Carrel name: keyword-virus-cord Creating study carrel named keyword-virus-cord Initializing database file: cache/cord-001065-j4hvyyoi.json key: cord-001065-j4hvyyoi authors: Boncristiani, Humberto F.; Evans, Jay D.; Chen, Yanping; Pettis, Jeff; Murphy, Charles; Lopez, Dawn L.; Simone-Finstrom, Michael; Strand, Micheline; Tarpy, David R.; Rueppell, Olav title: In Vitro Infection of Pupae with Israeli Acute Paralysis Virus Suggests Disturbance of Transcriptional Homeostasis in Honey Bees (Apis mellifera) date: 2013-09-05 journal: PLoS One DOI: 10.1371/journal.pone.0073429 sha: doc_id: 1065 cord_uid: j4hvyyoi file: cache/cord-000180-howix091.json key: cord-000180-howix091 authors: MacLeod, Iain J.; Minson, Tony title: Binding of Herpes Simplex Virus Type-1 Virions Leads to the Induction of Intracellular Signalling in the Absence of Virus Entry date: 2010-03-05 journal: PLoS One DOI: 10.1371/journal.pone.0009560 sha: doc_id: 180 cord_uid: howix091 file: cache/cord-000708-iuo2cw23.json key: cord-000708-iuo2cw23 authors: Lippé, Roger title: Deciphering Novel Host–Herpesvirus Interactions by Virion Proteomics date: 2012-05-28 journal: Front Microbiol DOI: 10.3389/fmicb.2012.00181 sha: doc_id: 708 cord_uid: iuo2cw23 file: cache/cord-003232-nquw7qga.json key: cord-003232-nquw7qga authors: Kuchipudi, Suresh V.; Nissly, Ruth H. title: Novel Flu Viruses in Bats and Cattle: “Pushing the Envelope” of Influenza Infection date: 2018-08-06 journal: Vet Sci DOI: 10.3390/vetsci5030071 sha: doc_id: 3232 cord_uid: nquw7qga file: cache/cord-001834-6xf4o3oy.json key: cord-001834-6xf4o3oy authors: Sung, Pil Soo; Shin, Eui-Cheol; Yoon, Seung Kew title: Interferon Response in Hepatitis C Virus (HCV) Infection: Lessons from Cell Culture Systems of HCV Infection date: 2015-10-07 journal: Int J Mol Sci DOI: 10.3390/ijms161023683 sha: doc_id: 1834 cord_uid: 6xf4o3oy file: cache/cord-002274-6rddtogo.json key: cord-002274-6rddtogo authors: James, Joe; Howard, Wendy; Iqbal, Munir; Nair, Venugopal K.; Barclay, Wendy S.; Shelton, Holly title: Influenza A virus PB1-F2 protein prolongs viral shedding in chickens lengthening the transmission window date: 2016-10-13 journal: J Gen Virol DOI: 10.1099/jgv.0.000584 sha: doc_id: 2274 cord_uid: 6rddtogo file: cache/cord-001542-f089bs8r.json key: cord-001542-f089bs8r authors: Lai, Kang Yiu; Ng, Wing Yiu George; Cheng, Fan Fanny title: Human Ebola virus infection in West Africa: a review of available therapeutic agents that target different steps of the life cycle of Ebola virus date: 2014-11-28 journal: Infect Dis Poverty DOI: 10.1186/2049-9957-3-43 sha: doc_id: 1542 cord_uid: f089bs8r file: cache/cord-002423-1u44tdrj.json key: cord-002423-1u44tdrj authors: Geoghegan, Jemma L.; Duchêne, Sebastián; Holmes, Edward C. title: Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families date: 2017-02-08 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1006215 sha: doc_id: 2423 cord_uid: 1u44tdrj file: cache/cord-002601-d8908t93.json key: cord-002601-d8908t93 authors: Arellano-Llamas, Rocío; Alfaro-Ruiz, Luis; Arriaga Canon, Cristian; Imaz Rosshandler, Ivan; Cruz-Lagunas, Alfredo; Zúñiga, Joaquín; Rebollar Vega, Rosa; Wong, Christopher W.; Maurer-Stroh, Sebastian; Romero Córdoba, Sandra; Liu, Edison T.; Hidalgo-Miranda, Alfredo; Vázquez-Pérez, Joel A. title: Molecular features of influenza A (H1N1)pdm09 prevalent in Mexico during winter seasons 2012-2014 date: 2017-07-10 journal: PLoS One DOI: 10.1371/journal.pone.0180419 sha: doc_id: 2601 cord_uid: d8908t93 file: cache/cord-003092-3owcqt3d.json key: cord-003092-3owcqt3d authors: Iketani, Sho; Shean, Ryan C.; Ferren, Marion; Makhsous, Negar; Aquino, Dolly B.; des Georges, Amedee; Rima, Bert; Mathieu, Cyrille; Porotto, Matteo; Moscona, Anne; Greninger, Alexander L. title: Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation date: 2018-07-03 journal: mBio DOI: 10.1128/mbio.00898-18 sha: doc_id: 3092 cord_uid: 3owcqt3d file: cache/cord-003122-a3f4l6iu.json key: cord-003122-a3f4l6iu authors: Dou, Dan; Revol, Rebecca; Östbye, Henrik; Wang, Hao; Daniels, Robert title: Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement date: 2018-07-20 journal: Front Immunol DOI: 10.3389/fimmu.2018.01581 sha: doc_id: 3122 cord_uid: a3f4l6iu file: cache/cord-003004-iif2lnez.json key: cord-003004-iif2lnez authors: Linster, Martin; Do, Lien Anh Ha; Minh, Ngo Ngoc Quang; Chen, Yihui; Zhe, Zhu; Tuan, Tran Anh; Tuan, Ha Manh; Su, Yvonne C. F.; van Doorn, H. Rogier; Moorthy, Mahesh; Smith, Gavin J. D. title: Clinical and Molecular Epidemiology of Human Parainfluenza Viruses 1–4 in Children from Viet Nam date: 2018-05-01 journal: Sci Rep DOI: 10.1038/s41598-018-24767-4 sha: doc_id: 3004 cord_uid: iif2lnez file: cache/cord-000265-llilwq1u.json key: cord-000265-llilwq1u authors: Gao, Rongbao; Dong, Libo; Dong, Jie; Wen, Leying; Zhang, Ye; Yu, Hongjie; Feng, Zijian; Chen, Minmei; Tan, Yi; Mo, Zhaojun; Liu, Haiyan; Fan, Yunyan; Li, Kunxiong; Li, Chris Ka-Fai; Li, Dexin; Yang, Weizhong; Shu, Yuelong title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case date: 2010-10-12 journal: PLoS One DOI: 10.1371/journal.pone.0013315 sha: doc_id: 265 cord_uid: llilwq1u file: cache/cord-000012-p56v8wi1.json key: cord-000012-p56v8wi1 authors: Bigot, Yves; Samain, Sylvie; Augé-Gouillou, Corinne; Federici, Brian A title: Molecular evidence for the evolution of ichnoviruses from ascoviruses by symbiogenesis date: 2008-09-18 journal: BMC Evol Biol DOI: 10.1186/1471-2148-8-253 sha: doc_id: 12 cord_uid: p56v8wi1 file: cache/cord-002932-5e7xrd1y.json key: cord-002932-5e7xrd1y authors: Watanabe, Tokiko; Iwatsuki-Horimoto, Kiyoko; Kiso, Maki; Nakajima, Noriko; Takahashi, Kenta; Jose da Silva Lopes, Tiago; Ito, Mutsumi; Fukuyama, Satoshi; Hasegawa, Hideki; Kawaoka, Yoshihiro title: Experimental infection of Cynomolgus Macaques with highly pathogenic H5N1 influenza virus through the aerosol route date: 2018-03-19 journal: Sci Rep DOI: 10.1038/s41598-018-23022-0 sha: doc_id: 2932 cord_uid: 5e7xrd1y file: cache/cord-002937-7xauocti.json key: cord-002937-7xauocti authors: Huang, Chung-Guei; Lee, Li-Ang; Wu, Yi-Cheng; Hsiao, Mei-Jen; Horng, Jim-Tong; Kuo, Rei-Lin; Huang, Chih-Heng; Lin, Ya-Chu; Tsao, Kuo-Chien; Chen, Min-Chi; Chen, Tse-Ching; Shih, Shin-Ru title: A pilot study on primary cultures of human respiratory tract epithelial cells to predict patients’ responses to H7N9 infection date: 2018-02-20 journal: Oncotarget DOI: 10.18632/oncotarget.24537 sha: doc_id: 2937 cord_uid: 7xauocti file: cache/cord-000114-f0vud3gu.json key: cord-000114-f0vud3gu authors: Kim, Jeong‐Ki; Negovetich, Nicholas J.; Forrest, Heather L.; Webster, Robert G. title: Ducks: The “Trojan Horses” of H5N1 influenza date: 2009-05-31 journal: Influenza Other Respir Viruses DOI: 10.1111/j.1750-2659.2009.00084.x sha: doc_id: 114 cord_uid: f0vud3gu file: cache/cord-000902-ew8orn0z.json key: cord-000902-ew8orn0z authors: Zhao, Xiangyan; Tian, Yonglei; Yang, Ronghua; Feng, Haiping; Ouyang, Qingjian; Tian, You; Tan, Zhongyang; Li, Mingfu; Niu, Yile; Jiang, Jianhui; Shen, Guoli; Yu, Ruqin title: Coevolution between simple sequence repeats (SSRs) and virus genome size date: 2012-08-30 journal: BMC Genomics DOI: 10.1186/1471-2164-13-435 sha: doc_id: 902 cord_uid: ew8orn0z file: cache/cord-002581-r7mskri0.json key: cord-002581-r7mskri0 authors: Magnani, Diogo M.; Silveira, Cassia G. T.; Rosen, Brandon C.; Ricciardi, Michael J.; Pedreño-Lopez, Núria; Gutman, Martin J.; Bailey, Varian K.; Maxwell, Helen S.; Domingues, Aline; Gonzalez-Nieto, Lucas; Avelino-Silva, Vivian I.; Trindade, Mateus; Nogueira, Juliana; Oliveira, Consuelo S.; Maestri, Alvino; Felix, Alvina Clara; Levi, José Eduardo; Nogueira, Mauricio L.; Martins, Mauricio A.; Martinez-Navio, José M.; Fuchs, Sebastian P.; Whitehead, Stephen S.; Burton, Dennis R.; Desrosiers, Ronald C.; Kallas, Esper G.; Watkins, David I. title: A human inferred germline antibody binds to an immunodominant epitope and neutralizes Zika virus date: 2017-06-12 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0005655 sha: doc_id: 2581 cord_uid: r7mskri0 file: cache/cord-000539-uh3q65we.json key: cord-000539-uh3q65we authors: Zhang, Yi; Sun, Honglei; Fan, Lihong; Ma, Yuan; Sun, Yipeng; Pu, Juan; Yang, Jun; Qiao, Jian; Ma, Guangpeng; Liu, Jinhua title: Acute Respiratory Distress Syndrome Induced by a Swine 2009 H1N1 Variant in Mice date: 2012-01-03 journal: PLoS One DOI: 10.1371/journal.pone.0029347 sha: doc_id: 539 cord_uid: uh3q65we file: cache/cord-001616-9sc2xmqr.json key: cord-001616-9sc2xmqr authors: Erdem, Hakan; Ünal, Serhat title: New global viral threats date: 2015 journal: Saudi Med J DOI: 10.15537/smj.2015.4.10089 sha: doc_id: 1616 cord_uid: 9sc2xmqr file: cache/cord-000937-8vk89i4h.json key: cord-000937-8vk89i4h authors: Law, John; Jovel, Juan; Patterson, Jordan; Ford, Glenn; O’keefe, Sandra; Wang, Weiwei; Meng, Bo; Song, Deyong; Zhang, Yong; Tian, Zhijian; Wasilenko, Shawn T.; Rahbari, Mandana; Mitchell, Troy; Jordan, Tracy; Carpenter, Eric; Mason, Andrew L.; Wong, Gane Ka-Shu title: Identification of Hepatotropic Viruses from Plasma Using Deep Sequencing: A Next Generation Diagnostic Tool date: 2013-04-17 journal: PLoS One DOI: 10.1371/journal.pone.0060595 sha: doc_id: 937 cord_uid: 8vk89i4h file: cache/cord-001676-68y733y3.json key: cord-001676-68y733y3 authors: Shoemaker, Jason E.; Fukuyama, Satoshi; Eisfeld, Amie J.; Zhao, Dongming; Kawakami, Eiryo; Sakabe, Saori; Maemura, Tadashi; Gorai, Takeo; Katsura, Hiroaki; Muramoto, Yukiko; Watanabe, Shinji; Watanabe, Tokiko; Fuji, Ken; Matsuoka, Yukiko; Kitano, Hiroaki; Kawaoka, Yoshihiro title: An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation date: 2015-06-05 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1004856 sha: doc_id: 1676 cord_uid: 68y733y3 file: cache/cord-001985-iwfidoer.json key: cord-001985-iwfidoer authors: Urayama, Syun-ichi; Takaki, Yoshihiro; Nunoura, Takuro title: FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance date: 2016-02-13 journal: Microbes Environ DOI: 10.1264/jsme2.me15171 sha: doc_id: 1985 cord_uid: iwfidoer file: cache/cord-002072-qbh728ec.json key: cord-002072-qbh728ec authors: Bi, Yuhai; Liu, Jingyuan; Xiong, Haofeng; Zhang, Yue; Liu, Di; Liu, Yingxia; Gao, George F.; Wang, Beibei title: A new reassortment of influenza A (H7N9) virus causing human infection in Beijing, 2014 date: 2016-05-27 journal: Sci Rep DOI: 10.1038/srep26624 sha: doc_id: 2072 cord_uid: qbh728ec file: cache/cord-001958-2gt3fwpy.json key: cord-001958-2gt3fwpy authors: Meseda, Clement A.; Atukorale, Vajini; Kuhn, Jordan; Schmeisser, Falko; Weir, Jerry P. title: Percutaneous Vaccination as an Effective Method of Delivery of MVA and MVA-Vectored Vaccines date: 2016-02-19 journal: PLoS One DOI: 10.1371/journal.pone.0149364 sha: doc_id: 1958 cord_uid: 2gt3fwpy file: cache/cord-000113-d0eur1hq.json key: cord-000113-d0eur1hq authors: Fooks, Anthony R.; Johnson, Nicholas; Freuling, Conrad M.; Wakeley, Philip R.; Banyard, Ashley C.; McElhinney, Lorraine M.; Marston, Denise A.; Dastjerdi, Akbar; Wright, Edward; Weiss, Robin A.; Müller, Thomas title: Emerging Technologies for the Detection of Rabies Virus: Challenges and Hopes in the 21st Century date: 2009-09-29 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0000530 sha: doc_id: 113 cord_uid: d0eur1hq file: cache/cord-001420-b4zcvd04.json key: cord-001420-b4zcvd04 authors: Crescenzo-Chaigne, Bernadette; Barbezange, Cyril; Frigard, Vianney; Poulain, Damien; van der Werf, Sylvie title: Chimeric NP Non Coding Regions between Type A and C Influenza Viruses Reveal Their Role in Translation Regulation date: 2014-09-30 journal: PLoS One DOI: 10.1371/journal.pone.0109046 sha: doc_id: 1420 cord_uid: b4zcvd04 file: cache/cord-001528-33f94doo.json key: cord-001528-33f94doo authors: Fouchier, Ron A. M. title: Studies on Influenza Virus Transmission between Ferrets: the Public Health Risks Revisited date: 2015-01-23 journal: mBio DOI: 10.1128/mbio.02560-14 sha: doc_id: 1528 cord_uid: 33f94doo file: cache/cord-002136-mkl89qkt.json key: cord-002136-mkl89qkt authors: Nunes, Sandro F.; Murcia, Pablo R.; Tiley, Laurence S.; Brown, Ian H.; Tucker, Alexander W.; Maskell, Duncan J.; Wood, James Lionel N. title: An ex vivo swine tracheal organ culture for the study of influenza infection date: 2009-12-09 journal: Influenza Other Respir Viruses DOI: 10.1111/j.1750-2659.2009.00119.x sha: doc_id: 2136 cord_uid: mkl89qkt file: cache/cord-003523-byxuruk1.json key: cord-003523-byxuruk1 authors: Fritsch, Annemarie; Schweiger, Brunhilde; Biere, Barbara title: Influenza C virus in pre-school children with respiratory infections: retrospective analysis of data from the national influenza surveillance system in Germany, 2012 to 2014 date: 2019-03-07 journal: Euro Surveill DOI: 10.2807/1560-7917.es.2019.24.10.1800174 sha: doc_id: 3523 cord_uid: byxuruk1 file: cache/cord-001120-fxd533b4.json key: cord-001120-fxd533b4 authors: Everitt, Aaron R.; Clare, Simon; McDonald, Jacqueline U.; Kane, Leanne; Harcourt, Katherine; Ahras, Malika; Lall, Amar; Hale, Christine; Rodgers, Angela; Young, Douglas B.; Haque, Ashraful; Billker, Oliver; Tregoning, John S.; Dougan, Gordon; Kellam, Paul title: Defining the Range of Pathogens Susceptible to Ifitm3 Restriction Using a Knockout Mouse Model date: 2013-11-21 journal: PLoS One DOI: 10.1371/journal.pone.0080723 sha: doc_id: 1120 cord_uid: fxd533b4 file: cache/cord-000777-7cty5s6o.json key: cord-000777-7cty5s6o authors: Merten, O.-W. title: Virus contaminations of cell cultures – A biotechnological view date: 2002-01-01 journal: Cytotechnology DOI: 10.1023/a:1022969101804 sha: doc_id: 777 cord_uid: 7cty5s6o file: cache/cord-000804-0hlj6r10.json key: cord-000804-0hlj6r10 authors: Brauburger, Kristina; Hume, Adam J.; Mühlberger, Elke; Olejnik, Judith title: Forty-Five Years of Marburg Virus Research date: 2012-10-01 journal: Viruses DOI: 10.3390/v4101878 sha: doc_id: 804 cord_uid: 0hlj6r10 file: cache/cord-001142-puj74k7y.json key: cord-001142-puj74k7y authors: Crescenzo-Chaigne, Bernadette; Barbezange, Cyril; van der Werf, Sylvie title: The Panhandle Formed by Influenza A and C Virus NS Non-Coding Regions Determines NS Segment Expression date: 2013-11-21 journal: PLoS One DOI: 10.1371/journal.pone.0081550 sha: doc_id: 1142 cord_uid: puj74k7y file: cache/cord-001397-nrq4ncdf.json key: cord-001397-nrq4ncdf authors: Mlera, Luwanika; Melik, Wessam; Bloom, Marshall E. title: The role of viral persistence in flavivirus biology date: 2014-05-12 journal: Pathogens and Disease DOI: 10.1111/2049-632x.12178 sha: doc_id: 1397 cord_uid: nrq4ncdf file: cache/cord-001748-7e8px4vx.json key: cord-001748-7e8px4vx authors: Nobach, Daniel; Bourg, Manon; Herzog, Sibylle; Lange-Herbst, Hildburg; Encarnação, Jorge A.; Eickmann, Markus; Herden, Christiane title: Shedding of Infectious Borna Disease Virus-1 in Living Bicolored White-Toothed Shrews date: 2015-08-27 journal: PLoS One DOI: 10.1371/journal.pone.0137018 sha: doc_id: 1748 cord_uid: 7e8px4vx file: cache/cord-000238-om92cx5q.json key: cord-000238-om92cx5q authors: Ogbunugafor, C. Brandon; Pease, James B.; Turner, Paul E. title: On the possible role of robustness in the evolution of infectious diseases date: 2010-06-30 journal: Chaos DOI: 10.1063/1.3455189 sha: doc_id: 238 cord_uid: om92cx5q file: cache/cord-001974-wjf3c7a7.json key: cord-001974-wjf3c7a7 authors: Friis-Nielsen, Jens; Kjartansdóttir, Kristín Rós; Mollerup, Sarah; Asplund, Maria; Mourier, Tobias; Jensen, Randi Holm; Hansen, Thomas Arn; Rey-Iglesia, Alba; Richter, Stine Raith; Nielsen, Ida Broman; Alquezar-Planas, David E.; Olsen, Pernille V. S.; Vinner, Lasse; Fridholm, Helena; Nielsen, Lars Peter; Willerslev, Eske; Sicheritz-Pontén, Thomas; Lund, Ole; Hansen, Anders Johannes; Izarzugaza, Jose M. G.; Brunak, Søren title: Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers date: 2016-02-19 journal: Viruses DOI: 10.3390/v8020053 sha: doc_id: 1974 cord_uid: wjf3c7a7 file: cache/cord-000359-y0m1utug.json key: cord-000359-y0m1utug authors: Walpita, Pramila; Barr, Jennifer; Sherman, Michael; Basler, Christopher F.; Wang, Linfa title: Vaccine Potential of Nipah Virus-Like Particles date: 2011-04-06 journal: PLoS One DOI: 10.1371/journal.pone.0018437 sha: doc_id: 359 cord_uid: y0m1utug file: cache/cord-000729-iq30z094.json key: cord-000729-iq30z094 authors: Marsh, Glenn A.; de Jong, Carol; Barr, Jennifer A.; Tachedjian, Mary; Smith, Craig; Middleton, Deborah; Yu, Meng; Todd, Shawn; Foord, Adam J.; Haring, Volker; Payne, Jean; Robinson, Rachel; Broz, Ivano; Crameri, Gary; Field, Hume E.; Wang, Lin-Fa title: Cedar Virus: A Novel Henipavirus Isolated from Australian Bats date: 2012-08-02 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1002836 sha: doc_id: 729 cord_uid: iq30z094 file: cache/cord-001207-yjaiybwf.json key: cord-001207-yjaiybwf authors: Sachsenröder, Jana; Twardziok, Sven O.; Scheuch, Matthias; Johne, Reimar title: The General Composition of the Faecal Virome of Pigs Depends on Age, but Not on Feeding with a Probiotic Bacterium date: 2014-02-19 journal: PLoS One DOI: 10.1371/journal.pone.0088888 sha: doc_id: 1207 cord_uid: yjaiybwf file: cache/cord-001831-3aonqyub.json key: cord-001831-3aonqyub authors: Royle, Jamie; Dobson, Samuel John; Müller, Marietta; Macdonald, Andrew title: Emerging Roles of Viroporins Encoded by DNA Viruses: Novel Targets for Antivirals? date: 2015-10-16 journal: Viruses DOI: 10.3390/v7102880 sha: doc_id: 1831 cord_uid: 3aonqyub file: cache/cord-002337-8v907g24.json key: cord-002337-8v907g24 authors: Lipsitch, Marc; Barclay, Wendy; Raman, Rahul; Russell, Charles J; Belser, Jessica A; Cobey, Sarah; Kasson, Peter M; Lloyd-Smith, James O; Maurer-Stroh, Sebastian; Riley, Steven; Beauchemin, Catherine AA; Bedford, Trevor; Friedrich, Thomas C; Handel, Andreas; Herfst, Sander; Murcia, Pablo R; Roche, Benjamin; Wilke, Claus O; Russell, Colin A title: Viral factors in influenza pandemic risk assessment date: 2016-11-11 journal: nan DOI: 10.7554/elife.18491 sha: doc_id: 2337 cord_uid: 8v907g24 file: cache/cord-002338-ri7v2ka3.json key: cord-002338-ri7v2ka3 authors: Anderson, Tavis K.; Macken, Catherine A.; Lewis, Nicola S.; Scheuermann, Richard H.; Van Reeth, Kristien; Brown, Ian H.; Swenson, Sabrina L.; Simon, Gaëlle; Saito, Takehiko; Berhane, Yohannes; Ciacci-Zanella, Janice; Pereda, Ariel; Davis, C. Todd; Donis, Ruben O.; Webby, Richard J.; Vincent, Amy L. title: A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses date: 2016-12-14 journal: mSphere DOI: 10.1128/msphere.00275-16 sha: doc_id: 2338 cord_uid: ri7v2ka3 file: cache/cord-002728-6oyw5sqv.json key: cord-002728-6oyw5sqv authors: Carding, S. R.; Davis, N.; Hoyles, L. title: Review article: the human intestinal virome in health and disease date: 2017-09-04 journal: Aliment Pharmacol Ther DOI: 10.1111/apt.14280 sha: doc_id: 2728 cord_uid: 6oyw5sqv file: cache/cord-002921-i5jxn1vj.json key: cord-002921-i5jxn1vj authors: Morens, David M; Fauci, Anthony S title: Pandemic Zika: A Formidable Challenge to Medicine and Public Health date: 2017-12-15 journal: J Infect Dis DOI: 10.1093/infdis/jix383 sha: doc_id: 2921 cord_uid: i5jxn1vj file: cache/cord-002874-9rxv6fy9.json key: cord-002874-9rxv6fy9 authors: Welch, David; Buonanno, Manuela; Grilj, Veljko; Shuryak, Igor; Crickmore, Connor; Bigelow, Alan W.; Randers-Pehrson, Gerhard; Johnson, Gary W.; Brenner, David J. title: Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases date: 2018-02-09 journal: Sci Rep DOI: 10.1038/s41598-018-21058-w sha: doc_id: 2874 cord_uid: 9rxv6fy9 file: cache/cord-003130-p2h8p5bm.json key: cord-003130-p2h8p5bm authors: Lindqvist, Richard; Upadhyay, Arunkumar; Överby, Anna K. title: Tick-Borne Flaviviruses and the Type I Interferon Response date: 2018-06-21 journal: Viruses DOI: 10.3390/v10070340 sha: doc_id: 3130 cord_uid: p2h8p5bm file: cache/cord-002327-tocqabgu.json key: cord-002327-tocqabgu authors: de Vries, Rory D.; Rimmelzwaan, Guus F. title: Viral vector-based influenza vaccines date: 2016-07-25 journal: Hum Vaccin Immunother DOI: 10.1080/21645515.2016.1210729 sha: doc_id: 2327 cord_uid: tocqabgu file: cache/cord-003861-qeao4ghg.json key: cord-003861-qeao4ghg authors: Aris-Brosou, Stéphane; Parent, Louis; Ibeh, Neke title: Viral Long-Term Evolutionary Strategies Favor Stability over Proliferation date: 2019-07-24 journal: Viruses DOI: 10.3390/v11080677 sha: doc_id: 3861 cord_uid: qeao4ghg file: cache/cord-003926-ycdaw2vh.json key: cord-003926-ycdaw2vh authors: Maslow, Joel N. title: Zika Vaccine Development—Current Progress and Challenges for the Future date: 2019-07-14 journal: Trop Med Infect Dis DOI: 10.3390/tropicalmed4030104 sha: doc_id: 3926 cord_uid: ycdaw2vh file: cache/cord-003993-3bozjfv7.json key: cord-003993-3bozjfv7 authors: Cagliani, Rachele; Forni, Diego; Sironi, Manuela title: Mode and tempo of human hepatitis virus evolution date: 2019-10-25 journal: Comput Struct Biotechnol J DOI: 10.1016/j.csbj.2019.09.007 sha: doc_id: 3993 cord_uid: 3bozjfv7 file: cache/cord-004477-qu2o2iu1.json key: cord-004477-qu2o2iu1 authors: Vlasova, Anastasia N.; Butler, John E. title: Editorial: Porcine Anti-Viral Immunity date: 2020-03-06 journal: Front Immunol DOI: 10.3389/fimmu.2020.00399 sha: doc_id: 4477 cord_uid: qu2o2iu1 file: cache/cord-000501-qz68gtd4.json key: cord-000501-qz68gtd4 authors: Greatorex, Jane S.; Digard, Paul; Curran, Martin D.; Moynihan, Robert; Wensley, Harrison; Wreghitt, Tim; Varsani, Harsha; Garcia, Fayna; Enstone, Joanne; Nguyen-Van-Tam, Jonathan S. title: Survival of Influenza A(H1N1) on Materials Found in Households: Implications for Infection Control date: 2011-11-22 journal: PLoS One DOI: 10.1371/journal.pone.0027932 sha: doc_id: 501 cord_uid: qz68gtd4 file: cache/cord-000760-4yfohp9w.json key: cord-000760-4yfohp9w authors: Babapoor, Sankhiros; Neef, Tobias; Mittelholzer, Christian; Girshick, Theodore; Garmendia, Antonio; Shang, Hongwei; Khan, Mazhar I.; Burkhard, Peter title: A Novel Vaccine Using Nanoparticle Platform to Present Immunogenic M2e against Avian Influenza Infection date: 2012-01-12 journal: Influenza Res Treat DOI: 10.1155/2011/126794 sha: doc_id: 760 cord_uid: 4yfohp9w file: cache/cord-000050-tfcerilc.json key: cord-000050-tfcerilc authors: Rao, Srinivas; Kong, Wing-Pui; Wei, Chih-Jen; Yang, Zhi-Yong; Nason, Martha; Styles, Darrel; DeTolla, Louis J.; Sorrell, Erin M.; Song, Haichen; Wan, Hongquan; Ramirez-Nieto, Gloria C.; Perez, Daniel; Nabel, Gary J. title: Multivalent HA DNA Vaccination Protects against Highly Pathogenic H5N1 Avian Influenza Infection in Chickens and Mice date: 2008-06-18 journal: PLoS One DOI: 10.1371/journal.pone.0002432 sha: doc_id: 50 cord_uid: tfcerilc file: cache/cord-003166-k3jxvzfi.json key: cord-003166-k3jxvzfi authors: Noh, Ji Yeong; Jeong, Dae Gwin; Yoon, Sun-Woo; Kim, Ji Hyung; Choi, Yong Gun; Kang, Shien-Young; Kim, Hye Kwon title: Isolation and characterization of novel bat paramyxovirus B16-40 potentially belonging to the proposed genus Shaanvirus date: 2018-08-22 journal: Sci Rep DOI: 10.1038/s41598-018-30319-7 sha: doc_id: 3166 cord_uid: k3jxvzfi file: cache/cord-003492-rodqdtfj.json key: cord-003492-rodqdtfj authors: Montaner-Tarbes, Sergio; del Portillo, Hernando A.; Montoya, María; Fraile, Lorenzo title: Key Gaps in the Knowledge of the Porcine Respiratory Reproductive Syndrome Virus (PRRSV) date: 2019-02-20 journal: Front Vet Sci DOI: 10.3389/fvets.2019.00038 sha: doc_id: 3492 cord_uid: rodqdtfj file: cache/cord-004280-c470nlie.json key: cord-004280-c470nlie authors: Coleman, Kristen K.; Sigler, William V. title: Airborne Influenza A Virus Exposure in an Elementary School date: 2020-02-05 journal: Sci Rep DOI: 10.1038/s41598-020-58588-1 sha: doc_id: 4280 cord_uid: c470nlie file: cache/cord-002407-25cawzi0.json key: cord-002407-25cawzi0 authors: Nogales, Aitor; Martínez-Sobrido, Luis title: Reverse Genetics Approaches for the Development of Influenza Vaccines date: 2016-12-22 journal: Int J Mol Sci DOI: 10.3390/ijms18010020 sha: doc_id: 2407 cord_uid: 25cawzi0 file: cache/cord-003216-5qioku84.json key: cord-003216-5qioku84 authors: Rehman, Zaib Ur.; Meng, Chunchun; Sun, Yingjie; Mahrose, Khalid M.; Umar, Sajid; Ding, Chan; Munir, Muhammad title: Pathobiology of Avian avulavirus 1: special focus on waterfowl date: 2018-09-19 journal: Vet Res DOI: 10.1186/s13567-018-0587-x sha: doc_id: 3216 cord_uid: 5qioku84 file: cache/cord-004211-58x3nnsc.json key: cord-004211-58x3nnsc authors: Javelle, Emilie; Lesueur, Alexandre; Pommier de Santi, Vincent; de Laval, Franck; Lefebvre, Thibault; Holweck, Guillaume; Durand, Guillaume André; Leparc-Goffart, Isabelle; Texier, Gaëtan; Simon, Fabrice title: The challenging management of Rift Valley Fever in humans: literature review of the clinical disease and algorithm proposal date: 2020-01-22 journal: Ann Clin Microbiol Antimicrob DOI: 10.1186/s12941-020-0346-5 sha: doc_id: 4211 cord_uid: 58x3nnsc file: cache/cord-003880-uuuzfyjm.json key: cord-003880-uuuzfyjm authors: Shen, Meng-xin; Ma, Nian; Li, Min-ke; Liu, Yuan-yuan; Chen, Tian; Wei, Fei; Liu, Dong-ying; Hou, Wei; Xiong, Hai-rong; Yang, Zhan-qiu title: Antiviral Properties of R. tanguticum Nanoparticles on Herpes Simplex Virus Type I In Vitro and In Vivo date: 2019-09-04 journal: Front Pharmacol DOI: 10.3389/fphar.2019.00959 sha: doc_id: 3880 cord_uid: uuuzfyjm file: cache/cord-003482-f1uvohf0.json key: cord-003482-f1uvohf0 authors: Malmlov, Ashley; Bantle, Collin; Aboellail, Tawfik; Wagner, Kaitlyn; Campbell, Corey L.; Eckley, Miles; Chotiwan, Nunya; Gullberg, Rebekah C.; Perera, Rushika; Tjalkens, Ronald; Schountz, Tony title: Experimental Zika virus infection of Jamaican fruit bats (Artibeus jamaicensis) and possible entry of virus into brain via activated microglial cells date: 2019-02-04 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0007071 sha: doc_id: 3482 cord_uid: f1uvohf0 file: cache/cord-002410-2zi5iv2t.json key: cord-002410-2zi5iv2t authors: Bruening, Janina; Weigel, Bettina; Gerold, Gisa title: The Role of Type III Interferons in Hepatitis C Virus Infection and Therapy date: 2017-02-01 journal: J Immunol Res DOI: 10.1155/2017/7232361 sha: doc_id: 2410 cord_uid: 2zi5iv2t file: cache/cord-003302-vxk7uqlc.json key: cord-003302-vxk7uqlc authors: Fedson, David S title: Influenza, evolution, and the next pandemic date: 2018-10-03 journal: Evol Med Public Health DOI: 10.1093/emph/eoy027 sha: doc_id: 3302 cord_uid: vxk7uqlc file: cache/cord-000933-nn9gj0z1.json key: cord-000933-nn9gj0z1 authors: Krzyzaniak, Magdalena Anna; Zumstein, Michael Thomas; Gerez, Juan Atilio; Picotti, Paola; Helenius, Ari title: Host Cell Entry of Respiratory Syncytial Virus Involves Macropinocytosis Followed by Proteolytic Activation of the F Protein date: 2013-04-11 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1003309 sha: doc_id: 933 cord_uid: nn9gj0z1 file: cache/cord-003503-t6cnjwpd.json key: cord-003503-t6cnjwpd authors: Sung, Ming-Hua; Lin, Chao-Nan; Chiou, Ming-Tang; Cheng, I-Ju; Thanh, Quang-Hien; Chao, Day-Yu; Lan, Yu-Ching title: Phylogeographic investigation of 2014 porcine epidemic diarrhea virus (PEDV) transmission in Taiwan date: 2019-03-06 journal: PLoS One DOI: 10.1371/journal.pone.0213153 sha: doc_id: 3503 cord_uid: t6cnjwpd file: cache/cord-003817-k3m72uxw.json key: cord-003817-k3m72uxw authors: Braun, Elisabeth; Sauter, Daniel title: Furin‐mediated protein processing in infectious diseases and cancer date: 2019-08-05 journal: Clin Transl Immunology DOI: 10.1002/cti2.1073 sha: doc_id: 3817 cord_uid: k3m72uxw file: cache/cord-003044-9uqa39j9.json key: cord-003044-9uqa39j9 authors: Cervera, Héctor; Ambrós, Silvia; Bernet, Guillermo P; Rodrigo, Guillermo; Elena, Santiago F title: Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host’s Transcriptome: The Tobacco Etch Potyvirus—Tobacco Case Study date: 2018-03-19 journal: Mol Biol Evol DOI: 10.1093/molbev/msy038 sha: doc_id: 3044 cord_uid: 9uqa39j9 file: cache/cord-004608-3u00cpsc.json key: cord-004608-3u00cpsc authors: nan title: Arboviren—durch Arthropoden übertragbare Viren: Stellungnahmen des Arbeitskreises Blut des Bundesministeriums für Gesundheit und Soziale Sicherung date: 2004 journal: Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz DOI: 10.1007/s00103-004-0890-8 sha: doc_id: 4608 cord_uid: 3u00cpsc file: cache/cord-004761-cgby8bhz.json key: cord-004761-cgby8bhz authors: Fuchs, N.; Wigand, R. title: Virus isolation and titration at 33‡ and 37‡ C date: 1975 journal: Med Microbiol Immunol DOI: 10.1007/bf02121753 sha: doc_id: 4761 cord_uid: cgby8bhz file: cache/cord-002076-7t4d4vvo.json key: cord-002076-7t4d4vvo authors: Li, Yongfeng; Li, Lian-Feng; Yu, Shaoxiong; Wang, Xiao; Zhang, Lingkai; Yu, Jiahui; Xie, Libao; Li, Weike; Ali, Razim; Qiu, Hua-Ji title: Applications of Replicating-Competent Reporter-Expressing Viruses in Diagnostic and Molecular Virology date: 2016-05-06 journal: Viruses DOI: 10.3390/v8050127 sha: doc_id: 2076 cord_uid: 7t4d4vvo file: cache/cord-003707-fbe47bgi.json key: cord-003707-fbe47bgi authors: Russo, Alice G; Kelly, Andrew G; Enosi Tuipulotu, Daniel; Tanaka, Mark M; White, Peter A title: Novel insights into endogenous RNA viral elements in Ixodes scapularis and other arbovirus vector genomes date: 2019-06-18 journal: Virus Evol DOI: 10.1093/ve/vez010 sha: doc_id: 3707 cord_uid: fbe47bgi file: cache/cord-003466-599x0euj.json key: cord-003466-599x0euj authors: Nickol, Michaela E.; Kindrachuk, Jason title: A year of terror and a century of reflection: perspectives on the great influenza pandemic of 1918–1919 date: 2019-02-06 journal: BMC Infect Dis DOI: 10.1186/s12879-019-3750-8 sha: doc_id: 3466 cord_uid: 599x0euj file: cache/cord-002482-2t09zqqi.json key: cord-002482-2t09zqqi authors: Miras, Manuel; Miller, W. Allen; Truniger, Verónica; Aranda, Miguel A. title: Non-canonical Translation in Plant RNA Viruses date: 2017-04-06 journal: Front Plant Sci DOI: 10.3389/fpls.2017.00494 sha: doc_id: 2482 cord_uid: 2t09zqqi file: cache/cord-002933-zmx4k46v.json key: cord-002933-zmx4k46v authors: Stabell, Alex C; Meyerson, Nicholas R; Gullberg, Rebekah C; Gilchrist, Alison R; Webb, Kristofor J; Old, William M; Perera, Rushika; Sawyer, Sara L title: Dengue viruses cleave STING in humans but not in nonhuman primates, their presumed natural reservoir date: 2018-03-20 journal: nan DOI: 10.7554/elife.31919 sha: doc_id: 2933 cord_uid: zmx4k46v file: cache/cord-003767-9xbu4hnq.json key: cord-003767-9xbu4hnq authors: Slingenbergh, Jan title: Animal Virus Ecology and Evolution Are Shaped by the Virus Host-Body Infiltration and Colonization Pattern date: 2019-05-25 journal: Pathogens DOI: 10.3390/pathogens8020072 sha: doc_id: 3767 cord_uid: 9xbu4hnq file: cache/cord-003792-v48xeqdz.json key: cord-003792-v48xeqdz authors: Izquierdo-Suzán, Mónica; Zárate, Selene; Torres-Flores, Jesús; Correa-Morales, Fabián; González-Acosta, Cassandra; Sevilla-Reyes, Edgar E.; Lira, Rosalia; Alcaraz-Estrada, Sofía L.; Yocupicio-Monroy, Martha title: Natural Vertical Transmission of Zika Virus in Larval Aedes aegypti Populations, Morelos, Mexico date: 2019-08-17 journal: Emerg Infect Dis DOI: 10.3201/eid2508.181533 sha: doc_id: 3792 cord_uid: v48xeqdz file: cache/cord-003639-bjtxf1y8.json key: cord-003639-bjtxf1y8 authors: Vahey, Michael D; Fletcher, Daniel A title: Influenza A virus surface proteins are organized to help penetrate host mucus date: 2019-05-14 journal: nan DOI: 10.7554/elife.43764 sha: doc_id: 3639 cord_uid: bjtxf1y8 file: cache/cord-003961-gs75ebo4.json key: cord-003961-gs75ebo4 authors: Yin, Xin; Feng, Zongdi title: Hepatitis E Virus Entry date: 2019-09-20 journal: Viruses DOI: 10.3390/v11100883 sha: doc_id: 3961 cord_uid: gs75ebo4 file: cache/cord-002757-upwe0cpj.json key: cord-002757-upwe0cpj authors: Sullivan, Kathleen E.; Bassiri, Hamid; Bousfiha, Ahmed A.; Costa-Carvalho, Beatriz T.; Freeman, Alexandra F.; Hagin, David; Lau, Yu L.; Lionakis, Michail S.; Moreira, Ileana; Pinto, Jorge A.; de Moraes-Pinto, M. Isabel; Rawat, Amit; Reda, Shereen M.; Reyes, Saul Oswaldo Lugo; Seppänen, Mikko; Tang, Mimi L. K. title: Emerging Infections and Pertinent Infections Related to Travel for Patients with Primary Immunodeficiencies date: 2017-08-07 journal: J Clin Immunol DOI: 10.1007/s10875-017-0426-2 sha: doc_id: 2757 cord_uid: upwe0cpj file: cache/cord-004501-guiy89x8.json key: cord-004501-guiy89x8 authors: Cojocaru, Florina-Daniela; Botezat, Doru; Gardikiotis, Ioannis; Uritu, Cristina-Mariana; Dodi, Gianina; Trandafir, Laura; Rezus, Ciprian; Rezus, Elena; Tamba, Bogdan-Ionel; Mihai, Cosmin-Teodor title: Nanomaterials Designed for Antiviral Drug Delivery Transport across Biological Barriers date: 2020-02-18 journal: Pharmaceutics DOI: 10.3390/pharmaceutics12020171 sha: doc_id: 4501 cord_uid: guiy89x8 file: cache/cord-003598-m2fsrwvw.json key: cord-003598-m2fsrwvw authors: Elbahesh, Husni; Gerlach, Thomas; Saletti, Giulietta; Rimmelzwaan, Guus F. title: Response Modifiers: Tweaking the Immune Response Against Influenza A Virus date: 2019-04-12 journal: Front Immunol DOI: 10.3389/fimmu.2019.00809 sha: doc_id: 3598 cord_uid: m2fsrwvw file: cache/cord-004672-0lf5j8lo.json key: cord-004672-0lf5j8lo authors: Anderson, Kevin; Bond, Clifford W. title: Structural and physiological properties of mengovirus: Avirulent, hemagglutination-defective mutants express altered alpha (1 D) proteins and are adsorption-defective date: 1987 journal: Arch Virol DOI: 10.1007/bf01313891 sha: doc_id: 4672 cord_uid: 0lf5j8lo file: cache/cord-004771-4yinnncj.json key: cord-004771-4yinnncj authors: Tajima, M. title: Morphology of transmissible gastroenteritis virus of pigs: A possible member of coronaviruses date: 1970 journal: Arch Gesamte Virusforsch DOI: 10.1007/bf01253886 sha: doc_id: 4771 cord_uid: 4yinnncj file: cache/cord-004034-mjkixqhs.json key: cord-004034-mjkixqhs authors: Szilasi, Anna; Dénes, Lilla; Krikó, Eszter; Heenemann, Kristin; Ertl, Reinhard; Mándoki, Míra; Vahlenkamp, Thomas W; Balka, Gyula title: Prevalence of feline immunodeficiency virus and feline leukaemia virus in domestic cats in Hungary date: 2019-12-10 journal: JFMS Open Rep DOI: 10.1177/2055116919892094 sha: doc_id: 4034 cord_uid: mjkixqhs file: cache/cord-004751-4vl0cvyq.json key: cord-004751-4vl0cvyq authors: Mostow, S. R.; Tyrrell, D. A. J. title: The behaviour in vitro of attenuated recombinant influenza viruses date: 1973 journal: Arch Gesamte Virusforsch DOI: 10.1007/bf01556156 sha: doc_id: 4751 cord_uid: 4vl0cvyq file: cache/cord-003403-ypefqm71.json key: cord-003403-ypefqm71 authors: Roberts, Christine C.; Maslow, Joel N. title: Assay Challenges for Emerging Infectious Diseases: The Zika Experience date: 2018-10-02 journal: Vaccines (Basel) DOI: 10.3390/vaccines6040070 sha: doc_id: 3403 cord_uid: ypefqm71 file: cache/cord-004719-3stcx0dd.json key: cord-004719-3stcx0dd authors: Mushegian, A. R.; Koonin, E. V. title: Cell-to-cell movement of plant viruses: Insights from amino acid sequence comparisons of movement proteins and from analogies with cellular transport systems date: 1993 journal: Arch Virol DOI: 10.1007/bf01313766 sha: doc_id: 4719 cord_uid: 3stcx0dd file: cache/cord-003917-bswndfvk.json key: cord-003917-bswndfvk authors: Lalle, Eleonora; Biava, Mirella; Nicastri, Emanuele; Colavita, Francesca; Di Caro, Antonino; Vairo, Francesco; Lanini, Simone; Castilletti, Concetta; Langer, Martin; Zumla, Alimuddin; Kobinger, Gary; Capobianchi, Maria R.; Ippolito, Giuseppe title: Pulmonary Involvement during the Ebola Virus Disease date: 2019-08-24 journal: Viruses DOI: 10.3390/v11090780 sha: doc_id: 3917 cord_uid: bswndfvk file: cache/cord-004724-llex3yed.json key: cord-004724-llex3yed authors: Dea, S. A.; Bilodeau, R.; Martineau, G. P. title: Isolation of encephalomyocarditis virus among stillborn and post-weaning pigs in Quebec date: 1991 journal: Arch Virol DOI: 10.1007/bf01310497 sha: doc_id: 4724 cord_uid: llex3yed file: cache/cord-004774-fvf671jn.json key: cord-004774-fvf671jn authors: Kjeldsberg, Elisabeth; Hem, Annelise title: Detection of astroviruses in gut contents of nude and normal mice date: 1985 journal: Arch Virol DOI: 10.1007/bf01310560 sha: doc_id: 4774 cord_uid: fvf671jn file: cache/cord-004743-ido065mh.json key: cord-004743-ido065mh authors: Nagy, Éva; Lomniczi, B. title: Polypeptide patterns of infectious bronchitis virus serotypes fall into two categories date: 1979 journal: Arch Virol DOI: 10.1007/bf01315022 sha: doc_id: 4743 cord_uid: ido065mh file: cache/cord-004781-ajf9zig0.json key: cord-004781-ajf9zig0 authors: Ray, N. B.; Power, C.; Lynch, W. P.; Ewalt, L. C.; Lodmell, D. L. title: Rabies viruses infect primary cultures of murine, feline, and human microglia and astrocytes date: 2014-03-07 journal: Arch Virol DOI: 10.1007/s007050050136 sha: doc_id: 4781 cord_uid: ajf9zig0 file: cache/cord-004775-foaf3vyl.json key: cord-004775-foaf3vyl authors: Weiss, Marianne; Horzinek, M. C. title: The proposed family toroviridae: Agents of enteric infections date: 1987 journal: Arch Virol DOI: 10.1007/bf01310058 sha: doc_id: 4775 cord_uid: foaf3vyl file: cache/cord-004827-bnf3mvaf.json key: cord-004827-bnf3mvaf authors: Desselberger, U. title: Report on an ICTV-sponsored symposium on Virus Evolution date: 2005-01-13 journal: Arch Virol DOI: 10.1007/s00705-004-0466-9 sha: doc_id: 4827 cord_uid: bnf3mvaf file: cache/cord-004830-vmka378d.json key: cord-004830-vmka378d authors: Cursiefen, Dagmar; Becht, Hermann title: In vitro cultivation of cells from the chorioallantoic membrane of chick embryos date: 1975 journal: Med Microbiol Immunol DOI: 10.1007/bf02120764 sha: doc_id: 4830 cord_uid: vmka378d file: cache/cord-004841-wf0o3whi.json key: cord-004841-wf0o3whi authors: Sibalin, M.; Gerstl, F.; Pichler, L.; Bürki, F. title: Herpesvirus strigis, a new avian herpesvirus: II. Biochemical and biophysical properties date: 1974 journal: Arch Gesamte Virusforsch DOI: 10.1007/bf01251017 sha: doc_id: 4841 cord_uid: wf0o3whi file: cache/cord-005081-kxrzv16n.json key: cord-005081-kxrzv16n authors: Kiselev, O. I. title: Progress in the development of pandemic influenza vaccines and their production technologies date: 2010-11-12 journal: Appl DOI: 10.1134/s0003683810090024 sha: doc_id: 5081 cord_uid: kxrzv16n file: cache/cord-005876-d8sid7gd.json key: cord-005876-d8sid7gd authors: Varnholt, V.; Lasch, P.; Suske, G.; Koelfen, W.; Kachel, W. title: ARDS infolge schwerer RSV-Infektion Therapeutische Optionen: Therapeutische Optionen date: 1996 journal: Monatsschr Kinderheilkd DOI: 10.1007/s001120050095 sha: doc_id: 5876 cord_uid: d8sid7gd file: cache/cord-001521-l36f1gp7.json key: cord-001521-l36f1gp7 authors: nan title: Oral and Poster Manuscripts date: 2011-04-08 journal: Influenza Other Respir Viruses DOI: 10.1111/j.1750-2659.2011.00209.x sha: doc_id: 1521 cord_uid: l36f1gp7 file: cache/cord-005246-cskb0njm.json key: cord-005246-cskb0njm authors: Ludwig, George V.; Iacono-Connors, Lauren C. title: Insect-transmitted vertebrate viruses: Flaviviridae date: 1993 journal: In Vitro Cell Dev Biol Anim DOI: 10.1007/bf02633958 sha: doc_id: 5246 cord_uid: cskb0njm file: cache/cord-006819-sxz1s6kz.json key: cord-006819-sxz1s6kz authors: Daniel Givens, M.; Marley, M.S.D. title: Infectious causes of embryonic and fetal mortality date: 2008-05-27 journal: Theriogenology DOI: 10.1016/j.theriogenology.2008.04.018 sha: doc_id: 6819 cord_uid: sxz1s6kz file: cache/cord-005281-wy0zk9p8.json key: cord-005281-wy0zk9p8 authors: Blinov, V. M.; Zverev, V. V.; Krasnov, G. S.; Filatov, F. P.; Shargunov, A. V. title: Viral component of the human genome date: 2017-05-09 journal: Mol Biol DOI: 10.1134/s0026893317020066 sha: doc_id: 5281 cord_uid: wy0zk9p8 file: cache/cord-005885-r3qtoqu1.json key: cord-005885-r3qtoqu1 authors: Hellmich, Luisa; Rongisch, Robert; Rasokat, Heinrich; von Stebut, Esther; Fabri, Mario title: Exantheme nach Auslandsreisen date: 2019-10-09 journal: Hautarzt DOI: 10.1007/s00105-019-04489-y sha: doc_id: 5885 cord_uid: r3qtoqu1 file: cache/cord-005258-gps8rzb5.json key: cord-005258-gps8rzb5 authors: Liu, William J.; Liu, Di title: The triphibious warfare against viruses date: 2017-12-01 journal: Sci China Life Sci DOI: 10.1007/s11427-017-9252-y sha: doc_id: 5258 cord_uid: gps8rzb5 file: cache/cord-006790-lye0qjw8.json key: cord-006790-lye0qjw8 authors: Song, R.; Pang, X.; Yang, P.; Shu, Y.; Zhang, Y.; Wang, Q.; Chen, Z.; Liu, J.; Cheng, J.; Jiao, Y.; Jiang, R.; Lu, L.; Chen, L.; Ma, J.; Li, C.; Zeng, H.; Peng, X.; Huang, L.; Zheng, Y.; Deng, Y.; Li, X. title: Surveillance of the first case of human avian influenza A (H7N9) virus in Beijing, China date: 2013-10-16 journal: Infection DOI: 10.1007/s15010-013-0533-9 sha: doc_id: 6790 cord_uid: lye0qjw8 file: cache/cord-006997-sghhdjyi.json key: cord-006997-sghhdjyi authors: Rowland, M.G.M.; Davies, Heather; Patterson, S.; Dourmashkin, R.R.; Tyrrell, D.A.J.; Matthews, T.H.J.; Parry, J.; Hall, J.; Larson, H.E. title: Viruses and diarrhoea in West Africa and London: a collaborative study date: 1978-01-17 journal: Trans R Soc Trop Med Hyg DOI: 10.1016/0035-9203(78)90308-5 sha: doc_id: 6997 cord_uid: sghhdjyi file: cache/cord-004848-2cfphi88.json key: cord-004848-2cfphi88 authors: Carter, M. J. title: Transcription of feline calicivirus RNA date: 1990 journal: Arch Virol DOI: 10.1007/bf01310744 sha: doc_id: 4848 cord_uid: 2cfphi88 file: cache/cord-006089-08g206kf.json key: cord-006089-08g206kf authors: Stevens, James; Blixt, Ola; Paulson, James C.; Wilson, Ian A. title: Glycan microarray technologies: tools to survey host specificity of influenza viruses date: 2006-10-02 journal: Nat Rev Microbiol DOI: 10.1038/nrmicro1530 sha: doc_id: 6089 cord_uid: 08g206kf file: cache/cord-006129-5rog0s98.json key: cord-006129-5rog0s98 authors: Hemida, Maged Gomaa; Ye, Xin; Thair, Simone; Yang, Decheng title: Exploiting the Therapeutic Potential of MicroRNAs in Viral Diseases: Expectations and Limitations date: 2012-08-16 journal: Mol Diagn Ther DOI: 10.1007/bf03256383 sha: doc_id: 6129 cord_uid: 5rog0s98 file: cache/cord-004998-wuixnqy5.json key: cord-004998-wuixnqy5 authors: Arnold, W. title: Identic viral infections in four cases of malignant lymphoepithelioma date: 1978 journal: Arch Otorhinolaryngol DOI: 10.1007/bf00455364 sha: doc_id: 4998 cord_uid: wuixnqy5 file: cache/cord-007149-m4xsx9ev.json key: cord-007149-m4xsx9ev authors: Morahan, Pages S; Connor, Janice R; Leary, Kathryn R title: VIRUSES AND THE VERSATILE MACROPHAGE date: 1985-01-17 journal: Br Med Bull DOI: 10.1093/oxfordjournals.bmb.a072017 sha: doc_id: 7149 cord_uid: m4xsx9ev file: cache/cord-006954-ec9x8thb.json key: cord-006954-ec9x8thb authors: Aznar, María; Roca-Bonet, Sergi; Reguera, David title: Viral nanomechanics with a virtual atomic force microscope date: 2018-07-04 journal: J Phys Condens Matter DOI: 10.1088/1361-648x/aac57a sha: doc_id: 6954 cord_uid: ec9x8thb file: cache/cord-006252-cbelsymu.json key: cord-006252-cbelsymu authors: Gross, Peter A. title: Current Recommendations for the Prevention and Treatment of Influenza in the Older Population date: 2012-11-18 journal: Drugs Aging DOI: 10.2165/00002512-199101060-00003 sha: doc_id: 6252 cord_uid: cbelsymu file: cache/cord-007176-61e9obb3.json key: cord-007176-61e9obb3 authors: Jackson, George Gee; Muldoon, Robert Lee title: Viroses Causing Common Respiratory Infections in Man. III. Respiratory Syncytial Viroses and Coronavimses date: 1973-11-17 journal: J Infect Dis DOI: 10.1093/infdis/128.5.674 sha: doc_id: 7176 cord_uid: 61e9obb3 file: cache/cord-007796-zggk0x2q.json key: cord-007796-zggk0x2q authors: Lindemans, Caroline A.; Kimpen, Jan L. L. title: The Immune Response to Viral Lower Respiratory Tract Infection date: 2005 journal: Hot Topics in Infection and Immunity in Children II DOI: 10.1007/0-387-25342-4_4 sha: doc_id: 7796 cord_uid: zggk0x2q file: cache/cord-007898-nky7bo6u.json key: cord-007898-nky7bo6u authors: HUGHES, C.S.; GASKELL, R.M.; JONES, R.C.; BRADBURY, J.M.; JORDAN, F.T.W. title: Effects of certain stress factors on the re-excretion of infectious laryngotracheitis virus from latently infected carrier birds date: 2018-09-04 journal: Res Vet Sci DOI: 10.1016/s0034-5288(18)31158-5 sha: doc_id: 7898 cord_uid: nky7bo6u file: cache/cord-006106-u5npu6ng.json key: cord-006106-u5npu6ng authors: Attoui, H.; Mohd Jaafar, F.; Biagini, P.; Cantaloube, J.-F.; de Micco, P.; Murphy, F. A.; de Lamballerie, X. title: Genus Coltivirus (family Reoviridae): genomic and morphologic characterization of Old World and New World viruses date: 2002 journal: Arch Virol DOI: 10.1007/s007050200005 sha: doc_id: 6106 cord_uid: u5npu6ng file: cache/cord-007362-pjpkz6wv.json key: cord-007362-pjpkz6wv authors: Bielefeldt-Ohmann, Helle title: The Pathologies of Bovine Viral Diarrhea Virus Infection: A Window on the Pathogenesis date: 2016-01-06 journal: Vet Clin North Am Food Anim Pract DOI: 10.1016/s0749-0720(15)30461-8 sha: doc_id: 7362 cord_uid: pjpkz6wv file: cache/cord-008700-knbf8m4x.json key: cord-008700-knbf8m4x authors: Rodrigues, Merlyn R.; Lennette, David A.; Arentsen, Juan J.; Thompson, Charla title: Methods for Rapid Detection of Human Ocular Viral Infections date: 2013-10-30 journal: Ophthalmology DOI: 10.1016/s0161-6420(79)35507-5 sha: doc_id: 8700 cord_uid: knbf8m4x file: cache/cord-006892-n2ncamqh.json key: cord-006892-n2ncamqh authors: Donaldson, Braeden; Lateef, Zabeen; Walker, Greg F.; Young, Sarah L.; Ward, Vernon K. title: Virus-like particle vaccines: immunology and formulation for clinical translation date: 2018-09-19 journal: Expert Rev Vaccines DOI: 10.1080/14760584.2018.1516552 sha: doc_id: 6892 cord_uid: n2ncamqh file: cache/cord-008454-8brxpotx.json key: cord-008454-8brxpotx authors: Field, Anne M. title: Diagnostic Virology Using Electron Microscopic Techniques date: 2008-04-09 journal: Adv Virus Res DOI: 10.1016/s0065-3527(08)60432-7 sha: doc_id: 8454 cord_uid: 8brxpotx file: cache/cord-007733-zh8e76w7.json key: cord-007733-zh8e76w7 authors: DiMenna, Lauren J.; Ertl, Hildegund C. J. title: Pandemic Influenza Vaccines date: 2009-06-15 journal: Vaccines for Pandemic Influenza DOI: 10.1007/978-3-540-92165-3_15 sha: doc_id: 7733 cord_uid: zh8e76w7 file: cache/cord-007792-596jxrm5.json key: cord-007792-596jxrm5 authors: Luo, Ming title: Influenza Virus Entry date: 2011-08-26 journal: Viral Molecular Machines DOI: 10.1007/978-1-4614-0980-9_9 sha: doc_id: 7792 cord_uid: 596jxrm5 file: cache/cord-009615-xcz8m9a7.json key: cord-009615-xcz8m9a7 authors: Stoner, Gerald L. title: Polyomavirus Models of Brain Infection and the Pathogenesis of Multiple Sclerosis date: 2008-01-28 journal: Brain Pathol DOI: 10.1111/j.1750-3639.1993.tb00748.x sha: doc_id: 9615 cord_uid: xcz8m9a7 file: cache/cord-006640-25ykas09.json key: cord-006640-25ykas09 authors: Fedson, David S. title: What treating Ebola means for pandemic influenza date: 2018-07-16 journal: J Public Health Policy DOI: 10.1057/s41271-018-0138-8 sha: doc_id: 6640 cord_uid: 25ykas09 file: cache/cord-007575-5ekgabx5.json key: cord-007575-5ekgabx5 authors: Luby, James P. title: Southwestern Internal Medicine Conference: Pneumonias in Adults Due to Mycoplasma, Chlamydiae, and Viruses date: 2016-01-14 journal: Am J Med Sci DOI: 10.1097/00000441-198707000-00007 sha: doc_id: 7575 cord_uid: 5ekgabx5 file: cache/cord-008013-blf57r7u.json key: cord-008013-blf57r7u authors: Hartmann, K. title: Feline immunodeficiency virus infection: an overview date: 2005-03-02 journal: Vet J DOI: 10.1016/s1090-0233(98)80008-7 sha: doc_id: 8013 cord_uid: blf57r7u file: cache/cord-007445-2folsh35.json key: cord-007445-2folsh35 authors: Tuffaha, Amjad; Gern, James E.; Lemanske, Robert F. title: THE ROLE OF RESPIRATORY VIRUSES IN ACUTE AND CHRONIC ASTHMA date: 2000-06-01 journal: Clin Chest Med DOI: 10.1016/s0272-5231(05)70267-7 sha: doc_id: 7445 cord_uid: 2folsh35 file: cache/cord-006285-kkxdmzk9.json key: cord-006285-kkxdmzk9 authors: Smirnova, S. S.; Pisareva, M. M.; Smirnova, T. D.; Sivak, K. V.; Vorobiev, K. V. title: Long-Term Maintenance of the Functional Changes Induced by Influenza A Virus and/or LPS in Human Endothelial ECV-304 Cell Sublines date: 2019-08-26 journal: Cell tissue biol DOI: 10.1134/s1990519x19040084 sha: doc_id: 6285 cord_uid: kkxdmzk9 file: cache/cord-007094-ur9sz21s.json key: cord-007094-ur9sz21s authors: Mahabir, Esther; Bauer, Beth; Schmidt, Jörg title: Rodent and Germplasm Trafficking: Risks of Microbial Contamination in a High-Tech Biomedical World date: 2008-01-01 journal: ILAR J DOI: 10.1093/ilar.49.3.347 sha: doc_id: 7094 cord_uid: ur9sz21s file: cache/cord-008556-oetrdm8g.json key: cord-008556-oetrdm8g authors: Kozak, Marilyn title: Regulation of Protein Synthesis in Virus-Infected Animal Cells date: 2008-03-01 journal: Adv Virus Res DOI: 10.1016/s0065-3527(08)60265-1 sha: doc_id: 8556 cord_uid: oetrdm8g file: cache/cord-007717-7x1mqqmf.json key: cord-007717-7x1mqqmf authors: Lowen, Anice C.; Bouvier, Nicole M.; Steel, John title: Transmission in the Guinea Pig Model date: 2014-07-08 journal: Influenza Pathogenesis and Control - Volume I DOI: 10.1007/82_2014_390 sha: doc_id: 7717 cord_uid: 7x1mqqmf file: cache/cord-008149-kdlcaium.json key: cord-008149-kdlcaium authors: Blacklaws, B.A.; Daly, J.M. title: Emerging viruses of zoonotic and veterinary importance date: 2017-12-30 journal: Vet J DOI: 10.1016/j.tvjl.2017.12.022 sha: doc_id: 8149 cord_uid: kdlcaium file: cache/cord-007417-az8xd66p.json key: cord-007417-az8xd66p authors: Hansbro, Nicole G.; Horvat, Jay C.; Wark, Peter A.; Hansbro, Philip M. title: Understanding the mechanisms of viral induced asthma: New therapeutic directions date: 2008-01-29 journal: Pharmacol Ther DOI: 10.1016/j.pharmthera.2007.11.002 sha: doc_id: 7417 cord_uid: az8xd66p file: cache/cord-007764-7750z41g.json key: cord-007764-7750z41g authors: Smith, M. L.; Fitzmaurice, W. P.; Turpen, T. H.; Palmer, K. E. title: Display of Peptides on the Surface of Tobacco Mosaic Virus Particles date: 2009 journal: Plant-produced Microbial Vaccines DOI: 10.1007/978-3-540-70868-1_2 sha: doc_id: 7764 cord_uid: 7750z41g file: cache/cord-008686-9ybxuy00.json key: cord-008686-9ybxuy00 authors: Everett, Tom; Douglas, Jenny; May, Shoshanna; Horne, Simon; Marquis, Peter; Cunningham, Richard; Tang, Julian W title: Poor transmission of seasonal cold viruses in a British Antarctic Survey base date: 2019-03-14 journal: J Infect DOI: 10.1016/j.jinf.2019.03.007 sha: doc_id: 8686 cord_uid: 9ybxuy00 file: cache/cord-009383-ozx5u0t3.json key: cord-009383-ozx5u0t3 authors: Sheppard, Michael title: Viral Vectors for Veterinary Vaccines date: 2007-09-28 journal: Adv Vet Med DOI: 10.1016/s0065-3519(99)80014-7 sha: doc_id: 9383 cord_uid: ozx5u0t3 file: cache/cord-009504-sn00p8iw.json key: cord-009504-sn00p8iw authors: Taguchi, Fumihiro; Goto, Yoshitaka; Aiuchi, Masamine; Hayashi, Toshiharu; Fujiwara, Kôsaku title: Pathogenesis of Mouse Hepatitis Virus Infection: The Role of Nasal Epithelial Cells as a Primary Target of Low‐Virulence Virus, MHV‐S date: 2013-11-14 journal: Microbiol Immunol DOI: 10.1111/j.1348-0421.1979.tb00461.x sha: doc_id: 9504 cord_uid: sn00p8iw file: cache/cord-007784-fq2urilg.json key: cord-007784-fq2urilg authors: Elderfield, Ruth; Barclay, Wendy title: Influenza Pandemics date: 2011-09-22 journal: Hot Topics in Infection and Immunity in Children VIII DOI: 10.1007/978-1-4614-0204-6_8 sha: doc_id: 7784 cord_uid: fq2urilg file: cache/cord-008333-1wepke2o.json key: cord-008333-1wepke2o authors: Weisz, Ora A.; Machamer, Carolyn E. title: Chapter 7 Use of Recombinant Vaccinia Virus Vectors for Cell Biology date: 2008-02-28 journal: Methods Cell Biol DOI: 10.1016/s0091-679x(08)60602-0 sha: doc_id: 8333 cord_uid: 1wepke2o file: cache/cord-007170-svsfu7fj.json key: cord-007170-svsfu7fj authors: Richt, J. A.; VandeWoude, S.; Zink, M. C.; Clements, J. E.; Herzog, S.; Stitz, L.; Rott, R.; Narayan, O. title: Infection with Borna Disease Virus: Molecular and Immunobiological Characterization of the Agent date: 1992-06-17 journal: Clin Infect Dis DOI: 10.1093/clinids/14.6.1240 sha: doc_id: 7170 cord_uid: svsfu7fj file: cache/cord-008716-38sqkh9m.json key: cord-008716-38sqkh9m authors: Schmidt, Alexander C; Couch, Robert B; Galasso, George J; Hayden, Frederick G; Mills, John; Murphy, Brian R; Chanock, Robert M title: Current research on respiratory viral infections: Third International Symposium date: 2001-06-01 journal: Antiviral Res DOI: 10.1016/s0166-3542(01)00136-x sha: doc_id: 8716 cord_uid: 38sqkh9m file: cache/cord-009589-xfdgk2j6.json key: cord-009589-xfdgk2j6 authors: Spradbrow, P. B. title: VIRUS DISEASES OF DOMESTIC ANIMALS date: 2008-03-10 journal: Aust Vet J DOI: 10.1111/j.1751-0813.1972.tb05117.x sha: doc_id: 9589 cord_uid: xfdgk2j6 file: cache/cord-009820-fi54s0x7.json key: cord-009820-fi54s0x7 authors: Andries, K.; Pensaert, M.; Callebaut, P. title: Pathogenicity of Hemagglutinating Encephalomyelitis (Vomiting and Wasting Disease) Virus of Pigs, using Different Routes of Inoculation date: 2010-05-13 journal: J Vet Med B Infect Dis Vet Public Health DOI: 10.1111/j.1439-0450.1978.tb00754.x sha: doc_id: 9820 cord_uid: fi54s0x7 file: cache/cord-007710-0u5ot5h4.json key: cord-007710-0u5ot5h4 authors: Graham, Barney S.; Anderson, Larry J. title: Challenges and Opportunities for Respiratory Syncytial Virus Vaccines date: 2013-05-24 journal: Challenges and Opportunities for Respiratory Syncytial Virus Vaccines DOI: 10.1007/978-3-642-38919-1_20 sha: doc_id: 7710 cord_uid: 0u5ot5h4 file: cache/cord-007731-wu7i548j.json key: cord-007731-wu7i548j authors: Sriwilaijaroen, Nongluk; Suzuki, Yasuo title: Molecular Basis of a Pandemic of Avian-Type Influenza Virus date: 2014-05-27 journal: Lectins DOI: 10.1007/978-1-4939-1292-6_38 sha: doc_id: 7731 cord_uid: wu7i548j file: cache/cord-009561-pg4jmvw4.json key: cord-009561-pg4jmvw4 authors: Johnson, Richard T. title: The virology of demyelinating diseases date: 2004-10-08 journal: Ann Neurol DOI: 10.1002/ana.410360715 sha: doc_id: 9561 cord_uid: pg4jmvw4 file: cache/cord-009577-29u7pdpk.json key: cord-009577-29u7pdpk authors: Gonzalez‐Scarano, F.; Tyler, Kenneth L. title: Molecular pathogenesis of neurotropic viral infections date: 2004-10-08 journal: Ann Neurol DOI: 10.1002/ana.410220502 sha: doc_id: 9577 cord_uid: 29u7pdpk file: cache/cord-007843-yqdqm4rh.json key: cord-007843-yqdqm4rh authors: Shader, Richard I. title: Zoonotic Viruses: The Mysterious Leap From Animals to Man date: 2018-07-26 journal: Clin Ther DOI: 10.1016/j.clinthera.2018.06.016 sha: doc_id: 7843 cord_uid: yqdqm4rh file: cache/cord-009702-02bo7pnl.json key: cord-009702-02bo7pnl authors: SCOTT, G. R. title: Guidelines for the Control of Equine Viral Infections date: 2010-04-23 journal: Equine Vet J DOI: 10.1111/j.2042-3306.1971.tb04431.x sha: doc_id: 9702 cord_uid: 02bo7pnl file: cache/cord-009836-7o6htufh.json key: cord-009836-7o6htufh authors: Borrow, Persephone; Shaw, George M. title: Cytotoxic T‐lymphocyte escape viral variants: how important are they in viral evasion of immune clearance in vivo? date: 2006-04-28 journal: Immunol Rev DOI: 10.1111/j.1600-065x.1998.tb01206.x sha: doc_id: 9836 cord_uid: 7o6htufh file: cache/cord-010248-ln800g5z.json key: cord-010248-ln800g5z authors: Sissons, J.G. Patrick; Oldstone, Michael B.A. title: Antibody-Mediated Destruction of Virus-Infected Cells date: 2008-02-29 journal: Adv Immunol DOI: 10.1016/s0065-2776(08)60045-0 sha: doc_id: 10248 cord_uid: ln800g5z file: cache/cord-007530-eyk015n3.json key: cord-007530-eyk015n3 authors: Powell, H.C.; Lehrich, J.R.; Arnason, B.G. title: Electron-microscopic appearance of the DA virus, a demyelinating murine virus() date: 2003-03-06 journal: J Neurol Sci DOI: 10.1016/0022-510x(77)90087-9 sha: doc_id: 7530 cord_uid: eyk015n3 file: cache/cord-008551-yu71iewp.json key: cord-008551-yu71iewp authors: Parrish, Colin R. title: Emergence, Natural History, and Variation of Canine, Mink, and Feline Parvoviruses date: 2008-04-11 journal: Adv Virus Res DOI: 10.1016/s0065-3527(08)60867-2 sha: doc_id: 8551 cord_uid: yu71iewp file: cache/cord-009144-3slh1nbk.json key: cord-009144-3slh1nbk authors: Jacobs, J.W.; Peacock, D.B.; Corner, B.D.; Caul, E.O.; Clarke, S.K.R. title: RESPIRATORY SYNCYTIAL AND OTHER VIRUSES ASSOCIATED WITH RESPIRATORY DISEASE IN INFANTS date: 1971-05-01 journal: Lancet DOI: 10.1016/s0140-6736(71)92440-8 sha: doc_id: 9144 cord_uid: 3slh1nbk file: cache/cord-009791-k09vcq96.json key: cord-009791-k09vcq96 authors: Osterhaus, A.; Vries, J. Berghuis‐de; Steur, K. title: Antiviral Antibodies in Dogs in the Netherlands date: 2010-05-13 journal: J Vet Med B Infect Dis Vet Public Health DOI: 10.1111/j.1439-0450.1977.tb00982.x sha: doc_id: 9791 cord_uid: k09vcq96 file: cache/cord-010159-uo47oab1.json key: cord-010159-uo47oab1 authors: Jartti, Tuomas; Waris, Matti; Niesters, Hubert G.M.; Allander, Tobias; Ruuskanen, Olli title: Respiratory viruses and acute asthma in children date: 2007-04-02 journal: J Allergy Clin Immunol DOI: 10.1016/j.jaci.2007.02.025 sha: doc_id: 10159 cord_uid: uo47oab1 file: cache/cord-010016-fs8pjy1z.json key: cord-010016-fs8pjy1z authors: WEBB, H. E.; FAZAKERLEY, J. K. title: CAN VIRAL ENVELOPE GLYCOLIPIDS PRODUCE AUTO‐IMMUNITY, WITH REFERENCE TO THE CNS AND MULTIPLE SCLEROSIS? date: 2008-05-12 journal: Neuropathol Appl Neurobiol DOI: 10.1111/j.1365-2990.1984.tb00335.x sha: doc_id: 10016 cord_uid: fs8pjy1z file: cache/cord-010189-makhaypd.json key: cord-010189-makhaypd authors: Yamashita, Teruo; Sakae, Kenji title: VI, 3. Molecular biology and epidemiology of Aichi virus and other diarrhoeogenic enteroviruses date: 2004-09-14 journal: Perspect Med Virol DOI: 10.1016/s0168-7069(03)09040-2 sha: doc_id: 10189 cord_uid: makhaypd file: cache/cord-011917-6u0t4hy8.json key: cord-011917-6u0t4hy8 authors: Skarlupka, Amanda L.; Ross, Ted M. title: Immune Imprinting in the Influenza Ferret Model date: 2020-04-08 journal: Vaccines (Basel) DOI: 10.3390/vaccines8020173 sha: doc_id: 11917 cord_uid: 6u0t4hy8 file: cache/cord-008764-j9qmw4zy.json key: cord-008764-j9qmw4zy authors: nan title: Chapter 1 The need for chemotherapy and prophylaxis against viral diseases date: 2008-05-29 journal: Perspect Med Virol DOI: 10.1016/s0168-7069(08)70009-0 sha: doc_id: 8764 cord_uid: j9qmw4zy file: cache/cord-009846-o6wj8z6e.json key: cord-009846-o6wj8z6e authors: Wroblewska, Zofia; Wellish, Mary; Rorke, Lucy B.; Gilden, Donald H. title: Rat tracheal organ culture supports replication of parainfluenza 1 (6/94) virus and promotes 6/94 virus rescue from latently infected human brain cells date: 2005-12-06 journal: J Med Virol DOI: 10.1002/jmv.1890030204 sha: doc_id: 9846 cord_uid: o6wj8z6e file: cache/cord-010168-aiqbqnaa.json key: cord-010168-aiqbqnaa authors: Desselberger, Ulrich title: Classical and molecular techniques for the diagnosis of viral gastroenteritis() date: 1999-03-11 journal: Clin Diagn Virol DOI: 10.1016/0928-0197(96)00211-5 sha: doc_id: 10168 cord_uid: aiqbqnaa file: cache/cord-010188-884d196k.json key: cord-010188-884d196k authors: Schlesinger, Sondra title: Alphaviruses — vectors for the expression of heterologous genes date: 2004-08-26 journal: Trends Biotechnol DOI: 10.1016/0167-7799(93)90070-p sha: doc_id: 10188 cord_uid: 884d196k file: cache/cord-010235-hu6o1ggc.json key: cord-010235-hu6o1ggc authors: Atmar, Robert L.; Estes, Mary K. title: Nonculturable agents of viral gastroenteritis date: 1997-12-01 journal: Clin Microbiol Newsl DOI: 10.1016/s0196-4399(00)89189-8 sha: doc_id: 10235 cord_uid: hu6o1ggc file: cache/cord-011129-btaxvmsr.json key: cord-011129-btaxvmsr authors: Di Paola, Nicholas; Sanchez-Lockhart, Mariano; Zeng, Xiankun; Kuhn, Jens H.; Palacios, Gustavo title: Viral genomics in Ebola virus research date: 2020-05-04 journal: Nat Rev Microbiol DOI: 10.1038/s41579-020-0354-7 sha: doc_id: 11129 cord_uid: btaxvmsr file: cache/cord-010222-5oxie0zc.json key: cord-010222-5oxie0zc authors: Oldstone, Michael B.A. title: Virus-induced autoimmunity: Molecular mimicry as a route to autoimmune disease date: 2004-04-11 journal: J Autoimmun DOI: 10.1016/0896-8411(89)90130-3 sha: doc_id: 10222 cord_uid: 5oxie0zc file: cache/cord-010273-0c56x9f5.json key: cord-010273-0c56x9f5 authors: Simmonds, Peter title: Virology of hepatitis C virus date: 2001-10-10 journal: Clin Ther DOI: 10.1016/s0149-2918(96)80193-7 sha: doc_id: 10273 cord_uid: 0c56x9f5 file: cache/cord-011438-imbpgsub.json key: cord-011438-imbpgsub authors: Zhang, Yun; Xu, Zhichao; Cao, Yongchang title: Host–Virus Interaction: How Host Cells Defend against Influenza A Virus Infection date: 2020-03-29 journal: Viruses DOI: 10.3390/v12040376 sha: doc_id: 11438 cord_uid: imbpgsub file: cache/cord-010343-tqqt0hj7.json key: cord-010343-tqqt0hj7 authors: Alidjinou, Enagnon Kazali; Sane, Famara; Firquet, Swan; Lobert, Pierre-Emmanuel; Hober, Didier title: Resistance of Enteric Viruses on Fomites date: 2017-06-15 journal: Intervirology DOI: 10.1159/000448807 sha: doc_id: 10343 cord_uid: tqqt0hj7 file: cache/cord-010001-u0d5jkp1.json key: cord-010001-u0d5jkp1 authors: KOTWAL, GIRISH J.; KACZMAREK, JENNIFER N.; LEIVERS, STEVEN; GHEBREMARIAM, YOHANNES T.; KULKARNI, AMOD P.; BAUER, GABRIELE; DE BEER, CORENA; PREISER, WOLFGANG; MOHAMED, ABDU RAHMAN title: Anti‐HIV, Anti‐Poxvirus, and Anti‐SARS Activity of a Nontoxic, Acidic Plant Extract from the Trifollium Species Secomet‐V/anti‐Vac Suggests That It Contains a Novel Broad‐Spectrum Antiviral date: 2006-01-22 journal: Ann N Y Acad Sci DOI: 10.1196/annals.1352.014 sha: doc_id: 10001 cord_uid: u0d5jkp1 file: cache/cord-011457-hqxybv1k.json key: cord-011457-hqxybv1k authors: Kirui, James; Freed, Eric O. title: Generation and validation of a highly sensitive bioluminescent HIV-1 reporter vector that simplifies measurement of virus release date: 2020-05-19 journal: Retrovirology DOI: 10.1186/s12977-020-00521-5 sha: doc_id: 11457 cord_uid: hqxybv1k file: cache/cord-012582-k1mjik27.json key: cord-012582-k1mjik27 authors: Gallego, Iván; Lostalé-Seijo, Irene; Montenegro, Javier title: Stronger Together: Multivalent Phage Capsids Inhibit Virus Entry date: 2020-08-27 journal: Chembiochem DOI: 10.1002/cbic.202000536 sha: doc_id: 12582 cord_uid: k1mjik27 file: cache/cord-013073-siy7dvlo.json key: cord-013073-siy7dvlo authors: Pfäfflin, Albrecht title: Influenza virus-flow from insects to humans as causative for influenza seasonality date: 2020-10-09 journal: Biol Direct DOI: 10.1186/s13062-020-00272-5 sha: doc_id: 13073 cord_uid: siy7dvlo file: cache/cord-013412-gj443yei.json key: cord-013412-gj443yei authors: Lebedeva, Natalya Sh.; Gubarev, Yury A.; Koifman, Mikhail O.; Koifman, Oskar I. title: The Application of Porphyrins and Their Analogues for Inactivation of Viruses date: 2020-09-23 journal: Molecules DOI: 10.3390/molecules25194368 sha: doc_id: 13412 cord_uid: gj443yei file: cache/cord-011880-qlutgfu2.json key: cord-011880-qlutgfu2 authors: Barberis, Abdelheq; Boudaoud, Amine; Gorrill, Angelina; Loupias, Josianne; Ghram, Abdeljelil; Lachheb, Jihene; Alloui, Nadir; Ducatez, Mariette F. title: Full-length genome sequences of the first H9N2 avian influenza viruses isolated in the Northeast of Algeria date: 2020-07-17 journal: Virol J DOI: 10.1186/s12985-020-01377-z sha: doc_id: 11880 cord_uid: qlutgfu2 file: cache/cord-014541-2i0jga5v.json key: cord-014541-2i0jga5v authors: Breedlove, Byron; Arguin, Paul M. title: The Exploding Aliveness of the World date: 2017-04-17 journal: Emerg Infect Dis DOI: 10.3201/eid2304.ac2304 sha: doc_id: 14541 cord_uid: 2i0jga5v file: cache/cord-013176-6ckuya1w.json key: cord-013176-6ckuya1w authors: Ninfali, Paolino; Antonelli, Antonella; Magnani, Mauro; Scarpa, Emanuele Salvatore title: Antiviral Properties of Flavonoids and Delivery Strategies date: 2020-08-21 journal: Nutrients DOI: 10.3390/nu12092534 sha: doc_id: 13176 cord_uid: 6ckuya1w file: cache/cord-015871-1tuf4zxi.json key: cord-015871-1tuf4zxi authors: Ergonul, Onder; Mirazimi, Ali; Dimitrov, Dimiter S. title: Treatment of Crimean-Congo Hemorrhagic Fever date: 2007 journal: Crimean-Congo Hemorrhagic Fever DOI: 10.1007/978-1-4020-6106-6_19 sha: doc_id: 15871 cord_uid: 1tuf4zxi file: cache/cord-014462-11ggaqf1.json key: cord-014462-11ggaqf1 authors: nan title: Abstracts of the Papers Presented in the XIX National Conference of Indian Virological Society, “Recent Trends in Viral Disease Problems and Management”, on 18–20 March, 2010, at S.V. University, Tirupati, Andhra Pradesh date: 2011-04-21 journal: Indian J Virol DOI: 10.1007/s13337-011-0027-2 sha: doc_id: 14462 cord_uid: 11ggaqf1 file: cache/cord-016171-17ut32bu.json key: cord-016171-17ut32bu authors: Lane, J. Michael; Summer, Lila title: Smallpox as a Weapon for Bioterrorism date: 2009 journal: Bioterrorism and Infectious Agents: A New Dilemma for the 21st Century DOI: 10.1007/978-1-4419-1266-4_5 sha: doc_id: 16171 cord_uid: 17ut32bu file: cache/cord-014397-7b88ycv8.json key: cord-014397-7b88ycv8 authors: Gavora, JS title: Resistance of livestock to viruses: mechanisms and strategies for genetic engineering date: 1996-12-15 journal: Genet Sel Evol DOI: 10.1186/1297-9686-28-5-385 sha: doc_id: 14397 cord_uid: 7b88ycv8 file: cache/cord-014796-6rw2wk1q.json key: cord-014796-6rw2wk1q authors: Fayyadh, Thaer Kadhim; Ma, Fuying; Qin, Chong; Zhang, Xiaowei; Li, Wei; Zhang, Xian-En; Zhang, Zhiping; Cui, Zongqiang title: Simultaneous detection of multiple viruses in their co-infected cells using multicolour imaging with self-assembled quantum dot probes date: 2017-05-06 journal: Mikrochim Acta DOI: 10.1007/s00604-017-2300-6 sha: doc_id: 14796 cord_uid: 6rw2wk1q file: cache/cord-010374-z9ygudv6.json key: cord-010374-z9ygudv6 authors: Siddell, S.G.; Anderson, R.; Cavanagh, D.; Fujiwara, K.; Klenk, H.D.; Macnaughton, M.R.; Pensaert, M.; Stohlman, S.A.; Sturman, L.; van der Zeijst, B.A.M. title: Coronaviridae1 date: 2008-07-24 journal: Intervirology DOI: 10.1159/000149390 sha: doc_id: 10374 cord_uid: z9ygudv6 file: cache/cord-012418-6ralcn8p.json key: cord-012418-6ralcn8p authors: Schwanke, Hella; Stempel, Markus; Brinkmann, Melanie M. title: Of Keeping and Tipping the Balance: Host Regulation and Viral Modulation of IRF3-Dependent IFNB1 Expression date: 2020-07-07 journal: Viruses DOI: 10.3390/v12070733 sha: doc_id: 12418 cord_uid: 6ralcn8p file: cache/cord-016070-e9ix35x3.json key: cord-016070-e9ix35x3 authors: Perret Pérez, Cecilia; Ferrés Garrido, Marcela title: Pneumonia Caused by Emerging Viral Agents date: 2020-02-01 journal: Pediatric Respiratory Diseases DOI: 10.1007/978-3-030-26961-6_34 sha: doc_id: 16070 cord_uid: e9ix35x3 file: cache/cord-011106-h20vbmbo.json key: cord-011106-h20vbmbo authors: Takeda, Yohei; Okuyama, Yuko; Nakano, Hiroto; Yaoita, Yasunori; Machida, Koich; Ogawa, Haruko; Imai, Kunitoshi title: Antiviral Activities of Hibiscus sabdariffa L. Tea Extract Against Human Influenza A Virus Rely Largely on Acidic pH but Partially on a Low-pH-Independent Mechanism date: 2019-10-16 journal: Food Environ Virol DOI: 10.1007/s12560-019-09408-x sha: doc_id: 11106 cord_uid: h20vbmbo file: cache/cord-015023-ishxfinx.json key: cord-015023-ishxfinx authors: Jones, David title: Hard water date: 1995 journal: Nature DOI: 10.1038/377106a0 sha: doc_id: 15023 cord_uid: ishxfinx file: cache/cord-015619-msicix98.json key: cord-015619-msicix98 authors: nan title: Virus Structure & Assembly date: 2009-02-24 journal: Biophys J DOI: 10.1016/s0006-3495(08)79065-9 sha: doc_id: 15619 cord_uid: msicix98 file: cache/cord-015764-ly68q5z0.json key: cord-015764-ly68q5z0 authors: Poissy, J.; Terrier, O.; Lina, B.; Textoris, J.; Rosa-Calatrava, M. title: La modulation de la signature transcriptomique de l’hôte infecté : une nouvelle stratégie thérapeutique dans les viroses graves ? Exemple de la grippe date: 2016-04-07 journal: Reanimation DOI: 10.1007/s13546-016-1188-1 sha: doc_id: 15764 cord_uid: ly68q5z0 file: cache/cord-016475-7ldxvbpz.json key: cord-016475-7ldxvbpz authors: Pleschka, Stephan; Ludwig, Stephan; Wolff, Thorsten; Planz, Oliver title: Anti-viral approaches against influenza viruses date: 2006 journal: New Concepts of Antiviral Therapy DOI: 10.1007/978-0-387-31047-3_5 sha: doc_id: 16475 cord_uid: 7ldxvbpz file: cache/cord-016928-yigz9qiz.json key: cord-016928-yigz9qiz authors: Bhattacharyya, Sankar title: Inflammation During Virus Infection: Swings and Roundabouts date: 2019-11-05 journal: Dynamics of Immune Activation in Viral Diseases DOI: 10.1007/978-981-15-1045-8_3 sha: doc_id: 16928 cord_uid: yigz9qiz file: cache/cord-016796-g4kqqpy1.json key: cord-016796-g4kqqpy1 authors: Bramhachari, Pallaval Veera; Mohana Sheela, Ganugula; Prathyusha, A. M. V. N.; Madhavi, M.; Satish Kumar, K.; Reddy, Neelapu Nageswara Rao; Berde, Chanda Parulekar title: Advanced Immunotechnological Methods for Detection and Diagnosis of Viral Infections: Current Applications and Future Challenges date: 2019-11-05 journal: Dynamics of Immune Activation in Viral Diseases DOI: 10.1007/978-981-15-1045-8_17 sha: doc_id: 16796 cord_uid: g4kqqpy1 file: cache/cord-013526-6fip93l2.json key: cord-013526-6fip93l2 authors: Labadie, Thomas; Roy, Polly title: A non-enveloped arbovirus released in lysosome-derived extracellular vesicles induces super-infection exclusion date: 2020-10-19 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1009015 sha: doc_id: 13526 cord_uid: 6fip93l2 file: cache/cord-016663-qnp99m7o.json key: cord-016663-qnp99m7o authors: Taylor, Robert B. title: Medical Words Linked to Places date: 2017-02-01 journal: The Amazing Language of Medicine DOI: 10.1007/978-3-319-50328-8_5 sha: doc_id: 16663 cord_uid: qnp99m7o file: cache/cord-016309-6mw8okmt.json key: cord-016309-6mw8okmt authors: Bule, Mohammed; Khan, Fazlullah; Niaz, Kamal title: Antivirals: Past, Present and Future date: 2019-06-06 journal: Recent Advances in Animal Virology DOI: 10.1007/978-981-13-9073-9_22 sha: doc_id: 16309 cord_uid: 6mw8okmt file: cache/cord-016652-x8t3lf1x.json key: cord-016652-x8t3lf1x authors: Matthews, David; Emmott, Edward; Hiscox, Julian title: Viruses and the Nucleolus date: 2011-05-23 journal: The Nucleolus DOI: 10.1007/978-1-4614-0514-6_14 sha: doc_id: 16652 cord_uid: x8t3lf1x file: cache/cord-016798-tv2ntug6.json key: cord-016798-tv2ntug6 authors: Gautam, Ablesh; Tiwari, Ashish; Malik, Yashpal Singh title: Bioinformatics Applications in Advancing Animal Virus Research date: 2019-06-06 journal: Recent Advances in Animal Virology DOI: 10.1007/978-981-13-9073-9_23 sha: doc_id: 16798 cord_uid: tv2ntug6 file: cache/cord-014908-jys1y0k9.json key: cord-014908-jys1y0k9 authors: Yadav, Rakesh; Dwivedi, Sadhana; Kumar, Sandeep; Chaudhury, Ashok title: Trends and Perspectives of Biosensors for Food and Environmental Virology date: 2010-05-19 journal: Food Environ Virol DOI: 10.1007/s12560-010-9034-5 sha: doc_id: 14908 cord_uid: jys1y0k9 file: cache/cord-016754-6fv8mjld.json key: cord-016754-6fv8mjld authors: Iturriza-Gómara, Miren; Gallimore, Chris I.; Gray, Jim title: Gastroenteric Viruses date: 2007 journal: Foodborne Diseases DOI: 10.1007/978-1-59745-501-5_8 sha: doc_id: 16754 cord_uid: 6fv8mjld file: cache/cord-016576-1yqwci0y.json key: cord-016576-1yqwci0y authors: Hu, Xiaohua; Yoo, Illhoi; Rumm, Peter; Atwood, Michael title: Mining Candidate Viruses as Potential Bio-terrorism Weapons from Biomedical Literature date: 2005 journal: Intelligence and Security Informatics DOI: 10.1007/11427995_6 sha: doc_id: 16576 cord_uid: 1yqwci0y file: cache/cord-016808-gy8d8285.json key: cord-016808-gy8d8285 authors: Agol, Vadim I. title: The Origin and Evolution of Viruses date: 2008 journal: Evolution from Cellular to Social Scales DOI: 10.1007/978-1-4020-8761-5_7 sha: doc_id: 16808 cord_uid: gy8d8285 file: cache/cord-016451-k8m2xz0e.json key: cord-016451-k8m2xz0e authors: Chertow, Daniel S.; Kindrachuk, Jason title: Influenza, Measles, SARS, MERS, and Smallpox date: 2020-01-03 journal: Highly Infectious Diseases in Critical Care DOI: 10.1007/978-3-030-33803-9_5 sha: doc_id: 16451 cord_uid: k8m2xz0e file: cache/cord-017070-05vlz5dn.json key: cord-017070-05vlz5dn authors: Dimitrov, Dimiter S. title: Human Monoclonal Antibodies Against HIV and Emerging Viruses date: 2008 journal: National Institute of Allergy and Infectious Diseases, NIH DOI: 10.1007/978-1-59745-569-5_34 sha: doc_id: 17070 cord_uid: 05vlz5dn file: cache/cord-016990-ot1wi3xi.json key: cord-016990-ot1wi3xi authors: Zaki, Sherif R.; Paddock, Christopher D. title: Viral Infections of the Lung date: 2008 journal: Dail and Hammar’s Pulmonary Pathology DOI: 10.1007/978-0-387-68792-6_11 sha: doc_id: 16990 cord_uid: ot1wi3xi file: cache/cord-016499-5iqpl23p.json key: cord-016499-5iqpl23p authors: Mackay, Ian M.; Arden, Katherine E. title: Rhinoviruses date: 2014-02-27 journal: Viral Infections of Humans DOI: 10.1007/978-1-4899-7448-8_29 sha: doc_id: 16499 cord_uid: 5iqpl23p file: cache/cord-016538-4og05fuo.json key: cord-016538-4og05fuo authors: Dolja, V. V.; Meng, B. title: Biotechnology Applications of Grapevine Viruses date: 2017-03-30 journal: Grapevine Viruses: Molecular Biology, Diagnostics and Management DOI: 10.1007/978-3-319-57706-7_31 sha: doc_id: 16538 cord_uid: 4og05fuo file: cache/cord-016995-5izyl234.json key: cord-016995-5izyl234 authors: Auewarakul, Prasert title: The Past and Present Threat of Avian Influenza in Thailand date: 2008 journal: Emerging Infections in Asia DOI: 10.1007/978-0-387-75722-3_2 sha: doc_id: 16995 cord_uid: 5izyl234 file: cache/cord-017249-la5sum39.json key: cord-017249-la5sum39 authors: Feldblyum, Tamara V.; Segal, David M. title: Seasonal and Pandemic Influenza Surveillance and Disease Severity date: 2015-05-12 journal: Global Virology I - Identifying and Investigating Viral Diseases DOI: 10.1007/978-1-4939-2410-3_29 sha: doc_id: 17249 cord_uid: la5sum39 file: cache/cord-017158-w2tlq6ho.json key: cord-017158-w2tlq6ho authors: Moriones, Enrique; García-Andrés, Susana; Navas-Castillo, Jesús title: Recombination in the TYLCV Complex: a Mechanism to Increase Genetic Diversity. Implications for Plant Resistance Development date: 2007 journal: Tomato Yellow Leaf Curl Virus Disease DOI: 10.1007/978-1-4020-4769-5_7 sha: doc_id: 17158 cord_uid: w2tlq6ho file: cache/cord-016882-c9ts2g7w.json key: cord-016882-c9ts2g7w authors: Ribeiro, Edna; Leitão, Céu; Cristovam, Elisabete; Dias, Ana title: Viruses Present Indoors and Analyses Approaches date: 2017-06-12 journal: Exposure to Microbiological Agents in Indoor and Occupational Environments DOI: 10.1007/978-3-319-61688-9_7 sha: doc_id: 16882 cord_uid: c9ts2g7w file: cache/cord-017429-3evwlfac.json key: cord-017429-3evwlfac authors: Hubálek, Zdenek; Rudolf, Ivo title: Vertebrates as Hosts and Reservoirs of Zoonotic Microbial Agents date: 2010-11-10 journal: Microbial Zoonoses and Sapronoses DOI: 10.1007/978-90-481-9657-9_7 sha: doc_id: 17429 cord_uid: 3evwlfac file: cache/cord-017008-c7skxte0.json key: cord-017008-c7skxte0 authors: Méthot, Pierre-Olivier; Alizon, Samuel title: Emerging Disease and the Evolution of Virulence: The Case of the 1918–1919 Influenza Pandemic date: 2014-08-22 journal: Classification, Disease and Evidence DOI: 10.1007/978-94-017-8887-8_5 sha: doc_id: 17008 cord_uid: c7skxte0 file: cache/cord-017489-ftz9190a.json key: cord-017489-ftz9190a authors: Richards, Guy A.; Schleicher, Gunter; Mer, Mervyn title: Viruses in the Intensive Care Unit (ICU) date: 2005 journal: Tropical and Parasitic Infections in the Intensive Care Unit DOI: 10.1007/0-387-23380-6_3 sha: doc_id: 17489 cord_uid: ftz9190a file: cache/cord-017364-d9zmdm23.json key: cord-017364-d9zmdm23 authors: Crowe, James E.; Williams, John V. title: Paramyxoviruses: Respiratory Syncytial Virus and Human Metapneumovirus date: 2014-02-27 journal: Viral Infections of Humans DOI: 10.1007/978-1-4899-7448-8_26 sha: doc_id: 17364 cord_uid: d9zmdm23 file: cache/cord-017326-1caeui30.json key: cord-017326-1caeui30 authors: Seay, Montrell; Dinesh-Kumar, Savithramma; Levine, Beth title: Digesting Oneself and Digesting Microbes: Autophagy as a Host Response to Viral Infection date: 2005 journal: Modulation of Host Gene Expression and Innate Immunity by Viruses DOI: 10.1007/1-4020-3242-0_11 sha: doc_id: 17326 cord_uid: 1caeui30 file: cache/cord-017537-ztdz4a2s.json key: cord-017537-ztdz4a2s authors: Bologna, Mauro title: Biological Agents and Bioterrorism date: 2014-09-18 journal: Detection of Chemical, Biological, Radiological and Nuclear Agents for the Prevention of Terrorism DOI: 10.1007/978-94-017-9238-7_1 sha: doc_id: 17537 cord_uid: ztdz4a2s file: cache/cord-017748-xy26tk0t.json key: cord-017748-xy26tk0t authors: Georgiev, Vassil St. title: Influenza date: 2009 journal: National Institute of Allergy and Infectious Diseases, NIH DOI: 10.1007/978-1-60327-297-1_13 sha: doc_id: 17748 cord_uid: xy26tk0t file: cache/cord-017287-70lk77zb.json key: cord-017287-70lk77zb authors: Sánchez, Gloria; Bosch, Albert title: Survival of Enteric Viruses in the Environment and Food date: 2016-08-26 journal: Viruses in Foods DOI: 10.1007/978-3-319-30723-7_13 sha: doc_id: 17287 cord_uid: 70lk77zb file: cache/cord-017527-ylng1us2.json key: cord-017527-ylng1us2 authors: Herman, Philippe; Pauwels, Katia title: Biosafety Recommendations on the Handling of Animal Cell Cultures date: 2014-11-05 journal: Animal Cell Culture DOI: 10.1007/978-3-319-10320-4_22 sha: doc_id: 17527 cord_uid: ylng1us2 file: cache/cord-017959-g0nf1iwm.json key: cord-017959-g0nf1iwm authors: Lipkin, W. Ian; Briese, Thomas title: Diagnosis, Discovery and Dissection of Viral Diseases date: 2014-02-27 journal: Viral Infections of Humans DOI: 10.1007/978-1-4899-7448-8_2 sha: doc_id: 17959 cord_uid: g0nf1iwm file: cache/cord-017568-8fnr4zzv.json key: cord-017568-8fnr4zzv authors: Wang, Lin-Fa; Mackenzie, John S.; Eaton, Bryan T. title: Disease Outbreaks Caused by Emerging Paramyxoviruses of Bat Origin date: 2008 journal: Emerging Infections in Asia DOI: 10.1007/978-0-387-75722-3_12 sha: doc_id: 17568 cord_uid: 8fnr4zzv file: cache/cord-017764-h1w9gbxk.json key: cord-017764-h1w9gbxk authors: Meanwell, Nicholas A.; Belema, Makonen title: The Discovery and Development of Daclatasvir: An Inhibitor of the Hepatitis C Virus NS5A Replication Complex date: 2018-06-08 journal: HCV: The Journey from Discovery to a Cure DOI: 10.1007/7355_2018_47 sha: doc_id: 17764 cord_uid: h1w9gbxk file: cache/cord-018164-h5k1zsyg.json key: cord-018164-h5k1zsyg authors: Taylor, Milton W. title: What Is a Virus? date: 2014-07-22 journal: Viruses and Man: A History of Interactions DOI: 10.1007/978-3-319-07758-1_2 sha: doc_id: 18164 cord_uid: h5k1zsyg file: cache/cord-017331-ru7mvfc0.json key: cord-017331-ru7mvfc0 authors: Samanta, Indranil; Bandyopadhyay, Samiran title: Infectious Diseases date: 2017-02-25 journal: Pet bird diseases and care DOI: 10.1007/978-981-10-3674-3_2 sha: doc_id: 17331 cord_uid: ru7mvfc0 file: cache/cord-018058-n3majqes.json key: cord-018058-n3majqes authors: Modrow, Susanne; Falke, Dietrich; Truyen, Uwe; Schätzl, Hermann title: Historical Overview date: 2013-08-12 journal: Molecular Virology DOI: 10.1007/978-3-642-20718-1_1 sha: doc_id: 18058 cord_uid: n3majqes file: cache/cord-017167-8cdbcrh7.json key: cord-017167-8cdbcrh7 authors: Ahola, Tero; Merits, Andres title: Functions of Chikungunya Virus Nonstructural Proteins date: 2016-12-03 journal: Chikungunya Virus DOI: 10.1007/978-3-319-42958-8_6 sha: doc_id: 17167 cord_uid: 8cdbcrh7 file: cache/cord-018078-clxzp1ph.json key: cord-018078-clxzp1ph authors: Weber, Olaf; Schmidt, Axel title: Coronavirus infections in veterinary medicine date: 2005 journal: Coronaviruses with Special Emphasis on First Insights Concerning SARS DOI: 10.1007/3-7643-7339-3_2 sha: doc_id: 18078 cord_uid: clxzp1ph file: cache/cord-017824-0pinevfc.json key: cord-017824-0pinevfc authors: Tekes, Gergely title: Vaccinia Virus-Based Reverse Genetics for Feline Coronaviruses date: 2015-09-10 journal: Animal Coronaviruses DOI: 10.1007/978-1-4939-3414-0_7 sha: doc_id: 17824 cord_uid: 0pinevfc file: cache/cord-017752-ofzm3x3a.json key: cord-017752-ofzm3x3a authors: nan title: Theories of Carcinogenesis date: 2007 journal: Molecular Mechanisms of Cancer DOI: 10.1007/978-1-4020-6016-8_1 sha: doc_id: 17752 cord_uid: ofzm3x3a file: cache/cord-017758-zfudssm9.json key: cord-017758-zfudssm9 authors: Fong, I. W. title: Emergence of New Tickborne Infections date: 2017-02-08 journal: Emerging Zoonoses DOI: 10.1007/978-3-319-50890-0_5 sha: doc_id: 17758 cord_uid: zfudssm9 file: cache/cord-018364-b06084r1.json key: cord-018364-b06084r1 authors: LaBrunda, Michelle; Amin, Naushad title: The Emerging Threat of Ebola date: 2019-06-07 journal: Global Health Security DOI: 10.1007/978-3-030-23491-1_6 sha: doc_id: 18364 cord_uid: b06084r1 file: cache/cord-018040-k0h5ejjt.json key: cord-018040-k0h5ejjt authors: Ilyinskii, P. title: Aspects of Microparticle Utilization for Potentiation of Novel Vaccines: Promises and Risks date: 2009 journal: Silicon Versus Carbon DOI: 10.1007/978-90-481-2523-4_26 sha: doc_id: 18040 cord_uid: k0h5ejjt file: cache/cord-018166-savdgy0u.json key: cord-018166-savdgy0u authors: Bosch, Albert; Pintó, Rosa M.; Abad, F. Xavier title: Survival and Transport of Enteric Viruses in the Environment date: 2006 journal: Viruses in Foods DOI: 10.1007/0-387-29251-9_6 sha: doc_id: 18166 cord_uid: savdgy0u file: cache/cord-018463-a6qu0cuv.json key: cord-018463-a6qu0cuv authors: Wimmer, Eckard title: Synthetic Biology, Dual Use Research, and Possibilities for Control date: 2018-03-23 journal: Defence Against Bioterrorism DOI: 10.1007/978-94-024-1263-5_2 sha: doc_id: 18463 cord_uid: a6qu0cuv file: cache/cord-018302-lmly43rd.json key: cord-018302-lmly43rd authors: Renaud, Christian; Englund, Janet title: Respiratory Syncytial Virus and Human Metapneumovirus Infection in Transplant Recipients date: 2016-02-15 journal: Transplant Infections DOI: 10.1007/978-3-319-28797-3_31 sha: doc_id: 18302 cord_uid: lmly43rd file: cache/cord-018165-afzjx2ci.json key: cord-018165-afzjx2ci authors: Modrow, Susanne; Falke, Dietrich; Truyen, Uwe; Schätzl, Hermann title: Vaccines date: 2013-08-12 journal: Molecular Virology DOI: 10.1007/978-3-642-20718-1_10 sha: doc_id: 18165 cord_uid: afzjx2ci file: cache/cord-018319-tylkbh4h.json key: cord-018319-tylkbh4h authors: Chemaly, Roy F.; Rathod, Dhanesh B.; Couch, Robert title: Respiratory Viruses date: 2011-01-04 journal: Principles and Practice of Cancer Infectious Diseases DOI: 10.1007/978-1-60761-644-3_32 sha: doc_id: 18319 cord_uid: tylkbh4h file: cache/cord-018555-3lta1tbp.json key: cord-018555-3lta1tbp authors: Overstreet, Robin M.; Lotz, Jeffrey M. title: Host–Symbiont Relationships: Understanding the Change from Guest to Pest date: 2016-01-06 journal: The Rasputin Effect: When Commensals and Symbionts Become Parasitic DOI: 10.1007/978-3-319-28170-4_2 sha: doc_id: 18555 cord_uid: 3lta1tbp file: cache/cord-018265-twp33bb6.json key: cord-018265-twp33bb6 authors: Becker, Pablo D.; Guzmán, Carlos A. title: Community-acquired pneumonia: paving the way towards new vaccination concepts date: 2007 journal: Community-Acquired Pneumonia DOI: 10.1007/978-3-7643-7563-8_10 sha: doc_id: 18265 cord_uid: twp33bb6 file: cache/cord-018089-m94q75xn.json key: cord-018089-m94q75xn authors: Mubareka, Samira; Palese, Peter title: Influenza Virus: The Biology of a Changing Virus date: 2010-06-18 journal: Influenza Vaccines for the Future DOI: 10.1007/978-3-0346-0279-2_1 sha: doc_id: 18089 cord_uid: m94q75xn file: cache/cord-018816-v3ylisbt.json key: cord-018816-v3ylisbt authors: Alroy, Joseph; Lyons, Jeremiah A.; Kavirayani, Anoop M. title: Viral Pulmonary Disorders in Animals: Neoplastic and Nonneoplastic date: 2013-08-26 journal: Viruses and the Lung DOI: 10.1007/978-3-642-40605-8_24 sha: doc_id: 18816 cord_uid: v3ylisbt file: cache/cord-019982-hyxrgamj.json key: cord-019982-hyxrgamj authors: Brookfield, D.S.K.; Cosgrove, B.P.; Bell, E.J.; Madeley, C.R. title: Viruses demonstrated in children in Tanzania: Studies in diarrhoea and measles date: 2005-04-14 journal: J Infect DOI: 10.1016/s0163-4453(79)91285-4 sha: doc_id: 19982 cord_uid: hyxrgamj file: cache/cord-018724-ss8x2g3b.json key: cord-018724-ss8x2g3b authors: Stobbe, Anthony; Roossinck, Marilyn J. title: Plant Virus Diversity and Evolution date: 2016-06-22 journal: Current Research Topics in Plant Virology DOI: 10.1007/978-3-319-32919-2_8 sha: doc_id: 18724 cord_uid: ss8x2g3b file: cache/cord-018393-5jlqn7wq.json key: cord-018393-5jlqn7wq authors: Finke, Ernst-Jürgen; Tomaso, Herbert; Frangoulidis, Dimitrios title: Bioterrorismus, infektiologische Aspekte date: 2011-12-14 journal: Lexikon der Infektionskrankheiten des Menschen DOI: 10.1007/978-3-642-17158-1_3 sha: doc_id: 18393 cord_uid: 5jlqn7wq file: cache/cord-018017-c8myq6bi.json key: cord-018017-c8myq6bi authors: Iversen, Patrick L. title: The Threat from Viruses date: 2018-09-30 journal: Molecular Basis of Resilience DOI: 10.1007/978-3-319-98164-2_3 sha: doc_id: 18017 cord_uid: c8myq6bi file: cache/cord-018437-yjvwa1ot.json key: cord-018437-yjvwa1ot authors: Mitchell, Michael title: Taxonomy date: 2013-08-26 journal: Viruses and the Lung DOI: 10.1007/978-3-642-40605-8_3 sha: doc_id: 18437 cord_uid: yjvwa1ot file: cache/cord-020101-5rib7pe8.json key: cord-020101-5rib7pe8 authors: nan title: Cumulative Author Index for 2008 date: 2008-11-17 journal: Virus Res DOI: 10.1016/s0168-1702(08)00367-5 sha: doc_id: 20101 cord_uid: 5rib7pe8 file: cache/cord-020789-slsfhrkx.json key: cord-020789-slsfhrkx authors: Kleines, Michael title: Virale Atemwegserkrankungen – Influenza, RSV und neue Viren date: 2017-10-27 journal: nan DOI: 10.1055/s-0043-114856 sha: doc_id: 20789 cord_uid: slsfhrkx file: cache/cord-018477-hgvqd1ej.json key: cord-018477-hgvqd1ej authors: Modrow, Susanne; Falke, Dietrich; Truyen, Uwe; Schätzl, Hermann title: Pathogenesis date: 2013-08-12 journal: Molecular Virology DOI: 10.1007/978-3-642-20718-1_4 sha: doc_id: 18477 cord_uid: hgvqd1ej file: cache/cord-018639-0g1ov96t.json key: cord-018639-0g1ov96t authors: Kurpiers, Laura A.; Schulte-Herbrüggen, Björn; Ejotre, Imran; Reeder, DeeAnn M. title: Bushmeat and Emerging Infectious Diseases: Lessons from Africa date: 2015-09-21 journal: Problematic Wildlife DOI: 10.1007/978-3-319-22246-2_24 sha: doc_id: 18639 cord_uid: 0g1ov96t file: cache/cord-018811-zhwr3h07.json key: cord-018811-zhwr3h07 authors: Oxford, John; Gilbert, Anthony; Lambkin-Williams, Robert title: Influenza Vaccines Have a Short but Illustrious History of Dedicated Science Enabling the Rapid Global Production of A/Swine (H1N1) Vaccine in the Current Pandemic date: 2010-06-18 journal: Influenza Vaccines for the Future DOI: 10.1007/978-3-0346-0279-2_6 sha: doc_id: 18811 cord_uid: zhwr3h07 file: cache/cord-018804-wj35q88f.json key: cord-018804-wj35q88f authors: Lázaro, Ester title: Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity date: 2007 journal: Structural Approaches to Sequence Evolution DOI: 10.1007/978-3-540-35306-5_15 sha: doc_id: 18804 cord_uid: wj35q88f file: cache/cord-020087-gs0pc6ee.json key: cord-020087-gs0pc6ee authors: nan title: Cumulative Contents for 2010 date: 2010-11-18 journal: Virus Res DOI: 10.1016/s0168-1702(10)00397-7 sha: doc_id: 20087 cord_uid: gs0pc6ee file: cache/cord-021034-hnw7a3a1.json key: cord-021034-hnw7a3a1 authors: Mahony, James B.; Chernesky, Max A. title: Negative staining in the detection of viruses in clinical specimens date: 2002-10-09 journal: nan DOI: 10.1016/0739-6260(91)90062-5 sha: doc_id: 21034 cord_uid: hnw7a3a1 file: cache/cord-020235-stcrozdw.json key: cord-020235-stcrozdw authors: nan title: Abstracts of Papers Presented at the 38th Meeting of the Deutsche Gesellschaft für Hygiene und Mikrobiologie, Virology Section, Göttingen, 5.–8.10.1981 date: 2012-03-15 journal: Zentralbl Bakteriol Mikrobiol Hyg A DOI: 10.1016/s0174-3031(82)80128-5 sha: doc_id: 20235 cord_uid: stcrozdw file: cache/cord-018441-r6wwpfcy.json key: cord-018441-r6wwpfcy authors: Taylor, Milton W. title: Emerging Viruses date: 2014-07-22 journal: Viruses and Man: A History of Interactions DOI: 10.1007/978-3-319-07758-1_20 sha: doc_id: 18441 cord_uid: r6wwpfcy file: cache/cord-021069-v9f9874x.json key: cord-021069-v9f9874x authors: Morrison, Lynda A.; Fields, Bernard N. title: Viral pathogenesis and central nervous system infection date: 2004-11-23 journal: nan DOI: 10.1016/1044-5765(91)90002-6 sha: doc_id: 21069 cord_uid: v9f9874x file: cache/cord-020097-eh5deunk.json key: cord-020097-eh5deunk authors: nan title: Cumulative Author Index for 2006 (Volumes 115–122) date: 2006-10-27 journal: Virus Res DOI: 10.1016/s0168-1702(06)00318-2 sha: doc_id: 20097 cord_uid: eh5deunk file: cache/cord-020714-h1fevqcw.json key: cord-020714-h1fevqcw authors: Compans, Richard W.; Kemp, Maurice C. title: Membrane Glycoproteins of Enveloped Viruses date: 2008-05-30 journal: Curr Top Membr Transp DOI: 10.1016/s0070-2161(08)60750-9 sha: doc_id: 20714 cord_uid: h1fevqcw file: cache/cord-018706-gykw2nvt.json key: cord-018706-gykw2nvt authors: Yadav, Mahendra Pal; Singh, Raj Kumar; Malik, Yashpal Singh title: Emerging and Transboundary Animal Viral Diseases: Perspectives and Preparedness date: 2020-02-23 journal: Emerging and Transboundary Animal Viruses DOI: 10.1007/978-981-15-0402-0_1 sha: doc_id: 18706 cord_uid: gykw2nvt file: cache/cord-020969-lh2ergpm.json key: cord-020969-lh2ergpm authors: STRAUSS, JAMES H.; STRAUSS, ELLEN G. title: Gene Therapy date: 2012-07-27 journal: Viruses and Human Disease DOI: 10.1016/b978-0-12-373741-0.50014-3 sha: doc_id: 20969 cord_uid: lh2ergpm file: cache/cord-020712-l9cn0n99.json key: cord-020712-l9cn0n99 authors: Ohnishi, Shun-Ichi title: Chapter 9 Fusion of Viral Envelopes with Cellular Membranes date: 2008-05-30 journal: Curr Top Membr Transp DOI: 10.1016/s0070-2161(08)60137-9 sha: doc_id: 20712 cord_uid: l9cn0n99 file: cache/cord-021413-1ht1xm88.json key: cord-021413-1ht1xm88 authors: Kraft, Lisbeth M. title: Viral Diseases of the Digestive System date: 2013-10-21 journal: Diseases DOI: 10.1016/b978-0-12-262502-2.50016-x sha: doc_id: 21413 cord_uid: 1ht1xm88 file: cache/cord-021588-ec7udsmw.json key: cord-021588-ec7udsmw authors: Craighead, John E. title: Enteric Viral Disease date: 2007-05-09 journal: Pathology and Pathogenesis of Human Viral Disease DOI: 10.1016/b978-012195160-3/50033-9 sha: doc_id: 21588 cord_uid: ec7udsmw file: cache/cord-021894-lq8yr710.json key: cord-021894-lq8yr710 authors: Cunningham, Steve title: Bronchiolitis date: 2018-03-13 journal: Kendig's Disorders of the Respiratory Tract in Children DOI: 10.1016/b978-0-323-44887-1.00024-9 sha: doc_id: 21894 cord_uid: lq8yr710 file: cache/cord-019051-gtruu1op.json key: cord-019051-gtruu1op authors: Weber, Olaf title: The role of viruses in the etiology and pathogenesis of common cold date: 2009-11-10 journal: Common Cold DOI: 10.1007/978-3-7643-9912-2_5 sha: doc_id: 19051 cord_uid: gtruu1op file: cache/cord-021499-up5vftj4.json key: cord-021499-up5vftj4 authors: Brayton, Cory; Mähler, Michael; Nicklas, Werner title: Viral Infections date: 2007-09-02 journal: The Laboratory Mouse DOI: 10.1016/b978-012336425-8/50076-5 sha: doc_id: 21499 cord_uid: up5vftj4 file: cache/cord-020756-d9f5fd7x.json key: cord-020756-d9f5fd7x authors: de Jong, Menno Douwe title: Avian Influenza Viruses and Pandemic Influenza date: 2007 journal: New and Evolving Infections of the 21st Century DOI: 10.1007/978-0-387-32830-0_9 sha: doc_id: 20756 cord_uid: d9f5fd7x file: cache/cord-021116-rh0e4n2w.json key: cord-021116-rh0e4n2w authors: Lippens, Ronnie title: Viral Contagion and Anti-Terrorism: Notes on Medical Emergency, Legality and Diplomacy date: 2004 journal: nan DOI: 10.1023/b:sela.0000033617.97749.13 sha: doc_id: 21116 cord_uid: rh0e4n2w file: cache/cord-021770-zn7na974.json key: cord-021770-zn7na974 authors: Slifka, Mark K.; Amanna, Ian J. title: Passive Immunization date: 2017-07-17 journal: Plotkin's Vaccines DOI: 10.1016/b978-0-323-35761-6.00008-0 sha: doc_id: 21770 cord_uid: zn7na974 file: cache/cord-021375-lca26xum.json key: cord-021375-lca26xum authors: Voelkner, Nadine title: Riding the Shi: From Infection Barriers to the Microbial City date: 2019-08-23 journal: nan DOI: 10.1093/ips/olz016 sha: doc_id: 21375 cord_uid: lca26xum file: cache/cord-021805-2j07zw6q.json key: cord-021805-2j07zw6q authors: Epstein, Jonathan H. title: Emerging Diseases in Bats date: 2018-09-28 journal: Fowler's Zoo and Wild Animal Medicine Current Therapy, Volume 9 DOI: 10.1016/b978-0-323-55228-8.00040-0 sha: doc_id: 21805 cord_uid: 2j07zw6q file: cache/cord-021552-6jbm869r.json key: cord-021552-6jbm869r authors: HURST, CHRISTON J.; ADCOCK, NOREEN J. title: Relationship Between Humans and Their Viruses date: 2007-05-09 journal: Viral Ecology DOI: 10.1016/b978-012362675-2/50015-x sha: doc_id: 21552 cord_uid: 6jbm869r file: cache/cord-022254-8y5sq72c.json key: cord-022254-8y5sq72c authors: Nathanson, Neal; Gonzalez-Scarano, Francisco title: IMMUNOSUPPRESSION AND VIRUS INFECTION OF RODENTS date: 2012-12-02 journal: Viral and Mycoplasmal of Laboratory Rodents DOI: 10.1016/b978-0-12-095785-9.50036-6 sha: doc_id: 22254 cord_uid: 8y5sq72c file: cache/cord-020010-q58x6xb0.json key: cord-020010-q58x6xb0 authors: nan title: 19th ICAR Abstracts: date: 2006-03-13 journal: Antiviral Res DOI: 10.1016/j.antiviral.2006.02.001 sha: doc_id: 20010 cord_uid: q58x6xb0 file: cache/cord-021465-2pj26fmv.json key: cord-021465-2pj26fmv authors: PERDUE, MICHAEL L.; SEAL, BRUCE S. title: Impact of Avian Viruses date: 2007-05-09 journal: Viral Ecology DOI: 10.1016/b978-012362675-2/50016-1 sha: doc_id: 21465 cord_uid: 2pj26fmv file: cache/cord-022084-hap7flng.json key: cord-022084-hap7flng authors: ARRUDA, EURICO; CINTRA, OTAVIO A.L.; HAYDEN, FREDERICK G. title: Respiratory Tract Viral Infections date: 2009-05-15 journal: Tropical Infectious Diseases DOI: 10.1016/b978-0-443-06668-9.50064-8 sha: doc_id: 22084 cord_uid: hap7flng file: cache/cord-022348-w7z97wir.json key: cord-022348-w7z97wir authors: Sola, Monica; Wain-Hobson, Simon title: Drift and Conservatism in RNA Virus Evolution: Are They Adapting or Merely Changing? date: 2007-09-02 journal: Origin and Evolution of Viruses DOI: 10.1016/b978-012220360-2/50007-6 sha: doc_id: 22348 cord_uid: w7z97wir file: cache/cord-022324-tcltmhi7.json key: cord-022324-tcltmhi7 authors: Barthold, Stephen W. title: MOUSE HEPATITIS VIRUS BIOLOGY AND EPIZOOTIOLOGY date: 2012-12-02 journal: Viral and Mycoplasmal of Laboratory Rodents DOI: 10.1016/b978-0-12-095785-9.50032-9 sha: doc_id: 22324 cord_uid: tcltmhi7 file: cache/cord-021990-a8ku5rke.json key: cord-021990-a8ku5rke authors: Tyring, Stephen K. title: Syndromal Tropical Dermatology date: 2016-12-02 journal: Tropical Dermatology DOI: 10.1016/b978-0-323-29634-2.00001-8 sha: doc_id: 21990 cord_uid: a8ku5rke file: cache/cord-022163-7klzsrpu.json key: cord-022163-7klzsrpu authors: Broder, Christopher C.; Wong, Kum Thong title: Henipaviruses date: 2016-09-09 journal: Neurotropic Viral Infections DOI: 10.1007/978-3-319-33133-1_3 sha: doc_id: 22163 cord_uid: 7klzsrpu file: cache/cord-022196-1tionxun.json key: cord-022196-1tionxun authors: FENNER, FRANK; McAUSLAN, B.R.; MIMS, C.A.; SAMBROOK, J.; WHITE, DAVID O. title: The Nature and Classification of Animal Viruses date: 2013-11-17 journal: The Biology of Animal Viruses DOI: 10.1016/b978-0-12-253040-1.50006-3 sha: doc_id: 22196 cord_uid: 1tionxun file: cache/cord-022305-uvor9rts.json key: cord-022305-uvor9rts authors: Jacoby, Robert O.; Bhatt, Pravin N.; Jonas, Albert M. title: Viral Diseases date: 2013-11-17 journal: The Laboratory Rat DOI: 10.1016/b978-0-12-074901-0.50018-6 sha: doc_id: 22305 cord_uid: uvor9rts file: cache/cord-022349-z8w1wkm8.json key: cord-022349-z8w1wkm8 authors: Beeler, Judy A. title: Human and Animal Viruses date: 2007-09-02 journal: Maintaining Cultures for Biotechnology and Industry DOI: 10.1016/b978-012361946-4/50010-7 sha: doc_id: 22349 cord_uid: z8w1wkm8 file: cache/cord-022674-90g0461f.json key: cord-022674-90g0461f authors: Hurst, Christon J.; Benton, William H.; Stetler, Ronald E. title: Detecting Viruses in Water date: 1989-09-01 journal: J Am Water Works Assoc DOI: 10.1002/j.1551-8833.1989.tb03273.x sha: doc_id: 22674 cord_uid: 90g0461f file: cache/cord-022262-ck2lhojz.json key: cord-022262-ck2lhojz authors: Gromeier, Matthias; Wimmer, Eckard; Gorbalenya, Alexander E. title: Genetics, Pathogenesis and Evolution of Picornaviruses date: 2007-09-02 journal: Origin and Evolution of Viruses DOI: 10.1016/b978-012220360-2/50013-1 sha: doc_id: 22262 cord_uid: ck2lhojz file: cache/cord-021555-rrverrsj.json key: cord-021555-rrverrsj authors: Delano, Margaret L.; Mischler, Scott A.; Underwood, Wendy J. title: Biology and Diseases of Ruminants: Sheep, Goats, and Cattle date: 2007-09-02 journal: Laboratory Animal Medicine DOI: 10.1016/b978-012263951-7/50017-x sha: doc_id: 21555 cord_uid: rrverrsj file: cache/cord-022378-ovxmy1as.json key: cord-022378-ovxmy1as authors: Cook, Jane K.A. title: Coronaviridae date: 2009-05-15 journal: Poultry Diseases DOI: 10.1016/b978-0-7020-2862-5.50033-7 sha: doc_id: 22378 cord_uid: ovxmy1as file: cache/cord-022439-8wy7rpqv.json key: cord-022439-8wy7rpqv authors: DENMAN, A.M. title: Viral Etiology of Polymyositis/Dermatomyositis date: 2013-11-17 journal: Polymyositis and Dermatomyositis DOI: 10.1016/b978-0-409-95191-2.50010-0 sha: doc_id: 22439 cord_uid: 8wy7rpqv file: cache/cord-022947-ruizhgwh.json key: cord-022947-ruizhgwh authors: Elliot, Elisa L; Colwell, Rita R title: Indicator organisms for estuarine and marine waters date: 2006-03-27 journal: FEMS Microbiol Lett DOI: 10.1111/j.1574-6968.1985.tb01183.x sha: doc_id: 22947 cord_uid: ruizhgwh file: cache/cord-022399-66mzbynu.json key: cord-022399-66mzbynu authors: Hopkins, Graham; Pearson, Richard title: Basic microbiology date: 2009-05-15 journal: Ophthalmic Drugs DOI: 10.1016/b978-0-7506-8864-2.50005-2 sha: doc_id: 22399 cord_uid: 66mzbynu file: cache/cord-022822-7346069t.json key: cord-022822-7346069t authors: nan title: Infections, Immunity & their Effects on Asthma date: 2006-10-02 journal: Clin Exp Allergy DOI: 10.1111/j.1365-2222.2006.02583_7.x sha: doc_id: 22822 cord_uid: 7346069t file: cache/cord-023584-yaxawqhj.json key: cord-023584-yaxawqhj authors: Bucknall, R.A. title: The Continuing Search for Antiviral Drugs date: 2008-04-10 journal: Adv Pharmacol DOI: 10.1016/s1054-3589(08)60460-3 sha: doc_id: 23584 cord_uid: yaxawqhj file: cache/cord-021966-5m21bsrw.json key: cord-021966-5m21bsrw authors: Shaw, Alan R.; Feinberg, Mark B. title: Vaccines date: 2009-05-15 journal: Clinical Immunology DOI: 10.1016/b978-0-323-04404-2.10092-2 sha: doc_id: 21966 cord_uid: 5m21bsrw file: cache/cord-022453-xe5v7947.json key: cord-022453-xe5v7947 authors: BABIUK, L.A. title: Viral Gastroenteritis in Ruminants date: 2013-11-17 journal: Virus Infections of Ruminants DOI: 10.1016/b978-0-444-87312-5.50076-x sha: doc_id: 22453 cord_uid: xe5v7947 file: cache/cord-023034-j8zwcfys.json key: cord-023034-j8zwcfys authors: Osterhaus, Albert D. M. E.; Horzinek, Marian C.; Wirahadiredja, R. M. S. title: Feline Infectious Peritonitis Virus: II. Propagation in Suckling Mouse Brain date: 2010-05-13 journal: J Vet Med B Infect Dis Vet Public Health DOI: 10.1111/j.1439-0450.1978.tb01683.x sha: doc_id: 23034 cord_uid: j8zwcfys file: cache/cord-023608-w2g7v7g1.json key: cord-023608-w2g7v7g1 authors: nan title: ISAR News date: 2017-10-20 journal: Antiviral Res DOI: 10.1016/s0166-3542(17)30664-2 sha: doc_id: 23608 cord_uid: w2g7v7g1 file: cache/cord-022354-aqtceqqo.json key: cord-022354-aqtceqqo authors: HUNTER, ERIC title: Membrane Insertion and Transport of Viral Glycoproteins: A Mutational Analysis date: 2012-12-02 journal: Protein Transfer and Organelle Biogenesis DOI: 10.1016/b978-0-12-203460-2.50007-x sha: doc_id: 22354 cord_uid: aqtceqqo file: cache/cord-022128-r8el8nqm.json key: cord-022128-r8el8nqm authors: Domingo, Esteban title: Molecular basis of genetic variation of viruses: error-prone replication date: 2019-11-08 journal: Virus as Populations DOI: 10.1016/b978-0-12-816331-3.00002-7 sha: doc_id: 22128 cord_uid: r8el8nqm file: cache/cord-023092-unjv71qv.json key: cord-023092-unjv71qv authors: Horzinek, Prof. Dr Marian C. title: Feline leukaemia prophylaxis date: 2008-04-10 journal: J Small Anim Pract DOI: 10.1111/j.1748-5827.1986.tb02146.x sha: doc_id: 23092 cord_uid: unjv71qv file: cache/cord-022383-pz0htccp.json key: cord-022383-pz0htccp authors: Kohn, Dennis F.; Barthold, Stephen W. title: Biology and Diseases of Rats date: 2013-11-17 journal: Laboratory Animal Medicine DOI: 10.1016/b978-0-12-263620-2.50010-0 sha: doc_id: 22383 cord_uid: pz0htccp file: cache/cord-022393-s26d54ew.json key: cord-022393-s26d54ew authors: E. Newcomer, Christian; G. Fox, James title: Zoonoses and Other Human Health Hazards date: 2007-09-02 journal: The Mouse in Biomedical Research DOI: 10.1016/b978-012369454-6/50054-6 sha: doc_id: 22393 cord_uid: s26d54ew file: cache/cord-022830-tvt58gtn.json key: cord-022830-tvt58gtn authors: Li, Dan; De Keuckelaere, Ann; Uyttendaele, Mieke title: Fate of Foodborne Viruses in the “Farm to Fork” Chain of Fresh Produce date: 2015-10-08 journal: Compr Rev Food Sci Food Saf DOI: 10.1111/1541-4337.12163 sha: doc_id: 22830 cord_uid: tvt58gtn file: cache/cord-023200-3caevjvh.json key: cord-023200-3caevjvh authors: Falanga, Annarita; Galdiero, Massimiliano; Morelli, Giancarlo; Galdiero, Stefania title: Membranotropic peptides mediating viral entry date: 2018-02-13 journal: Pept Sci (Hoboken) DOI: 10.1002/pep2.24040 sha: doc_id: 23200 cord_uid: 3caevjvh file: cache/cord-025181-eg108wcd.json key: cord-025181-eg108wcd authors: Zheng, Zhihang; Li, Min; Liu, Zhihua; Jin, Xia; Sun, Jin title: Establishment of Murine Infection Models with Biological Clones of Dengue Viruses Derived from a Single Clinical Viral Isolate date: 2020-05-25 journal: Virol Sin DOI: 10.1007/s12250-020-00229-y sha: doc_id: 25181 cord_uid: eg108wcd file: cache/cord-022960-u4s23x1r.json key: cord-022960-u4s23x1r authors: Pihlstrom, Bruce Lee title: Selections from the current literature date: 2020-04-17 journal: J Am Dent Assoc DOI: 10.1016/j.aime.2020.04.020 sha: doc_id: 22960 cord_uid: u4s23x1r file: cache/cord-022980-tkii8se4.json key: cord-022980-tkii8se4 authors: nan title: Diarrhea date: 2008-03-05 journal: Int J Dermatol DOI: 10.1111/j.1365-4362.1980.tb00268.x sha: doc_id: 22980 cord_uid: tkii8se4 file: cache/cord-023622-tul7bonh.json key: cord-023622-tul7bonh authors: nan title: Rotaviruses of Man and Animals date: 1975-02-01 journal: Lancet DOI: 10.1016/s0140-6736(75)91148-4 sha: doc_id: 23622 cord_uid: tul7bonh file: cache/cord-023678-9q68ftr9.json key: cord-023678-9q68ftr9 authors: Hierholzer, J.C.; Killington, R.A. title: Virus isolation and quantitation date: 2007-09-02 journal: Virology Methods Manual DOI: 10.1016/b978-012465330-6/50003-8 sha: doc_id: 23678 cord_uid: 9q68ftr9 file: cache/cord-022252-9yiuuye3.json key: cord-022252-9yiuuye3 authors: Mims, Cedric A.; Dimmock, Nigel J.; Nash, Anthony; Stephen, John title: Mechanisms of Cell and Tissue Damage date: 2013-11-17 journal: Mims' Pathogenesis of Infectious Disease DOI: 10.1016/b978-0-12-498262-8.50015-1 sha: doc_id: 22252 cord_uid: 9yiuuye3 file: cache/cord-023564-kpqvyxxe.json key: cord-023564-kpqvyxxe authors: nan title: Viral gastroenteritis: Causes, pathophysiology, immunology, treatment, and epidemiology date: 2004-09-14 journal: Perspect Med Virol DOI: 10.1016/s0168-7069(03)09001-3 sha: doc_id: 23564 cord_uid: kpqvyxxe file: cache/cord-023740-g84fa45m.json key: cord-023740-g84fa45m authors: Oldstone, Michael B.A.; Schwimmbeck, Peter; Dyrberg, Thomas; Fujinami, Robert title: Mimicry by Virus of Host Molecules: Implications for Autoimmune Disease date: 2014-06-27 journal: Progress in Immunology DOI: 10.1016/b978-0-12-174685-8.50079-2 sha: doc_id: 23740 cord_uid: g84fa45m file: cache/cord-023831-93xqrblk.json key: cord-023831-93xqrblk authors: Rosenberg, Helene F.; Domachowske, Joseph B. title: Pneumonia Virus of Mice (PVM): Exploring Novel Therapeutic Options In a Severe Respiratory Disease Model date: 2010-03-30 journal: National Institute of Allergy and Infectious Diseases, NIH DOI: 10.1007/978-1-60761-512-5_35 sha: doc_id: 23831 cord_uid: 93xqrblk file: cache/cord-026641-eemp6b5j.json key: cord-026641-eemp6b5j authors: Kabiljo, Julijan; Laengle, Johannes; Bergmann, Michael title: From threat to cure: understanding of virus-induced cell death leads to highly immunogenic oncolytic influenza viruses date: 2020-06-11 journal: Cell Death Discov DOI: 10.1038/s41420-020-0284-1 sha: doc_id: 26641 cord_uid: eemp6b5j file: cache/cord-023293-te0n2vvp.json key: cord-023293-te0n2vvp authors: Carter, M. J.; Milton, I. D.; Madeley, C. R. title: Caliciviruses date: 2005-10-18 journal: Rev Med Virol DOI: 10.1002/rmv.1980010307 sha: doc_id: 23293 cord_uid: te0n2vvp file: cache/cord-026130-ki7bn67o.json key: cord-026130-ki7bn67o authors: Sharma, Anand Kumar title: Novel Coronavirus Disease (COVID-19) date: 2020-06-05 journal: Reson DOI: 10.1007/s12045-020-0981-3 sha: doc_id: 26130 cord_uid: ki7bn67o file: cache/cord-025995-nxeg03xj.json key: cord-025995-nxeg03xj authors: Gerba, Charles P.; Goyal, Sagar M. title: Pathogen Removal from Wastewater during Groundwater Recharge date: 2013-11-17 journal: Artificial Recharge of Groundwater DOI: 10.1016/b978-0-250-40549-7.50015-1 sha: doc_id: 25995 cord_uid: nxeg03xj file: cache/cord-023488-jf2xl3vl.json key: cord-023488-jf2xl3vl authors: Le Duc, James W.; Nathanson, Neal title: Emerging Viral Diseases: Why We Need to Worry about Bats, Camels, and Airplanes date: 2016-02-12 journal: Viral Pathogenesis DOI: 10.1016/b978-0-12-800964-2.00016-1 sha: doc_id: 23488 cord_uid: jf2xl3vl file: cache/cord-023721-e0zp2gux.json key: cord-023721-e0zp2gux authors: Meissner, H. Cody title: Bronchiolitis date: 2013-02-10 journal: Principles and Practice of Pediatric Infectious Diseases DOI: 10.1016/b978-1-4377-2702-9.00033-7 sha: doc_id: 23721 cord_uid: e0zp2gux file: cache/cord-023731-jqgervt7.json key: cord-023731-jqgervt7 authors: FENNER, FRANK; BACHMANN, PETER A.; GIBBS, E. PAUL J.; MURPHY, FREDERICK A.; STUDDERT, MICHAEL J.; WHITE, DAVID O. title: Laboratory Diagnosis of Viral Diseases date: 2014-06-27 journal: Veterinary Virology DOI: 10.1016/b978-0-12-253055-5.50017-7 sha: doc_id: 23731 cord_uid: jqgervt7 file: cache/cord-024188-d7tnku8z.json key: cord-024188-d7tnku8z authors: Nissen, Michael D.; Lambert, Stephen B.; Whiley, David M.; Sloots, Theo P. title: Respiratory Infections date: 2010-03-27 journal: PCR for Clinical Microbiology DOI: 10.1007/978-90-481-9039-3_5 sha: doc_id: 24188 cord_uid: d7tnku8z file: cache/cord-023726-2fduzqyb.json key: cord-023726-2fduzqyb authors: STRAUSS, JAMES H.; STRAUSS, ELLEN G. title: The Structure of Viruses date: 2012-07-27 journal: Viruses and Human Disease DOI: 10.1016/b978-0-12-373741-0.50005-2 sha: doc_id: 23726 cord_uid: 2fduzqyb file: cache/cord-027654-k0uby99n.json key: cord-027654-k0uby99n authors: Nabel, Gary J. title: The development of gene-based vectors for immunization date: 2020-06-22 journal: Vaccines DOI: 10.1016/b978-1-4160-3611-1.50066-0 sha: doc_id: 27654 cord_uid: k0uby99n file: cache/cord-023724-5at0rhqk.json key: cord-023724-5at0rhqk authors: Cann, Alan J. title: Infection date: 2015-07-24 journal: Principles of Molecular Virology DOI: 10.1016/b978-0-12-801946-7.00006-7 sha: doc_id: 23724 cord_uid: 5at0rhqk file: cache/cord-023925-qrr7jcwe.json key: cord-023925-qrr7jcwe authors: Verhoef, Jan; van Kessel, Kok; Snippe, Harm title: A8 Immune response in human pathology: Infections caused by bacteria, viruses, fungi, and parasites date: 2011-07-12 journal: Principles of Immunopharmacology DOI: 10.1007/978-3-0346-0136-8_8 sha: doc_id: 23925 cord_uid: qrr7jcwe file: cache/cord-027752-xcpv9k22.json key: cord-027752-xcpv9k22 authors: Bresalier, Michael title: Uses of a Pandemic: Forging the Identities of Influenza and Virus Research in Interwar Britain date: 2011-12-15 journal: Soc Hist Med DOI: 10.1093/shm/hkr162 sha: doc_id: 27752 cord_uid: xcpv9k22 file: cache/cord-031840-k9l91unc.json key: cord-031840-k9l91unc authors: Lu, Li; Lankala, Srinivas; Gong, Yuan; Feng, Xuefeng; Chang, Briankle G. title: Forum: COVID-19 Dispatches date: 2020-09-11 journal: Cult Stud Crit Methodol DOI: 10.1177/1532708620953190 sha: doc_id: 31840 cord_uid: k9l91unc file: cache/cord-023705-3q9yr6np.json key: cord-023705-3q9yr6np authors: FENNER, FRANK; BACHMANN, PETER A.; GIBBS, E. PAUL J.; MURPHY, FREDERICK A.; STUDDERT, MICHAEL J.; WHITE, DAVID O. title: Viral Replication date: 2014-06-27 journal: Veterinary Virology DOI: 10.1016/b978-0-12-253055-5.50008-6 sha: doc_id: 23705 cord_uid: 3q9yr6np file: cache/cord-027550-yyqsatqw.json key: cord-027550-yyqsatqw authors: Mammas, Ioannis N.; Drysdale, Simon B.; Rath, Barbara; Theodoridou, Maria; Papaioannou, Georgia; Papatheodoropoulou, Alexia; koutsounaki, Eirini; Koutsaftiki, Chryssie; Kozanidou, Eleftheria; Achtsidis, Vassilis; Korovessi, Paraskevi; Chrousos, George P.; Spandidos, Demetrios A. title: Update on current views and advances on RSV infection (Review) date: 2020-06-15 journal: Int J Mol Med DOI: 10.3892/ijmm.2020.4641 sha: doc_id: 27550 cord_uid: yyqsatqw file: cache/cord-025704-icedihm2.json key: cord-025704-icedihm2 authors: Pawestri, Hana A.; Nugraha, Arie A.; Han, Alvin X.; Pratiwi, Eka; Parker, Edyth; Richard, Mathilde; van der Vliet, Stefan; Fouchier, Ron A. M.; Muljono, David H.; de Jong, Menno D.; Setiawaty, Vivi; Eggink, Dirk title: Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008–2015 date: 2020-06-01 journal: Virus Genes DOI: 10.1007/s11262-020-01765-1 sha: doc_id: 25704 cord_uid: icedihm2 file: cache/cord-023143-fcno330z.json key: cord-023143-fcno330z authors: nan title: Molecular aspects of viral immunity date: 2004-02-19 journal: J Cell Biochem DOI: 10.1002/jcb.240591009 sha: doc_id: 23143 cord_uid: fcno330z file: cache/cord-029419-b0w9nomq.json key: cord-029419-b0w9nomq authors: Matthews, Adam title: Review of Mark Honigsbaum (2020). The Pandemic Century—A History of Global Contagion from the Spanish Flu to Covid-19: Cambridge, MA: Penguin. 321 pp. ISBN 9780753558287 date: 2020-07-20 journal: Postdigit Sci Educ DOI: 10.1007/s42438-020-00170-z sha: doc_id: 29419 cord_uid: b0w9nomq file: cache/cord-026340-2nf97zvc.json key: cord-026340-2nf97zvc authors: Singh, Ranjana; Vijayan, Viji title: Chloroquine: A Potential Drug in the COVID-19 Scenario date: 2020-06-07 journal: Trans Indian Natl DOI: 10.1007/s41403-020-00114-w sha: doc_id: 26340 cord_uid: 2nf97zvc file: cache/cord-027473-8zerjwa0.json key: cord-027473-8zerjwa0 authors: Roos, Yrjö H. title: Water and Pathogenic Viruses Inactivation—Food Engineering Perspectives date: 2020-06-20 journal: Food Eng Rev DOI: 10.1007/s12393-020-09234-z sha: doc_id: 27473 cord_uid: 8zerjwa0 file: cache/cord-030961-5gzc7193.json key: cord-030961-5gzc7193 authors: Wang, Jiajun; Lapinski, Nicole; Zhang, Xiaohui; Jagota, Anand title: Adhesive contact between cylindrical (Ebola) and spherical (SARS-CoV-2) viral particles and a cell membrane date: 2020-08-28 journal: Mech Soft Mater DOI: 10.1007/s42558-020-00026-3 sha: doc_id: 30961 cord_uid: 5gzc7193 file: cache/cord-103135-nly9vojr.json key: cord-103135-nly9vojr authors: Fletcher, Nicola F.; Meredith, Luke W.; Tidswell, Emma; Bryden, Steven R; Gonçalves-Carneiro, Daniel; Chaudhry, Yasmin; Lowe, Claire Shannon; Folan, Michael A.; Lefteri, Daniella A; Pingen, Marieke; Bailey, Dalan; McKimmie, Clive S.; Baird, Alan W. title: A novel antiviral formulation inhibits a range of enveloped viruses date: 2020-03-30 journal: bioRxiv DOI: 10.1101/2020.03.29.009464 sha: doc_id: 103135 cord_uid: nly9vojr file: cache/cord-102704-wfuzk2dp.json key: cord-102704-wfuzk2dp authors: Meza, Diana K.; Broos, Alice; Becker, Daniel J.; Behdenna, Abdelkader; Willett, Brian J.; Viana, Mafalda; Streicker, Daniel G. title: Predicting the presence and titer of rabies virus neutralizing antibodies from low-volume serum samples in low-containment facilities date: 2020-04-30 journal: bioRxiv DOI: 10.1101/2020.04.24.060095 sha: doc_id: 102704 cord_uid: wfuzk2dp file: cache/cord-030279-pv770doe.json key: cord-030279-pv770doe authors: Novossiolova, Tatyana title: Twenty-first Century Governance Challenges in the Life Sciences date: 2016-11-29 journal: Governance of Biotechnology in Post-Soviet Russia DOI: 10.1007/978-3-319-51004-0_4 sha: doc_id: 30279 cord_uid: pv770doe file: cache/cord-030028-s6sxi8uj.json key: cord-030028-s6sxi8uj authors: Rubio, Luis; Galipienso, Luis; Ferriol, Inmaculada title: Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution date: 2020-07-17 journal: Front Plant Sci DOI: 10.3389/fpls.2020.01092 sha: doc_id: 30028 cord_uid: s6sxi8uj file: cache/cord-035163-tqh5wv12.json key: cord-035163-tqh5wv12 authors: Ijaz, M. Khalid; Sattar, Syed A.; Rubino, Joseph R.; Nims, Raymond W.; Gerba, Charles P. title: Combating SARS-CoV-2: leveraging microbicidal experiences with other emerging/re-emerging viruses date: 2020-09-08 journal: PeerJ DOI: 10.7717/peerj.9914 sha: doc_id: 35163 cord_uid: tqh5wv12 file: cache/cord-102862-oq54sfx6.json key: cord-102862-oq54sfx6 authors: Dastjerdi, Akbar M.; Snodgrass, David R.; Bridger, Janice C. title: Characterisation of the bovine enteric calici-like virus, Newbury agent 1 date: 2000-11-01 journal: FEMS Microbiology Letters DOI: 10.1016/s0378-1097(00)00422-5 sha: doc_id: 102862 cord_uid: oq54sfx6 file: cache/cord-048368-wm4c7rk6.json key: cord-048368-wm4c7rk6 authors: Evseenko, Vasily A; Bukin, Eugeny K; Zaykovskaya, Anna V; Sharshov, Kirill A; Ternovoi, Vladimir A; Ignatyev, George M; Shestopalov, Alexander M title: Experimental infection of H5N1 HPAI in BALB/c mice date: 2007-07-27 journal: Virol J DOI: 10.1186/1743-422x-4-77 sha: doc_id: 48368 cord_uid: wm4c7rk6 file: cache/cord-076082-4kpkhz0o.json key: cord-076082-4kpkhz0o authors: Lam, Tommy Tsan-Yuk; Hon, Chung-Chau; Pybus, Oliver G.; Kosakovsky Pond, Sergei L.; Wong, Raymond Tze-Yeung; Yip, Chi-Wai; Zeng, Fanya; Leung, Frederick Chi-Ching title: Evolutionary and Transmission Dynamics of Reassortant H5N1 Influenza Virus in Indonesia date: 2008-08-22 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1000130 sha: doc_id: 76082 cord_uid: 4kpkhz0o file: cache/cord-103688-n7hzpbyf.json key: cord-103688-n7hzpbyf authors: Wang, Lina; Chen, Fengzhen; Guo, Xueqin; You, Lijin; Yang, Xiaoxia; Yang, Fan; Yang, Tao; Gao, Fei; Hua, Cong; Ding, Yuantong; Cai, Jia; Yang, Linlin; Huang, Wei; Xu, Zhicheng; Wan, Bo; Tong, Jiawei; Peng, Chunhua; Yang, Yawen; Zhang, Lei; Liu, Ke; Zhou, Feiyu; Zhang, Minwen; Tan, Cong; Zeng, Wenjun; Wang, Bo; Wei, Xiaofeng title: VirusDIP: Virus Data Integration Platform date: 2020-06-09 journal: bioRxiv DOI: 10.1101/2020.06.08.139451 sha: doc_id: 103688 cord_uid: n7hzpbyf file: cache/cord-102908-sr7j8z9c.json key: cord-102908-sr7j8z9c authors: Mersmann, Sophia F.; Johns, Emma; Yong, Tracer; McEwan, Will A.; James, Leo C.; Cohen, Edward A.K.; Grove, Joe title: Learning to count: determining the stoichiometry of bio-molecular complexes using fluorescence microscopy and statistical modelling date: 2020-07-24 journal: bioRxiv DOI: 10.1101/2020.07.23.217745 sha: doc_id: 102908 cord_uid: sr7j8z9c file: cache/cord-102383-m5ahicqb.json key: cord-102383-m5ahicqb authors: Romano, Alessandra; Casazza, Marco; Gonella, Francesco title: Energy dynamics for systemic configurations of virus-host co-evolution date: 2020-05-15 journal: bioRxiv DOI: 10.1101/2020.05.13.092866 sha: doc_id: 102383 cord_uid: m5ahicqb file: cache/cord-035015-slgywe0c.json key: cord-035015-slgywe0c authors: Nunn, Alistair V. W.; Guy, Geoffrey W.; Brysch, Wolfgang; Botchway, Stanley W.; Frasch, Wayne; Calabrese, Edward J.; Bell, Jimmy D. title: SARS-CoV-2 and mitochondrial health: implications of lifestyle and ageing date: 2020-11-09 journal: Immun Ageing DOI: 10.1186/s12979-020-00204-x sha: doc_id: 35015 cord_uid: slgywe0c file: cache/cord-104286-5yw4zwo4.json key: cord-104286-5yw4zwo4 authors: Doane, F. W. title: Virus morphology as an aid for rapid diagnosis. date: 1980 journal: Yale J Biol Med DOI: nan sha: doc_id: 104286 cord_uid: 5yw4zwo4 file: cache/cord-214795-8jweuq50.json key: cord-214795-8jweuq50 authors: Mongia, Aanchal; Jain, Stuti; Chouzenoux, Emilie; Majumda, Angshul title: DeepVir -- Graphical Deep Matrix Factorization for"In Silico"Antiviral Repositioning: Application to COVID-19 date: 2020-09-22 journal: nan DOI: nan sha: doc_id: 214795 cord_uid: 8jweuq50 file: cache/cord-161674-nk0wie0w.json key: cord-161674-nk0wie0w authors: Liu, Zhi; Wang, Jianwei; Xu, Yuyu; Guo, Mengchen; Mi, Kai; Xu, Rui; Pei, Yang; Zhang, Qiangkun; Luan, Xiaoting; Hu, Zhibin; Liu, Xingyin title: Implications of the virus-encoded miRNA and host miRNA in the pathogenicity of SARS-CoV-2 date: 2020-04-10 journal: nan DOI: nan sha: doc_id: 161674 cord_uid: nk0wie0w file: cache/cord-203232-1nnqx1g9.json key: cord-203232-1nnqx1g9 authors: Canturk, Semih; Singh, Aman; St-Amant, Patrick; Behrmann, Jason title: Machine-Learning Driven Drug Repurposing for COVID-19 date: 2020-06-25 journal: nan DOI: nan sha: doc_id: 203232 cord_uid: 1nnqx1g9 file: cache/cord-048466-fj9l8che.json key: cord-048466-fj9l8che authors: Bragstad, Karoline; Nielsen, Lars P; Fomsgaard, Anders title: The evolution of human influenza A viruses from 1999 to 2006: A complete genome study date: 2008-03-07 journal: Virol J DOI: 10.1186/1743-422x-5-40 sha: doc_id: 48466 cord_uid: fj9l8che file: cache/cord-171099-d0qr84xg.json key: cord-171099-d0qr84xg authors: Buehler, Markus J. title: Nanomechanical sonification of the 2019-nCoV coronavirus spike protein through a materiomusical approach date: 2020-03-30 journal: nan DOI: nan sha: doc_id: 171099 cord_uid: d0qr84xg file: cache/cord-104317-t30dg6oj.json key: cord-104317-t30dg6oj authors: Parker, Michael T. title: An Ecological Framework of the Human Virome Provides Classification of Current Knowledge and Identifies Areas of Forthcoming Discovery date: 2016-09-30 journal: Yale J Biol Med DOI: nan sha: doc_id: 104317 cord_uid: t30dg6oj file: cache/cord-252456-971d0sir.json key: cord-252456-971d0sir authors: Hemida, Maged Gomaa; Ba Abduallah, Mohammed M. title: The SARS-CoV-2 outbreak from a one health perspective date: 2020-03-16 journal: One Health DOI: 10.1016/j.onehlt.2020.100127 sha: doc_id: 252456 cord_uid: 971d0sir file: cache/cord-102898-eyyd7ent.json key: cord-102898-eyyd7ent authors: Rizvi, Vaseef A.; Sarkar, Maharnob; Roy, Rahul title: Translation regulation of Japanese encephalitis virus revealed by ribosome profiling date: 2020-07-17 journal: bioRxiv DOI: 10.1101/2020.07.16.206920 sha: doc_id: 102898 cord_uid: eyyd7ent file: cache/cord-102905-rlee32x7.json key: cord-102905-rlee32x7 authors: Leis, Jonathan; Luan, Chi-Hao; Audia, James E.; Dunne, Sara F.; Heath, Carissa M. title: Ilaprazole and other novel prazole-based compounds that bind Tsg101 inhibit viral budding of HSV-1/2 and HIV from cells date: 2020-05-04 journal: bioRxiv DOI: 10.1101/2020.05.04.075036 sha: doc_id: 102905 cord_uid: rlee32x7 file: cache/cord-245161-xbw72k4m.json key: cord-245161-xbw72k4m authors: Castano, Nicolas; Cordts, Seth; Jalil, Myra Kurosu; Zhang, Kevin; Koppaka, Saisneha; Bick, Alison; Paul, Rajorshi; Tang, Sindy KY title: Fomite transmission and disinfection strategies for SARS-CoV-2 and related viruses date: 2020-05-23 journal: nan DOI: nan sha: doc_id: 245161 cord_uid: xbw72k4m file: cache/cord-252012-hdjbxah8.json key: cord-252012-hdjbxah8 authors: McErlean, Peter; Greiman, Alyssa; Favoreto, Silvio; Avila, Pedro C. title: Viral diversity in asthma: Immunology and Allergy Clinics of North America: Asthma and Infectious Disease date: 2010-11-01 journal: Immunology and Allergy Clinics of North America DOI: 10.1016/j.iac.2010.08.001 sha: doc_id: 252012 cord_uid: hdjbxah8 file: cache/cord-252397-qlu7dilh.json key: cord-252397-qlu7dilh authors: Johnson, Reed F.; Via, Laura E.; Kumar, Mia R.; Cornish, Joseph P.; Yellayi, Srikanth; Huzella, Louis; Postnikova, Elena; Oberlander, Nicholas; Bartos, Christopher; Ork, Britini L.; Mazur, Steven; Allan, Cindy; Holbrook, Michael R.; Solomon, Jeffrey; Johnson, Joshua C.; Pickel, James; Hensley, Lisa E.; Jahrling, Peter B. title: Intratracheal exposure of common marmosets to MERS-CoV Jordan-n3/2012 or MERS-CoV EMC/2012 isolates does not result in lethal disease date: 2015-11-01 journal: Virology DOI: 10.1016/j.virol.2015.07.013 sha: doc_id: 252397 cord_uid: qlu7dilh file: cache/cord-212761-4bwatc2r.json key: cord-212761-4bwatc2r authors: Contoyiannis, Y.; Stavrinides, S. G.; Hanias, M. P.; Kampitakis, M.; Papadopoulos, P.; Potirakis, S. title: On the effectiveness of imposing restrictive measures in a graded Self-Organized Criticality epidemic spread model The case of COVID-19 date: 2020-04-01 journal: nan DOI: nan sha: doc_id: 212761 cord_uid: 4bwatc2r file: cache/cord-252466-usrpodjx.json key: cord-252466-usrpodjx authors: Yun, Nadezhda E.; Walker, David H. title: Pathogenesis of Lassa Fever date: 2012-10-09 journal: Viruses DOI: 10.3390/v4102031 sha: doc_id: 252466 cord_uid: usrpodjx file: cache/cord-253143-73dsc6q3.json key: cord-253143-73dsc6q3 authors: Tang, Julian W.; Shetty, Nandini; Lam, Tommy T.Y.; Hon, K.L. Ellis title: Emerging, Novel, and Known Influenza Virus Infections in Humans date: 2010-08-02 journal: Infect Dis Clin North Am DOI: 10.1016/j.idc.2010.04.001 sha: doc_id: 253143 cord_uid: 73dsc6q3 file: cache/cord-253594-9gbo8viu.json key: cord-253594-9gbo8viu authors: Konieczny, Leszek; Roterman, Irena title: The COVID-19 Puzzle date: 2020-05-31 journal: Bioinformation DOI: 10.6026/97320630016418 sha: doc_id: 253594 cord_uid: 9gbo8viu file: cache/cord-151024-qe7c2uks.json key: cord-151024-qe7c2uks authors: Koca, Caglar; Civas, Meltem; Sahin, Selin M.; Ergonul, Onder; Akan, Ozgur B. title: Molecular Communication Theoretical Modeling and Analysis of SARS-CoV2 Transmission in Human Respiratory System date: 2020-11-07 journal: nan DOI: nan sha: doc_id: 151024 cord_uid: qe7c2uks file: cache/cord-252725-e3pazjdi.json key: cord-252725-e3pazjdi authors: Khalil, Ayman; Tazeddinova, Diana title: The upshot of Polyphenolic compounds on immunity amid COVID-19 pandemic and other emerging communicable diseases: An appraisal date: 2020-10-15 journal: Nat Prod Bioprospect DOI: 10.1007/s13659-020-00271-z sha: doc_id: 252725 cord_uid: e3pazjdi file: cache/cord-254200-9bpdfxrt.json key: cord-254200-9bpdfxrt authors: Barin, F. title: La sécurité virale des médicaments d’origine biologique date: 2008-06-30 journal: Annales Pharmaceutiques Françaises DOI: 10.1016/j.pharma.2008.05.004 sha: doc_id: 254200 cord_uid: 9bpdfxrt file: cache/cord-253705-utp8po48.json key: cord-253705-utp8po48 authors: Sriwilaijaroen, Nongluk; Suzuki, Yasuo title: Sialoglycovirology of Lectins: Sialyl Glycan Binding of Enveloped and Non-enveloped Viruses date: 2020-04-19 journal: Lectin Purification and Analysis DOI: 10.1007/978-1-0716-0430-4_47 sha: doc_id: 253705 cord_uid: utp8po48 file: cache/cord-232446-vvb2ffhv.json key: cord-232446-vvb2ffhv authors: Mongia, Aanchal; Saha, Sanjay Kr.; Chouzenoux, Emilie; Majumdar, Angshul title: A computational approach to aid clinicians in selecting anti-viral drugs for COVID-19 trials date: 2020-07-03 journal: nan DOI: nan sha: doc_id: 232446 cord_uid: vvb2ffhv file: cache/cord-252769-fe50u028.json key: cord-252769-fe50u028 authors: Mendes, J. Pinto title: Infecção na modulaçâo da asma 1 1 Trabalho apresentado no XXIII Congresso de Pneumologia da SPP – Guarda, Novembro 2007 / Paper presented at the XXIII Congresso de Pneumologia da SPP / PSP Pulmonology Congress, Guarda, November 2007 date: 2008-10-31 journal: Revista Portuguesa de Pneumologia DOI: 10.1016/s0873-2159(15)30275-0 sha: doc_id: 252769 cord_uid: fe50u028 file: cache/cord-252871-qfrpuy3t.json key: cord-252871-qfrpuy3t authors: Nasir, Arshan; Romero-Severson, Ethan; Claverie, Jean-Michel title: Investigating the Concept and Origin of Viruses date: 2020-11-03 journal: Trends Microbiol DOI: 10.1016/j.tim.2020.08.003 sha: doc_id: 252871 cord_uid: qfrpuy3t file: cache/cord-253466-7gpije5d.json key: cord-253466-7gpije5d authors: Netherton, Christopher; Moffat, Katy; Brooks, Elizabeth; Wileman, Thomas title: A Guide to Viral Inclusions, Membrane Rearrangements, Factories, and Viroplasm Produced During Virus Replication date: 2007-08-31 journal: Adv Virus Res DOI: 10.1016/s0065-3527(07)70004-0 sha: doc_id: 253466 cord_uid: 7gpije5d file: cache/cord-254932-b447w202.json key: cord-254932-b447w202 authors: Panda, Aruna; Huang, Zhuhui; Elankumaran, Subbiah; Rockemann, Daniel D; Samal, Siba K title: Role of fusion protein cleavage site in the virulence of Newcastle disease virus date: 2003-11-18 journal: Microb Pathog DOI: 10.1016/j.micpath.2003.07.003 sha: doc_id: 254932 cord_uid: b447w202 file: cache/cord-252147-bvtchcbt.json key: cord-252147-bvtchcbt authors: Domingo-Espín, Joan; Unzueta, Ugutz; Saccardo, Paolo; Rodríguez-Carmona, Escarlata; Corchero, José Luís; Vázquez, Esther; Ferrer-Miralles, Neus title: Engineered Biological Entities for Drug Delivery and Gene Therapy: Protein Nanoparticles date: 2011-11-15 journal: Prog Mol Biol Transl Sci DOI: 10.1016/b978-0-12-416020-0.00006-1 sha: doc_id: 252147 cord_uid: bvtchcbt file: cache/cord-254090-x8tnweih.json key: cord-254090-x8tnweih authors: Yang, Szu-Chi; Lin, Huan-Chun; Liu, Tzu-Ming; Lu, Jen-Tang; Hung, Wan-Ting; Huang, Yu-Ru; Tsai, Yi-Chun; Kao, Chuan-Liang; Chen, Shih-Yuan; Sun, Chi-Kuang title: Efficient Structure Resonance Energy Transfer from Microwaves to Confined Acoustic Vibrations in Viruses date: 2015-12-09 journal: Sci Rep DOI: 10.1038/srep18030 sha: doc_id: 254090 cord_uid: x8tnweih file: cache/cord-254592-wa5il5go.json key: cord-254592-wa5il5go authors: Brierley, Liam; Pedersen, Amy B.; Woolhouse, Mark E. J. title: Tissue tropism and transmission ecology predict virulence of human RNA viruses date: 2019-11-26 journal: PLoS Biol DOI: 10.1371/journal.pbio.3000206 sha: doc_id: 254592 cord_uid: wa5il5go file: cache/cord-255026-fdp6mies.json key: cord-255026-fdp6mies authors: Belák, Sándor title: Molecular diagnosis of viral diseases, present trends and future aspects: A view from the OIE Collaborating Centre for the Application of Polymerase Chain Reaction Methods for Diagnosis of Viral Diseases in Veterinary Medicine date: 2007-07-26 journal: Vaccine DOI: 10.1016/j.vaccine.2006.11.068 sha: doc_id: 255026 cord_uid: fdp6mies file: cache/cord-255075-6azu6k3h.json key: cord-255075-6azu6k3h authors: Zhuang, Jianjian; Yin, Juxin; Lv, Shaowu; Wang, Ben; Mu, Ying title: Advanced “lab-on-a-chip” to detect viruses – Current challenges and future perspectives date: 2020-05-12 journal: Biosens Bioelectron DOI: 10.1016/j.bios.2020.112291 sha: doc_id: 255075 cord_uid: 6azu6k3h file: cache/cord-255479-yd5cbwnx.json key: cord-255479-yd5cbwnx authors: Vu, David M.; Jungkind, Donald; Angelle Desiree LaBeaud, title: Chikungunya Virus date: 2017-06-30 journal: Clinics in Laboratory Medicine DOI: 10.1016/j.cll.2017.01.008 sha: doc_id: 255479 cord_uid: yd5cbwnx file: cache/cord-254527-zddwajzg.json key: cord-254527-zddwajzg authors: Junter, Guy-Alain; Lebrun, Laurent title: Polysaccharide-based chromatographic adsorbents for virus purification and viral clearance date: 2020-01-13 journal: J Pharm Anal DOI: 10.1016/j.jpha.2020.01.002 sha: doc_id: 254527 cord_uid: zddwajzg file: cache/cord-253825-d9borky8.json key: cord-253825-d9borky8 authors: Blaising, Julie; Polyak, Stephen J.; Pécheur, Eve-Isabelle title: Arbidol as a broad-spectrum antiviral: An update date: 2014-04-24 journal: Antiviral Res DOI: 10.1016/j.antiviral.2014.04.006 sha: doc_id: 253825 cord_uid: d9borky8 file: cache/cord-254194-962vynwk.json key: cord-254194-962vynwk authors: Galdiero, Stefania; Falanga, Annarita; Vitiello, Mariateresa; Cantisani, Marco; Marra, Veronica; Galdiero, Massimiliano title: Silver Nanoparticles as Potential Antiviral Agents date: 2011-10-24 journal: Molecules DOI: 10.3390/molecules16108894 sha: doc_id: 254194 cord_uid: 962vynwk file: cache/cord-252974-pwx27kdi.json key: cord-252974-pwx27kdi authors: Fornek, Jamie L.; Korth, Marcus J.; Katze, Michael G. title: Use of Functional Genomics to Understand Influenza–Host Interactions date: 2007-08-31 journal: Adv Virus Res DOI: 10.1016/s0065-3527(07)70003-9 sha: doc_id: 252974 cord_uid: pwx27kdi file: cache/cord-255623-qdpdsye9.json key: cord-255623-qdpdsye9 authors: Pham, Hien T.; Nguyen, Phuc T. T.; Tran, Sinh T.; Phung, Thuy T. B. title: Clinical and Pathogenic Characteristics of Lower Respiratory Tract Infection Treated at the Vietnam National Children's Hospital date: 2020-03-11 journal: Can J Infect Dis Med Microbiol DOI: 10.1155/2020/7931950 sha: doc_id: 255623 cord_uid: qdpdsye9 file: cache/cord-255137-utg8k7qs.json key: cord-255137-utg8k7qs authors: Yinda, Claude Kwe; Vanhulle, Emiel; Conceição-Neto, Nádia; Beller, Leen; Deboutte, Ward; Shi, Chenyan; Ghogomu, Stephen Mbigha; Maes, Piet; Van Ranst, Marc; Matthijnssens, Jelle title: Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses date: 2019-01-23 journal: mSphere DOI: 10.1128/msphere.00585-18 sha: doc_id: 255137 cord_uid: utg8k7qs file: cache/cord-254963-cnvxlv6h.json key: cord-254963-cnvxlv6h authors: Paskey, Adrian C.; Frey, Kenneth G.; Schroth, Gary; Gross, Stephen; Hamilton, Theron; Bishop-Lilly, Kimberly A. title: Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples date: 2019-02-26 journal: BMC Genomics DOI: 10.1186/s12864-019-5543-2 sha: doc_id: 254963 cord_uid: cnvxlv6h file: cache/cord-252048-ftbjsoup.json key: cord-252048-ftbjsoup authors: McKinley, Enid T.; Jackwood, Mark W.; Hilt, Deborah A.; Kissinger, Jessica C.; Robertson, Jon S.; Lemke, Cornelia; Paterson, Andrew H. title: Attenuated live vaccine usage affects accurate measures of virus diversity and mutation rates in avian coronavirus infectious bronchitis virus date: 2011-04-22 journal: Virus Res DOI: 10.1016/j.virusres.2011.04.006 sha: doc_id: 252048 cord_uid: ftbjsoup file: cache/cord-254100-u6x5zd4i.json key: cord-254100-u6x5zd4i authors: Taliansky, M.E.; Brown, J.W.S.; Rajamäki, M.L.; Valkonen, J.P.T.; Kalinina, N.O. title: Involvement of the Plant Nucleolus in Virus and Viroid Infections: Parallels with Animal Pathosystems date: 2010-10-15 journal: Adv Virus Res DOI: 10.1016/b978-0-12-385034-8.00005-3 sha: doc_id: 254100 cord_uid: u6x5zd4i file: cache/cord-254890-4ynsgu6c.json key: cord-254890-4ynsgu6c authors: Heldens, J.G.M.; Patel, J.R.; Chanter, N.; ten Thij, G.J.; Gravendijck, M.; Schijns, V.E.J.C.; Langen, A.; Schetters, Th.P.M. title: Veterinary vaccine development from an industrial perspective date: 2008-03-03 journal: Vet J DOI: 10.1016/j.tvjl.2007.11.009 sha: doc_id: 254890 cord_uid: 4ynsgu6c file: cache/cord-255096-27dfbhsl.json key: cord-255096-27dfbhsl authors: Sweet, Michael J.; Bateman, Kelly S. title: Reprint of ‘Diseases in marine invertebrates associated with mariculture and commercial fisheries’ date: 2016-06-19 journal: J Sea Res DOI: 10.1016/j.seares.2016.06.001 sha: doc_id: 255096 cord_uid: 27dfbhsl file: cache/cord-255217-l2ak5ygj.json key: cord-255217-l2ak5ygj authors: Eccles, Ronald title: Why is temperature sensitivity important for the success of common respiratory viruses? date: 2020-08-10 journal: Rev Med Virol DOI: 10.1002/rmv.2153 sha: doc_id: 255217 cord_uid: l2ak5ygj file: cache/cord-257064-iafm3pcc.json key: cord-257064-iafm3pcc authors: Kint, Joeri; Maier, Helena Jane; Jagt, Erik title: Quantification of Infectious Bronchitis Coronavirus by Titration In Vitro and In Ovo date: 2014-12-18 journal: Coronaviruses DOI: 10.1007/978-1-4939-2438-7_9 sha: doc_id: 257064 cord_uid: iafm3pcc file: cache/cord-255697-trig04hd.json key: cord-255697-trig04hd authors: Cheng, Vincent Chi-Chung; Chan, Jasper Fuk-Woo; Hung, Ivan Fan-Ngai; Yuen, Kwok-Yung title: Viral Infections, an Overview with a Focus on Prevention of Transmission date: 2016-10-24 journal: International Encyclopedia of Public Health DOI: 10.1016/b978-0-12-803678-5.00514-2 sha: doc_id: 255697 cord_uid: trig04hd file: cache/cord-256325-q70rky3r.json key: cord-256325-q70rky3r authors: Stewart, Cameron R.; Deffrasnes, Celine; Foo, Chwan Hong; Bean, Andrew G. D.; Wang, Lin-Fa title: A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease date: 2017-07-04 journal: Roles of Host Gene and Non-coding RNA Expression in Virus Infection DOI: 10.1007/82_2017_28 sha: doc_id: 256325 cord_uid: q70rky3r file: cache/cord-256510-orr2roxz.json key: cord-256510-orr2roxz authors: de Castro, Isabel Fernández; Volonté, Luca; Risco, Cristina title: Virus factories: biogenesis and structural design date: 2012-10-04 journal: Cell Microbiol DOI: 10.1111/cmi.12029 sha: doc_id: 256510 cord_uid: orr2roxz file: cache/cord-256837-100ir651.json key: cord-256837-100ir651 authors: Smith, Steven B.; Dampier, William; Tozeren, Aydin; Brown, James R.; Magid-Slav, Michal title: Identification of Common Biological Pathways and Drug Targets Across Multiple Respiratory Viruses Based on Human Host Gene Expression Analysis date: 2012-03-14 journal: PLoS One DOI: 10.1371/journal.pone.0033174 sha: doc_id: 256837 cord_uid: 100ir651 file: cache/cord-257569-36qx1sy9.json key: cord-257569-36qx1sy9 authors: Hanada, Kousuke; Suzuki, Yoshiyuki; Gojobori, Takashi title: A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes date: 2004-06-17 journal: Mol Biol Evol DOI: 10.1093/molbev/msh109 sha: doc_id: 257569 cord_uid: 36qx1sy9 file: cache/cord-255181-du6rqc6i.json key: cord-255181-du6rqc6i authors: Louz, Derrick; Bergmans, Hans E.; Loos, Birgit P.; Hoeben, Rob C. title: Cross‐species transfer of viruses: implications for the use of viral vectors in biomedical research, gene therapy and as live‐virus vaccines date: 2005-06-29 journal: J Gene Med DOI: 10.1002/jgm.794 sha: doc_id: 255181 cord_uid: du6rqc6i file: cache/cord-255690-xc4bxin4.json key: cord-255690-xc4bxin4 authors: Rolain, Jean-Marc; Colson, Philippe; Raoult, Didier title: Recycling of chloroquine and its hydroxyl analogue to face bacterial, fungal and viral infections in the 21st century date: 2007-07-16 journal: Int J Antimicrob Agents DOI: 10.1016/j.ijantimicag.2007.05.015 sha: doc_id: 255690 cord_uid: xc4bxin4 file: cache/cord-256917-6h1ip37z.json key: cord-256917-6h1ip37z authors: Habibi-Yangjeh, Aziz; Asadzadeh-Khaneghah, Soheila; Feizpoor, Solmaz; Rouhi, Afsar title: Review on heterogeneous photocatalytic disinfection of waterborne, airborne, and foodborne viruses: Can we win against pathogenic viruses? date: 2020-07-15 journal: J Colloid Interface Sci DOI: 10.1016/j.jcis.2020.07.047 sha: doc_id: 256917 cord_uid: 6h1ip37z file: cache/cord-257019-lj1yzjn0.json key: cord-257019-lj1yzjn0 authors: ter MEULEN, V.; CARTER, M. J.; WEGE, H.; WATANABE, R. title: Mechanisms and Consequences of Virus Persistence in the Human Nervous System date: 2006-12-16 journal: Ann N Y Acad Sci DOI: 10.1111/j.1749-6632.1984.tb14778.x sha: doc_id: 257019 cord_uid: lj1yzjn0 file: cache/cord-255339-oudj079q.json key: cord-255339-oudj079q authors: Al-Tayib, Omar A. title: An Overview of the Most Significant Zoonotic Viral Pathogens Transmitted from Animal to Human in Saudi Arabia date: 2019-02-22 journal: Pathogens DOI: 10.3390/pathogens8010025 sha: doc_id: 255339 cord_uid: oudj079q file: cache/cord-255734-038xu4hq.json key: cord-255734-038xu4hq authors: Taylor, Deborah R. title: Obstacles and advances in SARS vaccine development date: 2006-02-13 journal: Vaccine DOI: 10.1016/j.vaccine.2005.08.102 sha: doc_id: 255734 cord_uid: 038xu4hq file: cache/cord-256036-gd53s4dv.json key: cord-256036-gd53s4dv authors: Sandmann, Lisa; Ploss, Alexander title: Barriers of hepatitis C virus interspecies transmission date: 2013-01-01 journal: Virology DOI: 10.1016/j.virol.2012.09.044 sha: doc_id: 256036 cord_uid: gd53s4dv file: cache/cord-256370-cz88t29n.json key: cord-256370-cz88t29n authors: Jansen van Vuren, Petrus; Wiley, Michael; Palacios, Gustavo; Storm, Nadia; McCulloch, Stewart; Markotter, Wanda; Birkhead, Monica; Kemp, Alan; Paweska, Janusz T. title: Isolation of a Novel Fusogenic Orthoreovirus from Eucampsipoda africana Bat Flies in South Africa date: 2016-02-29 journal: Viruses DOI: 10.3390/v8030065 sha: doc_id: 256370 cord_uid: cz88t29n file: cache/cord-257321-l1swyr6g.json key: cord-257321-l1swyr6g authors: Chen, Lihong; Liu, Bo; Wu, Zhiqiang; Jin, Qi; Yang, Jian title: DRodVir: A resource for exploring the virome diversity in rodents date: 2017-05-20 journal: J Genet Genomics DOI: 10.1016/j.jgg.2017.04.004 sha: doc_id: 257321 cord_uid: l1swyr6g file: cache/cord-257220-fe2sacjj.json key: cord-257220-fe2sacjj authors: Butler, J. E.; Lager, K. M.; Golde, William; Faaberg, Kay S.; Sinkora, Marek; Loving, Crystal; Zhang, Y. I. title: Porcine reproductive and respiratory syndrome (PRRS): an immune dysregulatory pandemic date: 2014-07-01 journal: Immunol Res DOI: 10.1007/s12026-014-8549-5 sha: doc_id: 257220 cord_uid: fe2sacjj file: cache/cord-257299-z9u12yqb.json key: cord-257299-z9u12yqb authors: Mansi, N.; de Maio, V.; della Volpe, A.; Ripa, G.; Malafronte, L.; de Filippis, C. title: Ear, nose and throat manifestation of viral systemic infections in pediatric patients date: 2009-12-31 journal: International Journal of Pediatric Otorhinolaryngology DOI: 10.1016/s0165-5876(09)70006-0 sha: doc_id: 257299 cord_uid: z9u12yqb file: cache/cord-258489-pyfc7jde.json key: cord-258489-pyfc7jde authors: Lico, Chiara; Chen, Qiang; Santi, Luca title: Viral vectors for production of recombinant proteins in plants date: 2008-03-10 journal: J Cell Physiol DOI: 10.1002/jcp.21423 sha: doc_id: 258489 cord_uid: pyfc7jde file: cache/cord-259505-7hiss0j3.json key: cord-259505-7hiss0j3 authors: Kong, Qingming; Xue, Chunyi; Ren, Xiangpeng; Zhang, Chengwen; Li, Linlin; Shu, Dingming; Bi, Yingzuo; Cao, Yongchang title: Proteomic analysis of purified coronavirus infectious bronchitis virus particles date: 2010-06-09 journal: Proteome Sci DOI: 10.1186/1477-5956-8-29 sha: doc_id: 259505 cord_uid: 7hiss0j3 file: cache/cord-257163-hodykbcb.json key: cord-257163-hodykbcb authors: Sanz, Ivan; Tamames, Sonia; Rojo, Silvia; Justel, Mar; Lozano, José Eugenio; Disdier, Carlos; Vega, Tomás; Ortiz de Lejarazu, Raúl title: Viral Etiology of Chronic Obstructive Pulmonary Disease Exacerbations during the A/H1N1pdm09 Pandemic and Postpandemic Period date: 2015-05-07 journal: Adv Virol DOI: 10.1155/2015/560679 sha: doc_id: 257163 cord_uid: hodykbcb file: cache/cord-257255-n5o368ih.json key: cord-257255-n5o368ih authors: Barker, J.; Stevens, D.; Bloomfield, S.F. title: Spread and prevention of some common viral infections in community facilities and domestic homes date: 2001-12-21 journal: J Appl Microbiol DOI: 10.1046/j.1365-2672.2001.01364.x sha: doc_id: 257255 cord_uid: n5o368ih file: cache/cord-257553-479x7av6.json key: cord-257553-479x7av6 authors: Kortepeter, Mark G.; Seaworth, Barbara J.; Tasker, Sybil A.; Burgess, Timothy H.; Coldren, Rodney L.; Aronson, Naomi E. title: Health Care Workers and Researchers Traveling to Developing-World Clinical Settings: Disease Transmission Risk and Mitigation date: 2010-12-01 journal: Clin Infect Dis DOI: 10.1086/657115 sha: doc_id: 257553 cord_uid: 479x7av6 file: cache/cord-258333-jmk8hdk2.json key: cord-258333-jmk8hdk2 authors: Sivier, V; Odelin, M.F; Gonthier, R; Pozzetto, B title: Place des viroses respiratoires dans les hyperthermies de sujets âgés hospitalisés au cours d’une saison hivernale date: 2001-12-10 journal: Rev Med Interne DOI: 10.1016/s0248-8663(01)00489-1 sha: doc_id: 258333 cord_uid: jmk8hdk2 file: cache/cord-259458-o2yts5pq.json key: cord-259458-o2yts5pq authors: O’Grady, Kerry‐Ann F.; Torzillo, Paul J.; Rockett, Rebecca J.; Whiley, David M.; Nissen, Michael D.; Sloots, Theo P.; Lambert, Stephen B. title: Successful application of a simple specimen transport method for the conduct of respiratory virus surveillance in remote Indigenous communities in Australia date: 2011-03-21 journal: Trop Med Int Health DOI: 10.1111/j.1365-3156.2011.02757.x sha: doc_id: 259458 cord_uid: o2yts5pq file: cache/cord-256615-gvq8uyfk.json key: cord-256615-gvq8uyfk authors: Rosenberg, Ronald title: Detecting the emergence of novel, zoonotic viruses pathogenic to humans date: 2014-11-22 journal: Cell Mol Life Sci DOI: 10.1007/s00018-014-1785-y sha: doc_id: 256615 cord_uid: gvq8uyfk file: cache/cord-259627-8stewshp.json key: cord-259627-8stewshp authors: Huang, Qing; Fu, Wei-Ling; Chen, Bing; Huang, Jun-Fu; Zhang, Xue; Xue, Qiang title: Inactivation of dengue virus by methylene blue/narrow bandwidth light system date: 2004-12-02 journal: Journal of Photochemistry and Photobiology B: Biology DOI: 10.1016/j.jphotobiol.2004.08.005 sha: doc_id: 259627 cord_uid: 8stewshp file: cache/cord-259233-smmhhroe.json key: cord-259233-smmhhroe authors: de Armas‐Rillo, Laura; Valera, María‐Soledad; Marrero‐Hernández, Sara; Valenzuela‐Fernández, Agustín title: Membrane dynamics associated with viral infection date: 2016-01-28 journal: Rev Med Virol DOI: 10.1002/rmv.1872 sha: doc_id: 259233 cord_uid: smmhhroe file: cache/cord-260420-4s7akmdp.json key: cord-260420-4s7akmdp authors: Mubareka, Samira; Groulx, Nicolas; Savory, Eric; Cutts, Todd; Theriault, Steven; Scott, James A.; Roy, Chad J.; Turgeon, Nathalie; Bryce, Elizabeth; Astrakianakis, George; Kirychuk, Shelley; Girard, Matthieu; Kobinger, Gary; Zhang, Chao; Duchaine, Caroline title: Bioaerosols and Transmission, a Diverse and Growing Community of Practice date: 2019-02-21 journal: Front Public Health DOI: 10.3389/fpubh.2019.00023 sha: doc_id: 260420 cord_uid: 4s7akmdp file: cache/cord-259927-xh9cw9ao.json key: cord-259927-xh9cw9ao authors: Papadopoulos, Nikolaos G.; Megremis, Spyridon; Kitsioulis, Nikolaos A.; Vangelatou, Olympia; West, Peter; Xepapadaki, Paraskevi title: Promising approaches for the treatment and prevention of viral respiratory illnesses date: 2017-07-21 journal: J Allergy Clin Immunol DOI: 10.1016/j.jaci.2017.07.001 sha: doc_id: 259927 cord_uid: xh9cw9ao file: cache/cord-257665-12gyrmh2.json key: cord-257665-12gyrmh2 authors: Liu, Shan-Lu; Saif, Linda title: Emerging Viruses without Borders: The Wuhan Coronavirus date: 2020-01-22 journal: Viruses DOI: 10.3390/v12020130 sha: doc_id: 257665 cord_uid: 12gyrmh2 file: cache/cord-258027-f3rr5el1.json key: cord-258027-f3rr5el1 authors: Østby, Anne‐Cathrine; Gubbels, Sophie; Baake, Gerben; Nielsen, Lars Peter; Riedel, Casper; Arpi, Magnus title: Respiratory virology and microbiology in intensive care units: a prospective cohort study date: 2013-05-18 journal: APMIS DOI: 10.1111/apm.12089 sha: doc_id: 258027 cord_uid: f3rr5el1 file: cache/cord-258389-1u05w7r4.json key: cord-258389-1u05w7r4 authors: Verma, Anju; Verma, Megha; Singh, Anchal title: Animal tissue culture principles and applications date: 2020-06-26 journal: Animal Biotechnology DOI: 10.1016/b978-0-12-811710-1.00012-4 sha: doc_id: 258389 cord_uid: 1u05w7r4 file: cache/cord-260472-xvvfguht.json key: cord-260472-xvvfguht authors: Papadopoulos, Nikolaos G.; Konstantinou, George N. title: Antimicrobial strategies: An option to treat allergy? date: 2007-01-31 journal: Biomedicine & Pharmacotherapy DOI: 10.1016/j.biopha.2006.10.004 sha: doc_id: 260472 cord_uid: xvvfguht file: cache/cord-257008-7q5s1vu1.json key: cord-257008-7q5s1vu1 authors: Sharma, Virender K.; Jinadatha, Chetan; Lichtfouse, Eric title: Environmental chemistry is most relevant to study coronavirus pandemics date: 2020-05-20 journal: Environ Chem Lett DOI: 10.1007/s10311-020-01017-6 sha: doc_id: 257008 cord_uid: 7q5s1vu1 file: cache/cord-257652-ndt8f812.json key: cord-257652-ndt8f812 authors: Zhang, Yong-Zhen; Wu, Wei-Chen; Shi, Mang; Holmes, Edward C title: The diversity, evolution and origins of vertebrate RNA viruses date: 2018-08-13 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2018.07.017 sha: doc_id: 257652 cord_uid: ndt8f812 file: cache/cord-260554-nao59qx4.json key: cord-260554-nao59qx4 authors: Wargo, Andrew R; Kurath, Gael title: Viral fitness: definitions, measurement, and current insights date: 2012-09-15 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2012.07.007 sha: doc_id: 260554 cord_uid: nao59qx4 file: cache/cord-261417-4pf5nsw2.json key: cord-261417-4pf5nsw2 authors: Harwig, Alex; Landick, Robert; Berkhout, Ben title: The Battle of RNA Synthesis: Virus versus Host date: 2017-10-21 journal: Viruses DOI: 10.3390/v9100309 sha: doc_id: 261417 cord_uid: 4pf5nsw2 file: cache/cord-260705-huyyw5z6.json key: cord-260705-huyyw5z6 authors: Moshe, Adi; Gorovits, Rena title: Virus-Induced Aggregates in Infected Cells date: 2012-10-17 journal: Viruses DOI: 10.3390/v4102218 sha: doc_id: 260705 cord_uid: huyyw5z6 file: cache/cord-260168-rb7j94dh.json key: cord-260168-rb7j94dh authors: Gu, Jiang; Xie, Zhigang; Gao, Zhancheng; Liu, Jinhua; Korteweg, Christine; Ye, Juxiang; Lau, Lok Ting; Lu, Jie; Gao, Zifen; Zhang, Bo; McNutt, Michael A; Lu, Min; Anderson, Virginia M; Gong, Encong; Yu, Albert Cheung Hoi; Lipkin, W Ian title: H5N1 infection of the respiratory tract and beyond: a molecular pathology study date: 2007-09-27 journal: Lancet DOI: 10.1016/s0140-6736(07)61515-3 sha: doc_id: 260168 cord_uid: rb7j94dh file: cache/cord-262722-cz3ce29n.json key: cord-262722-cz3ce29n authors: Kuzmanovic, Deborah A.; Elashvili, Ilya; O’Connell, Catherine; Krueger, Susan title: A novel application of small-angle scattering techniques: Quality assurance testing of virus quantification technology date: 2008-03-31 journal: Radiation Physics and Chemistry DOI: 10.1016/j.radphyschem.2007.10.004 sha: doc_id: 262722 cord_uid: cz3ce29n file: cache/cord-260147-w19hl2vs.json key: cord-260147-w19hl2vs authors: Gröner, Albrecht; Broumis, Connie; Fang, Randel; Nowak, Thomas; Popp, Birgit; Schäfer, Wolfram; Roth, Nathan J. title: Effective inactivation of a wide range of viruses by pasteurization date: 2017-11-16 journal: Transfusion DOI: 10.1111/trf.14390 sha: doc_id: 260147 cord_uid: w19hl2vs file: cache/cord-261160-g92zhv19.json key: cord-261160-g92zhv19 authors: Rowland, Raymond R.R; Lawson, Steven; Rossow, Kurt; Benfield, David A title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero date: 2003-10-30 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2003.07.006 sha: doc_id: 261160 cord_uid: g92zhv19 file: cache/cord-258783-ev0h95b9.json key: cord-258783-ev0h95b9 authors: Kapil, Sanjay; Yeary, Teresa J. title: Canine Distemper Spillover in Domestic Dogs from Urban Wildlife date: 2011-11-30 journal: Veterinary Clinics of North America: Small Animal Practice DOI: 10.1016/j.cvsm.2011.08.005 sha: doc_id: 258783 cord_uid: ev0h95b9 file: cache/cord-260014-q5sug7uu.json key: cord-260014-q5sug7uu authors: Szűcs, Zsolt; Naesens, Lieve; Stevaert, Annelies; Ostorházi, Eszter; Batta, Gyula; Herczegh, Pál; Borbás, Anikó title: Reprogramming of the Antibacterial Drug Vancomycin Results in Potent Antiviral Agents Devoid of Antibacterial Activity date: 2020-06-29 journal: Pharmaceuticals (Basel) DOI: 10.3390/ph13070139 sha: doc_id: 260014 cord_uid: q5sug7uu file: cache/cord-258626-p469ysi8.json key: cord-258626-p469ysi8 authors: Davis-Wurzler, Gina M. title: 2013 Update on Current Vaccination Strategies in Puppies and Kittens date: 2014-02-26 journal: Vet Clin North Am Small Anim Pract DOI: 10.1016/j.cvsm.2013.11.006 sha: doc_id: 258626 cord_uid: p469ysi8 file: cache/cord-260956-w6wxsg4p.json key: cord-260956-w6wxsg4p authors: Dimitrov, Kiril M.; Afonso, Claudio L.; Yu, Qingzhong; Miller, Patti J. title: Newcastle disease vaccines—A solved problem or a continuous challenge? date: 2017-07-31 journal: Veterinary Microbiology DOI: 10.1016/j.vetmic.2016.12.019 sha: doc_id: 260956 cord_uid: w6wxsg4p file: cache/cord-259235-p0yj9qug.json key: cord-259235-p0yj9qug authors: de Lamballerie, Xavier title: Diagnostic et traitement des viroses émergentes : comment aller de l’avant ? date: 2016-12-31 journal: Bulletin de l'Académie Nationale de Médecine DOI: 10.1016/s0001-4079(19)30571-0 sha: doc_id: 259235 cord_uid: p0yj9qug file: cache/cord-259260-qcfgigga.json key: cord-259260-qcfgigga authors: Ibrahim, Ibrahim M.; Abdelmalek, Doaa H.; Elfiky, Abdo A. title: GRP78: A cell's response to stress date: 2019-06-01 journal: Life Sciences DOI: 10.1016/j.lfs.2019.04.022 sha: doc_id: 259260 cord_uid: qcfgigga file: cache/cord-260496-s2ba7uy3.json key: cord-260496-s2ba7uy3 authors: Moncany, Maurice L.J.; Dalet, Karine; Courtois, Pascal R.R. title: Identification of conserved lentiviral sequences as landmarks of genomic flexibility date: 2006-08-08 journal: C R Biol DOI: 10.1016/j.crvi.2006.07.001 sha: doc_id: 260496 cord_uid: s2ba7uy3 file: cache/cord-260708-l9w5jhsw.json key: cord-260708-l9w5jhsw authors: Lasecka, Lidia; Baron, Michael D. title: The molecular biology of nairoviruses, an emerging group of tick-borne arboviruses date: 2013-12-11 journal: Arch Virol DOI: 10.1007/s00705-013-1940-z sha: doc_id: 260708 cord_uid: l9w5jhsw file: cache/cord-263017-rh86g4jk.json key: cord-263017-rh86g4jk authors: Wigginton, Krista Rule; Kohn, Tamar title: Virus disinfection mechanisms: the role of virus composition, structure, and function date: 2011-12-09 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2011.11.003 sha: doc_id: 263017 cord_uid: rh86g4jk file: cache/cord-261961-u4d0vvmq.json key: cord-261961-u4d0vvmq authors: St-Germain, Jonathan R.; Astori, Audrey; Samavarchi-Tehrani, Payman; Abdouni, Hala; Macwan, Vinitha; Kim, Dae-Kyum; Knapp, Jennifer J.; Roth, Frederick P.; Gingras, Anne-Claude; Raught, Brian title: A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research date: 2020-08-28 journal: bioRxiv DOI: 10.1101/2020.08.28.269175 sha: doc_id: 261961 cord_uid: u4d0vvmq file: cache/cord-262776-6k7tcgfs.json key: cord-262776-6k7tcgfs authors: Burnouf, Thierry; Griffiths, Elwyn; Padilla, Ana; Seddik, Salwa; Stephano, Marco Antonio; Gutiérrez, José-María title: Assessment of the viral safety of antivenoms fractionated from equine plasma date: 2004-09-30 journal: Biologicals DOI: 10.1016/j.biologicals.2004.07.001 sha: doc_id: 262776 cord_uid: 6k7tcgfs file: cache/cord-262752-bwofzbwa.json key: cord-262752-bwofzbwa authors: Li, Qianqian; Liu, Qiang; Huang, Weijin; Li, Xuguang; Wang, Youchun title: Current status on the development of pseudoviruses for enveloped viruses date: 2017-12-07 journal: Rev Med Virol DOI: 10.1002/rmv.1963 sha: doc_id: 262752 cord_uid: bwofzbwa file: cache/cord-263245-2qub96mz.json key: cord-263245-2qub96mz authors: Singh, D.; Joshi, K.; Samuel, A.; Patra, J.; Mahindroo, N. title: Alcohol-based hand sanitisers as first line of defence against SARS-CoV-2: a review of biology, chemistry and formulations date: 2020-09-29 journal: Epidemiol Infect DOI: 10.1017/s0950268820002319 sha: doc_id: 263245 cord_uid: 2qub96mz file: cache/cord-260690-h5pjv2dw.json key: cord-260690-h5pjv2dw authors: Druce, Julian; Tran, Thomas; Kelly, Heath; Kaye, Matthew; Chibo, Doris; Kostecki, Renata; Amiri, Abdul; Catton, Mike; Birch, Chris title: Laboratory diagnosis and surveillance of human respiratory viruses by PCR in Victoria, Australia, 2002–2003 date: 2004-11-12 journal: J Med Virol DOI: 10.1002/jmv.20246 sha: doc_id: 260690 cord_uid: h5pjv2dw file: cache/cord-262748-v4xue7ha.json key: cord-262748-v4xue7ha authors: Xu, Yongtao; Yu, Shui; Zou, Jian-Wei; Hu, Guixiang; Rahman, Noorsaadah A. B. D.; Othman, Rozana Binti; Tao, Xia; Huang, Meilan title: Identification of Peptide Inhibitors of Enveloped Viruses Using Support Vector Machine date: 2015-12-04 journal: PLoS One DOI: 10.1371/journal.pone.0144171 sha: doc_id: 262748 cord_uid: v4xue7ha file: cache/cord-261241-eqf6ame6.json key: cord-261241-eqf6ame6 authors: van Beek, Josine; Veenhoven, Reinier H; Bruin, Jacob P; van Boxtel, Renée A J; de Lange, Marit M A; Meijer, Adam; Sanders, Elisabeth A M; Rots, Nynke Y; Luytjes, Willem title: Influenza-like Illness Incidence Is Not Reduced by Influenza Vaccination in a Cohort of Older Adults, Despite Effectively Reducing Laboratory-Confirmed Influenza Virus Infections date: 2017-08-15 journal: J Infect Dis DOI: 10.1093/infdis/jix268 sha: doc_id: 261241 cord_uid: eqf6ame6 file: cache/cord-263165-bv4dh9eu.json key: cord-263165-bv4dh9eu authors: Möstl, Karin title: Coronaviridae, pathogenetic and clinical aspects: An update date: 1990-12-31 journal: Comparative Immunology, Microbiology and Infectious Diseases DOI: 10.1016/0147-9571(90)90085-8 sha: doc_id: 263165 cord_uid: bv4dh9eu file: cache/cord-263315-g7os15m1.json key: cord-263315-g7os15m1 authors: Martins-da-Silva, Andrea; Telleria, Erich Loza; Batista, Michel; Marchini, Fabricio Klerynton; Traub-Csekö, Yara Maria; Tempone, Antonio Jorge title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response date: 2018-01-18 journal: Viruses DOI: 10.3390/v10010043 sha: doc_id: 263315 cord_uid: g7os15m1 file: cache/cord-262514-1e2bc0bi.json key: cord-262514-1e2bc0bi authors: Harrison, Alyne K; Murphy, Frederick A; Gardner, Jared J title: Visceral target organs in systemic St. Louis encephalitis virus infection of hamsters date: 1982-12-31 journal: Experimental and Molecular Pathology DOI: 10.1016/0014-4800(82)90043-0 sha: doc_id: 262514 cord_uid: 1e2bc0bi file: cache/cord-264291-0czphube.json key: cord-264291-0czphube authors: Varfolomeev, S. D.; Panin, A. A.; Bykov, V. I.; Tsybenova, S. B.; Shogenova, L. V.; Chuchalin, A. G. title: Kinetic model of development of acute viral infection in the human body. Critical conditions, control mechanisms, “thermoheliox” date: 2020-07-20 journal: Russ Chem Bull DOI: 10.1007/s11172-020-2886-4 sha: doc_id: 264291 cord_uid: 0czphube file: cache/cord-263157-8jin6oru.json key: cord-263157-8jin6oru authors: Martínez, Miguel Angel title: Progress in the Therapeutic Applications of siRNAs Against HIV-1 date: 2008-10-13 journal: siRNA and miRNA Gene Silencing DOI: 10.1007/978-1-60327-547-7_17 sha: doc_id: 263157 cord_uid: 8jin6oru file: cache/cord-261171-iknoqb4d.json key: cord-261171-iknoqb4d authors: Roingeard, Philippe title: Viral detection by electron microscopy: past, present and future date: 2012-01-09 journal: Biol Cell DOI: 10.1042/bc20070173 sha: doc_id: 261171 cord_uid: iknoqb4d file: cache/cord-264264-7j3xirfg.json key: cord-264264-7j3xirfg authors: TüRsen, Ümit; Türsen, Belma; Lotti, Torello title: CORONAVIRUS‐DAYS IN DERMATOLOGY date: 2020-04-15 journal: Dermatol Ther DOI: 10.1111/dth.13421 sha: doc_id: 264264 cord_uid: 7j3xirfg file: cache/cord-265445-bazcczdj.json key: cord-265445-bazcczdj authors: Arias-Bravo, Guisselle; Valderrama, Gustavo; Inostroza, Jaime; Reyes-Farías, Marjorie; Garcia-Diaz, Diego F.; Zorondo-Rodríguez, Francisco; Fuenzalida, Loreto F. 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 journal: Front Pediatr DOI: 10.3389/fped.2020.00044 sha: doc_id: 265445 cord_uid: bazcczdj file: cache/cord-263484-afcgqjwq.json key: cord-263484-afcgqjwq authors: Ladner, Jason T.; Grubaugh, Nathan D.; Pybus, Oliver G.; Andersen, Kristian G. title: Precision epidemiology for infectious disease control date: 2019-02-06 journal: Nat Med DOI: 10.1038/s41591-019-0345-2 sha: doc_id: 263484 cord_uid: afcgqjwq file: cache/cord-263764-2ewz8ok4.json key: cord-263764-2ewz8ok4 authors: Kutter, Jasmin S; Spronken, Monique I; Fraaij, Pieter L; Fouchier, Ron AM; Herfst, Sander title: Transmission routes of respiratory viruses among humans date: 2018-01-17 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2018.01.001 sha: doc_id: 263764 cord_uid: 2ewz8ok4 file: cache/cord-263785-0iift8zy.json key: cord-263785-0iift8zy authors: Zhang, Xiaorong; Liao, Kai; Chen, Shuqin; Yan, Kun; Du, Xubin; Zhang, Chengcheng; Guo, Mengjiao; Wu, Yantao title: Evaluation of the reproductive system development and egg-laying performance of hens infected with TW I-type infectious bronchitis virus date: 2020-07-31 journal: Vet Res DOI: 10.1186/s13567-020-00819-4 sha: doc_id: 263785 cord_uid: 0iift8zy file: cache/cord-263868-ewnf96cz.json key: cord-263868-ewnf96cz authors: Srivastava, Mayank; Zhang, Ying; Chen, Jian; Sirohi, Devika; Miller, Andrew; Zhang, Yang; Chen, Zhilu; Lu, Haojie; Xu, Jianqing; Kuhn, Richard J.; Andy Tao, W. title: Chemical proteomics tracks virus entry and uncovers NCAM1 as Zika virus receptor date: 2020-08-04 journal: Nat Commun DOI: 10.1038/s41467-020-17638-y sha: doc_id: 263868 cord_uid: ewnf96cz file: cache/cord-263619-p17oomzn.json key: cord-263619-p17oomzn authors: Moss, William J.; Griffin, Diane E.; Feinstone, W. Harry title: Measles date: 2009-01-30 journal: Vaccines for Biodefense and Emerging and Neglected Diseases DOI: 10.1016/b978-0-12-369408-9.00030-5 sha: doc_id: 263619 cord_uid: p17oomzn file: cache/cord-264794-bgygebgx.json key: cord-264794-bgygebgx authors: Lundgren, A.-L. title: Feline non-suppurative meningoencephalomyelitis. A clinical and pathological study date: 1992-11-30 journal: Journal of Comparative Pathology DOI: 10.1016/0021-9975(92)90015-m sha: doc_id: 264794 cord_uid: bgygebgx file: cache/cord-264350-4zxp3uae.json key: cord-264350-4zxp3uae authors: Kelley, James L. title: Chapter 12. Antiviral Agents date: 1984-12-31 journal: Annual Reports in Medicinal Chemistry DOI: 10.1016/s0065-7743(08)60688-0 sha: doc_id: 264350 cord_uid: 4zxp3uae file: cache/cord-264308-y6xuxj16.json key: cord-264308-y6xuxj16 authors: Liu, Rui; An, Liwei; Liu, Ge; Li, Xiaoyu; Tang, Wei; Chen, Xulin title: Mouse lung slices: An ex vivo model for the evaluation of antiviral and anti-inflammatory agents against influenza viruses date: 2015-05-26 journal: Antiviral Res DOI: 10.1016/j.antiviral.2015.05.008 sha: doc_id: 264308 cord_uid: y6xuxj16 file: cache/cord-264406-s5c0grz0.json key: cord-264406-s5c0grz0 authors: Miró-Cañís, Sílvia; Capilla-Rubio, Sílvia; Marzo-Checa, Laura; Fontanals-Aymerich, Dionisia; Sanfeliu-Sala, Isabel; Espasa-Soley, Mateu; Asensio-de-la-Cruz, Oscar title: Multiplex PCR reveals that viruses are more frequent than bacteria in children with cystic fibrosis date: 2016-11-13 journal: J Clin Virol DOI: 10.1016/j.jcv.2016.11.004 sha: doc_id: 264406 cord_uid: s5c0grz0 file: cache/cord-264699-l8db5gll.json key: cord-264699-l8db5gll authors: Kino, Tomoshige; Chrousos, George P. title: Virus-mediated modulation of the host endocrine signaling systems: clinical implications date: 2007-06-30 journal: Trends in Endocrinology & Metabolism DOI: 10.1016/j.tem.2007.03.003 sha: doc_id: 264699 cord_uid: l8db5gll file: cache/cord-264884-ydkigome.json key: cord-264884-ydkigome authors: Villarreal, Luis P. title: The Widespread Evolutionary Significance of Viruses date: 2008-07-05 journal: Origin and Evolution of Viruses DOI: 10.1016/b978-0-12-374153-0.00021-7 sha: doc_id: 264884 cord_uid: ydkigome file: cache/cord-266136-81sx505i.json key: cord-266136-81sx505i authors: Freymuth, F.; Vabret, A.; Dina, J.; Cuvillon-Nimal, D.; Lubin, C.; Vaudecrane, A.; Guillois, B.; Gouarin, S.; Petitjean, J.; Lafaix-Delaire, F.; Brouard, J. title: Les virus des bronchiolites aiguës date: 2010-06-16 journal: Arch Pediatr DOI: 10.1016/j.arcped.2010.05.006 sha: doc_id: 266136 cord_uid: 81sx505i file: cache/cord-264916-c4n0kyog.json key: cord-264916-c4n0kyog authors: Zimmerman, Keith; Kearns, Fiona; Tzekov, Radouil title: Natural protection of ocular surface from viral infections – a hypothesis date: 2020-07-09 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.110082 sha: doc_id: 264916 cord_uid: c4n0kyog file: cache/cord-266138-yibbiiij.json key: cord-266138-yibbiiij authors: Wege, Helmut title: Immunopathological aspects of coronavirus infections date: 1995 journal: Springer Semin Immunopathol DOI: 10.1007/bf00196162 sha: doc_id: 266138 cord_uid: yibbiiij file: cache/cord-265461-hj2b1wc4.json key: cord-265461-hj2b1wc4 authors: Decroly, Etienne; Canard, Bruno title: Biochemical principles and inhibitors to interfere with viral capping pathways date: 2017-05-18 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2017.04.003 sha: doc_id: 265461 cord_uid: hj2b1wc4 file: cache/cord-265681-ab8j4o1u.json key: cord-265681-ab8j4o1u authors: Boroomand, Zahra; Asasi, Keramat; Mohammadi, Ali title: Pathogenesis and Tissue Distribution of Avian Infectious Bronchitis Virus Isolate IRFIBV32 (793/B Serotype) in Experimentally Infected Broiler Chickens date: 2012-04-01 journal: ScientificWorldJournal DOI: 10.1100/2012/402537 sha: doc_id: 265681 cord_uid: ab8j4o1u file: cache/cord-265751-q1ecpfyg.json key: cord-265751-q1ecpfyg authors: Shahani, Lokesh; Ariza-Heredia, Ella J.; Chemaly, Roy F. title: Antiviral therapy for respiratory viral infections in immunocompromised patients date: 2017-01-16 journal: Expert Rev Anti Infect Ther DOI: 10.1080/14787210.2017.1279970 sha: doc_id: 265751 cord_uid: q1ecpfyg file: cache/cord-267326-355q6k6k.json key: cord-267326-355q6k6k authors: Gu, Xiaoqiong; Tay, Qi Xiang Martin; Te, Shu Harn; Saeidi, Nazanin; Goh, Shin Giek; Kushmaro, Ariel; Thompson, Janelle R.; Gin, Karina Yew-Hoong title: Geospatial distribution of viromes in tropical freshwater ecosystems date: 2018-06-15 journal: Water Res DOI: 10.1016/j.watres.2018.03.017 sha: doc_id: 267326 cord_uid: 355q6k6k file: cache/cord-266985-9qwttt2y.json key: cord-266985-9qwttt2y authors: Gale, P.; Hill, A.; Kelly, L.; Bassett, J.; McClure, P.; Le Marc, Y.; Soumpasis, I. title: Applications of omics approaches to the development of microbiological risk assessment using RNA virus dose–response models as a case study date: 2014-11-04 journal: J Appl Microbiol DOI: 10.1111/jam.12656 sha: doc_id: 266985 cord_uid: 9qwttt2y file: cache/cord-265642-7mu530yp.json key: cord-265642-7mu530yp authors: Syomin, B. V.; Ilyin, Y. V. title: Virus-Like Particles as an Instrument of Vaccine Production date: 2019-06-17 journal: Mol Biol DOI: 10.1134/s0026893319030154 sha: doc_id: 265642 cord_uid: 7mu530yp file: cache/cord-264408-vk4lt83x.json key: cord-264408-vk4lt83x authors: Ruiz, Sara I.; Zumbrun, Elizabeth E.; Nalca, Aysegul title: Animal Models of Human Viral Diseases date: 2017-06-23 journal: Animal Models for the Study of Human Disease DOI: 10.1016/b978-0-12-809468-6.00033-4 sha: doc_id: 264408 cord_uid: vk4lt83x file: cache/cord-266822-ecq50ye2.json key: cord-266822-ecq50ye2 authors: Rath, Barbara; Conrad, Tim; Myles, Puja; Alchikh, Maren; Ma, Xiaolin; Hoppe, Christian; Tief, Franziska; Chen, Xi; Obermeier, Patrick; Kisler, Bron; Schweiger, Brunhilde title: Influenza and other respiratory viruses: standardizing disease severity in surveillance and clinical trials date: 2017-05-12 journal: Expert Rev Anti Infect Ther DOI: 10.1080/14787210.2017.1295847 sha: doc_id: 266822 cord_uid: ecq50ye2 file: cache/cord-267003-k7eo2c26.json key: cord-267003-k7eo2c26 authors: Hendaus, Mohamed A; Jomha, Fatima A; Alhammadi, Ahmed H title: Virus-induced secondary bacterial infection: a concise review date: 2015-08-24 journal: Ther Clin Risk Manag DOI: 10.2147/tcrm.s87789 sha: doc_id: 267003 cord_uid: k7eo2c26 file: cache/cord-267194-i6vetquk.json key: cord-267194-i6vetquk authors: Carman, William F.; Mahony, James B. title: The pathogens date: 2007-10-31 journal: Journal of Clinical Virology DOI: 10.1016/s1386-6532(07)70003-3 sha: doc_id: 267194 cord_uid: i6vetquk file: cache/cord-267134-5gz2dotn.json key: cord-267134-5gz2dotn authors: Sallenave, Jean-Michel; Guillot, Loïc title: Innate Immune Signaling and Proteolytic Pathways in the Resolution or Exacerbation of SARS-CoV-2 in Covid-19: Key Therapeutic Targets? date: 2020-05-28 journal: Front Immunol DOI: 10.3389/fimmu.2020.01229 sha: doc_id: 267134 cord_uid: 5gz2dotn file: cache/cord-268999-6748c617.json key: cord-268999-6748c617 authors: Gibson, Kristen E title: Viral pathogens in water: occurrence, public health impact, and available control strategies date: 2014-01-14 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2013.12.005 sha: doc_id: 268999 cord_uid: 6748c617 file: cache/cord-266199-smlq11y9.json key: cord-266199-smlq11y9 authors: Dhakal, Santosh; Renukaradhya, Gourapura J. title: Nanoparticle-based vaccine development and evaluation against viral infections in pigs date: 2019-11-06 journal: Vet Res DOI: 10.1186/s13567-019-0712-5 sha: doc_id: 266199 cord_uid: smlq11y9 file: cache/cord-267831-uu883ofc.json key: cord-267831-uu883ofc authors: Kang, Yuan-Lin; Chou, Yi-Ying; Rothlauf, Paul W.; Liu, Zhuoming; Soh, Timothy K.; Cureton, David; Case, James Brett; Chen, Rita E.; Diamond, Michael S.; Whelan, Sean P. J.; Kirchhausen, Tom title: Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2 date: 2020-06-15 journal: bioRxiv DOI: 10.1101/2020.04.21.053058 sha: doc_id: 267831 cord_uid: uu883ofc file: cache/cord-267140-vdcf6vok.json key: cord-267140-vdcf6vok authors: Trudel, M.; Marchessault, F.; Payment, P. title: Purification of infectious rubella virus by gel filtration on sepharose 2B compared to gradient centrifugation in sucrose, sodium metrizoate and metrizamide date: 1981-02-28 journal: Journal of Virological Methods DOI: 10.1016/0166-0934(81)90032-x sha: doc_id: 267140 cord_uid: vdcf6vok file: cache/cord-269324-zh1a3gwh.json key: cord-269324-zh1a3gwh authors: Mubareka, Samira; Palese, Peter title: Human Genes and Influenza date: 2008-01-01 journal: J Infect Dis DOI: 10.1086/524067 sha: doc_id: 269324 cord_uid: zh1a3gwh file: cache/cord-266762-z08rn959.json key: cord-266762-z08rn959 authors: Rouse, Barry T.; Mueller, Scott N. title: 25 Host Defenses to Viruses date: 2019-12-31 journal: Clinical Immunology DOI: 10.1016/b978-0-7020-6896-6.00025-9 sha: doc_id: 266762 cord_uid: z08rn959 file: cache/cord-268501-z4oztgi0.json key: cord-268501-z4oztgi0 authors: Palatnik-de-Sousa, Clarisa B. title: What Would Jenner and Pasteur Have Done About COVID-19 Coronavirus? The Urges of a Vaccinologist date: 2020-08-26 journal: Front Immunol DOI: 10.3389/fimmu.2020.02173 sha: doc_id: 268501 cord_uid: z4oztgi0 file: cache/cord-269623-9pxdeva3.json key: cord-269623-9pxdeva3 authors: Nicholson, Karl G; Wood, John M; Zambon, Maria title: Influenza date: 2003-11-22 journal: Lancet DOI: 10.1016/s0140-6736(03)14854-4 sha: doc_id: 269623 cord_uid: 9pxdeva3 file: cache/cord-269519-8hr8wyrr.json key: cord-269519-8hr8wyrr authors: Hirotsu, Yosuke; Maejima, Makoto; Shibusawa, Masahiro; Amemiya, Kenji; Nagakubo, Yuki; Hosaka, Kazuhiro; Sueki, Hitomi; Mochizuki, Hitoshi; Tsutsui, Toshiharu; Kakizaki, Yumiko; Miyashita, Yoshihiro; Omata, Masao title: Analysis of Covid-19 and non-Covid-19 viruses, including influenza viruses, to determine the influence of intensive preventive measures in Japan date: 2020-07-07 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104543 sha: doc_id: 269519 cord_uid: 8hr8wyrr file: cache/cord-269975-1ebmq7t8.json key: cord-269975-1ebmq7t8 authors: Duplantier, Allen J.; Shurtleff, Amy C.; Miller, Cheryl; Chiang, Chih-Yuan; Panchal, Rekha G.; Sunay, Melek title: Combating biothreat pathogens: ongoing efforts for countermeasure development and unique challenges date: 2020-05-27 journal: Drug Discovery Targeting Drug-Resistant Bacteria DOI: 10.1016/b978-0-12-818480-6.00007-2 sha: doc_id: 269975 cord_uid: 1ebmq7t8 file: cache/cord-267567-w39f584z.json key: cord-267567-w39f584z authors: Pombo, Joao Palma; Sanyal, Sumana title: Perturbation of Intracellular Cholesterol and Fatty Acid Homeostasis During Flavivirus Infections date: 2018-06-04 journal: Front Immunol DOI: 10.3389/fimmu.2018.01276 sha: doc_id: 267567 cord_uid: w39f584z file: cache/cord-267261-8z4aqfff.json key: cord-267261-8z4aqfff authors: Su, John R. title: Emerging viral infections date: 2005-03-01 journal: Clin Lab Med DOI: 10.1016/j.cll.2004.05.002 sha: doc_id: 267261 cord_uid: 8z4aqfff file: cache/cord-268417-6eyetb5i.json key: cord-268417-6eyetb5i authors: Mandel, Benjamin title: Neutralization of Animal Viruses date: 1978-12-31 journal: Advances in Virus Research DOI: 10.1016/s0065-3527(08)60101-3 sha: doc_id: 268417 cord_uid: 6eyetb5i file: cache/cord-267733-fuz8r3vj.json key: cord-267733-fuz8r3vj authors: Al Ali, Sally; Baldanta, Sara; Fernández-Escobar, Mercedes; Guerra, Susana title: Use of Reporter Genes in the Generation of Vaccinia Virus-Derived Vectors date: 2016-05-21 journal: Viruses DOI: 10.3390/v8050134 sha: doc_id: 267733 cord_uid: fuz8r3vj file: cache/cord-268788-jcu3pasy.json key: cord-268788-jcu3pasy authors: Thor, Sharmi W.; Hilt, Deborah A.; Kissinger, Jessica C.; Paterson, Andrew H.; Jackwood, Mark W. title: Recombination in Avian Gamma-Coronavirus Infectious Bronchitis Virus date: 2011-09-23 journal: Viruses DOI: 10.3390/v3091777 sha: doc_id: 268788 cord_uid: jcu3pasy file: cache/cord-268593-rvxxv1dn.json key: cord-268593-rvxxv1dn authors: Wang, Mingyang; Veit, Michael title: Hemagglutinin-esterase-fusion (HEF) protein of influenza C virus date: 2015-07-28 journal: Protein Cell DOI: 10.1007/s13238-015-0193-x sha: doc_id: 268593 cord_uid: rvxxv1dn file: cache/cord-269193-a647hwu9.json key: cord-269193-a647hwu9 authors: Lin, Debby A.; Roychoudhury, Sonali; Palese, Peter; Clay, William C.; Fuller, Frederick J. title: Evolutionary relatedness of the predicted gene product of RNA segment 2 of the Tick-Borne Dhori virus and the PB1 polymerase gene of influenza viruses date: 1991-05-31 journal: Virology DOI: 10.1016/0042-6822(91)90641-n sha: doc_id: 269193 cord_uid: a647hwu9 file: cache/cord-270243-moxleyjg.json key: cord-270243-moxleyjg authors: Cholleti, Harindranath; Hayer, Juliette; Mulandane, Fernando Chanisso; Falk, Kerstin; Fafetine, Jose; Berg, Mikael; Blomström, Anne-Lie title: Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique date: 2018-05-28 journal: Infect Ecol Epidemiol DOI: 10.1080/20008686.2018.1478585 sha: doc_id: 270243 cord_uid: moxleyjg file: cache/cord-270772-zshjrc87.json key: cord-270772-zshjrc87 authors: To, Kelvin Kai-Wang; Zhou, Jie; Chan, Jasper Fuk-Woo; Yuen, Kwok-Yung title: Host genes and influenza pathogenesis in humans: an emerging paradigm date: 2015-06-14 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2015.04.010 sha: doc_id: 270772 cord_uid: zshjrc87 file: cache/cord-271105-eyigl0wz.json key: cord-271105-eyigl0wz authors: Ionidis, Georgios; Hübscher, Judith; Jack, Thomas; Becker, Britta; Bischoff, Birte; Todt, Daniel; Hodasa, Veronika; Brill, Florian H. H.; Steinmann, Eike; Steinmann, Jochen title: Development and virucidal activity of a novel alcohol-based hand disinfectant supplemented with urea and citric acid date: 2016-02-11 journal: BMC Infect Dis DOI: 10.1186/s12879-016-1410-9 sha: doc_id: 271105 cord_uid: eyigl0wz file: cache/cord-270911-z637eh2z.json key: cord-270911-z637eh2z authors: Zhou, Jie; Li, Cun; Sachs, Norman; Chiu, Man Chun; Wong, Bosco Ho-Yin; Chu, Hin; Poon, Vincent Kwok-Man; Wang, Dong; Zhao, Xiaoyu; Wen, Lei; Song, Wenjun; Yuan, Shuofeng; Wong, Kenneth Kak-Yuen; Chan, Jasper Fuk-Woo; To, Kelvin Kai-Wang; Chen, Honglin; Clevers, Hans; Yuen, Kwok-Yung title: Differentiated human airway organoids to assess infectivity of emerging influenza virus date: 2018-06-26 journal: Proc Natl Acad Sci U S A DOI: 10.1073/pnas.1806308115 sha: doc_id: 270911 cord_uid: z637eh2z file: cache/cord-271709-5frm3dnb.json key: cord-271709-5frm3dnb authors: Arden, Katherine E.; Greer, Ristan M.; Wang, Claire Y.T.; Mackay, Ian M. title: Genotypic diversity, circulation patterns and co-detections among rhinoviruses in Queensland, 2001 date: 2019-11-04 journal: Access Microbiol DOI: 10.1099/acmi.0.000075 sha: doc_id: 271709 cord_uid: 5frm3dnb file: cache/cord-268645-5op2m7pu.json key: cord-268645-5op2m7pu authors: Wu, Zhiqiang; Yang, Li; Ren, Xianwen; He, Guimei; Zhang, Junpeng; Yang, Jian; Qian, Zhaohui; Dong, Jie; Sun, Lilian; Zhu, Yafang; Du, Jiang; Yang, Fan; Zhang, Shuyi; Jin, Qi title: Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases date: 2015-08-11 journal: The ISME Journal DOI: 10.1038/ismej.2015.138 sha: doc_id: 268645 cord_uid: 5op2m7pu file: cache/cord-270091-sqrh8ylt.json key: cord-270091-sqrh8ylt authors: Cohen, Pascal; Guillevin, Loïc title: Vascularites associées aux infections virales date: 2004-11-30 journal: La Presse Médicale DOI: 10.1016/s0755-4982(04)98936-1 sha: doc_id: 270091 cord_uid: sqrh8ylt file: cache/cord-270161-vaejyy4i.json key: cord-270161-vaejyy4i authors: Reicks, Darwin L. title: Effective biosecurity to protect North American studs and clients from emerging infectious disease date: 2019-10-01 journal: Theriogenology DOI: 10.1016/j.theriogenology.2019.05.041 sha: doc_id: 270161 cord_uid: vaejyy4i file: cache/cord-269126-d81z6t0a.json key: cord-269126-d81z6t0a authors: Jayaseelan, Vijayashree Priyadharsini; Paramasivam, Arumugam title: Repurposing calcium channel blockers as antiviral drugs date: 2020-08-19 journal: J Cell Commun Signal DOI: 10.1007/s12079-020-00579-y sha: doc_id: 269126 cord_uid: d81z6t0a file: cache/cord-268540-wrjzr3ws.json key: cord-268540-wrjzr3ws authors: Park, You Jeong; Farooq, Jeffrey; Cho, Justin; Sadanandan, Nadia; Cozene, Blaise; Gonzales-Portillo, Bella; Saft, Madeline; Borlongan, Maximillian C.; Borlongan, Mia C.; Shytle, R. Douglas; Willing, Alison E.; Garbuzova-Davis, Svitlana; Sanberg, Paul R.; Borlongan, Cesar V. title: Fighting the War Against COVID-19 via Cell-Based Regenerative Medicine: Lessons Learned from 1918 Spanish Flu and Other Previous Pandemics date: 2020-08-13 journal: Stem Cell Rev Rep DOI: 10.1007/s12015-020-10026-5 sha: doc_id: 268540 cord_uid: wrjzr3ws file: cache/cord-270803-jtv5jmkn.json key: cord-270803-jtv5jmkn authors: Wang, Lin-Fa; Walker, Peter J.; Poon, Leo L.M. title: Mass extinctions, biodiversity and mitochondrial function: are bats ‘special’ as reservoirs for emerging viruses? date: 2011-11-09 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2011.10.013 sha: doc_id: 270803 cord_uid: jtv5jmkn file: cache/cord-271171-tohbzenc.json key: cord-271171-tohbzenc authors: Bhola, J.; Revathi Venkateswaran, V.; Koul, M. title: Corona Epidemic in Indian context: Predictive Mathematical Modelling date: 2020-04-07 journal: nan DOI: 10.1101/2020.04.03.20047175 sha: doc_id: 271171 cord_uid: tohbzenc file: cache/cord-271692-60nlid3c.json key: cord-271692-60nlid3c authors: Guo, Wen-Ping; Lin, Xian-Dan; Wang, Wen; Tian, Jun-Hua; Cong, Mei-Li; Zhang, Hai-Lin; Wang, Miao-Ruo; Zhou, Run-Hong; Wang, Jian-Bo; Li, Ming-Hui; Xu, Jianguo; Holmes, Edward C.; Zhang, Yong-Zhen title: Phylogeny and Origins of Hantaviruses Harbored by Bats, Insectivores, and Rodents date: 2013-02-07 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1003159 sha: doc_id: 271692 cord_uid: 60nlid3c file: cache/cord-271927-u8p6c9w4.json key: cord-271927-u8p6c9w4 authors: Stefanacci, Richard G.; Riddle, Albert title: Learnings to Operate LTC Better from the COVID-19 Crisis date: 2020-09-07 journal: Geriatr Nurs DOI: 10.1016/j.gerinurse.2020.07.014 sha: doc_id: 271927 cord_uid: u8p6c9w4 file: cache/cord-270940-acwkh6ed.json key: cord-270940-acwkh6ed authors: Kallio-Kokko, Hannimari; Uzcategui, Nathalie; Vapalahti, Olli; Vaheri, Antti title: Viral zoonoses in Europe date: 2005-06-29 journal: FEMS Microbiol Rev DOI: 10.1016/j.femsre.2005.04.012 sha: doc_id: 270940 cord_uid: acwkh6ed file: cache/cord-267671-ys43n672.json key: cord-267671-ys43n672 authors: Whary, Mark T.; Baumgarth, Nicole; Fox, James G.; Barthold, Stephen W. title: Biology and Diseases of Mice date: 2015-07-10 journal: Laboratory Animal Medicine DOI: 10.1016/b978-0-12-409527-4.00003-1 sha: doc_id: 267671 cord_uid: ys43n672 file: cache/cord-272052-8vvpm4tx.json key: cord-272052-8vvpm4tx authors: Hartmann, Katrin title: Clinical aspects of feline immunodeficiency and feline leukemia virus infection date: 2011-10-15 journal: Vet Immunol Immunopathol DOI: 10.1016/j.vetimm.2011.06.003 sha: doc_id: 272052 cord_uid: 8vvpm4tx file: cache/cord-270335-8vqi9c68.json key: cord-270335-8vqi9c68 authors: Seifert, Stephanie N; Letko, Michael C; Bushmaker, Trenton; Laing, Eric D; Saturday, Greg; Meade-White, Kimberly; van Doremalen, Neeltje; Broder, Christopher C; Munster, Vincent J title: Rousettus aegyptiacus Bats Do Not Support Productive Nipah Virus Replication date: 2019-11-04 journal: J Infect Dis DOI: 10.1093/infdis/jiz429 sha: doc_id: 270335 cord_uid: 8vqi9c68 file: cache/cord-270647-vn4kirrx.json key: cord-270647-vn4kirrx authors: Romero-Espinoza, Jose A.; Moreno-Valencia, Yazmin; Coronel-Tellez, Rodrigo H.; Castillejos-Lopez, Manuel; Hernandez, Andres; Dominguez, Aaron; Miliar-Garcia, Angel; Barbachano-Guerrero, Arturo; Perez-Padilla, Rogelio; Alejandre-Garcia, Alejandro; Vazquez-Perez, Joel 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 journal: PLoS One DOI: 10.1371/journal.pone.0192878 sha: doc_id: 270647 cord_uid: vn4kirrx file: cache/cord-272099-26nhza2s.json key: cord-272099-26nhza2s authors: IKEDA, KEIKO; TSUJIMOTO, KAZUKO; SUZUKI, YUKIKO; KOYAMA, AUGUSTINE HAJIME title: Survival of influenza A virus on contaminated student clothing date: 2015-02-09 journal: Exp Ther Med DOI: 10.3892/etm.2015.2278 sha: doc_id: 272099 cord_uid: 26nhza2s file: cache/cord-272405-jmwn8pdn.json key: cord-272405-jmwn8pdn authors: Parvez, Mohammad K.; Parveen, Shama title: Evolution and Emergence of Pathogenic Viruses: Past, Present, and Future date: 2017-08-04 journal: Intervirology DOI: 10.1159/000478729 sha: doc_id: 272405 cord_uid: jmwn8pdn file: cache/cord-273343-als886fe.json key: cord-273343-als886fe authors: McClenahan, Shasta D.; Scherba, Gail; Borst, Luke; Fredrickson, Richard L.; Krause, Philip R.; Uhlenhaut, Christine title: Discovery of a Bovine Enterovirus in Alpaca date: 2013-08-12 journal: PLoS One DOI: 10.1371/journal.pone.0068777 sha: doc_id: 273343 cord_uid: als886fe file: cache/cord-269426-82g5eiyg.json key: cord-269426-82g5eiyg authors: Holman, David H.; Wang, Danher; Woraratanadharm, Jan; Dong, John Y. title: Viral Vectors date: 2009-01-30 journal: Vaccines for Biodefense and Emerging and Neglected Diseases DOI: 10.1016/b978-0-12-369408-9.00007-x sha: doc_id: 269426 cord_uid: 82g5eiyg file: cache/cord-271076-436nxsua.json key: cord-271076-436nxsua authors: Paul-Pierre, Pastoret title: Emerging diseases, zoonoses and vaccines to control them date: 2009-10-30 journal: Vaccine DOI: 10.1016/j.vaccine.2009.06.021 sha: doc_id: 271076 cord_uid: 436nxsua file: cache/cord-271172-y48dovux.json key: cord-271172-y48dovux authors: Potter, Christopher William title: Chapter 25 Respiratory tract viruses date: 1998-12-31 journal: Principles of Medical Biology DOI: 10.1016/s1569-2582(97)80009-8 sha: doc_id: 271172 cord_uid: y48dovux file: cache/cord-271568-qgpi2kcs.json key: cord-271568-qgpi2kcs authors: Jackwood, M.W.; Rosenbloom, R.; Petteruti, M.; Hilt, D.A.; McCall, A.W.; Williams, S.M. title: Avian coronavirus infectious bronchitis virus susceptibility to botanical oleoresins and essential oils in vitro and in vivo date: 2010-01-21 journal: Virus Res DOI: 10.1016/j.virusres.2010.01.006 sha: doc_id: 271568 cord_uid: qgpi2kcs file: cache/cord-272829-i4jh6bcn.json key: cord-272829-i4jh6bcn authors: ZANETTI, A. R.; ZAPPA, A. title: Emerging and re‐emerging infections at the turn of the millennium date: 2010-01-04 journal: Haemophilia DOI: 10.1111/j.1365-2516.2009.02174.x sha: doc_id: 272829 cord_uid: i4jh6bcn file: cache/cord-271313-h9v0nmx5.json key: cord-271313-h9v0nmx5 authors: Bagust, T. J. title: A REVIEW OF VIRAL INFECTIONS OF HORSES date: 2008-03-10 journal: Aust Vet J DOI: 10.1111/j.1751-0813.1972.tb02314.x sha: doc_id: 271313 cord_uid: h9v0nmx5 file: cache/cord-273372-69rlh9or.json key: cord-273372-69rlh9or authors: Litterman, Nadia; Lipinski, Christopher; Ekins, Sean title: Small molecules with antiviral activity against the Ebola virus date: 2015-02-09 journal: F1000Res DOI: 10.12688/f1000research.6120.1 sha: doc_id: 273372 cord_uid: 69rlh9or file: cache/cord-271884-86yl9ren.json key: cord-271884-86yl9ren authors: Traavik, T. title: Development of a modified immunoelectroosmophoresis method for Uukuniemi and Runde virus serology date: 1977 journal: Arch Virol DOI: 10.1007/bf01314789 sha: doc_id: 271884 cord_uid: 86yl9ren file: cache/cord-270670-cubh9jxc.json key: cord-270670-cubh9jxc authors: Domingo, E.; Martín, V.; Perales, C.; Grande-Pérez, A.; García-Arriaza, J.; Arias, A. title: Viruses as Quasispecies: Biological Implications date: 2006 journal: Quasispecies: Concept and Implications for Virology DOI: 10.1007/3-540-26397-7_3 sha: doc_id: 270670 cord_uid: cubh9jxc file: cache/cord-274765-3wzht843.json key: cord-274765-3wzht843 authors: Kweon, Chang-Hee; Kwon, Byung-Joon; Lee, Jae-Gil; Kwon, Geon-Oh; Kang, Yung-Bai title: Derivation of attenuated porcine epidemic diarrhea virus (PEDV) as vaccine candidate date: 1999-06-04 journal: Vaccine DOI: 10.1016/s0264-410x(99)00059-6 sha: doc_id: 274765 cord_uid: 3wzht843 file: cache/cord-271650-biq0chyn.json key: cord-271650-biq0chyn authors: Torres, Juan M; Ramírez, Miguel A; Morales, Mónica; Bárcena, Juan; Vázquez, Belén; Espuña, Enric; Pagès-Manté, Albert; Sánchez-Vizcaíno, José M title: Safety evaluation of a recombinant myxoma-RHDV virus inducing horizontal transmissible protection against myxomatosis and rabbit haemorrhagic disease date: 2000-09-15 journal: Vaccine DOI: 10.1016/s0264-410x(00)00183-3 sha: doc_id: 271650 cord_uid: biq0chyn file: cache/cord-272981-8gahvdt0.json key: cord-272981-8gahvdt0 authors: Wege, Helmut; Watanabe, Rihito; ter Meulen, Volker title: Relapsing subacute demyelinating encephalomyelitis in rats during the course of coronavirus JHM infection date: 1984-08-31 journal: Journal of Neuroimmunology DOI: 10.1016/0165-5728(84)90022-5 sha: doc_id: 272981 cord_uid: 8gahvdt0 file: cache/cord-274112-6t0wpiqy.json key: cord-274112-6t0wpiqy authors: Webby, RJ; Perez, DR; Coleman, JS; Guan, Y; Knight, JH; Govorkova, EA; McClain-Moss, LR; Peiris, JS; Rehg, JE; Tuomanen, EI; Webster, RG title: Responsiveness to a pandemic alert: use of reverse genetics for rapid development of influenza vaccines date: 2004-04-03 journal: Lancet DOI: 10.1016/s0140-6736(04)15892-3 sha: doc_id: 274112 cord_uid: 6t0wpiqy file: cache/cord-275013-na6319rg.json key: cord-275013-na6319rg authors: Singh, Indra P.; Baron, Samuel title: Innate defences against viraemia date: 2000-11-23 journal: Rev Med Virol DOI: 10.1002/1099-1654(200011/12)10:6<395::aid-rmv298>3.0.co;2-v sha: doc_id: 275013 cord_uid: na6319rg file: cache/cord-271790-3s8o774l.json key: cord-271790-3s8o774l authors: Pinto Mendes, J. title: The role of infection in asthma date: 2008-10-31 journal: Revista Portuguesa de Pneumologia (English Edition) DOI: 10.1016/s2173-5115(08)70297-5 sha: doc_id: 271790 cord_uid: 3s8o774l file: cache/cord-271091-ffn59sgf.json key: cord-271091-ffn59sgf authors: Galao, Rui P; Scheller, Nicoletta; Alves-Rodrigues, Isabel; Breinig, Tanja; Meyerhans, Andreas; Díez, Juana title: Saccharomyces cerevisiae: a versatile eukaryotic system in virology date: 2007-10-10 journal: Microb Cell Fact DOI: 10.1186/1475-2859-6-32 sha: doc_id: 271091 cord_uid: ffn59sgf file: cache/cord-273019-hbpfz8rt.json key: cord-273019-hbpfz8rt authors: Glingston, R. Sahaya; Deb, Rachayeeta; Kumar, Sachin; Nagotu, Shirisha title: Organelle dynamics and viral infections: at cross roads date: 2018-06-25 journal: Microbes Infect DOI: 10.1016/j.micinf.2018.06.002 sha: doc_id: 273019 cord_uid: hbpfz8rt file: cache/cord-274306-cxvnv8dy.json key: cord-274306-cxvnv8dy authors: Chastel, C. title: Émergence de virus nouveaux en Asie : les changements climatiques sont-ils en cause ? date: 2004-11-30 journal: Médecine et Maladies Infectieuses DOI: 10.1016/j.medmal.2004.07.027 sha: doc_id: 274306 cord_uid: cxvnv8dy file: cache/cord-274643-vjb2yt93.json key: cord-274643-vjb2yt93 authors: Kang, G. title: Viral Diarrhea date: 2008-08-26 journal: International Encyclopedia of Public Health DOI: 10.1016/b978-012373960-5.00571-2 sha: doc_id: 274643 cord_uid: vjb2yt93 file: cache/cord-275602-cog4nma0.json key: cord-275602-cog4nma0 authors: Watkins, Kevin title: Emerging Infectious Diseases: a Review date: 2018-06-22 journal: Curr Emerg Hosp Med Rep DOI: 10.1007/s40138-018-0162-9 sha: doc_id: 275602 cord_uid: cog4nma0 file: cache/cord-272066-f6q6q3io.json key: cord-272066-f6q6q3io authors: Shim, Byoung-Shik; Choi, Youngjoo; Cheon, In Su; Song, Man Ki title: Sublingual Delivery of Vaccines for the Induction of Mucosal Immunity date: 2013-06-30 journal: Immune Netw DOI: 10.4110/in.2013.13.3.81 sha: doc_id: 272066 cord_uid: f6q6q3io file: cache/cord-271122-3fsl5589.json key: cord-271122-3fsl5589 authors: Wathes, D. Claire; Oguejiofor, Chike F.; Thomas, Carole; Cheng, Zhangrui title: Importance of Viral Disease in Dairy Cow Fertility date: 2019-07-24 journal: Engineering (Beijing) DOI: 10.1016/j.eng.2019.07.020 sha: doc_id: 271122 cord_uid: 3fsl5589 file: cache/cord-273326-gmw8gl2r.json key: cord-273326-gmw8gl2r authors: Saiz, Juan-Carlos; de Oya, Nereida Jiménez; Blázquez, Ana-Belén; Escribano-Romero, Estela; Martín-Acebes, Miguel A. title: Host-Directed Antivirals: A Realistic Alternative to Fight Zika Virus date: 2018-08-24 journal: Viruses DOI: 10.3390/v10090453 sha: doc_id: 273326 cord_uid: gmw8gl2r file: cache/cord-273708-2q64at3z.json key: cord-273708-2q64at3z authors: Annunziata, Giuseppe; Sanduzzi Zamparelli, Marco; Santoro, Ciro; Ciampaglia, Roberto; Stornaiuolo, Mariano; Tenore, Gian Carlo; Sanduzzi, Alessandro; Novellino, Ettore title: May Polyphenols Have a Role Against Coronavirus Infection? An Overview of in vitro Evidence date: 2020-05-15 journal: Front Med (Lausanne) DOI: 10.3389/fmed.2020.00240 sha: doc_id: 273708 cord_uid: 2q64at3z file: cache/cord-276006-mjjnkqv6.json key: cord-276006-mjjnkqv6 authors: Jarach, Natanel; Dodiuk, Hanna; Kenig, Samuel title: Polymers in the Medical Antiviral Front-Line date: 2020-07-31 journal: Polymers (Basel) DOI: 10.3390/polym12081727 sha: doc_id: 276006 cord_uid: mjjnkqv6 file: cache/cord-273777-qb0vp9gr.json key: cord-273777-qb0vp9gr authors: Happel, Anna-Ursula; Varsani, Arvind; Balle, Christina; Passmore, Jo-Ann; Jaspan, Heather title: The Vaginal Virome—Balancing Female Genital Tract Bacteriome, Mucosal Immunity, and Sexual and Reproductive Health Outcomes? date: 2020-07-30 journal: Viruses DOI: 10.3390/v12080832 sha: doc_id: 273777 cord_uid: qb0vp9gr file: cache/cord-276193-cngz535o.json key: cord-276193-cngz535o authors: Volz, A.; Sutter, G. title: Modified Vaccinia Virus Ankara: History, Value in Basic Research, and Current Perspectives for Vaccine Development date: 2016-08-01 journal: Adv Virus Res DOI: 10.1016/bs.aivir.2016.07.001 sha: doc_id: 276193 cord_uid: cngz535o file: cache/cord-276348-vr5fit8r.json key: cord-276348-vr5fit8r authors: Ogra, Pearay L. title: Respiratory syncytial virus: The virus, the disease and the immune response date: 2004-01-31 journal: Paediatric Respiratory Reviews DOI: 10.1016/s1526-0542(04)90023-1 sha: doc_id: 276348 cord_uid: vr5fit8r file: cache/cord-276585-m1dkkbq7.json key: cord-276585-m1dkkbq7 authors: Pulliam, Juliet R. C. title: Viral Host Jumps: Moving toward a Predictive Framework date: 2008-02-13 journal: Ecohealth DOI: 10.1007/s10393-007-0149-6 sha: doc_id: 276585 cord_uid: m1dkkbq7 file: cache/cord-276212-ys5njiw0.json key: cord-276212-ys5njiw0 authors: Wei, L.; Chan, K.-H.; Ip, D.K.M.; Fang, V.J.; Fung, R.O.P.; Leung, G.M.; Peiris, M.J.S.; Cowling, B.J. title: Burden, seasonal pattern and symptomatology of acute respiratory illnesses with different viral aetiologies in children presenting at outpatient clinics in Hong Kong date: 2015-05-30 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2015.05.027 sha: doc_id: 276212 cord_uid: ys5njiw0 file: cache/cord-275719-ru33ubss.json key: cord-275719-ru33ubss authors: Roingeard, Philippe; Raynal, Pierre‐Ivan; Eymieux, Sébastien; Blanchard, Emmanuelle title: Virus detection by transmission electron microscopy: Still useful for diagnosis and a plus for biosafety date: 2018-11-09 journal: Rev Med Virol DOI: 10.1002/rmv.2019 sha: doc_id: 275719 cord_uid: ru33ubss file: cache/cord-276052-gk6n8slx.json key: cord-276052-gk6n8slx authors: Yadav, Pragya; Sarkale, Prasad; Patil, Deepak; Shete, Anita; Kokate, Prasad; Kumar, Vimal; Jain, Rajlaxmi; Jadhav, Santosh; Basu, Atanu; Pawar, Shailesh; Sudeep, Anakkathil; Gokhale, Mangesh; Lakra, Rajen; Mourya, Devendra title: Isolation of Tioman virus from Pteropus giganteus bat in North-East region of India date: 2016-09-09 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2016.09.010 sha: doc_id: 276052 cord_uid: gk6n8slx file: cache/cord-276009-p98wjtjb.json key: cord-276009-p98wjtjb authors: Iyer, Arun V.; Pahar, Bapi; Boudreaux, Marc J.; Wakamatsu, Nobuko; Roy, Alma F.; Chouljenko, Vladimir N.; Baghian, Abolghasem; Apetrei, Cristian; Marx, Preston A.; Kousoulas, Konstantin G. title: Recombinant vesicular stomatitis virus-based west Nile vaccine elicits strong humoral and cellular immune responses and protects mice against lethal challenge with the virulent west Nile virus strain LSU-AR01 date: 2009-02-05 journal: Vaccine DOI: 10.1016/j.vaccine.2008.11.087 sha: doc_id: 276009 cord_uid: p98wjtjb file: cache/cord-276715-d1nh2dvb.json key: cord-276715-d1nh2dvb authors: Raha, Syamal; Mallick, Rahul; Basak, Sanjay; Duttaroy, Asim K. title: Is Copper beneficial for COVID-19 patients? date: 2020-05-05 journal: Med Hypotheses DOI: 10.1016/j.mehy.2020.109814 sha: doc_id: 276715 cord_uid: d1nh2dvb file: cache/cord-275570-i9fw0afj.json key: cord-275570-i9fw0afj authors: Lau, Susanna K. P. title: Molecular Research on Emerging Viruses: Evolution, Diagnostics, Pathogenesis, and Therapeutics date: 2018-01-30 journal: Int J Mol Sci DOI: 10.3390/ijms19020398 sha: doc_id: 275570 cord_uid: i9fw0afj file: cache/cord-275821-yu39aw54.json key: cord-275821-yu39aw54 authors: Ciminski, Kevin; Thamamongood, Thiprampai; Zimmer, Gert; Schwemmle, Martin title: Novel insights into bat influenza A viruses date: 2017-09-14 journal: J Gen Virol DOI: 10.1099/jgv.0.000927 sha: doc_id: 275821 cord_uid: yu39aw54 file: cache/cord-275795-ee7qyw5h.json key: cord-275795-ee7qyw5h authors: Monette, Anne; Mouland, Andrew J. title: T Lymphocytes as Measurable Targets of Protection and Vaccination Against Viral Disorders date: 2018-10-24 journal: Int Rev Cell Mol Biol DOI: 10.1016/bs.ircmb.2018.07.006 sha: doc_id: 275795 cord_uid: ee7qyw5h file: cache/cord-274080-884x48on.json key: cord-274080-884x48on authors: Rumlová, Michaela; Ruml, Tomáš title: In vitro methods for testing antiviral drugs date: 2018-06-30 journal: Biotechnology Advances DOI: 10.1016/j.biotechadv.2017.12.016 sha: doc_id: 274080 cord_uid: 884x48on file: cache/cord-277392-s0bldxg9.json key: cord-277392-s0bldxg9 authors: Cann, Alan J. title: Replication date: 2012-02-29 journal: Principles of Molecular Virology DOI: 10.1016/b978-0-12-384939-7.10004-3 sha: doc_id: 277392 cord_uid: s0bldxg9 file: cache/cord-277107-gs7j6fxo.json key: cord-277107-gs7j6fxo authors: Yamin, Mohammad title: Counting the cost of COVID-19 date: 2020-05-13 journal: Int J Inf Technol DOI: 10.1007/s41870-020-00466-0 sha: doc_id: 277107 cord_uid: gs7j6fxo file: cache/cord-276583-j8bf0eme.json key: cord-276583-j8bf0eme authors: Ghalyanchi Langeroudi, Arash; Karimi, Vahid; Tavasoti Kheiri, Masoumeh; Barin, Abbas title: Full-length characterization and phylogenetic analysis of hemagglutinin gene of H9N2 virus isolated from broilers in Iran during 1998–2007 date: 2012-01-21 journal: Comp Clin Path DOI: 10.1007/s00580-012-1405-x sha: doc_id: 276583 cord_uid: j8bf0eme file: cache/cord-277327-il8uaavn.json key: cord-277327-il8uaavn authors: Couch, MD, Robert B.; Englund, MD, Janet A. title: Respiratory Viral Infections in Immunocompetent and Immunocompromised Persons date: 1997-03-17 journal: Am J Med DOI: 10.1016/s0002-9343(97)00003-x sha: doc_id: 277327 cord_uid: il8uaavn file: cache/cord-278093-0twnkv93.json key: cord-278093-0twnkv93 authors: Perveen, Shagufta; Orfali, Raha; Azam, Shafiq; Aati, Hanan Y.; Bukhari, Khulud; Bukhari, Sara I.; Al-Taweel, Areej title: Coronavirus nCOVID-19: A Pandemic Disease and the Saudi precautions date: 2020-06-18 journal: Saudi Pharm J DOI: 10.1016/j.jsps.2020.06.006 sha: doc_id: 278093 cord_uid: 0twnkv93 file: cache/cord-275683-1qj9ri18.json key: cord-275683-1qj9ri18 authors: Roux, Simon; Matthijnssens, Jelle; Dutilh, Bas E. title: Metagenomics in Virology date: 2019-06-12 journal: Reference Module in Life Sciences DOI: 10.1016/b978-0-12-809633-8.20957-6 sha: doc_id: 275683 cord_uid: 1qj9ri18 file: cache/cord-277010-2iecsho0.json key: cord-277010-2iecsho0 authors: Wen, Xiaohong; Huang, Qiuling; Tao, Hong; Zou, Weihua; Gao, Min; Guo, Huihui; Yao, Xing; Cui, Dawei; Wang, Xiang title: Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study date: 2019-01-08 journal: BMC Infect Dis DOI: 10.1186/s12879-018-3668-6 sha: doc_id: 277010 cord_uid: 2iecsho0 file: cache/cord-276039-nqqwnmwc.json key: cord-276039-nqqwnmwc authors: Rua, Rejane; Gessain, Antoine title: Origin, evolution and innate immune control of simian foamy viruses in humans date: 2015-02-17 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2014.12.003 sha: doc_id: 276039 cord_uid: nqqwnmwc file: cache/cord-278250-dwok857k.json key: cord-278250-dwok857k authors: Li, Heng; Li, Hongzhe; Wang, Jingjing; Guo, Lei; Fan, Haitao; Zheng, Huiwen; Yang, Zening; Huang, Xing; Chu, Manman; Yang, Fengmei; He, Zhanlong; Li, Nan; Yang, Jinxi; Wu, Qiongwen; Shi, Haijing; Liu, Longding title: The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites date: 2019-08-19 journal: Virol J DOI: 10.1186/s12985-019-1211-z sha: doc_id: 278250 cord_uid: dwok857k file: cache/cord-275538-c44gmu22.json key: cord-275538-c44gmu22 authors: Davis-Wurzler, Gina M. title: Current Vaccination Strategies in Puppies and Kittens date: 2006-03-24 journal: Vet Clin North Am Small Anim Pract DOI: 10.1016/j.cvsm.2005.12.003 sha: doc_id: 275538 cord_uid: c44gmu22 file: cache/cord-277400-w7mvk3x4.json key: cord-277400-w7mvk3x4 authors: Nasir, Arshan; Caetano-Anollés, Gustavo title: Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification date: 2017-03-10 journal: Front Microbiol DOI: 10.3389/fmicb.2017.00380 sha: doc_id: 277400 cord_uid: w7mvk3x4 file: cache/cord-278099-ypov9ha3.json key: cord-278099-ypov9ha3 authors: Kumar, Surender; Subbarao, Burra L.; Kumari, Reenu; Hallan, Vipin title: Molecular characterization of a novel cryptic virus infecting pigeonpea plants date: 2017-08-03 journal: PLoS One DOI: 10.1371/journal.pone.0181829 sha: doc_id: 278099 cord_uid: ypov9ha3 file: cache/cord-277641-nb1p1akx.json key: cord-277641-nb1p1akx authors: Shaw, D. M. title: Invisible Enemies: Coronavirus and Other Hidden Threats date: 2020-08-25 journal: J Bioeth Inq DOI: 10.1007/s11673-020-10015-w sha: doc_id: 277641 cord_uid: nb1p1akx file: cache/cord-276506-dj7dyo0x.json key: cord-276506-dj7dyo0x authors: Coria, M. F. title: Protective effect of an inactivated avian coronavirus vaccine administered by aerosol date: 1973 journal: Arch Gesamte Virusforsch DOI: 10.1007/bf01249930 sha: doc_id: 276506 cord_uid: dj7dyo0x file: cache/cord-276616-odmnvv7m.json key: cord-276616-odmnvv7m authors: Darcel, C. title: Reflections on scrapie and related disorders, with consideration of the possibility of a viral aetiology date: 1995 journal: Vet Res Commun DOI: 10.1007/bf01839302 sha: doc_id: 276616 cord_uid: odmnvv7m file: cache/cord-277309-kelebqr6.json key: cord-277309-kelebqr6 authors: Wang, Lin-Fa; Anderson, Danielle E title: Viruses in bats and potential spillover to animals and humans date: 2019-01-18 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2018.12.007 sha: doc_id: 277309 cord_uid: kelebqr6 file: cache/cord-278456-gsv6dh36.json key: cord-278456-gsv6dh36 authors: Qureshi, Abid; Kaur, Gazaldeep; Kumar, Manoj title: AVCpred: an integrated web server for prediction and design of antiviral compounds date: 2016-09-09 journal: Chem Biol Drug Des DOI: 10.1111/cbdd.12834 sha: doc_id: 278456 cord_uid: gsv6dh36 file: cache/cord-278635-vwdxr1bl.json key: cord-278635-vwdxr1bl authors: Świętoń, Edyta; Tarasiuk, Karolina; Śmietanka, Krzysztof title: Low pathogenic avian influenza virus isolates with different levels of defective genome segments vary in pathogenicity and transmission efficiency date: 2020-08-28 journal: Vet Res DOI: 10.1186/s13567-020-00833-6 sha: doc_id: 278635 cord_uid: vwdxr1bl file: cache/cord-277970-sb1wjd3b.json key: cord-277970-sb1wjd3b authors: Kang, Qianli; Wang, Yanyan; Cui, Qinghua; Gong, Lili; Yang, Yong; Jiang, Haiqiang; Rong, Lijun; Rong, Rong; Du, Ruikun title: Screening for Anti-Influenza Actives of Prefractionated Traditional Chinese Medicines date: 2020-10-14 journal: Evid Based Complement Alternat Med DOI: 10.1155/2020/4979850 sha: doc_id: 277970 cord_uid: sb1wjd3b file: cache/cord-278465-tjjkz16y.json key: cord-278465-tjjkz16y authors: Wille, Michelle; Lindqvist, Kristine; Muradrasoli, Shaman; Olsen, Björn; Järhult, Josef D. title: Urbanization and the dynamics of RNA viruses in Mallards (Anas platyrhynchos) date: 2017-03-18 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2017.03.019 sha: doc_id: 278465 cord_uid: tjjkz16y file: cache/cord-276364-zyw5aukk.json key: cord-276364-zyw5aukk authors: Wong, Ho Him; Sanyal, Sumana title: Manipulation of autophagy by (+) RNA viruses date: 2019-08-08 journal: Semin Cell Dev Biol DOI: 10.1016/j.semcdb.2019.07.013 sha: doc_id: 276364 cord_uid: zyw5aukk file: cache/cord-279694-25rblhwb.json key: cord-279694-25rblhwb authors: Mahy, B.W.J title: Emerging and Reemerging Virus Diseases of Vertebrates date: 2014-11-28 journal: Reference Module in Biomedical Sciences DOI: 10.1016/b978-0-12-801238-3.02564-2 sha: doc_id: 279694 cord_uid: 25rblhwb file: cache/cord-279798-b5tduubu.json key: cord-279798-b5tduubu authors: Sano, Daisuke; Amarasiri, Mohan; Hata, Akihiko; Watanabe, Toru; Katayama, Hiroyuki title: Risk management of viral infectious diseases in wastewater reclamation and reuse: Review date: 2016-03-14 journal: Environ Int DOI: 10.1016/j.envint.2016.03.001 sha: doc_id: 279798 cord_uid: b5tduubu file: cache/cord-276908-9jthjf24.json key: cord-276908-9jthjf24 authors: Gupta, Akanksha; Kumar, Sanjay; Kumar, Ravinder; Choudhary, Ashish Kumar; Kumari, Kamlesh; Singh, Prashant; Kumar, Vinod title: COVID‐19: Emergence of Infectious Diseases, Nanotechnology Aspects, Challenges, and Future Perspectives date: 2020-07-06 journal: ChemistrySelect DOI: 10.1002/slct.202001709 sha: doc_id: 276908 cord_uid: 9jthjf24 file: cache/cord-278973-82n0d1dh.json key: cord-278973-82n0d1dh authors: Li, Zhijie; Liu, Dafei; Ran, Xuhua; Liu, Chunguo; Guo, Dongchun; Hu, Xiaoliang; Tian, Jin; Zhang, Xiaozhan; Shao, Yuhao; Liu, Shengwang; Qu, Liandong title: Characterization and pathogenicity of a novel mammalian orthoreovirus from wild short-nosed fruit bats date: 2016-05-31 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2016.05.039 sha: doc_id: 278973 cord_uid: 82n0d1dh file: cache/cord-279617-xuzu55cg.json key: cord-279617-xuzu55cg authors: Tuladhar, E.; Bouwknegt, M.; Zwietering, M.H.; Koopmans, M.; Duizer, E. title: Thermal stability of structurally different viruses with proven or potential relevance to food safety date: 2012-03-30 journal: J Appl Microbiol DOI: 10.1111/j.1365-2672.2012.05282.x sha: doc_id: 279617 cord_uid: xuzu55cg file: cache/cord-277417-f71jwdzj.json key: cord-277417-f71jwdzj authors: Geoghegan, Jemma L.; Holmes, Edward C. title: The phylogenomics of evolving virus virulence date: 2018-10-10 journal: Nat Rev Genet DOI: 10.1038/s41576-018-0055-5 sha: doc_id: 277417 cord_uid: f71jwdzj file: cache/cord-278482-j5zlismf.json key: cord-278482-j5zlismf authors: Taylor, Raymond; Kotian, Pravin; Warren, Travis; Panchal, Rekha; Bavari, Sina; Julander, Justin; Dobo, Sylvia; Rose, Angela; El-Kattan, Yahya; Taubenheim, Brian; Babu, Yarlagadda; Sheridan, William P. title: BCX4430 – A broad-spectrum antiviral adenosine nucleoside analog under development for the treatment of Ebola virus disease date: 2016-06-30 journal: Journal of Infection and Public Health DOI: 10.1016/j.jiph.2016.04.002 sha: doc_id: 278482 cord_uid: j5zlismf file: cache/cord-280854-cxpgwwjd.json key: cord-280854-cxpgwwjd authors: Kumarasamy, Dhanabal; Roy, Biswajit Gopal; Rocha-Pereira, Joana; Neyts, Johan; Nanjappan, Satheeshkumar; Maity, Subhasis; Mookerjee, Musfiqua; Naesens, Lieve title: Synthesis and in vitro antiviral evaluation of 4-substituted 3,4-dihydropyrimidinones date: 2017-01-15 journal: Bioorganic & Medicinal Chemistry Letters DOI: 10.1016/j.bmcl.2016.12.010 sha: doc_id: 280854 cord_uid: cxpgwwjd file: cache/cord-280987-uhxk5b1b.json key: cord-280987-uhxk5b1b authors: Turtle, L.; Solomon, T. title: Encephalitis, Viral date: 2014-05-01 journal: Encyclopedia of the Neurological Sciences DOI: 10.1016/b978-0-12-385157-4.00375-4 sha: doc_id: 280987 cord_uid: uhxk5b1b file: cache/cord-279557-hk77e3pp.json key: cord-279557-hk77e3pp authors: Drosten, Christian; Seilmaier, Michael; Corman, Victor M; Hartmann, Wulf; Scheible, Gregor; Sack, Stefan; Guggemos, Wolfgang; Kallies, Rene; Muth, Doreen; Junglen, Sandra; Müller, Marcel A; Haas, Walter; Guberina, Hana; Röhnisch, Tim; Schmid-Wendtner, Monika; Aldabbagh, Souhaib; Dittmer, Ulf; Gold, Hermann; Graf, Petra; Bonin, Frank; Rambaut, Andrew; Wendtner, Clemens-Martin title: Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection date: 2013-06-17 journal: Lancet Infect Dis DOI: 10.1016/s1473-3099(13)70154-3 sha: doc_id: 279557 cord_uid: hk77e3pp file: cache/cord-280048-b4dz1lnn.json key: cord-280048-b4dz1lnn authors: Domingo, Esteban; Perales, Celia title: Viral quasispecies date: 2019-10-17 journal: PLoS Genet DOI: 10.1371/journal.pgen.1008271 sha: doc_id: 280048 cord_uid: b4dz1lnn file: cache/cord-280391-5kiu2pb6.json key: cord-280391-5kiu2pb6 authors: Akinloye, Oluwabukola M.; Rönkkö, Esa; Savolainen-Kopra, Carita; Ziegler, Thedi; Iwalokun, Bamidele A.; Deji-Agboola, Mope A.; Oluwadun, Afolabi; Roivainen, Merja; Adu, Festus D.; Hovi, Tapani title: Specific Viruses Detected in Nigerian Children in Association with Acute Respiratory Disease date: 2011-10-11 journal: J Trop Med DOI: 10.1155/2011/690286 sha: doc_id: 280391 cord_uid: 5kiu2pb6 file: cache/cord-278479-vl296i1b.json key: cord-278479-vl296i1b authors: Samuel, Arthur S; Subbiah, Madhuri; Shive, Heather; Collins, Peter L; Samal, Siba K title: Experimental infection of hamsters with avian paramyxovirus serotypes 1 to 9 date: 2011-02-23 journal: Vet Res DOI: 10.1186/1297-9716-42-38 sha: doc_id: 278479 cord_uid: vl296i1b file: cache/cord-278876-il7g78w1.json key: cord-278876-il7g78w1 authors: Akkina, Ramesh; Ellerbrok, Heinz; Hall, William; Hasegawa, Hideki; Kawaguchi, Yasushi; Kleanthous, Harold; McSweegan, Edward; Mercer, Natalia; Romanowski, Victor; Sawa, Hirofumi; Vahlne, Anders title: 2016 International meeting of the Global Virus Network date: 2017-03-16 journal: Antiviral Res DOI: 10.1016/j.antiviral.2017.03.005 sha: doc_id: 278876 cord_uid: il7g78w1 file: cache/cord-278913-u6vihq3u.json key: cord-278913-u6vihq3u authors: Allam, Zaheer title: The Rise of Machine Intelligence in the COVID-19 Pandemic and Its Impact on Health Policy date: 2020-07-24 journal: Surveying the Covid-19 Pandemic and its Implications DOI: 10.1016/b978-0-12-824313-8.00006-1 sha: doc_id: 278913 cord_uid: u6vihq3u file: cache/cord-280986-i27mge10.json key: cord-280986-i27mge10 authors: Mallia, Patrick; Johnston, Sebastian L. title: How Viral Infections Cause Exacerbation of Airway Diseases date: 2017-01-25 journal: Chest DOI: 10.1378/chest.130.4.1203 sha: doc_id: 280986 cord_uid: i27mge10 file: cache/cord-281332-5mddyv0n.json key: cord-281332-5mddyv0n authors: Wilson, Michael R.; Suan, Dan; Duggins, Andrew; Schubert, Ryan D.; Khan, Lillian M.; Sample, Hannah A.; Zorn, Kelsey C.; Rodrigues Hoffman, Aline; Blick, Anna; Shingde, Meena; DeRisi, Joseph L. title: A novel cause of chronic viral meningoencephalitis: Cache Valley virus date: 2017-07-25 journal: Ann Neurol DOI: 10.1002/ana.24982 sha: doc_id: 281332 cord_uid: 5mddyv0n file: cache/cord-278511-je1509ar.json key: cord-278511-je1509ar authors: Wang, David title: 5 challenges in understanding the role of the virome in health and disease date: 2020-03-26 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1008318 sha: doc_id: 278511 cord_uid: je1509ar file: cache/cord-280429-4fota9rl.json key: cord-280429-4fota9rl authors: Medvedev, Kirill E.; Kinch, Lisa N.; Grishin, Nick V. title: Functional and evolutionary analysis of viral proteins containing a Rossmann‐like fold date: 2018-06-13 journal: Protein Science DOI: 10.1002/pro.3438 sha: doc_id: 280429 cord_uid: 4fota9rl file: cache/cord-278684-txlvla0j.json key: cord-278684-txlvla0j authors: Gonzalez–Dunia, Daniel; Sauder, Christian; de la Torre, Juan Carlos title: Borna Disease Virus and the Brain date: 1998-01-30 journal: Brain Res Bull DOI: 10.1016/s0361-9230(97)00276-1 sha: doc_id: 278684 cord_uid: txlvla0j file: cache/cord-280427-smqc23vr.json key: cord-280427-smqc23vr authors: Singla, Rubal; Mishra, Abhishek; Joshi, Rupa; Jha, Sonali; Sharma, Amit Raj; Upadhyay, Sujata; Sarma, Phulen; Prakash, Ajay; Medhi, Bikash title: Human animal interface of SARS-CoV-2 (COVID-19) transmission: a critical appraisal of scientific evidence date: 2020-09-14 journal: Vet Res Commun DOI: 10.1007/s11259-020-09781-0 sha: doc_id: 280427 cord_uid: smqc23vr file: cache/cord-279691-v5kpmk0b.json key: cord-279691-v5kpmk0b authors: Hagemeijer, Marne C.; Rottier, Peter J.M.; de Haan, Cornelis A.M. title: Biogenesis and Dynamics of the Coronavirus Replicative Structures date: 2012-11-21 journal: Viruses DOI: 10.3390/v4113245 sha: doc_id: 279691 cord_uid: v5kpmk0b file: cache/cord-280130-ewqe9edq.json key: cord-280130-ewqe9edq authors: Weber, Friedemann; Haller, Otto title: Viral suppression of the interferon system date: 2007-01-27 journal: Biochimie DOI: 10.1016/j.biochi.2007.01.005 sha: doc_id: 280130 cord_uid: ewqe9edq file: cache/cord-280564-kgoczioe.json key: cord-280564-kgoczioe authors: Conceição-Neto, Nádia; Theuns, Sebastiaan; Cui, Tingting; Zeller, Mark; Yinda, Claude Kwe; Christiaens, Isaura; Heylen, Elisabeth; Van Ranst, Marc; Carpentier, Sebastien; Nauwynck, Hans J.; Matthijnssens, Jelle title: Identification of an enterovirus recombinant with a torovirus-like gene insertion during a diarrhea outbreak in fattening pigs date: 2017-09-08 journal: Virus Evol DOI: 10.1093/ve/vex024 sha: doc_id: 280564 cord_uid: kgoczioe file: cache/cord-282628-6uoberfu.json key: cord-282628-6uoberfu authors: Tiwari, Bhagyashree; Sellamuthu, Balasubramanian; Drogui, Patrick; Tyagi, R.D. title: Future impacts and trends in treatment of hospital wastewater date: 2020-05-01 journal: Current Developments in Biotechnology and Bioengineering DOI: 10.1016/b978-0-12-819722-6.00017-1 sha: doc_id: 282628 cord_uid: 6uoberfu file: cache/cord-279849-zzkliu76.json key: cord-279849-zzkliu76 authors: DaPalma, T.; Doonan, B.P.; Trager, N.M.; Kasman, L.M. title: A systematic approach to virus–virus interactions date: 2010-01-20 journal: Virus Res DOI: 10.1016/j.virusres.2010.01.002 sha: doc_id: 279849 cord_uid: zzkliu76 file: cache/cord-281061-uoszpnst.json key: cord-281061-uoszpnst authors: Watanabe, Yohei; Ito, Tetsuo; Ibrahim, Madiha S.; Arai, Yasuha; Hotta, Kozue; Phuong, Hoang Vu Mai; Hang, Nguyen Le Khanh; Mai, Le Quynh; Soda, Kosuke; Yamaoka, Masaoki; Poetranto, Emmanuel Djoko; Wulandari, Laksmi; Hiramatsu, Hiroaki; Daidoji, Tomo; Kubota-Koketsu, Ritsuko; Sriwilaijaroen, Nongluk; Nakaya, Takaaki; Okuno, Yoshinobu; Takahashi, Tadanobu; Suzuki, Takashi; Ito, Toshihiro; Hotta, Hak; Yamashiro, Tetsu; Hayashi, Tsukasa; Morita, Kouichi; Ikuta, Kazuyoshi; Suzuki, Yasuo title: A novel immunochromatographic system for easy-to-use detection of group 1 avian influenza viruses with acquired human-type receptor binding specificity date: 2015-03-15 journal: Biosens Bioelectron DOI: 10.1016/j.bios.2014.10.036 sha: doc_id: 281061 cord_uid: uoszpnst file: cache/cord-280878-1kt51viz.json key: cord-280878-1kt51viz authors: To, Janet; Surya, Wahyu; Torres, Jaume title: Targeting the Channel Activity of Viroporins date: 2016-01-07 journal: Adv Protein Chem Struct Biol DOI: 10.1016/bs.apcsb.2015.12.003 sha: doc_id: 280878 cord_uid: 1kt51viz file: cache/cord-281593-bq12grqo.json key: cord-281593-bq12grqo authors: Liu, Zheng; Liu, Shuyu; Cui, Jinming; Tan, Yurong; He, Jian; Zhang, Jingqiang title: Transmission Electron Microscopy Studies of Cellular Responses to Entry of Virions: One Kind of Natural Nanobiomaterial date: 2012-04-11 journal: Int J Cell Biol DOI: 10.1155/2012/596589 sha: doc_id: 281593 cord_uid: bq12grqo file: cache/cord-281158-vjh9z7l4.json key: cord-281158-vjh9z7l4 authors: Storch, Gregory A title: Respiratory Viruses in Babies: Important Insights From Down Under date: 2018-02-01 journal: J Infect Dis DOI: 10.1093/infdis/jix600 sha: doc_id: 281158 cord_uid: vjh9z7l4 file: cache/cord-280781-u3wd27rn.json key: cord-280781-u3wd27rn authors: Stohlman, S. A.; Weiner, Leslie P. title: Stability of neurotropic mouse hepatitis virus (JHM strain) during chronic infection of neuroblastoma cells date: 1978 journal: Arch Virol DOI: 10.1007/bf01315637 sha: doc_id: 280781 cord_uid: u3wd27rn file: cache/cord-282344-o1rkx2z4.json key: cord-282344-o1rkx2z4 authors: Kim, Seung Won; Ramakrishnan, M. A.; Raynor, Peter C.; Goyal, Sagar M. title: Effects of humidity and other factors on the generation and sampling of a coronavirus aerosol date: 2007-07-25 journal: Aerobiologia (Bologna) DOI: 10.1007/s10453-007-9068-9 sha: doc_id: 282344 cord_uid: o1rkx2z4 file: cache/cord-283405-aozxvxxs.json key: cord-283405-aozxvxxs authors: Vermillion, Meghan S.; Klein, Sabra L. title: Pregnancy and infection: using disease pathogenesis to inform vaccine strategy date: 2018-02-01 journal: NPJ Vaccines DOI: 10.1038/s41541-017-0042-4 sha: doc_id: 283405 cord_uid: aozxvxxs file: cache/cord-283641-2u16otbf.json key: cord-283641-2u16otbf authors: Vainionpää, R.; Waris, M.; Leinikki, P. title: Diagnostic Techniques: Serological and Molecular Approaches date: 2015-03-06 journal: Reference Module in Biomedical Sciences DOI: 10.1016/b978-0-12-801238-3.02558-7 sha: doc_id: 283641 cord_uid: 2u16otbf file: cache/cord-279418-3r1ijafm.json key: cord-279418-3r1ijafm authors: Nevers, Quentin; Albertini, Aurélie A.; Lagaudrière-Gesbert, Cécile; Gaudin, Yves title: Negri bodies and other virus membrane-less replication compartments() date: 2020-08-21 journal: Biochim Biophys Acta Mol Cell Res DOI: 10.1016/j.bbamcr.2020.118831 sha: doc_id: 279418 cord_uid: 3r1ijafm file: cache/cord-281429-6lv3di4x.json key: cord-281429-6lv3di4x authors: García-Nicolás, Obdulio; Braun, Roman O.; Milona, Panagiota; Lewandowska, Marta; Dijkman, Ronald; Alves, Marco P.; Summerfield, Artur title: Targeting of the Nasal Mucosa by Japanese Encephalitis Virus for Non-Vector-Borne Transmission date: 2018-11-27 journal: J Virol DOI: 10.1128/jvi.01091-18 sha: doc_id: 281429 cord_uid: 6lv3di4x file: cache/cord-284523-lknyehsa.json key: cord-284523-lknyehsa authors: da Mata, Élida Cleyse Gomes; Mourão, Caroline Barbosa Farias; Rangel, Marisa; Schwartz, Elisabeth Ferroni title: Antiviral activity of animal venom peptides and related compounds date: 2017-01-06 journal: J Venom Anim Toxins Incl Trop Dis DOI: 10.1186/s40409-016-0089-0 sha: doc_id: 284523 cord_uid: lknyehsa file: cache/cord-282204-j1slaefb.json key: cord-282204-j1slaefb authors: Silva, José V.J.; Ludwig-Begall, Louisa F.; Oliveira-Filho, Edmilson F. de; Oliveira, Renato A.S.; Durães-Carvalho, Ricardo; Lopes, Thaísa R.R.; Silva, Daisy E.A.; Gil, Laura H.V.G. title: A scoping review of Chikungunya virus infection: epidemiology, clinical characteristics, viral co-circulation complications, and control date: 2018-12-31 journal: Acta Tropica DOI: 10.1016/j.actatropica.2018.09.003 sha: doc_id: 282204 cord_uid: j1slaefb file: cache/cord-281844-c0uhcatg.json key: cord-281844-c0uhcatg authors: Costa, Lusmaia D.C.; Costa, Paulo Sucasas; Camargos, Paulo A.M. title: Exacerbation of asthma and airway infection: is the virus the villain? date: 2014-12-31 journal: Jornal de Pediatria DOI: 10.1016/j.jped.2014.07.001 sha: doc_id: 281844 cord_uid: c0uhcatg file: cache/cord-284880-xsh3wkqy.json key: cord-284880-xsh3wkqy authors: Bandaly, Victor; Joubert, Aurélie; Le Cann, Pierre; Andres, Yves title: The Fate of Mengovirus on Fiberglass Filter of Air Handling Units date: 2017-06-28 journal: Food Environ Virol DOI: 10.1007/s12560-017-9310-8 sha: doc_id: 284880 cord_uid: xsh3wkqy file: cache/cord-282343-cko4curf.json key: cord-282343-cko4curf authors: Cheng, Han; Koning, Katie; O’Hearn, Aileen; Wang, Minxiu; Rumschlag-Booms, Emily; Varhegyi, Elizabeth; Rong, Lijun title: A parallel genome-wide RNAi screening strategy to identify host proteins important for entry of Marburg virus and H5N1 influenza virus date: 2015-11-24 journal: Virol J DOI: 10.1186/s12985-015-0420-3 sha: doc_id: 282343 cord_uid: cko4curf file: cache/cord-281281-knelqmzx.json key: cord-281281-knelqmzx authors: Villas-Boas, Gustavo R.; Rescia, Vanessa C.; Paes, Marina M.; Lavorato, Stefânia N.; de Magalhães-Filho, Manoel F.; Cunha, Mila S.; Simões, Rafael da C.; de Lacerda, Roseli B.; de Freitas-Júnior, Renilson S.; Ramos, Bruno H. da S.; Mapeli, Ana M.; Henriques, Matheus da S. T.; de Freitas, William R.; Lopes, Luiz A. F.; Oliveira, Luiz G. R.; da Silva, Jonatas G.; Silva-Filho, Saulo E.; da Silveira, Ana P. S.; Leão, Katyuscya V.; Matos, Maria M. de S.; Fernandes, Jamille S.; Cuman, Roberto K. N.; Silva-Comar, Francielli M. de S.; Comar, Jurandir F.; Brasileiro, Luana do A.; dos Santos, Jussileide N.; Oesterreich, Silvia A. title: The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents date: 2020-09-07 journal: Molecules DOI: 10.3390/molecules25184086 sha: doc_id: 281281 cord_uid: knelqmzx file: cache/cord-285462-9i61rsei.json key: cord-285462-9i61rsei authors: Almomani, Hesham; Al-Qur'an, Wael title: L'ampleur de la réaction des gens aux rumeurs et aux fausses nouvelles à la lumière de la crise du virus Corona date: 2020-06-25 journal: Ann Med Psychol (Paris) DOI: 10.1016/j.amp.2020.06.011 sha: doc_id: 285462 cord_uid: 9i61rsei file: cache/cord-285148-bch7814v.json key: cord-285148-bch7814v authors: Singanayagam, Aran; Joshi, Priya V; Mallia, Patrick; Johnston, Sebastian L title: Viruses exacerbating chronic pulmonary disease: the role of immune modulation date: 2012-03-15 journal: BMC Med DOI: 10.1186/1741-7015-10-27 sha: doc_id: 285148 cord_uid: bch7814v file: cache/cord-283880-lrrkuist.json key: cord-283880-lrrkuist authors: Kumar, Arvind; Murthy, Satyapramod; Kapoor, Amit title: Evolution of selective-sequencing approaches for virus discovery and virome analysis date: 2017-07-15 journal: Virus Research DOI: 10.1016/j.virusres.2017.06.005 sha: doc_id: 283880 cord_uid: lrrkuist file: cache/cord-285367-jxlt0gby.json key: cord-285367-jxlt0gby authors: Johnson, Richard T.; Power, Christopher title: Emerging Issues in Neurovirology: New Viruses, Diagnostic Tools, and Therapeutics date: 2008-08-31 journal: Neurologic Clinics DOI: 10.1016/j.ncl.2008.04.003 sha: doc_id: 285367 cord_uid: jxlt0gby file: cache/cord-284941-wfn0pnev.json key: cord-284941-wfn0pnev authors: Samal, S.K. title: Paramyxoviruses of Animals date: 2008-07-30 journal: Encyclopedia of Virology DOI: 10.1016/b978-012374410-4.00460-x sha: doc_id: 284941 cord_uid: wfn0pnev file: cache/cord-285856-0sw3wt1i.json key: cord-285856-0sw3wt1i authors: Naesens, Lieve; Vanderlinden, Evelien; Rőth, Erzsébet; Jekő, József; Andrei, Graciela; Snoeck, Robert; Pannecouque, Christophe; Illyés, Eszter; Batta, Gyula; Herczegh, Pál; Sztaricskai, Ferenc title: Anti-influenza virus activity and structure–activity relationship of aglycoristocetin derivatives with cyclobutenedione carrying hydrophobic chains date: 2009-02-05 journal: Antiviral Res DOI: 10.1016/j.antiviral.2009.01.003 sha: doc_id: 285856 cord_uid: 0sw3wt1i file: cache/cord-284266-tbndldhr.json key: cord-284266-tbndldhr authors: Schippa, Serena; Frassanito, Antonella; Marazzato, Massimiliano; Nenna, Raffaella; Petrarca, Laura; Neroni, Bruna; Bonfiglio, Giulia; Guerrieri, Francesca; Frasca, Federica; Oliveto, Giuseppe; Pierangeli, Alessandra; Midulla, Fabio title: Nasal Microbiota in RSV Bronchiolitis date: 2020-05-13 journal: Microorganisms DOI: 10.3390/microorganisms8050731 sha: doc_id: 284266 cord_uid: tbndldhr file: cache/cord-290034-4b0mshqa.json key: cord-290034-4b0mshqa authors: Le, Yen H.; Nguyen, Khanh C.; Coleman, Kristen K.; Nguyen, Tham T.; Than, Son T.; Phan, Hai H.; Nguyen, Manh D.; Ngu, Nghia D.; Phan, Dan T.; Hoang, Phuong V. M.; Trieu, Long P.; Bailey, Emily S.; Warkentien, Tyler E.; Gray, Gregory C. title: Virus detections among patients with severe acute respiratory illness, Northern Vietnam date: 2020-05-12 journal: PLoS One DOI: 10.1371/journal.pone.0233117 sha: doc_id: 290034 cord_uid: 4b0mshqa file: cache/cord-285330-td4vr0zv.json key: cord-285330-td4vr0zv authors: Mohammadi, Ali; Asasi, Keramat; Boroomand, Zahra; Namazi, Fatemeh; Hosseinian, Seyedeh Alemeh title: Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus date: 2015-11-12 journal: VirusDisease DOI: 10.1007/s13337-015-0286-4 sha: doc_id: 285330 cord_uid: td4vr0zv file: cache/cord-282742-eyukbot7.json key: cord-282742-eyukbot7 authors: Diosa-Toro, Mayra; Urcuqui-Inchima, Silvio; Smit, Jolanda M. title: Arthropod-Borne Flaviviruses and RNA Interference: Seeking New Approaches for Antiviral Therapy date: 2013-02-20 journal: Adv Virus Res DOI: 10.1016/b978-0-12-408116-1.00004-5 sha: doc_id: 282742 cord_uid: eyukbot7 file: cache/cord-286137-4cbh3u3z.json key: cord-286137-4cbh3u3z authors: Honce, Rebekah; Schultz-Cherry, Stacey title: They are what you eat: Shaping of viral populations through nutrition and consequences for virulence date: 2020-08-13 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1008711 sha: doc_id: 286137 cord_uid: 4cbh3u3z file: cache/cord-284372-v95fzp8n.json key: cord-284372-v95fzp8n authors: Coyle, Peter V; Ong, Grace M; O'Neill, Hugh J; McCaughey, Conall; De Ornellas, Dennis; Mitchell, Frederick; Mitchell, Suzanne J; Feeney, Susan A; Wyatt, Dorothy E; Forde, Marian; Stockton, Joanne 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 journal: BMC Microbiol DOI: 10.1186/1471-2180-4-41 sha: doc_id: 284372 cord_uid: v95fzp8n file: cache/cord-286708-igu984oc.json key: cord-286708-igu984oc authors: Chua, Kaw Bing; Voon, Kenny; Crameri, Gary; Tan, Hui Siu; Rosli, Juliana; McEachern, Jennifer A.; Suluraju, Sivagami; Yu, Meng; Wang, Lin-Fa title: Identification and Characterization of a New Orthoreovirus from Patients with Acute Respiratory Infections date: 2008-11-25 journal: PLoS One DOI: 10.1371/journal.pone.0003803 sha: doc_id: 286708 cord_uid: igu984oc file: cache/cord-283756-ycjzitlk.json key: cord-283756-ycjzitlk authors: Simons, Robin R. L.; Gale, Paul; Horigan, Verity; Snary, Emma L.; Breed, Andrew C. title: Potential for Introduction of Bat-Borne Zoonotic Viruses into the EU: A Review date: 2014-05-16 journal: Viruses DOI: 10.3390/v6052084 sha: doc_id: 283756 cord_uid: ycjzitlk file: cache/cord-286219-qcx5ehnh.json key: cord-286219-qcx5ehnh authors: Calistri, Arianna; Munegato, Denis; Carli, Ilaria; Parolin, Cristina; Palù, Giorgio title: The Ubiquitin-Conjugating System: Multiple Roles in Viral Replication and Infection date: 2014-05-06 journal: Cells DOI: 10.3390/cells3020386 sha: doc_id: 286219 cord_uid: qcx5ehnh file: cache/cord-283964-k3hy2ewx.json key: cord-283964-k3hy2ewx authors: Chan, Jasper Fuk-Woo; To, Kelvin Kai-Wang; Chen, Honglin; Yuen, Kwok-Yung title: Cross-species transmission and emergence of novel viruses from birds date: 2015-01-31 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2015.01.006 sha: doc_id: 283964 cord_uid: k3hy2ewx file: cache/cord-288703-wdh1jiry.json key: cord-288703-wdh1jiry authors: Ishtiaq, Farah title: A Call to Introduce Structured Zika Surveillance in India date: 2017-11-15 journal: Trends Parasitol DOI: 10.1016/j.pt.2017.10.008 sha: doc_id: 288703 cord_uid: wdh1jiry file: cache/cord-285935-5rsk6g7l.json key: cord-285935-5rsk6g7l authors: Kinast, Volker; Burkard, Thomas L; Todt, Daniel; Steinmann, Eike title: Hepatitis E Virus Drug Development date: 2019-05-28 journal: Viruses DOI: 10.3390/v11060485 sha: doc_id: 285935 cord_uid: 5rsk6g7l file: cache/cord-286298-pn9nwl64.json key: cord-286298-pn9nwl64 authors: Helmy, Yosra A.; Fawzy, Mohamed; Elaswad, Ahmed; Sobieh, Ahmed; Kenney, Scott P.; Shehata, Awad A. title: The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control date: 2020-04-24 journal: J Clin Med DOI: 10.3390/jcm9041225 sha: doc_id: 286298 cord_uid: pn9nwl64 file: cache/cord-284156-btb4oodz.json key: cord-284156-btb4oodz authors: Liu, Yiliu; Olagnier, David; Lin, Rongtuan title: Host and Viral Modulation of RIG-I-Mediated Antiviral Immunity date: 2017-01-03 journal: Front Immunol DOI: 10.3389/fimmu.2016.00662 sha: doc_id: 284156 cord_uid: btb4oodz file: cache/cord-287286-4l963z2q.json key: cord-287286-4l963z2q authors: Green, Victoria A.; Munshi, Saif U.; Marakalala, Mohlopheni J.; Mourão, Marina M. title: Molecular mechanisms of viral infection and propagation: An overview of the second Advanced Summer School in Africa date: 2010-07-28 journal: IUBMB Life DOI: 10.1002/iub.364 sha: doc_id: 287286 cord_uid: 4l963z2q file: cache/cord-288111-0ufc54kw.json key: cord-288111-0ufc54kw authors: ter MEULEN, VOLKER title: Autoimmune Reactions Against Myelin Basic Protein Induced by Corona and Measles Viruses date: 2006-12-17 journal: Ann N Y Acad Sci DOI: 10.1111/j.1749-6632.1988.tb27062.x sha: doc_id: 288111 cord_uid: 0ufc54kw file: cache/cord-288348-b10e023s.json key: cord-288348-b10e023s authors: Estes, Mary Kolb; Graham, David Yates title: Epidemic viral gastroenteritis date: 1979-06-30 journal: The American Journal of Medicine DOI: 10.1016/0002-9343(79)90457-1 sha: doc_id: 288348 cord_uid: b10e023s file: cache/cord-284479-75zgljet.json key: cord-284479-75zgljet authors: García-Serradilla, Moisés; Risco, Cristina; Pacheco, Beatriz title: Drug repurposing for new, efficient, broad spectrum antivirals date: 2019-04-15 journal: Virus Res DOI: 10.1016/j.virusres.2019.02.011 sha: doc_id: 284479 cord_uid: 75zgljet file: cache/cord-286719-1xjmlwqr.json key: cord-286719-1xjmlwqr authors: Draz, Mohamed Shehata; Shafiee, Hadi title: Applications of gold nanoparticles in virus detection date: 2018-02-15 journal: Theranostics DOI: 10.7150/thno.23856 sha: doc_id: 286719 cord_uid: 1xjmlwqr file: cache/cord-287348-00yaxpkp.json key: cord-287348-00yaxpkp authors: Martinez, Maria Jose Abad; Olmo, Luis Miguel Bedoya Del; Benito, Paulina Bermejo title: Antiviral Activities of Polysaccharides from Natural Sources date: 2005-12-31 journal: Studies in Natural Products Chemistry DOI: 10.1016/s1572-5995(05)80038-9 sha: doc_id: 287348 cord_uid: 00yaxpkp file: cache/cord-287711-gw8mgg4m.json key: cord-287711-gw8mgg4m authors: Junter, Guy-Alain; Lebrun, Laurent title: Cellulose-based virus-retentive filters: a review date: 2017-06-01 journal: Rev Environ Sci Biotechnol DOI: 10.1007/s11157-017-9434-1 sha: doc_id: 287711 cord_uid: gw8mgg4m file: cache/cord-287337-2ljbsia2.json key: cord-287337-2ljbsia2 authors: Ludwig, Christine; Wagner, Ralf title: Virus-like particles—universal molecular toolboxes date: 2008-01-04 journal: Curr Opin Biotechnol DOI: 10.1016/j.copbio.2007.10.013 sha: doc_id: 287337 cord_uid: 2ljbsia2 file: cache/cord-288372-48wao8a0.json key: cord-288372-48wao8a0 authors: Dia, Ndongo; Richard, Vincent; Kiori, Davy; Cisse, El Hadj Abdoul Khadir; Sarr, Fatoumata Diène; Faye, Abdourahmane; Goudiaby, Déborah G; Diop, Ousmane M; Niang, Mbayame N title: Respiratory viruses associated with patients older than 50 years presenting with ILI in Senegal, 2009 to 2011 date: 2014-04-08 journal: BMC Infect Dis DOI: 10.1186/1471-2334-14-189 sha: doc_id: 288372 cord_uid: 48wao8a0 file: cache/cord-287554-2lqy2ix9.json key: cord-287554-2lqy2ix9 authors: Amarelle, Luciano; Lecuona, Emilia; Sznajder, Jacob I. title: Tratamiento antigripal: fármacos actualmente utilizados y nuevos agentes en desarrollo date: 2017-01-31 journal: Archivos de Bronconeumología DOI: 10.1016/j.arbres.2016.07.004 sha: doc_id: 287554 cord_uid: 2lqy2ix9 file: cache/cord-288231-vg8bwed9.json key: cord-288231-vg8bwed9 authors: Haagmans, Bart L.; Andeweg, Arno C.; Osterhaus, Albert D. M. E. title: The Application of Genomics to Emerging Zoonotic Viral Diseases date: 2009-10-26 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1000557 sha: doc_id: 288231 cord_uid: vg8bwed9 file: cache/cord-288238-36hiiw91.json key: cord-288238-36hiiw91 authors: Keshavarz, Mohsen; Solaymani-Mohammadi, Farid; Namdari, Haideh; Arjeini, Yaser; Mousavi, Mohammad Javad; Rezaei, Farhad title: Metabolic host response and therapeutic approaches to influenza infection date: 2020-03-05 journal: Cell Mol Biol Lett DOI: 10.1186/s11658-020-00211-2 sha: doc_id: 288238 cord_uid: 36hiiw91 file: cache/cord-286559-y8z0pwgn.json key: cord-286559-y8z0pwgn authors: Ding, Nai-Zheng; Xu, Dong-Shuai; Sun, Yuan-Yuan; He, Hong-Bin; He, Cheng-Qiang title: A permanent host shift of rabies virus from Chiroptera to Carnivora associated with recombination date: 2017-03-21 journal: Sci Rep DOI: 10.1038/s41598-017-00395-2 sha: doc_id: 286559 cord_uid: y8z0pwgn file: cache/cord-287151-4hlvrfeh.json key: cord-287151-4hlvrfeh authors: Steinmann, J title: Surrogate viruses for testing virucidal efficacy of chemical disinfectants date: 2004-04-30 journal: Journal of Hospital Infection DOI: 10.1016/j.jhin.2003.12.030 sha: doc_id: 287151 cord_uid: 4hlvrfeh file: cache/cord-287466-ag5y781z.json key: cord-287466-ag5y781z authors: Cowley, J.A. title: Nidoviruses of Fish and Crustaceans date: 2016-09-09 journal: Aquaculture Virology DOI: 10.1016/b978-0-12-801573-5.00032-2 sha: doc_id: 287466 cord_uid: ag5y781z file: cache/cord-285547-7m3dh8hu.json key: cord-285547-7m3dh8hu authors: Nomura, Naoki; Sakoda, Yoshihiro; Endo, Mayumi; Yoshida, Hiromi; Yamamoto, Naoki; Okamatsu, Masatoshi; Sakurai, Kenji; Hoang, Nam Van; Nguyen, Long Van; Chu, Huy Duc; Tien, Tien Ngoc; Kida, Hiroshi title: Characterization of avian influenza viruses isolated from domestic ducks in Vietnam in 2009 and 2010 date: 2011-11-09 journal: Arch Virol DOI: 10.1007/s00705-011-1152-3 sha: doc_id: 285547 cord_uid: 7m3dh8hu file: cache/cord-288879-rj03dsib.json key: cord-288879-rj03dsib authors: Schein, Catherine H. title: Polyglutamine Repeats in Viruses date: 2018-09-04 journal: Mol Neurobiol DOI: 10.1007/s12035-018-1269-4 sha: doc_id: 288879 cord_uid: rj03dsib file: cache/cord-286741-h3oix9zc.json key: cord-286741-h3oix9zc authors: Park, Mee Sook; Kim, Jin Il; Bae, Joon-Yong; Park, Man-Seong title: Animal models for the risk assessment of viral pandemic potential date: 2020-04-22 journal: Lab Anim Res DOI: 10.1186/s42826-020-00040-6 sha: doc_id: 286741 cord_uid: h3oix9zc file: cache/cord-287770-oxfnt2n4.json key: cord-287770-oxfnt2n4 authors: Caricati, C. P.; Oliveira‐Nascimento, L.; Yoshida, J. T.; Stephano, M. A.; Caricati, A. T. P.; Raw, I. title: Safety of snake antivenom immunoglobulins: Efficacy of viral inactivation in a complete downstream process date: 2013-06-27 journal: Biotechnol Prog DOI: 10.1002/btpr.1758 sha: doc_id: 287770 cord_uid: oxfnt2n4 file: cache/cord-287851-9p0dr7rl.json key: cord-287851-9p0dr7rl authors: Fedson, David S title: Confronting an influenza pandemic with inexpensive generic agents: can it be done? date: 2008-09-30 journal: The Lancet Infectious Diseases DOI: 10.1016/s1473-3099(08)70070-7 sha: doc_id: 287851 cord_uid: 9p0dr7rl file: cache/cord-288945-c9ow1q5c.json key: cord-288945-c9ow1q5c authors: Spengler, Ulrich title: Liver Disease Associated with Non-Hepatitis Viruses date: 2019-11-01 journal: Encyclopedia of Gastroenterology DOI: 10.1016/b978-0-12-801238-3.65782-3 sha: doc_id: 288945 cord_uid: c9ow1q5c file: cache/cord-288930-h13cxuh3.json key: cord-288930-h13cxuh3 authors: Lim, Faye J; Wake, Zoe V; Levy, Avram; Tempone, Simone; Moore, Hannah C; Richmond, Peter C; de Klerk, Nicholas; Conway, Nicholas T; Keil, Anthony D; Effler, Paul V; Smith, David W; Blyth, Christopher C title: Viral Etiology and the Impact of Codetection in Young Children Presenting With Influenza-Like Illness date: 2016-07-20 journal: J Pediatric Infect Dis Soc DOI: 10.1093/jpids/piw042 sha: doc_id: 288930 cord_uid: h13cxuh3 file: cache/cord-289360-h6wvx7gw.json key: cord-289360-h6wvx7gw authors: Imperiale, Michael J.; Casadevall, Arturo title: The Importance of Virology at a Time of Great Need and Great Jeopardy date: 2015-03-10 journal: mBio DOI: 10.1128/mbio.00236-15 sha: doc_id: 289360 cord_uid: h6wvx7gw file: cache/cord-288734-xinkqs6u.json key: cord-288734-xinkqs6u authors: Muñoz-Fontela, César; McElroy, Anita K. title: Ebola Virus Disease in Humans: Pathophysiology and Immunity date: 2017-03-30 journal: Marburg- and Ebolaviruses DOI: 10.1007/82_2017_11 sha: doc_id: 288734 cord_uid: xinkqs6u file: cache/cord-289593-81vu2kbu.json key: cord-289593-81vu2kbu authors: de Blic, J.; Brouard, J.; Vabret, A.; Deschildre, A. title: Interactions micro-organismes et voies aériennes distales : spécificités pédiatriques date: 2017-03-03 journal: Rev Mal Respir DOI: 10.1016/j.rmr.2016.02.012 sha: doc_id: 289593 cord_uid: 81vu2kbu file: cache/cord-289406-54vyzxjf.json key: cord-289406-54vyzxjf authors: Edwards, Suzanne; Small, J. David; Geratz, Joachim Dieter; Alexander, Lorraine K.; Baric, Ralph S. title: An Experimental Model for Myocarditis and Congestive Heart Failure after Rabbit Coronavirus Infection date: 1992-01-17 journal: J Infect Dis DOI: 10.1093/infdis/165.1.134 sha: doc_id: 289406 cord_uid: 54vyzxjf file: cache/cord-290481-i2ppvsh5.json key: cord-290481-i2ppvsh5 authors: Dolja, Valerian V.; Kreuze, Jan F.; Valkonen, Jari P.T. title: Comparative and functional genomics of closteroviruses date: 2006-03-09 journal: Virus Res DOI: 10.1016/j.virusres.2006.02.002 sha: doc_id: 290481 cord_uid: i2ppvsh5 file: cache/cord-290385-0smnl70i.json key: cord-290385-0smnl70i authors: Chan, Jasper F.W.; Choi, Garnet K.Y.; Yip, Cyril C.Y.; Cheng, Vincent C.C.; Yuen, Kwok-Yung title: Zika fever and congenital Zika syndrome: An unexpected emerging arboviral disease date: 2016-03-03 journal: J Infect DOI: 10.1016/j.jinf.2016.02.011 sha: doc_id: 290385 cord_uid: 0smnl70i file: cache/cord-290231-4m9lj0uq.json key: cord-290231-4m9lj0uq authors: Guirakhoo, Farshad; Bolin, Richard A.; Roehrig, John T. title: The Murray Valley encephalitis virus prM protein confers acid resistance to virus particles and alters the expression of epitopes within the R2 domain of E glycoprotein date: 1992-12-31 journal: Virology DOI: 10.1016/0042-6822(92)90267-s sha: doc_id: 290231 cord_uid: 4m9lj0uq file: cache/cord-290556-x7t7zqjd.json key: cord-290556-x7t7zqjd authors: Middleton, Peter J title: Viruses that multiply in the gut and cause endemic and epidemic gastroenteritis date: 1996-08-31 journal: Clinical and Diagnostic Virology DOI: 10.1016/0928-0197(96)00231-0 sha: doc_id: 290556 cord_uid: x7t7zqjd file: cache/cord-290133-4ou7ubb4.json key: cord-290133-4ou7ubb4 authors: Weiss, Martin M.; Weiss, Peter D.; Mathisen, Glenn; Guze, Phyllis; Henderson, Donald A.; Inglesby, Thomas V.; O'Toole, Tara title: Rethinking Smallpox date: 2004-12-01 journal: Clin Infect Dis DOI: 10.1086/425745 sha: doc_id: 290133 cord_uid: 4ou7ubb4 file: cache/cord-289093-si8btsab.json key: cord-289093-si8btsab authors: Beard, Philippa M.; Griffiths, Samantha J.; Gonzalez, Orland; Haga, Ismar R.; Pechenick Jowers, Tali; Reynolds, Danielle K.; Wildenhain, Jan; Tekotte, Hille; Auer, Manfred; Tyers, Mike; Ghazal, Peter; Zimmer, Ralf; Haas, Jürgen title: A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference date: 2014-06-05 journal: PLoS One DOI: 10.1371/journal.pone.0098431 sha: doc_id: 289093 cord_uid: si8btsab file: cache/cord-290352-0pc5eji4.json key: cord-290352-0pc5eji4 authors: de Jong, Menno D.; Hien, Tran Tinh title: Avian influenza A (H5N1) date: 2005-10-06 journal: J Clin Virol DOI: 10.1016/j.jcv.2005.09.002 sha: doc_id: 290352 cord_uid: 0pc5eji4 file: cache/cord-291294-w5ecsht4.json key: cord-291294-w5ecsht4 authors: Foulongne, V.; Segondy, M. title: Le bocavirus humain (HBoV) date: 2008-03-17 journal: Pathol Biol (Paris) DOI: 10.1016/j.patbio.2008.01.001 sha: doc_id: 291294 cord_uid: w5ecsht4 file: cache/cord-290282-oxyzndsj.json key: cord-290282-oxyzndsj authors: Ortego, Javier; Sola, Isabel; Almazán, Fernando; Ceriani, Juan E; Riquelme, Cristina; Balasch, Monica; Plana, Juan; Enjuanes, Luis title: Transmissible gastroenteritis coronavirus gene 7 is not essential but influences in vivo virus replication and virulence date: 2003-03-30 journal: Virology DOI: 10.1016/s0042-6822(02)00096-x sha: doc_id: 290282 cord_uid: oxyzndsj file: cache/cord-289017-vwye3pk9.json key: cord-289017-vwye3pk9 authors: Comach, Guillermo; Teneza-Mora, Nimfa; Kochel, Tadeusz J.; Espino, Carlos; Sierra, Gloria; Camacho, Daria E.; Laguna-Torres, V. Alberto; Garcia, Josefina; Chauca, Gloria; Gamero, Maria E.; Sovero, Merly; Bordones, Slave; Villalobos, Iris; Melchor, Angel; Halsey, Eric S. title: Sentinel Surveillance of Influenza-Like Illness in Two Hospitals in Maracay, Venezuela: 2006–2010 date: 2012-09-11 journal: PLoS One DOI: 10.1371/journal.pone.0044511 sha: doc_id: 289017 cord_uid: vwye3pk9 file: cache/cord-290432-4dli5emd.json key: cord-290432-4dli5emd authors: O’Grady, Kerry-Ann F.; Hall, Kerry K.; Sloots, Theo P.; Anderson, Jennie; Chang, Anne B. title: Upper airway viruses and bacteria in urban Aboriginal and Torres Strait Islander children in Brisbane, Australia: a cross-sectional study date: 2017-04-04 journal: BMC Infect Dis DOI: 10.1186/s12879-017-2349-1 sha: doc_id: 290432 cord_uid: 4dli5emd file: cache/cord-291707-dzmvjh7j.json key: cord-291707-dzmvjh7j authors: Tupper, G. T.; Evermann, J. F.; Russell, R. G.; Thouless, M. E. title: Antigenic and biological diversity of feline coronaviruses: feline infectious peritonitis and feline enteritis virus date: 1987 journal: Arch Virol DOI: 10.1007/bf01310988 sha: doc_id: 291707 cord_uid: dzmvjh7j file: cache/cord-290149-eed4v2jl.json key: cord-290149-eed4v2jl authors: ODEND'HAL, STEWART title: Porcine Hemagglutinating Encephalomyelitis Virus date: 2012-12-02 journal: The Geographical Distribution of Animal Viral Diseases DOI: 10.1016/b978-0-12-524180-9.50087-x sha: doc_id: 290149 cord_uid: eed4v2jl file: cache/cord-290509-56pfww0l.json key: cord-290509-56pfww0l authors: Fleet, Graham H; Heiskanen, Paul; Reid, Iona; Buckle, Ken A title: Foodborne viral illness - status in Australia date: 2000-07-25 journal: Int J Food Microbiol DOI: 10.1016/s0168-1605(00)00249-x sha: doc_id: 290509 cord_uid: 56pfww0l file: cache/cord-290851-1e5e033r.json key: cord-290851-1e5e033r authors: Gerlier, Denis title: Emerging zoonotic viruses: new lessons on receptor and entry mechanisms date: 2011-06-12 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2011.05.014 sha: doc_id: 290851 cord_uid: 1e5e033r file: cache/cord-290855-6umgvt28.json key: cord-290855-6umgvt28 authors: Ma, Li; Yao, Lei title: Antiviral Effects of Plant-Derived Essential Oils and Their Components: An Updated Review date: 2020-06-05 journal: Molecules DOI: 10.3390/molecules25112627 sha: doc_id: 290855 cord_uid: 6umgvt28 file: cache/cord-290539-8ak2tths.json key: cord-290539-8ak2tths authors: Cagno, Valeria; Tintori, Cristina; Civra, Andrea; Cavalli, Roberta; Tiberi, Marika; Botta, Lorenzo; Brai, Annalaura; Poli, Giulio; Tapparel, Caroline; Lembo, David; Botta, Maurizio title: Novel broad spectrum virucidal molecules against enveloped viruses date: 2018-12-07 journal: PLoS One DOI: 10.1371/journal.pone.0208333 sha: doc_id: 290539 cord_uid: 8ak2tths file: cache/cord-291816-d4j8samu.json key: cord-291816-d4j8samu authors: Diniz Beduschi Travassos Alves, Christian; da Fontoura Budaszewski, Renata; Cibulski, Samuel Paulo; Nunes Weber, Matheus; Quoos Mayer, Fabiana; Viezzer Bianchi, Matheus; Zafalon-Silva, Bruna; Konradt, Guilherme; Slaviero, Mônica; Sonne, Luciana; Driemeier, David; Meller Alievi, Marcelo; Wageck Canal, Cláudio title: Mamastrovirus 5 detected in a crab-eating fox (Cerdocyon thous): Expanding wildlife host range of astroviruses date: 2018-08-15 journal: Comp Immunol Microbiol Infect Dis DOI: 10.1016/j.cimid.2018.08.002 sha: doc_id: 291816 cord_uid: d4j8samu file: cache/cord-291860-dw1sfzqx.json key: cord-291860-dw1sfzqx authors: van Boheemen, Sander; van Rijn, Anneloes L.; Pappas, Nikos; Carbo, Ellen C.; Vorderman, Ruben H.P.; Sidorov, Igor; van `t Hof, Peter J.; Mei, Hailiang; Claas, Eric C.J.; Kroes, Aloys C.M.; de Vries, Jutte J.C. title: Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients date: 2019-12-16 journal: J Mol Diagn DOI: 10.1016/j.jmoldx.2019.10.007 sha: doc_id: 291860 cord_uid: dw1sfzqx file: cache/cord-290540-r0d6oaez.json key: cord-290540-r0d6oaez authors: Rottier, Peter J.M. title: The molecular dynamics of feline coronaviruses date: 1999-09-01 journal: Vet Microbiol DOI: 10.1016/s0378-1135(99)00099-1 sha: doc_id: 290540 cord_uid: r0d6oaez file: cache/cord-290617-45be6gxe.json key: cord-290617-45be6gxe authors: Poulain, Florian; Lejeune, Noémie; Willemart, Kévin; Gillet, Nicolas A. title: Footprint of the host restriction factors APOBEC3 on the genome of human viruses date: 2020-08-14 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1008718 sha: doc_id: 290617 cord_uid: 45be6gxe file: cache/cord-290548-0wezrr1b.json key: cord-290548-0wezrr1b authors: Watanabe, Tokiko; Kawaoka, Yoshihiro title: Villains or heroes? The raison d'être of viruses date: 2020-02-19 journal: Clin Transl Immunology DOI: 10.1002/cti2.1114 sha: doc_id: 290548 cord_uid: 0wezrr1b file: cache/cord-291534-c6cjxq07.json key: cord-291534-c6cjxq07 authors: Gwyer Findlay, Emily; Currie, Silke M.; Davidson, Donald J. title: Cationic Host Defence Peptides: Potential as Antiviral Therapeutics date: 2013-05-07 journal: BioDrugs DOI: 10.1007/s40259-013-0039-0 sha: doc_id: 291534 cord_uid: c6cjxq07 file: cache/cord-291561-sxvgue36.json key: cord-291561-sxvgue36 authors: Haixu, Liang; Haibin, Wang; Lili, Ren title: Detection of 20 respiratory viruses and bacteria by influenza-like illness surveillance in Beijing, China, 2016–2018 date: 2019-11-25 journal: J Infect DOI: 10.1016/j.jinf.2019.11.014 sha: doc_id: 291561 cord_uid: sxvgue36 file: cache/cord-291156-zxg3dsm3.json key: cord-291156-zxg3dsm3 authors: Bernasconi, Anna; Canakoglu, Arif; Pinoli, Pietro; Ceri, Stefano title: Empowering Virus Sequences Research through Conceptual Modeling date: 2020-05-01 journal: bioRxiv DOI: 10.1101/2020.04.29.067637 sha: doc_id: 291156 cord_uid: zxg3dsm3 file: cache/cord-290993-bsnja161.json key: cord-290993-bsnja161 authors: McAuliffe, Josephine; Vogel, Leatrice; Roberts, Anjeanette; Fahle, Gary; Fischer, Steven; Shieh, Wun-Ju; Butler, Emily; Zaki, Sherif; St. Claire, Marisa; Murphy, Brian; Subbarao, Kanta title: Replication of SARS coronavirus administered into the respiratory tract of African Green, rhesus and cynomolgus monkeys date: 2004-12-05 journal: Virology DOI: 10.1016/j.virol.2004.09.030 sha: doc_id: 290993 cord_uid: bsnja161 file: cache/cord-292075-t9z7zqz4.json key: cord-292075-t9z7zqz4 authors: Gessain, Antoine title: Mécanismes d’émergence virale et transmission interespèces : l’exemple des rétrovirus Foamy simiens chezl’Homme en Afrique Centrale date: 2013-12-31 journal: Bulletin de l'Académie Nationale de Médecine DOI: 10.1016/s0001-4079(19)31387-1 sha: doc_id: 292075 cord_uid: t9z7zqz4 file: cache/cord-293375-qcy56ui7.json key: cord-293375-qcy56ui7 authors: Strauss, Ellen G.; De Groot, Raoul J.; Levinson, Randy; Strauss, James H. title: Identification of the active site residues in the nsP2 proteinase of sindbis virus date: 1992-12-31 journal: Virology DOI: 10.1016/0042-6822(92)90268-t sha: doc_id: 293375 cord_uid: qcy56ui7 file: cache/cord-293472-d3iwlpsr.json key: cord-293472-d3iwlpsr authors: Afilalo, Marc; Stern, Errol; Oughton, Matthew title: Evaluation and Management of Seasonal Influenza in the Emergency Department date: 2012-04-06 journal: Emerg Med Clin North Am DOI: 10.1016/j.emc.2011.10.011 sha: doc_id: 293472 cord_uid: d3iwlpsr file: cache/cord-292643-n6xp5mlz.json key: cord-292643-n6xp5mlz authors: Hall, Richard J.; Wang, Jing; Todd, Angela K.; Bissielo, Ange B.; Yen, Seiha; Strydom, Hugo; Moore, Nicole E.; Ren, Xiaoyun; Huang, Q. Sue; Carter, Philip E.; Peacey, Matthew title: Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery date: 2013-09-13 journal: J Virol Methods DOI: 10.1016/j.jviromet.2013.08.035 sha: doc_id: 292643 cord_uid: n6xp5mlz file: cache/cord-292830-gcfx1095.json key: cord-292830-gcfx1095 authors: Ianevski, Aleksandr; Zusinaite, Eva; Kuivanen, Suvi; Strand, Mårten; Lysvand, Hilde; Teppor, Mona; Kakkola, Laura; Paavilainen, Henrik; Laajala, Mira; Kallio-Kokko, Hannimari; Valkonen, Miia; Kantele, Anu; Telling, Kaidi; Lutsar, Irja; Letjuka, Pille; Metelitsa, Natalja; Oksenych, Valentyn; Bjørås, Magnar; Nordbø, Svein Arne; Dumpis, Uga; Vitkauskiene, Astra; Öhrmalm, Christina; Bondeson, Kåre; Bergqvist, Anders; Aittokallio, Tero; Cox, Rebecca J.; Evander, Magnus; Hukkanen, Veijo; Marjomaki, Varpu; Julkunen, Ilkka; Vapalahti, Olli; Tenson, Tanel; Merits, Andres; Kainov, Denis title: Novel activities of safe-in-human broad-spectrum antiviral agents date: 2018-04-23 journal: Antiviral Res DOI: 10.1016/j.antiviral.2018.04.016 sha: doc_id: 292830 cord_uid: gcfx1095 file: cache/cord-293975-np9xdag5.json key: cord-293975-np9xdag5 authors: Barnett, E. M.; Cassell, M. D.; Perlman, S. title: Two neurotropic viruses, herpes simplex virus type 1 and mouse hepatitis virus, spread along different neural pathways from the main olfactory bulb date: 1993-12-31 journal: Neuroscience DOI: 10.1016/0306-4522(93)90045-h sha: doc_id: 293975 cord_uid: np9xdag5 file: cache/cord-291113-iizj932l.json key: cord-291113-iizj932l authors: Cumbo, Enzo; Gallina, Giuseppe; Messina, Pietro; Scardina, Giuseppe Alessandro title: Alternative Methods of Sterilization in Dental Practices Against COVID-19 date: 2020-08-08 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17165736 sha: doc_id: 291113 cord_uid: iizj932l file: cache/cord-292286-ygomb3oi.json key: cord-292286-ygomb3oi authors: Zakaryan, Hovakim; Arabyan, Erik; Oo, Adrian; Zandi, Keivan title: Flavonoids: promising natural compounds against viral infections date: 2017-05-25 journal: Arch Virol DOI: 10.1007/s00705-017-3417-y sha: doc_id: 292286 cord_uid: ygomb3oi file: cache/cord-292353-z86rjwle.json key: cord-292353-z86rjwle authors: Hussein, Islam T.M.; Haseeb, Abdul; Haque, Absarul; Mir, Mohammad A. title: Recent Advances in Hantavirus Molecular Biology and Disease date: 2011-04-01 journal: Adv Appl Microbiol DOI: 10.1016/b978-0-12-387022-3.00006-9 sha: doc_id: 292353 cord_uid: z86rjwle file: cache/cord-291946-kq0rsuxj.json key: cord-291946-kq0rsuxj authors: Etienne, Lucie; Emerman, Michael title: The Mongoose, the Pheasant, the Pox, and the Retrovirus date: 2013-08-27 journal: PLoS Biol DOI: 10.1371/journal.pbio.1001641 sha: doc_id: 291946 cord_uid: kq0rsuxj file: cache/cord-291063-de7v4e5s.json key: cord-291063-de7v4e5s authors: Moens, Ugo title: Silencing Viral MicroRNA as a Novel Antiviral Therapy? date: 2009-05-28 journal: J Biomed Biotechnol DOI: 10.1155/2009/419539 sha: doc_id: 291063 cord_uid: de7v4e5s file: cache/cord-294568-12eyo13f.json key: cord-294568-12eyo13f authors: Fernandes-Matano, Larissa; Monroy-Muñoz, Irma Eloísa; Angeles-Martínez, Javier; Sarquiz-Martinez, Brenda; Palomec-Nava, Iliana Donají; Pardavé-Alejandre, Hector Daniel; Santos Coy-Arechavaleta, Andrea; Santacruz-Tinoco, Clara Esperanza; González-Ibarra, Joaquín; González-Bonilla, Cesar Raúl; Muñoz-Medina, José Esteban title: Prevalence of non-influenza respiratory viruses in acute respiratory infection cases in Mexico date: 2017-05-03 journal: PLoS One DOI: 10.1371/journal.pone.0176298 sha: doc_id: 294568 cord_uid: 12eyo13f file: cache/cord-297339-et2305rz.json key: cord-297339-et2305rz authors: Lauber, Chris; Gorbalenya, Alexander E. title: Genetics-Based Classification of Filoviruses Calls for Expanded Sampling of Genomic Sequences date: 2012-08-31 journal: Viruses DOI: 10.3390/v4091425 sha: doc_id: 297339 cord_uid: et2305rz file: cache/cord-292416-3hhi4wps.json key: cord-292416-3hhi4wps authors: Sarid, Ronit title: Investigating an Emerging Virus During a Sudden Pandemic Outbreak date: 2020-07-31 journal: Rambam Maimonides Med J DOI: 10.5041/rmmj.10414 sha: doc_id: 292416 cord_uid: 3hhi4wps file: cache/cord-292657-gq3965se.json key: cord-292657-gq3965se authors: Das, Piyanki; Choudhuri, Tathagata title: Decoding the global outbreak of COVID-19: the nature is behind the scene date: 2020-06-22 journal: Virusdisease DOI: 10.1007/s13337-020-00605-y sha: doc_id: 292657 cord_uid: gq3965se file: cache/cord-293540-45awgabp.json key: cord-293540-45awgabp authors: Drancourt, Michel; Gaydos, Charlotte A; Summersgill, James T; Raoult, Didier title: Point-of-care testing for community-acquired pneumonia date: 2013-07-23 journal: Lancet Infect Dis DOI: 10.1016/s1473-3099(13)70165-8 sha: doc_id: 293540 cord_uid: 45awgabp file: cache/cord-295189-bz3gi15h.json key: cord-295189-bz3gi15h authors: Jennings, Lance C.; Priest, Patricia C.; Psutka, Rebecca A.; Duncan, Alasdair R.; Anderson, Trevor; Mahagamasekera, Patalee; Strathdee, Andrew; Baker, Michael G. title: Respiratory viruses in airline travellers with influenza symptoms: Results of an airport screening study date: 2015-03-14 journal: J Clin Virol DOI: 10.1016/j.jcv.2015.03.011 sha: doc_id: 295189 cord_uid: bz3gi15h file: cache/cord-295640-mhfu0e9r.json key: cord-295640-mhfu0e9r authors: Wang, Wenling; Huang, Baoying; Wang, Xiuping; Tan, Wenjie; Ruan, Li title: Improving Cross-Protection against Influenza Virus Using Recombinant Vaccinia Vaccine Expressing NP and M2 Ectodomain Tandem Repeats date: 2019-06-25 journal: Virol Sin DOI: 10.1007/s12250-019-00138-9 sha: doc_id: 295640 cord_uid: mhfu0e9r file: cache/cord-295792-hajvtzj9.json key: cord-295792-hajvtzj9 authors: Álvez, Fernando title: SARS-CoV2 coronavirus: So far polite with children. Debatable immunological and non-immunological evidence date: 2020-07-03 journal: Allergol Immunopathol (Madr) DOI: 10.1016/j.aller.2020.05.003 sha: doc_id: 295792 cord_uid: hajvtzj9 file: cache/cord-294323-mryiqmsw.json key: cord-294323-mryiqmsw authors: Kumar, Binod; Asha, Kumari; Khanna, Madhu; Ronsard, Larance; Meseko, Clement Adebajo; Sanicas, Melvin title: The emerging influenza virus threat: status and new prospects for its therapy and control date: 2018-01-10 journal: Arch Virol DOI: 10.1007/s00705-018-3708-y sha: doc_id: 294323 cord_uid: mryiqmsw file: cache/cord-294544-iutcduix.json key: cord-294544-iutcduix authors: Kesson, Alison M. title: Respiratory virus infections date: 2007-09-06 journal: Paediatr Respir Rev DOI: 10.1016/j.prrv.2007.07.003 sha: doc_id: 294544 cord_uid: iutcduix file: cache/cord-292828-29jbf9ik.json key: cord-292828-29jbf9ik authors: Alsaleh, Asma N; Whiley, David M; Bialasiewicz, Seweryn; Lambert, Stephen B; Ware, Robert S; Nissen, Michael D; Sloots, Theo P; Grimwood, Keith 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 journal: BMC Infect Dis DOI: 10.1186/1471-2334-14-15 sha: doc_id: 292828 cord_uid: 29jbf9ik file: cache/cord-293097-poh1y6o7.json key: cord-293097-poh1y6o7 authors: V, Antony Aroul Raj; R, Velraj; Haghighat, Fariborz title: The contribution of dry indoor built environment on the spread of Coronavirus: Data from various Indian states date: 2020-07-02 journal: Sustain Cities Soc DOI: 10.1016/j.scs.2020.102371 sha: doc_id: 293097 cord_uid: poh1y6o7 file: cache/cord-294478-3ickafd3.json key: cord-294478-3ickafd3 authors: Kapil, Sanjay; Yeary, Teresa; Johnson, Bill title: Diagnostic Investigation of Emerging Viruses of Companion Animals date: 2008-05-22 journal: Vet Clin North Am Small Anim Pract DOI: 10.1016/j.cvsm.2008.02.009 sha: doc_id: 294478 cord_uid: 3ickafd3 file: cache/cord-292575-vsswxwdi.json key: cord-292575-vsswxwdi authors: Hammou, Rahma Ait; Benhassou, Mustapha; Bessi, Hlima; Ennaji, Moulay Mustapha title: Chapter 7 Scientific Advances in the Diagnosis of Emerging and Reemerging Viral Human Pathogens date: 2020-12-31 journal: Emerging and Reemerging Viral Pathogens DOI: 10.1016/b978-0-12-814966-9.00007-x sha: doc_id: 292575 cord_uid: vsswxwdi file: cache/cord-293387-0m1ngob3.json key: cord-293387-0m1ngob3 authors: Wood, A.; Payne, D. title: The action of three antiseptics/disinfectants against enveloped and non-enveloped viruses date: 1998-04-30 journal: Journal of Hospital Infection DOI: 10.1016/s0195-6701(98)90077-9 sha: doc_id: 293387 cord_uid: 0m1ngob3 file: cache/cord-293421-0ksn0fc7.json key: cord-293421-0ksn0fc7 authors: Rodriguez, J. M. title: Detection of animal pathogens by using the polymerasechain reaction (PCR) date: 1997-05-31 journal: The Veterinary Journal DOI: 10.1016/s1090-0233(97)80063-9 sha: doc_id: 293421 cord_uid: 0ksn0fc7 file: cache/cord-294312-ju6vuywm.json key: cord-294312-ju6vuywm authors: Rohde, Rodney E. title: Common Myths and Legends of Rabies date: 2019-04-19 journal: Rabies DOI: 10.1016/b978-0-323-63979-8.00005-2 sha: doc_id: 294312 cord_uid: ju6vuywm file: cache/cord-296935-y77c4ro4.json key: cord-296935-y77c4ro4 authors: Couch, Robert B.; Atmar, Robert L.; Franco, Luis M.; Quarles, John M.; Niño, Diane; Wells, Janet M.; Arden, Nancy; Cheung, Sheree; Belmont, John W. title: Prior Infections With Seasonal Influenza A/H1N1 Virus Reduced the Illness Severity and Epidemic Intensity of Pandemic H1N1 Influenza in Healthy Adults date: 2011-11-10 journal: Clinical Infectious Diseases DOI: 10.1093/cid/cir809 sha: doc_id: 296935 cord_uid: y77c4ro4 file: cache/cord-294812-nnlzwaf1.json key: cord-294812-nnlzwaf1 authors: Desforges, Marc; Le Coupanec, Alain; Brison, Élodie; Meessen-Pinard, Mathieu; Talbot, Pierre J. title: Neuroinvasive and Neurotropic Human Respiratory Coronaviruses: Potential Neurovirulent Agents in Humans date: 2014-03-12 journal: Infectious Diseases and Nanomedicine I DOI: 10.1007/978-81-322-1777-0_6 sha: doc_id: 294812 cord_uid: nnlzwaf1 file: cache/cord-294842-aesiff1f.json key: cord-294842-aesiff1f authors: Romero-Brey, Inés; Bartenschlager, Ralf title: Membranous Replication Factories Induced by Plus-Strand RNA Viruses date: 2014-07-22 journal: Viruses DOI: 10.3390/v6072826 sha: doc_id: 294842 cord_uid: aesiff1f file: cache/cord-294125-v2dr4hm0.json key: cord-294125-v2dr4hm0 authors: Albert, Manuel; Bécares, Martina; Falqui, Michela; Fernández-Lozano, Carlos; Guerra, Susana title: ISG15, a Small Molecule with Huge Implications: Regulation of Mitochondrial Homeostasis date: 2018-11-13 journal: Viruses DOI: 10.3390/v10110629 sha: doc_id: 294125 cord_uid: v2dr4hm0 file: cache/cord-295041-5vpawtef.json key: cord-295041-5vpawtef authors: Jakhmola, Shweta; Indari, Omkar; Chatterjee, Sayantani; Jha, Hem Chandra title: SARS-CoV-2, an Underestimated Pathogen of the Nervous System date: 2020-09-28 journal: SN Compr Clin Med DOI: 10.1007/s42399-020-00522-7 sha: doc_id: 295041 cord_uid: 5vpawtef file: cache/cord-297203-f3f31h4r.json key: cord-297203-f3f31h4r authors: Afrough, B.; Dowall, S.; Hewson, R. title: Emerging viruses and current strategies for vaccine intervention date: 2019-04-16 journal: Clin Exp Immunol DOI: 10.1111/cei.13295 sha: doc_id: 297203 cord_uid: f3f31h4r file: cache/cord-293732-rxd1lyi7.json key: cord-293732-rxd1lyi7 authors: Manoj, M.G.; Satheesh Kumar, M.K.; Valsaraj, K.T.; Sivan, C.; Vijayan, Soumya K. title: Potential link between compromised air quality and transmission of the novel corona virus (SARS-CoV-2) in affected areas date: 2020-08-01 journal: Environ Res DOI: 10.1016/j.envres.2020.110001 sha: doc_id: 293732 cord_uid: rxd1lyi7 file: cache/cord-294585-dl5v9p50.json key: cord-294585-dl5v9p50 authors: Klein, H. G.; Bryant, B. J. title: Pathogen‐reduction methods: advantages and limits date: 2009-02-13 journal: ISBT Sci Ser DOI: 10.1111/j.1751-2824.2009.01224.x sha: doc_id: 294585 cord_uid: dl5v9p50 file: cache/cord-295191-xu26mvc3.json key: cord-295191-xu26mvc3 authors: Avirutnan, Panisadee; Mehlhop, Erin; Diamond, Michael S. title: Complement and its role in protection and pathogenesis of flavivirus infections date: 2008-12-30 journal: Vaccine DOI: 10.1016/j.vaccine.2008.11.061 sha: doc_id: 295191 cord_uid: xu26mvc3 file: cache/cord-295531-zojb3cew.json key: cord-295531-zojb3cew authors: Huggett, Kathryn D.; Knoop, Floyd C. title: Influenza A date: 2008-01-10 journal: xPharm: The Comprehensive Pharmacology Reference DOI: 10.1016/b978-008055232-3.60922-5 sha: doc_id: 295531 cord_uid: zojb3cew file: cache/cord-298032-3zlu8g8y.json key: cord-298032-3zlu8g8y authors: Nan, Yuchen; Zhang, Yan-Jin title: Antisense Phosphorodiamidate Morpholino Oligomers as Novel Antiviral Compounds date: 2018-04-20 journal: Front Microbiol DOI: 10.3389/fmicb.2018.00750 sha: doc_id: 298032 cord_uid: 3zlu8g8y file: cache/cord-296309-i1mpov7k.json key: cord-296309-i1mpov7k authors: Houldcroft, Charlotte J.; Beale, Mathew A.; Breuer, Judith title: Clinical and biological insights from viral genome sequencing date: 2017-01-16 journal: Nat Rev Microbiol DOI: 10.1038/nrmicro.2016.182 sha: doc_id: 296309 cord_uid: i1mpov7k file: cache/cord-296819-gztmidn2.json key: cord-296819-gztmidn2 authors: Sambri, Vittorio; Capobianchi, Maria R.; Cavrini, Francesca; Charrel, Rémi; Donoso-Mantke, Olivier; Escadafal, Camille; Franco, Leticia; Gaibani, Paolo; Gould, Ernest A.; Niedrig, Matthias; Papa, Anna; Pierro, Anna; Rossini, Giada; Sanchini, Andrea; Tenorio, Antonio; Varani, Stefania; Vázquez, Ana; Vocale, Caterina; Zeller, Herve title: Diagnosis of West Nile Virus Human Infections: Overview and Proposal of Diagnostic Protocols Considering the Results of External Quality Assessment Studies date: 2013-09-25 journal: Viruses DOI: 10.3390/v5102329 sha: doc_id: 296819 cord_uid: gztmidn2 file: cache/cord-297494-6yxmaihl.json key: cord-297494-6yxmaihl authors: Katsurada, Naoko; Suzuki, Motoi; Aoshima, Masahiro; Yaegashi, Makito; Ishifuji, Tomoko; Asoh, Norichika; Hamashige, Naohisa; Abe, Masahiko; Ariyoshi, Koya; Morimoto, Konosuke title: The impact of virus infections on pneumonia mortality is complex in adults: a prospective multicentre observational study date: 2017-12-06 journal: BMC Infect Dis DOI: 10.1186/s12879-017-2858-y sha: doc_id: 297494 cord_uid: 6yxmaihl file: cache/cord-297834-me1ajoyb.json key: cord-297834-me1ajoyb authors: Schountz, Tony; Prescott, Joseph title: Hantavirus Immunology of Rodent Reservoirs: Current Status and Future Directions date: 2014-03-14 journal: Viruses DOI: 10.3390/v6031317 sha: doc_id: 297834 cord_uid: me1ajoyb file: cache/cord-294108-uvnh0s9r.json key: cord-294108-uvnh0s9r authors: Dube, Taru; Ghosh, Amrito; Mishra, Jibanananda; Kompella, Uday B.; Panda, Jiban Jyoti title: Repurposed Drugs, Molecular Vaccines, Immune‐Modulators, and Nanotherapeutics to Treat and Prevent COVID‐19 Associated with SARS‐CoV‐2, a Deadly Nanovector date: 2020-10-25 journal: Adv Ther (Weinh) DOI: 10.1002/adtp.202000172 sha: doc_id: 294108 cord_uid: uvnh0s9r file: cache/cord-297131-3a9vjpvn.json key: cord-297131-3a9vjpvn authors: Charlton Hume, Hayley K.; Vidigal, João; Carrondo, Manuel J. T.; Middelberg, Anton P. J.; Roldão, António; Lua, Linda H. L. title: Synthetic biology for bioengineering virus‐like particle vaccines date: 2018-12-31 journal: Biotechnol Bioeng DOI: 10.1002/bit.26890 sha: doc_id: 297131 cord_uid: 3a9vjpvn file: cache/cord-295062-8rl4kswe.json key: cord-295062-8rl4kswe authors: Marsh, Mark; Helenius, Ari title: Virus Entry: Open Sesame date: 2006-02-24 journal: Cell DOI: 10.1016/j.cell.2006.02.007 sha: doc_id: 295062 cord_uid: 8rl4kswe file: cache/cord-295873-kykyubdq.json key: cord-295873-kykyubdq authors: Morikawa, Saeko; Kohdera, Urara; Hosaka, Taisuke; Ishii, Kousuke; Akagawa, Shohei; Hiroi, Satoshi; Kase, Tetsuo title: Seasonal variations of respiratory viruses and etiology of human rhinovirus infection in children date: 2015-10-22 journal: J Clin Virol DOI: 10.1016/j.jcv.2015.10.001 sha: doc_id: 295873 cord_uid: kykyubdq file: cache/cord-298905-c2uuvfm5.json key: cord-298905-c2uuvfm5 authors: Horzinek, M. C. title: Molecular pathogenesis of virus infections date: 1987 journal: Experientia DOI: 10.1007/bf01945522 sha: doc_id: 298905 cord_uid: c2uuvfm5 file: cache/cord-295445-f4p00yaw.json key: cord-295445-f4p00yaw authors: Wang, Hao; Sikora, Per; Rutgersson, Carolin; Lindh, Magnus; Brodin, Tomas; Björlenius, Berndt; Larsson, D.G. Joakim; Norder, Heléne title: Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments date: 2018-02-01 journal: Int J Hyg Environ Health DOI: 10.1016/j.ijheh.2018.01.012 sha: doc_id: 295445 cord_uid: f4p00yaw file: cache/cord-298036-2zurc60t.json key: cord-298036-2zurc60t authors: Imre, Gergely title: Cell death signalling in virus infection date: 2020-09-12 journal: Cell Signal DOI: 10.1016/j.cellsig.2020.109772 sha: doc_id: 298036 cord_uid: 2zurc60t file: cache/cord-300020-edolh7ww.json key: cord-300020-edolh7ww authors: Nielsen, Anne Ahlmann; Skovgård, Henrik; Stockmarr, Anders; Handberg, Kurt Jensen; Jørgensen, Poul H. title: Persistence of Low-Pathogenic Avian Influenza H5N7 and H7N1 Subtypes in House Flies (Diptera: Muscidae) date: 2011-05-01 journal: J Med Entomol DOI: 10.1603/me11017 sha: doc_id: 300020 cord_uid: edolh7ww file: cache/cord-297960-4x1j0iqg.json key: cord-297960-4x1j0iqg authors: Bösl, Korbinian; Ianevski, Aleksandr; Than, Thoa T.; Andersen, Petter I.; Kuivanen, Suvi; Teppor, Mona; Zusinaite, Eva; Dumpis, Uga; Vitkauskiene, Astra; Cox, Rebecca J.; Kallio-Kokko, Hannimari; Bergqvist, Anders; Tenson, Tanel; Merits, Andres; Oksenych, Valentyn; Bjørås, Magnar; Anthonsen, Marit W.; Shum, David; Kaarbø, Mari; Vapalahti, Olli; Windisch, Marc P.; Superti-Furga, Giulio; Snijder, Berend; Kainov, Denis; Kandasamy, Richard K. title: Common Nodes of Virus–Host Interaction Revealed Through an Integrated Network Analysis date: 2019-10-04 journal: Front Immunol DOI: 10.3389/fimmu.2019.02186 sha: doc_id: 297960 cord_uid: 4x1j0iqg file: cache/cord-296635-8r3tm966.json key: cord-296635-8r3tm966 authors: Breed, Andrew C.; Breed, Martin F.; Meers, Joanne; Field, Hume E. title: Evidence of Endemic Hendra Virus Infection in Flying-Foxes (Pteropus conspicillatus)—Implications for Disease Risk Management date: 2011-12-14 journal: PLoS One DOI: 10.1371/journal.pone.0028816 sha: doc_id: 296635 cord_uid: 8r3tm966 file: cache/cord-295433-olmein3q.json key: cord-295433-olmein3q authors: Banerjee, Arinjay; Kulcsar, Kirsten; Misra, Vikram; Frieman, Matthew; Mossman, Karen title: Bats and Coronaviruses date: 2019-01-09 journal: Viruses DOI: 10.3390/v11010041 sha: doc_id: 295433 cord_uid: olmein3q file: cache/cord-298214-ivu4erpq.json key: cord-298214-ivu4erpq authors: Castrignano, Silvana Beres; Nagasse-Sugahara, Teresa Keico title: The metagenomic approach and causality in virology date: 2015-04-01 journal: Rev Saude Publica DOI: 10.1590/s0034-8910.2015049005475 sha: doc_id: 298214 cord_uid: ivu4erpq file: cache/cord-297662-slmlhqnb.json key: cord-297662-slmlhqnb authors: Yap, Sally S. L.; Nguyen-Khuong, Terry; Rudd, Pauline M.; Alonso, Sylvie title: Dengue Virus Glycosylation: What Do We Know? date: 2017-07-25 journal: Front Microbiol DOI: 10.3389/fmicb.2017.01415 sha: doc_id: 297662 cord_uid: slmlhqnb file: cache/cord-300189-gsp1dozg.json key: cord-300189-gsp1dozg authors: Franci, Gianluigi; Falanga, Annarita; Zannella, Carla; Folliero, Veronica; Martora, Francesca; Galdiero, Marilena; Galdiero, Stefania; Morelli, Giancarlo; Galdiero, Massimiliano title: Infectivity inhibition by overlapping synthetic peptides derived from the gH/gL heterodimer of herpes simplex virus type 1 date: 2017-02-14 journal: J Pept Sci DOI: 10.1002/psc.2979 sha: doc_id: 300189 cord_uid: gsp1dozg file: cache/cord-298051-ej8qxkce.json key: cord-298051-ej8qxkce authors: Louten, Jennifer title: Detection and Diagnosis of Viral Infections date: 2016-05-06 journal: Essential Human Virology DOI: 10.1016/b978-0-12-800947-5.00007-7 sha: doc_id: 298051 cord_uid: ej8qxkce file: cache/cord-298862-8bijio30.json key: cord-298862-8bijio30 authors: Eltom, Kamal H.; Samy, Abdallah M.; Abd El Wahed, Ahmed; Czerny, Claus-Peter title: Buffalopox Virus: An Emerging Virus in Livestock and Humans date: 2020-08-20 journal: Pathogens DOI: 10.3390/pathogens9090676 sha: doc_id: 298862 cord_uid: 8bijio30 file: cache/cord-298019-gf2asni1.json key: cord-298019-gf2asni1 authors: Galdiero, Stefania; Falanga, Annarita; Morelli, Giancarlo; Galdiero, Massimiliano title: gH625: A milestone in understanding the many roles of membranotropic peptides date: 2014-10-12 journal: Biochim Biophys Acta Biomembr DOI: 10.1016/j.bbamem.2014.10.006 sha: doc_id: 298019 cord_uid: gf2asni1 file: cache/cord-302277-c66xm2n4.json key: cord-302277-c66xm2n4 authors: Bakaletz, Lauren O. title: Developing animal models for polymicrobial diseases date: 2004 journal: Nat Rev Microbiol DOI: 10.1038/nrmicro928 sha: doc_id: 302277 cord_uid: c66xm2n4 file: cache/cord-302425-aaxvlktp.json key: cord-302425-aaxvlktp authors: Cortey, Martí; Díaz, Ivan; Vidal, Anna; Martín-Valls, Gerard; Franzo, Giovanni; Gómez de Nova, Pedro José; Darwich, Laila; Puente, Héctor; Carvajal, Ana; Martín, Marga; Mateu, Enric title: High levels of unreported intraspecific diversity among RNA viruses in faeces of neonatal piglets with diarrhoea date: 2019-12-05 journal: BMC Vet Res DOI: 10.1186/s12917-019-2204-2 sha: doc_id: 302425 cord_uid: aaxvlktp file: cache/cord-302111-kg0dmgq0.json key: cord-302111-kg0dmgq0 authors: Darden, Dijoia B.; Hawkins, Russell B.; Larson, Shawn D.; Iovine, Nicole M.; Prough, Donald S.; Efron, Philip A. title: The Clinical Presentation and Immunology of Viral Pneumonia and Implications for Management of Coronavirus Disease 2019 date: 2020-04-29 journal: Crit Care Explor DOI: 10.1097/cce.0000000000000109 sha: doc_id: 302111 cord_uid: kg0dmgq0 file: cache/cord-298033-kzdp9edn.json key: cord-298033-kzdp9edn authors: Domingo, Esteban title: Quasispecies dynamics in disease prevention and control date: 2019-11-08 journal: Virus as Populations DOI: 10.1016/b978-0-12-816331-3.00008-8 sha: doc_id: 298033 cord_uid: kzdp9edn file: cache/cord-300837-d0a8y5qh.json key: cord-300837-d0a8y5qh authors: Khetawat, Dimple; Broder, Christopher C title: A Functional Henipavirus Envelope Glycoprotein Pseudotyped Lentivirus Assay System date: 2010-11-12 journal: Virol J DOI: 10.1186/1743-422x-7-312 sha: doc_id: 300837 cord_uid: d0a8y5qh file: cache/cord-301064-ex6qb6zj.json key: cord-301064-ex6qb6zj authors: Elena, Santiago F.; Pybus, Oliver G. title: Editorial: A home for virology, ecology, epidemiology, and evolutionary biology date: 2015-03-26 journal: Virus Evol DOI: 10.1093/ve/vev001 sha: doc_id: 301064 cord_uid: ex6qb6zj file: cache/cord-298489-uqrzzh0e.json key: cord-298489-uqrzzh0e authors: Bale, James F. title: Emerging Viral Infections date: 2012-08-11 journal: Semin Pediatr Neurol DOI: 10.1016/j.spen.2012.02.001 sha: doc_id: 298489 cord_uid: uqrzzh0e file: cache/cord-298733-jole21wq.json key: cord-298733-jole21wq authors: Tyrrell, D.A.J. title: A view from the common cold unit date: 1992-06-30 journal: Antiviral Research DOI: 10.1016/0166-3542(92)90032-z sha: doc_id: 298733 cord_uid: jole21wq file: cache/cord-300133-yc2wxgid.json key: cord-300133-yc2wxgid authors: Martínez, Miguel J.; Salim, Abdulbaset M.; Hurtado, Juan C.; Kilgore, Paul E. title: Ebola Virus Infection: Overview and Update on Prevention and Treatment date: 2015-09-12 journal: Infect Dis Ther DOI: 10.1007/s40121-015-0079-5 sha: doc_id: 300133 cord_uid: yc2wxgid file: cache/cord-297790-tpjxt0w5.json key: cord-297790-tpjxt0w5 authors: Mandl, Judith N.; Schneider, Caitlin; Schneider, David S.; Baker, Michelle L. title: Going to Bat(s) for Studies of Disease Tolerance date: 2018-09-20 journal: Front Immunol DOI: 10.3389/fimmu.2018.02112 sha: doc_id: 297790 cord_uid: tpjxt0w5 file: cache/cord-299207-lw0cv74b.json key: cord-299207-lw0cv74b authors: Upadhyay, Ranjit Kumar; Kumari, Nitu; Rao, V. Sree Hari title: Modeling the spread of bird flu and predicting outbreak diversity date: 2007-05-08 journal: Nonlinear Anal Real World Appl DOI: 10.1016/j.nonrwa.2007.04.009 sha: doc_id: 299207 cord_uid: lw0cv74b file: cache/cord-300810-a1skdp67.json key: cord-300810-a1skdp67 authors: Lafay, F.; Coulon, P.; Astic, L.; Saucier, D.; Riche, D.; Holley, A.; Flamand, A. title: Spread of the CVS strain of rabies virus and of the avirulent mutant AvO1 along the olfactory pathways of the mouse after intranasal inoculation date: 1991-07-31 journal: Virology DOI: 10.1016/0042-6822(91)90145-2 sha: doc_id: 300810 cord_uid: a1skdp67 file: cache/cord-299379-ch7a39d6.json key: cord-299379-ch7a39d6 authors: De Conto, Flora; Conversano, Francesca; Medici, Maria Cristina; Ferraglia, Francesca; Pinardi, Federica; Arcangeletti, Maria Cristina; Chezzi, Carlo; Calderaro, Adriana 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 journal: Diagn Microbiol Infect Dis DOI: 10.1016/j.diagmicrobio.2019.01.008 sha: doc_id: 299379 cord_uid: ch7a39d6 file: cache/cord-299786-wuve0tjz.json key: cord-299786-wuve0tjz authors: Anderson, Robert title: Manipulation of cell surface macromolecules by flaviviruses date: 2004-02-27 journal: Adv Virus Res DOI: 10.1016/s0065-3527(03)59007-8 sha: doc_id: 299786 cord_uid: wuve0tjz file: cache/cord-301285-p83ondy8.json key: cord-301285-p83ondy8 authors: Kautz, Tiffany F; Guerbois, Mathilde; Khanipov, Kamil; Patterson, Edward I; Langsjoen, Rose M; Yun, Ruimei; Warmbrod, Kelsey L; Fofanov, Yuriy; Weaver, Scott C; Forrester, Naomi L title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy date: 2018-03-06 journal: Virus Evol DOI: 10.1093/ve/vey004 sha: doc_id: 301285 cord_uid: p83ondy8 file: cache/cord-301592-n5ns3m34.json key: cord-301592-n5ns3m34 authors: Ivaska, Lauri; Niemelä, Jussi; Lempainen, Johanna; Österback, Riikka; Waris, Matti; Vuorinen, Tytti; Hytönen, Jukka; Rantakokko-Jalava, Kaisu; Peltola, Ville title: Aetiology of febrile pharyngitis in children: Potential of myxovirus resistance protein A (MxA) as a biomarker of viral infection date: 2017-01-07 journal: J Infect DOI: 10.1016/j.jinf.2017.01.002 sha: doc_id: 301592 cord_uid: n5ns3m34 file: cache/cord-303040-ha8gufh8.json key: cord-303040-ha8gufh8 authors: Park, Won-Ju; Yoo, Seok-Ju; Lee, Suk-Ho; Chung, Jae-Woo; Jang, Keun-Ho; Moon, Jai-Dong title: Respiratory Syncytial Virus Outbreak in the Basic Military Training Camp of the Republic of Korea Air Force date: 2015-01-14 journal: J Prev Med Public Health DOI: 10.3961/jpmph.14.037 sha: doc_id: 303040 cord_uid: ha8gufh8 file: cache/cord-298736-9bvyp21d.json key: cord-298736-9bvyp21d authors: Gerold, Gisa; Bruening, Janina; Pietschmann, Thomas title: Decoding protein networks during virus entry by quantitative proteomics date: 2016-06-15 journal: Virus Research DOI: 10.1016/j.virusres.2015.09.006 sha: doc_id: 298736 cord_uid: 9bvyp21d file: cache/cord-298678-hjxph9jm.json key: cord-298678-hjxph9jm authors: Petrović, T.; D'Agostino, M. title: Viral Contamination of Food date: 2016-02-05 journal: Antimicrobial Food Packaging DOI: 10.1016/b978-0-12-800723-5.00005-x sha: doc_id: 298678 cord_uid: hjxph9jm file: cache/cord-300711-yibdumij.json key: cord-300711-yibdumij authors: Shatizadeh, Somayeh; Yavarian, Jila; Rezaie, Farhad; Mahmoodi, Mahmood; Naseri, Maryam; Mokhtari Azad, Talat title: Epidemiological and clinical evaluation of children with respiratory virus infections date: 2014-09-22 journal: Med J Islam Repub Iran DOI: nan sha: doc_id: 300711 cord_uid: yibdumij file: cache/cord-302716-wfla3l20.json key: cord-302716-wfla3l20 authors: Popov, Vsevolod L.; Tesh, Robert B.; Weaver, Scott C.; Vasilakis, Nikos title: Electron Microscopy in Discovery of Novel and Emerging Viruses from the Collection of the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA) date: 2019-05-25 journal: Viruses DOI: 10.3390/v11050477 sha: doc_id: 302716 cord_uid: wfla3l20 file: cache/cord-302047-vv5gpldi.json key: cord-302047-vv5gpldi authors: Willemsen, Anouk; Zwart, Mark P title: On the stability of sequences inserted into viral genomes date: 2019-11-14 journal: Virus Evol DOI: 10.1093/ve/vez045 sha: doc_id: 302047 cord_uid: vv5gpldi file: cache/cord-298745-3rrlap70.json key: cord-298745-3rrlap70 authors: Field, H. E.; Mackenzie, John S.; Daszak, P. title: Henipaviruses: Emerging Paramyxoviruses Associated with Fruit Bats date: 2007 journal: Wildlife and Emerging Zoonotic Diseases: The Biology, Circumstances and Consequences of Cross-Species Transmission DOI: 10.1007/978-3-540-70962-6_7 sha: doc_id: 298745 cord_uid: 3rrlap70 file: cache/cord-302021-42vqmndl.json key: cord-302021-42vqmndl authors: Stanley, Mathew; Mayr, Juliane; Huber, Wolfgang; Vlasak, Reinhard; Streicher, Hansjörg title: Synthesis and inhibitory activity of sialic acid derivatives targeted at viral sialate-O-acetylesterases date: 2011-04-08 journal: Eur J Med Chem DOI: 10.1016/j.ejmech.2011.04.008 sha: doc_id: 302021 cord_uid: 42vqmndl file: cache/cord-302055-s155i4e9.json key: cord-302055-s155i4e9 authors: Mitchell, Edith P. title: Corona Virus: Global Pandemic Causing World-Wide Shutdown date: 2020-04-03 journal: J Natl Med Assoc DOI: 10.1016/j.jnma.2020.03.015 sha: doc_id: 302055 cord_uid: s155i4e9 file: cache/cord-302486-z36hcvrx.json key: cord-302486-z36hcvrx authors: Cobo, Fernando; Talavera, Paloma; Concha, Ángel title: Diagnostic approaches for viruses and prions in stem cell banks date: 2006-03-30 journal: Virology DOI: 10.1016/j.virol.2005.11.026 sha: doc_id: 302486 cord_uid: z36hcvrx file: cache/cord-299549-bjqwwzam.json key: cord-299549-bjqwwzam authors: Zhang, Lei; Wang, Hao; Zhang, Yi-qing title: Against Ebola: type I interferon guard risk and mesenchymal stromal cell combat sepsis date: 2015-01-01 journal: Journal of Zhejiang University-SCIENCE B DOI: 10.1631/jzus.b1400365 sha: doc_id: 299549 cord_uid: bjqwwzam file: cache/cord-302614-siyyve9e.json key: cord-302614-siyyve9e authors: Shigeta, Shiro; Mori, Shuichi; Yamase, Toshihiro; Yamamoto, Norio; Yamamoto, Naoki title: Anti-RNA virus activity of polyoxometalates date: 2006-05-24 journal: Biomed Pharmacother DOI: 10.1016/j.biopha.2006.03.009 sha: doc_id: 302614 cord_uid: siyyve9e file: cache/cord-303297-fiievwy7.json key: cord-303297-fiievwy7 authors: Oberemok, Volodymyr V.; Laikova, Kateryna V.; Yurchenko, Kseniya A.; Fomochkina, Irina I.; Kubyshkin, Anatolii V. title: SARS-CoV-2 will continue to circulate in the human population: an opinion from the point of view of the virus-host relationship date: 2020-04-30 journal: Inflamm Res DOI: 10.1007/s00011-020-01352-y sha: doc_id: 303297 cord_uid: fiievwy7 file: cache/cord-300522-okbupw61.json key: cord-300522-okbupw61 authors: Sansone, Clementina; Brunet, Christophe; Noonan, Douglas M.; Albini, Adriana title: Marine Algal Antioxidants as Potential Vectors for Controlling Viral Diseases date: 2020-05-07 journal: Antioxidants (Basel) DOI: 10.3390/antiox9050392 sha: doc_id: 300522 cord_uid: okbupw61 file: cache/cord-304481-yqc8r3ll.json key: cord-304481-yqc8r3ll authors: Luis, Angela D.; O'Shea, Thomas J.; Hayman, David T. S.; Wood, James L. N.; Cunningham, Andrew A.; Gilbert, Amy T.; Mills, James N.; Webb, Colleen T. title: Network analysis of host–virus communities in bats and rodents reveals determinants of cross‐species transmission date: 2015-08-24 journal: Ecol Lett DOI: 10.1111/ele.12491 sha: doc_id: 304481 cord_uid: yqc8r3ll file: cache/cord-303186-2hxlx1j2.json key: cord-303186-2hxlx1j2 authors: Won, Hokeun; Lee, Dong-Uk; Jang, Guehwan; Noh, Yun-Hee; Lee, Seung-Chul; Choi, Hwan-Won; Yoon, In-Joong; Yoo, Han Sang; Lee, Changhee title: Generation and protective efficacy of a cold-adapted attenuated genotype 2b porcine epidemic diarrhea virus date: 2019-07-09 journal: J Vet Sci DOI: 10.4142/jvs.2019.20.e32 sha: doc_id: 303186 cord_uid: 2hxlx1j2 file: cache/cord-304278-0qy1nngs.json key: cord-304278-0qy1nngs authors: Raj, G. Dhinakar; Jones, R. C. title: Infectious bronchitis virus: immunopathogenesis of infection in the chicken date: 2007-11-12 journal: Avian Pathol DOI: 10.1080/03079459708419246 sha: doc_id: 304278 cord_uid: 0qy1nngs file: cache/cord-304807-j2k1oel2.json key: cord-304807-j2k1oel2 authors: Herrera-Rodriguez, José; Signorazzi, Aurora; Holtrop, Marijke; de Vries-Idema, Jacqueline; Huckriede, Anke title: Inactivated or damaged? Comparing the effect of inactivation methods on influenza virions to optimize vaccine production date: 2019-03-14 journal: Vaccine DOI: 10.1016/j.vaccine.2019.01.086 sha: doc_id: 304807 cord_uid: j2k1oel2 file: cache/cord-300435-vs0ntcsb.json key: cord-300435-vs0ntcsb authors: Katz, Al; Peña, Stephanie; Alimova, Alexandra; Gottlieb, Paul; Xu, Min; Block, Karin A. title: Heteroaggregation of an enveloped bacteriophage with colloidal sediments and effect on virus viability date: 2018-10-01 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2018.04.425 sha: doc_id: 300435 cord_uid: vs0ntcsb file: cache/cord-304251-dohglrm1.json key: cord-304251-dohglrm1 authors: Scully, C; Samaranayake, LP title: Emerging and changing viral diseases in the new millennium date: 2015-08-06 journal: Oral Dis DOI: 10.1111/odi.12356 sha: doc_id: 304251 cord_uid: dohglrm1 file: cache/cord-301362-f3lp10lm.json key: cord-301362-f3lp10lm authors: Delgui, Laura R.; Colombo, María I. title: A Novel Mechanism Underlying the Innate Immune Response Induction upon Viral-Dependent Replication of Host Cell mRNA: A Mistake of +sRNA Viruses' Replicases date: 2017-01-20 journal: Front Cell Infect Microbiol DOI: 10.3389/fcimb.2017.00005 sha: doc_id: 301362 cord_uid: f3lp10lm file: cache/cord-303533-6s01qplg.json key: cord-303533-6s01qplg authors: Neuman, Benjamin W.; Angelini, Megan M.; Buchmeier, Michael J. title: Does form meet function in the coronavirus replicative organelle? date: 2014-07-15 journal: Trends Microbiol DOI: 10.1016/j.tim.2014.06.003 sha: doc_id: 303533 cord_uid: 6s01qplg file: cache/cord-304850-9xetsc2c.json key: cord-304850-9xetsc2c authors: Drosten, Christian title: Virus ecology: a gap between detection and prediction date: 2013-05-22 journal: Emerg Microbes Infect DOI: 10.1038/emi.2013.25 sha: doc_id: 304850 cord_uid: 9xetsc2c file: cache/cord-305336-wxiazglk.json key: cord-305336-wxiazglk authors: Li, Ji Lian; Cornman, R. Scott; Evans, Jay D.; Pettis, Jeffery S.; Zhao, Yan; Murphy, Charles; Peng, Wen Jun; Wu, Jie; Hamilton, Michele; Boncristiani, Humberto F.; Zhou, Liang; Hammond, John; Chen, Yan Ping title: Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera date: 2014-01-21 journal: mBio DOI: 10.1128/mbio.00898-13 sha: doc_id: 305336 cord_uid: wxiazglk file: cache/cord-304343-m7tbdfri.json key: cord-304343-m7tbdfri authors: Khandia, Rekha; Dadar, Maryam; Munjal, Ashok; Dhama, Kuldeep; Karthik, Kumaragurubaran; Tiwari, Ruchi; Yatoo, Mohd. Iqbal; Iqbal, Hafiz M.N.; Singh, Karam Pal; Joshi, Sunil K.; Chaicumpa, Wanpen title: A Comprehensive Review of Autophagy and Its Various Roles in Infectious, Non-Infectious, and Lifestyle Diseases: Current Knowledge and Prospects for Disease Prevention, Novel Drug Design, and Therapy date: 2019-07-03 journal: Cells DOI: 10.3390/cells8070674 sha: doc_id: 304343 cord_uid: m7tbdfri file: cache/cord-303665-l57e54hu.json key: cord-303665-l57e54hu authors: Lahrich, S.; Laghrib, F.; Farahi, A.; Bakasse, M.; Saqrane, S.; El Mhammedi, M. A. title: Review on the contamination of wastewater by COVID-19 virus: Impact and treatment date: 2020-09-10 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.142325 sha: doc_id: 303665 cord_uid: l57e54hu file: cache/cord-306983-6w2fvtfy.json key: cord-306983-6w2fvtfy authors: Wang, Siye; Le, Trong Quang; Kurihara, Naoki; Chida, Junji; Cisse, Youssouf; Yano, Mihiro; Kido, Hiroshi title: Influenza Virus—Cytokine-Protease Cycle in the Pathogenesis of Vascular Hyperpermeability in Severe Influenza date: 2010-10-01 journal: J Infect Dis DOI: 10.1086/656044 sha: doc_id: 306983 cord_uid: 6w2fvtfy file: cache/cord-305263-fgwf6wy3.json key: cord-305263-fgwf6wy3 authors: Wang, Ben X.; Fish, Eleanor N. title: The yin and yang of viruses and interferons date: 2012-02-07 journal: Trends Immunol DOI: 10.1016/j.it.2012.01.004 sha: doc_id: 305263 cord_uid: fgwf6wy3 file: cache/cord-304498-ty41xob0.json key: cord-304498-ty41xob0 authors: Denison, Mark R; Graham, Rachel L; Donaldson, Eric F; Eckerle, Lance D; Baric, Ralph S title: Coronaviruses: An RNA proofreading machine regulates replication fidelity and diversity date: 2011-03-01 journal: RNA Biology DOI: 10.4161/rna.8.2.15013 sha: doc_id: 304498 cord_uid: ty41xob0 file: cache/cord-307893-mvl0wrsj.json key: cord-307893-mvl0wrsj authors: Goulter-Thorsen, R.M.; Jaykus, L-A title: Disciplines Associated with Food Safety: Food Virology date: 2014-01-13 journal: Encyclopedia of Food Safety DOI: 10.1016/b978-0-12-378612-8.00024-x sha: doc_id: 307893 cord_uid: mvl0wrsj file: cache/cord-304876-txaoz7oh.json key: cord-304876-txaoz7oh authors: Jordan, Paul C; Stevens, Sarah K; Deval, Jerome title: Nucleosides for the treatment of respiratory RNA virus infections date: 2018-03-21 journal: Antivir Chem Chemother DOI: 10.1177/2040206618764483 sha: doc_id: 304876 cord_uid: txaoz7oh file: cache/cord-306733-df36w6l7.json key: cord-306733-df36w6l7 authors: Rosales-Mendoza, Sergio; Márquez-Escobar, Verónica A.; González-Ortega, Omar; Nieto-Gómez, Ricardo; Arévalo-Villalobos, Jaime I. title: What Does Plant-Based Vaccine Technology Offer to the Fight against COVID-19? date: 2020-04-14 journal: Vaccines (Basel) DOI: 10.3390/vaccines8020183 sha: doc_id: 306733 cord_uid: df36w6l7 file: cache/cord-308385-bcph664h.json key: cord-308385-bcph664h authors: Yan, Zishuo; Lan, Yueheng title: Modeling COVID-19 infection in a confined space date: 2020-07-15 journal: Nonlinear Dyn DOI: 10.1007/s11071-020-05802-4 sha: doc_id: 308385 cord_uid: bcph664h file: cache/cord-305302-go87uu06.json key: cord-305302-go87uu06 authors: Gessain, Antoine; García-Arenal, Fernando title: Editorial overview: Emerging viruses: interspecies transmission date: 2015-02-28 journal: Current Opinion in Virology DOI: 10.1016/j.coviro.2015.02.001 sha: doc_id: 305302 cord_uid: go87uu06 file: cache/cord-302529-43pd2qsp.json key: cord-302529-43pd2qsp authors: El Moussi, Awatef; Pozo, Francisco; Ben Hadj Kacem, Mohamed Ali; Ledesma, Juan; Cuevas, Maria Teresa; Casas, Inmaculada; Slim, Amine title: Virological Surveillance of Influenza Viruses during the 2008–09, 2009–10 and 2010–11 Seasons in Tunisia date: 2013-09-19 journal: PLoS One DOI: 10.1371/journal.pone.0074064 sha: doc_id: 302529 cord_uid: 43pd2qsp file: cache/cord-304747-ojyxs3cp.json key: cord-304747-ojyxs3cp authors: Gaynor, Anne M; Nissen, Michael D; Whiley, David M; Mackay, Ian M; Lambert, Stephen B; Wu, Guang; Brennan, Daniel C; Storch, Gregory A; Sloots, Theo P; Wang, David title: Identification of a Novel Polyomavirus from Patients with Acute Respiratory Tract Infections date: 2007-05-04 journal: PLoS Pathog DOI: 10.1371/journal.ppat.0030064 sha: doc_id: 304747 cord_uid: ojyxs3cp file: cache/cord-305807-n3fs7533.json key: cord-305807-n3fs7533 authors: Ferreira, T B; Alves, P M; Aunins, J G; Carrondo, M J T title: Use of adenoviral vectors as veterinary vaccines date: 2005-10-18 journal: Gene Ther DOI: 10.1038/sj.gt.3302618 sha: doc_id: 305807 cord_uid: n3fs7533 file: cache/cord-307817-2vy28i4m.json key: cord-307817-2vy28i4m authors: Lou, Zhiyong; Sun, Yuna; Rao, Zihe title: Current progress in antiviral strategies date: 2014-01-14 journal: Trends Pharmacol Sci DOI: 10.1016/j.tips.2013.11.006 sha: doc_id: 307817 cord_uid: 2vy28i4m file: cache/cord-304424-048xo7jn.json key: cord-304424-048xo7jn authors: Greninger, Alexander L. title: A decade of RNA virus metagenomics is (not) enough date: 2018-01-15 journal: Virus Res DOI: 10.1016/j.virusres.2017.10.014 sha: doc_id: 304424 cord_uid: 048xo7jn file: cache/cord-305165-3twlnkac.json key: cord-305165-3twlnkac authors: Bourgueil, E.; Hutet, E.; Cariolet, R.; Vannier, P. title: Experimental infection of pigs with the porcine respiratory coronavirus (PRCV): measure of viral excretion date: 1992-04-30 journal: Veterinary Microbiology DOI: 10.1016/0378-1135(92)90136-h sha: doc_id: 305165 cord_uid: 3twlnkac file: cache/cord-305742-wf6qxplf.json key: cord-305742-wf6qxplf authors: Gomez, Santiago A.; Rojas-Valencia, Natalia; Gomez, Sara; Egidi, Franco; Cappelli, Chiara; Restrepo, Albeiro title: Binding of SARS–CoV–2 to cell receptors: a tale of molecular evolution date: 2020-09-28 journal: Chembiochem DOI: 10.1002/cbic.202000618 sha: doc_id: 305742 cord_uid: wf6qxplf file: cache/cord-309048-emmtplv3.json key: cord-309048-emmtplv3 authors: Lomonossoff, George P.; Wege, Christina title: TMV Particles: The Journey From Fundamental Studies to Bionanotechnology Applications date: 2018-07-26 journal: Adv Virus Res DOI: 10.1016/bs.aivir.2018.06.003 sha: doc_id: 309048 cord_uid: emmtplv3 file: cache/cord-307744-wbr84taq.json key: cord-307744-wbr84taq authors: Jayadevan, Rajeev; Raveendran, A.V. title: Does a younger host make the virus weaker? Presenting a new hypothesis date: 2020-09-13 journal: Diabetes Metab Syndr DOI: 10.1016/j.dsx.2020.09.011 sha: doc_id: 307744 cord_uid: wbr84taq file: cache/cord-305488-vk59ghjm.json key: cord-305488-vk59ghjm authors: Choi, Kang-Seuk title: Newcastle disease virus vectored vaccines as bivalent or antigen delivery vaccines date: 2017-07-26 journal: Clin Exp Vaccine Res DOI: 10.7774/cevr.2017.6.2.72 sha: doc_id: 305488 cord_uid: vk59ghjm file: cache/cord-304569-o39kl5k4.json key: cord-304569-o39kl5k4 authors: Nguyen-Van-Tam, Jonathan S title: From the Editor's desk date: 2015-04-23 journal: Influenza Other Respir Viruses DOI: 10.1111/irv.12311 sha: doc_id: 304569 cord_uid: o39kl5k4 file: cache/cord-309489-ubf55eux.json key: cord-309489-ubf55eux authors: Carvalho, John J. title: OUR COMMON ENEMY: COMBATTING THE WORLD'S DEADLIEST VIRUSES TO ENSURE EQUITY HEALTH CARE IN DEVELOPING NATIONS date: 2009-02-19 journal: Zygon DOI: 10.1111/j.1467-9744.2009.00985.x sha: doc_id: 309489 cord_uid: ubf55eux file: cache/cord-309346-4mdxe6ri.json key: cord-309346-4mdxe6ri authors: López-Medrano, Francisco; María Aguado, José title: Virus respiratorios: los más frecuentes, los más olvidados date: 2008-02-29 journal: Enfermedades Infecciosas y Microbiología Clínica DOI: 10.1157/13115538 sha: doc_id: 309346 cord_uid: 4mdxe6ri file: cache/cord-307046-ko3bdvo0.json key: cord-307046-ko3bdvo0 authors: Vasilakis, Nikos; Tesh, Robert B.; Popov, Vsevolod L.; Widen, Steve G.; Wood, Thomas G.; Forrester, Naomi L.; Gonzalez, Jean Paul; Saluzzo, Jean Francois; Alkhovsky, Sergey; Lam, Sai Kit; Mackenzie, John S.; Walker, Peter J. title: Exploiting the Legacy of the Arbovirus Hunters date: 2019-05-23 journal: Viruses DOI: 10.3390/v11050471 sha: doc_id: 307046 cord_uid: ko3bdvo0 file: cache/cord-307813-elom30nx.json key: cord-307813-elom30nx authors: Yip, Tsz-Fung; Selim, Aisha Sami Mohammed; Lian, Ida; Lee, Suki Man-Yan title: Advancements in Host-Based Interventions for Influenza Treatment date: 2018-07-10 journal: Front Immunol DOI: 10.3389/fimmu.2018.01547 sha: doc_id: 307813 cord_uid: elom30nx file: cache/cord-309179-5hlatbqe.json key: cord-309179-5hlatbqe authors: Bosch, Albert; Guix, Susana; Sano, Daisuke; Pintó, Rosa M title: New tools for the study and direct surveillance of viral pathogens in water date: 2008-05-26 journal: Curr Opin Biotechnol DOI: 10.1016/j.copbio.2008.04.006 sha: doc_id: 309179 cord_uid: 5hlatbqe file: cache/cord-309120-05bg7rfa.json key: cord-309120-05bg7rfa authors: Niazi, Sadegh; Groth, Robert; Spann, Kirsten; Johnson, Graham R. title: The role of respiratory droplet physicochemistry in limiting and promoting the airborne transmission of human coronaviruses: A critical review() date: 2020-11-06 journal: Environ Pollut DOI: 10.1016/j.envpol.2020.115767 sha: doc_id: 309120 cord_uid: 05bg7rfa file: cache/cord-308201-lavcsqov.json key: cord-308201-lavcsqov authors: Desforges, Marc; Le Coupanec, Alain; Dubeau, Philippe; Bourgouin, Andréanne; Lajoie, Louise; Dubé, Mathieu; Talbot, Pierre J. title: Human Coronaviruses and Other Respiratory Viruses: Underestimated Opportunistic Pathogens of the Central Nervous System? date: 2019-12-20 journal: Viruses DOI: 10.3390/v12010014 sha: doc_id: 308201 cord_uid: lavcsqov file: cache/cord-308857-otsrexqu.json key: cord-308857-otsrexqu authors: Goel, Saurav; Hawi, Sara; Goel, Gaurav; Thakur, Vijay Kumar; Pearce, Oliver; Hoskins, Clare; Hussain, Tanvir; Agrawal, Anupam; Upadhyaya, Hari M.; Cross, Graham; Barber, Asa H. title: Resilient and Agile Engineering Solutions to Address Societal Challenges such as Coronavirus Pandemic date: 2020-05-28 journal: Mater Today Chem DOI: 10.1016/j.mtchem.2020.100300 sha: doc_id: 308857 cord_uid: otsrexqu file: cache/cord-309067-aemjbkfj.json key: cord-309067-aemjbkfj authors: Kennedy, Melissa title: Methodology in diagnostic virology date: 2005-03-01 journal: Vet Clin North Am Exot Anim Pract DOI: 10.1016/j.cvex.2004.09.009 sha: doc_id: 309067 cord_uid: aemjbkfj file: cache/cord-307918-8y89p11a.json key: cord-307918-8y89p11a authors: Onyango, Clayton O.; Njeru, Regina; Kazungu, Sidi; Achilla, Rachel; Bulimo, Wallace; Welch, Stephen R.; Cane, Patricia A.; Gunson, Rory N.; Hammitt, Laura L.; Scott, J. Anthony G.; Berkley, James A.; Nokes, D. James title: Influenza Surveillance Among Children With Pneumonia Admitted to a District Hospital in Coastal Kenya, 2007–2010 date: 2012-12-15 journal: J Infect Dis DOI: 10.1093/infdis/jis536 sha: doc_id: 307918 cord_uid: 8y89p11a file: cache/cord-310141-2jofy8fo.json key: cord-310141-2jofy8fo authors: Qureshi, Abid; Tantray, Vaqar Gani; Kirmani, Altaf Rehman; Ahangar, Abdul Ghani title: A review on current status of antiviral siRNA date: 2018-04-15 journal: Rev Med Virol DOI: 10.1002/rmv.1976 sha: doc_id: 310141 cord_uid: 2jofy8fo file: cache/cord-303265-v6ci69n0.json key: cord-303265-v6ci69n0 authors: Domingo, Esteban title: Introduction to virus origins and their role in biological evolution date: 2019-11-08 journal: Virus as Populations DOI: 10.1016/b978-0-12-816331-3.00001-5 sha: doc_id: 303265 cord_uid: v6ci69n0 file: cache/cord-307632-x9bxnrtn.json key: cord-307632-x9bxnrtn authors: Wu, Zhiqiang; Lu, Liang; Du, Jiang; Yang, Li; Ren, Xianwen; Liu, Bo; Jiang, Jinyong; Yang, Jian; Dong, Jie; Sun, Lilian; Zhu, Yafang; Li, Yuhui; Zheng, Dandan; Zhang, Chi; Su, Haoxiang; Zheng, Yuting; Zhou, Hongning; Zhu, Guangjian; Li, Hongying; Chmura, Aleksei; Yang, Fan; Daszak, Peter; Wang, Jianwei; Liu, Qiyong; Jin, Qi title: Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases date: 2018-10-03 journal: Microbiome DOI: 10.1186/s40168-018-0554-9 sha: doc_id: 307632 cord_uid: x9bxnrtn file: cache/cord-307899-427a7i3h.json key: cord-307899-427a7i3h authors: BITTLE, JAMES L.; MUIR, SUSIE title: Vaccines Produced by Conventional Means to Control Major Infectious Diseases of Man and Animals date: 1989-12-31 journal: Advances in Veterinary Science and Comparative Medicine DOI: 10.1016/b978-0-12-039233-9.50005-6 sha: doc_id: 307899 cord_uid: 427a7i3h file: cache/cord-309381-cb80ntxs.json key: cord-309381-cb80ntxs authors: Nogales, Aitor; L. DeDiego, Marta title: Host Single Nucleotide Polymorphisms Modulating Influenza A Virus Disease in Humans date: 2019-09-30 journal: Pathogens DOI: 10.3390/pathogens8040168 sha: doc_id: 309381 cord_uid: cb80ntxs file: cache/cord-305327-hayhbs5u.json key: cord-305327-hayhbs5u authors: Gonzalez, Jean-Paul; Souris, Marc; Valdivia-Granda, Willy title: Global Spread of Hemorrhagic Fever Viruses: Predicting Pandemics date: 2017-09-19 journal: Hemorrhagic Fever Viruses DOI: 10.1007/978-1-4939-6981-4_1 sha: doc_id: 305327 cord_uid: hayhbs5u file: cache/cord-306083-juysx6yo.json key: cord-306083-juysx6yo authors: Choe, Young June; Park, Sangshin; Michelow, Ian C. title: Co-seasonality and co-detection of respiratory viruses and bacteraemia in children: a retrospective analysis date: 2020-09-10 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.09.006 sha: doc_id: 306083 cord_uid: juysx6yo file: cache/cord-310255-aixq5mhf.json key: cord-310255-aixq5mhf authors: Charlton, Frank W.; Pearson, Hayley M.; Hover, Samantha; Lippiat, Jon D.; Fontana, Juan; Barr, John N.; Mankouri, Jamel title: Ion Channels as Therapeutic Targets for Viral Infections: Further Discoveries and Future Perspectives date: 2020-08-03 journal: Viruses DOI: 10.3390/v12080844 sha: doc_id: 310255 cord_uid: aixq5mhf file: cache/cord-310371-pylrg91h.json key: cord-310371-pylrg91h authors: Bishop, R.F.; Kirkwood, C.D. title: Enteric Viruses date: 2008-07-30 journal: Encyclopedia of Virology DOI: 10.1016/b978-012374410-4.00386-1 sha: doc_id: 310371 cord_uid: pylrg91h file: cache/cord-306948-wkisfz1m.json key: cord-306948-wkisfz1m authors: Han, Mingyuan; Yoo, Dongwan title: Engineering the PRRS virus genome: Updates and perspectives date: 2014-12-05 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2014.10.007 sha: doc_id: 306948 cord_uid: wkisfz1m file: cache/cord-308686-tbwecf7o.json key: cord-308686-tbwecf7o authors: Mortamet, G.; Morello, R.; Jokic, M.; Vabret, A.; Leroux, M.; Brouard, J.; Dina, J. title: Étude prospective de l’écologie virale hivernale dans un service de réanimation pédiatrique date: 2015-04-30 journal: Archives de Pédiatrie DOI: 10.1016/j.arcped.2014.10.025 sha: doc_id: 308686 cord_uid: tbwecf7o file: cache/cord-309635-1tgovkr7.json key: cord-309635-1tgovkr7 authors: Wu, Nicholas C.; Wilson, Ian A. title: Structural Biology of Influenza Hemagglutinin: An Amaranthine Adventure date: 2020-09-22 journal: Viruses DOI: 10.3390/v12091053 sha: doc_id: 309635 cord_uid: 1tgovkr7 file: cache/cord-311748-yr2ep7uf.json key: cord-311748-yr2ep7uf authors: Kahyaoglu, L. N.; Irudayaraj, J. title: 11 New approaches in microbial pathogen detection date: 2013-12-31 journal: Advances in Microbial Food Safety DOI: 10.1533/9780857098740.3.202 sha: doc_id: 311748 cord_uid: yr2ep7uf file: cache/cord-310140-h7uwl0pb.json key: cord-310140-h7uwl0pb authors: Templeton, K.E.; Forde, C.B.; Loon, A.M. van; Claas, E.C.J.; Niesters, H.G.M.; Wallace, P.; Carman, W.F. title: A multi-centre pilot proficiency programme to assess the quality of molecular detection of respiratory viruses date: 2005-07-12 journal: J Clin Virol DOI: 10.1016/j.jcv.2005.05.005 sha: doc_id: 310140 cord_uid: h7uwl0pb file: cache/cord-312964-vsrqmmv7.json key: cord-312964-vsrqmmv7 authors: Doyle, William J.; Alper, Cuneyt M. title: Prevention of otitis media caused by viral upper respiratory tract infection: Vaccines, antivirals, and other approaches date: 2003 journal: Curr Allergy Asthma Rep DOI: 10.1007/s11882-003-0093-7 sha: doc_id: 312964 cord_uid: vsrqmmv7 file: cache/cord-311823-85wj08gr.json key: cord-311823-85wj08gr authors: Katze, Michael G.; Fornek, Jamie L.; Palermo, Robert E.; Walters, Kathie-Anne; Korth, Marcus J. title: Innate immune modulation by RNA viruses: emerging insights from functional genomics date: 2008 journal: Nat Rev Immunol DOI: 10.1038/nri2377 sha: doc_id: 311823 cord_uid: 85wj08gr file: cache/cord-308066-lrbi5198.json key: cord-308066-lrbi5198 authors: Childs, James E. title: Pre-spillover Prevention of Emerging Zoonotic Diseases: What Are the Targets and What Are the Tools? date: 2007 journal: Wildlife and Emerging Zoonotic Diseases: The Biology, Circumstances and Consequences of Cross-Species Transmission DOI: 10.1007/978-3-540-70962-6_16 sha: doc_id: 308066 cord_uid: lrbi5198 file: cache/cord-309488-8guapzke.json key: cord-309488-8guapzke authors: Dodd, R. title: Other emerging viral pathogens date: 2006-08-15 journal: ISBT Sci Ser DOI: 10.1111/j.1751-2824.2006.00043.x sha: doc_id: 309488 cord_uid: 8guapzke file: cache/cord-307364-j86t65qu.json key: cord-307364-j86t65qu authors: Uccellini, Lorenzo; Ossiboff, Robert J; de Matos, Ricardo EC; Morrisey, James K; Petrosov, Alexandra; Navarrete-Macias, Isamara; Jain, Komal; Hicks, Allison L; Buckles, Elizabeth L; Tokarz, Rafal; McAloose, Denise; Lipkin, Walter Ian title: Identification of a novel nidovirus in an outbreak of fatal respiratory disease in ball pythons (Python regius) date: 2014-08-08 journal: Virol J DOI: 10.1186/1743-422x-11-144 sha: doc_id: 307364 cord_uid: j86t65qu file: cache/cord-310942-191m0e65.json key: cord-310942-191m0e65 authors: Boga, Jose Antonio; Coto‐Montes, Ana; Rosales‐Corral, Sergio A.; Tan, Dun‐Xian; Reiter, Russel J. title: Beneficial actions of melatonin in the management of viral infections: a new use for this “molecular handyman”? date: 2012-04-18 journal: Rev Med Virol DOI: 10.1002/rmv.1714 sha: doc_id: 310942 cord_uid: 191m0e65 file: cache/cord-312431-de7zhswl.json key: cord-312431-de7zhswl authors: Ganesh, Atheesha; Lin, Johnson; Singh, Moganavelli title: Detecting Virus‐Like Particles from the Umgeni River, South Africa date: 2013-08-30 journal: Clean (Weinh) DOI: 10.1002/clen.201200564 sha: doc_id: 312431 cord_uid: de7zhswl file: cache/cord-314254-9ye8tfvz.json key: cord-314254-9ye8tfvz authors: Pfaender, Stephanie; Brown, Richard JP; Pietschmann, Thomas; Steinmann, Eike title: Natural reservoirs for homologs of hepatitis C virus date: 2014-03-26 journal: Emerg Microbes Infect DOI: 10.1038/emi.2014.19 sha: doc_id: 314254 cord_uid: 9ye8tfvz file: cache/cord-306424-gf0bglm0.json key: cord-306424-gf0bglm0 authors: Scutigliani, Enzo Maxim; Kikkert, Marjolein title: Interaction of the innate immune system with positive-strand RNA virus replication organelles date: 2017-06-27 journal: Cytokine Growth Factor Rev DOI: 10.1016/j.cytogfr.2017.05.007 sha: doc_id: 306424 cord_uid: gf0bglm0 file: cache/cord-310920-itqwhi6a.json key: cord-310920-itqwhi6a authors: Haddad, Christina; Davila-Calderon, Jesse; Tolbert, Blanton S. title: Integrated Approaches to Reveal Mechanisms by which RNA Viruses Reprogram the Cellular Environment date: 2020-07-02 journal: Methods DOI: 10.1016/j.ymeth.2020.06.013 sha: doc_id: 310920 cord_uid: itqwhi6a file: cache/cord-310795-n78s0sg2.json key: cord-310795-n78s0sg2 authors: Brand, H. Kim; de Groot, Ronald; Galama, Joep M.D.; Brouwer, Marianne L.; Teuwen, Karin; Hermans, Peter W.M.; Melchers, Willem J.G.; Warris, Adilia title: Infection with multiple viruses is not associated with increased disease severity in children with bronchiolitis date: 2011-09-07 journal: Pediatr Pulmonol DOI: 10.1002/ppul.21552 sha: doc_id: 310795 cord_uid: n78s0sg2 file: cache/cord-310171-1fmsxx2s.json key: cord-310171-1fmsxx2s authors: Goffard, Anne; Lambert, Valérie; Salleron, Julia; Herwegh, Stéphanie; Engelmann, Ilka; Pinel, Claudine; Pin, Isabelle; Perrez, Thierry; Prévotat, Anne; Dewilde, Anny; Delhaes, Laurence title: Virus and cystic fibrosis: Rhinoviruses are associated with exacerbations in adult patients() date: 2014-02-25 journal: J Clin Virol DOI: 10.1016/j.jcv.2014.02.005 sha: doc_id: 310171 cord_uid: 1fmsxx2s file: cache/cord-311410-lgqup9ug.json key: cord-311410-lgqup9ug authors: Ayers, M.; Adachi, D.; Johnson, G.; Andonova, M.; Drebot, M.; Tellier, R. title: A single tube RT-PCR assay for the detection of mosquito-borne flaviviruses date: 2006-05-02 journal: J Virol Methods DOI: 10.1016/j.jviromet.2006.03.009 sha: doc_id: 311410 cord_uid: lgqup9ug file: cache/cord-312461-5qzpo6l1.json key: cord-312461-5qzpo6l1 authors: Adalja, Amesh A.; Watson, Matthew; Toner, Eric S.; Cicero, Anita; Inglesby, Thomas V. title: Characteristics of Microbes Most Likely to Cause Pandemics and Global Catastrophes date: 2019-08-30 journal: Global Catastrophic Biological Risks DOI: 10.1007/82_2019_176 sha: doc_id: 312461 cord_uid: 5qzpo6l1 file: cache/cord-313356-ninzeazy.json key: cord-313356-ninzeazy authors: Fiorillo, Luca; Cervino, Gabriele; Matarese, Marco; D’Amico, Cesare; Surace, Giovanni; Paduano, Valeria; Fiorillo, Maria Teresa; Moschella, Antonio; La Bruna, Alessia; Romano, Giovanni Luca; Laudicella, Riccardo; Baldari, Sergio; Cicciù, Marco title: COVID-19 Surface Persistence: A Recent Data Summary and Its Importance for Medical and Dental Settings date: 2020-04-30 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17093132 sha: doc_id: 313356 cord_uid: ninzeazy file: cache/cord-314190-fvdock94.json key: cord-314190-fvdock94 authors: Florin, Todd A; Plint, Amy C; Zorc, Joseph J title: Viral bronchiolitis date: 2017-01-01 journal: The Lancet DOI: 10.1016/s0140-6736(16)30951-5 sha: doc_id: 314190 cord_uid: fvdock94 file: cache/cord-310439-z0bxsjug.json key: cord-310439-z0bxsjug authors: Martin, R. R.; Tzanetakis, I. E. title: Pathogen-Tested Planting Material date: 2014-12-31 journal: Encyclopedia of Agriculture and Food Systems DOI: 10.1016/b978-0-444-52512-3.00173-x sha: doc_id: 310439 cord_uid: z0bxsjug file: cache/cord-311908-sgdq6j6x.json key: cord-311908-sgdq6j6x authors: Atkins, G. J.; McQuaid, S.; Morris‐Downes, M. M.; Galbraith, S. E.; Amor, S.; Cosby, S. L.; Sheahan, B. J. title: Transient virus infection and multiple sclerosis date: 2000-09-28 journal: Rev Med Virol DOI: 10.1002/1099-1654(200009/10)10:5<291::aid-rmv278>3.0.co;2-u sha: doc_id: 311908 cord_uid: sgdq6j6x file: cache/cord-309642-wwaa6ls0.json key: cord-309642-wwaa6ls0 authors: Potgieter, Leon N.D. title: Pathogenesis of Viral Infections date: 1986-11-30 journal: Veterinary Clinics of North America: Small Animal Practice DOI: 10.1016/s0195-5616(86)50129-7 sha: doc_id: 309642 cord_uid: wwaa6ls0 file: cache/cord-310870-w8wu8vno.json key: cord-310870-w8wu8vno authors: Shorten, Robert J.; Wilson-Davies, Eleri title: The risk of transmission of a viral haemorrhagic fever infection in a United Kingdom laboratory date: 2017-05-18 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0005358 sha: doc_id: 310870 cord_uid: w8wu8vno file: cache/cord-313312-h607itv2.json key: cord-313312-h607itv2 authors: Mok, Darren Z. L.; Chan, Kuan Rong title: The Effects of Pre-Existing Antibodies on Live-Attenuated Viral Vaccines date: 2020-05-08 journal: Viruses DOI: 10.3390/v12050520 sha: doc_id: 313312 cord_uid: h607itv2 file: cache/cord-314390-q36ye9ff.json key: cord-314390-q36ye9ff authors: Kang, Gagandeep title: Viral Diarrhea date: 2016-10-24 journal: International Encyclopedia of Public Health DOI: 10.1016/b978-0-12-803678-5.00486-0 sha: doc_id: 314390 cord_uid: q36ye9ff file: cache/cord-315346-ebfjba4y.json key: cord-315346-ebfjba4y authors: Cummings, Kristin J.; Martin, Stephen B.; Lindsley, William G.; Othumpangat, Sreekumar; Blachere, Francoise M.; Noti, John D.; Beezhold, Donald H.; Roidad, Nasira; Parker, John E.; Weissman, David N. title: Exposure to Influenza Virus Aerosols in the Hospital Setting: Is Routine Patient Care an Aerosol Generating Procedure? date: 2014-03-04 journal: Journal of Infectious Diseases DOI: 10.1093/infdis/jiu127 sha: doc_id: 315346 cord_uid: ebfjba4y file: cache/cord-314325-nquov2i0.json key: cord-314325-nquov2i0 authors: Murphy, F.A. title: Epidemiology of Human and Animal Viral Diseases date: 2008-07-30 journal: Encyclopedia of Virology DOI: 10.1016/b978-012374410-4.00390-3 sha: doc_id: 314325 cord_uid: nquov2i0 file: cache/cord-314166-79323mzd.json key: cord-314166-79323mzd authors: Vanderford, Thomas H.; Demma, Linda J.; Feinberg, Mark B.; Staprans, Silvija I.; Logsdon, John M. title: Adaptation of a Diverse Simian Immunodeficiency Virus Population to a New Host Is Revealed through a Systematic Approach to Identify Amino Acid Sites under Selection date: 2006-12-11 journal: Mol Biol Evol DOI: 10.1093/molbev/msl194 sha: doc_id: 314166 cord_uid: 79323mzd file: cache/cord-311382-ioemd0ij.json key: cord-311382-ioemd0ij authors: Tellier, Raymond; Li, Yuguo; Cowling, Benjamin J.; Tang, Julian W. title: Recognition of aerosol transmission of infectious agents: a commentary date: 2019-01-31 journal: BMC Infect Dis DOI: 10.1186/s12879-019-3707-y sha: doc_id: 311382 cord_uid: ioemd0ij file: cache/cord-313301-7mkadtp9.json key: cord-313301-7mkadtp9 authors: Duffy, Siobain; Burch, Christina L.; Turner, Paul E. title: EVOLUTION OF HOST SPECIFICITY DRIVES REPRODUCTIVE ISOLATION AMONG RNA VIRUSES date: 2007-08-23 journal: Evolution DOI: 10.1111/j.1558-5646.2007.00226.x sha: doc_id: 313301 cord_uid: 7mkadtp9 file: cache/cord-316295-x636ux34.json key: cord-316295-x636ux34 authors: Roth, Bernhard; Mohr, Hannah; Enders, Martin; Garten, Wolfgang; Gregersen, Jens-Peter title: Isolation of influenza viruses in MDCK 33016PF cells and clearance of contaminating respiratory viruses date: 2012-01-11 journal: Vaccine DOI: 10.1016/j.vaccine.2011.11.063 sha: doc_id: 316295 cord_uid: x636ux34 file: cache/cord-316245-n6tmn4ph.json key: cord-316245-n6tmn4ph authors: Cui, Binglin; Zhang, Dangui; Pan, Hui; Zhang, Fan; Farrar, Jeremy; Law, Frieda; van Doorn, H Rogier; Wu, Beiyan; Ba-Thein, William title: Viral aetiology of acute respiratory infections among children and associated meteorological factors in southern China date: 2015-03-13 journal: BMC Infect Dis DOI: 10.1186/s12879-015-0863-6 sha: doc_id: 316245 cord_uid: n6tmn4ph file: cache/cord-315037-lmur80te.json key: cord-315037-lmur80te authors: Lin, Chien-Yu; Hwang, David; Chiu, Nan-Chang; Weng, Li-Chuan; Liu, Hsin-Fu; Mu, Jung-Jung; Liu, Chang-Pan; Chi, Hsin title: Increased Detection of Viruses in Children with Respiratory Tract Infection Using PCR date: 2020-01-15 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17020564 sha: doc_id: 315037 cord_uid: lmur80te file: cache/cord-311012-wyglrpqh.json key: cord-311012-wyglrpqh authors: Meyers, Craig; Kass, Rena; Goldenberg, David; Milici, Janice; Alam, Samina; Robison, Richard title: Ethanol and Isopropanol Inactivation of Human Coronavirus on Hard Surfaces date: 2020-09-28 journal: J Hosp Infect DOI: 10.1016/j.jhin.2020.09.026 sha: doc_id: 311012 cord_uid: wyglrpqh file: cache/cord-315781-dejh8q22.json key: cord-315781-dejh8q22 authors: Konishi, Tomokazu title: Re-evaluation of the evolution of influenza H1 viruses using direct PCA date: 2019-12-17 journal: Sci Rep DOI: 10.1038/s41598-019-55254-z sha: doc_id: 315781 cord_uid: dejh8q22 file: cache/cord-316951-1swlhdz5.json key: cord-316951-1swlhdz5 authors: Kennedy, Melissa; Greenacre, Cheryl B. title: General concepts of virology date: 2005-03-01 journal: Vet Clin North Am Exot Anim Pract DOI: 10.1016/j.cvex.2004.09.010 sha: doc_id: 316951 cord_uid: 1swlhdz5 file: cache/cord-315167-ph15z424.json key: cord-315167-ph15z424 authors: Goka, E. A.; Vallely, P. J.; Mutton, K. J.; Klapper, P. E. title: Pan-human coronavirus and human bocavirus SYBR Green and TaqMan PCR assays; use in studying influenza A viruses co-infection and risk of hospitalization date: 2014-12-05 journal: Infection DOI: 10.1007/s15010-014-0710-5 sha: doc_id: 315167 cord_uid: ph15z424 file: cache/cord-314201-6njwigco.json key: cord-314201-6njwigco authors: Maher-Sturgess, Sheryl L; Forrester, Naomi L; Wayper, Paul J; Gould, Ernest A; Hall, Roy A; Barnard, Ross T; Gibbs, Mark J title: Universal primers that amplify RNA from all three flavivirus subgroups date: 2008-01-24 journal: Virol J DOI: 10.1186/1743-422x-5-16 sha: doc_id: 314201 cord_uid: 6njwigco file: cache/cord-312688-12san3m7.json key: cord-312688-12san3m7 authors: Martin, Baptiste; Hoenen, Thomas; Canard, Bruno; Decroly, Etienne title: Filovirus proteins for antiviral drug discovery: A structure/function analysis of surface glycoproteins and virus entry date: 2016-09-14 journal: Antiviral Res DOI: 10.1016/j.antiviral.2016.09.001 sha: doc_id: 312688 cord_uid: 12san3m7 file: cache/cord-312332-rwmuucsp.json key: cord-312332-rwmuucsp authors: Dicker, Kate; Järvelin, Aino I.; Garcia-Moreno, Manuel; Castello, Alfredo title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity date: 2020-09-10 journal: Semin Cell Dev Biol DOI: 10.1016/j.semcdb.2020.08.002 sha: doc_id: 312332 cord_uid: rwmuucsp file: cache/cord-315131-4yb2b70g.json key: cord-315131-4yb2b70g authors: Hammerschmidt, Sven; Hacker, Jörg; Klenk, Hans-Dieter title: Threat of infection: Microbes of high pathogenic potential – strategies for detection, control and eradication date: 2005-06-28 journal: International Journal of Medical Microbiology DOI: 10.1016/j.ijmm.2005.03.004 sha: doc_id: 315131 cord_uid: 4yb2b70g file: cache/cord-315339-dcui85lw.json key: cord-315339-dcui85lw authors: Broadbent, Andrew J.; Boonnak, Kobporn; Subbarao, Kanta title: Respiratory Virus Vaccines date: 2015-03-13 journal: Mucosal Immunology DOI: 10.1016/b978-0-12-415847-4.00059-8 sha: doc_id: 315339 cord_uid: dcui85lw file: cache/cord-317198-mean7sj9.json key: cord-317198-mean7sj9 authors: Giamberardin, Heloisa I.G.; Homsani, Sheila; Bricks, Lucia F.; Pacheco, Ana P.O.; Guedes, Matilde; Debur, Maria C.; Raboni, Sonia M. title: Clinical and epidemiological features of respiratory virus infections in preschool children over two consecutive influenza seasons in southern Brazil date: 2016-02-09 journal: J Med Virol DOI: 10.1002/jmv.24477 sha: doc_id: 317198 cord_uid: mean7sj9 file: cache/cord-317244-4su5on6s.json key: cord-317244-4su5on6s authors: Maganga, Gael D.; Bourgarel, Mathieu; Obame Nkoghe, Judicael; N'Dilimabaka, Nadine; Drosten, Christian; Paupy, Christophe; Morand, Serge; Drexler, Jan Felix; Leroy, Eric M. title: Identification of an Unclassified Paramyxovirus in Coleura afra: A Potential Case of Host Specificity date: 2014-12-31 journal: PLoS One DOI: 10.1371/journal.pone.0115588 sha: doc_id: 317244 cord_uid: 4su5on6s file: cache/cord-317404-jvtozj4v.json key: cord-317404-jvtozj4v authors: Santos, Marfran C.D.; Morais, Camilo L.M.; Nascimento, Yasmin M.; Araujo, Josélio M.G.; Lima, Kássio M.G. title: Spectroscopy with computational analysis in virological studies: A decade (2006–2016) date: 2017-09-21 journal: Trends Analyt Chem DOI: 10.1016/j.trac.2017.09.015 sha: doc_id: 317404 cord_uid: jvtozj4v file: cache/cord-313598-2t40ss6h.json key: cord-313598-2t40ss6h authors: Ali, Mohsin; Han, Sangsu; Gunst, Chris J.; Lim, Steve; Luinstra, Kathy; Smieja, Marek title: Throat and nasal swabs for molecular detection of respiratory viruses in acute pharyngitis date: 2015-10-29 journal: Virol J DOI: 10.1186/s12985-015-0408-z sha: doc_id: 313598 cord_uid: 2t40ss6h file: cache/cord-316063-9bg2dm8e.json key: cord-316063-9bg2dm8e authors: Morgan, Marcus title: Why meaning-making matters: the case of the UK Government’s COVID-19 response date: 2020-10-15 journal: Am J Cult Sociol DOI: 10.1057/s41290-020-00121-y sha: doc_id: 316063 cord_uid: 9bg2dm8e file: cache/cord-316996-8yimrpaz.json key: cord-316996-8yimrpaz authors: Nicholls, John M.; Moss, Ronald B.; Haslam, Stuart M. title: The use of sialidase therapy for respiratory viral infections date: 2013-04-17 journal: Antiviral Res DOI: 10.1016/j.antiviral.2013.04.012 sha: doc_id: 316996 cord_uid: 8yimrpaz file: cache/cord-316273-vo6j8zb0.json key: cord-316273-vo6j8zb0 authors: Cosset, François-Loic; Lavillette, Dimitri title: Cell Entry of Enveloped Viruses date: 2011-02-08 journal: Adv Genet DOI: 10.1016/b978-0-12-380860-8.00004-5 sha: doc_id: 316273 cord_uid: vo6j8zb0 file: cache/cord-315918-12rbbe8c.json key: cord-315918-12rbbe8c authors: Mukherjee, Pulok K. title: Antiviral Evaluation of Herbal Drugs date: 2019-06-21 journal: Quality Control and Evaluation of Herbal Drugs DOI: 10.1016/b978-0-12-813374-3.00016-8 sha: doc_id: 315918 cord_uid: 12rbbe8c file: cache/cord-314825-fzba05wn.json key: cord-314825-fzba05wn authors: Chauhan, Ravendra P.; Gordon, Michelle L. title: A Systematic Review Analyzing the Prevalence and Circulation of Influenza Viruses in Swine Population Worldwide date: 2020-05-08 journal: Pathogens DOI: 10.3390/pathogens9050355 sha: doc_id: 314825 cord_uid: fzba05wn file: cache/cord-316682-4360s2yu.json key: cord-316682-4360s2yu authors: Fischer, William A.; Weber, David J.; Wohl, David A. title: Personal Protective Equipment: Protecting Health Care Providers in an Ebola Outbreak date: 2015-11-01 journal: Clinical Therapeutics DOI: 10.1016/j.clinthera.2015.07.007 sha: doc_id: 316682 cord_uid: 4360s2yu file: cache/cord-318172-bdotp9ko.json key: cord-318172-bdotp9ko authors: Blanco, Jorge C. G.; Core, Susan; Pletneva, Lioubov M.; March, Thomas H.; Boukhvalova, Marina S.; Kajon, Adriana E. title: PROPHYLACTIC ANTIBODY TREATMENT AND INTRAMUSCULAR IMMUNIZATION REDUCE INFECTIOUS HUMAN RHINOVIRUS 16 LOAD IN THE LOWER RESPIRATORY TRACT OF CHALLENGED COTTON RATS date: 2014-01-01 journal: Trials in Vaccinology DOI: 10.1016/j.trivac.2014.02.003 sha: doc_id: 318172 cord_uid: bdotp9ko file: cache/cord-317501-yblzopc3.json key: cord-317501-yblzopc3 authors: Kuhn, Philipp; Fühner, Viola; Unkauf, Tobias; Moreira, Gustavo Marcal Schmidt Garcia; Frenzel, André; Miethe, Sebastian; Hust, Michael title: Recombinant antibodies for diagnostics and therapy against pathogens and toxins generated by phage display date: 2016-06-21 journal: Proteomics Clin Appl DOI: 10.1002/prca.201600002 sha: doc_id: 317501 cord_uid: yblzopc3 file: cache/cord-317277-rr9zue4l.json key: cord-317277-rr9zue4l authors: Cifuentes-Munoz, Nicolas; El Najjar, Farah; Dutch, Rebecca Ellis title: Viral cell-to-cell spread: Conventional and non-conventional ways date: 2020-09-29 journal: Adv Virus Res DOI: 10.1016/bs.aivir.2020.09.002 sha: doc_id: 317277 cord_uid: rr9zue4l file: cache/cord-317851-lj07947c.json key: cord-317851-lj07947c authors: Elena, S F; Agudelo-Romero, P; Carrasco, P; Codoñer, F M; Martín, S; Torres-Barceló, C; Sanjuán, R title: Experimental evolution of plant RNA viruses date: 2008-02-06 journal: Heredity (Edinb) DOI: 10.1038/sj.hdy.6801088 sha: doc_id: 317851 cord_uid: lj07947c file: cache/cord-317971-kuwargnp.json key: cord-317971-kuwargnp authors: Opatz, Till; Senn‐Bilfinger, Joerg; Richert, Clemens title: Thoughts on What Chemists Can Contribute to Fighting SARS‐CoV‐2 – A Short Note on Hand Sanitizers, Drug Candidates and Outreach date: 2020-05-08 journal: Angew Chem Int Ed Engl DOI: 10.1002/anie.202004721 sha: doc_id: 317971 cord_uid: kuwargnp file: cache/cord-318725-09a32vyg.json key: cord-318725-09a32vyg authors: Dong, Rui; Zheng, Hui; Tian, Kun; Yau, Shek-Chung; Mao, Weiguang; Yu, Wenping; Yin, Changchuan; Yu, Chenglong; He, Rong Lucy; Yang, Jie; Yau, Stephen ST title: Virus Database and Online Inquiry System Based on Natural Vectors date: 2017-12-17 journal: Evol Bioinform Online DOI: 10.1177/1176934317746667 sha: doc_id: 318725 cord_uid: 09a32vyg file: cache/cord-319746-6bccxgbd.json key: cord-319746-6bccxgbd authors: Saxena, Latika; Khanna, Madhu title: Production and Characterization of Human Monoclonal Antibodies from the Cells of A(H1N1)pdm2009 Influenza Virus Infected Indian Donors date: 2015-12-31 journal: Procedia in Vaccinology DOI: 10.1016/j.provac.2015.05.009 sha: doc_id: 319746 cord_uid: 6bccxgbd file: cache/cord-317496-6o2upns3.json key: cord-317496-6o2upns3 authors: Pascual-Iglesias, Alejandro; Sanchez, Carlos M.; Penzes, Zoltan; Sola, Isabel; Enjuanes, Luis; Zuñiga, Sonia title: Recombinant Chimeric Transmissible Gastroenteritis Virus (TGEV)—Porcine Epidemic Diarrhea Virus (PEDV) Virus Provides Protection against Virulent PEDV date: 2019-07-25 journal: Viruses DOI: 10.3390/v11080682 sha: doc_id: 317496 cord_uid: 6o2upns3 file: cache/cord-316894-zhmuzv7z.json key: cord-316894-zhmuzv7z authors: Stetzenbach, L.D. title: Airborne Infectious Microorganisms date: 2009-02-17 journal: Encyclopedia of Microbiology DOI: 10.1016/b978-012373944-5.00177-2 sha: doc_id: 316894 cord_uid: zhmuzv7z file: cache/cord-318786-qd0k8174.json key: cord-318786-qd0k8174 authors: Mauriz, Elba title: Recent Progress in Plasmonic Biosensing Schemes for Virus Detection date: 2020-08-22 journal: Sensors (Basel) DOI: 10.3390/s20174745 sha: doc_id: 318786 cord_uid: qd0k8174 file: cache/cord-319208-jrxz59bb.json key: cord-319208-jrxz59bb authors: Ting, Chun Yi; Cheng, Daryl R.; Kotsanas, Despina; Kirkwood, Carl D.; Bogdanovic-Sakran, Nada; Stuart, Rhonda L.; Buttery, Jim P. title: Are identity badges and lanyards in pediatrics potentially contaminated with viral pathogens? date: 2015-11-01 journal: American Journal of Infection Control DOI: 10.1016/j.ajic.2015.06.024 sha: doc_id: 319208 cord_uid: jrxz59bb file: cache/cord-319754-5isw53wl.json key: cord-319754-5isw53wl authors: Balgoma, David; Gil-de-Gómez, Luis; Montero, Olimpio title: Lipidomics Issues on Human Positive ssRNA Virus Infection: An Update date: 2020-08-31 journal: Metabolites DOI: 10.3390/metabo10090356 sha: doc_id: 319754 cord_uid: 5isw53wl file: cache/cord-317508-03u2vtzk.json key: cord-317508-03u2vtzk authors: Oldstone, M.B.A. title: History of Virology date: 2019-08-28 journal: Encyclopedia of Microbiology DOI: 10.1016/b978-0-12-801238-3.00078-7 sha: doc_id: 317508 cord_uid: 03u2vtzk file: cache/cord-318495-1w74wf02.json key: cord-318495-1w74wf02 authors: Vignuzzi, Marco; López, Carolina B. title: Defective viral genomes are key drivers of the virus–host interaction date: 2019-06-03 journal: Nat Microbiol DOI: 10.1038/s41564-019-0465-y sha: doc_id: 318495 cord_uid: 1w74wf02 file: cache/cord-319210-yqimufdh.json key: cord-319210-yqimufdh authors: KENNEDY, P.G.E.; STEINER, I. title: On the possible viral aetiology of multiple sclerosis date: 1994-09-17 journal: QJM DOI: 10.1093/oxfordjournals.qjmed.a068963 sha: doc_id: 319210 cord_uid: yqimufdh file: cache/cord-317412-f3ua8ks3.json key: cord-317412-f3ua8ks3 authors: Zhang, Xing; Zhang, Yunshan; Shi, Xiu; Dai, Kun; Liang, Zi; Zhu, Min; Zhang, Ziyao; Shen, Zenen; Pan, Jun; Wang, Chonglong; Hu, Xiaolong; Gong, Chengliang title: Characterization of the lipidomic profile of BmN cells in response to Bombyx mori cytoplasmic polyhedrosis virus infection date: 2020-08-15 journal: Dev Comp Immunol DOI: 10.1016/j.dci.2020.103822 sha: doc_id: 317412 cord_uid: f3ua8ks3 file: cache/cord-319814-tyqb473m.json key: cord-319814-tyqb473m authors: Zhang, Dingmei; He, Zhenjian; Xu, Lin; Zhu, Xun; Wu, Jueheng; Wen, Weitao; Zheng, Yun; Deng, Yu; Chen, Jieling; Hu, Yiwen; Li, Mengfeng; Cao, Kaiyuan title: Epidemiology characteristics of respiratory viruses found in children and adults with respiratory tract infections in southern China date: 2014-06-11 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2014.02.019 sha: doc_id: 319814 cord_uid: tyqb473m file: cache/cord-322748-a5131tv9.json key: cord-322748-a5131tv9 authors: Yates, Mary K.; Raje, Mithun R.; Chatterjee, Payel; Spiropoulou, Christina F.; Bavari, Sina; Flint, Mike; Soloveva, Veronica; Seley-Radtke, Katherine L. title: Flex-nucleoside analogues – Novel therapeutics against filoviruses date: 2017-06-15 journal: Bioorganic & Medicinal Chemistry Letters DOI: 10.1016/j.bmcl.2017.04.069 sha: doc_id: 322748 cord_uid: a5131tv9 file: cache/cord-318551-c1qr27lg.json key: cord-318551-c1qr27lg authors: Boguszewska‐Chachulska, Anna M.; Haenni, Anne‐Lise title: Rna Viruses Redirect Host Factors to Better Amplify Their Genome date: 2005-12-29 journal: Adv Virus Res DOI: 10.1016/s0065-3527(05)65002-6 sha: doc_id: 318551 cord_uid: c1qr27lg file: cache/cord-319761-bu5pzbnv.json key: cord-319761-bu5pzbnv authors: Miller, Craig S. title: Pleiotropic mechanisms of virus survival and persistence date: 2005-07-16 journal: Oral Surg Oral Med Oral Pathol Oral Radiol Endod DOI: 10.1016/j.tripleo.2005.03.017 sha: doc_id: 319761 cord_uid: bu5pzbnv file: cache/cord-321562-hk4hzl13.json key: cord-321562-hk4hzl13 authors: Liu, Xuan; Li, Dengfeng; Liu, Gang title: Cell membrane-derived biomimetic nanodecoys for viruses date: 2020-05-12 journal: Sci China Life Sci DOI: 10.1007/s11427-020-1669-x sha: doc_id: 321562 cord_uid: hk4hzl13 file: cache/cord-317619-o7qfugjw.json key: cord-317619-o7qfugjw authors: Nye, Steven; Whitley, Richard J.; Kong, Michele title: Viral Infection in the Development and Progression of Pediatric Acute Respiratory Distress Syndrome date: 2016-11-24 journal: Front Pediatr DOI: 10.3389/fped.2016.00128 sha: doc_id: 317619 cord_uid: o7qfugjw file: cache/cord-321756-a7eh4dkb.json key: cord-321756-a7eh4dkb authors: Kwofie, Theophilus B; Anane, Yaw A; Nkrumah, Bernard; Annan, Augustina; Nguah, Samuel B; Owusu, Michael title: Respiratory viruses in children hospitalized for acute lower respiratory tract infection in Ghana date: 2012-04-10 journal: Virol J DOI: 10.1186/1743-422x-9-78 sha: doc_id: 321756 cord_uid: a7eh4dkb file: cache/cord-320030-ojtp90na.json key: cord-320030-ojtp90na authors: Montero, Antonio title: Fiebre chikungunya - Una nueva amenaza global date: 2015-08-07 journal: Medicina Clínica DOI: 10.1016/j.medcli.2014.05.031 sha: doc_id: 320030 cord_uid: ojtp90na file: cache/cord-320935-3n157yl4.json key: cord-320935-3n157yl4 authors: Kumar, Manish; Mohapatra, Sanjeeb; Mazumder, Payal; Singh, Ashwin; Honda, Ryo; Lin, Chuxia; Kumari, Rina; Goswami, Ritusmita; Jha, Pawan Kumar; Vithanage, Meththika; Kuroda, Keisuke title: Making Waves Perspectives of Modelling and Monitoring of SARS-CoV-2 in Aquatic Environment for COVID-19 Pandemic date: 2020-09-12 journal: Curr Pollut Rep DOI: 10.1007/s40726-020-00161-5 sha: doc_id: 320935 cord_uid: 3n157yl4 file: cache/cord-321053-lgae22f8.json key: cord-321053-lgae22f8 authors: Gerold, Gisa; Pietschmann, Thomas title: Opportunities and Risks of Host-targeting Antiviral Strategies for Hepatitis C date: 2013-10-04 journal: Curr Hepat Rep DOI: 10.1007/s11901-013-0187-1 sha: doc_id: 321053 cord_uid: lgae22f8 file: cache/cord-318686-we6pveus.json key: cord-318686-we6pveus authors: Ehlen, Lukas; Tödtmann, Jan; Specht, Sabine; Kallies, René; Papies, Jan; Müller, Marcel A.; Junglen, Sandra; Drosten, Christian; Eckerle, Isabella title: Epithelial cell lines of the cotton rat (Sigmodon hispidus) are highly susceptible in vitro models to zoonotic Bunya-, Rhabdo-, and Flaviviruses date: 2016-05-04 journal: Virol J DOI: 10.1186/s12985-016-0531-5 sha: doc_id: 318686 cord_uid: we6pveus file: cache/cord-320693-de1lmzl1.json key: cord-320693-de1lmzl1 authors: Hu, Han; Guo, Nan; Chen, Shuhua; Guo, Xiaozhen; Liu, Xiaoli; Ye, Shiyi; Chai, Qingqing; Wang, Yang; Liu, Binlei; He, Qigai title: Antiviral activity of Piscidin 1 against pseudorabies virus both in vitro and in vivo date: 2019-07-31 journal: Virol J DOI: 10.1186/s12985-019-1199-4 sha: doc_id: 320693 cord_uid: de1lmzl1 file: cache/cord-319933-yp9ofhi8.json key: cord-319933-yp9ofhi8 authors: Ruiz, Sara I.; Zumbrun, Elizabeth E.; Nalca, Aysegul title: Chapter 38 Animal Models of Human Viral Diseases date: 2013-12-31 journal: Animal Models for the Study of Human Disease DOI: 10.1016/b978-0-12-415894-8.00038-5 sha: doc_id: 319933 cord_uid: yp9ofhi8 file: cache/cord-323333-keshu99t.json key: cord-323333-keshu99t authors: Schleis, Thomas G. title: The Process: New Methods of Purification and Viral Safety date: 2013-01-16 journal: Pharmacotherapy DOI: 10.1592/phco.2005.25.11part2.73s sha: doc_id: 323333 cord_uid: keshu99t file: cache/cord-320055-6ycp8m89.json key: cord-320055-6ycp8m89 authors: Elliot, Elisa L; Colwell, Rita R title: Indicator organisms for estuarine and marine waters date: 1985-07-31 journal: FEMS Microbiology Letters DOI: 10.1016/0378-1097(85)90057-6 sha: doc_id: 320055 cord_uid: 6ycp8m89 file: cache/cord-318853-mxyxwkhx.json key: cord-318853-mxyxwkhx authors: Sallie, Richard title: Replicative homeostasis II: Influence of polymerase fidelity on RNA virus quasispecies biology: Implications for immune recognition, viral autoimmunity and other "virus receptor" diseases date: 2005-08-22 journal: Virol J DOI: 10.1186/1743-422x-2-70 sha: doc_id: 318853 cord_uid: mxyxwkhx file: cache/cord-320713-b37c8aye.json key: cord-320713-b37c8aye authors: Roberts, Lisa O.; Jopling, Catherine L.; Jackson, Richard J.; Willis, Anne E. title: Chapter 9 Viral Strategies to Subvert the Mammalian Translation Machinery date: 2009-10-27 journal: Prog Mol Biol Transl Sci DOI: 10.1016/s1877-1173(09)90009-6 sha: doc_id: 320713 cord_uid: b37c8aye file: cache/cord-321835-qn33sx8x.json key: cord-321835-qn33sx8x authors: Bailey, Emily S.; Fieldhouse, Jane K.; Choi, Jessica Y.; Gray, Gregory C. title: A Mini Review of the Zoonotic Threat Potential of Influenza Viruses, Coronaviruses, Adenoviruses, and Enteroviruses date: 2018-04-09 journal: Front Public Health DOI: 10.3389/fpubh.2018.00104 sha: doc_id: 321835 cord_uid: qn33sx8x file: cache/cord-319379-qe56u93a.json key: cord-319379-qe56u93a authors: Patil, Vaishali M.; Singhal, Shipra; Masand, Neeraj title: A systematic review on use of aminoquinolines for the therapeutic management of COVID-19: Efficacy, safety and clinical trials date: 2020-05-11 journal: Life Sci DOI: 10.1016/j.lfs.2020.117775 sha: doc_id: 319379 cord_uid: qe56u93a file: cache/cord-321741-aq76s37x.json key: cord-321741-aq76s37x authors: Andersen, Petter I.; Ianevski, Aleksandr; Lysvand, Hilde; Vitkauskiene, Astra; Oksenych, Valentyn; Bjørås, Magnar; Telling, Kaidi; Lutsar, Irja; Dumpis, Uga; Irie, Yasuhiko; Tenson, Tanel; Kantele, Anu; Kainov, Denis E. title: Discovery and development of safe-in-man broad-spectrum antiviral agents date: 2020-04-30 journal: International Journal of Infectious Diseases DOI: 10.1016/j.ijid.2020.02.018 sha: doc_id: 321741 cord_uid: aq76s37x file: cache/cord-320015-lbr2q4qh.json key: cord-320015-lbr2q4qh authors: Chinchar, V. Gregory; Yu, Kwang H.; Jancovich, James K. title: The Molecular Biology of Frog Virus 3 and other Iridoviruses Infecting Cold-Blooded Vertebrates date: 2011-10-20 journal: Viruses DOI: 10.3390/v3101959 sha: doc_id: 320015 cord_uid: lbr2q4qh file: cache/cord-322082-80ym2rsq.json key: cord-322082-80ym2rsq authors: Monto, Arnold S; Fukuda, Keiji title: Lessons From Influenza Pandemics of the Last 100 Years date: 2020-03-01 journal: Clin Infect Dis DOI: 10.1093/cid/ciz803 sha: doc_id: 322082 cord_uid: 80ym2rsq file: cache/cord-324775-3x5os79m.json key: cord-324775-3x5os79m authors: Crowe, J.E. title: Human Respiratory Viruses date: 2008-07-30 journal: Encyclopedia of Virology DOI: 10.1016/b978-012374410-4.00488-x sha: doc_id: 324775 cord_uid: 3x5os79m file: cache/cord-323195-buzcb8ya.json key: cord-323195-buzcb8ya authors: Valtonen, Maarit; Waris, Matti; Vuorinen, Tytti; Eerola, Erkki; Hakanen, Antti J; Mjosund, Katja; Grönroos, Wilma; Heinonen, Olli J; Ruuskanen, Olli title: Common cold in Team Finland during 2018 Winter Olympic Games (PyeongChang): epidemiology, diagnosis including molecular point-of-care testing (POCT) and treatment date: 2019-05-29 journal: Br J Sports Med DOI: 10.1136/bjsports-2018-100487 sha: doc_id: 323195 cord_uid: buzcb8ya file: cache/cord-323358-05bk91lm.json key: cord-323358-05bk91lm authors: Bhaskar, Sathyamoorthy; Lim, Sierin title: Engineering protein nanocages as carriers for biomedical applications date: 2017-04-07 journal: NPG Asia Mater DOI: 10.1038/am.2016.128 sha: doc_id: 323358 cord_uid: 05bk91lm file: cache/cord-321112-w7x1dkds.json key: cord-321112-w7x1dkds authors: Zhao, Xuesen; Li, Jiarui; Winkler, Cheryl A.; An, Ping; Guo, Ju-Tao title: IFITM Genes, Variants, and Their Roles in the Control and Pathogenesis of Viral Infections date: 2019-01-08 journal: Front Microbiol DOI: 10.3389/fmicb.2018.03228 sha: doc_id: 321112 cord_uid: w7x1dkds file: cache/cord-322234-1zyy536y.json key: cord-322234-1zyy536y authors: Lorusso, Alessio; Faaberg, Kay S.; Killian, Mary Lea; Koster, Leo; Vincent, Amy L. title: One-step real-time RT-PCR for pandemic influenza A virus (H1N1) 2009 matrix gene detection in swine samples date: 2009-12-17 journal: J Virol Methods DOI: 10.1016/j.jviromet.2009.12.002 sha: doc_id: 322234 cord_uid: 1zyy536y file: cache/cord-323009-frej2qmb.json key: cord-323009-frej2qmb authors: Nakouné, Emmanuel; Tricou, Vianney; Manirakiza, Alexandre; Komoyo, Francis; Selekon, Benjamin; Gody, Jean Chrysostome; Victoir, Kathleen; Buchy, Philippe; Kazanji, Mirdad title: First introduction of pandemic influenza A/H1N1 and detection of respiratory viruses in pediatric patients in Central African Republic date: 2013-02-08 journal: Virol J DOI: 10.1186/1743-422x-10-49 sha: doc_id: 323009 cord_uid: frej2qmb file: cache/cord-323404-3mw4q7m3.json key: cord-323404-3mw4q7m3 authors: Bomsel, Morgane; Alfsen, Annette title: Entry of viruses through the epithelial barrier: pathogenic trickery date: 2003 journal: Nat Rev Mol Cell Biol DOI: 10.1038/nrm1005 sha: doc_id: 323404 cord_uid: 3mw4q7m3 file: cache/cord-322904-9mta0aem.json key: cord-322904-9mta0aem authors: Neu, Ursula; Stehle, Thilo; Atwood, Walter J. title: The Polyomaviridae: Contributions of virus structure to our understanding of virus receptors and infectious entry date: 2009-02-01 journal: Virology DOI: 10.1016/j.virol.2008.12.021 sha: doc_id: 322904 cord_uid: 9mta0aem file: cache/cord-323311-xl2fv0qx.json key: cord-323311-xl2fv0qx authors: Kahn, R. E.; Morozov, I.; Feldmann, H.; Richt, J. A. title: 6th International Conference on Emerging Zoonoses date: 2012-09-07 journal: Zoonoses Public Health DOI: 10.1111/j.1863-2378.2012.01539.x sha: doc_id: 323311 cord_uid: xl2fv0qx file: cache/cord-322206-roxa3ix6.json key: cord-322206-roxa3ix6 authors: I. Sardi, Silvia; H. Carvalho, Rejane; C. Pacheco, Luis G.; P. d. Almeida, João P.; M. d. A. Belitardo, Emilia M.; S. Pinheiro, Carina; S. Campos, Gúbio; R. G. R. Aguiar, Eric title: High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics date: 2020-07-21 journal: Viruses DOI: 10.3390/v12070782 sha: doc_id: 322206 cord_uid: roxa3ix6 file: cache/cord-323987-gh1m05gi.json key: cord-323987-gh1m05gi authors: Dziąbowska, Karolina; Czaczyk, Elżbieta; Nidzworski, Dawid title: Detection Methods of Human and Animal Influenza Virus—Current Trends date: 2018-10-18 journal: Biosensors (Basel) DOI: 10.3390/bios8040094 sha: doc_id: 323987 cord_uid: gh1m05gi file: cache/cord-324950-ux7shvji.json key: cord-324950-ux7shvji authors: Saade, Georges; Deblanc, Céline; Bougon, Juliette; Marois-Créhan, Corinne; Fablet, Christelle; Auray, Gaël; Belloc, Catherine; Leblanc-Maridor, Mily; Gagnon, Carl A.; Zhu, Jianzhong; Gottschalk, Marcelo; Summerfield, Artur; Simon, Gaëlle; Bertho, Nicolas; Meurens, François title: Coinfections and their molecular consequences in the porcine respiratory tract date: 2020-06-16 journal: Vet Res DOI: 10.1186/s13567-020-00807-8 sha: doc_id: 324950 cord_uid: ux7shvji file: cache/cord-324280-e8mj6ecl.json key: cord-324280-e8mj6ecl authors: Shaman, Jeffrey; Morita, Haruka; Birger, Ruthie; Boyle, Mary; Comito, Devon; Lane, Benjamin; Ligon, Chanel; Smith, Hannah; Desalle, Rob; Planet, Paul title: Asymptomatic Summertime Shedding of Respiratory Viruses date: 2018-04-01 journal: J Infect Dis DOI: 10.1093/infdis/jix685 sha: doc_id: 324280 cord_uid: e8mj6ecl file: cache/cord-325280-4whzcmqv.json key: cord-325280-4whzcmqv authors: Takizawa, Naoki; Yamasaki, Manabu title: Current landscape and future prospects of antiviral drugs derived from microbial products date: 2017-10-11 journal: J Antibiot (Tokyo) DOI: 10.1038/ja.2017.115 sha: doc_id: 325280 cord_uid: 4whzcmqv file: cache/cord-321481-vrfwczve.json key: cord-321481-vrfwczve authors: Watashi, Koichi; Urban, Stephan; Li, Wenhui; Wakita, Takaji title: NTCP and Beyond: Opening the Door to Unveil Hepatitis B Virus Entry date: 2014-02-19 journal: Int J Mol Sci DOI: 10.3390/ijms15022892 sha: doc_id: 321481 cord_uid: vrfwczve file: cache/cord-323700-5awng7h1.json key: cord-323700-5awng7h1 authors: Goggin, Rachel K.; Bennett, Catherine A.; Bassiouni, Ahmed; Bialasiewicz, Seweryn; Vreugde, Sarah; Wormald, Peter-John; Psaltis, Alkis J. title: Comparative Viral Sampling in the Sinonasal Passages; Different Viruses at Different Sites date: 2018-09-19 journal: Front Cell Infect Microbiol DOI: 10.3389/fcimb.2018.00334 sha: doc_id: 323700 cord_uid: 5awng7h1 file: cache/cord-325825-0lyt8gfq.json key: cord-325825-0lyt8gfq authors: Griffiths, Samantha J.; Koegl, Manfred; Boutell, Chris; Zenner, Helen L.; Crump, Colin M.; Pica, Francesca; Gonzalez, Orland; Friedel, Caroline C.; Barry, Gerald; Martin, Kim; Craigon, Marie H.; Chen, Rui; Kaza, Lakshmi N.; Fossum, Even; Fazakerley, John K.; Efstathiou, Stacey; Volpi, Antonio; Zimmer, Ralf; Ghazal, Peter; Haas, Jürgen title: A Systematic Analysis of Host Factors Reveals a Med23-Interferon-λ Regulatory Axis against Herpes Simplex Virus Type 1 Replication date: 2013-08-08 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1003514 sha: doc_id: 325825 cord_uid: 0lyt8gfq file: cache/cord-323793-c69joaqs.json key: cord-323793-c69joaqs authors: Palmieri, V.; Papi, M. title: Can graphene take part in the fight against COVID-19? date: 2020-05-07 journal: Nano Today DOI: 10.1016/j.nantod.2020.100883 sha: doc_id: 323793 cord_uid: c69joaqs file: cache/cord-324984-ojrpsdt9.json key: cord-324984-ojrpsdt9 authors: Ji, Xingyue; Li, Zhuorong title: Medicinal chemistry strategies toward host targeting antiviral agents date: 2020-02-14 journal: Med Res Rev DOI: 10.1002/med.21664 sha: doc_id: 324984 cord_uid: ojrpsdt9 file: cache/cord-324696-htx0ul4o.json key: cord-324696-htx0ul4o authors: Chothe, Shubhada K.; Bhushan, Gitanjali; Nissly, Ruth H.; Yeh, Yin-Ting; Brown, Justin; Turner, Gregory; Fisher, Jenny; Sewall, Brent J.; Reeder, DeeAnn M.; Terrones, Mauricio; Jayarao, Bhushan M.; Kuchipudi, Suresh V. title: Avian and human influenza virus compatible sialic acid receptors in little brown bats date: 2017-04-06 journal: Sci Rep DOI: 10.1038/s41598-017-00793-6 sha: doc_id: 324696 cord_uid: htx0ul4o file: cache/cord-323710-cmbg0ty8.json key: cord-323710-cmbg0ty8 authors: Mühlebach, Michael D.; Hutzler, Stefan title: Development of Recombinant Measles Virus-Based Vaccines date: 2016-11-26 journal: Recombinant Virus Vaccines DOI: 10.1007/978-1-4939-6869-5_9 sha: doc_id: 323710 cord_uid: cmbg0ty8 file: cache/cord-325875-93krp81r.json key: cord-325875-93krp81r authors: Henao-Diaz, Alexandra; Giménez-Lirola, Luis; Baum, David H.; Zimmerman, Jeffrey title: Guidelines for oral fluid-based surveillance of viral pathogens in swine date: 2020-10-19 journal: Porcine Health Manag DOI: 10.1186/s40813-020-00168-w sha: doc_id: 325875 cord_uid: 93krp81r file: cache/cord-326719-p1ma4akz.json key: cord-326719-p1ma4akz authors: Enjuanes, Luis; Almazán, Fernando; Ortego, Javier title: Virus-based vectors for gene expression in mammalian cells: Coronavirus date: 2003-12-31 journal: New Comprehensive Biochemistry DOI: 10.1016/s0167-7306(03)38010-x sha: doc_id: 326719 cord_uid: p1ma4akz file: cache/cord-323930-pl3qlcpo.json key: cord-323930-pl3qlcpo authors: Sohail, Ayesha; Nutini, Alessandro title: Forecasting the timeframe of coronavirus and human cells interaction with reverse engineering date: 2020-04-29 journal: Prog Biophys Mol Biol DOI: 10.1016/j.pbiomolbio.2020.04.002 sha: doc_id: 323930 cord_uid: pl3qlcpo file: cache/cord-325635-don9qjpz.json key: cord-325635-don9qjpz authors: Turner, Paul; Turner, Claudia; Watthanaworawit, Wanitda; Carrara, Verena; Cicelia, Naw; Deglise, Carole; Phares, Christina; Ortega, Luis; Nosten, Francois title: Respiratory virus surveillance in hospitalised pneumonia patients on the Thailand-Myanmar border date: 2013-09-16 journal: BMC Infect Dis DOI: 10.1186/1471-2334-13-434 sha: doc_id: 325635 cord_uid: don9qjpz file: cache/cord-325830-mrtpihc7.json key: cord-325830-mrtpihc7 authors: Nelson, Philipp P.; Rath, Barbara A.; Fragkou, Paraskevi C.; Antalis, Emmanouil; Tsiodras, Sotirios; Skevaki, Chrysanthi title: Current and Future Point-of-Care Tests for Emerging and New Respiratory Viruses and Future Perspectives date: 2020-04-29 journal: Front Cell Infect Microbiol DOI: 10.3389/fcimb.2020.00181 sha: doc_id: 325830 cord_uid: mrtpihc7 file: cache/cord-325230-3kg4oe4g.json key: cord-325230-3kg4oe4g authors: Agol, Vadim I.; Gmyl, Anatoly P. title: Viral security proteins: counteracting host defences date: 2010-11-09 journal: Nat Rev Microbiol DOI: 10.1038/nrmicro2452 sha: doc_id: 325230 cord_uid: 3kg4oe4g file: cache/cord-324295-9c1zxjng.json key: cord-324295-9c1zxjng authors: Bonilla-Aldana, D. Katterine; Jimenez-Diaz, S. Daniela; Arango-Duque, J. Sebastian; Aguirre-Florez, Mateo; Balbin-Ramon, Graciela J.; Paniz-Mondolfi, Alberto; Suárez, Jose Antonio; Pachar, Monica R.; Perez-Garcia, Luis A.; Delgado-Noguera, Lourdes A.; Sierra, Manuel Antonio; Muñoz-Lara, Fausto; Zambrano, Lysien I.; Rodriguez-Morales, Alfonso J. title: Bats in Ecosystems and their Wide Spectrum of Viral Infectious Threats: SARS-CoV-2 and other emerging viruses date: 2020-08-20 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.08.050 sha: doc_id: 324295 cord_uid: 9c1zxjng file: cache/cord-325750-x7jpsnxg.json key: cord-325750-x7jpsnxg authors: Mokili, John L; Rohwer, Forest; Dutilh, Bas E title: Metagenomics and future perspectives in virus discovery date: 2012-01-20 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2011.12.004 sha: doc_id: 325750 cord_uid: x7jpsnxg file: cache/cord-326225-crtpzad7.json key: cord-326225-crtpzad7 authors: Neill, John D.; Bayles, Darrell O.; Ridpath, Julia F. title: Simultaneous rapid sequencing of multiple RNA virus genomes date: 2014-06-01 journal: J Virol Methods DOI: 10.1016/j.jviromet.2014.02.016 sha: doc_id: 326225 cord_uid: crtpzad7 file: cache/cord-325326-2bbqz4o7.json key: cord-325326-2bbqz4o7 authors: Beitzel, Brett F.; Bakken, Russell R.; Smith, Jeffrey M.; Schmaljohn, Connie S. title: High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and Massively Parallel Sequencing date: 2010-10-14 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1001146 sha: doc_id: 325326 cord_uid: 2bbqz4o7 file: cache/cord-325969-9zhmmvdg.json key: cord-325969-9zhmmvdg authors: To, Kelvin KW; Lu, Lu; Yip, Cyril CY; Poon, Rosana WS; Fung, Ami MY; Cheng, Andrew; Lui, Daniel HK; Ho, Deborah TY; Hung, Ivan FN; Chan, Kwok-Hung; Yuen, Kwok-Yung title: Additional molecular testing of saliva specimens improves the detection of respiratory viruses date: 2017-06-07 journal: Emerg Microbes Infect DOI: 10.1038/emi.2017.35 sha: doc_id: 325969 cord_uid: 9zhmmvdg file: cache/cord-325827-492xi3ee.json key: cord-325827-492xi3ee authors: Evermann, J. F.; Heeney, J. L.; Roelke, M. E.; McKeirnan, A. J.; O'Brien, S. J. title: Biological and pathological consequences of feline infectious peritonitis virus infection in the cheetah date: 1988 journal: Arch Virol DOI: 10.1007/bf01310822 sha: doc_id: 325827 cord_uid: 492xi3ee file: cache/cord-327013-gc6o8ou3.json key: cord-327013-gc6o8ou3 authors: Kim, Heui Man; Lee, Namjoo; Kim, Mi-Seon; Kang, Chun; Chung, Yoon-Seok title: Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea date: 2020-07-06 journal: Virol J DOI: 10.1186/s12985-020-01375-1 sha: doc_id: 327013 cord_uid: gc6o8ou3 file: cache/cord-327199-ggomuomb.json key: cord-327199-ggomuomb authors: Moerdyk-Schauwecker, Megan; Hwang, Sun-Il; Grdzelishvili, Valery Z. title: Cellular Proteins Associated with the Interior and Exterior of Vesicular Stomatitis Virus Virions date: 2014-08-08 journal: PLoS One DOI: 10.1371/journal.pone.0104688 sha: doc_id: 327199 cord_uid: ggomuomb file: cache/cord-325915-dw989txm.json key: cord-325915-dw989txm authors: Wolf, Michael W; Reichl, Udo title: Downstream processing of cell culture-derived virus particles date: 2014-01-09 journal: Expert Rev Vaccines DOI: 10.1586/erv.11.111 sha: doc_id: 325915 cord_uid: dw989txm file: cache/cord-325925-010xj69x.json key: cord-325925-010xj69x authors: Mordecai, Gideon J; Miller, Kristina M; Di Cicco, Emiliano; Schulze, Angela D; Kaukinen, Karia H; Ming, Tobi J; Li, Shaorong; Tabata, Amy; Teffer, Amy; Patterson, David A; Ferguson, Hugh W; Suttle, Curtis A title: Endangered wild salmon infected by newly discovered viruses date: 2019-09-03 journal: eLife DOI: 10.7554/elife.47615 sha: doc_id: 325925 cord_uid: 010xj69x file: cache/cord-326725-0jgw083h.json key: cord-326725-0jgw083h authors: Klamroth, Robert; Gröner, Albrecht; Simon, Toby L. title: Pathogen inactivation and removal methods for plasma‐derived clotting factor concentrates date: 2013-09-30 journal: Transfusion DOI: 10.1111/trf.12423 sha: doc_id: 326725 cord_uid: 0jgw083h file: cache/cord-327000-oyg3oyx1.json key: cord-327000-oyg3oyx1 authors: Li, Shasha; Yang, Jinping; Zhu, Zixiang; Zheng, Haixue title: Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response date: 2020-05-11 journal: Pathogens DOI: 10.3390/pathogens9050367 sha: doc_id: 327000 cord_uid: oyg3oyx1 file: cache/cord-325325-xw7627x9.json key: cord-325325-xw7627x9 authors: Skeik, Nedaa; Jabr, Fadi I. title: Influenza viruses and the evolution of avian influenza virus H5N1 date: 2007-10-02 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2007.07.002 sha: doc_id: 325325 cord_uid: xw7627x9 file: cache/cord-326027-58whwspe.json key: cord-326027-58whwspe authors: Hernaez, Bruno; Escribano, Jose M.; Alonso, Covadonga title: Visualization of the African swine fever virus infection in living cells by incorporation into the virus particle of green fluorescent protein-p54 membrane protein chimera date: 2006-06-20 journal: Virology DOI: 10.1016/j.virol.2006.01.021 sha: doc_id: 326027 cord_uid: 58whwspe file: cache/cord-328252-dk54w8z9.json key: cord-328252-dk54w8z9 authors: Kikkert, Marjolein title: Innate Immune Evasion by Human Respiratory RNA Viruses date: 2019-10-14 journal: Journal of Innate Immunity DOI: 10.1159/000503030 sha: doc_id: 328252 cord_uid: dk54w8z9 file: cache/cord-325712-9kbnyqt3.json key: cord-325712-9kbnyqt3 authors: Nathan, Lakshmi; Daniel, Susan title: Single Virion Tracking Microscopy for the Study of Virus Entry Processes in Live Cells and Biomimetic Platforms date: 2019-07-18 journal: Physical Virology DOI: 10.1007/978-3-030-14741-9_2 sha: doc_id: 325712 cord_uid: 9kbnyqt3 file: cache/cord-326177-zzsaf3bl.json key: cord-326177-zzsaf3bl authors: Khatri, Mahesh; Richardson, Levi Arthur; Meulia, Tea title: Mesenchymal stem cell-derived extracellular vesicles attenuate influenza virus-induced acute lung injury in a pig model date: 2018-01-29 journal: Stem Cell Res Ther DOI: 10.1186/s13287-018-0774-8 sha: doc_id: 326177 cord_uid: zzsaf3bl file: cache/cord-326960-9phlylce.json key: cord-326960-9phlylce authors: Felberbaum, Rachael S. title: The baculovirus expression vector system: A commercial manufacturing platform for viral vaccines and gene therapy vectors date: 2015-03-20 journal: Biotechnol J DOI: 10.1002/biot.201400438 sha: doc_id: 326960 cord_uid: 9phlylce file: cache/cord-327660-p1b07b4t.json key: cord-327660-p1b07b4t authors: Wolf, Yuri I.; Kazlauskas, Darius; Iranzo, Jaime; Lucía-Sanz, Adriana; Kuhn, Jens H.; Krupovic, Mart; Dolja, Valerian V.; Koonin, Eugene V. title: Origins and Evolution of the Global RNA Virome date: 2018-11-27 journal: mBio DOI: 10.1128/mbio.02329-18 sha: doc_id: 327660 cord_uid: p1b07b4t file: cache/cord-327855-txryqil7.json key: cord-327855-txryqil7 authors: Kulka, M.; Chen, A.; Ngo, D.; Bhattacharya, S. S.; Cebula, T. A.; Goswami, B. B. title: The cytopathic 18f strain of Hepatitis A virus induces RNA degradation in FrhK4 cells date: 2003 journal: Arch Virol DOI: 10.1007/s00705-003-0110-0 sha: doc_id: 327855 cord_uid: txryqil7 file: cache/cord-329145-424vv8a8.json key: cord-329145-424vv8a8 authors: Kuhn, Jens H.; Bao, Yiming; Bavari, Sina; Becker, Stephan; Bradfute, Steven; Brister, J. Rodney; Bukreyev, Alexander A.; Chandran, Kartik; Davey, Robert A.; Dolnik, Olga; Dye, John M.; Enterlein, Sven; Hensley, Lisa E.; Honko, Anna N.; Jahrling, Peter B.; Johnson, Karl M.; Kobinger, Gary; Leroy, Eric M.; Lever, Mark S.; Mühlberger, Elke; Netesov, Sergey V.; Olinger, Gene G.; Palacios, Gustavo; Patterson, Jean L.; Paweska, Janusz T.; Pitt, Louise; Radoshitzky, Sheli R.; Saphire, Erica Ollmann; Smither, Sophie J.; Swanepoel, Robert; Towner, Jonathan S.; van der Groen, Guido; Volchkov, Viktor E.; Wahl-Jensen, Victoria; Warren, Travis K.; Weidmann, Manfred; Nichol, Stuart T. title: Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae date: 2012-09-23 journal: Arch Virol DOI: 10.1007/s00705-012-1454-0 sha: doc_id: 329145 cord_uid: 424vv8a8 file: cache/cord-325611-tu1bn4hu.json key: cord-325611-tu1bn4hu authors: Pérez-Sautu, Unai; Wiley, Michael Ross; Iglesias-Caballero, María; Pozo, Francisco; Prieto, Karla; Chitty, Joseph Alex; García-García, María Luz; Calvo, Cristina; Casas, Inmaculada; Palacios, Gustavo 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 journal: Emerg Microbes Infect DOI: 10.1080/22221751.2019.1640587 sha: doc_id: 325611 cord_uid: tu1bn4hu file: cache/cord-329050-vzsy6xw1.json key: cord-329050-vzsy6xw1 authors: Nabi, Ghulam; Wang, Yang; Lv, Liang; Jiang, Chuan; Ahmad, Shahid; Wu, Yufeng; Li, Dongming title: Bats and birds as viral reservoirs: A physiological and ecological perspective date: 2020-09-22 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.142372 sha: doc_id: 329050 cord_uid: vzsy6xw1 file: cache/cord-328621-3jda0k2u.json key: cord-328621-3jda0k2u authors: Laporte, Manon; Naesens, Lieve title: Airway proteases: an emerging drug target for influenza and other respiratory virus infections date: 2017-04-14 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2017.03.018 sha: doc_id: 328621 cord_uid: 3jda0k2u file: cache/cord-329857-pcsuu597.json key: cord-329857-pcsuu597 authors: Chan, Kuan Rong; Ong, Eugenia Z; Mok, Darren ZL; Ooi, Eng Eong title: Fc receptors and their influence on efficacy of therapeutic antibodies for treatment of viral diseases date: 2015-11-02 journal: Expert Rev Anti Infect Ther DOI: 10.1586/14787210.2015.1079127 sha: doc_id: 329857 cord_uid: pcsuu597 file: cache/cord-329078-gnnis7pl.json key: cord-329078-gnnis7pl authors: Musella, Simona; di Sarno, Veronica; Ciaglia, Tania; Sala, Marina; Spensiero, Antonia; Scala, Maria Carmina; Ostacolo, Carmine; Andrei, Graciela; Balzarini, Jan; Snoeck, Robert; Novellino, Ettore; Campiglia, Pietro; Bertamino, Alessia; Gomez-Monterrey, Isabel M. title: Identification of an indol-based derivative as potent and selective varicella zoster virus (VZV) inhibitor date: 2016-11-29 journal: Eur J Med Chem DOI: 10.1016/j.ejmech.2016.09.014 sha: doc_id: 329078 cord_uid: gnnis7pl file: cache/cord-326160-mf0vh6iu.json key: cord-326160-mf0vh6iu authors: de Wit, Emmie; Rasmussen, Angela L.; Feldmann, Friederike; Bushmaker, Trenton; Martellaro, Cynthia; Haddock, Elaine; Okumura, Atsushi; Proll, Sean C.; Chang, Jean; Gardner, Don; Katze, Michael G.; Munster, Vincent J.; Feldmann, Heinz title: Influenza Virus A/Anhui/1/2013 (H7N9) Replicates Efficiently in the Upper and Lower Respiratory Tracts of Cynomolgus Macaques date: 2014-08-12 journal: mBio DOI: 10.1128/mbio.01331-14 sha: doc_id: 326160 cord_uid: mf0vh6iu file: cache/cord-327777-pg98zc6o.json key: cord-327777-pg98zc6o authors: Delogu, Mauro; Cotti, Claudia; Lelli, Davide; Sozzi, Enrica; Trogu, Tiziana; Lavazza, Antonio; Garuti, Giacomo; Castrucci, Maria Rita; Vaccari, Gabriele; De Marco, Maria Alessandra; Moreno, Ana title: Eco-Virological Preliminary Study of Potentially Emerging Pathogens in Hedgehogs (Erinaceus europaeus) Recovered at a Wildlife Treatment and Rehabilitation Center in Northern Italy date: 2020-03-01 journal: Animals (Basel) DOI: 10.3390/ani10030407 sha: doc_id: 327777 cord_uid: pg98zc6o file: cache/cord-330827-gu2mt6zp.json key: cord-330827-gu2mt6zp authors: Shanmugaraj, Balamurugan; Malla, Ashwini; Phoolcharoen, Waranyoo title: Emergence of Novel Coronavirus 2019-nCoV: Need for Rapid Vaccine and Biologics Development date: 2020-02-22 journal: Pathogens DOI: 10.3390/pathogens9020148 sha: doc_id: 330827 cord_uid: gu2mt6zp file: cache/cord-327392-9psblokc.json key: cord-327392-9psblokc authors: Srivastava, A.K.; Dwivedi, Neeraj; Dhand, Chetna; Khan, Raju; Sathish, N.; Gupta, Manoj K.; Kumar, Rajeev; Kumar, Surender title: Potential of Graphene-based Materials to Combat COVID-19: Properties, Perspectives and Prospects date: 2020-10-21 journal: Mater Today Chem DOI: 10.1016/j.mtchem.2020.100385 sha: doc_id: 327392 cord_uid: 9psblokc file: cache/cord-328753-qwdxgk4z.json key: cord-328753-qwdxgk4z authors: Lafaye, Pierre; Li, Tengfei title: Use of camel single-domain antibodies for the diagnosis and treatment of zoonotic diseases date: 2018-09-25 journal: Comp Immunol Microbiol Infect Dis DOI: 10.1016/j.cimid.2018.09.009 sha: doc_id: 328753 cord_uid: qwdxgk4z file: cache/cord-330296-706hf4qw.json key: cord-330296-706hf4qw authors: Romette, J. L.; Prat, C. M.; Gould, E. A.; de Lamballerie, X.; Charrel, R.; Coutard, B.; Fooks, A. R.; Bardsley, M.; Carroll, M.; Drosten, C.; Drexler, J. F.; Günther, S.; Klempa, B.; Pinschewer, D.; Klimkait, T.; Avsic-Zupanc, T.; Capobianchi, M. R.; Dicaro, A.; Ippolito, G.; Nitsche, A.; Koopmans, M.; Reusken, C.; Gorbalenya, A.; Raoul, H.; Bourhy, H.; Mettenleiter, T.; Reiche, S.; Batten, C.; Sabeta, C.; Paweska, J. T.; Eropkin, M.; Zverev, V.; Hu, Z.; Mac Cullough, S.; Mirazimi, A.; Pradel, F.; Lieutaud, P. title: The European Virus Archive goes global: A growing resource for research date: 2018-10-31 journal: Antiviral Research DOI: 10.1016/j.antiviral.2018.07.017 sha: doc_id: 330296 cord_uid: 706hf4qw file: cache/cord-329527-0rlotyz3.json key: cord-329527-0rlotyz3 authors: Bohmwald, Karen; Gálvez, Nicolás M. S.; Ríos, Mariana; Kalergis, Alexis M. title: Neurologic Alterations Due to Respiratory Virus Infections date: 2018-10-26 journal: Front Cell Neurosci DOI: 10.3389/fncel.2018.00386 sha: doc_id: 329527 cord_uid: 0rlotyz3 file: cache/cord-330508-uilejxmi.json key: cord-330508-uilejxmi authors: van den Hoogen, Bernadette; Santoni, Angela; Sciumé, Giuseppe; Bowie, Andrew; O’Farrelly, Cliona; O’Neill, Luke; Anthonsen, Marit; Pardalli, Katerina; Young, Simon; Bergthaler, Andreas; Manel, Nicolas; Zahn, Ronald; Kikkert, Marjolein; Snijder, Eric; van Kuppeveld, Frank; Fouchier, Ron; Hiscott, John title: Immunometabolism pathways as the basis for innovative anti-viral strategies (INITIATE): A Marie Sklodowska-Curie innovative training network date: 2020-07-28 journal: Virus Res DOI: 10.1016/j.virusres.2020.198094 sha: doc_id: 330508 cord_uid: uilejxmi file: cache/cord-329493-ueqlhgn0.json key: cord-329493-ueqlhgn0 authors: Stadler, Konrad; Masignani, Vega; Eickmann, Markus; Becker, Stephan; Abrignani, Sergio; Klenk, Hans-Dieter; Rappuoli, Rino title: SARS — beginning to understand a new virus date: 2003 journal: Nat Rev Microbiol DOI: 10.1038/nrmicro775 sha: doc_id: 329493 cord_uid: ueqlhgn0 file: cache/cord-327883-s9nbr5y8.json key: cord-327883-s9nbr5y8 authors: nan title: Section Virology date: 1990-03-31 journal: Zentralblatt für Bakteriologie DOI: 10.1016/s0934-8840(11)80039-3 sha: doc_id: 327883 cord_uid: s9nbr5y8 file: cache/cord-329429-ur8g68vp.json key: cord-329429-ur8g68vp authors: Miłek, Justyna; Blicharz-Domańska, Katarzyna title: Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds date: 2018-12-10 journal: J Vet Res DOI: 10.2478/jvetres-2018-0035 sha: doc_id: 329429 cord_uid: ur8g68vp file: cache/cord-331217-uup16bhm.json key: cord-331217-uup16bhm authors: Murphy, Frederick A.; Osburn, Bennie I. title: Adventitious Agents and Smallpox Vaccine in Strategic National Stockpile date: 2005-07-17 journal: Emerg Infect Dis DOI: 10.3201/eid1107.050277 sha: doc_id: 331217 cord_uid: uup16bhm file: cache/cord-329902-db7hl770.json key: cord-329902-db7hl770 authors: Li, Desheng; Zhu, Ling; Cui, Hengmin; Ling, Shanshan; Fan, Shengtao; Yu, Zhijun; Zhou, Yuancheng; Wang, Tiecheng; Qian, Jun; Xia, Xianzhu; Xu, Zhiwen; Gao, Yuwei; Wang, Chengdong title: Influenza A(H1N1)pdm09 Virus Infection in Giant Pandas, China date: 2014-03-17 journal: Emerg Infect Dis DOI: 10.3201/eid2003.131531 sha: doc_id: 329902 cord_uid: db7hl770 file: cache/cord-331020-lyxje82u.json key: cord-331020-lyxje82u authors: M. Najimudeen, Shahnas; H. Hassan, Mohamed S.; C. Cork, Susan; Abdul-Careem, Mohamed Faizal title: Infectious Bronchitis Coronavirus Infection in Chickens: Multiple System Disease with Immune Suppression date: 2020-09-24 journal: Pathogens DOI: 10.3390/pathogens9100779 sha: doc_id: 331020 cord_uid: lyxje82u file: cache/cord-331673-xv1tcugl.json key: cord-331673-xv1tcugl authors: Reina, Giacomo; Peng, Shiyuan; Jacquemin, Lucas; Andrade, Andrés Felipe; Bianco, Alberto title: Hard Nanomaterials in Time of Viral Pandemics date: 2020-07-15 journal: ACS Nano DOI: 10.1021/acsnano.0c04117 sha: doc_id: 331673 cord_uid: xv1tcugl file: cache/cord-330131-yfhrmbvx.json key: cord-330131-yfhrmbvx authors: Danchin, Antoine; Marlière, Philippe title: Cytosine drives evolution of SARS‐CoV‐2 date: 2020-04-27 journal: Environ Microbiol DOI: 10.1111/1462-2920.15025 sha: doc_id: 330131 cord_uid: yfhrmbvx file: cache/cord-323683-9h9mld6x.json key: cord-323683-9h9mld6x authors: Butler, M. title: Virus Removal by Disinfection of Effluents date: 2013-11-17 journal: Viruses and Wastewater Treatment DOI: 10.1016/b978-0-08-026401-1.50025-7 sha: doc_id: 323683 cord_uid: 9h9mld6x file: cache/cord-330647-w1bpeqzg.json key: cord-330647-w1bpeqzg authors: Wong, Samson Sai-Yin; Wong, Sally Cheuk-Ying title: Ebola virus disease in nonendemic countries date: 2015-05-31 journal: Journal of the Formosan Medical Association DOI: 10.1016/j.jfma.2015.01.012 sha: doc_id: 330647 cord_uid: w1bpeqzg file: cache/cord-331244-zaguyxm5.json key: cord-331244-zaguyxm5 authors: Stephenson, Iain; Nicholson, Karl G; Wood, John M; Zambon, Maria C; Katz, Jacqueline M title: Confronting the avian influenza threat: vaccine development for a potential pandemic date: 2004-07-30 journal: Lancet Infect Dis DOI: 10.1016/s1473-3099(04)01105-3 sha: doc_id: 331244 cord_uid: zaguyxm5 file: cache/cord-332165-31tbc31x.json key: cord-332165-31tbc31x authors: Rustmeier, Nils H.; Strebl, Michael; Stehle, Thilo title: The Symmetry of Viral Sialic Acid Binding Sites—Implications for Antiviral Strategies date: 2019-10-14 journal: Viruses DOI: 10.3390/v11100947 sha: doc_id: 332165 cord_uid: 31tbc31x file: cache/cord-331584-z43ifmr3.json key: cord-331584-z43ifmr3 authors: Mahy, B.W.J. title: Emerging and Reemerging Virus Diseases of Vertebrates date: 2008-07-30 journal: Encyclopedia of Virology DOI: 10.1016/b978-012374410-4.00383-6 sha: doc_id: 331584 cord_uid: z43ifmr3 file: cache/cord-331739-y1d0leic.json key: cord-331739-y1d0leic authors: Kempf, Christoph; Stucki, Martin; Boschetti, Nicola title: Pathogen inactivation and removal procedures used in the production of intravenous immunoglobulins date: 2007-03-31 journal: Biologicals DOI: 10.1016/j.biologicals.2006.01.002 sha: doc_id: 331739 cord_uid: y1d0leic file: cache/cord-332361-pdoln3nr.json key: cord-332361-pdoln3nr authors: Khor, Chee-Sieng; Sam, I-Ching; Hooi, Poh-Sim; Quek, Kia-Fatt; Chan, Yoke-Fun 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 journal: BMC Pediatr DOI: 10.1186/1471-2431-12-32 sha: doc_id: 332361 cord_uid: pdoln3nr file: cache/cord-332457-gan10za0.json key: cord-332457-gan10za0 authors: de Ángel Solá, David E.; Wang, Leyao; Vázquez, Marietta; Méndez Lázaro, Pablo A. title: Weathering the pandemic: How the Caribbean Basin can use viral and environmental patterns to predict, prepare and respond to COVID‐19 date: 2020-04-10 journal: J Med Virol DOI: 10.1002/jmv.25864 sha: doc_id: 332457 cord_uid: gan10za0 file: cache/cord-331652-oc5s1if2.json key: cord-331652-oc5s1if2 authors: Trudeau, Michaela P.; Verma, Harsha; Sampedro, Fernando; Urriola, Pedro E.; Shurson, Gerald C.; McKelvey, Jessica; Pillai, Suresh D.; Goyal, Sagar M. title: Comparison of Thermal and Non-Thermal Processing of Swine Feed and the Use of Selected Feed Additives on Inactivation of Porcine Epidemic Diarrhea Virus (PEDV) date: 2016-06-24 journal: PLoS One DOI: 10.1371/journal.pone.0158128 sha: doc_id: 331652 cord_uid: oc5s1if2 file: cache/cord-331289-02411gfv.json key: cord-331289-02411gfv authors: Di Minno, Giovanni; Perno, Carlo Federico; Tiede, Andreas; Navarro, David; Canaro, Mariana; Güertler, Lutz; Ironside, James W. title: Current concepts in the prevention of pathogen transmission via blood/plasma-derived products for bleeding disorders() date: 2015-07-20 journal: Blood Rev DOI: 10.1016/j.blre.2015.07.004 sha: doc_id: 331289 cord_uid: 02411gfv file: cache/cord-332088-5c77h0of.json key: cord-332088-5c77h0of authors: Beena, V.; Saikumar, G. title: Emerging horizon for bat borne viral zoonoses date: 2019-10-26 journal: Virusdisease DOI: 10.1007/s13337-019-00548-z sha: doc_id: 332088 cord_uid: 5c77h0of file: cache/cord-332181-k90i33gp.json key: cord-332181-k90i33gp authors: Degeling, Chris; Kerridge, Ian title: Hendra in the news: Public policy meets public morality in times of zoonotic uncertainty date: 2012-12-29 journal: Soc Sci Med DOI: 10.1016/j.socscimed.2012.12.024 sha: doc_id: 332181 cord_uid: k90i33gp file: cache/cord-333043-fe24ezt6.json key: cord-333043-fe24ezt6 authors: Traavik, T.; Mehl, R.; Kjeldsberg, Elisabeth title: “Runde“ virus, a coronavirus-like agent associated with seabirds and ticks date: 1977 journal: Arch Virol DOI: 10.1007/bf01314476 sha: doc_id: 333043 cord_uid: fe24ezt6 file: cache/cord-332632-u2ud0vmq.json key: cord-332632-u2ud0vmq authors: Lussi, Carmela; Schweizer, Matthias title: What can pestiviral endonucleases teach us about innate immunotolerance? date: 2016-03-17 journal: Cytokine Growth Factor Rev DOI: 10.1016/j.cytogfr.2016.03.003 sha: doc_id: 332632 cord_uid: u2ud0vmq file: cache/cord-332205-ydijp66b.json key: cord-332205-ydijp66b authors: Hufsky, Franziska; Ibrahim, Bashar; Beer, Martin; Deng, Li; Mercier, Philippe Le; McMahon, Dino P.; Palmarini, Massimo; Thiel, Volker; Marz, Manja title: Virologists—Heroes need weapons date: 2018-02-08 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1006771 sha: doc_id: 332205 cord_uid: ydijp66b file: cache/cord-332046-ihc031ly.json key: cord-332046-ihc031ly authors: Li, Yan‐Chao; Bai, Wan‐Zhu; Hirano, Norio; Hayashida, Tsuyako; Taniguchi, Takahide; Sugita, Yoichi; Tohyama, Koujiro; Hashikawa, Tsutomu title: Neurotropic virus tracing suggests a membranous‐coating‐mediated mechanism for transsynaptic communication date: 2013-01-01 journal: J Comp Neurol DOI: 10.1002/cne.23171 sha: doc_id: 332046 cord_uid: ihc031ly file: cache/cord-332992-8rmqg4rf.json key: cord-332992-8rmqg4rf authors: de Vries, A. A. F. title: SARS-CoV-2/COVID-19: a primer for cardiologists date: 2020-07-15 journal: Neth Heart J DOI: 10.1007/s12471-020-01475-1 sha: doc_id: 332992 cord_uid: 8rmqg4rf file: cache/cord-331343-qzvwwca9.json key: cord-331343-qzvwwca9 authors: Mason, Andrew L.; Doucette, Karen; Wong, Gane Ka‐Shu title: Metagenomics and the case of the deadly hamster date: 2008-06-09 journal: Hepatology DOI: 10.1002/hep.22452 sha: doc_id: 331343 cord_uid: qzvwwca9 file: cache/cord-333730-qsx0m68e.json key: cord-333730-qsx0m68e authors: Tsai, Y. C.; Tsai, T. F. title: Oral disease-modifying antirheumatic drugs and immunosuppressants with antiviral potential, including SARS-CoV-2 infection: a review date: 2020-09-03 journal: Ther Adv Musculoskelet Dis DOI: 10.1177/1759720x20947296 sha: doc_id: 333730 cord_uid: qsx0m68e file: cache/cord-333228-ejkgune0.json key: cord-333228-ejkgune0 authors: Ball, Andrew S; Patil, Sayali; Soni, Sarvesh title: Chapter 1 Introduction into nanotechnology and microbiology date: 2019-12-31 journal: Methods in Microbiology DOI: 10.1016/bs.mim.2019.04.003 sha: doc_id: 333228 cord_uid: ejkgune0 file: cache/cord-333853-p2kbjwpy.json key: cord-333853-p2kbjwpy authors: Smee, Donald F.; Wong, Min-Hui; Russell, Andrew; Ennis, Jane; Turner, Jeffrey D. title: Therapy and Long-Term Prophylaxis of Vaccinia Virus Respiratory Infections in Mice with an Adenovirus-Vectored Interferon Alpha (mDEF201) date: 2011-10-13 journal: PLoS One DOI: 10.1371/journal.pone.0026330 sha: doc_id: 333853 cord_uid: p2kbjwpy file: cache/cord-330852-n7j0c4ne.json key: cord-330852-n7j0c4ne authors: Fischer, Wolfgang B.; Wang, Yi-Ting; Schindler, Christina; Chen, Chin-Pei title: Mechanism of Function of Viral Channel Proteins and Implications for Drug Development date: 2012-02-23 journal: Int Rev Cell Mol Biol DOI: 10.1016/b978-0-12-394305-7.00006-9 sha: doc_id: 330852 cord_uid: n7j0c4ne file: cache/cord-333351-homxj9uz.json key: cord-333351-homxj9uz authors: Rodhain, F. title: Bats and Viruses: complex relationships date: 2015-10-10 journal: Bull Soc Pathol Exot DOI: 10.1007/s13149-015-0448-z sha: doc_id: 333351 cord_uid: homxj9uz file: cache/cord-334010-gxu0refq.json key: cord-334010-gxu0refq authors: Banerjee, Nilotpal; Mukhopadhyay, Sumi title: Viral glycoproteins: biological role and application in diagnosis date: 2016-01-18 journal: VirusDisease DOI: 10.1007/s13337-015-0293-5 sha: doc_id: 334010 cord_uid: gxu0refq file: cache/cord-334947-pa0p5dif.json key: cord-334947-pa0p5dif authors: Rozen-Gagnon, Kathryn; Stapleford, Kenneth A.; Mongelli, Vanesa; Blanc, Hervé; Failloux, Anna-Bella; Saleh, Maria-Carla; Vignuzzi, Marco title: Alphavirus Mutator Variants Present Host-Specific Defects and Attenuation in Mammalian and Insect Models date: 2014-01-16 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1003877 sha: doc_id: 334947 cord_uid: pa0p5dif file: cache/cord-334027-xhfmio7k.json key: cord-334027-xhfmio7k authors: Fagre, Anna C.; Kading, Rebekah C. title: Can Bats Serve as Reservoirs for Arboviruses? date: 2019-03-03 journal: Viruses DOI: 10.3390/v11030215 sha: doc_id: 334027 cord_uid: xhfmio7k file: cache/cord-334941-6uattdti.json key: cord-334941-6uattdti authors: Espmark, Åke; Grandien, Monica title: Other viruses date: 2014-06-27 journal: Textbook of Medical Virology DOI: 10.1016/b978-0-407-00253-1.50038-4 sha: doc_id: 334941 cord_uid: 6uattdti file: cache/cord-334560-1j9zmuub.json key: cord-334560-1j9zmuub authors: Hunt, Catherine L.; Lennemann, Nicholas J.; Maury, Wendy title: Filovirus Entry: A Novelty in the Viral Fusion World date: 2012-02-07 journal: Viruses DOI: 10.3390/v4020258 sha: doc_id: 334560 cord_uid: 1j9zmuub file: cache/cord-333655-lylt7qld.json key: cord-333655-lylt7qld authors: Van Breedam, Wander; Pöhlmann, Stefan; Favoreel, Herman W.; de Groot, Raoul J.; Nauwynck, Hans J. title: Bitter‐sweet symphony: glycan–lectin interactions in virus biology date: 2013-12-06 journal: FEMS Microbiol Rev DOI: 10.1111/1574-6976.12052 sha: doc_id: 333655 cord_uid: lylt7qld file: cache/cord-334082-fyxn0g3v.json key: cord-334082-fyxn0g3v authors: O’Carroll, I.P.; Rein, A. title: Viral Nucleic Acids date: 2015-08-20 journal: Encyclopedia of Cell Biology DOI: 10.1016/b978-0-12-394447-4.10061-6 sha: doc_id: 334082 cord_uid: fyxn0g3v file: cache/cord-334771-uy3s6443.json key: cord-334771-uy3s6443 authors: Rao, BL; Basu, Atanu; Wairagkar, Niteen S; Gore, Milind M; Arankalle, Vidya A; Thakare, Jyotsna P; Jadi, Ramesh S; Rao, KA; Mishra, AC title: A large outbreak of acute encephalitis with high fatality rate in children in Andhra Pradesh, India, in 2003, associated with Chandipura virus date: 2004-09-09 journal: Lancet DOI: 10.1016/s0140-6736(04)16982-1 sha: doc_id: 334771 cord_uid: uy3s6443 file: cache/cord-333810-57d4oopv.json key: cord-333810-57d4oopv authors: Leroy, Éric Maurice title: L’Émergence du virus EBOLA chez l’homme: un long processus pas totalement élucidé date: 2015-05-31 journal: Bulletin de l'Académie Nationale de Médecine DOI: 10.1016/s0001-4079(19)30940-9 sha: doc_id: 333810 cord_uid: 57d4oopv file: cache/cord-335116-c83xyev5.json key: cord-335116-c83xyev5 authors: Proença-Módena, José Luiz; Buzatto, Guilherme P.; Paula, Flávia E.; Saturno, Tamara H.; Delcaro, Luana S.; Prates, Mirela C.; Tamashiro, Edwin; Valera, Fabiana C.P.; Arruda, Eurico; Anselmo-Lima, Wilma T. title: Respiratory viruses are continuously detected in children with chronic tonsillitis throughout the year date: 2014-07-21 journal: Int J Pediatr Otorhinolaryngol DOI: 10.1016/j.ijporl.2014.07.015 sha: doc_id: 335116 cord_uid: c83xyev5 file: cache/cord-336212-ueh4q408.json key: cord-336212-ueh4q408 authors: Koenig, Kristi L.; Almadhyan, Abdulmajeed; Burns, Michael J. title: Identify-Isolate-Inform: A Tool for Initial Detection and Management of Zika Virus Patients in the Emergency Department date: 2016-04-04 journal: West J Emerg Med DOI: 10.5811/westjem.2016.3.30188 sha: doc_id: 336212 cord_uid: ueh4q408 file: cache/cord-333463-u7je0d1o.json key: cord-333463-u7je0d1o authors: Diaz-Salazar, Carlos; Sun, Joseph C title: Natural killer cell responses to emerging viruses of zoonotic origin date: 2020-08-09 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2020.07.003 sha: doc_id: 333463 cord_uid: u7je0d1o file: cache/cord-333262-xvfl7ycj.json key: cord-333262-xvfl7ycj authors: Robson, B. title: COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles’ heel conserved region to minimize probability of escape mutations and drug resistance date: 2020-04-11 journal: Comput Biol Med DOI: 10.1016/j.compbiomed.2020.103749 sha: doc_id: 333262 cord_uid: xvfl7ycj file: cache/cord-336157-aqc9zrrm.json key: cord-336157-aqc9zrrm authors: Liang, Guodong; Gao, Xiaoyan; Gould, Ernest A title: Factors responsible for the emergence of arboviruses; strategies, challenges and limitations for their control date: 2015-03-25 journal: Emerg Microbes Infect DOI: 10.1038/emi.2015.18 sha: doc_id: 336157 cord_uid: aqc9zrrm file: cache/cord-334365-idjvbcy4.json key: cord-334365-idjvbcy4 authors: Gooding, J. Justin; Ligler, Frances S. title: Virus Detection: What Were We Doing before COVID-19 Changed the World? date: 2020-05-29 journal: ACS Sens DOI: 10.1021/acssensors.0c01029 sha: doc_id: 334365 cord_uid: idjvbcy4 file: cache/cord-335948-qkfxfmxb.json key: cord-335948-qkfxfmxb authors: Ampofo, William K.; Baylor, Norman; Cobey, Sarah; Cox, Nancy J.; Daves, Sharon; Edwards, Steven; Ferguson, Neil; Grohmann, Gary; Hay, Alan; Katz, Jacqueline; Kullabutr, Kornnika; Lambert, Linda; Levandowski, Roland; Mishra, A. C.; Monto, Arnold; Siqueira, Marilda; Tashiro, Masato; Waddell, Anthony L.; Wairagkar, Niteen; Wood, John; Zambon, Maria; Zhang, Wenqing title: Improving influenza vaccine virus selectionReport of a WHO informal consultation held at WHO headquarters, Geneva, Switzerland, 14–16 June 2010 date: 2011-08-08 journal: Influenza Other Respir Viruses DOI: 10.1111/j.1750-2659.2011.00277.x sha: doc_id: 335948 cord_uid: qkfxfmxb file: cache/cord-335774-15fhg8o9.json key: cord-335774-15fhg8o9 authors: Mull, Nathaniel; Jackson, Reilly; Sironen, Tarja; Forbes, Kristian M. title: Ecology of Neglected Rodent-Borne American Orthohantaviruses date: 2020-04-26 journal: Pathogens DOI: 10.3390/pathogens9050325 sha: doc_id: 335774 cord_uid: 15fhg8o9 file: cache/cord-336045-8qcj5uiy.json key: cord-336045-8qcj5uiy authors: Langlois, Isabelle title: Viral diseases of ferrets date: 2005-03-01 journal: Vet Clin North Am Exot Anim Pract DOI: 10.1016/j.cvex.2004.09.008 sha: doc_id: 336045 cord_uid: 8qcj5uiy file: cache/cord-331714-2qj2rrgd.json key: cord-331714-2qj2rrgd authors: Lvov, Dimitry Konstantinovich; Shchelkanov, Mikhail Yurievich; Alkhovsky, Sergey Vladimirovich; Deryabin, Petr Grigorievich title: Single-Stranded RNA Viruses date: 2015-05-29 journal: Zoonotic Viruses in Northern Eurasia DOI: 10.1016/b978-0-12-801742-5.00008-8 sha: doc_id: 331714 cord_uid: 2qj2rrgd file: cache/cord-335279-cfv18qn0.json key: cord-335279-cfv18qn0 authors: Paillot, Romain title: Special Issue “Equine Viruses”: Old “Friends” and New Foes? date: 2020-01-29 journal: Viruses DOI: 10.3390/v12020153 sha: doc_id: 335279 cord_uid: cfv18qn0 file: cache/cord-334108-4ey725dv.json key: cord-334108-4ey725dv authors: Seymour, I.J.; Appleton, H. title: Foodborne viruses and fresh produce date: 2008-07-07 journal: J Appl Microbiol DOI: 10.1046/j.1365-2672.2001.01427.x sha: doc_id: 334108 cord_uid: 4ey725dv file: cache/cord-336447-hpnkou41.json key: cord-336447-hpnkou41 authors: Pitlik, Silvio Daniel title: COVID-19 Compared to Other Pandemic Diseases date: 2020-07-31 journal: Rambam Maimonides Med J DOI: 10.5041/rmmj.10418 sha: doc_id: 336447 cord_uid: hpnkou41 file: cache/cord-336493-ggo9wsrm.json key: cord-336493-ggo9wsrm authors: Huang, Stephen S. H.; Lin, Zhen; Banner, David; León, Alberto J.; Paquette, Stéphane G.; Rubin, Barry; Rubino, Salvatore; Guan, Yi; Kelvin, David J.; Kelvin, Alyson A. title: Immunity toward H1N1 influenza hemagglutinin of historical and contemporary strains suggests protection and vaccine failure date: 2013-04-23 journal: Sci Rep DOI: 10.1038/srep01698 sha: doc_id: 336493 cord_uid: ggo9wsrm file: cache/cord-337149-cjon7ihb.json key: cord-337149-cjon7ihb authors: Van Vliet, Kim M.; Blouin, Veronique; Brument, Nicole; Agbandje-McKenna, Mavis; Snyder, Richard O. title: The Role of the Adeno-Associated Virus Capsid in Gene Transfer date: 2008 journal: Drug Delivery Systems DOI: 10.1007/978-1-59745-210-6_2 sha: doc_id: 337149 cord_uid: cjon7ihb file: cache/cord-336929-2rnkotqy.json key: cord-336929-2rnkotqy authors: Vieira, Flávia Sarmento; Corrêa, Gladys; Einicker‐Lamas, Marcelo; Coutinho‐Silva, Robson title: Host‐cell lipid rafts: a safe door for micro‐organisms? date: 2012-01-03 journal: Biol Cell DOI: 10.1042/bc20090138 sha: doc_id: 336929 cord_uid: 2rnkotqy file: cache/cord-336554-n8n5ii5k.json key: cord-336554-n8n5ii5k authors: Singh, Thakur Uttam; Parida, Subhashree; Lingaraju, Madhu Cholenahalli; Kesavan, Manickam; Kumar, Dinesh; Singh, Raj Kumar title: Drug repurposing approach to fight COVID-19 date: 2020-09-05 journal: Pharmacol Rep DOI: 10.1007/s43440-020-00155-6 sha: doc_id: 336554 cord_uid: n8n5ii5k file: cache/cord-337285-t6qr41wc.json key: cord-337285-t6qr41wc authors: Ikeda, Masanori; Kato, Nobuyuki title: Modulation of host metabolism as a target of new antivirals() date: 2007-10-10 journal: Adv Drug Deliv Rev DOI: 10.1016/j.addr.2007.03.021 sha: doc_id: 337285 cord_uid: t6qr41wc file: cache/cord-336225-ijodhrwf.json key: cord-336225-ijodhrwf authors: Chang, Mee Soo; Woo, Jun Hee title: Severe Fever with Thrombocytopenia Syndrome: Tick-Mediated Viral Disease date: 2013-06-03 journal: J Korean Med Sci DOI: 10.3346/jkms.2013.28.6.795 sha: doc_id: 336225 cord_uid: ijodhrwf file: cache/cord-337361-salby0fu.json key: cord-337361-salby0fu authors: Bujarski, Jozef J. title: Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives date: 2013-03-26 journal: Front Plant Sci DOI: 10.3389/fpls.2013.00068 sha: doc_id: 337361 cord_uid: salby0fu file: cache/cord-337673-1nau263l.json key: cord-337673-1nau263l authors: Wu, Chang-Jer; Chan, Yi-Lin title: Antiviral applications of RNAi for coronavirus date: 2006-01-24 journal: Expert Opin Investig Drugs DOI: 10.1517/13543784.15.2.89 sha: doc_id: 337673 cord_uid: 1nau263l file: cache/cord-337914-1hwnxkdd.json key: cord-337914-1hwnxkdd authors: Ehlkes, L.; Kreuels, B.; Schwarz, N.G.; May, Jürgen title: Epidemiologie des Ebolafiebers und anderer, in Deutschland seltener hochkontagiöser, lebensbedrohlicher Erkrankungen date: 2015-05-22 journal: Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz DOI: 10.1007/s00103-015-2165-y sha: doc_id: 337914 cord_uid: 1hwnxkdd file: cache/cord-336948-8yqdhcnz.json key: cord-336948-8yqdhcnz authors: Löhner, Rainald; Antil, Harbir; Idelsohn, Sergio; Oñate, Eugenio title: Detailed simulation of viral propagation in the built environment date: 2020-08-05 journal: Comput Mech DOI: 10.1007/s00466-020-01881-7 sha: doc_id: 336948 cord_uid: 8yqdhcnz file: cache/cord-337577-dqikrmk7.json key: cord-337577-dqikrmk7 authors: Greenberg, Harry B.; Dormitzer, Philip R. title: Vaccination against Viruses date: 2016-05-09 journal: Encyclopedia of Immunobiology DOI: 10.1016/b978-0-12-374279-7.14016-0 sha: doc_id: 337577 cord_uid: dqikrmk7 file: cache/cord-338400-30vl2hks.json key: cord-338400-30vl2hks authors: Epstein, Jonathan H.; Quan, Phenix-Lan; Briese, Thomas; Street, Craig; Jabado, Omar; Conlan, Sean; Ali Khan, Shahneaz; Verdugo, Dawn; Hossain, M. Jahangir; Hutchison, Stephen K.; Egholm, Michael; Luby, Stephen P.; Daszak, Peter; Lipkin, W. Ian title: Identification of GBV-D, a Novel GB-like Flavivirus from Old World Frugivorous Bats (Pteropus giganteus) in Bangladesh date: 2010-07-01 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1000972 sha: doc_id: 338400 cord_uid: 30vl2hks file: cache/cord-335647-dhcxj7cj.json key: cord-335647-dhcxj7cj authors: Vanderlinden, Evelien; Naesens, Lieve title: Emerging Antiviral Strategies to Interfere with Influenza Virus Entry date: 2013-06-25 journal: Med Res Rev DOI: 10.1002/med.21289 sha: doc_id: 335647 cord_uid: dhcxj7cj file: cache/cord-338083-77re4l0w.json key: cord-338083-77re4l0w authors: Bolin, Steven R.; Grooms, Daniel L. title: Origination and consequences of bovine viral diarrhea virus diversity date: 2005-03-04 journal: Vet Clin North Am Food Anim Pract DOI: 10.1016/j.cvfa.2003.11.009 sha: doc_id: 338083 cord_uid: 77re4l0w file: cache/cord-336510-qzm9wgde.json key: cord-336510-qzm9wgde authors: Ellermann-Eriksen, Svend title: Macrophages and cytokines in the early defence against herpes simplex virus date: 2005-08-03 journal: Virol J DOI: 10.1186/1743-422x-2-59 sha: doc_id: 336510 cord_uid: qzm9wgde file: cache/cord-337659-x4oywbrj.json key: cord-337659-x4oywbrj authors: Wilson, Brenda A. title: Global biosecurity in a complex, dynamic world date: 2008-07-31 journal: Complexity DOI: 10.1002/cplx.20246 sha: doc_id: 337659 cord_uid: x4oywbrj file: cache/cord-338081-ggw5l1qm.json key: cord-338081-ggw5l1qm authors: Gorbalenya, Alexander E.; Lauber, C. title: Phylogeny of Viruses date: 2017-06-26 journal: Reference Module in Biomedical Sciences DOI: 10.1016/b978-0-12-801238-3.95723-4 sha: doc_id: 338081 cord_uid: ggw5l1qm file: cache/cord-338727-1kodz527.json key: cord-338727-1kodz527 authors: Ilinskaya, O. N.; Mahmud, R. Shah title: Ribonucleases as antiviral agents date: 2014-10-11 journal: Mol Biol DOI: 10.1134/s0026893314040050 sha: doc_id: 338727 cord_uid: 1kodz527 file: cache/cord-338804-nreqluol.json key: cord-338804-nreqluol authors: Heise, M.T. title: Viral Pathogenesis date: 2014-11-28 journal: Reference Module in Biomedical Sciences DOI: 10.1016/b978-0-12-801238-3.00079-9 sha: doc_id: 338804 cord_uid: nreqluol file: cache/cord-339209-oe8onyr9.json key: cord-339209-oe8onyr9 authors: Vasilakis, Nikos; Guzman, Hilda; Firth, Cadhla; Forrester, Naomi L; Widen, Steven G; Wood, Thomas G; Rossi, Shannan L; Ghedin, Elodie; Popov, Vsevolov; Blasdell, Kim R; Walker, Peter J; Tesh, Robert B title: Mesoniviruses are mosquito-specific viruses with extensive geographic distribution and host range date: 2014-05-20 journal: Virol J DOI: 10.1186/1743-422x-11-97 sha: doc_id: 339209 cord_uid: oe8onyr9 file: cache/cord-339172-210dwhgj.json key: cord-339172-210dwhgj authors: Knoops, Kèvin; Kikkert, Marjolein; van den Worm, Sjoerd H. E.; Zevenhoven-Dobbe, Jessika C; van der Meer, Yvonne; Koster, Abraham J; Mommaas, A. Mieke; Snijder, Eric J title: SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum date: 2008-09-16 journal: PLoS Biol DOI: 10.1371/journal.pbio.0060226 sha: doc_id: 339172 cord_uid: 210dwhgj file: cache/cord-339062-tq0f6d01.json key: cord-339062-tq0f6d01 authors: Weaver, Scott C.; Barrett, Alan D. T. title: Transmission cycles, host range, evolution and emergence of arboviral disease date: 2004 journal: Nat Rev Microbiol DOI: 10.1038/nrmicro1006 sha: doc_id: 339062 cord_uid: tq0f6d01 file: cache/cord-339854-scb7pz87.json key: cord-339854-scb7pz87 authors: Overend, Christopher; Yuan, Lijuan; Peccoud, Jean title: The synthetic futures of vesicular stomatitis virus date: 2012-07-11 journal: Trends Biotechnol DOI: 10.1016/j.tibtech.2012.06.002 sha: doc_id: 339854 cord_uid: scb7pz87 file: cache/cord-339744-xrit0w5i.json key: cord-339744-xrit0w5i authors: Feng, Bo; Zhao, Lihong; Wang, Wei; Wang, Jianfang; Wang, Hongyan; Duan, Huiqin; Zhang, Jianjun; Qiao, Jian title: Investigation of antiviral state mediated by interferon-inducible transmembrane protein 1 induced by H9N2 virus and inactivated viral particle in human endothelial cells date: 2017-11-03 journal: Virol J DOI: 10.1186/s12985-017-0875-5 sha: doc_id: 339744 cord_uid: xrit0w5i file: cache/cord-339885-mpzgrogd.json key: cord-339885-mpzgrogd authors: Zhan, Yangqing; Yang, Zifeng; Chen, Rongchang; Wang, Yutao; Guan, Wenda; Zhao, Suishan title: Respiratory virus is a real pathogen in immunocompetent community-acquired pneumonia: comparing to influenza like illness and volunteer controls date: 2014-09-02 journal: BMC Pulm Med DOI: 10.1186/1471-2466-14-144 sha: doc_id: 339885 cord_uid: mpzgrogd file: cache/cord-340907-j9i1wlak.json key: cord-340907-j9i1wlak authors: Zarai, Yoram; Zafrir, Zohar; Siridechadilok, Bunpote; Suphatrakul, Amporn; Roopin, Modi; Julander, Justin; Tuller, Tamir title: Evolutionary selection against short nucleotide sequences in viruses and their related hosts date: 2020-04-27 journal: DNA Res DOI: 10.1093/dnares/dsaa008 sha: doc_id: 340907 cord_uid: j9i1wlak file: cache/cord-339423-5qym9dsf.json key: cord-339423-5qym9dsf authors: Lina, B. title: Virus émergents ou menaces à répétition date: 2005-05-31 journal: Antibiotiques DOI: 10.1016/s1294-5501(05)80175-x sha: doc_id: 339423 cord_uid: 5qym9dsf file: cache/cord-337712-ylqgraos.json key: cord-337712-ylqgraos authors: Heinz, Franz X.; Stiasny, Karin title: Profile of SARS-CoV-2 date: 2020-10-30 journal: Wien Klin Wochenschr DOI: 10.1007/s00508-020-01763-1 sha: doc_id: 337712 cord_uid: ylqgraos file: cache/cord-339382-ii4xurmr.json key: cord-339382-ii4xurmr authors: Bachofen, Claudia title: Selected Viruses Detected on and in our Food date: 2018-03-21 journal: Curr Clin Microbiol Rep DOI: 10.1007/s40588-018-0087-9 sha: doc_id: 339382 cord_uid: ii4xurmr file: cache/cord-340481-i3qrxnpr.json key: cord-340481-i3qrxnpr authors: Pozo, Francisco; Casas, Inmaculada; Ruiz, Guillermo; Falcón, Ana; Pérez-Breña, Pilar title: Aplicación de los métodos moleculares al diagnóstico y el estudio epidemiológico de las infecciones respiratorias causadas por virus date: 2008-07-31 journal: Enfermedades Infecciosas y Microbiología Clínica DOI: 10.1016/s0213-005x(08)76537-6 sha: doc_id: 340481 cord_uid: i3qrxnpr file: cache/cord-341050-hnuogpqn.json key: cord-341050-hnuogpqn authors: Acharya, Dhiraj; Bai, Fengwei title: An Overview of Current Approaches Toward the Treatment and Prevention of West Nile Virus Infection date: 2016-05-18 journal: West Nile Virus DOI: 10.1007/978-1-4939-3670-0_19 sha: doc_id: 341050 cord_uid: hnuogpqn file: cache/cord-338331-27ic5zen.json key: cord-338331-27ic5zen authors: Boulagnon, Camille; Leveque, Nicolas; Renois, Fanny; Andreoletti, Laurent; Fornes, Paul title: Influenza A/H1N1 (2009) Infection as a Cause of Unexpected Out‐of‐Hospital Death in the Young date: 2012-05-14 journal: J Forensic Sci DOI: 10.1111/j.1556-4029.2012.02180.x sha: doc_id: 338331 cord_uid: 27ic5zen file: cache/cord-339230-cc7gcy5b.json key: cord-339230-cc7gcy5b authors: Smith, Amber M.; McCullers, Jonathan A. title: Secondary Bacterial Infections in Influenza Virus Infection Pathogenesis date: 2014-07-16 journal: Influenza Pathogenesis and Control - Volume I DOI: 10.1007/82_2014_394 sha: doc_id: 339230 cord_uid: cc7gcy5b file: cache/cord-339386-sxyeuiw1.json key: cord-339386-sxyeuiw1 authors: McIntosh, Kenneth; Perlman, Stanley title: 157 Coronaviruses, Including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) date: 2015-12-31 journal: Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases DOI: 10.1016/b978-1-4557-4801-3.00157-0 sha: doc_id: 339386 cord_uid: sxyeuiw1 file: cache/cord-340537-pdvpmydk.json key: cord-340537-pdvpmydk authors: Bañon-Gonzalez, Rafael; Carnicero-Caceres, Silvia; Suarez-Mier, M. Paz; Diaz, Francisco J. title: Autopsies of suspected SARS-CoV-2 cases date: 2020-07-15 journal: nan DOI: 10.1016/j.remle.2020.05.002 sha: doc_id: 340537 cord_uid: pdvpmydk file: cache/cord-340503-zwdewiu1.json key: cord-340503-zwdewiu1 authors: Mokhtarzadeh, Ahad; Eivazzadeh-Keihan, Reza; Pashazadeh, Paria; Hejazi, Maryam; Gharaatifar, Nasrin; Hasanzadeh, Mohammad; Baradaran, Behzad; de la Guardia, Miguel title: Nanomaterial-based biosensors for detection of pathogenic virus date: 2017-10-13 journal: Trends Analyt Chem DOI: 10.1016/j.trac.2017.10.005 sha: doc_id: 340503 cord_uid: zwdewiu1 file: cache/cord-340423-f8ab7413.json key: cord-340423-f8ab7413 authors: Barr, J.N.; Fearns, R. title: Genetic Instability of RNA Viruses date: 2016-09-09 journal: Genome Stability DOI: 10.1016/b978-0-12-803309-8.00002-1 sha: doc_id: 340423 cord_uid: f8ab7413 file: cache/cord-340610-ex2yjyum.json key: cord-340610-ex2yjyum authors: Wang, De-Yun; Li, Yingying; Yan, Yan; Li, Chunwei; Shi, Li title: Upper Airway Stem Cells: Understanding the Nose and Role for Future Cell Therapy date: 2014-11-28 journal: Curr Allergy Asthma Rep DOI: 10.1007/s11882-014-0490-0 sha: doc_id: 340610 cord_uid: ex2yjyum file: cache/cord-341303-1iayp8oa.json key: cord-341303-1iayp8oa authors: McINTOSH, KENNETH title: Immunofluorescence in Diagnostic Virology date: 2006-12-16 journal: Ann N Y Acad Sci DOI: 10.1111/j.1749-6632.1983.tb22226.x sha: doc_id: 341303 cord_uid: 1iayp8oa file: cache/cord-339973-kj56zi59.json key: cord-339973-kj56zi59 authors: Coleman, Kristen K.; Nguyen, Tham T.; Yadana, Su; Hansen-Estruch, Christophe; Lindsley, William G.; Gray, Gregory C. title: Bioaerosol Sampling for Respiratory Viruses in Singapore’s Mass Rapid Transit Network date: 2018-11-30 journal: Sci Rep DOI: 10.1038/s41598-018-35896-1 sha: doc_id: 339973 cord_uid: kj56zi59 file: cache/cord-339152-wfakzb6w.json key: cord-339152-wfakzb6w authors: Trovato, Maria; Sartorius, Rossella; D’Apice, Luciana; Manco, Roberta; De Berardinis, Piergiuseppe title: Viral Emerging Diseases: Challenges in Developing Vaccination Strategies date: 2020-09-03 journal: Front Immunol DOI: 10.3389/fimmu.2020.02130 sha: doc_id: 339152 cord_uid: wfakzb6w file: cache/cord-340042-intxyu46.json key: cord-340042-intxyu46 authors: Chaudhry, Sundas Nasir; Hazafa, Abu; Mumtaz, Muhummad; Kalsoom, Ume; Abbas, Saima; Kainaat, Amna; Bilal, Shahid; Zafar, Nauman; Siddique, Aleena; Zafar, Ayesha title: New insight on possible vaccine development against SARS-CoV-2 date: 2020-09-11 journal: Life Sci DOI: 10.1016/j.lfs.2020.118421 sha: doc_id: 340042 cord_uid: intxyu46 file: cache/cord-341923-jwckbdnb.json key: cord-341923-jwckbdnb authors: To, Kelvin Kai-Wang; Li, Iris Wai-Sum; Hung, Ivan Fan-Ngai; Cheng, Vincent Chi-Chung; Yuen, Kwok-Yung title: Pathogenesis of pandemic H1N1 2009 influenza virus infection and the implication on management date: 2010-04-28 journal: Front Med China DOI: 10.1007/s11684-010-0030-9 sha: doc_id: 341923 cord_uid: jwckbdnb file: cache/cord-341298-mqpovrms.json key: cord-341298-mqpovrms authors: Morse, S.A.; Meyer, R.F. title: Viruses and Bioterrorism date: 2016-10-31 journal: Reference Module in Life Sciences DOI: 10.1016/b978-0-12-809633-8.11007-6 sha: doc_id: 341298 cord_uid: mqpovrms file: cache/cord-341138-mxjsp3cm.json key: cord-341138-mxjsp3cm authors: Denner, Joachim title: Transspecies Transmission of Gammaretroviruses and the Origin of the Gibbon Ape Leukaemia Virus (GaLV) and the Koala Retrovirus (KoRV) date: 2016-12-20 journal: Viruses DOI: 10.3390/v8120336 sha: doc_id: 341138 cord_uid: mxjsp3cm file: cache/cord-339288-y8woqsii.json key: cord-339288-y8woqsii authors: Tews, Birke Andrea; Meyers, Gregor title: Self-Replicating RNA date: 2016-06-11 journal: RNA Vaccines DOI: 10.1007/978-1-4939-6481-9_2 sha: doc_id: 339288 cord_uid: y8woqsii file: cache/cord-340331-51yq1rdo.json key: cord-340331-51yq1rdo authors: Tonelli, Michele; Naesens, Lieve; Gazzarrini, Sabrina; Santucci, Matteo; Cichero, Elena; Tasso, Bruno; Moroni, Anna; Costi, Maria Paola; Loddo, Roberta title: Host dihydrofolate reductase (DHFR)-directed cycloguanil analogues endowed with activity against influenza virus and respiratory syncytial virus date: 2017-07-28 journal: Eur J Med Chem DOI: 10.1016/j.ejmech.2017.04.070 sha: doc_id: 340331 cord_uid: 51yq1rdo file: cache/cord-338737-phv12m1q.json key: cord-338737-phv12m1q authors: Amor, A.; Sánchez-Conde, M. title: Infecciones víricas. Clasificación. Infecciones por virus herpes date: 2006-06-30 journal: Medicine - Programa de Formación Médica Continuada Acreditado DOI: 10.1016/s0211-3449(06)74333-8 sha: doc_id: 338737 cord_uid: phv12m1q file: cache/cord-342412-azkamnpa.json key: cord-342412-azkamnpa authors: Ecker, David J; Sampath, Rangarajan; Willett, Paul; Wyatt, Jacqueline R; Samant, Vivek; Massire, Christian; Hall, Thomas A; Hari, Kumar; McNeil, John A; Büchen-Osmond, Cornelia; Budowle, Bruce title: The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents date: 2005-04-25 journal: BMC Microbiol DOI: 10.1186/1471-2180-5-19 sha: doc_id: 342412 cord_uid: azkamnpa file: cache/cord-341155-3d64mso0.json key: cord-341155-3d64mso0 authors: Slots, Jørgen; Slots, Henrik title: Bacterial and viral pathogens in saliva: disease relationship and infectious risk date: 2010-12-07 journal: Periodontol 2000 DOI: 10.1111/j.1600-0757.2010.00361.x sha: doc_id: 341155 cord_uid: 3d64mso0 file: cache/cord-340489-yo3cp5vs.json key: cord-340489-yo3cp5vs authors: nan title: KAPITEL 13 Infektionskrankheiten date: 2008-12-31 journal: Innere Medizin DOI: 10.1016/b978-3-437-42831-9.10013-0 sha: doc_id: 340489 cord_uid: yo3cp5vs file: cache/cord-340629-1fle5fpz.json key: cord-340629-1fle5fpz authors: O’Shea, Helen; Blacklaws, Barbara A.; Collins, Patrick J.; McKillen, John; Fitzgerald, Rose title: Viruses Associated With Foodborne Infections date: 2019-05-21 journal: Reference Module in Life Sciences DOI: 10.1016/b978-0-12-809633-8.90273-5 sha: doc_id: 340629 cord_uid: 1fle5fpz file: cache/cord-342151-1e6x589e.json key: cord-342151-1e6x589e authors: Talbot, Pierre J. title: Hemagglutination by Murine Hepatitis Viruses date: 2008-07-29 journal: Intervirology DOI: 10.1159/000150083 sha: doc_id: 342151 cord_uid: 1e6x589e file: cache/cord-341968-uc8i9h0m.json key: cord-341968-uc8i9h0m authors: Izaguirre, Gonzalo title: The Proteolytic Regulation of Virus Cell Entry by Furin and Other Proprotein Convertases date: 2019-09-09 journal: Viruses DOI: 10.3390/v11090837 sha: doc_id: 341968 cord_uid: uc8i9h0m file: cache/cord-341029-49360l2a.json key: cord-341029-49360l2a authors: Nasir, Arshan; Caetano-Anollés, Gustavo title: A phylogenomic data-driven exploration of viral origins and evolution date: 2015-09-25 journal: Sci Adv DOI: 10.1126/sciadv.1500527 sha: doc_id: 341029 cord_uid: 49360l2a file: cache/cord-340194-ibli36rq.json key: cord-340194-ibli36rq authors: To, Kelvin K.W.; Chan, Jasper F.W.; Tsang, Alan K.L.; Cheng, Vincent C.C.; Yuen, Kwok-Yung title: Ebola virus disease: a highly fatal infectious disease reemerging in West Africa date: 2014-11-29 journal: Microbes Infect DOI: 10.1016/j.micinf.2014.11.007 sha: doc_id: 340194 cord_uid: ibli36rq file: cache/cord-344006-0iq9s94n.json key: cord-344006-0iq9s94n authors: Atzrodt, Cassandra L.; Maknojia, Insha; McCarthy, Robert D.P.; Oldfield, Tiara M.; Po, Jonathan; Ta, Kenny T.L.; Stepp, Hannah E.; Clements, Thomas P. title: A Guide to COVID‐19: a global pandemic caused by the novel coronavirus SARS‐CoV‐2 date: 2020-05-23 journal: FEBS J DOI: 10.1111/febs.15375 sha: doc_id: 344006 cord_uid: 0iq9s94n file: cache/cord-344009-hm36pepp.json key: cord-344009-hm36pepp authors: Nathanson, N. title: Virus perpetuation in populations: biological variables that determine persistence or eradication date: 2005 journal: Infectious Diseases from Nature: Mechanisms of Viral Emergence and Persistence DOI: 10.1007/3-211-29981-5_2 sha: doc_id: 344009 cord_uid: hm36pepp file: cache/cord-342936-43u7afl3.json key: cord-342936-43u7afl3 authors: Balzarini, Jan title: Targeting the glycans of glycoproteins: a novel paradigm for antiviral therapy date: 2007 journal: Nat Rev Microbiol DOI: 10.1038/nrmicro1707 sha: doc_id: 342936 cord_uid: 43u7afl3 file: cache/cord-343690-rafvxgx1.json key: cord-343690-rafvxgx1 authors: Hartmann, Katrin title: Clinical Aspects of Feline Retroviruses: A Review date: 2012-10-31 journal: Viruses DOI: 10.3390/v4112684 sha: doc_id: 343690 cord_uid: rafvxgx1 file: cache/cord-341101-5yvjbr5q.json key: cord-341101-5yvjbr5q authors: Hashem, Anwar M.; Alghamdi, Badrah S.; Algaissi, Abdullah A.; Alshehri, Fahad S.; Bukhari, Abdullah; Alfaleh, Mohamed A.; Memish, Ziad A. title: Therapeutic use of chloroquine and hydroxychloroquine in COVID-19 and other viral infections: A narrative review date: 2020-05-06 journal: Travel Med Infect Dis DOI: 10.1016/j.tmaid.2020.101735 sha: doc_id: 341101 cord_uid: 5yvjbr5q file: cache/cord-342915-r9kv67we.json key: cord-342915-r9kv67we authors: Hayden, Frederick G. title: Advances in antivirals for non‐influenza respiratory virus infections date: 2013-11-01 journal: Influenza and Other Respiratory Viruses DOI: 10.1111/irv.12173 sha: doc_id: 342915 cord_uid: r9kv67we file: cache/cord-342277-v6310fjh.json key: cord-342277-v6310fjh authors: Carducci, A.; Verani, M.; Lombardi, R.; Casini, B.; Privitera, G. title: Environmental survey to assess viral contamination of air and surfaces in hospital settings date: 2011-01-31 journal: J Hosp Infect DOI: 10.1016/j.jhin.2010.10.010 sha: doc_id: 342277 cord_uid: v6310fjh file: cache/cord-344408-4ko557n1.json key: cord-344408-4ko557n1 authors: Cunningham, Andrew A.; Daszak, Peter; Wood, James L. N. title: One Health, emerging infectious diseases and wildlife: two decades of progress? date: 2017-07-19 journal: Philos Trans R Soc Lond B Biol Sci DOI: 10.1098/rstb.2016.0167 sha: doc_id: 344408 cord_uid: 4ko557n1 file: cache/cord-341765-ml6eo8r3.json key: cord-341765-ml6eo8r3 authors: Widhidewi, Ni Wayan; Wiyatno, Ageng; Dewantari, Aghnianditya Kresno; Paramasatiari, Lila; Aryastuti, Sri Agung; Artika, I Nengah; Setiawan, Wayan Doddy; Soebandrio, Amin; Aye Myint, Khin Saw; safari, Dodi title: Identification of viral etiology of acute respiratory tract infections in children and adults in Tabanan, Bali, Indonesia date: 2020-03-25 journal: Access Microbiol DOI: 10.1099/acmi.0.000120 sha: doc_id: 341765 cord_uid: ml6eo8r3 file: cache/cord-345168-3w32v2fm.json key: cord-345168-3w32v2fm authors: To, Kelvin K.W.; Chan, Kwok‐Hung; Li, Iris W.S.; Tsang, Tak‐Yin; Tse, Herman; Chan, Jasper F.W.; Hung, Ivan F.N.; Lai, Sik‐To; Leung, Chi‐Wai; Kwan, Yat‐Wah; Lau, Yu‐Lung; Ng, Tak‐Keung; Cheng, Vincent C.C.; Peiris, Joseph S.M.; Yuen, Kwok‐Yung title: Viral load in patients infected with pandemic H1N1 2009 influenza A virus date: 2009-11-30 journal: J Med Virol DOI: 10.1002/jmv.21664 sha: doc_id: 345168 cord_uid: 3w32v2fm file: cache/cord-343350-04e6wvov.json key: cord-343350-04e6wvov authors: Liu, Haipeng; Söderhäll, Kenneth; Jiravanichpaisal, Pikul title: Antiviral immunity in crustaceans date: 2009-02-15 journal: Fish Shellfish Immunol DOI: 10.1016/j.fsi.2009.02.009 sha: doc_id: 343350 cord_uid: 04e6wvov file: cache/cord-343784-zgvxl4h3.json key: cord-343784-zgvxl4h3 authors: Cho, Chi Hyun; Lee, Chang Kyu; Nam, Myung-Hyun; Yoon, Soo-Young; Lim, Chae Seung; Cho, Yunjung; Kim, Young Kee title: Evaluation of the AdvanSure™ real-time RT-PCR compared with culture and Seeplex RV15 for simultaneous detection of respiratory viruses date: 2014-05-31 journal: Diagnostic Microbiology and Infectious Disease DOI: 10.1016/j.diagmicrobio.2014.01.016 sha: doc_id: 343784 cord_uid: zgvxl4h3 file: cache/cord-342906-51296y8d.json key: cord-342906-51296y8d authors: Li, Zhiping; Li, Jinsong; Zhang, Yandong; Li, Lin; Ma, Limin; Li, Dan; Gao, Feng; Xia, Zhiping title: Aerosolized avian influenza virus by laboratory manipulations date: 2012-08-06 journal: Virol J DOI: 10.1186/1743-422x-9-146 sha: doc_id: 342906 cord_uid: 51296y8d file: cache/cord-345359-okmkgsbr.json key: cord-345359-okmkgsbr authors: Ohno, Marumi; Sekiya, Toshiki; Nomura, Naoki; Daito, Taku ji; Shingai, Masashi; Kida, Hiroshi title: Influenza virus infection affects insulin signaling, fatty acid-metabolizing enzyme expressions, and the tricarboxylic acid cycle in mice date: 2020-07-02 journal: Sci Rep DOI: 10.1038/s41598-020-67879-6 sha: doc_id: 345359 cord_uid: okmkgsbr file: cache/cord-344749-omzhhr0k.json key: cord-344749-omzhhr0k authors: Kaya, Sariye Irem; Karadurmus, Leyla; Ozcelikay, Goksu; Bakirhan, Nurgul K.; Ozkan, Sibel A. title: Electrochemical virus detections with nanobiosensors date: 2020-02-14 journal: Nanosensors for Smart Cities DOI: 10.1016/b978-0-12-819870-4.00017-7 sha: doc_id: 344749 cord_uid: omzhhr0k file: cache/cord-345157-fhmhpobi.json key: cord-345157-fhmhpobi authors: Qi, Dan; Guan, Jitian; Wu, Erxi title: Virus infection-induced host mRNA degradation and potential application of live cell imaging date: 2018-12-12 journal: Radiol Infect Dis DOI: 10.1016/j.jrid.2018.12.002 sha: doc_id: 345157 cord_uid: fhmhpobi 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-341324-f9g9gitn.json key: cord-341324-f9g9gitn authors: Rojas, José M.; Alejo, Alí; Martín, Verónica; Sevilla, Noemí title: Viral pathogen-induced mechanisms to antagonize mammalian interferon (IFN) signaling pathway date: 2020-10-21 journal: Cell Mol Life Sci DOI: 10.1007/s00018-020-03671-z sha: doc_id: 341324 cord_uid: f9g9gitn file: cache/cord-344782-ond1ziu5.json key: cord-344782-ond1ziu5 authors: Zhang, Jing; Finlaison, Deborah S.; Frost, Melinda J.; Gestier, Sarah; Gu, Xingnian; Hall, Jane; Jenkins, Cheryl; Parrish, Kate; Read, Andrew J.; Srivastava, Mukesh; Rose, Karrie; Kirkland, Peter D. title: Identification of a novel nidovirus as a potential cause of large scale mortalities in the endangered Bellinger River snapping turtle (Myuchelys georgesi) date: 2018-10-24 journal: PLoS One DOI: 10.1371/journal.pone.0205209 sha: doc_id: 344782 cord_uid: ond1ziu5 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-343963-99rd3o79.json key: cord-343963-99rd3o79 authors: Wong, Mun-Teng; Chen, Steve S-L title: Emerging roles of interferon-stimulated genes in the innate immune response to hepatitis C virus infection date: 2014-12-29 journal: Cell Mol Immunol DOI: 10.1038/cmi.2014.127 sha: doc_id: 343963 cord_uid: 99rd3o79 file: cache/cord-344576-upsc9cf8.json key: cord-344576-upsc9cf8 authors: Taylor-Robinson, Andrew W title: A vaccine effective against Zika virus is theoretically possible but may not be delivered anytime soon date: 2016-07-05 journal: Res Rep Trop Med DOI: 10.2147/rrtm.s108992 sha: doc_id: 344576 cord_uid: upsc9cf8 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-345020-ai5tib7h.json key: cord-345020-ai5tib7h authors: Price, O. H.; Sullivan, S. G.; Sutterby, C.; Druce, J.; Carville, K. S. title: Using routine testing data to understand circulation patterns of influenza A, respiratory syncytial virus and other respiratory viruses in Victoria, Australia date: 2019-06-17 journal: Epidemiol Infect DOI: 10.1017/s0950268819001055 sha: doc_id: 345020 cord_uid: ai5tib7h file: cache/cord-344093-3bniy5b5.json key: cord-344093-3bniy5b5 authors: Peteranderl, Christin; Herold, Susanne title: The Impact of the Interferon/TNF-Related Apoptosis-Inducing Ligand Signaling Axis on Disease Progression in Respiratory Viral Infection and Beyond date: 2017-03-22 journal: Front Immunol DOI: 10.3389/fimmu.2017.00313 sha: doc_id: 344093 cord_uid: 3bniy5b5 file: cache/cord-343347-guciupc8.json key: cord-343347-guciupc8 authors: Hajj Hussein, Inaya; Chams, Nour; Chams, Sana; El Sayegh, Skye; Badran, Reina; Raad, Mohamad; Gerges-Geagea, Alice; Leone, Angelo; Jurjus, Abdo title: Vaccines Through Centuries: Major Cornerstones of Global Health date: 2015-11-26 journal: Front Public Health DOI: 10.3389/fpubh.2015.00269 sha: doc_id: 343347 cord_uid: guciupc8 file: cache/cord-343918-5yk1j4ms.json key: cord-343918-5yk1j4ms authors: Gorbalenya, A.E. title: Phylogeny of Viruses date: 2008-07-30 journal: Encyclopedia of Virology DOI: 10.1016/b978-012374410-4.00712-3 sha: doc_id: 343918 cord_uid: 5yk1j4ms 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-346836-6jyv0q5e.json key: cord-346836-6jyv0q5e authors: Ikegami, Tetsuro; Makino, Shinji title: The Pathogenesis of Rift Valley Fever date: 2011-05-06 journal: Viruses DOI: 10.3390/v3050493 sha: doc_id: 346836 cord_uid: 6jyv0q5e file: cache/cord-346853-0c1qdjb5.json key: cord-346853-0c1qdjb5 authors: Holmes, E. C.; Drummond, A. J. title: The Evolutionary Genetics of Viral Emergence date: 2007 journal: Wildlife and Emerging Zoonotic Diseases: The Biology, Circumstances and Consequences of Cross-Species Transmission DOI: 10.1007/978-3-540-70962-6_3 sha: doc_id: 346853 cord_uid: 0c1qdjb5 file: cache/cord-346906-1wmp43ti.json key: cord-346906-1wmp43ti authors: Lewandowski, Kuiama; Xu, Yifei; Pullan, Steven T.; Lumley, Sheila F.; Foster, Dona; Sanderson, Nicholas; Vaughan, Alison; Morgan, Marcus; Bright, Nicole; Kavanagh, James; Vipond, Richard; Carroll, Miles; Marriott, Anthony C.; Gooch, Karen E.; Andersson, Monique; Jeffery, Katie; Peto, Timothy E. A.; Crook, Derrick W.; Walker, A. Sarah; Matthews, Philippa C. title: Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples date: 2019-12-23 journal: J Clin Microbiol DOI: 10.1128/jcm.00963-19 sha: doc_id: 346906 cord_uid: 1wmp43ti file: cache/cord-347577-p0a2rboi.json key: cord-347577-p0a2rboi authors: Bibby, Kyle; Fischer, Robert J.; Casson, Leonard W.; Stachler, Elyse; Haas, Charles N.; Munster, Vincent J. title: Persistence of Ebola Virus in Sterilized Wastewater date: 2015-08-17 journal: Environ Sci Technol Lett DOI: 10.1021/acs.estlett.5b00193 sha: doc_id: 347577 cord_uid: p0a2rboi 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-346904-aa88gtzr.json key: cord-346904-aa88gtzr authors: Bao, Y.; Kapustin, Y.; Tatusova, T. title: Virus Classification by Pairwise Sequence Comparison (PASC) date: 2008-07-30 journal: Encyclopedia of Virology DOI: 10.1016/b978-012374410-4.00710-x sha: doc_id: 346904 cord_uid: aa88gtzr file: cache/cord-342124-jdv17u86.json key: cord-342124-jdv17u86 authors: Nieto‐Rabiela, Fabiola; Wiratsudakul, Anuwat; Suzán, Gerardo; Rico‐Chávez, Oscar title: Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis date: 2019-06-20 journal: Zoonoses Public Health DOI: 10.1111/zph.12618 sha: doc_id: 342124 cord_uid: jdv17u86 file: cache/cord-348876-v55piprx.json key: cord-348876-v55piprx authors: Zhao, Guangyu; Lin, Yongping; Du, Lanying; Guan, Jie; Sun, Shihui; Sui, Hongyan; Kou, Zhihua; Chan, Chris CS; Guo, Yan; Jiang, Shibo; Zheng, Bo-Jian; Zhou, Yusen title: An M2e-based multiple antigenic peptide vaccine protects mice from lethal challenge with divergent H5N1 influenza viruses date: 2010-01-18 journal: Virol J DOI: 10.1186/1743-422x-7-9 sha: doc_id: 348876 cord_uid: v55piprx 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-348141-eskefcwk.json key: cord-348141-eskefcwk authors: Herrington, CS; Coates, PJ; Duprex, WP title: Viruses and disease: emerging concepts for prevention, diagnosis and treatment date: 2014-12-11 journal: J Pathol DOI: 10.1002/path.4476 sha: doc_id: 348141 cord_uid: eskefcwk file: cache/cord-348860-zaimorg0.json key: cord-348860-zaimorg0 authors: Ratra, Ruchi; Lal, Sunil K. title: Functional genomics as a tool in virus research date: 2008-06-01 journal: Indian Journal of Microbiology DOI: 10.1007/s12088-008-0032-3 sha: doc_id: 348860 cord_uid: zaimorg0 file: cache/cord-348161-757c51xw.json key: cord-348161-757c51xw authors: Petrosova, A.; Konry, T.; Cosnier, S.; Trakht, I.; Lutwama, J.; Rwaguma, E.; Chepurnov, A.; Mühlberger, E.; Lobel, L.; Marks, R.S. title: Development of a highly sensitive, field operable biosensor for serological studies of Ebola virus in central Africa date: 2007-03-26 journal: Sens Actuators B Chem DOI: 10.1016/j.snb.2006.07.005 sha: doc_id: 348161 cord_uid: 757c51xw file: cache/cord-348427-worgd0xu.json key: cord-348427-worgd0xu authors: Hatcher, Eneida L.; Zhdanov, Sergey A.; Bao, Yiming; Blinkova, Olga; Nawrocki, Eric P.; Ostapchuck, Yuri; Schäffer, Alejandro A.; Brister, J. Rodney title: Virus Variation Resource – improved response to emergent viral outbreaks date: 2017-01-04 journal: Nucleic Acids Res DOI: 10.1093/nar/gkw1065 sha: doc_id: 348427 cord_uid: worgd0xu file: cache/cord-346063-7u1a198p.json key: cord-346063-7u1a198p authors: De Clercq, Erik; Neyts, Johan title: Avian influenza A (H5N1) infection: targets and strategies for chemotherapeutic intervention date: 2007-05-04 journal: Trends Pharmacol Sci DOI: 10.1016/j.tips.2007.04.005 sha: doc_id: 346063 cord_uid: 7u1a198p file: cache/cord-346916-jj4l9ydl.json key: cord-346916-jj4l9ydl authors: Girardi, Erika; Pfeffer, Sebastien; Baumert, Thomas F.; Majzoub, Karim title: Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell date: 2020-08-23 journal: Semin Cell Dev Biol DOI: 10.1016/j.semcdb.2020.08.006 sha: doc_id: 346916 cord_uid: jj4l9ydl file: cache/cord-348163-9q1rt8i7.json key: cord-348163-9q1rt8i7 authors: Hussein, Hosni A. M.; Walker, Lia R.; Abdel-Raouf, Usama M.; Desouky, Sayed A.; Montasser, Abdel Khalek M.; Akula, Shaw M. title: Beyond RGD: virus interactions with integrins date: 2015-09-01 journal: Arch Virol DOI: 10.1007/s00705-015-2579-8 sha: doc_id: 348163 cord_uid: 9q1rt8i7 file: cache/cord-348867-c0xpzd4d.json key: cord-348867-c0xpzd4d authors: Zhai, Jun-Qiong; Zhai, Shao-Lun; Lin, Tao; Liu, Jian-Kui; Wang, He-Xing; Li, Bing; Zhang, He; Zou, Shu-Zhan; Zhou, Xia; Wu, Meng-Fan; Chen, Wu; Luo, Man-Lin title: First complete genome sequence of parainfluenza virus 5 isolated from lesser panda date: 2017-01-30 journal: Arch Virol DOI: 10.1007/s00705-017-3245-0 sha: doc_id: 348867 cord_uid: c0xpzd4d file: cache/cord-349225-504kr50e.json key: cord-349225-504kr50e authors: Alcami, Antonio; Koszinowski, Ulrich H. title: Viral mechanisms of immune evasion date: 2000-09-01 journal: Mol Med Today DOI: 10.1016/s1357-4310(00)01775-5 sha: doc_id: 349225 cord_uid: 504kr50e file: cache/cord-349249-jwvz1ux2.json key: cord-349249-jwvz1ux2 authors: Singh, Gagandeep; Singh, Pankaj; Pillatzki, Angela; Nelson, Eric; Webb, Brett; Dillberger-Lawson, Steven; Ramamoorthy, Sheela title: A Minimally Replicative Vaccine Protects Vaccinated Piglets Against Challenge With the Porcine Epidemic Diarrhea Virus date: 2019-10-22 journal: Front Vet Sci DOI: 10.3389/fvets.2019.00347 sha: doc_id: 349249 cord_uid: jwvz1ux2 file: cache/cord-345654-vyz6f3he.json key: cord-345654-vyz6f3he authors: Dennehy, John J. title: Evolutionary ecology of virus emergence date: 2016-12-30 journal: Ann N Y Acad Sci DOI: 10.1111/nyas.13304 sha: doc_id: 345654 cord_uid: vyz6f3he file: cache/cord-345848-s84lxe6l.json key: cord-345848-s84lxe6l authors: Everitt, Aaron R.; Clare, Simon; Pertel, Thomas; John, Sinu P.; Wash, Rachael S.; Smith, Sarah E.; Chin, Christopher R.; Feeley, Eric M.; Sims, Jennifer S.; Adams, David J.; Wise, Helen M.; Kane, Leanne; Goulding, David A.; Digard, Paul; Anttila, Verneri; Baillie, J. Kenneth; Walsh, Tim S.; Hume, David A.; Palotie, Aarno; Xue, Yali; Colonna, Vincenza; Tyler-Smith, Chris; Dunning, Jake; Gordon, Stephen B.; Smyth, Rosalind L.; Openshaw, Peter; Dougan, Gordon; Brass, Abraham L.; Kellam, Paul title: IFITM3 restricts the morbidity and mortality associated with influenza date: 2012-03-25 journal: Nature DOI: 10.1038/nature10921 sha: doc_id: 345848 cord_uid: s84lxe6l file: cache/cord-345689-5ns1onkw.json key: cord-345689-5ns1onkw authors: Kusters, Inca C.; Matthews, James; Saluzzo, Jean François title: Manufacturing Vaccines for an Emerging Viral Infection–Specific Issues Associated with the Development of a Prototype SARS Vaccine date: 2009-01-30 journal: Vaccines for Biodefense and Emerging and Neglected Diseases DOI: 10.1016/b978-0-12-369408-9.00011-1 sha: doc_id: 345689 cord_uid: 5ns1onkw 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-347727-wka9q98s.json key: cord-347727-wka9q98s authors: Vong, Sirenda; Samuel, Reuben; Gould, Philip; El Sakka, Hammam; Rana, Bardan J; Pinyowiwat, Vason; Bezbaruah, Supriya; Ofrin, Roderico title: Assessment of Ebola virus disease preparedness in the WHO South-East Asia Region date: 2016-12-01 journal: Bull World Health Organ DOI: 10.2471/blt.16.174441 sha: doc_id: 347727 cord_uid: wka9q98s file: cache/cord-344970-ud1lhkyi.json key: cord-344970-ud1lhkyi authors: Fecchi, Katia; Anticoli, Simona; Peruzzu, Daniela; Iessi, Elisabetta; Gagliardi, Maria Cristina; Matarrese, Paola; Ruggieri, Anna title: Coronavirus Interplay With Lipid Rafts and Autophagy Unveils Promising Therapeutic Targets date: 2020-08-11 journal: Front Microbiol DOI: 10.3389/fmicb.2020.01821 sha: doc_id: 344970 cord_uid: ud1lhkyi file: cache/cord-349011-kxhpdvri.json key: cord-349011-kxhpdvri authors: Grandvaux, Nathalie; McCormick, Craig title: CSV2018: The 2nd Symposium of the Canadian Society for Virology date: 2019-01-18 journal: Viruses DOI: 10.3390/v11010079 sha: doc_id: 349011 cord_uid: kxhpdvri file: cache/cord-347039-eap592i7.json key: cord-347039-eap592i7 authors: Lee, Seung-Hwan; Dimock, Ken; Gray, Douglas A; Beauchemin, Nicole; Holmes, Kathryn V.; Belouchi, Majid; Realson, John; Vidal, Silvia M. title: Maneuvering for advantage: the genetics of mouse susceptibility to virus infection date: 2003-08-31 journal: Trends in Genetics DOI: 10.1016/s0168-9525(03)00172-0 sha: doc_id: 347039 cord_uid: eap592i7 file: cache/cord-349358-leicos9j.json key: cord-349358-leicos9j authors: Ketzinel‐Gilad, Mali; Shaul, Yosef; Galun, Eithan title: RNA interference for antiviral therapy date: 2006-06-16 journal: J Gene Med DOI: 10.1002/jgm.929 sha: doc_id: 349358 cord_uid: leicos9j file: cache/cord-350964-0jtfc271.json key: cord-350964-0jtfc271 authors: Van Nguyen, Dung; Van Nguyen, Cuong; Bonsall, David; Ngo, Tue Tri; Carrique-Mas, Juan; Pham, Anh Hong; Bryant, Juliet E.; Thwaites, Guy; Baker, Stephen; Woolhouse, Mark; Simmonds, Peter title: Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam date: 2018-02-28 journal: Viruses DOI: 10.3390/v10030102 sha: doc_id: 350964 cord_uid: 0jtfc271 file: cache/cord-348669-mizygp4j.json key: cord-348669-mizygp4j authors: Beall, Anne; Yount, Boyd; Lin, Chun-Ming; Hou, Yixuan; Wang, Qiuhong; Saif, Linda; Baric, Ralph title: Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A date: 2016-01-05 journal: mBio DOI: 10.1128/mbio.01451-15 sha: doc_id: 348669 cord_uid: mizygp4j file: cache/cord-350467-18bvwxci.json key: cord-350467-18bvwxci authors: Clark, K.J; Sarr, A.B; Grant, P.G; Phillips, T.D; Woode, G.N title: In vitro studies on the use of clay, clay minerals and charcoal to adsorb bovine rotavirus and bovine coronavirus date: 1998-10-01 journal: Vet Microbiol DOI: 10.1016/s0378-1135(98)00241-7 sha: doc_id: 350467 cord_uid: 18bvwxci file: cache/cord-347710-ff64y6ef.json key: cord-347710-ff64y6ef authors: Wan, Qianya; Song, Dan; Li, Huangcan; He, Ming-liang title: Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development date: 2020-07-13 journal: Signal Transduct Target Ther DOI: 10.1038/s41392-020-00233-4 sha: doc_id: 347710 cord_uid: ff64y6ef file: cache/cord-351197-xv6ymc4l.json key: cord-351197-xv6ymc4l authors: Cibulski, Samuel; Alves de Lima, Diane; Fernandes dos Santos, Helton; Teixeira, Thais Fumaco; Tochetto, Caroline; Mayer, Fabiana Quoos; Roehe, Paulo Michel title: A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil date: 2020-09-28 journal: Virology DOI: 10.1016/j.virol.2020.09.005 sha: doc_id: 351197 cord_uid: xv6ymc4l file: cache/cord-351170-belbcrcd.json key: cord-351170-belbcrcd authors: Symonds, Erin M.; Breitbart, Mya title: Affordable Enteric Virus Detection Techniques Are Needed to Support Changing Paradigms in Water Quality Management date: 2014-10-16 journal: Clean (Weinh) DOI: 10.1002/clen.201400235 sha: doc_id: 351170 cord_uid: belbcrcd file: cache/cord-350151-s75d1hat.json key: cord-350151-s75d1hat authors: Wiramus, S.; Martin, C. title: Rianimazione e influenza grave: pandemia influenzale A (H1N1) date: 2013-04-30 journal: EMC - Anestesia-Rianimazione DOI: 10.1016/s1283-0771(13)64502-8 sha: doc_id: 350151 cord_uid: s75d1hat file: cache/cord-350235-yoy3hj3j.json key: cord-350235-yoy3hj3j authors: Sansonetti, Philippe J title: COVID‐19, chronicle of an expected pandemic date: 2020-05-04 journal: EMBO Mol Med DOI: 10.15252/emmm.202012463 sha: doc_id: 350235 cord_uid: yoy3hj3j file: cache/cord-351482-hzh5tyoo.json key: cord-351482-hzh5tyoo authors: Peng, Xinxia; Gralinski, Lisa; Ferris, Martin T.; Frieman, Matthew B.; Thomas, Matthew J.; Proll, Sean; Korth, Marcus J.; Tisoncik, Jennifer R.; Heise, Mark; Luo, Shujun; Schroth, Gary P.; Tumpey, Terrence M.; Li, Chengjun; Kawaoka, Yoshihiro; Baric, Ralph S.; Katze, Michael G. title: Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection date: 2011-11-15 journal: mBio DOI: 10.1128/mbio.00198-11 sha: doc_id: 351482 cord_uid: hzh5tyoo file: cache/cord-350703-vrqltz3s.json key: cord-350703-vrqltz3s authors: nan title: ISAR News date: 2016-01-31 journal: Antiviral Research DOI: 10.1016/s0166-3542(15)00286-7 sha: doc_id: 350703 cord_uid: vrqltz3s file: cache/cord-351377-xorj8tnz.json key: cord-351377-xorj8tnz authors: Kao, Chi-Fei; Chiou, Hue-Ying; Chang, Yen-Chen; Hsueh, Cheng-Shun; Jeng, Chian-Ren; Tsai, Pei-Shiue; Cheng, Ivan-Chen; Pang, Victor Fei; Chang, Hui-Wen title: The Characterization of Immunoprotection Induced by a cDNA Clone Derived from the Attenuated Taiwan Porcine Epidemic Diarrhea Virus Pintung 52 Strain date: 2018-10-04 journal: Viruses DOI: 10.3390/v10100543 sha: doc_id: 351377 cord_uid: xorj8tnz file: cache/cord-350948-oog6m4h3.json key: cord-350948-oog6m4h3 authors: Leclercq, Loïc; Nardello-Rataj, Véronique title: How to improve the chemical disinfection of contaminated surfaces by viruses, bacteria and fungus? date: 2020-09-17 journal: Eur J Pharm Sci DOI: 10.1016/j.ejps.2020.105559 sha: doc_id: 350948 cord_uid: oog6m4h3 file: cache/cord-351571-gwtkrt5u.json key: cord-351571-gwtkrt5u authors: Mackay, Ian M.; Lambert, Stephen B.; Faux, Cassandra E.; Arden, Katherine E.; Nissen, Michael D.; Sloots, Theo P.; Nolan, Terence M. title: Community-Wide, Contemporaneous Circulation of a Broad Spectrum of Human Rhinoviruses in Healthy Australian Preschool-Aged Children During a 12-Month Period date: 2013-05-01 journal: J Infect Dis DOI: 10.1093/infdis/jis476 sha: doc_id: 351571 cord_uid: gwtkrt5u file: cache/cord-352054-g7q2z4l5.json key: cord-352054-g7q2z4l5 authors: Kolivoška, Viliam; Weiss, Victor U.; Kremser, Leopold; Gaš, Bohuslav; Blaas, Dieter; Kenndler, Ernst title: Electrophoresis on a microfluidic chip for analysis of fluorescence‐labeled human rhinovirus date: 2007-11-15 journal: Electrophoresis DOI: 10.1002/elps.200700397 sha: doc_id: 352054 cord_uid: g7q2z4l5 file: cache/cord-352475-cmmpy5u7.json key: cord-352475-cmmpy5u7 authors: Pemmada, Rakesh; Zhu, Xiaoxian; Dash, Madhusmita; Zhou, Yubin; Ramakrishna, Seeram; Peng, Xinsheng; Thomas, Vinoy; Jain, Sanjeev; Nanda, Himansu Sekhar title: Science-Based Strategies of Antiviral Coatings with Viricidal Properties for the COVID-19 Like Pandemics date: 2020-09-11 journal: Materials (Basel) DOI: 10.3390/ma13184041 sha: doc_id: 352475 cord_uid: cmmpy5u7 file: cache/cord-352379-q5inrxcm.json key: cord-352379-q5inrxcm authors: Lai, Michael M. C. title: SARS virus: The beginning of the unraveling of a new coronavirus date: 2003-10-17 journal: J Biomed Sci DOI: 10.1007/bf02256318 sha: doc_id: 352379 cord_uid: q5inrxcm file: cache/cord-350747-5t5xthk6.json key: cord-350747-5t5xthk6 authors: Gmyl, A. P.; Agol, V. I. title: Diverse Mechanisms of RNA Recombination date: 2005 journal: Mol Biol DOI: 10.1007/s11008-005-0069-x sha: doc_id: 350747 cord_uid: 5t5xthk6 file: cache/cord-351365-dc9t3vh3.json key: cord-351365-dc9t3vh3 authors: Todt, Daniel; Walter, Stephanie; Brown, Richard J. P.; Steinmann, Eike title: Mutagenic Effects of Ribavirin on Hepatitis E Virus—Viral Extinction versus Selection of Fitness-Enhancing Mutations date: 2016-10-13 journal: Viruses DOI: 10.3390/v8100283 sha: doc_id: 351365 cord_uid: dc9t3vh3 file: cache/cord-352178-irjhmxsg.json key: cord-352178-irjhmxsg authors: Saxton-Shaw, Kali D.; Ledermann, Jeremy P.; Borland, Erin M.; Stovall, Janae L.; Mossel, Eric C.; Singh, Amber J.; Wilusz, Jeffrey; Powers, Ann M. title: O'nyong nyong Virus Molecular Determinants of Unique Vector Specificity Reside in Non-Structural Protein 3 date: 2013-01-24 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0001931 sha: doc_id: 352178 cord_uid: irjhmxsg file: cache/cord-353290-1wi1dhv6.json key: cord-353290-1wi1dhv6 authors: Kustin, Talia; Stern, Adi title: Biased mutation and selection in RNA viruses date: 2020-09-28 journal: Mol Biol Evol DOI: 10.1093/molbev/msaa247 sha: doc_id: 353290 cord_uid: 1wi1dhv6 file: cache/cord-354536-c9v9kbw8.json key: cord-354536-c9v9kbw8 authors: Han, Yan-Jie; Ren, Zhi-Guang; Li, Xin-Xin; Yan, Ji-Liang; Ma, Chun-Yan; Wu, Dong-Dong; Ji, Xin-Ying title: Advances and challenges in the prevention and treatment of COVID-19 date: 2020-07-09 journal: Int J Med Sci DOI: 10.7150/ijms.47836 sha: doc_id: 354536 cord_uid: c9v9kbw8 file: cache/cord-350925-1h6pbfwp.json key: cord-350925-1h6pbfwp authors: da Silva, Priscilla Gomes; Nascimento, Maria São José; Soares, Ruben R.G.; Sousa, Sofia I.V.; Mesquita, João R. title: Airborne spread of infectious SARS-CoV-2: moving forward using lessons from SARS-CoV and MERS-CoV date: 2020-10-08 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.142802 sha: doc_id: 350925 cord_uid: 1h6pbfwp file: cache/cord-353509-yfkiaq80.json key: cord-353509-yfkiaq80 authors: Nugraha, Rhea Veda; Ridwansyah, Hastono; Ghozali, Mohammad; Khairani, Astrid Feinisa; Atik, Nur title: Traditional Herbal Medicine Candidates as Complementary Treatments for COVID-19: A Review of Their Mechanisms, Pros and Cons date: 2020-10-10 journal: Evid Based Complement Alternat Med DOI: 10.1155/2020/2560645 sha: doc_id: 353509 cord_uid: yfkiaq80 file: cache/cord-353297-jizitnfl.json key: cord-353297-jizitnfl authors: Meyer, R.F.; Morse, S.A. title: Viruses and Bioterrorism date: 2008-07-30 journal: Encyclopedia of Virology DOI: 10.1016/b978-012374410-4.00549-5 sha: doc_id: 353297 cord_uid: jizitnfl file: cache/cord-352619-s2x53grh.json key: cord-352619-s2x53grh authors: Payne, Natalie; Kraberger, Simona; Fontenele, Rafaela S; Schmidlin, Kara; Bergeman, Melissa H; Cassaigne, Ivonne; Culver, Melanie; Varsani, Arvind; Van Doorslaer, Koenraad title: Novel Circoviruses Detected in Feces of Sonoran Felids date: 2020-09-15 journal: Viruses DOI: 10.3390/v12091027 sha: doc_id: 352619 cord_uid: s2x53grh file: cache/cord-352200-i05h8csb.json key: cord-352200-i05h8csb authors: Xu, Yi; Zhou, Wenwu; Zhou, Yijun; Wu, Jianxiang; Zhou, Xueping title: Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus date: 2012-04-27 journal: PLoS One DOI: 10.1371/journal.pone.0036238 sha: doc_id: 352200 cord_uid: i05h8csb file: cache/cord-353609-no3mbg5d.json key: cord-353609-no3mbg5d authors: Vandegrift, Kurt J.; Wale, Nina; Epstein, Jonathan H. title: An Ecological and Conservation Perspective on Advances in the Applied Virology of Zoonoses date: 2011-04-15 journal: Viruses DOI: 10.3390/v3040379 sha: doc_id: 353609 cord_uid: no3mbg5d file: cache/cord-354109-mli0c97c.json key: cord-354109-mli0c97c authors: Faezi, Nasim Asadi; Bialvaei, Abed Zahedi; Leylabadlo, Hamed Ebrahimzadeh; Soleimani, Hossein; Yousefi, Mehdi; Kafil, Hossein Samadi title: Viral infections in patients with acute respiratory infection in Northwest of Iran date: 2017-01-22 journal: Mol DOI: 10.3103/s0891416816030046 sha: doc_id: 354109 cord_uid: mli0c97c file: cache/cord-354035-i3sl2r0k.json key: cord-354035-i3sl2r0k authors: Wylie, Kristine M. title: The Virome of the Human Respiratory Tract date: 2016-12-10 journal: Clin Chest Med DOI: 10.1016/j.ccm.2016.11.001 sha: doc_id: 354035 cord_uid: i3sl2r0k file: cache/cord-355181-affuyn8z.json key: cord-355181-affuyn8z authors: Poggio, Claudio; Colombo, Marco; Arciola, Carla Renata; Greggi, Tiziana; Scribante, Andrea; Dagna, Alberto title: Copper-Alloy Surfaces and Cleaning Regimens against the Spread of SARS-CoV-2 in Dentistry and Orthopedics. From Fomites to Anti-Infective Nanocoatings date: 2020-07-22 journal: Materials (Basel) DOI: 10.3390/ma13153244 sha: doc_id: 355181 cord_uid: affuyn8z file: cache/cord-354151-psog34u3.json key: cord-354151-psog34u3 authors: van Asten, Liselotte; Bijkerk, Paul; Fanoy, Ewout; van Ginkel, Annemarijn; Suijkerbuijk, Anita; van der Hoek, Wim; Meijer, Adam; Vennema, Harry title: Early occurrence of influenza A epidemics coincided with changes in occurrence of other respiratory virus infections date: 2015-12-11 journal: Influenza Other Respir Viruses DOI: 10.1111/irv.12348 sha: doc_id: 354151 cord_uid: psog34u3 file: cache/cord-354848-7aakik9a.json key: cord-354848-7aakik9a authors: Sayres, Lauren; Hughes, Brenna L. title: Contemporary Understanding of Ebola and Zika Virus in Pregnancy date: 2020-10-16 journal: Clin Perinatol DOI: 10.1016/j.clp.2020.08.005 sha: doc_id: 354848 cord_uid: 7aakik9a file: cache/cord-353869-l53ms3q8.json key: cord-353869-l53ms3q8 authors: Friesen, Robert H. E.; Koudstaal, Wouter; Koldijk, Martin H.; Weverling, Gerrit Jan; Brakenhoff, Just P. J.; Lenting, Peter J.; Stittelaar, Koert J.; Osterhaus, Albert D. M. E.; Kompier, Ronald; Goudsmit, Jaap title: New Class of Monoclonal Antibodies against Severe Influenza: Prophylactic and Therapeutic Efficacy in Ferrets date: 2010-02-08 journal: PLoS One DOI: 10.1371/journal.pone.0009106 sha: doc_id: 353869 cord_uid: l53ms3q8 file: cache/cord-355489-tkvfneje.json key: cord-355489-tkvfneje authors: Mendez, Jairo A; Usme-Ciro, Jose A; Domingo, Cristina; Rey, Gloria J; Sanchez, Juan A; Tenorio, Antonio; Gallego-Gomez, Juan C title: Phylogenetic history demonstrates two different lineages of dengue type 1 virus in Colombia date: 2010-09-14 journal: Virol J DOI: 10.1186/1743-422x-7-226 sha: doc_id: 355489 cord_uid: tkvfneje file: cache/cord-355872-z6vsjmxn.json key: cord-355872-z6vsjmxn authors: Colón-López, Daisy D.; Stefan, Christopher P.; Koehler, Jeffrey W. title: Emerging viral infections date: 2019-08-15 journal: Genomic and Precision Medicine DOI: 10.1016/b978-0-12-801496-7.00010-1 sha: doc_id: 355872 cord_uid: z6vsjmxn file: cache/cord-355685-wgad0eoh.json key: cord-355685-wgad0eoh authors: Francesconi, Valeria; Cichero, Elena; Schenone, Silvia; Naesens, Lieve; Tonelli, Michele title: Synthesis and Biological Evaluation of Novel (thio)semicarbazone-Based Benzimidazoles as Antiviral Agents against Human Respiratory Viruses date: 2020-03-25 journal: Molecules DOI: 10.3390/molecules25071487 sha: doc_id: 355685 cord_uid: wgad0eoh file: cache/cord-353190-7qcoxl81.json key: cord-353190-7qcoxl81 authors: Nicklas, Werner; Bleich, André; Mähler, Michael title: Viral Infections of Laboratory Mice date: 2012-05-17 journal: The Laboratory Mouse DOI: 10.1016/b978-0-12-382008-2.00019-2 sha: doc_id: 353190 cord_uid: 7qcoxl81 file: cache/cord-354068-4qlk6y7h.json key: cord-354068-4qlk6y7h authors: Friedrich, Brian M.; Trefry, John C.; Biggins, Julia E.; Hensley, Lisa E.; Honko, Anna N.; Smith, Darci R.; Olinger, Gene G. title: Potential Vaccines and Post-Exposure Treatments for Filovirus Infections date: 2012-09-21 journal: Viruses DOI: 10.3390/v4091619 sha: doc_id: 354068 cord_uid: 4qlk6y7h file: cache/cord-355771-pxkkd3s1.json key: cord-355771-pxkkd3s1 authors: Olagnier, David; Alain, Tommy title: Oncolytic Viral Immunotherapy in the Time of COVID-19 date: 2020-11-04 journal: Cytokine Growth Factor Rev DOI: 10.1016/j.cytogfr.2020.10.009 sha: doc_id: 355771 cord_uid: pxkkd3s1 file: cache/cord-356176-1nwjjgul.json key: cord-356176-1nwjjgul authors: Atherton, J. G.; Kratzing, C. C.; Fisher, Anne title: The effect of ascorbic acid on infection of chick-embryo ciliated tracheal organ cultures by coronavirus date: 1978 journal: Arch Virol DOI: 10.1007/bf01317848 sha: doc_id: 356176 cord_uid: 1nwjjgul file: cache/cord-355259-779czzzx.json key: cord-355259-779czzzx authors: Yang, Xiaoyun; Steukers, Lennert; Forier, Katrien; Xiong, Ranhua; Braeckmans, Kevin; Van Reeth, Kristien; Nauwynck, Hans title: A Beneficiary Role for Neuraminidase in Influenza Virus Penetration through the Respiratory Mucus date: 2014-10-15 journal: PLoS One DOI: 10.1371/journal.pone.0110026 sha: doc_id: 355259 cord_uid: 779czzzx file: cache/cord-355535-01h8yyqj.json key: cord-355535-01h8yyqj authors: Zheng, Xue-yan; Xu, Yan-jun; Guan, Wei-jie; Lin, Li-feng title: Regional, age and respiratory-secretion-specific prevalence of respiratory viruses associated with asthma exacerbation: a literature review date: 2018-01-11 journal: Arch Virol DOI: 10.1007/s00705-017-3700-y sha: doc_id: 355535 cord_uid: 01h8yyqj file: cache/cord-356188-rwf78stz.json key: cord-356188-rwf78stz authors: Oshansky, Christine M.; Thomas, Paul G. title: The human side of influenza date: 2012-07-01 journal: Journal of Leukocyte Biology DOI: 10.1189/jlb.1011506 sha: doc_id: 356188 cord_uid: rwf78stz file: cache/cord-355913-fhvt1ht1.json key: cord-355913-fhvt1ht1 authors: Burrell, Christopher J.; Howard, Colin R.; Murphy, Frederick A. title: Virus Replication date: 2016-11-11 journal: Fenner and White's Medical Virology DOI: 10.1016/b978-0-12-375156-0.00004-7 sha: doc_id: 355913 cord_uid: fhvt1ht1 file: cache/cord-355906-yeaw9nr8.json key: cord-355906-yeaw9nr8 authors: Nedjadi, Taoufik; El-Kafrawy, Sherif; Sohrab, Sayed S.; Desprès, Philippe; Damanhouri, Ghazi; Azhar, Esam title: Tackling dengue fever: Current status and challenges date: 2015-12-09 journal: Virol J DOI: 10.1186/s12985-015-0444-8 sha: doc_id: 355906 cord_uid: yeaw9nr8 file: cache/cord-354582-fniymnmf.json key: cord-354582-fniymnmf authors: Ma, Zhiqian; Li, Zhiwei; Dong, Linfang; Yang, Ting; Xiao, Shuqi title: Reverse genetic systems: Rational design of coronavirus live attenuated vaccines with immune sequelae date: 2020-06-30 journal: Adv Virus Res DOI: 10.1016/bs.aivir.2020.06.003 sha: doc_id: 354582 cord_uid: fniymnmf Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named keyword-virus-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: 30938 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 30816 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 30133 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 28606 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 30463 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 30996 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 31480 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: 30969 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 31094 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 31555 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 30773 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 31268 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. /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 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 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 === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 28718 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 29253 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 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. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 30836 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 92. 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. /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. /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 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. parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /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 90. 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 89. 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 92. 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. /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: 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 parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /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 /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/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: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/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-003232-nquw7qga author: Kuchipudi, Suresh V. title: Novel Flu Viruses in Bats and Cattle: “Pushing the Envelope” of Influenza Infection date: 2018-08-06 pages: extension: .txt txt: ./txt/cord-003232-nquw7qga.txt cache: ./cache/cord-003232-nquw7qga.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-003232-nquw7qga.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 31507 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: 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: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /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/txt2adr.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/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-002072-qbh728ec author: Bi, Yuhai title: A new reassortment of influenza A (H7N9) virus causing human infection in Beijing, 2014 date: 2016-05-27 pages: extension: .txt txt: ./txt/cord-002072-qbh728ec.txt cache: ./cache/cord-002072-qbh728ec.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002072-qbh728ec.txt' /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-004761-cgby8bhz author: Fuchs, N. title: Virus isolation and titration at 33‡ and 37‡ C date: 1975 pages: extension: .txt txt: ./txt/cord-004761-cgby8bhz.txt cache: ./cache/cord-004761-cgby8bhz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004761-cgby8bhz.txt' === file2bib.sh === id: cord-004608-3u00cpsc author: nan title: Arboviren—durch Arthropoden übertragbare Viren: Stellungnahmen des Arbeitskreises Blut des Bundesministeriums für Gesundheit und Soziale Sicherung date: 2004 pages: extension: .txt txt: ./txt/cord-004608-3u00cpsc.txt cache: ./cache/cord-004608-3u00cpsc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004608-3u00cpsc.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-004477-qu2o2iu1 author: Vlasova, Anastasia N. title: Editorial: Porcine Anti-Viral Immunity date: 2020-03-06 pages: extension: .txt txt: ./txt/cord-004477-qu2o2iu1.txt cache: ./cache/cord-004477-qu2o2iu1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-004477-qu2o2iu1.txt' === file2bib.sh === id: cord-002921-i5jxn1vj author: Morens, David M title: Pandemic Zika: A Formidable Challenge to Medicine and Public Health date: 2017-12-15 pages: extension: .txt txt: ./txt/cord-002921-i5jxn1vj.txt cache: ./cache/cord-002921-i5jxn1vj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002921-i5jxn1vj.txt' === file2bib.sh === id: cord-002932-5e7xrd1y author: Watanabe, Tokiko title: Experimental infection of Cynomolgus Macaques with highly pathogenic H5N1 influenza virus through the aerosol route date: 2018-03-19 pages: extension: .txt txt: ./txt/cord-002932-5e7xrd1y.txt cache: ./cache/cord-002932-5e7xrd1y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-002932-5e7xrd1y.txt' === file2bib.sh === id: cord-003926-ycdaw2vh author: Maslow, Joel N. title: Zika Vaccine Development—Current Progress and Challenges for the Future date: 2019-07-14 pages: extension: .txt txt: ./txt/cord-003926-ycdaw2vh.txt cache: ./cache/cord-003926-ycdaw2vh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003926-ycdaw2vh.txt' === file2bib.sh === id: cord-003004-iif2lnez author: Linster, Martin title: Clinical and Molecular Epidemiology of Human Parainfluenza Viruses 1–4 in Children from Viet Nam date: 2018-05-01 pages: extension: .txt txt: ./txt/cord-003004-iif2lnez.txt cache: ./cache/cord-003004-iif2lnez.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003004-iif2lnez.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-002601-d8908t93 author: Arellano-Llamas, Rocío title: Molecular features of influenza A (H1N1)pdm09 prevalent in Mexico during winter seasons 2012-2014 date: 2017-07-10 pages: extension: .txt txt: ./txt/cord-002601-d8908t93.txt cache: ./cache/cord-002601-d8908t93.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002601-d8908t93.txt' === file2bib.sh === id: cord-004751-4vl0cvyq author: Mostow, S. R. title: The behaviour in vitro of attenuated recombinant influenza viruses date: 1973 pages: extension: .txt txt: ./txt/cord-004751-4vl0cvyq.txt cache: ./cache/cord-004751-4vl0cvyq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004751-4vl0cvyq.txt' === file2bib.sh === id: cord-002136-mkl89qkt author: Nunes, Sandro F. title: An ex vivo swine tracheal organ culture for the study of influenza infection date: 2009-12-09 pages: extension: .txt txt: ./txt/cord-002136-mkl89qkt.txt cache: ./cache/cord-002136-mkl89qkt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002136-mkl89qkt.txt' === file2bib.sh === id: cord-001616-9sc2xmqr author: Erdem, Hakan title: New global viral threats date: 2015 pages: extension: .txt txt: ./txt/cord-001616-9sc2xmqr.txt cache: ./cache/cord-001616-9sc2xmqr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001616-9sc2xmqr.txt' === file2bib.sh === id: cord-000708-iuo2cw23 author: Lippé, Roger title: Deciphering Novel Host–Herpesvirus Interactions by Virion Proteomics date: 2012-05-28 pages: extension: .txt txt: ./txt/cord-000708-iuo2cw23.txt cache: ./cache/cord-000708-iuo2cw23.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000708-iuo2cw23.txt' === file2bib.sh === id: cord-002874-9rxv6fy9 author: Welch, David title: Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases date: 2018-02-09 pages: extension: .txt txt: ./txt/cord-002874-9rxv6fy9.txt cache: ./cache/cord-002874-9rxv6fy9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002874-9rxv6fy9.txt' === file2bib.sh === id: cord-002728-6oyw5sqv author: Carding, S. R. title: Review article: the human intestinal virome in health and disease date: 2017-09-04 pages: extension: .txt txt: ./txt/cord-002728-6oyw5sqv.txt cache: ./cache/cord-002728-6oyw5sqv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-002728-6oyw5sqv.txt' === file2bib.sh === id: cord-001120-fxd533b4 author: Everitt, Aaron R. title: Defining the Range of Pathogens Susceptible to Ifitm3 Restriction Using a Knockout Mouse Model date: 2013-11-21 pages: extension: .txt txt: ./txt/cord-001120-fxd533b4.txt cache: ./cache/cord-001120-fxd533b4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001120-fxd533b4.txt' === file2bib.sh === id: cord-001065-j4hvyyoi author: Boncristiani, Humberto F. title: In Vitro Infection of Pupae with Israeli Acute Paralysis Virus Suggests Disturbance of Transcriptional Homeostasis in Honey Bees (Apis mellifera) date: 2013-09-05 pages: extension: .txt txt: ./txt/cord-001065-j4hvyyoi.txt cache: ./cache/cord-001065-j4hvyyoi.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-001065-j4hvyyoi.txt' === file2bib.sh === id: cord-001834-6xf4o3oy author: Sung, Pil Soo title: Interferon Response in Hepatitis C Virus (HCV) Infection: Lessons from Cell Culture Systems of HCV Infection date: 2015-10-07 pages: extension: .txt txt: ./txt/cord-001834-6xf4o3oy.txt cache: ./cache/cord-001834-6xf4o3oy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001834-6xf4o3oy.txt' === file2bib.sh === id: cord-001528-33f94doo author: Fouchier, Ron A. M. title: Studies on Influenza Virus Transmission between Ferrets: the Public Health Risks Revisited date: 2015-01-23 pages: extension: .txt txt: ./txt/cord-001528-33f94doo.txt cache: ./cache/cord-001528-33f94doo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001528-33f94doo.txt' === file2bib.sh === id: cord-001985-iwfidoer author: Urayama, Syun-ichi title: FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance date: 2016-02-13 pages: extension: .txt txt: ./txt/cord-001985-iwfidoer.txt cache: ./cache/cord-001985-iwfidoer.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001985-iwfidoer.txt' === file2bib.sh === id: cord-001142-puj74k7y author: Crescenzo-Chaigne, Bernadette title: The Panhandle Formed by Influenza A and C Virus NS Non-Coding Regions Determines NS Segment Expression date: 2013-11-21 pages: extension: .txt txt: ./txt/cord-001142-puj74k7y.txt cache: ./cache/cord-001142-puj74k7y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001142-puj74k7y.txt' === file2bib.sh === id: cord-000501-qz68gtd4 author: Greatorex, Jane S. title: Survival of Influenza A(H1N1) on Materials Found in Households: Implications for Infection Control date: 2011-11-22 pages: extension: .txt txt: ./txt/cord-000501-qz68gtd4.txt cache: ./cache/cord-000501-qz68gtd4.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-000501-qz68gtd4.txt' === file2bib.sh === id: cord-002274-6rddtogo author: James, Joe title: Influenza A virus PB1-F2 protein prolongs viral shedding in chickens lengthening the transmission window date: 2016-10-13 pages: extension: .txt txt: ./txt/cord-002274-6rddtogo.txt cache: ./cache/cord-002274-6rddtogo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002274-6rddtogo.txt' === file2bib.sh === id: cord-000114-f0vud3gu author: Kim, Jeong‐Ki title: Ducks: The “Trojan Horses” of H5N1 influenza date: 2009-05-31 pages: extension: .txt txt: ./txt/cord-000114-f0vud3gu.txt cache: ./cache/cord-000114-f0vud3gu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000114-f0vud3gu.txt' === file2bib.sh === id: cord-003861-qeao4ghg author: Aris-Brosou, Stéphane title: Viral Long-Term Evolutionary Strategies Favor Stability over Proliferation date: 2019-07-24 pages: extension: .txt txt: ./txt/cord-003861-qeao4ghg.txt cache: ./cache/cord-003861-qeao4ghg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003861-qeao4ghg.txt' === file2bib.sh === id: cord-004774-fvf671jn author: Kjeldsberg, Elisabeth title: Detection of astroviruses in gut contents of nude and normal mice date: 1985 pages: extension: .txt txt: ./txt/cord-004774-fvf671jn.txt cache: ./cache/cord-004774-fvf671jn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-004774-fvf671jn.txt' === file2bib.sh === id: cord-004280-c470nlie author: Coleman, Kristen K. title: Airborne Influenza A Virus Exposure in an Elementary School date: 2020-02-05 pages: extension: .txt txt: ./txt/cord-004280-c470nlie.txt cache: ./cache/cord-004280-c470nlie.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004280-c470nlie.txt' === file2bib.sh === id: cord-002581-r7mskri0 author: Magnani, Diogo M. title: A human inferred germline antibody binds to an immunodominant epitope and neutralizes Zika virus date: 2017-06-12 pages: extension: .txt txt: ./txt/cord-002581-r7mskri0.txt cache: ./cache/cord-002581-r7mskri0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002581-r7mskri0.txt' === file2bib.sh === id: cord-003523-byxuruk1 author: Fritsch, Annemarie title: Influenza C virus in pre-school children with respiratory infections: retrospective analysis of data from the national influenza surveillance system in Germany, 2012 to 2014 date: 2019-03-07 pages: extension: .txt txt: ./txt/cord-003523-byxuruk1.txt cache: ./cache/cord-003523-byxuruk1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003523-byxuruk1.txt' === file2bib.sh === id: cord-003166-k3jxvzfi author: Noh, Ji Yeong title: Isolation and characterization of novel bat paramyxovirus B16-40 potentially belonging to the proposed genus Shaanvirus date: 2018-08-22 pages: extension: .txt txt: ./txt/cord-003166-k3jxvzfi.txt cache: ./cache/cord-003166-k3jxvzfi.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-003166-k3jxvzfi.txt' === file2bib.sh === id: cord-003503-t6cnjwpd author: Sung, Ming-Hua title: Phylogeographic investigation of 2014 porcine epidemic diarrhea virus (PEDV) transmission in Taiwan date: 2019-03-06 pages: extension: .txt txt: ./txt/cord-003503-t6cnjwpd.txt cache: ./cache/cord-003503-t6cnjwpd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003503-t6cnjwpd.txt' === file2bib.sh === id: cord-004781-ajf9zig0 author: Ray, N. B. title: Rabies viruses infect primary cultures of murine, feline, and human microglia and astrocytes date: 2014-03-07 pages: extension: .txt txt: ./txt/cord-004781-ajf9zig0.txt cache: ./cache/cord-004781-ajf9zig0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-004781-ajf9zig0.txt' === file2bib.sh === id: cord-000539-uh3q65we author: Zhang, Yi title: Acute Respiratory Distress Syndrome Induced by a Swine 2009 H1N1 Variant in Mice date: 2012-01-03 pages: extension: .txt txt: ./txt/cord-000539-uh3q65we.txt cache: ./cache/cord-000539-uh3q65we.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000539-uh3q65we.txt' === file2bib.sh === id: cord-002338-ri7v2ka3 author: Anderson, Tavis K. title: A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses date: 2016-12-14 pages: extension: .txt txt: ./txt/cord-002338-ri7v2ka3.txt cache: ./cache/cord-002338-ri7v2ka3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-002338-ri7v2ka3.txt' === file2bib.sh === id: cord-003216-5qioku84 author: Rehman, Zaib Ur. title: Pathobiology of Avian avulavirus 1: special focus on waterfowl date: 2018-09-19 pages: extension: .txt txt: ./txt/cord-003216-5qioku84.txt cache: ./cache/cord-003216-5qioku84.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003216-5qioku84.txt' === file2bib.sh === id: cord-004724-llex3yed author: Dea, S. A. title: Isolation of encephalomyocarditis virus among stillborn and post-weaning pigs in Quebec date: 1991 pages: extension: .txt txt: ./txt/cord-004724-llex3yed.txt cache: ./cache/cord-004724-llex3yed.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-004724-llex3yed.txt' === file2bib.sh === id: cord-000265-llilwq1u author: Gao, Rongbao title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case date: 2010-10-12 pages: extension: .txt txt: ./txt/cord-000265-llilwq1u.txt cache: ./cache/cord-000265-llilwq1u.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-000265-llilwq1u.txt' === file2bib.sh === id: cord-000902-ew8orn0z author: Zhao, Xiangyan title: Coevolution between simple sequence repeats (SSRs) and virus genome size date: 2012-08-30 pages: extension: .txt txt: ./txt/cord-000902-ew8orn0z.txt cache: ./cache/cord-000902-ew8orn0z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000902-ew8orn0z.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-001831-3aonqyub author: Royle, Jamie title: Emerging Roles of Viroporins Encoded by DNA Viruses: Novel Targets for Antivirals? date: 2015-10-16 pages: extension: .txt txt: ./txt/cord-001831-3aonqyub.txt cache: ./cache/cord-001831-3aonqyub.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001831-3aonqyub.txt' === file2bib.sh === id: cord-001748-7e8px4vx author: Nobach, Daniel title: Shedding of Infectious Borna Disease Virus-1 in Living Bicolored White-Toothed Shrews date: 2015-08-27 pages: extension: .txt txt: ./txt/cord-001748-7e8px4vx.txt cache: ./cache/cord-001748-7e8px4vx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001748-7e8px4vx.txt' === file2bib.sh === id: cord-001207-yjaiybwf author: Sachsenröder, Jana title: The General Composition of the Faecal Virome of Pigs Depends on Age, but Not on Feeding with a Probiotic Bacterium date: 2014-02-19 pages: extension: .txt txt: ./txt/cord-001207-yjaiybwf.txt cache: ./cache/cord-001207-yjaiybwf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001207-yjaiybwf.txt' === file2bib.sh === id: cord-000760-4yfohp9w author: Babapoor, Sankhiros title: A Novel Vaccine Using Nanoparticle Platform to Present Immunogenic M2e against Avian Influenza Infection date: 2012-01-12 pages: extension: .txt txt: ./txt/cord-000760-4yfohp9w.txt cache: ./cache/cord-000760-4yfohp9w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000760-4yfohp9w.txt' === file2bib.sh === id: cord-002937-7xauocti author: Huang, Chung-Guei title: A pilot study on primary cultures of human respiratory tract epithelial cells to predict patients’ responses to H7N9 infection date: 2018-02-20 pages: extension: .txt txt: ./txt/cord-002937-7xauocti.txt cache: ./cache/cord-002937-7xauocti.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002937-7xauocti.txt' === file2bib.sh === id: cord-000729-iq30z094 author: Marsh, Glenn A. title: Cedar Virus: A Novel Henipavirus Isolated from Australian Bats date: 2012-08-02 pages: extension: .txt txt: ./txt/cord-000729-iq30z094.txt cache: ./cache/cord-000729-iq30z094.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000729-iq30z094.txt' === file2bib.sh === id: cord-000937-8vk89i4h author: Law, John title: Identification of Hepatotropic Viruses from Plasma Using Deep Sequencing: A Next Generation Diagnostic Tool date: 2013-04-17 pages: extension: .txt txt: ./txt/cord-000937-8vk89i4h.txt cache: ./cache/cord-000937-8vk89i4h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000937-8vk89i4h.txt' === file2bib.sh === id: cord-001420-b4zcvd04 author: Crescenzo-Chaigne, Bernadette title: Chimeric NP Non Coding Regions between Type A and C Influenza Viruses Reveal Their Role in Translation Regulation date: 2014-09-30 pages: extension: .txt txt: ./txt/cord-001420-b4zcvd04.txt cache: ./cache/cord-001420-b4zcvd04.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001420-b4zcvd04.txt' === file2bib.sh === id: cord-002076-7t4d4vvo author: Li, Yongfeng title: Applications of Replicating-Competent Reporter-Expressing Viruses in Diagnostic and Molecular Virology date: 2016-05-06 pages: extension: .txt txt: ./txt/cord-002076-7t4d4vvo.txt cache: ./cache/cord-002076-7t4d4vvo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002076-7t4d4vvo.txt' === file2bib.sh === id: cord-000180-howix091 author: MacLeod, Iain J. title: Binding of Herpes Simplex Virus Type-1 Virions Leads to the Induction of Intracellular Signalling in the Absence of Virus Entry date: 2010-03-05 pages: extension: .txt txt: ./txt/cord-000180-howix091.txt cache: ./cache/cord-000180-howix091.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000180-howix091.txt' === file2bib.sh === id: cord-004211-58x3nnsc author: Javelle, Emilie title: The challenging management of Rift Valley Fever in humans: literature review of the clinical disease and algorithm proposal date: 2020-01-22 pages: extension: .txt txt: ./txt/cord-004211-58x3nnsc.txt cache: ./cache/cord-004211-58x3nnsc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004211-58x3nnsc.txt' === file2bib.sh === id: cord-003792-v48xeqdz author: Izquierdo-Suzán, Mónica title: Natural Vertical Transmission of Zika Virus in Larval Aedes aegypti Populations, Morelos, Mexico date: 2019-08-17 pages: extension: .txt txt: ./txt/cord-003792-v48xeqdz.txt cache: ./cache/cord-003792-v48xeqdz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003792-v48xeqdz.txt' === file2bib.sh === id: cord-002423-1u44tdrj author: Geoghegan, Jemma L. title: Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families date: 2017-02-08 pages: extension: .txt txt: ./txt/cord-002423-1u44tdrj.txt cache: ./cache/cord-002423-1u44tdrj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002423-1u44tdrj.txt' === file2bib.sh === id: cord-001974-wjf3c7a7 author: Friis-Nielsen, Jens title: Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers date: 2016-02-19 pages: extension: .txt txt: ./txt/cord-001974-wjf3c7a7.txt cache: ./cache/cord-001974-wjf3c7a7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001974-wjf3c7a7.txt' === file2bib.sh === id: cord-000113-d0eur1hq author: Fooks, Anthony R. title: Emerging Technologies for the Detection of Rabies Virus: Challenges and Hopes in the 21st Century date: 2009-09-29 pages: extension: .txt txt: ./txt/cord-000113-d0eur1hq.txt cache: ./cache/cord-000113-d0eur1hq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000113-d0eur1hq.txt' === file2bib.sh === id: cord-000050-tfcerilc author: Rao, Srinivas title: Multivalent HA DNA Vaccination Protects against Highly Pathogenic H5N1 Avian Influenza Infection in Chickens and Mice date: 2008-06-18 pages: extension: .txt txt: ./txt/cord-000050-tfcerilc.txt cache: ./cache/cord-000050-tfcerilc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000050-tfcerilc.txt' === file2bib.sh === id: cord-000012-p56v8wi1 author: Bigot, Yves title: Molecular evidence for the evolution of ichnoviruses from ascoviruses by symbiogenesis date: 2008-09-18 pages: extension: .txt txt: ./txt/cord-000012-p56v8wi1.txt cache: ./cache/cord-000012-p56v8wi1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000012-p56v8wi1.txt' === file2bib.sh === id: cord-003880-uuuzfyjm author: Shen, Meng-xin title: Antiviral Properties of R. tanguticum Nanoparticles on Herpes Simplex Virus Type I In Vitro and In Vivo date: 2019-09-04 pages: extension: .txt txt: ./txt/cord-003880-uuuzfyjm.txt cache: ./cache/cord-003880-uuuzfyjm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003880-uuuzfyjm.txt' === file2bib.sh === id: cord-003130-p2h8p5bm author: Lindqvist, Richard title: Tick-Borne Flaviviruses and the Type I Interferon Response date: 2018-06-21 pages: extension: .txt txt: ./txt/cord-003130-p2h8p5bm.txt cache: ./cache/cord-003130-p2h8p5bm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003130-p2h8p5bm.txt' === file2bib.sh === id: cord-003302-vxk7uqlc author: Fedson, David S title: Influenza, evolution, and the next pandemic date: 2018-10-03 pages: extension: .txt txt: ./txt/cord-003302-vxk7uqlc.txt cache: ./cache/cord-003302-vxk7uqlc.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-003302-vxk7uqlc.txt' === file2bib.sh === id: cord-003993-3bozjfv7 author: Cagliani, Rachele title: Mode and tempo of human hepatitis virus evolution date: 2019-10-25 pages: extension: .txt txt: ./txt/cord-003993-3bozjfv7.txt cache: ./cache/cord-003993-3bozjfv7.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-003993-3bozjfv7.txt' === file2bib.sh === id: cord-002410-2zi5iv2t author: Bruening, Janina title: The Role of Type III Interferons in Hepatitis C Virus Infection and Therapy date: 2017-02-01 pages: extension: .txt txt: ./txt/cord-002410-2zi5iv2t.txt cache: ./cache/cord-002410-2zi5iv2t.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-002410-2zi5iv2t.txt' === file2bib.sh === id: cord-003466-599x0euj author: Nickol, Michaela E. title: A year of terror and a century of reflection: perspectives on the great influenza pandemic of 1918–1919 date: 2019-02-06 pages: extension: .txt txt: ./txt/cord-003466-599x0euj.txt cache: ./cache/cord-003466-599x0euj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003466-599x0euj.txt' === file2bib.sh === id: cord-000238-om92cx5q author: Ogbunugafor, C. Brandon title: On the possible role of robustness in the evolution of infectious diseases date: 2010-06-30 pages: extension: .txt txt: ./txt/cord-000238-om92cx5q.txt cache: ./cache/cord-000238-om92cx5q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-000238-om92cx5q.txt' === file2bib.sh === id: cord-003767-9xbu4hnq author: Slingenbergh, Jan title: Animal Virus Ecology and Evolution Are Shaped by the Virus Host-Body Infiltration and Colonization Pattern date: 2019-05-25 pages: extension: .txt txt: ./txt/cord-003767-9xbu4hnq.txt cache: ./cache/cord-003767-9xbu4hnq.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-003767-9xbu4hnq.txt' === file2bib.sh === id: cord-003482-f1uvohf0 author: Malmlov, Ashley title: Experimental Zika virus infection of Jamaican fruit bats (Artibeus jamaicensis) and possible entry of virus into brain via activated microglial cells date: 2019-02-04 pages: extension: .txt txt: ./txt/cord-003482-f1uvohf0.txt cache: ./cache/cord-003482-f1uvohf0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003482-f1uvohf0.txt' === file2bib.sh === id: cord-001958-2gt3fwpy author: Meseda, Clement A. title: Percutaneous Vaccination as an Effective Method of Delivery of MVA and MVA-Vectored Vaccines date: 2016-02-19 pages: extension: .txt txt: ./txt/cord-001958-2gt3fwpy.txt cache: ./cache/cord-001958-2gt3fwpy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001958-2gt3fwpy.txt' === file2bib.sh === id: cord-003092-3owcqt3d author: Iketani, Sho title: Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation date: 2018-07-03 pages: extension: .txt txt: ./txt/cord-003092-3owcqt3d.txt cache: ./cache/cord-003092-3owcqt3d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003092-3owcqt3d.txt' === file2bib.sh === id: cord-003817-k3m72uxw author: Braun, Elisabeth title: Furin‐mediated protein processing in infectious diseases and cancer date: 2019-08-05 pages: extension: .txt txt: ./txt/cord-003817-k3m72uxw.txt cache: ./cache/cord-003817-k3m72uxw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003817-k3m72uxw.txt' === file2bib.sh === id: cord-000359-y0m1utug author: Walpita, Pramila title: Vaccine Potential of Nipah Virus-Like Particles date: 2011-04-06 pages: extension: .txt txt: ./txt/cord-000359-y0m1utug.txt cache: ./cache/cord-000359-y0m1utug.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-000359-y0m1utug.txt' === file2bib.sh === id: cord-001676-68y733y3 author: Shoemaker, Jason E. title: An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation date: 2015-06-05 pages: extension: .txt txt: ./txt/cord-001676-68y733y3.txt cache: ./cache/cord-001676-68y733y3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001676-68y733y3.txt' === file2bib.sh === id: cord-004830-vmka378d author: Cursiefen, Dagmar title: In vitro cultivation of cells from the chorioallantoic membrane of chick embryos date: 1975 pages: extension: .txt txt: ./txt/cord-004830-vmka378d.txt cache: ./cache/cord-004830-vmka378d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-004830-vmka378d.txt' === file2bib.sh === id: cord-005876-d8sid7gd author: Varnholt, V. title: ARDS infolge schwerer RSV-Infektion Therapeutische Optionen: Therapeutische Optionen date: 1996 pages: extension: .txt txt: ./txt/cord-005876-d8sid7gd.txt cache: ./cache/cord-005876-d8sid7gd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-005876-d8sid7gd.txt' === file2bib.sh === id: cord-002933-zmx4k46v author: Stabell, Alex C title: Dengue viruses cleave STING in humans but not in nonhuman primates, their presumed natural reservoir date: 2018-03-20 pages: extension: .txt txt: ./txt/cord-002933-zmx4k46v.txt cache: ./cache/cord-002933-zmx4k46v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002933-zmx4k46v.txt' === 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' === file2bib.sh === id: cord-004841-wf0o3whi author: Sibalin, M. title: Herpesvirus strigis, a new avian herpesvirus: II. Biochemical and biophysical properties date: 1974 pages: extension: .txt txt: ./txt/cord-004841-wf0o3whi.txt cache: ./cache/cord-004841-wf0o3whi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-004841-wf0o3whi.txt' === file2bib.sh === id: cord-004827-bnf3mvaf author: Desselberger, U. title: Report on an ICTV-sponsored symposium on Virus Evolution date: 2005-01-13 pages: extension: .txt txt: ./txt/cord-004827-bnf3mvaf.txt cache: ./cache/cord-004827-bnf3mvaf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-004827-bnf3mvaf.txt' === file2bib.sh === id: cord-001542-f089bs8r author: Lai, Kang Yiu title: Human Ebola virus infection in West Africa: a review of available therapeutic agents that target different steps of the life cycle of Ebola virus date: 2014-11-28 pages: extension: .txt txt: ./txt/cord-001542-f089bs8r.txt cache: ./cache/cord-001542-f089bs8r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001542-f089bs8r.txt' === file2bib.sh === id: cord-004775-foaf3vyl author: Weiss, Marianne title: The proposed family toroviridae: Agents of enteric infections date: 1987 pages: extension: .txt txt: ./txt/cord-004775-foaf3vyl.txt cache: ./cache/cord-004775-foaf3vyl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004775-foaf3vyl.txt' === file2bib.sh === id: cord-005885-r3qtoqu1 author: Hellmich, Luisa title: Exantheme nach Auslandsreisen date: 2019-10-09 pages: extension: .txt txt: ./txt/cord-005885-r3qtoqu1.txt cache: ./cache/cord-005885-r3qtoqu1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-005885-r3qtoqu1.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-005258-gps8rzb5 author: Liu, William J. title: The triphibious warfare against viruses date: 2017-12-01 pages: extension: .txt txt: ./txt/cord-005258-gps8rzb5.txt cache: ./cache/cord-005258-gps8rzb5.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-005258-gps8rzb5.txt' === file2bib.sh === id: cord-003707-fbe47bgi author: Russo, Alice G title: Novel insights into endogenous RNA viral elements in Ixodes scapularis and other arbovirus vector genomes date: 2019-06-18 pages: extension: .txt txt: ./txt/cord-003707-fbe47bgi.txt cache: ./cache/cord-003707-fbe47bgi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003707-fbe47bgi.txt' === file2bib.sh === id: cord-003122-a3f4l6iu author: Dou, Dan title: Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement date: 2018-07-20 pages: extension: .txt txt: ./txt/cord-003122-a3f4l6iu.txt cache: ./cache/cord-003122-a3f4l6iu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003122-a3f4l6iu.txt' === file2bib.sh === id: cord-004998-wuixnqy5 author: Arnold, W. title: Identic viral infections in four cases of malignant lymphoepithelioma date: 1978 pages: extension: .txt txt: ./txt/cord-004998-wuixnqy5.txt cache: ./cache/cord-004998-wuixnqy5.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-004998-wuixnqy5.txt' === file2bib.sh === id: cord-007898-nky7bo6u author: HUGHES, C.S. title: Effects of certain stress factors on the re-excretion of infectious laryngotracheitis virus from latently infected carrier birds date: 2018-09-04 pages: extension: .txt txt: ./txt/cord-007898-nky7bo6u.txt cache: ./cache/cord-007898-nky7bo6u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007898-nky7bo6u.txt' === file2bib.sh === id: cord-002407-25cawzi0 author: Nogales, Aitor title: Reverse Genetics Approaches for the Development of Influenza Vaccines date: 2016-12-22 pages: extension: .txt txt: ./txt/cord-002407-25cawzi0.txt cache: ./cache/cord-002407-25cawzi0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002407-25cawzi0.txt' === file2bib.sh === id: cord-006997-sghhdjyi author: Rowland, M.G.M. title: Viruses and diarrhoea in West Africa and London: a collaborative study date: 1978-01-17 pages: extension: .txt txt: ./txt/cord-006997-sghhdjyi.txt cache: ./cache/cord-006997-sghhdjyi.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-006997-sghhdjyi.txt' === file2bib.sh === id: cord-006790-lye0qjw8 author: Song, R. title: Surveillance of the first case of human avian influenza A (H7N9) virus in Beijing, China date: 2013-10-16 pages: extension: .txt txt: ./txt/cord-006790-lye0qjw8.txt cache: ./cache/cord-006790-lye0qjw8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006790-lye0qjw8.txt' === file2bib.sh === id: cord-004848-2cfphi88 author: Carter, M. J. title: Transcription of feline calicivirus RNA date: 1990 pages: extension: .txt txt: ./txt/cord-004848-2cfphi88.txt cache: ./cache/cord-004848-2cfphi88.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-004848-2cfphi88.txt' === file2bib.sh === id: cord-008149-kdlcaium author: Blacklaws, B.A. title: Emerging viruses of zoonotic and veterinary importance date: 2017-12-30 pages: extension: .txt txt: ./txt/cord-008149-kdlcaium.txt cache: ./cache/cord-008149-kdlcaium.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-008149-kdlcaium.txt' === file2bib.sh === id: cord-008700-knbf8m4x author: Rodrigues, Merlyn R. title: Methods for Rapid Detection of Human Ocular Viral Infections date: 2013-10-30 pages: extension: .txt txt: ./txt/cord-008700-knbf8m4x.txt cache: ./cache/cord-008700-knbf8m4x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-008700-knbf8m4x.txt' === file2bib.sh === id: cord-009589-xfdgk2j6 author: Spradbrow, P. B. title: VIRUS DISEASES OF DOMESTIC ANIMALS date: 2008-03-10 pages: extension: .txt txt: ./txt/cord-009589-xfdgk2j6.txt cache: ./cache/cord-009589-xfdgk2j6.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-009589-xfdgk2j6.txt' === file2bib.sh === id: cord-000777-7cty5s6o author: Merten, O.-W. title: Virus contaminations of cell cultures – A biotechnological view date: 2002-01-01 pages: extension: .txt txt: ./txt/cord-000777-7cty5s6o.txt cache: ./cache/cord-000777-7cty5s6o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000777-7cty5s6o.txt' === file2bib.sh === id: cord-007843-yqdqm4rh author: Shader, Richard I. title: Zoonotic Viruses: The Mysterious Leap From Animals to Man date: 2018-07-26 pages: extension: .txt txt: ./txt/cord-007843-yqdqm4rh.txt cache: ./cache/cord-007843-yqdqm4rh.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-007843-yqdqm4rh.txt' === file2bib.sh === id: cord-005081-kxrzv16n author: Kiselev, O. I. title: Progress in the development of pandemic influenza vaccines and their production technologies date: 2010-11-12 pages: extension: .txt txt: ./txt/cord-005081-kxrzv16n.txt cache: ./cache/cord-005081-kxrzv16n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-005081-kxrzv16n.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 2 resourceName b'cord-007176-61e9obb3.txt' === file2bib.sh === id: cord-010159-uo47oab1 author: Jartti, Tuomas title: Respiratory viruses and acute asthma in children date: 2007-04-02 pages: extension: .txt txt: ./txt/cord-010159-uo47oab1.txt cache: ./cache/cord-010159-uo47oab1.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-010159-uo47oab1.txt' === file2bib.sh === id: cord-005281-wy0zk9p8 author: Blinov, V. M. title: Viral component of the human genome date: 2017-05-09 pages: extension: .txt txt: ./txt/cord-005281-wy0zk9p8.txt cache: ./cache/cord-005281-wy0zk9p8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-005281-wy0zk9p8.txt' === file2bib.sh === id: cord-009504-sn00p8iw author: Taguchi, Fumihiro title: Pathogenesis of Mouse Hepatitis Virus Infection: The Role of Nasal Epithelial Cells as a Primary Target of Low‐Virulence Virus, MHV‐S date: 2013-11-14 pages: extension: .txt txt: ./txt/cord-009504-sn00p8iw.txt cache: ./cache/cord-009504-sn00p8iw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-009504-sn00p8iw.txt' === file2bib.sh === id: cord-006089-08g206kf author: Stevens, James title: Glycan microarray technologies: tools to survey host specificity of influenza viruses date: 2006-10-02 pages: extension: .txt txt: ./txt/cord-006089-08g206kf.txt cache: ./cache/cord-006089-08g206kf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-006089-08g206kf.txt' === file2bib.sh === id: cord-007530-eyk015n3 author: Powell, H.C. title: Electron-microscopic appearance of the DA virus, a demyelinating murine virus() date: 2003-03-06 pages: extension: .txt txt: ./txt/cord-007530-eyk015n3.txt cache: ./cache/cord-007530-eyk015n3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-007530-eyk015n3.txt' === file2bib.sh === id: cord-009846-o6wj8z6e author: Wroblewska, Zofia title: Rat tracheal organ culture supports replication of parainfluenza 1 (6/94) virus and promotes 6/94 virus rescue from latently infected human brain cells date: 2005-12-06 pages: extension: .txt txt: ./txt/cord-009846-o6wj8z6e.txt cache: ./cache/cord-009846-o6wj8z6e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-009846-o6wj8z6e.txt' === file2bib.sh === id: cord-006819-sxz1s6kz author: Daniel Givens, M. title: Infectious causes of embryonic and fetal mortality date: 2008-05-27 pages: extension: .txt txt: ./txt/cord-006819-sxz1s6kz.txt cache: ./cache/cord-006819-sxz1s6kz.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-006819-sxz1s6kz.txt' === file2bib.sh === id: cord-006285-kkxdmzk9 author: Smirnova, S. S. title: Long-Term Maintenance of the Functional Changes Induced by Influenza A Virus and/or LPS in Human Endothelial ECV-304 Cell Sublines date: 2019-08-26 pages: extension: .txt txt: ./txt/cord-006285-kkxdmzk9.txt cache: ./cache/cord-006285-kkxdmzk9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006285-kkxdmzk9.txt' === 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 3 resourceName b'cord-007445-2folsh35.txt' === file2bib.sh === id: cord-007149-m4xsx9ev author: Morahan, Pages S title: VIRUSES AND THE VERSATILE MACROPHAGE date: 1985-01-17 pages: extension: .txt txt: ./txt/cord-007149-m4xsx9ev.txt cache: ./cache/cord-007149-m4xsx9ev.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007149-m4xsx9ev.txt' === file2bib.sh === id: cord-009383-ozx5u0t3 author: Sheppard, Michael title: Viral Vectors for Veterinary Vaccines date: 2007-09-28 pages: extension: .txt txt: ./txt/cord-009383-ozx5u0t3.txt cache: ./cache/cord-009383-ozx5u0t3.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-009383-ozx5u0t3.txt' === file2bib.sh === id: cord-010189-makhaypd author: Yamashita, Teruo title: VI, 3. Molecular biology and epidemiology of Aichi virus and other diarrhoeogenic enteroviruses date: 2004-09-14 pages: extension: .txt txt: ./txt/cord-010189-makhaypd.txt cache: ./cache/cord-010189-makhaypd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010189-makhaypd.txt' === file2bib.sh === id: cord-007710-0u5ot5h4 author: Graham, Barney S. title: Challenges and Opportunities for Respiratory Syncytial Virus Vaccines date: 2013-05-24 pages: extension: .txt txt: ./txt/cord-007710-0u5ot5h4.txt cache: ./cache/cord-007710-0u5ot5h4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-007710-0u5ot5h4.txt' === file2bib.sh === id: cord-009791-k09vcq96 author: Osterhaus, A. title: Antiviral Antibodies in Dogs in the Netherlands date: 2010-05-13 pages: extension: .txt txt: ./txt/cord-009791-k09vcq96.txt cache: ./cache/cord-009791-k09vcq96.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-009791-k09vcq96.txt' === file2bib.sh === id: cord-006640-25ykas09 author: Fedson, David S. title: What treating Ebola means for pandemic influenza date: 2018-07-16 pages: extension: .txt txt: ./txt/cord-006640-25ykas09.txt cache: ./cache/cord-006640-25ykas09.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-006640-25ykas09.txt' === file2bib.sh === id: cord-002482-2t09zqqi author: Miras, Manuel title: Non-canonical Translation in Plant RNA Viruses date: 2017-04-06 pages: extension: .txt txt: ./txt/cord-002482-2t09zqqi.txt cache: ./cache/cord-002482-2t09zqqi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002482-2t09zqqi.txt' === file2bib.sh === id: cord-006252-cbelsymu author: Gross, Peter A. title: Current Recommendations for the Prevention and Treatment of Influenza in the Older Population date: 2012-11-18 pages: extension: .txt txt: ./txt/cord-006252-cbelsymu.txt cache: ./cache/cord-006252-cbelsymu.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-006252-cbelsymu.txt' === file2bib.sh === id: cord-010188-884d196k author: Schlesinger, Sondra title: Alphaviruses — vectors for the expression of heterologous genes date: 2004-08-26 pages: extension: .txt txt: ./txt/cord-010188-884d196k.txt cache: ./cache/cord-010188-884d196k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-010188-884d196k.txt' === file2bib.sh === id: cord-014541-2i0jga5v author: Breedlove, Byron title: The Exploding Aliveness of the World date: 2017-04-17 pages: extension: .txt txt: ./txt/cord-014541-2i0jga5v.txt cache: ./cache/cord-014541-2i0jga5v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-014541-2i0jga5v.txt' === file2bib.sh === id: cord-009144-3slh1nbk author: Jacobs, J.W. title: RESPIRATORY SYNCYTIAL AND OTHER VIRUSES ASSOCIATED WITH RESPIRATORY DISEASE IN INFANTS date: 1971-05-01 pages: extension: .txt txt: ./txt/cord-009144-3slh1nbk.txt cache: ./cache/cord-009144-3slh1nbk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-009144-3slh1nbk.txt' === file2bib.sh === id: cord-009820-fi54s0x7 author: Andries, K. title: Pathogenicity of Hemagglutinating Encephalomyelitis (Vomiting and Wasting Disease) Virus of Pigs, using Different Routes of Inoculation date: 2010-05-13 pages: extension: .txt txt: ./txt/cord-009820-fi54s0x7.txt cache: ./cache/cord-009820-fi54s0x7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-009820-fi54s0x7.txt' === file2bib.sh === id: cord-009702-02bo7pnl author: SCOTT, G. R. title: Guidelines for the Control of Equine Viral Infections date: 2010-04-23 pages: extension: .txt txt: ./txt/cord-009702-02bo7pnl.txt cache: ./cache/cord-009702-02bo7pnl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-009702-02bo7pnl.txt' === file2bib.sh === id: cord-013073-siy7dvlo author: Pfäfflin, Albrecht title: Influenza virus-flow from insects to humans as causative for influenza seasonality date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-013073-siy7dvlo.txt cache: ./cache/cord-013073-siy7dvlo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-013073-siy7dvlo.txt' === file2bib.sh === id: cord-006106-u5npu6ng author: Attoui, H. title: Genus Coltivirus (family Reoviridae): genomic and morphologic characterization of Old World and New World viruses date: 2002 pages: extension: .txt txt: ./txt/cord-006106-u5npu6ng.txt cache: ./cache/cord-006106-u5npu6ng.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006106-u5npu6ng.txt' === file2bib.sh === id: cord-009615-xcz8m9a7 author: Stoner, Gerald L. title: Polyomavirus Models of Brain Infection and the Pathogenesis of Multiple Sclerosis date: 2008-01-28 pages: extension: .txt txt: ./txt/cord-009615-xcz8m9a7.txt cache: ./cache/cord-009615-xcz8m9a7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-009615-xcz8m9a7.txt' === file2bib.sh === id: cord-009561-pg4jmvw4 author: Johnson, Richard T. title: The virology of demyelinating diseases date: 2004-10-08 pages: extension: .txt txt: ./txt/cord-009561-pg4jmvw4.txt cache: ./cache/cord-009561-pg4jmvw4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-009561-pg4jmvw4.txt' === file2bib.sh === id: cord-010222-5oxie0zc author: Oldstone, Michael B.A. title: Virus-induced autoimmunity: Molecular mimicry as a route to autoimmune disease date: 2004-04-11 pages: extension: .txt txt: ./txt/cord-010222-5oxie0zc.txt cache: ./cache/cord-010222-5oxie0zc.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-010222-5oxie0zc.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-005246-cskb0njm author: Ludwig, George V. title: Insect-transmitted vertebrate viruses: Flaviviridae date: 1993 pages: extension: .txt txt: ./txt/cord-005246-cskb0njm.txt cache: ./cache/cord-005246-cskb0njm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-005246-cskb0njm.txt' === file2bib.sh === id: cord-006954-ec9x8thb author: Aznar, María title: Viral nanomechanics with a virtual atomic force microscope date: 2018-07-04 pages: extension: .txt txt: ./txt/cord-006954-ec9x8thb.txt cache: ./cache/cord-006954-ec9x8thb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006954-ec9x8thb.txt' === file2bib.sh === id: cord-010001-u0d5jkp1 author: KOTWAL, GIRISH J. title: Anti‐HIV, Anti‐Poxvirus, and Anti‐SARS Activity of a Nontoxic, Acidic Plant Extract from the Trifollium Species Secomet‐V/anti‐Vac Suggests That It Contains a Novel Broad‐Spectrum Antiviral date: 2006-01-22 pages: extension: .txt txt: ./txt/cord-010001-u0d5jkp1.txt cache: ./cache/cord-010001-u0d5jkp1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010001-u0d5jkp1.txt' === file2bib.sh === id: cord-012582-k1mjik27 author: Gallego, Iván title: Stronger Together: Multivalent Phage Capsids Inhibit Virus Entry date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-012582-k1mjik27.txt cache: ./cache/cord-012582-k1mjik27.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-012582-k1mjik27.txt' === file2bib.sh === id: cord-010016-fs8pjy1z author: WEBB, H. E. title: CAN VIRAL ENVELOPE GLYCOLIPIDS PRODUCE AUTO‐IMMUNITY, WITH REFERENCE TO THE CNS AND MULTIPLE SCLEROSIS? date: 2008-05-12 pages: extension: .txt txt: ./txt/cord-010016-fs8pjy1z.txt cache: ./cache/cord-010016-fs8pjy1z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010016-fs8pjy1z.txt' === file2bib.sh === id: cord-006129-5rog0s98 author: Hemida, Maged Gomaa title: Exploiting the Therapeutic Potential of MicroRNAs in Viral Diseases: Expectations and Limitations date: 2012-08-16 pages: extension: .txt txt: ./txt/cord-006129-5rog0s98.txt cache: ./cache/cord-006129-5rog0s98.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-006129-5rog0s98.txt' === file2bib.sh === id: cord-007362-pjpkz6wv author: Bielefeldt-Ohmann, Helle title: The Pathologies of Bovine Viral Diarrhea Virus Infection: A Window on the Pathogenesis date: 2016-01-06 pages: extension: .txt txt: ./txt/cord-007362-pjpkz6wv.txt cache: ./cache/cord-007362-pjpkz6wv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007362-pjpkz6wv.txt' === file2bib.sh === id: cord-007094-ur9sz21s author: Mahabir, Esther title: Rodent and Germplasm Trafficking: Risks of Microbial Contamination in a High-Tech Biomedical World date: 2008-01-01 pages: extension: .txt txt: ./txt/cord-007094-ur9sz21s.txt cache: ./cache/cord-007094-ur9sz21s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007094-ur9sz21s.txt' === file2bib.sh === id: cord-007717-7x1mqqmf author: Lowen, Anice C. title: Transmission in the Guinea Pig Model date: 2014-07-08 pages: extension: .txt txt: ./txt/cord-007717-7x1mqqmf.txt cache: ./cache/cord-007717-7x1mqqmf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-007717-7x1mqqmf.txt' === file2bib.sh === id: cord-010235-hu6o1ggc author: Atmar, Robert L. title: Nonculturable agents of viral gastroenteritis date: 1997-12-01 pages: extension: .txt txt: ./txt/cord-010235-hu6o1ggc.txt cache: ./cache/cord-010235-hu6o1ggc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010235-hu6o1ggc.txt' === file2bib.sh === id: cord-010168-aiqbqnaa author: Desselberger, Ulrich title: Classical and molecular techniques for the diagnosis of viral gastroenteritis() date: 1999-03-11 pages: extension: .txt txt: ./txt/cord-010168-aiqbqnaa.txt cache: ./cache/cord-010168-aiqbqnaa.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-010168-aiqbqnaa.txt' === file2bib.sh === id: cord-008686-9ybxuy00 author: Everett, Tom title: Poor transmission of seasonal cold viruses in a British Antarctic Survey base date: 2019-03-14 pages: extension: .txt txt: ./txt/cord-008686-9ybxuy00.txt cache: ./cache/cord-008686-9ybxuy00.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-008686-9ybxuy00.txt' === file2bib.sh === id: cord-010343-tqqt0hj7 author: Alidjinou, Enagnon Kazali title: Resistance of Enteric Viruses on Fomites date: 2017-06-15 pages: extension: .txt txt: ./txt/cord-010343-tqqt0hj7.txt cache: ./cache/cord-010343-tqqt0hj7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-010343-tqqt0hj7.txt' === file2bib.sh === id: cord-009577-29u7pdpk author: Gonzalez‐Scarano, F. title: Molecular pathogenesis of neurotropic viral infections date: 2004-10-08 pages: extension: .txt txt: ./txt/cord-009577-29u7pdpk.txt cache: ./cache/cord-009577-29u7pdpk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-009577-29u7pdpk.txt' === file2bib.sh === id: cord-007170-svsfu7fj author: Richt, J. A. title: Infection with Borna Disease Virus: Molecular and Immunobiological Characterization of the Agent date: 1992-06-17 pages: extension: .txt txt: ./txt/cord-007170-svsfu7fj.txt cache: ./cache/cord-007170-svsfu7fj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-007170-svsfu7fj.txt' === file2bib.sh === id: cord-008764-j9qmw4zy author: nan title: Chapter 1 The need for chemotherapy and prophylaxis against viral diseases date: 2008-05-29 pages: extension: .txt txt: ./txt/cord-008764-j9qmw4zy.txt cache: ./cache/cord-008764-j9qmw4zy.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-008764-j9qmw4zy.txt' === file2bib.sh === id: cord-010374-z9ygudv6 author: Siddell, S.G. title: Coronaviridae1 date: 2008-07-24 pages: extension: .txt txt: ./txt/cord-010374-z9ygudv6.txt cache: ./cache/cord-010374-z9ygudv6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010374-z9ygudv6.txt' === file2bib.sh === id: cord-008013-blf57r7u author: Hartmann, K. title: Feline immunodeficiency virus infection: an overview date: 2005-03-02 pages: extension: .txt txt: ./txt/cord-008013-blf57r7u.txt cache: ./cache/cord-008013-blf57r7u.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-008013-blf57r7u.txt' === file2bib.sh === id: cord-015023-ishxfinx author: Jones, David title: Hard water date: 1995 pages: extension: .txt txt: ./txt/cord-015023-ishxfinx.txt cache: ./cache/cord-015023-ishxfinx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-015023-ishxfinx.txt' === file2bib.sh === id: cord-007764-7750z41g author: Smith, M. L. title: Display of Peptides on the Surface of Tobacco Mosaic Virus Particles date: 2009 pages: extension: .txt txt: ./txt/cord-007764-7750z41g.txt cache: ./cache/cord-007764-7750z41g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-007764-7750z41g.txt' === 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 === id: cord-011457-hqxybv1k author: Kirui, James title: Generation and validation of a highly sensitive bioluminescent HIV-1 reporter vector that simplifies measurement of virus release date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-011457-hqxybv1k.txt cache: ./cache/cord-011457-hqxybv1k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-011457-hqxybv1k.txt' === file2bib.sh === id: cord-008333-1wepke2o author: Weisz, Ora A. title: Chapter 7 Use of Recombinant Vaccinia Virus Vectors for Cell Biology date: 2008-02-28 pages: extension: .txt txt: ./txt/cord-008333-1wepke2o.txt cache: ./cache/cord-008333-1wepke2o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-008333-1wepke2o.txt' === file2bib.sh === id: cord-002337-8v907g24 author: Lipsitch, Marc title: Viral factors in influenza pandemic risk assessment date: 2016-11-11 pages: extension: .txt txt: ./txt/cord-002337-8v907g24.txt cache: ./cache/cord-002337-8v907g24.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002337-8v907g24.txt' === file2bib.sh === id: cord-014796-6rw2wk1q author: Fayyadh, Thaer Kadhim title: Simultaneous detection of multiple viruses in their co-infected cells using multicolour imaging with self-assembled quantum dot probes date: 2017-05-06 pages: extension: .txt txt: ./txt/cord-014796-6rw2wk1q.txt cache: ./cache/cord-014796-6rw2wk1q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-014796-6rw2wk1q.txt' === file2bib.sh === id: cord-006892-n2ncamqh author: Donaldson, Braeden title: Virus-like particle vaccines: immunology and formulation for clinical translation date: 2018-09-19 pages: extension: .txt txt: ./txt/cord-006892-n2ncamqh.txt cache: ./cache/cord-006892-n2ncamqh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-006892-n2ncamqh.txt' === 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-009836-7o6htufh author: Borrow, Persephone title: Cytotoxic T‐lymphocyte escape viral variants: how important are they in viral evasion of immune clearance in vivo? date: 2006-04-28 pages: extension: .txt txt: ./txt/cord-009836-7o6htufh.txt cache: ./cache/cord-009836-7o6htufh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-009836-7o6htufh.txt' === file2bib.sh === id: cord-007784-fq2urilg author: Elderfield, Ruth title: Influenza Pandemics date: 2011-09-22 pages: extension: .txt txt: ./txt/cord-007784-fq2urilg.txt cache: ./cache/cord-007784-fq2urilg.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-007784-fq2urilg.txt' === file2bib.sh === id: cord-010273-0c56x9f5 author: Simmonds, Peter title: Virology of hepatitis C virus date: 2001-10-10 pages: extension: .txt txt: ./txt/cord-010273-0c56x9f5.txt cache: ./cache/cord-010273-0c56x9f5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010273-0c56x9f5.txt' === file2bib.sh === id: cord-015764-ly68q5z0 author: Poissy, J. title: La modulation de la signature transcriptomique de l’hôte infecté : une nouvelle stratégie thérapeutique dans les viroses graves ? Exemple de la grippe date: 2016-04-07 pages: extension: .txt txt: ./txt/cord-015764-ly68q5z0.txt cache: ./cache/cord-015764-ly68q5z0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-015764-ly68q5z0.txt' === file2bib.sh === id: cord-015619-msicix98 author: nan title: Virus Structure & Assembly date: 2009-02-24 pages: extension: .txt txt: ./txt/cord-015619-msicix98.txt cache: ./cache/cord-015619-msicix98.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-015619-msicix98.txt' === file2bib.sh === id: cord-011917-6u0t4hy8 author: Skarlupka, Amanda L. title: Immune Imprinting in the Influenza Ferret Model date: 2020-04-08 pages: extension: .txt txt: ./txt/cord-011917-6u0t4hy8.txt cache: ./cache/cord-011917-6u0t4hy8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-011917-6u0t4hy8.txt' === file2bib.sh === id: cord-007731-wu7i548j author: Sriwilaijaroen, Nongluk title: Molecular Basis of a Pandemic of Avian-Type Influenza Virus date: 2014-05-27 pages: extension: .txt txt: ./txt/cord-007731-wu7i548j.txt cache: ./cache/cord-007731-wu7i548j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007731-wu7i548j.txt' === file2bib.sh === id: cord-011129-btaxvmsr author: Di Paola, Nicholas title: Viral genomics in Ebola virus research date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-011129-btaxvmsr.txt cache: ./cache/cord-011129-btaxvmsr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-011129-btaxvmsr.txt' === file2bib.sh === id: cord-007575-5ekgabx5 author: Luby, James P. title: Southwestern Internal Medicine Conference: Pneumonias in Adults Due to Mycoplasma, Chlamydiae, and Viruses date: 2016-01-14 pages: extension: .txt txt: ./txt/cord-007575-5ekgabx5.txt cache: ./cache/cord-007575-5ekgabx5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007575-5ekgabx5.txt' === file2bib.sh === id: cord-013176-6ckuya1w author: Ninfali, Paolino title: Antiviral Properties of Flavonoids and Delivery Strategies date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-013176-6ckuya1w.txt cache: ./cache/cord-013176-6ckuya1w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-013176-6ckuya1w.txt' === file2bib.sh === id: cord-007792-596jxrm5 author: Luo, Ming title: Influenza Virus Entry date: 2011-08-26 pages: extension: .txt txt: ./txt/cord-007792-596jxrm5.txt cache: ./cache/cord-007792-596jxrm5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007792-596jxrm5.txt' === file2bib.sh === id: cord-011880-qlutgfu2 author: Barberis, Abdelheq title: Full-length genome sequences of the first H9N2 avian influenza viruses isolated in the Northeast of Algeria date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-011880-qlutgfu2.txt cache: ./cache/cord-011880-qlutgfu2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-011880-qlutgfu2.txt' === file2bib.sh === id: cord-011106-h20vbmbo author: Takeda, Yohei title: Antiviral Activities of Hibiscus sabdariffa L. Tea Extract Against Human Influenza A Virus Rely Largely on Acidic pH but Partially on a Low-pH-Independent Mechanism date: 2019-10-16 pages: extension: .txt txt: ./txt/cord-011106-h20vbmbo.txt cache: ./cache/cord-011106-h20vbmbo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-011106-h20vbmbo.txt' === file2bib.sh === id: cord-016576-1yqwci0y author: Hu, Xiaohua title: Mining Candidate Viruses as Potential Bio-terrorism Weapons from Biomedical Literature date: 2005 pages: extension: .txt txt: ./txt/cord-016576-1yqwci0y.txt cache: ./cache/cord-016576-1yqwci0y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-016576-1yqwci0y.txt' === file2bib.sh === id: cord-016808-gy8d8285 author: Agol, Vadim I. title: The Origin and Evolution of Viruses date: 2008 pages: extension: .txt txt: ./txt/cord-016808-gy8d8285.txt cache: ./cache/cord-016808-gy8d8285.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016808-gy8d8285.txt' === file2bib.sh === id: cord-011438-imbpgsub author: Zhang, Yun title: Host–Virus Interaction: How Host Cells Defend against Influenza A Virus Infection date: 2020-03-29 pages: extension: .txt txt: ./txt/cord-011438-imbpgsub.txt cache: ./cache/cord-011438-imbpgsub.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-011438-imbpgsub.txt' === file2bib.sh === id: cord-008551-yu71iewp author: Parrish, Colin R. title: Emergence, Natural History, and Variation of Canine, Mink, and Feline Parvoviruses date: 2008-04-11 pages: extension: .txt txt: ./txt/cord-008551-yu71iewp.txt cache: ./cache/cord-008551-yu71iewp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-008551-yu71iewp.txt' === file2bib.sh === id: cord-015871-1tuf4zxi author: Ergonul, Onder title: Treatment of Crimean-Congo Hemorrhagic Fever date: 2007 pages: extension: .txt txt: ./txt/cord-015871-1tuf4zxi.txt cache: ./cache/cord-015871-1tuf4zxi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-015871-1tuf4zxi.txt' === file2bib.sh === id: cord-016663-qnp99m7o author: Taylor, Robert B. title: Medical Words Linked to Places date: 2017-02-01 pages: extension: .txt txt: ./txt/cord-016663-qnp99m7o.txt cache: ./cache/cord-016663-qnp99m7o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016663-qnp99m7o.txt' === file2bib.sh === id: cord-007733-zh8e76w7 author: DiMenna, Lauren J. title: Pandemic Influenza Vaccines date: 2009-06-15 pages: extension: .txt txt: ./txt/cord-007733-zh8e76w7.txt cache: ./cache/cord-007733-zh8e76w7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-007733-zh8e76w7.txt' === file2bib.sh === id: cord-016928-yigz9qiz author: Bhattacharyya, Sankar title: Inflammation During Virus Infection: Swings and Roundabouts date: 2019-11-05 pages: extension: .txt txt: ./txt/cord-016928-yigz9qiz.txt cache: ./cache/cord-016928-yigz9qiz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-016928-yigz9qiz.txt' === file2bib.sh === id: cord-016754-6fv8mjld author: Iturriza-Gómara, Miren title: Gastroenteric Viruses date: 2007 pages: extension: .txt txt: ./txt/cord-016754-6fv8mjld.txt cache: ./cache/cord-016754-6fv8mjld.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016754-6fv8mjld.txt' === file2bib.sh === id: cord-016796-g4kqqpy1 author: Bramhachari, Pallaval Veera title: Advanced Immunotechnological Methods for Detection and Diagnosis of Viral Infections: Current Applications and Future Challenges date: 2019-11-05 pages: extension: .txt txt: ./txt/cord-016796-g4kqqpy1.txt cache: ./cache/cord-016796-g4kqqpy1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-016796-g4kqqpy1.txt' === file2bib.sh === id: cord-016171-17ut32bu author: Lane, J. Michael title: Smallpox as a Weapon for Bioterrorism date: 2009 pages: extension: .txt txt: ./txt/cord-016171-17ut32bu.txt cache: ./cache/cord-016171-17ut32bu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016171-17ut32bu.txt' === file2bib.sh === id: cord-016798-tv2ntug6 author: Gautam, Ablesh title: Bioinformatics Applications in Advancing Animal Virus Research date: 2019-06-06 pages: extension: .txt txt: ./txt/cord-016798-tv2ntug6.txt cache: ./cache/cord-016798-tv2ntug6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-016798-tv2ntug6.txt' === file2bib.sh === id: cord-016995-5izyl234 author: Auewarakul, Prasert title: The Past and Present Threat of Avian Influenza in Thailand date: 2008 pages: extension: .txt txt: ./txt/cord-016995-5izyl234.txt cache: ./cache/cord-016995-5izyl234.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016995-5izyl234.txt' === file2bib.sh === id: cord-017070-05vlz5dn author: Dimitrov, Dimiter S. title: Human Monoclonal Antibodies Against HIV and Emerging Viruses date: 2008 pages: extension: .txt txt: ./txt/cord-017070-05vlz5dn.txt cache: ./cache/cord-017070-05vlz5dn.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-017070-05vlz5dn.txt' === file2bib.sh === id: cord-014908-jys1y0k9 author: Yadav, Rakesh title: Trends and Perspectives of Biosensors for Food and Environmental Virology date: 2010-05-19 pages: extension: .txt txt: ./txt/cord-014908-jys1y0k9.txt cache: ./cache/cord-014908-jys1y0k9.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-014908-jys1y0k9.txt' === file2bib.sh === id: cord-013412-gj443yei author: Lebedeva, Natalya Sh. title: The Application of Porphyrins and Their Analogues for Inactivation of Viruses date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-013412-gj443yei.txt cache: ./cache/cord-013412-gj443yei.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-013412-gj443yei.txt' === file2bib.sh === id: cord-017537-ztdz4a2s author: Bologna, Mauro title: Biological Agents and Bioterrorism date: 2014-09-18 pages: extension: .txt txt: ./txt/cord-017537-ztdz4a2s.txt cache: ./cache/cord-017537-ztdz4a2s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017537-ztdz4a2s.txt' === file2bib.sh === id: cord-017489-ftz9190a author: Richards, Guy A. title: Viruses in the Intensive Care Unit (ICU) date: 2005 pages: extension: .txt txt: ./txt/cord-017489-ftz9190a.txt cache: ./cache/cord-017489-ftz9190a.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-017489-ftz9190a.txt' === file2bib.sh === id: cord-018463-a6qu0cuv author: Wimmer, Eckard title: Synthetic Biology, Dual Use Research, and Possibilities for Control date: 2018-03-23 pages: extension: .txt txt: ./txt/cord-018463-a6qu0cuv.txt cache: ./cache/cord-018463-a6qu0cuv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-018463-a6qu0cuv.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 523 resourceName b'cord-016451-k8m2xz0e.txt' === file2bib.sh === id: cord-016538-4og05fuo author: Dolja, V. V. title: Biotechnology Applications of Grapevine Viruses date: 2017-03-30 pages: extension: .txt txt: ./txt/cord-016538-4og05fuo.txt cache: ./cache/cord-016538-4og05fuo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-016538-4og05fuo.txt' === file2bib.sh === id: cord-019982-hyxrgamj author: Brookfield, D.S.K. title: Viruses demonstrated in children in Tanzania: Studies in diarrhoea and measles date: 2005-04-14 pages: extension: .txt txt: ./txt/cord-019982-hyxrgamj.txt cache: ./cache/cord-019982-hyxrgamj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-019982-hyxrgamj.txt' === file2bib.sh === id: cord-013526-6fip93l2 author: Labadie, Thomas title: A non-enveloped arbovirus released in lysosome-derived extracellular vesicles induces super-infection exclusion date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-013526-6fip93l2.txt cache: ./cache/cord-013526-6fip93l2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-013526-6fip93l2.txt' === file2bib.sh === id: cord-017158-w2tlq6ho author: Moriones, Enrique title: Recombination in the TYLCV Complex: a Mechanism to Increase Genetic Diversity. Implications for Plant Resistance Development date: 2007 pages: extension: .txt txt: ./txt/cord-017158-w2tlq6ho.txt cache: ./cache/cord-017158-w2tlq6ho.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-017158-w2tlq6ho.txt' === file2bib.sh === id: cord-020087-gs0pc6ee author: nan title: Cumulative Contents for 2010 date: 2010-11-18 pages: extension: .txt txt: ./txt/cord-020087-gs0pc6ee.txt cache: ./cache/cord-020087-gs0pc6ee.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-020087-gs0pc6ee.txt' === file2bib.sh === id: cord-017429-3evwlfac author: Hubálek, Zdenek title: Vertebrates as Hosts and Reservoirs of Zoonotic Microbial Agents date: 2010-11-10 pages: extension: .txt txt: ./txt/cord-017429-3evwlfac.txt cache: ./cache/cord-017429-3evwlfac.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017429-3evwlfac.txt' === file2bib.sh === id: cord-017824-0pinevfc author: Tekes, Gergely title: Vaccinia Virus-Based Reverse Genetics for Feline Coronaviruses date: 2015-09-10 pages: extension: .txt txt: ./txt/cord-017824-0pinevfc.txt cache: ./cache/cord-017824-0pinevfc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017824-0pinevfc.txt' === file2bib.sh === id: cord-016309-6mw8okmt author: Bule, Mohammed title: Antivirals: Past, Present and Future date: 2019-06-06 pages: extension: .txt txt: ./txt/cord-016309-6mw8okmt.txt cache: ./cache/cord-016309-6mw8okmt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016309-6mw8okmt.txt' === file2bib.sh === id: cord-017959-g0nf1iwm author: Lipkin, W. Ian title: Diagnosis, Discovery and Dissection of Viral Diseases date: 2014-02-27 pages: extension: .txt txt: ./txt/cord-017959-g0nf1iwm.txt cache: ./cache/cord-017959-g0nf1iwm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017959-g0nf1iwm.txt' === file2bib.sh === id: cord-018164-h5k1zsyg author: Taylor, Milton W. title: What Is a Virus? date: 2014-07-22 pages: extension: .txt txt: ./txt/cord-018164-h5k1zsyg.txt cache: ./cache/cord-018164-h5k1zsyg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018164-h5k1zsyg.txt' === file2bib.sh === id: cord-020101-5rib7pe8 author: nan title: Cumulative Author Index for 2008 date: 2008-11-17 pages: extension: .txt txt: ./txt/cord-020101-5rib7pe8.txt cache: ./cache/cord-020101-5rib7pe8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-020101-5rib7pe8.txt' === file2bib.sh === id: cord-016652-x8t3lf1x author: Matthews, David title: Viruses and the Nucleolus date: 2011-05-23 pages: extension: .txt txt: ./txt/cord-016652-x8t3lf1x.txt cache: ./cache/cord-016652-x8t3lf1x.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-016652-x8t3lf1x.txt' === file2bib.sh === id: cord-014397-7b88ycv8 author: Gavora, JS title: Resistance of livestock to viruses: mechanisms and strategies for genetic engineering date: 1996-12-15 pages: extension: .txt txt: ./txt/cord-014397-7b88ycv8.txt cache: ./cache/cord-014397-7b88ycv8.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-014397-7b88ycv8.txt' === file2bib.sh === id: cord-008454-8brxpotx author: Field, Anne M. title: Diagnostic Virology Using Electron Microscopic Techniques date: 2008-04-09 pages: extension: .txt txt: ./txt/cord-008454-8brxpotx.txt cache: ./cache/cord-008454-8brxpotx.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-008454-8brxpotx.txt' === file2bib.sh === id: cord-010248-ln800g5z author: Sissons, J.G. Patrick title: Antibody-Mediated Destruction of Virus-Infected Cells date: 2008-02-29 pages: extension: .txt txt: ./txt/cord-010248-ln800g5z.txt cache: ./cache/cord-010248-ln800g5z.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-010248-ln800g5z.txt' === file2bib.sh === id: cord-020097-eh5deunk author: nan title: Cumulative Author Index for 2006 (Volumes 115–122) date: 2006-10-27 pages: extension: .txt txt: ./txt/cord-020097-eh5deunk.txt cache: ./cache/cord-020097-eh5deunk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-020097-eh5deunk.txt' === file2bib.sh === id: cord-018816-v3ylisbt author: Alroy, Joseph title: Viral Pulmonary Disorders in Animals: Neoplastic and Nonneoplastic date: 2013-08-26 pages: extension: .txt txt: ./txt/cord-018816-v3ylisbt.txt cache: ./cache/cord-018816-v3ylisbt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-018816-v3ylisbt.txt' === file2bib.sh === id: cord-020789-slsfhrkx author: Kleines, Michael title: Virale Atemwegserkrankungen – Influenza, RSV und neue Viren date: 2017-10-27 pages: extension: .txt txt: ./txt/cord-020789-slsfhrkx.txt cache: ./cache/cord-020789-slsfhrkx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-020789-slsfhrkx.txt' === file2bib.sh === id: cord-018477-hgvqd1ej author: Modrow, Susanne title: Pathogenesis date: 2013-08-12 pages: extension: .txt txt: ./txt/cord-018477-hgvqd1ej.txt cache: ./cache/cord-018477-hgvqd1ej.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018477-hgvqd1ej.txt' === file2bib.sh === id: cord-018165-afzjx2ci author: Modrow, Susanne title: Vaccines date: 2013-08-12 pages: extension: .txt txt: ./txt/cord-018165-afzjx2ci.txt cache: ./cache/cord-018165-afzjx2ci.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018165-afzjx2ci.txt' === file2bib.sh === id: cord-002757-upwe0cpj author: Sullivan, Kathleen E. title: Emerging Infections and Pertinent Infections Related to Travel for Patients with Primary Immunodeficiencies date: 2017-08-07 pages: extension: .txt txt: ./txt/cord-002757-upwe0cpj.txt cache: ./cache/cord-002757-upwe0cpj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-002757-upwe0cpj.txt' === file2bib.sh === id: cord-018058-n3majqes author: Modrow, Susanne title: Historical Overview date: 2013-08-12 pages: extension: .txt txt: ./txt/cord-018058-n3majqes.txt cache: ./cache/cord-018058-n3majqes.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018058-n3majqes.txt' === file2bib.sh === id: cord-018078-clxzp1ph author: Weber, Olaf title: Coronavirus infections in veterinary medicine date: 2005 pages: extension: .txt txt: ./txt/cord-018078-clxzp1ph.txt cache: ./cache/cord-018078-clxzp1ph.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-018078-clxzp1ph.txt' === file2bib.sh === id: cord-021069-v9f9874x author: Morrison, Lynda A. title: Viral pathogenesis and central nervous system infection date: 2004-11-23 pages: extension: .txt txt: ./txt/cord-021069-v9f9874x.txt cache: ./cache/cord-021069-v9f9874x.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-021069-v9f9874x.txt' === file2bib.sh === id: cord-017568-8fnr4zzv author: Wang, Lin-Fa title: Disease Outbreaks Caused by Emerging Paramyxoviruses of Bat Origin date: 2008 pages: extension: .txt txt: ./txt/cord-017568-8fnr4zzv.txt cache: ./cache/cord-017568-8fnr4zzv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-017568-8fnr4zzv.txt' === file2bib.sh === id: cord-018724-ss8x2g3b author: Stobbe, Anthony title: Plant Virus Diversity and Evolution date: 2016-06-22 pages: extension: .txt txt: ./txt/cord-018724-ss8x2g3b.txt cache: ./cache/cord-018724-ss8x2g3b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-018724-ss8x2g3b.txt' === file2bib.sh === id: cord-017758-zfudssm9 author: Fong, I. W. title: Emergence of New Tickborne Infections date: 2017-02-08 pages: extension: .txt txt: ./txt/cord-017758-zfudssm9.txt cache: ./cache/cord-017758-zfudssm9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017758-zfudssm9.txt' === file2bib.sh === id: cord-017249-la5sum39 author: Feldblyum, Tamara V. title: Seasonal and Pandemic Influenza Surveillance and Disease Severity date: 2015-05-12 pages: extension: .txt txt: ./txt/cord-017249-la5sum39.txt cache: ./cache/cord-017249-la5sum39.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-017249-la5sum39.txt' === file2bib.sh === id: cord-018089-m94q75xn author: Mubareka, Samira title: Influenza Virus: The Biology of a Changing Virus date: 2010-06-18 pages: extension: .txt txt: ./txt/cord-018089-m94q75xn.txt cache: ./cache/cord-018089-m94q75xn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-018089-m94q75xn.txt' === file2bib.sh === id: cord-017287-70lk77zb author: Sánchez, Gloria title: Survival of Enteric Viruses in the Environment and Food date: 2016-08-26 pages: extension: .txt txt: ./txt/cord-017287-70lk77zb.txt cache: ./cache/cord-017287-70lk77zb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-017287-70lk77zb.txt' === file2bib.sh === id: cord-018441-r6wwpfcy author: Taylor, Milton W. title: Emerging Viruses date: 2014-07-22 pages: extension: .txt txt: ./txt/cord-018441-r6wwpfcy.txt cache: ./cache/cord-018441-r6wwpfcy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-018441-r6wwpfcy.txt' === file2bib.sh === id: cord-018040-k0h5ejjt author: Ilyinskii, P. title: Aspects of Microparticle Utilization for Potentiation of Novel Vaccines: Promises and Risks date: 2009 pages: extension: .txt txt: ./txt/cord-018040-k0h5ejjt.txt cache: ./cache/cord-018040-k0h5ejjt.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-018040-k0h5ejjt.txt' === file2bib.sh === id: cord-017764-h1w9gbxk author: Meanwell, Nicholas A. title: The Discovery and Development of Daclatasvir: An Inhibitor of the Hepatitis C Virus NS5A Replication Complex date: 2018-06-08 pages: extension: .txt txt: ./txt/cord-017764-h1w9gbxk.txt cache: ./cache/cord-017764-h1w9gbxk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017764-h1w9gbxk.txt' === file2bib.sh === id: cord-021034-hnw7a3a1 author: Mahony, James B. title: Negative staining in the detection of viruses in clinical specimens date: 2002-10-09 pages: extension: .txt txt: ./txt/cord-021034-hnw7a3a1.txt cache: ./cache/cord-021034-hnw7a3a1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-021034-hnw7a3a1.txt' === file2bib.sh === id: cord-017167-8cdbcrh7 author: Ahola, Tero title: Functions of Chikungunya Virus Nonstructural Proteins date: 2016-12-03 pages: extension: .txt txt: ./txt/cord-017167-8cdbcrh7.txt cache: ./cache/cord-017167-8cdbcrh7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017167-8cdbcrh7.txt' === file2bib.sh === id: cord-012418-6ralcn8p author: Schwanke, Hella title: Of Keeping and Tipping the Balance: Host Regulation and Viral Modulation of IRF3-Dependent IFNB1 Expression date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-012418-6ralcn8p.txt cache: ./cache/cord-012418-6ralcn8p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-012418-6ralcn8p.txt' === file2bib.sh === id: cord-021588-ec7udsmw author: Craighead, John E. title: Enteric Viral Disease date: 2007-05-09 pages: extension: .txt txt: ./txt/cord-021588-ec7udsmw.txt cache: ./cache/cord-021588-ec7udsmw.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-021588-ec7udsmw.txt' === file2bib.sh === id: cord-017326-1caeui30 author: Seay, Montrell title: Digesting Oneself and Digesting Microbes: Autophagy as a Host Response to Viral Infection date: 2005 pages: extension: .txt txt: ./txt/cord-017326-1caeui30.txt cache: ./cache/cord-017326-1caeui30.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017326-1caeui30.txt' === file2bib.sh === id: cord-018437-yjvwa1ot author: Mitchell, Michael title: Taxonomy date: 2013-08-26 pages: extension: .txt txt: ./txt/cord-018437-yjvwa1ot.txt cache: ./cache/cord-018437-yjvwa1ot.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018437-yjvwa1ot.txt' === 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 === id: cord-021805-2j07zw6q author: Epstein, Jonathan H. title: Emerging Diseases in Bats date: 2018-09-28 pages: extension: .txt txt: ./txt/cord-021805-2j07zw6q.txt cache: ./cache/cord-021805-2j07zw6q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-021805-2j07zw6q.txt' === 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' === file2bib.sh === id: cord-018804-wj35q88f author: Lázaro, Ester title: Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity date: 2007 pages: extension: .txt txt: ./txt/cord-018804-wj35q88f.txt cache: ./cache/cord-018804-wj35q88f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-018804-wj35q88f.txt' === file2bib.sh === id: cord-017527-ylng1us2 author: Herman, Philippe title: Biosafety Recommendations on the Handling of Animal Cell Cultures date: 2014-11-05 pages: extension: .txt txt: ./txt/cord-017527-ylng1us2.txt cache: ./cache/cord-017527-ylng1us2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-017527-ylng1us2.txt' === file2bib.sh === id: cord-017748-xy26tk0t author: Georgiev, Vassil St. title: Influenza date: 2009 pages: extension: .txt txt: ./txt/cord-017748-xy26tk0t.txt cache: ./cache/cord-017748-xy26tk0t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017748-xy26tk0t.txt' === file2bib.sh === id: cord-021116-rh0e4n2w author: Lippens, Ronnie title: Viral Contagion and Anti-Terrorism: Notes on Medical Emergency, Legality and Diplomacy date: 2004 pages: extension: .txt txt: ./txt/cord-021116-rh0e4n2w.txt cache: ./cache/cord-021116-rh0e4n2w.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-021116-rh0e4n2w.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-022254-8y5sq72c author: Nathanson, Neal title: IMMUNOSUPPRESSION AND VIRUS INFECTION OF RODENTS date: 2012-12-02 pages: extension: .txt txt: ./txt/cord-022254-8y5sq72c.txt cache: ./cache/cord-022254-8y5sq72c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022254-8y5sq72c.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-016475-7ldxvbpz author: Pleschka, Stephan title: Anti-viral approaches against influenza viruses date: 2006 pages: extension: .txt txt: ./txt/cord-016475-7ldxvbpz.txt cache: ./cache/cord-016475-7ldxvbpz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016475-7ldxvbpz.txt' === file2bib.sh === id: cord-018166-savdgy0u author: Bosch, Albert title: Survival and Transport of Enteric Viruses in the Environment date: 2006 pages: extension: .txt txt: ./txt/cord-018166-savdgy0u.txt cache: ./cache/cord-018166-savdgy0u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-018166-savdgy0u.txt' === file2bib.sh === id: cord-017752-ofzm3x3a author: nan title: Theories of Carcinogenesis date: 2007 pages: extension: .txt txt: ./txt/cord-017752-ofzm3x3a.txt cache: ./cache/cord-017752-ofzm3x3a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017752-ofzm3x3a.txt' === file2bib.sh === id: cord-022980-tkii8se4 author: nan title: Diarrhea date: 2008-03-05 pages: extension: .txt txt: ./txt/cord-022980-tkii8se4.txt cache: ./cache/cord-022980-tkii8se4.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-022980-tkii8se4.txt' === file2bib.sh === id: cord-023034-j8zwcfys author: Osterhaus, Albert D. M. E. title: Feline Infectious Peritonitis Virus: II. Propagation in Suckling Mouse Brain date: 2010-05-13 pages: extension: .txt txt: ./txt/cord-023034-j8zwcfys.txt cache: ./cache/cord-023034-j8zwcfys.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023034-j8zwcfys.txt' === file2bib.sh === id: cord-018706-gykw2nvt author: Yadav, Mahendra Pal title: Emerging and Transboundary Animal Viral Diseases: Perspectives and Preparedness date: 2020-02-23 pages: extension: .txt txt: ./txt/cord-018706-gykw2nvt.txt cache: ./cache/cord-018706-gykw2nvt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-018706-gykw2nvt.txt' === file2bib.sh === id: cord-022822-7346069t author: nan title: Infections, Immunity & their Effects on Asthma date: 2006-10-02 pages: extension: .txt txt: ./txt/cord-022822-7346069t.txt cache: ./cache/cord-022822-7346069t.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-022822-7346069t.txt' === file2bib.sh === id: cord-021552-6jbm869r author: HURST, CHRISTON J. title: Relationship Between Humans and Their Viruses date: 2007-05-09 pages: extension: .txt txt: ./txt/cord-021552-6jbm869r.txt cache: ./cache/cord-021552-6jbm869r.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-021552-6jbm869r.txt' === file2bib.sh === id: cord-023092-unjv71qv author: Horzinek, Prof. Dr Marian C. title: Feline leukaemia prophylaxis date: 2008-04-10 pages: extension: .txt txt: ./txt/cord-023092-unjv71qv.txt cache: ./cache/cord-023092-unjv71qv.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-023092-unjv71qv.txt' === file2bib.sh === id: cord-018017-c8myq6bi author: Iversen, Patrick L. title: The Threat from Viruses date: 2018-09-30 pages: extension: .txt txt: ./txt/cord-018017-c8myq6bi.txt cache: ./cache/cord-018017-c8myq6bi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-018017-c8myq6bi.txt' === file2bib.sh === id: cord-008556-oetrdm8g author: Kozak, Marilyn title: Regulation of Protein Synthesis in Virus-Infected Animal Cells date: 2008-03-01 pages: extension: .txt txt: ./txt/cord-008556-oetrdm8g.txt cache: ./cache/cord-008556-oetrdm8g.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-008556-oetrdm8g.txt' === file2bib.sh === id: cord-018364-b06084r1 author: LaBrunda, Michelle title: The Emerging Threat of Ebola date: 2019-06-07 pages: extension: .txt txt: ./txt/cord-018364-b06084r1.txt cache: ./cache/cord-018364-b06084r1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018364-b06084r1.txt' === file2bib.sh === id: cord-008716-38sqkh9m author: Schmidt, Alexander C title: Current research on respiratory viral infections: Third International Symposium date: 2001-06-01 pages: extension: .txt txt: ./txt/cord-008716-38sqkh9m.txt cache: ./cache/cord-008716-38sqkh9m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-008716-38sqkh9m.txt' === file2bib.sh === id: cord-023622-tul7bonh author: nan title: Rotaviruses of Man and Animals date: 1975-02-01 pages: extension: .txt txt: ./txt/cord-023622-tul7bonh.txt cache: ./cache/cord-023622-tul7bonh.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-023622-tul7bonh.txt' === file2bib.sh === id: cord-022349-z8w1wkm8 author: Beeler, Judy A. title: Human and Animal Viruses date: 2007-09-02 pages: extension: .txt txt: ./txt/cord-022349-z8w1wkm8.txt cache: ./cache/cord-022349-z8w1wkm8.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-022349-z8w1wkm8.txt' === file2bib.sh === id: cord-022453-xe5v7947 author: BABIUK, L.A. title: Viral Gastroenteritis in Ruminants date: 2013-11-17 pages: extension: .txt txt: ./txt/cord-022453-xe5v7947.txt cache: ./cache/cord-022453-xe5v7947.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-022453-xe5v7947.txt' === file2bib.sh === id: cord-022960-u4s23x1r author: Pihlstrom, Bruce Lee title: Selections from the current literature date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-022960-u4s23x1r.txt cache: ./cache/cord-022960-u4s23x1r.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-022960-u4s23x1r.txt' === file2bib.sh === id: cord-022324-tcltmhi7 author: Barthold, Stephen W. title: MOUSE HEPATITIS VIRUS BIOLOGY AND EPIZOOTIOLOGY date: 2012-12-02 pages: extension: .txt txt: ./txt/cord-022324-tcltmhi7.txt cache: ./cache/cord-022324-tcltmhi7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022324-tcltmhi7.txt' === file2bib.sh === id: cord-017008-c7skxte0 author: Méthot, Pierre-Olivier title: Emerging Disease and the Evolution of Virulence: The Case of the 1918–1919 Influenza Pandemic date: 2014-08-22 pages: extension: .txt txt: ./txt/cord-017008-c7skxte0.txt cache: ./cache/cord-017008-c7skxte0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017008-c7skxte0.txt' === file2bib.sh === id: cord-022378-ovxmy1as author: Cook, Jane K.A. title: Coronaviridae date: 2009-05-15 pages: extension: .txt txt: ./txt/cord-022378-ovxmy1as.txt cache: ./cache/cord-022378-ovxmy1as.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-022378-ovxmy1as.txt' === file2bib.sh === id: cord-021990-a8ku5rke author: Tyring, Stephen K. title: Syndromal Tropical Dermatology date: 2016-12-02 pages: extension: .txt txt: ./txt/cord-021990-a8ku5rke.txt cache: ./cache/cord-021990-a8ku5rke.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-021990-a8ku5rke.txt' === file2bib.sh === id: cord-023564-kpqvyxxe author: nan title: Viral gastroenteritis: Causes, pathophysiology, immunology, treatment, and epidemiology date: 2004-09-14 pages: extension: .txt txt: ./txt/cord-023564-kpqvyxxe.txt cache: ./cache/cord-023564-kpqvyxxe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-023564-kpqvyxxe.txt' === file2bib.sh === id: cord-018811-zhwr3h07 author: Oxford, John title: Influenza Vaccines Have a Short but Illustrious History of Dedicated Science Enabling the Rapid Global Production of A/Swine (H1N1) Vaccine in the Current Pandemic date: 2010-06-18 pages: extension: .txt txt: ./txt/cord-018811-zhwr3h07.txt cache: ./cache/cord-018811-zhwr3h07.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018811-zhwr3h07.txt' === file2bib.sh === id: cord-020969-lh2ergpm author: STRAUSS, JAMES H. title: Gene Therapy date: 2012-07-27 pages: extension: .txt txt: ./txt/cord-020969-lh2ergpm.txt cache: ./cache/cord-020969-lh2ergpm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-020969-lh2ergpm.txt' === file2bib.sh === id: cord-018555-3lta1tbp author: Overstreet, Robin M. title: Host–Symbiont Relationships: Understanding the Change from Guest to Pest date: 2016-01-06 pages: extension: .txt txt: ./txt/cord-018555-3lta1tbp.txt cache: ./cache/cord-018555-3lta1tbp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018555-3lta1tbp.txt' === file2bib.sh === id: cord-021375-lca26xum author: Voelkner, Nadine title: Riding the Shi: From Infection Barriers to the Microbial City date: 2019-08-23 pages: extension: .txt txt: ./txt/cord-021375-lca26xum.txt cache: ./cache/cord-021375-lca26xum.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-021375-lca26xum.txt' === file2bib.sh === id: cord-020235-stcrozdw author: nan title: Abstracts of Papers Presented at the 38th Meeting of the Deutsche Gesellschaft für Hygiene und Mikrobiologie, Virology Section, Göttingen, 5.–8.10.1981 date: 2012-03-15 pages: extension: .txt txt: ./txt/cord-020235-stcrozdw.txt cache: ./cache/cord-020235-stcrozdw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-020235-stcrozdw.txt' === file2bib.sh === id: cord-023740-g84fa45m author: Oldstone, Michael B.A. title: Mimicry by Virus of Host Molecules: Implications for Autoimmune Disease date: 2014-06-27 pages: extension: .txt txt: ./txt/cord-023740-g84fa45m.txt cache: ./cache/cord-023740-g84fa45m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023740-g84fa45m.txt' === file2bib.sh === id: cord-018265-twp33bb6 author: Becker, Pablo D. title: Community-acquired pneumonia: paving the way towards new vaccination concepts date: 2007 pages: extension: .txt txt: ./txt/cord-018265-twp33bb6.txt cache: ./cache/cord-018265-twp33bb6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-018265-twp33bb6.txt' === file2bib.sh === id: cord-020712-l9cn0n99 author: Ohnishi, Shun-Ichi title: Chapter 9 Fusion of Viral Envelopes with Cellular Membranes date: 2008-05-30 pages: extension: .txt txt: ./txt/cord-020712-l9cn0n99.txt cache: ./cache/cord-020712-l9cn0n99.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-020712-l9cn0n99.txt' === file2bib.sh === id: cord-023608-w2g7v7g1 author: nan title: ISAR News date: 2017-10-20 pages: extension: .txt txt: ./txt/cord-023608-w2g7v7g1.txt cache: ./cache/cord-023608-w2g7v7g1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-023608-w2g7v7g1.txt' === file2bib.sh === id: cord-025181-eg108wcd author: Zheng, Zhihang title: Establishment of Murine Infection Models with Biological Clones of Dengue Viruses Derived from a Single Clinical Viral Isolate date: 2020-05-25 pages: extension: .txt txt: ./txt/cord-025181-eg108wcd.txt cache: ./cache/cord-025181-eg108wcd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-025181-eg108wcd.txt' === file2bib.sh === id: cord-022674-90g0461f author: Hurst, Christon J. title: Detecting Viruses in Water date: 1989-09-01 pages: extension: .txt txt: ./txt/cord-022674-90g0461f.txt cache: ./cache/cord-022674-90g0461f.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-022674-90g0461f.txt' === file2bib.sh === id: cord-020714-h1fevqcw author: Compans, Richard W. title: Membrane Glycoproteins of Enveloped Viruses date: 2008-05-30 pages: extension: .txt txt: ./txt/cord-020714-h1fevqcw.txt cache: ./cache/cord-020714-h1fevqcw.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-020714-h1fevqcw.txt' === file2bib.sh === id: cord-023831-93xqrblk author: Rosenberg, Helene F. title: Pneumonia Virus of Mice (PVM): Exploring Novel Therapeutic Options In a Severe Respiratory Disease Model date: 2010-03-30 pages: extension: .txt txt: ./txt/cord-023831-93xqrblk.txt cache: ./cache/cord-023831-93xqrblk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-023831-93xqrblk.txt' === file2bib.sh === id: cord-018639-0g1ov96t author: Kurpiers, Laura A. title: Bushmeat and Emerging Infectious Diseases: Lessons from Africa date: 2015-09-21 pages: extension: .txt txt: ./txt/cord-018639-0g1ov96t.txt cache: ./cache/cord-018639-0g1ov96t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018639-0g1ov96t.txt' === file2bib.sh === id: cord-023200-3caevjvh author: Falanga, Annarita title: Membranotropic peptides mediating viral entry date: 2018-02-13 pages: extension: .txt txt: ./txt/cord-023200-3caevjvh.txt cache: ./cache/cord-023200-3caevjvh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023200-3caevjvh.txt' === file2bib.sh === id: cord-019051-gtruu1op author: Weber, Olaf title: The role of viruses in the etiology and pathogenesis of common cold date: 2009-11-10 pages: extension: .txt txt: ./txt/cord-019051-gtruu1op.txt cache: ./cache/cord-019051-gtruu1op.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-019051-gtruu1op.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-022399-66mzbynu author: Hopkins, Graham title: Basic microbiology date: 2009-05-15 pages: extension: .txt txt: ./txt/cord-022399-66mzbynu.txt cache: ./cache/cord-022399-66mzbynu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-022399-66mzbynu.txt' === file2bib.sh === id: cord-023293-te0n2vvp author: Carter, M. J. title: Caliciviruses date: 2005-10-18 pages: extension: .txt txt: ./txt/cord-023293-te0n2vvp.txt cache: ./cache/cord-023293-te0n2vvp.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-023293-te0n2vvp.txt' === file2bib.sh === id: cord-023584-yaxawqhj author: Bucknall, R.A. title: The Continuing Search for Antiviral Drugs date: 2008-04-10 pages: extension: .txt txt: ./txt/cord-023584-yaxawqhj.txt cache: ./cache/cord-023584-yaxawqhj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023584-yaxawqhj.txt' === file2bib.sh === id: cord-022348-w7z97wir author: Sola, Monica title: Drift and Conservatism in RNA Virus Evolution: Are They Adapting or Merely Changing? date: 2007-09-02 pages: extension: .txt txt: ./txt/cord-022348-w7z97wir.txt cache: ./cache/cord-022348-w7z97wir.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-022348-w7z97wir.txt' === file2bib.sh === id: cord-023678-9q68ftr9 author: Hierholzer, J.C. title: Virus isolation and quantitation date: 2007-09-02 pages: extension: .txt txt: ./txt/cord-023678-9q68ftr9.txt cache: ./cache/cord-023678-9q68ftr9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023678-9q68ftr9.txt' === file2bib.sh === id: cord-021770-zn7na974 author: Slifka, Mark K. title: Passive Immunization date: 2017-07-17 pages: extension: .txt txt: ./txt/cord-021770-zn7na974.txt cache: ./cache/cord-021770-zn7na974.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-021770-zn7na974.txt' === file2bib.sh === id: cord-023721-e0zp2gux author: Meissner, H. Cody title: Bronchiolitis date: 2013-02-10 pages: extension: .txt txt: ./txt/cord-023721-e0zp2gux.txt cache: ./cache/cord-023721-e0zp2gux.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-023721-e0zp2gux.txt' === file2bib.sh === id: cord-026130-ki7bn67o author: Sharma, Anand Kumar title: Novel Coronavirus Disease (COVID-19) date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-026130-ki7bn67o.txt cache: ./cache/cord-026130-ki7bn67o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-026130-ki7bn67o.txt' === file2bib.sh === id: cord-022196-1tionxun author: FENNER, FRANK title: The Nature and Classification of Animal Viruses date: 2013-11-17 pages: extension: .txt txt: ./txt/cord-022196-1tionxun.txt cache: ./cache/cord-022196-1tionxun.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-022196-1tionxun.txt' === file2bib.sh === id: cord-029419-b0w9nomq author: Matthews, Adam title: Review of Mark Honigsbaum (2020). The Pandemic Century—A History of Global Contagion from the Spanish Flu to Covid-19: Cambridge, MA: Penguin. 321 pp. ISBN 9780753558287 date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-029419-b0w9nomq.txt cache: ./cache/cord-029419-b0w9nomq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-029419-b0w9nomq.txt' === file2bib.sh === id: cord-021413-1ht1xm88 author: Kraft, Lisbeth M. title: Viral Diseases of the Digestive System date: 2013-10-21 pages: extension: .txt txt: ./txt/cord-021413-1ht1xm88.txt cache: ./cache/cord-021413-1ht1xm88.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-021413-1ht1xm88.txt' === file2bib.sh === id: cord-016990-ot1wi3xi author: Zaki, Sherif R. title: Viral Infections of the Lung date: 2008 pages: extension: .txt txt: ./txt/cord-016990-ot1wi3xi.txt cache: ./cache/cord-016990-ot1wi3xi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-016990-ot1wi3xi.txt' === file2bib.sh === id: cord-021465-2pj26fmv author: PERDUE, MICHAEL L. title: Impact of Avian Viruses date: 2007-05-09 pages: extension: .txt txt: ./txt/cord-021465-2pj26fmv.txt cache: ./cache/cord-021465-2pj26fmv.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-021465-2pj26fmv.txt' === file2bib.sh === id: cord-020756-d9f5fd7x author: de Jong, Menno Douwe title: Avian Influenza Viruses and Pandemic Influenza date: 2007 pages: extension: .txt txt: ./txt/cord-020756-d9f5fd7x.txt cache: ./cache/cord-020756-d9f5fd7x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-020756-d9f5fd7x.txt' === file2bib.sh === id: cord-103688-n7hzpbyf author: Wang, Lina title: VirusDIP: Virus Data Integration Platform date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-103688-n7hzpbyf.txt cache: ./cache/cord-103688-n7hzpbyf.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-103688-n7hzpbyf.txt' === file2bib.sh === id: cord-022439-8wy7rpqv author: DENMAN, A.M. title: Viral Etiology of Polymyositis/Dermatomyositis date: 2013-11-17 pages: extension: .txt txt: ./txt/cord-022439-8wy7rpqv.txt cache: ./cache/cord-022439-8wy7rpqv.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-022439-8wy7rpqv.txt' === file2bib.sh === id: cord-026641-eemp6b5j author: Kabiljo, Julijan title: From threat to cure: understanding of virus-induced cell death leads to highly immunogenic oncolytic influenza viruses date: 2020-06-11 pages: extension: .txt txt: ./txt/cord-026641-eemp6b5j.txt cache: ./cache/cord-026641-eemp6b5j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-026641-eemp6b5j.txt' === file2bib.sh === id: cord-024188-d7tnku8z author: Nissen, Michael D. title: Respiratory Infections date: 2010-03-27 pages: extension: .txt txt: ./txt/cord-024188-d7tnku8z.txt cache: ./cache/cord-024188-d7tnku8z.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-024188-d7tnku8z.txt' === file2bib.sh === id: cord-102704-wfuzk2dp author: Meza, Diana K. title: Predicting the presence and titer of rabies virus neutralizing antibodies from low-volume serum samples in low-containment facilities date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-102704-wfuzk2dp.txt cache: ./cache/cord-102704-wfuzk2dp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-102704-wfuzk2dp.txt' === file2bib.sh === id: cord-030961-5gzc7193 author: Wang, Jiajun title: Adhesive contact between cylindrical (Ebola) and spherical (SARS-CoV-2) viral particles and a cell membrane date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-030961-5gzc7193.txt cache: ./cache/cord-030961-5gzc7193.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-030961-5gzc7193.txt' === file2bib.sh === id: cord-102862-oq54sfx6 author: Dastjerdi, Akbar M. title: Characterisation of the bovine enteric calici-like virus, Newbury agent 1 date: 2000-11-01 pages: extension: .txt txt: ./txt/cord-102862-oq54sfx6.txt cache: ./cache/cord-102862-oq54sfx6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-102862-oq54sfx6.txt' === file2bib.sh === id: cord-023925-qrr7jcwe author: Verhoef, Jan title: A8 Immune response in human pathology: Infections caused by bacteria, viruses, fungi, and parasites date: 2011-07-12 pages: extension: .txt txt: ./txt/cord-023925-qrr7jcwe.txt cache: ./cache/cord-023925-qrr7jcwe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-023925-qrr7jcwe.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 4 resourceName b'cord-016499-5iqpl23p.txt' === file2bib.sh === id: cord-023731-jqgervt7 author: FENNER, FRANK title: Laboratory Diagnosis of Viral Diseases date: 2014-06-27 pages: extension: .txt txt: ./txt/cord-023731-jqgervt7.txt cache: ./cache/cord-023731-jqgervt7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-023731-jqgervt7.txt' === file2bib.sh === id: cord-022947-ruizhgwh author: Elliot, Elisa L title: Indicator organisms for estuarine and marine waters date: 2006-03-27 pages: extension: .txt txt: ./txt/cord-022947-ruizhgwh.txt cache: ./cache/cord-022947-ruizhgwh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-022947-ruizhgwh.txt' === file2bib.sh === id: cord-048368-wm4c7rk6 author: Evseenko, Vasily A title: Experimental infection of H5N1 HPAI in BALB/c mice date: 2007-07-27 pages: extension: .txt txt: ./txt/cord-048368-wm4c7rk6.txt cache: ./cache/cord-048368-wm4c7rk6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-048368-wm4c7rk6.txt' === file2bib.sh === id: cord-027654-k0uby99n author: Nabel, Gary J. title: The development of gene-based vectors for immunization date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-027654-k0uby99n.txt cache: ./cache/cord-027654-k0uby99n.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-027654-k0uby99n.txt' === file2bib.sh === id: cord-025704-icedihm2 author: Pawestri, Hana A. title: Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008–2015 date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-025704-icedihm2.txt cache: ./cache/cord-025704-icedihm2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-025704-icedihm2.txt' === file2bib.sh === id: cord-104286-5yw4zwo4 author: Doane, F. W. title: Virus morphology as an aid for rapid diagnosis. date: 1980 pages: extension: .txt txt: ./txt/cord-104286-5yw4zwo4.txt cache: ./cache/cord-104286-5yw4zwo4.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-104286-5yw4zwo4.txt' === file2bib.sh === id: cord-026340-2nf97zvc author: Singh, Ranjana title: Chloroquine: A Potential Drug in the COVID-19 Scenario date: 2020-06-07 pages: extension: .txt txt: ./txt/cord-026340-2nf97zvc.txt cache: ./cache/cord-026340-2nf97zvc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-026340-2nf97zvc.txt' === file2bib.sh === id: cord-023488-jf2xl3vl author: Le Duc, James W. title: Emerging Viral Diseases: Why We Need to Worry about Bats, Camels, and Airplanes date: 2016-02-12 pages: extension: .txt txt: ./txt/cord-023488-jf2xl3vl.txt cache: ./cache/cord-023488-jf2xl3vl.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-023488-jf2xl3vl.txt' === file2bib.sh === id: cord-023705-3q9yr6np author: FENNER, FRANK title: Viral Replication date: 2014-06-27 pages: extension: .txt txt: ./txt/cord-023705-3q9yr6np.txt cache: ./cache/cord-023705-3q9yr6np.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-023705-3q9yr6np.txt' === file2bib.sh === id: cord-022163-7klzsrpu author: Broder, Christopher C. title: Henipaviruses date: 2016-09-09 pages: extension: .txt txt: ./txt/cord-022163-7klzsrpu.txt cache: ./cache/cord-022163-7klzsrpu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022163-7klzsrpu.txt' === file2bib.sh === id: cord-102383-m5ahicqb author: Romano, Alessandra title: Energy dynamics for systemic configurations of virus-host co-evolution date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-102383-m5ahicqb.txt cache: ./cache/cord-102383-m5ahicqb.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-102383-m5ahicqb.txt' === file2bib.sh === id: cord-171099-d0qr84xg author: Buehler, Markus J. title: Nanomechanical sonification of the 2019-nCoV coronavirus spike protein through a materiomusical approach date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-171099-d0qr84xg.txt cache: ./cache/cord-171099-d0qr84xg.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-171099-d0qr84xg.txt' === file2bib.sh === id: cord-253594-9gbo8viu author: Konieczny, Leszek title: The COVID-19 Puzzle date: 2020-05-31 pages: extension: .txt txt: ./txt/cord-253594-9gbo8viu.txt cache: ./cache/cord-253594-9gbo8viu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253594-9gbo8viu.txt' === file2bib.sh === id: cord-161674-nk0wie0w author: Liu, Zhi title: Implications of the virus-encoded miRNA and host miRNA in the pathogenicity of SARS-CoV-2 date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-161674-nk0wie0w.txt cache: ./cache/cord-161674-nk0wie0w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-161674-nk0wie0w.txt' === file2bib.sh === id: cord-027752-xcpv9k22 author: Bresalier, Michael title: Uses of a Pandemic: Forging the Identities of Influenza and Virus Research in Interwar Britain date: 2011-12-15 pages: extension: .txt txt: ./txt/cord-027752-xcpv9k22.txt cache: ./cache/cord-027752-xcpv9k22.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-027752-xcpv9k22.txt' === file2bib.sh === id: cord-025995-nxeg03xj author: Gerba, Charles P. title: Pathogen Removal from Wastewater during Groundwater Recharge date: 2013-11-17 pages: extension: .txt txt: ./txt/cord-025995-nxeg03xj.txt cache: ./cache/cord-025995-nxeg03xj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-025995-nxeg03xj.txt' === 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' === file2bib.sh === id: cord-103135-nly9vojr author: Fletcher, Nicola F. title: A novel antiviral formulation inhibits a range of enveloped viruses date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-103135-nly9vojr.txt cache: ./cache/cord-103135-nly9vojr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-103135-nly9vojr.txt' === file2bib.sh === id: cord-022830-tvt58gtn author: Li, Dan title: Fate of Foodborne Viruses in the “Farm to Fork” Chain of Fresh Produce date: 2015-10-08 pages: extension: .txt txt: ./txt/cord-022830-tvt58gtn.txt cache: ./cache/cord-022830-tvt58gtn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022830-tvt58gtn.txt' === file2bib.sh === id: cord-102908-sr7j8z9c author: Mersmann, Sophia F. title: Learning to count: determining the stoichiometry of bio-molecular complexes using fluorescence microscopy and statistical modelling date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-102908-sr7j8z9c.txt cache: ./cache/cord-102908-sr7j8z9c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-102908-sr7j8z9c.txt' === file2bib.sh === id: cord-253143-73dsc6q3 author: Tang, Julian W. title: Emerging, Novel, and Known Influenza Virus Infections in Humans date: 2010-08-02 pages: extension: .txt txt: ./txt/cord-253143-73dsc6q3.txt cache: ./cache/cord-253143-73dsc6q3.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-253143-73dsc6q3.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 4 resourceName b'cord-022084-hap7flng.txt' === file2bib.sh === id: cord-102898-eyyd7ent author: Rizvi, Vaseef A. title: Translation regulation of Japanese encephalitis virus revealed by ribosome profiling date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-102898-eyyd7ent.txt cache: ./cache/cord-102898-eyyd7ent.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-102898-eyyd7ent.txt' === file2bib.sh === id: cord-023726-2fduzqyb author: STRAUSS, JAMES H. title: The Structure of Viruses date: 2012-07-27 pages: extension: .txt txt: ./txt/cord-023726-2fduzqyb.txt cache: ./cache/cord-023726-2fduzqyb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-023726-2fduzqyb.txt' === file2bib.sh === id: cord-076082-4kpkhz0o author: Lam, Tommy Tsan-Yuk title: Evolutionary and Transmission Dynamics of Reassortant H5N1 Influenza Virus in Indonesia date: 2008-08-22 pages: extension: .txt txt: ./txt/cord-076082-4kpkhz0o.txt cache: ./cache/cord-076082-4kpkhz0o.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-076082-4kpkhz0o.txt' === file2bib.sh === id: cord-203232-1nnqx1g9 author: Canturk, Semih title: Machine-Learning Driven Drug Repurposing for COVID-19 date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-203232-1nnqx1g9.txt cache: ./cache/cord-203232-1nnqx1g9.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-203232-1nnqx1g9.txt' === file2bib.sh === id: cord-212761-4bwatc2r author: Contoyiannis, Y. title: On the effectiveness of imposing restrictive measures in a graded Self-Organized Criticality epidemic spread model The case of COVID-19 date: 2020-04-01 pages: extension: .txt txt: ./txt/cord-212761-4bwatc2r.txt cache: ./cache/cord-212761-4bwatc2r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-212761-4bwatc2r.txt' === file2bib.sh === id: cord-214795-8jweuq50 author: Mongia, Aanchal title: DeepVir -- Graphical Deep Matrix Factorization for"In Silico"Antiviral Repositioning: Application to COVID-19 date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-214795-8jweuq50.txt cache: ./cache/cord-214795-8jweuq50.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-214795-8jweuq50.txt' === file2bib.sh === id: cord-022305-uvor9rts author: Jacoby, Robert O. title: Viral Diseases date: 2013-11-17 pages: extension: .txt txt: ./txt/cord-022305-uvor9rts.txt cache: ./cache/cord-022305-uvor9rts.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022305-uvor9rts.txt' === file2bib.sh === id: cord-035163-tqh5wv12 author: Ijaz, M. Khalid title: Combating SARS-CoV-2: leveraging microbicidal experiences with other emerging/re-emerging viruses date: 2020-09-08 pages: extension: .txt txt: ./txt/cord-035163-tqh5wv12.txt cache: ./cache/cord-035163-tqh5wv12.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-035163-tqh5wv12.txt' === file2bib.sh === id: cord-027473-8zerjwa0 author: Roos, Yrjö H. title: Water and Pathogenic Viruses Inactivation—Food Engineering Perspectives date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-027473-8zerjwa0.txt cache: ./cache/cord-027473-8zerjwa0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 8 resourceName b'cord-027473-8zerjwa0.txt' === 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 2 resourceName b'cord-252012-hdjbxah8.txt' === file2bib.sh === id: cord-252397-qlu7dilh author: Johnson, Reed F. title: Intratracheal exposure of common marmosets to MERS-CoV Jordan-n3/2012 or MERS-CoV EMC/2012 isolates does not result in lethal disease date: 2015-11-01 pages: extension: .txt txt: ./txt/cord-252397-qlu7dilh.txt cache: ./cache/cord-252397-qlu7dilh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252397-qlu7dilh.txt' === file2bib.sh === id: cord-102905-rlee32x7 author: Leis, Jonathan title: Ilaprazole and other novel prazole-based compounds that bind Tsg101 inhibit viral budding of HSV-1/2 and HIV from cells date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-102905-rlee32x7.txt cache: ./cache/cord-102905-rlee32x7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-102905-rlee32x7.txt' === file2bib.sh === id: cord-255075-6azu6k3h author: Zhuang, Jianjian title: Advanced “lab-on-a-chip” to detect viruses – Current challenges and future perspectives date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-255075-6azu6k3h.txt cache: ./cache/cord-255075-6azu6k3h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-255075-6azu6k3h.txt' === file2bib.sh === id: cord-252456-971d0sir author: Hemida, Maged Gomaa title: The SARS-CoV-2 outbreak from a one health perspective date: 2020-03-16 pages: extension: .txt txt: ./txt/cord-252456-971d0sir.txt cache: ./cache/cord-252456-971d0sir.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252456-971d0sir.txt' === file2bib.sh === id: cord-022393-s26d54ew author: E. Newcomer, Christian title: Zoonoses and Other Human Health Hazards date: 2007-09-02 pages: extension: .txt txt: ./txt/cord-022393-s26d54ew.txt cache: ./cache/cord-022393-s26d54ew.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-022393-s26d54ew.txt' === file2bib.sh === id: cord-022354-aqtceqqo author: HUNTER, ERIC title: Membrane Insertion and Transport of Viral Glycoproteins: A Mutational Analysis date: 2012-12-02 pages: extension: .txt txt: ./txt/cord-022354-aqtceqqo.txt cache: ./cache/cord-022354-aqtceqqo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-022354-aqtceqqo.txt' === file2bib.sh === id: cord-252466-usrpodjx author: Yun, Nadezhda E. title: Pathogenesis of Lassa Fever date: 2012-10-09 pages: extension: .txt txt: ./txt/cord-252466-usrpodjx.txt cache: ./cache/cord-252466-usrpodjx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252466-usrpodjx.txt' === file2bib.sh === id: cord-252871-qfrpuy3t author: Nasir, Arshan title: Investigating the Concept and Origin of Viruses date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-252871-qfrpuy3t.txt cache: ./cache/cord-252871-qfrpuy3t.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-252871-qfrpuy3t.txt' === file2bib.sh === id: cord-048466-fj9l8che author: Bragstad, Karoline title: The evolution of human influenza A viruses from 1999 to 2006: A complete genome study date: 2008-03-07 pages: extension: .txt txt: ./txt/cord-048466-fj9l8che.txt cache: ./cache/cord-048466-fj9l8che.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-048466-fj9l8che.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-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 3 resourceName b'cord-151024-qe7c2uks.txt' === file2bib.sh === id: cord-021499-up5vftj4 author: Brayton, Cory title: Viral Infections date: 2007-09-02 pages: extension: .txt txt: ./txt/cord-021499-up5vftj4.txt cache: ./cache/cord-021499-up5vftj4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-021499-up5vftj4.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-255623-qdpdsye9.txt cache: ./cache/cord-255623-qdpdsye9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255623-qdpdsye9.txt' === file2bib.sh === id: cord-022128-r8el8nqm author: Domingo, Esteban title: Molecular basis of genetic variation of viruses: error-prone replication date: 2019-11-08 pages: extension: .txt txt: ./txt/cord-022128-r8el8nqm.txt cache: ./cache/cord-022128-r8el8nqm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022128-r8el8nqm.txt' === file2bib.sh === id: cord-104317-t30dg6oj author: Parker, Michael T. title: An Ecological Framework of the Human Virome Provides Classification of Current Knowledge and Identifies Areas of Forthcoming Discovery date: 2016-09-30 pages: extension: .txt txt: ./txt/cord-104317-t30dg6oj.txt cache: ./cache/cord-104317-t30dg6oj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-104317-t30dg6oj.txt' === file2bib.sh === id: cord-254932-b447w202 author: Panda, Aruna title: Role of fusion protein cleavage site in the virulence of Newcastle disease virus date: 2003-11-18 pages: extension: .txt txt: ./txt/cord-254932-b447w202.txt cache: ./cache/cord-254932-b447w202.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-254932-b447w202.txt' === file2bib.sh === id: cord-014462-11ggaqf1 author: nan title: Abstracts of the Papers Presented in the XIX National Conference of Indian Virological Society, “Recent Trends in Viral Disease Problems and Management”, on 18–20 March, 2010, at S.V. University, Tirupati, Andhra Pradesh date: 2011-04-21 pages: extension: .txt txt: ./txt/cord-014462-11ggaqf1.txt cache: ./cache/cord-014462-11ggaqf1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-014462-11ggaqf1.txt' === file2bib.sh === id: cord-254200-9bpdfxrt author: Barin, F. title: La sécurité virale des médicaments d’origine biologique date: 2008-06-30 pages: extension: .txt txt: ./txt/cord-254200-9bpdfxrt.txt cache: ./cache/cord-254200-9bpdfxrt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254200-9bpdfxrt.txt' === file2bib.sh === id: cord-254090-x8tnweih author: Yang, Szu-Chi title: Efficient Structure Resonance Energy Transfer from Microwaves to Confined Acoustic Vibrations in Viruses date: 2015-12-09 pages: extension: .txt txt: ./txt/cord-254090-x8tnweih.txt cache: ./cache/cord-254090-x8tnweih.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-254090-x8tnweih.txt' === file2bib.sh === id: cord-023724-5at0rhqk author: Cann, Alan J. title: Infection date: 2015-07-24 pages: extension: .txt txt: ./txt/cord-023724-5at0rhqk.txt cache: ./cache/cord-023724-5at0rhqk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023724-5at0rhqk.txt' === file2bib.sh === id: cord-232446-vvb2ffhv author: Mongia, Aanchal title: A computational approach to aid clinicians in selecting anti-viral drugs for COVID-19 trials date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-232446-vvb2ffhv.txt cache: ./cache/cord-232446-vvb2ffhv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-232446-vvb2ffhv.txt' === file2bib.sh === id: cord-255479-yd5cbwnx author: Vu, David M. title: Chikungunya Virus date: 2017-06-30 pages: extension: .txt txt: ./txt/cord-255479-yd5cbwnx.txt cache: ./cache/cord-255479-yd5cbwnx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255479-yd5cbwnx.txt' === file2bib.sh === id: cord-255217-l2ak5ygj author: Eccles, Ronald title: Why is temperature sensitivity important for the success of common respiratory viruses? date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-255217-l2ak5ygj.txt cache: ./cache/cord-255217-l2ak5ygj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-255217-l2ak5ygj.txt' === file2bib.sh === id: cord-031840-k9l91unc author: Lu, Li title: Forum: COVID-19 Dispatches date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-031840-k9l91unc.txt cache: ./cache/cord-031840-k9l91unc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-031840-k9l91unc.txt' === file2bib.sh === id: cord-257064-iafm3pcc author: Kint, Joeri title: Quantification of Infectious Bronchitis Coronavirus by Titration In Vitro and In Ovo date: 2014-12-18 pages: extension: .txt txt: ./txt/cord-257064-iafm3pcc.txt cache: ./cache/cord-257064-iafm3pcc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257064-iafm3pcc.txt' === file2bib.sh === id: cord-255026-fdp6mies author: Belák, Sándor title: Molecular diagnosis of viral diseases, present trends and future aspects: A view from the OIE Collaborating Centre for the Application of Polymerase Chain Reaction Methods for Diagnosis of Viral Diseases in Veterinary Medicine date: 2007-07-26 pages: extension: .txt txt: ./txt/cord-255026-fdp6mies.txt cache: ./cache/cord-255026-fdp6mies.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255026-fdp6mies.txt' === file2bib.sh === id: cord-245161-xbw72k4m author: Castano, Nicolas title: Fomite transmission and disinfection strategies for SARS-CoV-2 and related viruses date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-245161-xbw72k4m.txt cache: ./cache/cord-245161-xbw72k4m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-245161-xbw72k4m.txt' === file2bib.sh === id: cord-252725-e3pazjdi author: Khalil, Ayman title: The upshot of Polyphenolic compounds on immunity amid COVID-19 pandemic and other emerging communicable diseases: An appraisal date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-252725-e3pazjdi.txt cache: ./cache/cord-252725-e3pazjdi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252725-e3pazjdi.txt' === file2bib.sh === id: cord-254963-cnvxlv6h author: Paskey, Adrian C. title: Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples date: 2019-02-26 pages: extension: .txt txt: ./txt/cord-254963-cnvxlv6h.txt cache: ./cache/cord-254963-cnvxlv6h.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-254963-cnvxlv6h.txt' === file2bib.sh === id: cord-254592-wa5il5go author: Brierley, Liam title: Tissue tropism and transmission ecology predict virulence of human RNA viruses date: 2019-11-26 pages: extension: .txt txt: ./txt/cord-254592-wa5il5go.txt cache: ./cache/cord-254592-wa5il5go.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-254592-wa5il5go.txt' === file2bib.sh === id: cord-257569-36qx1sy9 author: Hanada, Kousuke title: A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes date: 2004-06-17 pages: extension: .txt txt: ./txt/cord-257569-36qx1sy9.txt cache: ./cache/cord-257569-36qx1sy9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257569-36qx1sy9.txt' === file2bib.sh === id: cord-252974-pwx27kdi author: Fornek, Jamie L. title: Use of Functional Genomics to Understand Influenza–Host Interactions date: 2007-08-31 pages: extension: .txt txt: ./txt/cord-252974-pwx27kdi.txt cache: ./cache/cord-252974-pwx27kdi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252974-pwx27kdi.txt' === file2bib.sh === id: cord-030279-pv770doe author: Novossiolova, Tatyana title: Twenty-first Century Governance Challenges in the Life Sciences date: 2016-11-29 pages: extension: .txt txt: ./txt/cord-030279-pv770doe.txt cache: ./cache/cord-030279-pv770doe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-030279-pv770doe.txt' === file2bib.sh === id: cord-252048-ftbjsoup author: McKinley, Enid T. title: Attenuated live vaccine usage affects accurate measures of virus diversity and mutation rates in avian coronavirus infectious bronchitis virus date: 2011-04-22 pages: extension: .txt txt: ./txt/cord-252048-ftbjsoup.txt cache: ./cache/cord-252048-ftbjsoup.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252048-ftbjsoup.txt' === file2bib.sh === id: cord-256510-orr2roxz author: de Castro, Isabel Fernández title: Virus factories: biogenesis and structural design date: 2012-10-04 pages: extension: .txt txt: ./txt/cord-256510-orr2roxz.txt cache: ./cache/cord-256510-orr2roxz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-256510-orr2roxz.txt' === file2bib.sh === id: cord-257665-12gyrmh2 author: Liu, Shan-Lu title: Emerging Viruses without Borders: The Wuhan Coronavirus date: 2020-01-22 pages: extension: .txt txt: ./txt/cord-257665-12gyrmh2.txt cache: ./cache/cord-257665-12gyrmh2.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-257665-12gyrmh2.txt' === file2bib.sh === id: cord-021966-5m21bsrw author: Shaw, Alan R. title: Vaccines date: 2009-05-15 pages: extension: .txt txt: ./txt/cord-021966-5m21bsrw.txt cache: ./cache/cord-021966-5m21bsrw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-021966-5m21bsrw.txt' === file2bib.sh === id: cord-257163-hodykbcb author: Sanz, Ivan title: Viral Etiology of Chronic Obstructive Pulmonary Disease Exacerbations during the A/H1N1pdm09 Pandemic and Postpandemic Period date: 2015-05-07 pages: extension: .txt txt: ./txt/cord-257163-hodykbcb.txt cache: ./cache/cord-257163-hodykbcb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-257163-hodykbcb.txt' === file2bib.sh === id: cord-257321-l1swyr6g author: Chen, Lihong title: DRodVir: A resource for exploring the virome diversity in rodents date: 2017-05-20 pages: extension: .txt txt: ./txt/cord-257321-l1swyr6g.txt cache: ./cache/cord-257321-l1swyr6g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257321-l1swyr6g.txt' === file2bib.sh === id: cord-022383-pz0htccp author: Kohn, Dennis F. title: Biology and Diseases of Rats date: 2013-11-17 pages: extension: .txt txt: ./txt/cord-022383-pz0htccp.txt cache: ./cache/cord-022383-pz0htccp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022383-pz0htccp.txt' === file2bib.sh === id: cord-257019-lj1yzjn0 author: ter MEULEN, V. title: Mechanisms and Consequences of Virus Persistence in the Human Nervous System date: 2006-12-16 pages: extension: .txt txt: ./txt/cord-257019-lj1yzjn0.txt cache: ./cache/cord-257019-lj1yzjn0.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-257019-lj1yzjn0.txt' === file2bib.sh === id: cord-258333-jmk8hdk2 author: Sivier, V title: Place des viroses respiratoires dans les hyperthermies de sujets âgés hospitalisés au cours d’une saison hivernale date: 2001-12-10 pages: extension: .txt txt: ./txt/cord-258333-jmk8hdk2.txt cache: ./cache/cord-258333-jmk8hdk2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258333-jmk8hdk2.txt' === file2bib.sh === id: cord-259627-8stewshp author: Huang, Qing title: Inactivation of dengue virus by methylene blue/narrow bandwidth light system date: 2004-12-02 pages: extension: .txt txt: ./txt/cord-259627-8stewshp.txt cache: ./cache/cord-259627-8stewshp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259627-8stewshp.txt' === file2bib.sh === id: cord-255697-trig04hd author: Cheng, Vincent Chi-Chung title: Viral Infections, an Overview with a Focus on Prevention of Transmission date: 2016-10-24 pages: extension: .txt txt: ./txt/cord-255697-trig04hd.txt cache: ./cache/cord-255697-trig04hd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255697-trig04hd.txt' === file2bib.sh === id: cord-255137-utg8k7qs author: Yinda, Claude Kwe title: Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses date: 2019-01-23 pages: extension: .txt txt: ./txt/cord-255137-utg8k7qs.txt cache: ./cache/cord-255137-utg8k7qs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255137-utg8k7qs.txt' === file2bib.sh === id: cord-257008-7q5s1vu1 author: Sharma, Virender K. title: Environmental chemistry is most relevant to study coronavirus pandemics date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-257008-7q5s1vu1.txt cache: ./cache/cord-257008-7q5s1vu1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257008-7q5s1vu1.txt' === file2bib.sh === id: cord-256917-6h1ip37z author: Habibi-Yangjeh, Aziz title: Review on heterogeneous photocatalytic disinfection of waterborne, airborne, and foodborne viruses: Can we win against pathogenic viruses? date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-256917-6h1ip37z.txt cache: ./cache/cord-256917-6h1ip37z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256917-6h1ip37z.txt' === file2bib.sh === id: cord-256370-cz88t29n author: Jansen van Vuren, Petrus title: Isolation of a Novel Fusogenic Orthoreovirus from Eucampsipoda africana Bat Flies in South Africa date: 2016-02-29 pages: extension: .txt txt: ./txt/cord-256370-cz88t29n.txt cache: ./cache/cord-256370-cz88t29n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256370-cz88t29n.txt' === file2bib.sh === id: cord-259458-o2yts5pq author: O’Grady, Kerry‐Ann F. title: Successful application of a simple specimen transport method for the conduct of respiratory virus surveillance in remote Indigenous communities in Australia date: 2011-03-21 pages: extension: .txt txt: ./txt/cord-259458-o2yts5pq.txt cache: ./cache/cord-259458-o2yts5pq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259458-o2yts5pq.txt' === file2bib.sh === id: cord-255690-xc4bxin4 author: Rolain, Jean-Marc title: Recycling of chloroquine and its hydroxyl analogue to face bacterial, fungal and viral infections in the 21st century date: 2007-07-16 pages: extension: .txt txt: ./txt/cord-255690-xc4bxin4.txt cache: ./cache/cord-255690-xc4bxin4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255690-xc4bxin4.txt' === file2bib.sh === id: cord-030028-s6sxi8uj author: Rubio, Luis title: Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-030028-s6sxi8uj.txt cache: ./cache/cord-030028-s6sxi8uj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-030028-s6sxi8uj.txt' === file2bib.sh === id: cord-253825-d9borky8 author: Blaising, Julie title: Arbidol as a broad-spectrum antiviral: An update date: 2014-04-24 pages: extension: .txt txt: ./txt/cord-253825-d9borky8.txt cache: ./cache/cord-253825-d9borky8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-253825-d9borky8.txt' === file2bib.sh === id: cord-260554-nao59qx4 author: Wargo, Andrew R title: Viral fitness: definitions, measurement, and current insights date: 2012-09-15 pages: extension: .txt txt: ./txt/cord-260554-nao59qx4.txt cache: ./cache/cord-260554-nao59qx4.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-260554-nao59qx4.txt' === file2bib.sh === id: cord-255734-038xu4hq author: Taylor, Deborah R. title: Obstacles and advances in SARS vaccine development date: 2006-02-13 pages: extension: .txt txt: ./txt/cord-255734-038xu4hq.txt cache: ./cache/cord-255734-038xu4hq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255734-038xu4hq.txt' === file2bib.sh === id: cord-035015-slgywe0c author: Nunn, Alistair V. W. title: SARS-CoV-2 and mitochondrial health: implications of lifestyle and ageing date: 2020-11-09 pages: extension: .txt txt: ./txt/cord-035015-slgywe0c.txt cache: ./cache/cord-035015-slgywe0c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-035015-slgywe0c.txt' === file2bib.sh === id: cord-254890-4ynsgu6c author: Heldens, J.G.M. title: Veterinary vaccine development from an industrial perspective date: 2008-03-03 pages: extension: .txt txt: ./txt/cord-254890-4ynsgu6c.txt cache: ./cache/cord-254890-4ynsgu6c.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-254890-4ynsgu6c.txt' === file2bib.sh === id: cord-252769-fe50u028 author: Mendes, J. Pinto title: Infecção na modulaçâo da asma 1 1 Trabalho apresentado no XXIII Congresso de Pneumologia da SPP – Guarda, Novembro 2007 / Paper presented at the XXIII Congresso de Pneumologia da SPP / PSP Pulmonology Congress, Guarda, November 2007 date: 2008-10-31 pages: extension: .txt txt: ./txt/cord-252769-fe50u028.txt cache: ./cache/cord-252769-fe50u028.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-252769-fe50u028.txt' === file2bib.sh === id: cord-260420-4s7akmdp author: Mubareka, Samira title: Bioaerosols and Transmission, a Diverse and Growing Community of Practice date: 2019-02-21 pages: extension: .txt txt: ./txt/cord-260420-4s7akmdp.txt cache: ./cache/cord-260420-4s7akmdp.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-260420-4s7akmdp.txt' === file2bib.sh === id: cord-259235-p0yj9qug author: de Lamballerie, Xavier title: Diagnostic et traitement des viroses émergentes : comment aller de l’avant ? date: 2016-12-31 pages: extension: .txt txt: ./txt/cord-259235-p0yj9qug.txt cache: ./cache/cord-259235-p0yj9qug.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259235-p0yj9qug.txt' === file2bib.sh === id: cord-256325-q70rky3r author: Stewart, Cameron R. title: A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease date: 2017-07-04 pages: extension: .txt txt: ./txt/cord-256325-q70rky3r.txt cache: ./cache/cord-256325-q70rky3r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-256325-q70rky3r.txt' === file2bib.sh === id: cord-258027-f3rr5el1 author: Østby, Anne‐Cathrine title: Respiratory virology and microbiology in intensive care units: a prospective cohort study date: 2013-05-18 pages: extension: .txt txt: ./txt/cord-258027-f3rr5el1.txt cache: ./cache/cord-258027-f3rr5el1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258027-f3rr5el1.txt' === file2bib.sh === id: cord-257652-ndt8f812 author: Zhang, Yong-Zhen title: The diversity, evolution and origins of vertebrate RNA viruses date: 2018-08-13 pages: extension: .txt txt: ./txt/cord-257652-ndt8f812.txt cache: ./cache/cord-257652-ndt8f812.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-257652-ndt8f812.txt' === file2bib.sh === id: cord-256837-100ir651 author: Smith, Steven B. title: Identification of Common Biological Pathways and Drug Targets Across Multiple Respiratory Viruses Based on Human Host Gene Expression Analysis date: 2012-03-14 pages: extension: .txt txt: ./txt/cord-256837-100ir651.txt cache: ./cache/cord-256837-100ir651.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-256837-100ir651.txt' === file2bib.sh === id: cord-254194-962vynwk author: Galdiero, Stefania title: Silver Nanoparticles as Potential Antiviral Agents date: 2011-10-24 pages: extension: .txt txt: ./txt/cord-254194-962vynwk.txt cache: ./cache/cord-254194-962vynwk.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-254194-962vynwk.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-257553-479x7av6 author: Kortepeter, Mark G. title: Health Care Workers and Researchers Traveling to Developing-World Clinical Settings: Disease Transmission Risk and Mitigation date: 2010-12-01 pages: extension: .txt txt: ./txt/cord-257553-479x7av6.txt cache: ./cache/cord-257553-479x7av6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257553-479x7av6.txt' === file2bib.sh === id: cord-259505-7hiss0j3 author: Kong, Qingming title: Proteomic analysis of purified coronavirus infectious bronchitis virus particles date: 2010-06-09 pages: extension: .txt txt: ./txt/cord-259505-7hiss0j3.txt cache: ./cache/cord-259505-7hiss0j3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-259505-7hiss0j3.txt' === file2bib.sh === id: cord-256036-gd53s4dv author: Sandmann, Lisa title: Barriers of hepatitis C virus interspecies transmission date: 2013-01-01 pages: extension: .txt txt: ./txt/cord-256036-gd53s4dv.txt cache: ./cache/cord-256036-gd53s4dv.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-256036-gd53s4dv.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-259233-smmhhroe author: de Armas‐Rillo, Laura title: Membrane dynamics associated with viral infection date: 2016-01-28 pages: extension: .txt txt: ./txt/cord-259233-smmhhroe.txt cache: ./cache/cord-259233-smmhhroe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259233-smmhhroe.txt' === file2bib.sh === id: cord-255181-du6rqc6i author: Louz, Derrick title: Cross‐species transfer of viruses: implications for the use of viral vectors in biomedical research, gene therapy and as live‐virus vaccines date: 2005-06-29 pages: extension: .txt txt: ./txt/cord-255181-du6rqc6i.txt cache: ./cache/cord-255181-du6rqc6i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255181-du6rqc6i.txt' === file2bib.sh === id: cord-260147-w19hl2vs author: Gröner, Albrecht title: Effective inactivation of a wide range of viruses by pasteurization date: 2017-11-16 pages: extension: .txt txt: ./txt/cord-260147-w19hl2vs.txt cache: ./cache/cord-260147-w19hl2vs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260147-w19hl2vs.txt' === file2bib.sh === id: cord-262722-cz3ce29n author: Kuzmanovic, Deborah A. title: A novel application of small-angle scattering techniques: Quality assurance testing of virus quantification technology date: 2008-03-31 pages: extension: .txt txt: ./txt/cord-262722-cz3ce29n.txt cache: ./cache/cord-262722-cz3ce29n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262722-cz3ce29n.txt' === file2bib.sh === id: cord-263017-rh86g4jk author: Wigginton, Krista Rule title: Virus disinfection mechanisms: the role of virus composition, structure, and function date: 2011-12-09 pages: extension: .txt txt: ./txt/cord-263017-rh86g4jk.txt cache: ./cache/cord-263017-rh86g4jk.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-263017-rh86g4jk.txt' === file2bib.sh === id: cord-260014-q5sug7uu author: Szűcs, Zsolt title: Reprogramming of the Antibacterial Drug Vancomycin Results in Potent Antiviral Agents Devoid of Antibacterial Activity date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-260014-q5sug7uu.txt cache: ./cache/cord-260014-q5sug7uu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260014-q5sug7uu.txt' === file2bib.sh === id: cord-261961-u4d0vvmq author: St-Germain, Jonathan R. title: A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-261961-u4d0vvmq.txt cache: ./cache/cord-261961-u4d0vvmq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-261961-u4d0vvmq.txt' === file2bib.sh === id: cord-260168-rb7j94dh author: Gu, Jiang title: H5N1 infection of the respiratory tract and beyond: a molecular pathology study date: 2007-09-27 pages: extension: .txt txt: ./txt/cord-260168-rb7j94dh.txt cache: ./cache/cord-260168-rb7j94dh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260168-rb7j94dh.txt' === file2bib.sh === id: cord-256615-gvq8uyfk author: Rosenberg, Ronald title: Detecting the emergence of novel, zoonotic viruses pathogenic to humans date: 2014-11-22 pages: extension: .txt txt: ./txt/cord-256615-gvq8uyfk.txt cache: ./cache/cord-256615-gvq8uyfk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-256615-gvq8uyfk.txt' === file2bib.sh === id: cord-260705-huyyw5z6 author: Moshe, Adi title: Virus-Induced Aggregates in Infected Cells date: 2012-10-17 pages: extension: .txt txt: ./txt/cord-260705-huyyw5z6.txt cache: ./cache/cord-260705-huyyw5z6.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-260705-huyyw5z6.txt' === file2bib.sh === id: cord-022262-ck2lhojz author: Gromeier, Matthias title: Genetics, Pathogenesis and Evolution of Picornaviruses date: 2007-09-02 pages: extension: .txt txt: ./txt/cord-022262-ck2lhojz.txt cache: ./cache/cord-022262-ck2lhojz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022262-ck2lhojz.txt' === file2bib.sh === id: cord-259927-xh9cw9ao author: Papadopoulos, Nikolaos G. title: Promising approaches for the treatment and prevention of viral respiratory illnesses date: 2017-07-21 pages: extension: .txt txt: ./txt/cord-259927-xh9cw9ao.txt cache: ./cache/cord-259927-xh9cw9ao.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-259927-xh9cw9ao.txt' === file2bib.sh === id: cord-264264-7j3xirfg author: TüRsen, Ümit title: CORONAVIRUS‐DAYS IN DERMATOLOGY date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-264264-7j3xirfg.txt cache: ./cache/cord-264264-7j3xirfg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-264264-7j3xirfg.txt' === file2bib.sh === id: cord-263245-2qub96mz author: Singh, D. title: Alcohol-based hand sanitisers as first line of defence against SARS-CoV-2: a review of biology, chemistry and formulations date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-263245-2qub96mz.txt cache: ./cache/cord-263245-2qub96mz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263245-2qub96mz.txt' === file2bib.sh === id: cord-262514-1e2bc0bi author: Harrison, Alyne K title: Visceral target organs in systemic St. Louis encephalitis virus infection of hamsters date: 1982-12-31 pages: extension: .txt txt: ./txt/cord-262514-1e2bc0bi.txt cache: ./cache/cord-262514-1e2bc0bi.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-262514-1e2bc0bi.txt' === file2bib.sh === id: cord-260690-h5pjv2dw author: Druce, Julian title: Laboratory diagnosis and surveillance of human respiratory viruses by PCR in Victoria, Australia, 2002–2003 date: 2004-11-12 pages: extension: .txt txt: ./txt/cord-260690-h5pjv2dw.txt cache: ./cache/cord-260690-h5pjv2dw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260690-h5pjv2dw.txt' === file2bib.sh === id: cord-258489-pyfc7jde author: Lico, Chiara title: Viral vectors for production of recombinant proteins in plants date: 2008-03-10 pages: extension: .txt txt: ./txt/cord-258489-pyfc7jde.txt cache: ./cache/cord-258489-pyfc7jde.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258489-pyfc7jde.txt' === file2bib.sh === id: cord-262752-bwofzbwa author: Li, Qianqian title: Current status on the development of pseudoviruses for enveloped viruses date: 2017-12-07 pages: extension: .txt txt: ./txt/cord-262752-bwofzbwa.txt cache: ./cache/cord-262752-bwofzbwa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262752-bwofzbwa.txt' === file2bib.sh === id: cord-261160-g92zhv19 author: Rowland, Raymond R.R title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero date: 2003-10-30 pages: extension: .txt txt: ./txt/cord-261160-g92zhv19.txt cache: ./cache/cord-261160-g92zhv19.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261160-g92zhv19.txt' === file2bib.sh === id: cord-257255-n5o368ih author: Barker, J. title: Spread and prevention of some common viral infections in community facilities and domestic homes date: 2001-12-21 pages: extension: .txt txt: ./txt/cord-257255-n5o368ih.txt cache: ./cache/cord-257255-n5o368ih.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257255-n5o368ih.txt' === file2bib.sh === id: cord-259260-qcfgigga author: Ibrahim, Ibrahim M. title: GRP78: A cell's response to stress date: 2019-06-01 pages: extension: .txt txt: ./txt/cord-259260-qcfgigga.txt cache: ./cache/cord-259260-qcfgigga.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259260-qcfgigga.txt' === file2bib.sh === id: cord-260496-s2ba7uy3 author: Moncany, Maurice L.J. title: Identification of conserved lentiviral sequences as landmarks of genomic flexibility date: 2006-08-08 pages: extension: .txt txt: ./txt/cord-260496-s2ba7uy3.txt cache: ./cache/cord-260496-s2ba7uy3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260496-s2ba7uy3.txt' === file2bib.sh === id: cord-258783-ev0h95b9 author: Kapil, Sanjay title: Canine Distemper Spillover in Domestic Dogs from Urban Wildlife date: 2011-11-30 pages: extension: .txt txt: ./txt/cord-258783-ev0h95b9.txt cache: ./cache/cord-258783-ev0h95b9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258783-ev0h95b9.txt' === file2bib.sh === id: cord-254100-u6x5zd4i author: Taliansky, M.E. title: Involvement of the Plant Nucleolus in Virus and Viroid Infections: Parallels with Animal Pathosystems date: 2010-10-15 pages: extension: .txt txt: ./txt/cord-254100-u6x5zd4i.txt cache: ./cache/cord-254100-u6x5zd4i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-254100-u6x5zd4i.txt' === file2bib.sh === id: cord-264291-0czphube author: Varfolomeev, S. D. title: Kinetic model of development of acute viral infection in the human body. Critical conditions, control mechanisms, “thermoheliox” date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-264291-0czphube.txt cache: ./cache/cord-264291-0czphube.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264291-0czphube.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-252147-bvtchcbt author: Domingo-Espín, Joan title: Engineered Biological Entities for Drug Delivery and Gene Therapy: Protein Nanoparticles date: 2011-11-15 pages: extension: .txt txt: ./txt/cord-252147-bvtchcbt.txt cache: ./cache/cord-252147-bvtchcbt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252147-bvtchcbt.txt' === file2bib.sh === id: cord-261241-eqf6ame6 author: van Beek, Josine title: Influenza-like Illness Incidence Is Not Reduced by Influenza Vaccination in a Cohort of Older Adults, Despite Effectively Reducing Laboratory-Confirmed Influenza Virus Infections date: 2017-08-15 pages: extension: .txt txt: ./txt/cord-261241-eqf6ame6.txt cache: ./cache/cord-261241-eqf6ame6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261241-eqf6ame6.txt' === file2bib.sh === id: cord-263484-afcgqjwq author: Ladner, Jason T. title: Precision epidemiology for infectious disease control date: 2019-02-06 pages: extension: .txt txt: ./txt/cord-263484-afcgqjwq.txt cache: ./cache/cord-263484-afcgqjwq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263484-afcgqjwq.txt' === file2bib.sh === id: cord-262748-v4xue7ha author: Xu, Yongtao title: Identification of Peptide Inhibitors of Enveloped Viruses Using Support Vector Machine date: 2015-12-04 pages: extension: .txt txt: ./txt/cord-262748-v4xue7ha.txt cache: ./cache/cord-262748-v4xue7ha.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262748-v4xue7ha.txt' === file2bib.sh === id: cord-264350-4zxp3uae author: Kelley, James L. title: Chapter 12. Antiviral Agents date: 1984-12-31 pages: extension: .txt txt: ./txt/cord-264350-4zxp3uae.txt cache: ./cache/cord-264350-4zxp3uae.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-264350-4zxp3uae.txt' === file2bib.sh === id: cord-261171-iknoqb4d author: Roingeard, Philippe title: Viral detection by electron microscopy: past, present and future date: 2012-01-09 pages: extension: .txt txt: ./txt/cord-261171-iknoqb4d.txt cache: ./cache/cord-261171-iknoqb4d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-261171-iknoqb4d.txt' === file2bib.sh === id: cord-261417-4pf5nsw2 author: Harwig, Alex title: The Battle of RNA Synthesis: Virus versus Host date: 2017-10-21 pages: extension: .txt txt: ./txt/cord-261417-4pf5nsw2.txt cache: ./cache/cord-261417-4pf5nsw2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-261417-4pf5nsw2.txt' === file2bib.sh === id: cord-263165-bv4dh9eu author: Möstl, Karin title: Coronaviridae, pathogenetic and clinical aspects: An update date: 1990-12-31 pages: extension: .txt txt: ./txt/cord-263165-bv4dh9eu.txt cache: ./cache/cord-263165-bv4dh9eu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263165-bv4dh9eu.txt' === file2bib.sh === id: cord-264406-s5c0grz0 author: Miró-Cañís, Sílvia title: Multiplex PCR reveals that viruses are more frequent than bacteria in children with cystic fibrosis date: 2016-11-13 pages: extension: .txt txt: ./txt/cord-264406-s5c0grz0.txt cache: ./cache/cord-264406-s5c0grz0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-264406-s5c0grz0.txt' === file2bib.sh === id: cord-018393-5jlqn7wq author: Finke, Ernst-Jürgen title: Bioterrorismus, infektiologische Aspekte date: 2011-12-14 pages: extension: .txt txt: ./txt/cord-018393-5jlqn7wq.txt cache: ./cache/cord-018393-5jlqn7wq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-018393-5jlqn7wq.txt' === file2bib.sh === id: cord-262776-6k7tcgfs author: Burnouf, Thierry title: Assessment of the viral safety of antivenoms fractionated from equine plasma date: 2004-09-30 pages: extension: .txt txt: ./txt/cord-262776-6k7tcgfs.txt cache: ./cache/cord-262776-6k7tcgfs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262776-6k7tcgfs.txt' === file2bib.sh === id: cord-263785-0iift8zy author: Zhang, Xiaorong title: Evaluation of the reproductive system development and egg-laying performance of hens infected with TW I-type infectious bronchitis virus date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-263785-0iift8zy.txt cache: ./cache/cord-263785-0iift8zy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-263785-0iift8zy.txt' === file2bib.sh === id: cord-022252-9yiuuye3 author: Mims, Cedric A. title: Mechanisms of Cell and Tissue Damage date: 2013-11-17 pages: extension: .txt txt: ./txt/cord-022252-9yiuuye3.txt cache: ./cache/cord-022252-9yiuuye3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-022252-9yiuuye3.txt' === file2bib.sh === id: cord-263764-2ewz8ok4 author: Kutter, Jasmin S title: Transmission routes of respiratory viruses among humans date: 2018-01-17 pages: extension: .txt txt: ./txt/cord-263764-2ewz8ok4.txt cache: ./cache/cord-263764-2ewz8ok4.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-263764-2ewz8ok4.txt' === file2bib.sh === id: cord-267831-uu883ofc author: Kang, Yuan-Lin title: Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2 date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-267831-uu883ofc.txt cache: ./cache/cord-267831-uu883ofc.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-267831-uu883ofc.txt' === file2bib.sh === id: cord-258626-p469ysi8 author: Davis-Wurzler, Gina M. title: 2013 Update on Current Vaccination Strategies in Puppies and Kittens date: 2014-02-26 pages: extension: .txt txt: ./txt/cord-258626-p469ysi8.txt cache: ./cache/cord-258626-p469ysi8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258626-p469ysi8.txt' === file2bib.sh === id: cord-264794-bgygebgx author: Lundgren, A.-L. title: Feline non-suppurative meningoencephalomyelitis. A clinical and pathological study date: 1992-11-30 pages: extension: .txt txt: ./txt/cord-264794-bgygebgx.txt cache: ./cache/cord-264794-bgygebgx.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-264794-bgygebgx.txt' === file2bib.sh === id: cord-269324-zh1a3gwh author: Mubareka, Samira title: Human Genes and Influenza date: 2008-01-01 pages: extension: .txt txt: ./txt/cord-269324-zh1a3gwh.txt cache: ./cache/cord-269324-zh1a3gwh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269324-zh1a3gwh.txt' === file2bib.sh === id: cord-263315-g7os15m1 author: Martins-da-Silva, Andrea title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response date: 2018-01-18 pages: extension: .txt txt: ./txt/cord-263315-g7os15m1.txt cache: ./cache/cord-263315-g7os15m1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263315-g7os15m1.txt' === file2bib.sh === id: cord-264699-l8db5gll author: Kino, Tomoshige title: Virus-mediated modulation of the host endocrine signaling systems: clinical implications date: 2007-06-30 pages: extension: .txt txt: ./txt/cord-264699-l8db5gll.txt cache: ./cache/cord-264699-l8db5gll.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-264699-l8db5gll.txt' === file2bib.sh === id: cord-254527-zddwajzg author: Junter, Guy-Alain title: Polysaccharide-based chromatographic adsorbents for virus purification and viral clearance date: 2020-01-13 pages: extension: .txt txt: ./txt/cord-254527-zddwajzg.txt cache: ./cache/cord-254527-zddwajzg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-254527-zddwajzg.txt' === file2bib.sh === id: cord-266136-81sx505i author: Freymuth, F. title: Les virus des bronchiolites aiguës date: 2010-06-16 pages: extension: .txt txt: ./txt/cord-266136-81sx505i.txt cache: ./cache/cord-266136-81sx505i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-266136-81sx505i.txt' === file2bib.sh === id: cord-265681-ab8j4o1u author: Boroomand, Zahra title: Pathogenesis and Tissue Distribution of Avian Infectious Bronchitis Virus Isolate IRFIBV32 (793/B Serotype) in Experimentally Infected Broiler Chickens date: 2012-04-01 pages: extension: .txt txt: ./txt/cord-265681-ab8j4o1u.txt cache: ./cache/cord-265681-ab8j4o1u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-265681-ab8j4o1u.txt' === file2bib.sh === id: cord-260956-w6wxsg4p author: Dimitrov, Kiril M. title: Newcastle disease vaccines—A solved problem or a continuous challenge? date: 2017-07-31 pages: extension: .txt txt: ./txt/cord-260956-w6wxsg4p.txt cache: ./cache/cord-260956-w6wxsg4p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260956-w6wxsg4p.txt' === file2bib.sh === id: cord-267140-vdcf6vok author: Trudel, M. title: Purification of infectious rubella virus by gel filtration on sepharose 2B compared to gradient centrifugation in sucrose, sodium metrizoate and metrizamide date: 1981-02-28 pages: extension: .txt txt: ./txt/cord-267140-vdcf6vok.txt cache: ./cache/cord-267140-vdcf6vok.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267140-vdcf6vok.txt' === file2bib.sh === id: cord-255339-oudj079q author: Al-Tayib, Omar A. title: An Overview of the Most Significant Zoonotic Viral Pathogens Transmitted from Animal to Human in Saudi Arabia date: 2019-02-22 pages: extension: .txt txt: ./txt/cord-255339-oudj079q.txt cache: ./cache/cord-255339-oudj079q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255339-oudj079q.txt' === file2bib.sh === id: cord-258389-1u05w7r4 author: Verma, Anju title: Animal tissue culture principles and applications date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-258389-1u05w7r4.txt cache: ./cache/cord-258389-1u05w7r4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258389-1u05w7r4.txt' === file2bib.sh === id: cord-269519-8hr8wyrr author: Hirotsu, Yosuke title: Analysis of Covid-19 and non-Covid-19 viruses, including influenza viruses, to determine the influence of intensive preventive measures in Japan date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-269519-8hr8wyrr.txt cache: ./cache/cord-269519-8hr8wyrr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-269519-8hr8wyrr.txt' === file2bib.sh === id: cord-263157-8jin6oru author: Martínez, Miguel Angel title: Progress in the Therapeutic Applications of siRNAs Against HIV-1 date: 2008-10-13 pages: extension: .txt txt: ./txt/cord-263157-8jin6oru.txt cache: ./cache/cord-263157-8jin6oru.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 15 resourceName b'cord-263157-8jin6oru.txt' === file2bib.sh === id: cord-267003-k7eo2c26 author: Hendaus, Mohamed A title: Virus-induced secondary bacterial infection: a concise review date: 2015-08-24 pages: extension: .txt txt: ./txt/cord-267003-k7eo2c26.txt cache: ./cache/cord-267003-k7eo2c26.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267003-k7eo2c26.txt' === file2bib.sh === id: cord-260708-l9w5jhsw author: Lasecka, Lidia title: The molecular biology of nairoviruses, an emerging group of tick-borne arboviruses date: 2013-12-11 pages: extension: .txt txt: ./txt/cord-260708-l9w5jhsw.txt cache: ./cache/cord-260708-l9w5jhsw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260708-l9w5jhsw.txt' === file2bib.sh === id: cord-265461-hj2b1wc4 author: Decroly, Etienne title: Biochemical principles and inhibitors to interfere with viral capping pathways date: 2017-05-18 pages: extension: .txt txt: ./txt/cord-265461-hj2b1wc4.txt cache: ./cache/cord-265461-hj2b1wc4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-265461-hj2b1wc4.txt' === file2bib.sh === id: cord-264916-c4n0kyog author: Zimmerman, Keith title: Natural protection of ocular surface from viral infections – a hypothesis date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-264916-c4n0kyog.txt cache: ./cache/cord-264916-c4n0kyog.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264916-c4n0kyog.txt' === file2bib.sh === id: cord-255096-27dfbhsl author: Sweet, Michael J. title: Reprint of ‘Diseases in marine invertebrates associated with mariculture and commercial fisheries’ date: 2016-06-19 pages: extension: .txt txt: ./txt/cord-255096-27dfbhsl.txt cache: ./cache/cord-255096-27dfbhsl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255096-27dfbhsl.txt' === file2bib.sh === id: cord-269126-d81z6t0a author: Jayaseelan, Vijayashree Priyadharsini title: Repurposing calcium channel blockers as antiviral drugs date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-269126-d81z6t0a.txt cache: ./cache/cord-269126-d81z6t0a.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-269126-d81z6t0a.txt' === file2bib.sh === id: cord-263868-ewnf96cz author: Srivastava, Mayank title: Chemical proteomics tracks virus entry and uncovers NCAM1 as Zika virus receptor date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-263868-ewnf96cz.txt cache: ./cache/cord-263868-ewnf96cz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263868-ewnf96cz.txt' === file2bib.sh === id: cord-268999-6748c617 author: Gibson, Kristen E title: Viral pathogens in water: occurrence, public health impact, and available control strategies date: 2014-01-14 pages: extension: .txt txt: ./txt/cord-268999-6748c617.txt cache: ./cache/cord-268999-6748c617.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-268999-6748c617.txt' === file2bib.sh === id: cord-267194-i6vetquk author: Carman, William F. title: The pathogens date: 2007-10-31 pages: extension: .txt txt: ./txt/cord-267194-i6vetquk.txt cache: ./cache/cord-267194-i6vetquk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-267194-i6vetquk.txt' === file2bib.sh === id: cord-253705-utp8po48 author: Sriwilaijaroen, Nongluk title: Sialoglycovirology of Lectins: Sialyl Glycan Binding of Enveloped and Non-enveloped Viruses date: 2020-04-19 pages: extension: .txt txt: ./txt/cord-253705-utp8po48.txt cache: ./cache/cord-253705-utp8po48.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253705-utp8po48.txt' === file2bib.sh === id: cord-264308-y6xuxj16 author: Liu, Rui title: Mouse lung slices: An ex vivo model for the evaluation of antiviral and anti-inflammatory agents against influenza viruses date: 2015-05-26 pages: extension: .txt txt: ./txt/cord-264308-y6xuxj16.txt cache: ./cache/cord-264308-y6xuxj16.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264308-y6xuxj16.txt' === file2bib.sh === id: cord-267134-5gz2dotn author: Sallenave, Jean-Michel title: Innate Immune Signaling and Proteolytic Pathways in the Resolution or Exacerbation of SARS-CoV-2 in Covid-19: Key Therapeutic Targets? date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-267134-5gz2dotn.txt cache: ./cache/cord-267134-5gz2dotn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267134-5gz2dotn.txt' === file2bib.sh === id: cord-269193-a647hwu9 author: Lin, Debby A. title: Evolutionary relatedness of the predicted gene product of RNA segment 2 of the Tick-Borne Dhori virus and the PB1 polymerase gene of influenza viruses date: 1991-05-31 pages: extension: .txt txt: ./txt/cord-269193-a647hwu9.txt cache: ./cache/cord-269193-a647hwu9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269193-a647hwu9.txt' === file2bib.sh === id: cord-266138-yibbiiij author: Wege, Helmut title: Immunopathological aspects of coronavirus infections date: 1995 pages: extension: .txt txt: ./txt/cord-266138-yibbiiij.txt cache: ./cache/cord-266138-yibbiiij.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-266138-yibbiiij.txt' === file2bib.sh === id: cord-270243-moxleyjg author: Cholleti, Harindranath title: Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique date: 2018-05-28 pages: extension: .txt txt: ./txt/cord-270243-moxleyjg.txt cache: ./cache/cord-270243-moxleyjg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-270243-moxleyjg.txt' === file2bib.sh === id: cord-263619-p17oomzn author: Moss, William J. title: Measles date: 2009-01-30 pages: extension: .txt txt: ./txt/cord-263619-p17oomzn.txt cache: ./cache/cord-263619-p17oomzn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263619-p17oomzn.txt' === file2bib.sh === id: cord-271709-5frm3dnb author: Arden, Katherine E. title: Genotypic diversity, circulation patterns and co-detections among rhinoviruses in Queensland, 2001 date: 2019-11-04 pages: extension: .txt txt: ./txt/cord-271709-5frm3dnb.txt cache: ./cache/cord-271709-5frm3dnb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271709-5frm3dnb.txt' === file2bib.sh === id: cord-265642-7mu530yp author: Syomin, B. V. title: Virus-Like Particles as an Instrument of Vaccine Production date: 2019-06-17 pages: extension: .txt txt: ./txt/cord-265642-7mu530yp.txt cache: ./cache/cord-265642-7mu530yp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-265642-7mu530yp.txt' === file2bib.sh === id: cord-268501-z4oztgi0 author: Palatnik-de-Sousa, Clarisa B. title: What Would Jenner and Pasteur Have Done About COVID-19 Coronavirus? The Urges of a Vaccinologist date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-268501-z4oztgi0.txt cache: ./cache/cord-268501-z4oztgi0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-268501-z4oztgi0.txt' === file2bib.sh === id: cord-267567-w39f584z author: Pombo, Joao Palma title: Perturbation of Intracellular Cholesterol and Fatty Acid Homeostasis During Flavivirus Infections date: 2018-06-04 pages: extension: .txt txt: ./txt/cord-267567-w39f584z.txt cache: ./cache/cord-267567-w39f584z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267567-w39f584z.txt' === file2bib.sh === id: cord-271105-eyigl0wz author: Ionidis, Georgios title: Development and virucidal activity of a novel alcohol-based hand disinfectant supplemented with urea and citric acid date: 2016-02-11 pages: extension: .txt txt: ./txt/cord-271105-eyigl0wz.txt cache: ./cache/cord-271105-eyigl0wz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-271105-eyigl0wz.txt' === file2bib.sh === id: cord-271171-tohbzenc author: Bhola, J. title: Corona Epidemic in Indian context: Predictive Mathematical Modelling date: 2020-04-07 pages: extension: .txt txt: ./txt/cord-271171-tohbzenc.txt cache: ./cache/cord-271171-tohbzenc.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-271171-tohbzenc.txt' === file2bib.sh === id: cord-266199-smlq11y9 author: Dhakal, Santosh title: Nanoparticle-based vaccine development and evaluation against viral infections in pigs date: 2019-11-06 pages: extension: .txt txt: ./txt/cord-266199-smlq11y9.txt cache: ./cache/cord-266199-smlq11y9.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-266199-smlq11y9.txt' === file2bib.sh === id: cord-268788-jcu3pasy author: Thor, Sharmi W. title: Recombination in Avian Gamma-Coronavirus Infectious Bronchitis Virus date: 2011-09-23 pages: extension: .txt txt: ./txt/cord-268788-jcu3pasy.txt cache: ./cache/cord-268788-jcu3pasy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-268788-jcu3pasy.txt' === file2bib.sh === id: cord-266985-9qwttt2y author: Gale, P. title: Applications of omics approaches to the development of microbiological risk assessment using RNA virus dose–response models as a case study date: 2014-11-04 pages: extension: .txt txt: ./txt/cord-266985-9qwttt2y.txt cache: ./cache/cord-266985-9qwttt2y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-266985-9qwttt2y.txt' === file2bib.sh === id: cord-270772-zshjrc87 author: To, Kelvin Kai-Wang title: Host genes and influenza pathogenesis in humans: an emerging paradigm date: 2015-06-14 pages: extension: .txt txt: ./txt/cord-270772-zshjrc87.txt cache: ./cache/cord-270772-zshjrc87.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-270772-zshjrc87.txt' === file2bib.sh === id: cord-265751-q1ecpfyg author: Shahani, Lokesh title: Antiviral therapy for respiratory viral infections in immunocompromised patients date: 2017-01-16 pages: extension: .txt txt: ./txt/cord-265751-q1ecpfyg.txt cache: ./cache/cord-265751-q1ecpfyg.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-265751-q1ecpfyg.txt' === file2bib.sh === id: cord-271927-u8p6c9w4 author: Stefanacci, Richard G. title: Learnings to Operate LTC Better from the COVID-19 Crisis date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-271927-u8p6c9w4.txt cache: ./cache/cord-271927-u8p6c9w4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271927-u8p6c9w4.txt' === file2bib.sh === id: cord-270911-z637eh2z author: Zhou, Jie title: Differentiated human airway organoids to assess infectivity of emerging influenza virus date: 2018-06-26 pages: extension: .txt txt: ./txt/cord-270911-z637eh2z.txt cache: ./cache/cord-270911-z637eh2z.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-270911-z637eh2z.txt' === file2bib.sh === id: cord-272099-26nhza2s author: IKEDA, KEIKO title: Survival of influenza A virus on contaminated student clothing date: 2015-02-09 pages: extension: .txt txt: ./txt/cord-272099-26nhza2s.txt cache: ./cache/cord-272099-26nhza2s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-272099-26nhza2s.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-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 3 resourceName b'cord-257220-fe2sacjj.txt' === file2bib.sh === id: cord-266762-z08rn959 author: Rouse, Barry T. title: 25 Host Defenses to Viruses date: 2019-12-31 pages: extension: .txt txt: ./txt/cord-266762-z08rn959.txt cache: ./cache/cord-266762-z08rn959.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266762-z08rn959.txt' === file2bib.sh === id: cord-270161-vaejyy4i author: Reicks, Darwin L. title: Effective biosecurity to protect North American studs and clients from emerging infectious disease date: 2019-10-01 pages: extension: .txt txt: ./txt/cord-270161-vaejyy4i.txt cache: ./cache/cord-270161-vaejyy4i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270161-vaejyy4i.txt' === file2bib.sh === id: cord-274765-3wzht843 author: Kweon, Chang-Hee title: Derivation of attenuated porcine epidemic diarrhea virus (PEDV) as vaccine candidate date: 1999-06-04 pages: extension: .txt txt: ./txt/cord-274765-3wzht843.txt cache: ./cache/cord-274765-3wzht843.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274765-3wzht843.txt' === file2bib.sh === id: cord-267261-8z4aqfff author: Su, John R. title: Emerging viral infections date: 2005-03-01 pages: extension: .txt txt: ./txt/cord-267261-8z4aqfff.txt cache: ./cache/cord-267261-8z4aqfff.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-267261-8z4aqfff.txt' === file2bib.sh === id: cord-271076-436nxsua author: Paul-Pierre, Pastoret title: Emerging diseases, zoonoses and vaccines to control them date: 2009-10-30 pages: extension: .txt txt: ./txt/cord-271076-436nxsua.txt cache: ./cache/cord-271076-436nxsua.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-271076-436nxsua.txt' === file2bib.sh === id: cord-267326-355q6k6k author: Gu, Xiaoqiong title: Geospatial distribution of viromes in tropical freshwater ecosystems date: 2018-06-15 pages: extension: .txt txt: ./txt/cord-267326-355q6k6k.txt cache: ./cache/cord-267326-355q6k6k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267326-355q6k6k.txt' === file2bib.sh === id: cord-271313-h9v0nmx5 author: Bagust, T. J. title: A REVIEW OF VIRAL INFECTIONS OF HORSES date: 2008-03-10 pages: extension: .txt txt: ./txt/cord-271313-h9v0nmx5.txt cache: ./cache/cord-271313-h9v0nmx5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271313-h9v0nmx5.txt' === file2bib.sh === id: cord-270335-8vqi9c68 author: Seifert, Stephanie N title: Rousettus aegyptiacus Bats Do Not Support Productive Nipah Virus Replication date: 2019-11-04 pages: extension: .txt txt: ./txt/cord-270335-8vqi9c68.txt cache: ./cache/cord-270335-8vqi9c68.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270335-8vqi9c68.txt' === file2bib.sh === id: cord-273372-69rlh9or author: Litterman, Nadia title: Small molecules with antiviral activity against the Ebola virus date: 2015-02-09 pages: extension: .txt txt: ./txt/cord-273372-69rlh9or.txt cache: ./cache/cord-273372-69rlh9or.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273372-69rlh9or.txt' === file2bib.sh === id: cord-272829-i4jh6bcn author: ZANETTI, A. R. title: Emerging and re‐emerging infections at the turn of the millennium date: 2010-01-04 pages: extension: .txt txt: ./txt/cord-272829-i4jh6bcn.txt cache: ./cache/cord-272829-i4jh6bcn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-272829-i4jh6bcn.txt' === file2bib.sh === id: cord-271884-86yl9ren author: Traavik, T. title: Development of a modified immunoelectroosmophoresis method for Uukuniemi and Runde virus serology date: 1977 pages: extension: .txt txt: ./txt/cord-271884-86yl9ren.txt cache: ./cache/cord-271884-86yl9ren.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271884-86yl9ren.txt' === file2bib.sh === id: cord-270803-jtv5jmkn author: Wang, Lin-Fa title: Mass extinctions, biodiversity and mitochondrial function: are bats ‘special’ as reservoirs for emerging viruses? date: 2011-11-09 pages: extension: .txt txt: ./txt/cord-270803-jtv5jmkn.txt cache: ./cache/cord-270803-jtv5jmkn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-270803-jtv5jmkn.txt' === file2bib.sh === id: cord-267733-fuz8r3vj author: Al Ali, Sally title: Use of Reporter Genes in the Generation of Vaccinia Virus-Derived Vectors date: 2016-05-21 pages: extension: .txt txt: ./txt/cord-267733-fuz8r3vj.txt cache: ./cache/cord-267733-fuz8r3vj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-267733-fuz8r3vj.txt' === file2bib.sh === id: cord-268645-5op2m7pu author: Wu, Zhiqiang title: Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases date: 2015-08-11 pages: extension: .txt txt: ./txt/cord-268645-5op2m7pu.txt cache: ./cache/cord-268645-5op2m7pu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268645-5op2m7pu.txt' === file2bib.sh === id: cord-272405-jmwn8pdn author: Parvez, Mohammad K. title: Evolution and Emergence of Pathogenic Viruses: Past, Present, and Future date: 2017-08-04 pages: extension: .txt txt: ./txt/cord-272405-jmwn8pdn.txt cache: ./cache/cord-272405-jmwn8pdn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272405-jmwn8pdn.txt' === file2bib.sh === id: cord-271692-60nlid3c author: Guo, Wen-Ping title: Phylogeny and Origins of Hantaviruses Harbored by Bats, Insectivores, and Rodents date: 2013-02-07 pages: extension: .txt txt: ./txt/cord-271692-60nlid3c.txt cache: ./cache/cord-271692-60nlid3c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271692-60nlid3c.txt' === file2bib.sh === id: cord-275013-na6319rg author: Singh, Indra P. title: Innate defences against viraemia date: 2000-11-23 pages: extension: .txt txt: ./txt/cord-275013-na6319rg.txt cache: ./cache/cord-275013-na6319rg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275013-na6319rg.txt' === file2bib.sh === id: cord-270091-sqrh8ylt author: Cohen, Pascal title: Vascularites associées aux infections virales date: 2004-11-30 pages: extension: .txt txt: ./txt/cord-270091-sqrh8ylt.txt cache: ./cache/cord-270091-sqrh8ylt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-270091-sqrh8ylt.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-273343-als886fe author: McClenahan, Shasta D. title: Discovery of a Bovine Enterovirus in Alpaca date: 2013-08-12 pages: extension: .txt txt: ./txt/cord-273343-als886fe.txt cache: ./cache/cord-273343-als886fe.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273343-als886fe.txt' === file2bib.sh === id: cord-272981-8gahvdt0 author: Wege, Helmut title: Relapsing subacute demyelinating encephalomyelitis in rats during the course of coronavirus JHM infection date: 1984-08-31 pages: extension: .txt txt: ./txt/cord-272981-8gahvdt0.txt cache: ./cache/cord-272981-8gahvdt0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272981-8gahvdt0.txt' === file2bib.sh === id: cord-274112-6t0wpiqy author: Webby, RJ title: Responsiveness to a pandemic alert: use of reverse genetics for rapid development of influenza vaccines date: 2004-04-03 pages: extension: .txt txt: ./txt/cord-274112-6t0wpiqy.txt cache: ./cache/cord-274112-6t0wpiqy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274112-6t0wpiqy.txt' === file2bib.sh === id: cord-272066-f6q6q3io author: Shim, Byoung-Shik title: Sublingual Delivery of Vaccines for the Induction of Mucosal Immunity date: 2013-06-30 pages: extension: .txt txt: ./txt/cord-272066-f6q6q3io.txt cache: ./cache/cord-272066-f6q6q3io.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272066-f6q6q3io.txt' === file2bib.sh === id: cord-017331-ru7mvfc0 author: Samanta, Indranil title: Infectious Diseases date: 2017-02-25 pages: extension: .txt txt: ./txt/cord-017331-ru7mvfc0.txt cache: ./cache/cord-017331-ru7mvfc0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-017331-ru7mvfc0.txt' === file2bib.sh === id: cord-271568-qgpi2kcs author: Jackwood, M.W. title: Avian coronavirus infectious bronchitis virus susceptibility to botanical oleoresins and essential oils in vitro and in vivo date: 2010-01-21 pages: extension: .txt txt: ./txt/cord-271568-qgpi2kcs.txt cache: ./cache/cord-271568-qgpi2kcs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-271568-qgpi2kcs.txt' === file2bib.sh === id: cord-271650-biq0chyn author: Torres, Juan M title: Safety evaluation of a recombinant myxoma-RHDV virus inducing horizontal transmissible protection against myxomatosis and rabbit haemorrhagic disease date: 2000-09-15 pages: extension: .txt txt: ./txt/cord-271650-biq0chyn.txt cache: ./cache/cord-271650-biq0chyn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271650-biq0chyn.txt' === file2bib.sh === id: cord-268593-rvxxv1dn author: Wang, Mingyang title: Hemagglutinin-esterase-fusion (HEF) protein of influenza C virus date: 2015-07-28 pages: extension: .txt txt: ./txt/cord-268593-rvxxv1dn.txt cache: ./cache/cord-268593-rvxxv1dn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268593-rvxxv1dn.txt' === file2bib.sh === id: cord-269623-9pxdeva3 author: Nicholson, Karl G title: Influenza date: 2003-11-22 pages: extension: .txt txt: ./txt/cord-269623-9pxdeva3.txt cache: ./cache/cord-269623-9pxdeva3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-269623-9pxdeva3.txt' === file2bib.sh === id: cord-276715-d1nh2dvb author: Raha, Syamal title: Is Copper beneficial for COVID-19 patients? date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-276715-d1nh2dvb.txt cache: ./cache/cord-276715-d1nh2dvb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276715-d1nh2dvb.txt' === file2bib.sh === id: cord-275719-ru33ubss author: Roingeard, Philippe title: Virus detection by transmission electron microscopy: Still useful for diagnosis and a plus for biosafety date: 2018-11-09 pages: extension: .txt txt: ./txt/cord-275719-ru33ubss.txt cache: ./cache/cord-275719-ru33ubss.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275719-ru33ubss.txt' === file2bib.sh === id: cord-273708-2q64at3z author: Annunziata, Giuseppe title: May Polyphenols Have a Role Against Coronavirus Infection? An Overview of in vitro Evidence date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-273708-2q64at3z.txt cache: ./cache/cord-273708-2q64at3z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273708-2q64at3z.txt' === file2bib.sh === id: cord-276212-ys5njiw0 author: Wei, L. title: Burden, seasonal pattern and symptomatology of acute respiratory illnesses with different viral aetiologies in children presenting at outpatient clinics in Hong Kong date: 2015-05-30 pages: extension: .txt txt: ./txt/cord-276212-ys5njiw0.txt cache: ./cache/cord-276212-ys5njiw0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276212-ys5njiw0.txt' === file2bib.sh === id: cord-275570-i9fw0afj author: Lau, Susanna K. P. title: Molecular Research on Emerging Viruses: Evolution, Diagnostics, Pathogenesis, and Therapeutics date: 2018-01-30 pages: extension: .txt txt: ./txt/cord-275570-i9fw0afj.txt cache: ./cache/cord-275570-i9fw0afj.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-275570-i9fw0afj.txt' === file2bib.sh === id: cord-253466-7gpije5d author: Netherton, Christopher title: A Guide to Viral Inclusions, Membrane Rearrangements, Factories, and Viroplasm Produced During Virus Replication date: 2007-08-31 pages: extension: .txt txt: ./txt/cord-253466-7gpije5d.txt cache: ./cache/cord-253466-7gpije5d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-253466-7gpije5d.txt' === file2bib.sh === id: cord-274306-cxvnv8dy author: Chastel, C. title: Émergence de virus nouveaux en Asie : les changements climatiques sont-ils en cause ? date: 2004-11-30 pages: extension: .txt txt: ./txt/cord-274306-cxvnv8dy.txt cache: ./cache/cord-274306-cxvnv8dy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274306-cxvnv8dy.txt' === file2bib.sh === id: cord-275602-cog4nma0 author: Watkins, Kevin title: Emerging Infectious Diseases: a Review date: 2018-06-22 pages: extension: .txt txt: ./txt/cord-275602-cog4nma0.txt cache: ./cache/cord-275602-cog4nma0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275602-cog4nma0.txt' === file2bib.sh === id: cord-274643-vjb2yt93 author: Kang, G. title: Viral Diarrhea date: 2008-08-26 pages: extension: .txt txt: ./txt/cord-274643-vjb2yt93.txt cache: ./cache/cord-274643-vjb2yt93.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-274643-vjb2yt93.txt' === file2bib.sh === id: cord-276052-gk6n8slx author: Yadav, Pragya title: Isolation of Tioman virus from Pteropus giganteus bat in North-East region of India date: 2016-09-09 pages: extension: .txt txt: ./txt/cord-276052-gk6n8slx.txt cache: ./cache/cord-276052-gk6n8slx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276052-gk6n8slx.txt' === file2bib.sh === id: cord-269426-82g5eiyg author: Holman, David H. title: Viral Vectors date: 2009-01-30 pages: extension: .txt txt: ./txt/cord-269426-82g5eiyg.txt cache: ./cache/cord-269426-82g5eiyg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269426-82g5eiyg.txt' === file2bib.sh === id: cord-271172-y48dovux author: Potter, Christopher William title: Chapter 25 Respiratory tract viruses date: 1998-12-31 pages: extension: .txt txt: ./txt/cord-271172-y48dovux.txt cache: ./cache/cord-271172-y48dovux.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271172-y48dovux.txt' === file2bib.sh === id: cord-276348-vr5fit8r author: Ogra, Pearay L. title: Respiratory syncytial virus: The virus, the disease and the immune response date: 2004-01-31 pages: extension: .txt txt: ./txt/cord-276348-vr5fit8r.txt cache: ./cache/cord-276348-vr5fit8r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276348-vr5fit8r.txt' === file2bib.sh === id: cord-269975-1ebmq7t8 author: Duplantier, Allen J. title: Combating biothreat pathogens: ongoing efforts for countermeasure development and unique challenges date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-269975-1ebmq7t8.txt cache: ./cache/cord-269975-1ebmq7t8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269975-1ebmq7t8.txt' === file2bib.sh === id: cord-271091-ffn59sgf author: Galao, Rui P title: Saccharomyces cerevisiae: a versatile eukaryotic system in virology date: 2007-10-10 pages: extension: .txt txt: ./txt/cord-271091-ffn59sgf.txt cache: ./cache/cord-271091-ffn59sgf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271091-ffn59sgf.txt' === file2bib.sh === id: cord-273777-qb0vp9gr author: Happel, Anna-Ursula title: The Vaginal Virome—Balancing Female Genital Tract Bacteriome, Mucosal Immunity, and Sexual and Reproductive Health Outcomes? date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-273777-qb0vp9gr.txt cache: ./cache/cord-273777-qb0vp9gr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273777-qb0vp9gr.txt' === file2bib.sh === id: cord-278093-0twnkv93 author: Perveen, Shagufta title: Coronavirus nCOVID-19: A Pandemic Disease and the Saudi precautions date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-278093-0twnkv93.txt cache: ./cache/cord-278093-0twnkv93.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278093-0twnkv93.txt' === file2bib.sh === id: cord-277327-il8uaavn author: Couch, MD, Robert B. title: Respiratory Viral Infections in Immunocompetent and Immunocompromised Persons date: 1997-03-17 pages: extension: .txt txt: ./txt/cord-277327-il8uaavn.txt cache: ./cache/cord-277327-il8uaavn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277327-il8uaavn.txt' === file2bib.sh === id: cord-277010-2iecsho0 author: Wen, Xiaohong title: Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study date: 2019-01-08 pages: extension: .txt txt: ./txt/cord-277010-2iecsho0.txt cache: ./cache/cord-277010-2iecsho0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277010-2iecsho0.txt' === file2bib.sh === id: cord-271122-3fsl5589 author: Wathes, D. Claire title: Importance of Viral Disease in Dairy Cow Fertility date: 2019-07-24 pages: extension: .txt txt: ./txt/cord-271122-3fsl5589.txt cache: ./cache/cord-271122-3fsl5589.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-271122-3fsl5589.txt' === file2bib.sh === id: cord-277107-gs7j6fxo author: Yamin, Mohammad title: Counting the cost of COVID-19 date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-277107-gs7j6fxo.txt cache: ./cache/cord-277107-gs7j6fxo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277107-gs7j6fxo.txt' === file2bib.sh === id: cord-275821-yu39aw54 author: Ciminski, Kevin title: Novel insights into bat influenza A viruses date: 2017-09-14 pages: extension: .txt txt: ./txt/cord-275821-yu39aw54.txt cache: ./cache/cord-275821-yu39aw54.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275821-yu39aw54.txt' === file2bib.sh === id: cord-272052-8vvpm4tx author: Hartmann, Katrin title: Clinical aspects of feline immunodeficiency and feline leukemia virus infection date: 2011-10-15 pages: extension: .txt txt: ./txt/cord-272052-8vvpm4tx.txt cache: ./cache/cord-272052-8vvpm4tx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-272052-8vvpm4tx.txt' === file2bib.sh === id: cord-276506-dj7dyo0x author: Coria, M. F. title: Protective effect of an inactivated avian coronavirus vaccine administered by aerosol date: 1973 pages: extension: .txt txt: ./txt/cord-276506-dj7dyo0x.txt cache: ./cache/cord-276506-dj7dyo0x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276506-dj7dyo0x.txt' === file2bib.sh === id: cord-273326-gmw8gl2r author: Saiz, Juan-Carlos title: Host-Directed Antivirals: A Realistic Alternative to Fight Zika Virus date: 2018-08-24 pages: extension: .txt txt: ./txt/cord-273326-gmw8gl2r.txt cache: ./cache/cord-273326-gmw8gl2r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273326-gmw8gl2r.txt' === file2bib.sh === id: cord-276039-nqqwnmwc author: Rua, Rejane title: Origin, evolution and innate immune control of simian foamy viruses in humans date: 2015-02-17 pages: extension: .txt txt: ./txt/cord-276039-nqqwnmwc.txt cache: ./cache/cord-276039-nqqwnmwc.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-276039-nqqwnmwc.txt' === file2bib.sh === id: cord-276585-m1dkkbq7 author: Pulliam, Juliet R. C. title: Viral Host Jumps: Moving toward a Predictive Framework date: 2008-02-13 pages: extension: .txt txt: ./txt/cord-276585-m1dkkbq7.txt cache: ./cache/cord-276585-m1dkkbq7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276585-m1dkkbq7.txt' === file2bib.sh === id: cord-276583-j8bf0eme author: Ghalyanchi Langeroudi, Arash title: Full-length characterization and phylogenetic analysis of hemagglutinin gene of H9N2 virus isolated from broilers in Iran during 1998–2007 date: 2012-01-21 pages: extension: .txt txt: ./txt/cord-276583-j8bf0eme.txt cache: ./cache/cord-276583-j8bf0eme.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-276583-j8bf0eme.txt' === file2bib.sh === id: cord-277641-nb1p1akx author: Shaw, D. M. title: Invisible Enemies: Coronavirus and Other Hidden Threats date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-277641-nb1p1akx.txt cache: ./cache/cord-277641-nb1p1akx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-277641-nb1p1akx.txt' === file2bib.sh === id: cord-275683-1qj9ri18 author: Roux, Simon title: Metagenomics in Virology date: 2019-06-12 pages: extension: .txt txt: ./txt/cord-275683-1qj9ri18.txt cache: ./cache/cord-275683-1qj9ri18.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275683-1qj9ri18.txt' === file2bib.sh === id: cord-278456-gsv6dh36 author: Qureshi, Abid title: AVCpred: an integrated web server for prediction and design of antiviral compounds date: 2016-09-09 pages: extension: .txt txt: ./txt/cord-278456-gsv6dh36.txt cache: ./cache/cord-278456-gsv6dh36.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278456-gsv6dh36.txt' === file2bib.sh === id: cord-277970-sb1wjd3b author: Kang, Qianli title: Screening for Anti-Influenza Actives of Prefractionated Traditional Chinese Medicines date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-277970-sb1wjd3b.txt cache: ./cache/cord-277970-sb1wjd3b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277970-sb1wjd3b.txt' === file2bib.sh === id: cord-280854-cxpgwwjd author: Kumarasamy, Dhanabal title: Synthesis and in vitro antiviral evaluation of 4-substituted 3,4-dihydropyrimidinones date: 2017-01-15 pages: extension: .txt txt: ./txt/cord-280854-cxpgwwjd.txt cache: ./cache/cord-280854-cxpgwwjd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280854-cxpgwwjd.txt' === file2bib.sh === id: cord-278482-j5zlismf author: Taylor, Raymond title: BCX4430 – A broad-spectrum antiviral adenosine nucleoside analog under development for the treatment of Ebola virus disease date: 2016-06-30 pages: extension: .txt txt: ./txt/cord-278482-j5zlismf.txt cache: ./cache/cord-278482-j5zlismf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278482-j5zlismf.txt' === file2bib.sh === id: cord-280987-uhxk5b1b author: Turtle, L. title: Encephalitis, Viral date: 2014-05-01 pages: extension: .txt txt: ./txt/cord-280987-uhxk5b1b.txt cache: ./cache/cord-280987-uhxk5b1b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280987-uhxk5b1b.txt' === file2bib.sh === id: cord-270670-cubh9jxc author: Domingo, E. title: Viruses as Quasispecies: Biological Implications date: 2006 pages: extension: .txt txt: ./txt/cord-270670-cubh9jxc.txt cache: ./cache/cord-270670-cubh9jxc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270670-cubh9jxc.txt' === file2bib.sh === id: cord-280391-5kiu2pb6 author: Akinloye, Oluwabukola M. title: Specific Viruses Detected in Nigerian Children in Association with Acute Respiratory Disease date: 2011-10-11 pages: extension: .txt txt: ./txt/cord-280391-5kiu2pb6.txt cache: ./cache/cord-280391-5kiu2pb6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280391-5kiu2pb6.txt' === file2bib.sh === id: cord-276009-p98wjtjb author: Iyer, Arun V. title: Recombinant vesicular stomatitis virus-based west Nile vaccine elicits strong humoral and cellular immune responses and protects mice against lethal challenge with the virulent west Nile virus strain LSU-AR01 date: 2009-02-05 pages: extension: .txt txt: ./txt/cord-276009-p98wjtjb.txt cache: ./cache/cord-276009-p98wjtjb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276009-p98wjtjb.txt' === file2bib.sh === id: cord-278973-82n0d1dh author: Li, Zhijie title: Characterization and pathogenicity of a novel mammalian orthoreovirus from wild short-nosed fruit bats date: 2016-05-31 pages: extension: .txt txt: ./txt/cord-278973-82n0d1dh.txt cache: ./cache/cord-278973-82n0d1dh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278973-82n0d1dh.txt' === file2bib.sh === id: cord-273019-hbpfz8rt author: Glingston, R. Sahaya title: Organelle dynamics and viral infections: at cross roads date: 2018-06-25 pages: extension: .txt txt: ./txt/cord-273019-hbpfz8rt.txt cache: ./cache/cord-273019-hbpfz8rt.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-273019-hbpfz8rt.txt' === file2bib.sh === id: cord-278635-vwdxr1bl author: Świętoń, Edyta title: Low pathogenic avian influenza virus isolates with different levels of defective genome segments vary in pathogenicity and transmission efficiency date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-278635-vwdxr1bl.txt cache: ./cache/cord-278635-vwdxr1bl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278635-vwdxr1bl.txt' === file2bib.sh === id: cord-278511-je1509ar author: Wang, David title: 5 challenges in understanding the role of the virome in health and disease date: 2020-03-26 pages: extension: .txt txt: ./txt/cord-278511-je1509ar.txt cache: ./cache/cord-278511-je1509ar.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-278511-je1509ar.txt' === file2bib.sh === id: cord-278250-dwok857k author: Li, Heng title: The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites date: 2019-08-19 pages: extension: .txt txt: ./txt/cord-278250-dwok857k.txt cache: ./cache/cord-278250-dwok857k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278250-dwok857k.txt' === file2bib.sh === id: cord-279694-25rblhwb author: Mahy, B.W.J title: Emerging and Reemerging Virus Diseases of Vertebrates date: 2014-11-28 pages: extension: .txt txt: ./txt/cord-279694-25rblhwb.txt cache: ./cache/cord-279694-25rblhwb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279694-25rblhwb.txt' === file2bib.sh === id: cord-281593-bq12grqo author: Liu, Zheng title: Transmission Electron Microscopy Studies of Cellular Responses to Entry of Virions: One Kind of Natural Nanobiomaterial date: 2012-04-11 pages: extension: .txt txt: ./txt/cord-281593-bq12grqo.txt cache: ./cache/cord-281593-bq12grqo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281593-bq12grqo.txt' === file2bib.sh === id: cord-277400-w7mvk3x4 author: Nasir, Arshan title: Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification date: 2017-03-10 pages: extension: .txt txt: ./txt/cord-277400-w7mvk3x4.txt cache: ./cache/cord-277400-w7mvk3x4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277400-w7mvk3x4.txt' === file2bib.sh === id: cord-278465-tjjkz16y author: Wille, Michelle title: Urbanization and the dynamics of RNA viruses in Mallards (Anas platyrhynchos) date: 2017-03-18 pages: extension: .txt txt: ./txt/cord-278465-tjjkz16y.txt cache: ./cache/cord-278465-tjjkz16y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278465-tjjkz16y.txt' === file2bib.sh === id: cord-279617-xuzu55cg author: Tuladhar, E. title: Thermal stability of structurally different viruses with proven or potential relevance to food safety date: 2012-03-30 pages: extension: .txt txt: ./txt/cord-279617-xuzu55cg.txt cache: ./cache/cord-279617-xuzu55cg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-279617-xuzu55cg.txt' === file2bib.sh === id: cord-277392-s0bldxg9 author: Cann, Alan J. title: Replication date: 2012-02-29 pages: extension: .txt txt: ./txt/cord-277392-s0bldxg9.txt cache: ./cache/cord-277392-s0bldxg9.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-277392-s0bldxg9.txt' === file2bib.sh === id: cord-278913-u6vihq3u author: Allam, Zaheer title: The Rise of Machine Intelligence in the COVID-19 Pandemic and Its Impact on Health Policy date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-278913-u6vihq3u.txt cache: ./cache/cord-278913-u6vihq3u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-278913-u6vihq3u.txt' === file2bib.sh === id: cord-271790-3s8o774l author: Pinto Mendes, J. title: The role of infection in asthma date: 2008-10-31 pages: extension: .txt txt: ./txt/cord-271790-3s8o774l.txt cache: ./cache/cord-271790-3s8o774l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-271790-3s8o774l.txt' === file2bib.sh === id: cord-268540-wrjzr3ws author: Park, You Jeong title: Fighting the War Against COVID-19 via Cell-Based Regenerative Medicine: Lessons Learned from 1918 Spanish Flu and Other Previous Pandemics date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-268540-wrjzr3ws.txt cache: ./cache/cord-268540-wrjzr3ws.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268540-wrjzr3ws.txt' === file2bib.sh === id: cord-270940-acwkh6ed author: Kallio-Kokko, Hannimari title: Viral zoonoses in Europe date: 2005-06-29 pages: extension: .txt txt: ./txt/cord-270940-acwkh6ed.txt cache: ./cache/cord-270940-acwkh6ed.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-270940-acwkh6ed.txt' === file2bib.sh === id: cord-281158-vjh9z7l4 author: Storch, Gregory A title: Respiratory Viruses in Babies: Important Insights From Down Under date: 2018-02-01 pages: extension: .txt txt: ./txt/cord-281158-vjh9z7l4.txt cache: ./cache/cord-281158-vjh9z7l4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281158-vjh9z7l4.txt' === file2bib.sh === id: cord-276908-9jthjf24 author: Gupta, Akanksha title: COVID‐19: Emergence of Infectious Diseases, Nanotechnology Aspects, Challenges, and Future Perspectives date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-276908-9jthjf24.txt cache: ./cache/cord-276908-9jthjf24.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276908-9jthjf24.txt' === file2bib.sh === id: cord-280130-ewqe9edq author: Weber, Friedemann title: Viral suppression of the interferon system date: 2007-01-27 pages: extension: .txt txt: ./txt/cord-280130-ewqe9edq.txt cache: ./cache/cord-280130-ewqe9edq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280130-ewqe9edq.txt' === file2bib.sh === id: cord-277309-kelebqr6 author: Wang, Lin-Fa title: Viruses in bats and potential spillover to animals and humans date: 2019-01-18 pages: extension: .txt txt: ./txt/cord-277309-kelebqr6.txt cache: ./cache/cord-277309-kelebqr6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277309-kelebqr6.txt' === file2bib.sh === id: cord-280986-i27mge10 author: Mallia, Patrick title: How Viral Infections Cause Exacerbation of Airway Diseases date: 2017-01-25 pages: extension: .txt txt: ./txt/cord-280986-i27mge10.txt cache: ./cache/cord-280986-i27mge10.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-280986-i27mge10.txt' === file2bib.sh === id: cord-279557-hk77e3pp author: Drosten, Christian title: Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection date: 2013-06-17 pages: extension: .txt txt: ./txt/cord-279557-hk77e3pp.txt cache: ./cache/cord-279557-hk77e3pp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279557-hk77e3pp.txt' === file2bib.sh === id: cord-281332-5mddyv0n author: Wilson, Michael R. title: A novel cause of chronic viral meningoencephalitis: Cache Valley virus date: 2017-07-25 pages: extension: .txt txt: ./txt/cord-281332-5mddyv0n.txt cache: ./cache/cord-281332-5mddyv0n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-281332-5mddyv0n.txt' === file2bib.sh === id: cord-280781-u3wd27rn author: Stohlman, S. A. title: Stability of neurotropic mouse hepatitis virus (JHM strain) during chronic infection of neuroblastoma cells date: 1978 pages: extension: .txt txt: ./txt/cord-280781-u3wd27rn.txt cache: ./cache/cord-280781-u3wd27rn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280781-u3wd27rn.txt' === file2bib.sh === id: cord-279798-b5tduubu author: Sano, Daisuke title: Risk management of viral infectious diseases in wastewater reclamation and reuse: Review date: 2016-03-14 pages: extension: .txt txt: ./txt/cord-279798-b5tduubu.txt cache: ./cache/cord-279798-b5tduubu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-279798-b5tduubu.txt' === file2bib.sh === id: cord-278479-vl296i1b author: Samuel, Arthur S title: Experimental infection of hamsters with avian paramyxovirus serotypes 1 to 9 date: 2011-02-23 pages: extension: .txt txt: ./txt/cord-278479-vl296i1b.txt cache: ./cache/cord-278479-vl296i1b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-278479-vl296i1b.txt' === file2bib.sh === id: cord-276364-zyw5aukk author: Wong, Ho Him title: Manipulation of autophagy by (+) RNA viruses date: 2019-08-08 pages: extension: .txt txt: ./txt/cord-276364-zyw5aukk.txt cache: ./cache/cord-276364-zyw5aukk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276364-zyw5aukk.txt' === file2bib.sh === id: cord-282344-o1rkx2z4 author: Kim, Seung Won title: Effects of humidity and other factors on the generation and sampling of a coronavirus aerosol date: 2007-07-25 pages: extension: .txt txt: ./txt/cord-282344-o1rkx2z4.txt cache: ./cache/cord-282344-o1rkx2z4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282344-o1rkx2z4.txt' === file2bib.sh === id: cord-281061-uoszpnst author: Watanabe, Yohei title: A novel immunochromatographic system for easy-to-use detection of group 1 avian influenza viruses with acquired human-type receptor binding specificity date: 2015-03-15 pages: extension: .txt txt: ./txt/cord-281061-uoszpnst.txt cache: ./cache/cord-281061-uoszpnst.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-281061-uoszpnst.txt' === file2bib.sh === id: cord-283641-2u16otbf author: Vainionpää, R. title: Diagnostic Techniques: Serological and Molecular Approaches date: 2015-03-06 pages: extension: .txt txt: ./txt/cord-283641-2u16otbf.txt cache: ./cache/cord-283641-2u16otbf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-283641-2u16otbf.txt' === file2bib.sh === id: cord-020010-q58x6xb0 author: nan title: 19th ICAR Abstracts: date: 2006-03-13 pages: extension: .txt txt: ./txt/cord-020010-q58x6xb0.txt cache: ./cache/cord-020010-q58x6xb0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-020010-q58x6xb0.txt' === file2bib.sh === id: cord-276006-mjjnkqv6 author: Jarach, Natanel title: Polymers in the Medical Antiviral Front-Line date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-276006-mjjnkqv6.txt cache: ./cache/cord-276006-mjjnkqv6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276006-mjjnkqv6.txt' === file2bib.sh === id: cord-282343-cko4curf author: Cheng, Han title: A parallel genome-wide RNAi screening strategy to identify host proteins important for entry of Marburg virus and H5N1 influenza virus date: 2015-11-24 pages: extension: .txt txt: ./txt/cord-282343-cko4curf.txt cache: ./cache/cord-282343-cko4curf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282343-cko4curf.txt' === file2bib.sh === id: cord-285462-9i61rsei author: Almomani, Hesham title: L'ampleur de la réaction des gens aux rumeurs et aux fausses nouvelles à la lumière de la crise du virus Corona date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-285462-9i61rsei.txt cache: ./cache/cord-285462-9i61rsei.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285462-9i61rsei.txt' === file2bib.sh === id: cord-276616-odmnvv7m author: Darcel, C. title: Reflections on scrapie and related disorders, with consideration of the possibility of a viral aetiology date: 1995 pages: extension: .txt txt: ./txt/cord-276616-odmnvv7m.txt cache: ./cache/cord-276616-odmnvv7m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276616-odmnvv7m.txt' === file2bib.sh === id: cord-280427-smqc23vr author: Singla, Rubal title: Human animal interface of SARS-CoV-2 (COVID-19) transmission: a critical appraisal of scientific evidence date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-280427-smqc23vr.txt cache: ./cache/cord-280427-smqc23vr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-280427-smqc23vr.txt' === file2bib.sh === id: cord-275538-c44gmu22 author: Davis-Wurzler, Gina M. title: Current Vaccination Strategies in Puppies and Kittens date: 2006-03-24 pages: extension: .txt txt: ./txt/cord-275538-c44gmu22.txt cache: ./cache/cord-275538-c44gmu22.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-275538-c44gmu22.txt' === file2bib.sh === id: cord-264884-ydkigome author: Villarreal, Luis P. title: The Widespread Evolutionary Significance of Viruses date: 2008-07-05 pages: extension: .txt txt: ./txt/cord-264884-ydkigome.txt cache: ./cache/cord-264884-ydkigome.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264884-ydkigome.txt' === file2bib.sh === id: cord-280564-kgoczioe author: Conceição-Neto, Nádia title: Identification of an enterovirus recombinant with a torovirus-like gene insertion during a diarrhea outbreak in fattening pigs date: 2017-09-08 pages: extension: .txt txt: ./txt/cord-280564-kgoczioe.txt cache: ./cache/cord-280564-kgoczioe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280564-kgoczioe.txt' === file2bib.sh === id: cord-285367-jxlt0gby author: Johnson, Richard T. title: Emerging Issues in Neurovirology: New Viruses, Diagnostic Tools, and Therapeutics date: 2008-08-31 pages: extension: .txt txt: ./txt/cord-285367-jxlt0gby.txt cache: ./cache/cord-285367-jxlt0gby.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-285367-jxlt0gby.txt' === file2bib.sh === id: cord-277417-f71jwdzj author: Geoghegan, Jemma L. title: The phylogenomics of evolving virus virulence date: 2018-10-10 pages: extension: .txt txt: ./txt/cord-277417-f71jwdzj.txt cache: ./cache/cord-277417-f71jwdzj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277417-f71jwdzj.txt' === file2bib.sh === id: cord-280048-b4dz1lnn author: Domingo, Esteban title: Viral quasispecies date: 2019-10-17 pages: extension: .txt txt: ./txt/cord-280048-b4dz1lnn.txt cache: ./cache/cord-280048-b4dz1lnn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280048-b4dz1lnn.txt' === file2bib.sh === id: cord-285856-0sw3wt1i author: Naesens, Lieve title: Anti-influenza virus activity and structure–activity relationship of aglycoristocetin derivatives with cyclobutenedione carrying hydrophobic chains date: 2009-02-05 pages: extension: .txt txt: ./txt/cord-285856-0sw3wt1i.txt cache: ./cache/cord-285856-0sw3wt1i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285856-0sw3wt1i.txt' === file2bib.sh === id: cord-282628-6uoberfu author: Tiwari, Bhagyashree title: Future impacts and trends in treatment of hospital wastewater date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-282628-6uoberfu.txt cache: ./cache/cord-282628-6uoberfu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282628-6uoberfu.txt' === file2bib.sh === id: cord-280429-4fota9rl author: Medvedev, Kirill E. title: Functional and evolutionary analysis of viral proteins containing a Rossmann‐like fold date: 2018-06-13 pages: extension: .txt txt: ./txt/cord-280429-4fota9rl.txt cache: ./cache/cord-280429-4fota9rl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-280429-4fota9rl.txt' === file2bib.sh === id: cord-279418-3r1ijafm author: Nevers, Quentin title: Negri bodies and other virus membrane-less replication compartments() date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-279418-3r1ijafm.txt cache: ./cache/cord-279418-3r1ijafm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279418-3r1ijafm.txt' === file2bib.sh === id: cord-284880-xsh3wkqy author: Bandaly, Victor title: The Fate of Mengovirus on Fiberglass Filter of Air Handling Units date: 2017-06-28 pages: extension: .txt txt: ./txt/cord-284880-xsh3wkqy.txt cache: ./cache/cord-284880-xsh3wkqy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284880-xsh3wkqy.txt' === file2bib.sh === id: cord-286137-4cbh3u3z author: Honce, Rebekah title: They are what you eat: Shaping of viral populations through nutrition and consequences for virulence date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-286137-4cbh3u3z.txt cache: ./cache/cord-286137-4cbh3u3z.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-286137-4cbh3u3z.txt' === file2bib.sh === id: cord-290034-4b0mshqa author: Le, Yen H. title: Virus detections among patients with severe acute respiratory illness, Northern Vietnam date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-290034-4b0mshqa.txt cache: ./cache/cord-290034-4b0mshqa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290034-4b0mshqa.txt' === file2bib.sh === id: cord-278099-ypov9ha3 author: Kumar, Surender title: Molecular characterization of a novel cryptic virus infecting pigeonpea plants date: 2017-08-03 pages: extension: .txt txt: ./txt/cord-278099-ypov9ha3.txt cache: ./cache/cord-278099-ypov9ha3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278099-ypov9ha3.txt' === file2bib.sh === id: cord-278876-il7g78w1 author: Akkina, Ramesh title: 2016 International meeting of the Global Virus Network date: 2017-03-16 pages: extension: .txt txt: ./txt/cord-278876-il7g78w1.txt cache: ./cache/cord-278876-il7g78w1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278876-il7g78w1.txt' === file2bib.sh === id: cord-279849-zzkliu76 author: DaPalma, T. title: A systematic approach to virus–virus interactions date: 2010-01-20 pages: extension: .txt txt: ./txt/cord-279849-zzkliu76.txt cache: ./cache/cord-279849-zzkliu76.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279849-zzkliu76.txt' === file2bib.sh === id: cord-283964-k3hy2ewx author: Chan, Jasper Fuk-Woo title: Cross-species transmission and emergence of novel viruses from birds date: 2015-01-31 pages: extension: .txt txt: ./txt/cord-283964-k3hy2ewx.txt cache: ./cache/cord-283964-k3hy2ewx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283964-k3hy2ewx.txt' === file2bib.sh === id: cord-279691-v5kpmk0b author: Hagemeijer, Marne C. title: Biogenesis and Dynamics of the Coronavirus Replicative Structures date: 2012-11-21 pages: extension: .txt txt: ./txt/cord-279691-v5kpmk0b.txt cache: ./cache/cord-279691-v5kpmk0b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-279691-v5kpmk0b.txt' === file2bib.sh === id: cord-288703-wdh1jiry author: Ishtiaq, Farah title: A Call to Introduce Structured Zika Surveillance in India date: 2017-11-15 pages: extension: .txt txt: ./txt/cord-288703-wdh1jiry.txt cache: ./cache/cord-288703-wdh1jiry.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-288703-wdh1jiry.txt' === file2bib.sh === id: cord-285330-td4vr0zv author: Mohammadi, Ali title: Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus date: 2015-11-12 pages: extension: .txt txt: ./txt/cord-285330-td4vr0zv.txt cache: ./cache/cord-285330-td4vr0zv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285330-td4vr0zv.txt' === file2bib.sh === id: cord-283880-lrrkuist author: Kumar, Arvind title: Evolution of selective-sequencing approaches for virus discovery and virome analysis date: 2017-07-15 pages: extension: .txt txt: ./txt/cord-283880-lrrkuist.txt cache: ./cache/cord-283880-lrrkuist.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-283880-lrrkuist.txt' === file2bib.sh === id: cord-284941-wfn0pnev author: Samal, S.K. title: Paramyxoviruses of Animals date: 2008-07-30 pages: extension: .txt txt: ./txt/cord-284941-wfn0pnev.txt cache: ./cache/cord-284941-wfn0pnev.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284941-wfn0pnev.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-283405-aozxvxxs author: Vermillion, Meghan S. title: Pregnancy and infection: using disease pathogenesis to inform vaccine strategy date: 2018-02-01 pages: extension: .txt txt: ./txt/cord-283405-aozxvxxs.txt cache: ./cache/cord-283405-aozxvxxs.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-283405-aozxvxxs.txt' === file2bib.sh === id: cord-281429-6lv3di4x author: García-Nicolás, Obdulio title: Targeting of the Nasal Mucosa by Japanese Encephalitis Virus for Non-Vector-Borne Transmission date: 2018-11-27 pages: extension: .txt txt: ./txt/cord-281429-6lv3di4x.txt cache: ./cache/cord-281429-6lv3di4x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281429-6lv3di4x.txt' === file2bib.sh === id: cord-281844-c0uhcatg author: Costa, Lusmaia D.C. title: Exacerbation of asthma and airway infection: is the virus the villain? date: 2014-12-31 pages: extension: .txt txt: ./txt/cord-281844-c0uhcatg.txt cache: ./cache/cord-281844-c0uhcatg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281844-c0uhcatg.txt' === file2bib.sh === id: cord-288111-0ufc54kw author: ter MEULEN, VOLKER title: Autoimmune Reactions Against Myelin Basic Protein Induced by Corona and Measles Viruses date: 2006-12-17 pages: extension: .txt txt: ./txt/cord-288111-0ufc54kw.txt cache: ./cache/cord-288111-0ufc54kw.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-288111-0ufc54kw.txt' === file2bib.sh === id: cord-284523-lknyehsa author: da Mata, Élida Cleyse Gomes title: Antiviral activity of animal venom peptides and related compounds date: 2017-01-06 pages: extension: .txt txt: ./txt/cord-284523-lknyehsa.txt cache: ./cache/cord-284523-lknyehsa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284523-lknyehsa.txt' === file2bib.sh === id: cord-282204-j1slaefb author: Silva, José V.J. title: A scoping review of Chikungunya virus infection: epidemiology, clinical characteristics, viral co-circulation complications, and control date: 2018-12-31 pages: extension: .txt txt: ./txt/cord-282204-j1slaefb.txt cache: ./cache/cord-282204-j1slaefb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282204-j1slaefb.txt' === file2bib.sh === id: cord-286708-igu984oc author: Chua, Kaw Bing title: Identification and Characterization of a New Orthoreovirus from Patients with Acute Respiratory Infections date: 2008-11-25 pages: extension: .txt txt: ./txt/cord-286708-igu984oc.txt cache: ./cache/cord-286708-igu984oc.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-286708-igu984oc.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-023143-fcno330z author: nan title: Molecular aspects of viral immunity date: 2004-02-19 pages: extension: .txt txt: ./txt/cord-023143-fcno330z.txt cache: ./cache/cord-023143-fcno330z.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-023143-fcno330z.txt' === file2bib.sh === id: cord-276193-cngz535o author: Volz, A. title: Modified Vaccinia Virus Ankara: History, Value in Basic Research, and Current Perspectives for Vaccine Development date: 2016-08-01 pages: extension: .txt txt: ./txt/cord-276193-cngz535o.txt cache: ./cache/cord-276193-cngz535o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276193-cngz535o.txt' === file2bib.sh === id: cord-288231-vg8bwed9 author: Haagmans, Bart L. title: The Application of Genomics to Emerging Zoonotic Viral Diseases date: 2009-10-26 pages: extension: .txt txt: ./txt/cord-288231-vg8bwed9.txt cache: ./cache/cord-288231-vg8bwed9.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-288231-vg8bwed9.txt' === file2bib.sh === id: cord-289360-h6wvx7gw author: Imperiale, Michael J. title: The Importance of Virology at a Time of Great Need and Great Jeopardy date: 2015-03-10 pages: extension: .txt txt: ./txt/cord-289360-h6wvx7gw.txt cache: ./cache/cord-289360-h6wvx7gw.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-289360-h6wvx7gw.txt' === file2bib.sh === id: cord-288372-48wao8a0 author: Dia, Ndongo title: Respiratory viruses associated with patients older than 50 years presenting with ILI in Senegal, 2009 to 2011 date: 2014-04-08 pages: extension: .txt txt: ./txt/cord-288372-48wao8a0.txt cache: ./cache/cord-288372-48wao8a0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288372-48wao8a0.txt' === file2bib.sh === id: cord-285547-7m3dh8hu author: Nomura, Naoki title: Characterization of avian influenza viruses isolated from domestic ducks in Vietnam in 2009 and 2010 date: 2011-11-09 pages: extension: .txt txt: ./txt/cord-285547-7m3dh8hu.txt cache: ./cache/cord-285547-7m3dh8hu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285547-7m3dh8hu.txt' === file2bib.sh === id: cord-285148-bch7814v author: Singanayagam, Aran title: Viruses exacerbating chronic pulmonary disease: the role of immune modulation date: 2012-03-15 pages: extension: .txt txt: ./txt/cord-285148-bch7814v.txt cache: ./cache/cord-285148-bch7814v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285148-bch7814v.txt' === file2bib.sh === id: cord-287151-4hlvrfeh author: Steinmann, J title: Surrogate viruses for testing virucidal efficacy of chemical disinfectants date: 2004-04-30 pages: extension: .txt txt: ./txt/cord-287151-4hlvrfeh.txt cache: ./cache/cord-287151-4hlvrfeh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287151-4hlvrfeh.txt' === file2bib.sh === id: cord-282742-eyukbot7 author: Diosa-Toro, Mayra title: Arthropod-Borne Flaviviruses and RNA Interference: Seeking New Approaches for Antiviral Therapy date: 2013-02-20 pages: extension: .txt txt: ./txt/cord-282742-eyukbot7.txt cache: ./cache/cord-282742-eyukbot7.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-282742-eyukbot7.txt' === file2bib.sh === id: cord-288930-h13cxuh3 author: Lim, Faye J title: Viral Etiology and the Impact of Codetection in Young Children Presenting With Influenza-Like Illness date: 2016-07-20 pages: extension: .txt txt: ./txt/cord-288930-h13cxuh3.txt cache: ./cache/cord-288930-h13cxuh3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288930-h13cxuh3.txt' === file2bib.sh === id: cord-288348-b10e023s author: Estes, Mary Kolb title: Epidemic viral gastroenteritis date: 1979-06-30 pages: extension: .txt txt: ./txt/cord-288348-b10e023s.txt cache: ./cache/cord-288348-b10e023s.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-288348-b10e023s.txt' === file2bib.sh === id: cord-286559-y8z0pwgn author: Ding, Nai-Zheng title: A permanent host shift of rabies virus from Chiroptera to Carnivora associated with recombination date: 2017-03-21 pages: extension: .txt txt: ./txt/cord-286559-y8z0pwgn.txt cache: ./cache/cord-286559-y8z0pwgn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286559-y8z0pwgn.txt' === file2bib.sh === id: cord-285935-5rsk6g7l author: Kinast, Volker title: Hepatitis E Virus Drug Development date: 2019-05-28 pages: extension: .txt txt: ./txt/cord-285935-5rsk6g7l.txt cache: ./cache/cord-285935-5rsk6g7l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285935-5rsk6g7l.txt' === file2bib.sh === id: cord-268417-6eyetb5i author: Mandel, Benjamin title: Neutralization of Animal Viruses date: 1978-12-31 pages: extension: .txt txt: ./txt/cord-268417-6eyetb5i.txt cache: ./cache/cord-268417-6eyetb5i.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-268417-6eyetb5i.txt' === file2bib.sh === id: cord-287286-4l963z2q author: Green, Victoria A. title: Molecular mechanisms of viral infection and propagation: An overview of the second Advanced Summer School in Africa date: 2010-07-28 pages: extension: .txt txt: ./txt/cord-287286-4l963z2q.txt cache: ./cache/cord-287286-4l963z2q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-287286-4l963z2q.txt' === file2bib.sh === id: cord-290149-eed4v2jl author: ODEND'HAL, STEWART title: Porcine Hemagglutinating Encephalomyelitis Virus date: 2012-12-02 pages: extension: .txt txt: ./txt/cord-290149-eed4v2jl.txt cache: ./cache/cord-290149-eed4v2jl.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-290149-eed4v2jl.txt' === file2bib.sh === id: cord-287770-oxfnt2n4 author: Caricati, C. P. title: Safety of snake antivenom immunoglobulins: Efficacy of viral inactivation in a complete downstream process date: 2013-06-27 pages: extension: .txt txt: ./txt/cord-287770-oxfnt2n4.txt cache: ./cache/cord-287770-oxfnt2n4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287770-oxfnt2n4.txt' === file2bib.sh === id: cord-274080-884x48on author: Rumlová, Michaela title: In vitro methods for testing antiviral drugs date: 2018-06-30 pages: extension: .txt txt: ./txt/cord-274080-884x48on.txt cache: ./cache/cord-274080-884x48on.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274080-884x48on.txt' === file2bib.sh === id: cord-287554-2lqy2ix9 author: Amarelle, Luciano title: Tratamiento antigripal: fármacos actualmente utilizados y nuevos agentes en desarrollo date: 2017-01-31 pages: extension: .txt txt: ./txt/cord-287554-2lqy2ix9.txt cache: ./cache/cord-287554-2lqy2ix9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287554-2lqy2ix9.txt' === file2bib.sh === id: cord-287337-2ljbsia2 author: Ludwig, Christine title: Virus-like particles—universal molecular toolboxes date: 2008-01-04 pages: extension: .txt txt: ./txt/cord-287337-2ljbsia2.txt cache: ./cache/cord-287337-2ljbsia2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287337-2ljbsia2.txt' === file2bib.sh === id: cord-291294-w5ecsht4 author: Foulongne, V. title: Le bocavirus humain (HBoV) date: 2008-03-17 pages: extension: .txt txt: ./txt/cord-291294-w5ecsht4.txt cache: ./cache/cord-291294-w5ecsht4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-291294-w5ecsht4.txt' === file2bib.sh === id: cord-284156-btb4oodz author: Liu, Yiliu title: Host and Viral Modulation of RIG-I-Mediated Antiviral Immunity date: 2017-01-03 pages: extension: .txt txt: ./txt/cord-284156-btb4oodz.txt cache: ./cache/cord-284156-btb4oodz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-284156-btb4oodz.txt' === file2bib.sh === id: cord-278684-txlvla0j author: Gonzalez–Dunia, Daniel title: Borna Disease Virus and the Brain date: 1998-01-30 pages: extension: .txt txt: ./txt/cord-278684-txlvla0j.txt cache: ./cache/cord-278684-txlvla0j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-278684-txlvla0j.txt' === file2bib.sh === id: cord-289406-54vyzxjf author: Edwards, Suzanne title: An Experimental Model for Myocarditis and Congestive Heart Failure after Rabbit Coronavirus Infection date: 1992-01-17 pages: extension: .txt txt: ./txt/cord-289406-54vyzxjf.txt cache: ./cache/cord-289406-54vyzxjf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-289406-54vyzxjf.txt' === file2bib.sh === id: cord-290231-4m9lj0uq author: Guirakhoo, Farshad title: The Murray Valley encephalitis virus prM protein confers acid resistance to virus particles and alters the expression of epitopes within the R2 domain of E glycoprotein date: 1992-12-31 pages: extension: .txt txt: ./txt/cord-290231-4m9lj0uq.txt cache: ./cache/cord-290231-4m9lj0uq.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-290231-4m9lj0uq.txt' === file2bib.sh === id: cord-290133-4ou7ubb4 author: Weiss, Martin M. title: Rethinking Smallpox date: 2004-12-01 pages: extension: .txt txt: ./txt/cord-290133-4ou7ubb4.txt cache: ./cache/cord-290133-4ou7ubb4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290133-4ou7ubb4.txt' === file2bib.sh === id: cord-290556-x7t7zqjd author: Middleton, Peter J title: Viruses that multiply in the gut and cause endemic and epidemic gastroenteritis date: 1996-08-31 pages: extension: .txt txt: ./txt/cord-290556-x7t7zqjd.txt cache: ./cache/cord-290556-x7t7zqjd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290556-x7t7zqjd.txt' === file2bib.sh === id: cord-288879-rj03dsib author: Schein, Catherine H. title: Polyglutamine Repeats in Viruses date: 2018-09-04 pages: extension: .txt txt: ./txt/cord-288879-rj03dsib.txt cache: ./cache/cord-288879-rj03dsib.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288879-rj03dsib.txt' === file2bib.sh === id: cord-291707-dzmvjh7j author: Tupper, G. T. title: Antigenic and biological diversity of feline coronaviruses: feline infectious peritonitis and feline enteritis virus date: 1987 pages: extension: .txt txt: ./txt/cord-291707-dzmvjh7j.txt cache: ./cache/cord-291707-dzmvjh7j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291707-dzmvjh7j.txt' === file2bib.sh === id: cord-287851-9p0dr7rl author: Fedson, David S title: Confronting an influenza pandemic with inexpensive generic agents: can it be done? date: 2008-09-30 pages: extension: .txt txt: ./txt/cord-287851-9p0dr7rl.txt cache: ./cache/cord-287851-9p0dr7rl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287851-9p0dr7rl.txt' === file2bib.sh === id: cord-280878-1kt51viz author: To, Janet title: Targeting the Channel Activity of Viroporins date: 2016-01-07 pages: extension: .txt txt: ./txt/cord-280878-1kt51viz.txt cache: ./cache/cord-280878-1kt51viz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280878-1kt51viz.txt' === file2bib.sh === id: cord-286298-pn9nwl64 author: Helmy, Yosra A. title: The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-286298-pn9nwl64.txt cache: ./cache/cord-286298-pn9nwl64.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286298-pn9nwl64.txt' === file2bib.sh === id: cord-289593-81vu2kbu author: de Blic, J. title: Interactions micro-organismes et voies aériennes distales : spécificités pédiatriques date: 2017-03-03 pages: extension: .txt txt: ./txt/cord-289593-81vu2kbu.txt cache: ./cache/cord-289593-81vu2kbu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-289593-81vu2kbu.txt' === file2bib.sh === id: cord-290540-r0d6oaez author: Rottier, Peter J.M. title: The molecular dynamics of feline coronaviruses date: 1999-09-01 pages: extension: .txt txt: ./txt/cord-290540-r0d6oaez.txt cache: ./cache/cord-290540-r0d6oaez.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290540-r0d6oaez.txt' === file2bib.sh === id: cord-287348-00yaxpkp author: Martinez, Maria Jose Abad title: Antiviral Activities of Polysaccharides from Natural Sources date: 2005-12-31 pages: extension: .txt txt: ./txt/cord-287348-00yaxpkp.txt cache: ./cache/cord-287348-00yaxpkp.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-287348-00yaxpkp.txt' === file2bib.sh === id: cord-284479-75zgljet author: García-Serradilla, Moisés title: Drug repurposing for new, efficient, broad spectrum antivirals date: 2019-04-15 pages: extension: .txt txt: ./txt/cord-284479-75zgljet.txt cache: ./cache/cord-284479-75zgljet.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-284479-75zgljet.txt' === file2bib.sh === id: cord-290548-0wezrr1b author: Watanabe, Tokiko title: Villains or heroes? The raison d'être of viruses date: 2020-02-19 pages: extension: .txt txt: ./txt/cord-290548-0wezrr1b.txt cache: ./cache/cord-290548-0wezrr1b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290548-0wezrr1b.txt' === file2bib.sh === id: cord-290432-4dli5emd author: O’Grady, Kerry-Ann F. title: Upper airway viruses and bacteria in urban Aboriginal and Torres Strait Islander children in Brisbane, Australia: a cross-sectional study date: 2017-04-04 pages: extension: .txt txt: ./txt/cord-290432-4dli5emd.txt cache: ./cache/cord-290432-4dli5emd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290432-4dli5emd.txt' === file2bib.sh === id: cord-290851-1e5e033r author: Gerlier, Denis title: Emerging zoonotic viruses: new lessons on receptor and entry mechanisms date: 2011-06-12 pages: extension: .txt txt: ./txt/cord-290851-1e5e033r.txt cache: ./cache/cord-290851-1e5e033r.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-290851-1e5e033r.txt' === file2bib.sh === id: cord-291816-d4j8samu author: Diniz Beduschi Travassos Alves, Christian title: Mamastrovirus 5 detected in a crab-eating fox (Cerdocyon thous): Expanding wildlife host range of astroviruses date: 2018-08-15 pages: extension: .txt txt: ./txt/cord-291816-d4j8samu.txt cache: ./cache/cord-291816-d4j8samu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291816-d4j8samu.txt' === file2bib.sh === id: cord-292075-t9z7zqz4 author: Gessain, Antoine title: Mécanismes d’émergence virale et transmission interespèces : l’exemple des rétrovirus Foamy simiens chezl’Homme en Afrique Centrale date: 2013-12-31 pages: extension: .txt txt: ./txt/cord-292075-t9z7zqz4.txt cache: ./cache/cord-292075-t9z7zqz4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292075-t9z7zqz4.txt' === file2bib.sh === id: cord-290282-oxyzndsj author: Ortego, Javier title: Transmissible gastroenteritis coronavirus gene 7 is not essential but influences in vivo virus replication and virulence date: 2003-03-30 pages: extension: .txt txt: ./txt/cord-290282-oxyzndsj.txt cache: ./cache/cord-290282-oxyzndsj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290282-oxyzndsj.txt' === file2bib.sh === id: cord-289017-vwye3pk9 author: Comach, Guillermo title: Sentinel Surveillance of Influenza-Like Illness in Two Hospitals in Maracay, Venezuela: 2006–2010 date: 2012-09-11 pages: extension: .txt txt: ./txt/cord-289017-vwye3pk9.txt cache: ./cache/cord-289017-vwye3pk9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-289017-vwye3pk9.txt' === file2bib.sh === id: cord-291860-dw1sfzqx author: van Boheemen, Sander title: Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients date: 2019-12-16 pages: extension: .txt txt: ./txt/cord-291860-dw1sfzqx.txt cache: ./cache/cord-291860-dw1sfzqx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-291860-dw1sfzqx.txt' === file2bib.sh === id: cord-286219-qcx5ehnh author: Calistri, Arianna title: The Ubiquitin-Conjugating System: Multiple Roles in Viral Replication and Infection date: 2014-05-06 pages: extension: .txt txt: ./txt/cord-286219-qcx5ehnh.txt cache: ./cache/cord-286219-qcx5ehnh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286219-qcx5ehnh.txt' === file2bib.sh === id: cord-290385-0smnl70i author: Chan, Jasper F.W. title: Zika fever and congenital Zika syndrome: An unexpected emerging arboviral disease date: 2016-03-03 pages: extension: .txt txt: ./txt/cord-290385-0smnl70i.txt cache: ./cache/cord-290385-0smnl70i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290385-0smnl70i.txt' === file2bib.sh === id: cord-288238-36hiiw91 author: Keshavarz, Mohsen title: Metabolic host response and therapeutic approaches to influenza infection date: 2020-03-05 pages: extension: .txt txt: ./txt/cord-288238-36hiiw91.txt cache: ./cache/cord-288238-36hiiw91.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288238-36hiiw91.txt' === file2bib.sh === id: cord-293540-45awgabp author: Drancourt, Michel title: Point-of-care testing for community-acquired pneumonia date: 2013-07-23 pages: extension: .txt txt: ./txt/cord-293540-45awgabp.txt cache: ./cache/cord-293540-45awgabp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293540-45awgabp.txt' === file2bib.sh === id: cord-289093-si8btsab author: Beard, Philippa M. title: A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference date: 2014-06-05 pages: extension: .txt txt: ./txt/cord-289093-si8btsab.txt cache: ./cache/cord-289093-si8btsab.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289093-si8btsab.txt' === file2bib.sh === id: cord-290509-56pfww0l author: Fleet, Graham H title: Foodborne viral illness - status in Australia date: 2000-07-25 pages: extension: .txt txt: ./txt/cord-290509-56pfww0l.txt cache: ./cache/cord-290509-56pfww0l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-290509-56pfww0l.txt' === file2bib.sh === id: cord-290481-i2ppvsh5 author: Dolja, Valerian V. title: Comparative and functional genomics of closteroviruses date: 2006-03-09 pages: extension: .txt txt: ./txt/cord-290481-i2ppvsh5.txt cache: ./cache/cord-290481-i2ppvsh5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290481-i2ppvsh5.txt' === file2bib.sh === id: cord-290993-bsnja161 author: McAuliffe, Josephine title: Replication of SARS coronavirus administered into the respiratory tract of African Green, rhesus and cynomolgus monkeys date: 2004-12-05 pages: extension: .txt txt: ./txt/cord-290993-bsnja161.txt cache: ./cache/cord-290993-bsnja161.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-290993-bsnja161.txt' === file2bib.sh === id: cord-291946-kq0rsuxj author: Etienne, Lucie title: The Mongoose, the Pheasant, the Pox, and the Retrovirus date: 2013-08-27 pages: extension: .txt txt: ./txt/cord-291946-kq0rsuxj.txt cache: ./cache/cord-291946-kq0rsuxj.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-291946-kq0rsuxj.txt' === file2bib.sh === id: cord-291156-zxg3dsm3 author: Bernasconi, Anna title: Empowering Virus Sequences Research through Conceptual Modeling date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-291156-zxg3dsm3.txt cache: ./cache/cord-291156-zxg3dsm3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-291156-zxg3dsm3.txt' === file2bib.sh === id: cord-290539-8ak2tths author: Cagno, Valeria title: Novel broad spectrum virucidal molecules against enveloped viruses date: 2018-12-07 pages: extension: .txt txt: ./txt/cord-290539-8ak2tths.txt cache: ./cache/cord-290539-8ak2tths.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290539-8ak2tths.txt' === file2bib.sh === id: cord-288945-c9ow1q5c author: Spengler, Ulrich title: Liver Disease Associated with Non-Hepatitis Viruses date: 2019-11-01 pages: extension: .txt txt: ./txt/cord-288945-c9ow1q5c.txt cache: ./cache/cord-288945-c9ow1q5c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288945-c9ow1q5c.txt' === file2bib.sh === id: cord-281281-knelqmzx author: Villas-Boas, Gustavo R. title: The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-281281-knelqmzx.txt cache: ./cache/cord-281281-knelqmzx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281281-knelqmzx.txt' === file2bib.sh === id: cord-287711-gw8mgg4m author: Junter, Guy-Alain title: Cellulose-based virus-retentive filters: a review date: 2017-06-01 pages: extension: .txt txt: ./txt/cord-287711-gw8mgg4m.txt cache: ./cache/cord-287711-gw8mgg4m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-287711-gw8mgg4m.txt' === file2bib.sh === id: cord-286741-h3oix9zc author: Park, Mee Sook title: Animal models for the risk assessment of viral pandemic potential date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-286741-h3oix9zc.txt cache: ./cache/cord-286741-h3oix9zc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286741-h3oix9zc.txt' === file2bib.sh === id: cord-290855-6umgvt28 author: Ma, Li title: Antiviral Effects of Plant-Derived Essential Oils and Their Components: An Updated Review date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-290855-6umgvt28.txt cache: ./cache/cord-290855-6umgvt28.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290855-6umgvt28.txt' === file2bib.sh === id: cord-293375-qcy56ui7 author: Strauss, Ellen G. title: Identification of the active site residues in the nsP2 proteinase of sindbis virus date: 1992-12-31 pages: extension: .txt txt: ./txt/cord-293375-qcy56ui7.txt cache: ./cache/cord-293375-qcy56ui7.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-293375-qcy56ui7.txt' === file2bib.sh === id: cord-292643-n6xp5mlz author: Hall, Richard J. title: Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery date: 2013-09-13 pages: extension: .txt txt: ./txt/cord-292643-n6xp5mlz.txt cache: ./cache/cord-292643-n6xp5mlz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292643-n6xp5mlz.txt' === file2bib.sh === id: cord-292286-ygomb3oi author: Zakaryan, Hovakim title: Flavonoids: promising natural compounds against viral infections date: 2017-05-25 pages: extension: .txt txt: ./txt/cord-292286-ygomb3oi.txt cache: ./cache/cord-292286-ygomb3oi.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-292286-ygomb3oi.txt' === file2bib.sh === id: cord-293975-np9xdag5 author: Barnett, E. M. title: Two neurotropic viruses, herpes simplex virus type 1 and mouse hepatitis virus, spread along different neural pathways from the main olfactory bulb date: 1993-12-31 pages: extension: .txt txt: ./txt/cord-293975-np9xdag5.txt cache: ./cache/cord-293975-np9xdag5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-293975-np9xdag5.txt' === file2bib.sh === id: cord-293097-poh1y6o7 author: V, Antony Aroul Raj title: The contribution of dry indoor built environment on the spread of Coronavirus: Data from various Indian states date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-293097-poh1y6o7.txt cache: ./cache/cord-293097-poh1y6o7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293097-poh1y6o7.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-292416-3hhi4wps author: Sarid, Ronit title: Investigating an Emerging Virus During a Sudden Pandemic Outbreak date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-292416-3hhi4wps.txt cache: ./cache/cord-292416-3hhi4wps.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292416-3hhi4wps.txt' === file2bib.sh === id: cord-297339-et2305rz author: Lauber, Chris title: Genetics-Based Classification of Filoviruses Calls for Expanded Sampling of Genomic Sequences date: 2012-08-31 pages: extension: .txt txt: ./txt/cord-297339-et2305rz.txt cache: ./cache/cord-297339-et2305rz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297339-et2305rz.txt' === file2bib.sh === id: cord-292830-gcfx1095 author: Ianevski, Aleksandr title: Novel activities of safe-in-human broad-spectrum antiviral agents date: 2018-04-23 pages: extension: .txt txt: ./txt/cord-292830-gcfx1095.txt cache: ./cache/cord-292830-gcfx1095.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292830-gcfx1095.txt' === file2bib.sh === id: cord-288734-xinkqs6u author: Muñoz-Fontela, César title: Ebola Virus Disease in Humans: Pathophysiology and Immunity date: 2017-03-30 pages: extension: .txt txt: ./txt/cord-288734-xinkqs6u.txt cache: ./cache/cord-288734-xinkqs6u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-288734-xinkqs6u.txt' === file2bib.sh === id: cord-293387-0m1ngob3 author: Wood, A. title: The action of three antiseptics/disinfectants against enveloped and non-enveloped viruses date: 1998-04-30 pages: extension: .txt txt: ./txt/cord-293387-0m1ngob3.txt cache: ./cache/cord-293387-0m1ngob3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293387-0m1ngob3.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-294568-12eyo13f.txt cache: ./cache/cord-294568-12eyo13f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294568-12eyo13f.txt' === file2bib.sh === id: cord-283756-ycjzitlk author: Simons, Robin R. L. title: Potential for Introduction of Bat-Borne Zoonotic Viruses into the EU: A Review date: 2014-05-16 pages: extension: .txt txt: ./txt/cord-283756-ycjzitlk.txt cache: ./cache/cord-283756-ycjzitlk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-283756-ycjzitlk.txt' === file2bib.sh === id: cord-292828-29jbf9ik author: Alsaleh, Asma N title: Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control date: 2014-01-09 pages: extension: .txt txt: ./txt/cord-292828-29jbf9ik.txt cache: ./cache/cord-292828-29jbf9ik.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292828-29jbf9ik.txt' === file2bib.sh === id: cord-296935-y77c4ro4 author: Couch, Robert B. title: Prior Infections With Seasonal Influenza A/H1N1 Virus Reduced the Illness Severity and Epidemic Intensity of Pandemic H1N1 Influenza in Healthy Adults date: 2011-11-10 pages: extension: .txt txt: ./txt/cord-296935-y77c4ro4.txt cache: ./cache/cord-296935-y77c4ro4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-296935-y77c4ro4.txt' === file2bib.sh === id: cord-292657-gq3965se author: Das, Piyanki title: Decoding the global outbreak of COVID-19: the nature is behind the scene date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-292657-gq3965se.txt cache: ./cache/cord-292657-gq3965se.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-292657-gq3965se.txt' === file2bib.sh === id: cord-295640-mhfu0e9r author: Wang, Wenling title: Improving Cross-Protection against Influenza Virus Using Recombinant Vaccinia Vaccine Expressing NP and M2 Ectodomain Tandem Repeats date: 2019-06-25 pages: extension: .txt txt: ./txt/cord-295640-mhfu0e9r.txt cache: ./cache/cord-295640-mhfu0e9r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-295640-mhfu0e9r.txt' === file2bib.sh === id: cord-295792-hajvtzj9 author: Álvez, Fernando title: SARS-CoV2 coronavirus: So far polite with children. Debatable immunological and non-immunological evidence date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-295792-hajvtzj9.txt cache: ./cache/cord-295792-hajvtzj9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-295792-hajvtzj9.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-290352-0pc5eji4 author: de Jong, Menno D. title: Avian influenza A (H5N1) date: 2005-10-06 pages: extension: .txt txt: ./txt/cord-290352-0pc5eji4.txt cache: ./cache/cord-290352-0pc5eji4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-290352-0pc5eji4.txt' === file2bib.sh === id: cord-291113-iizj932l author: Cumbo, Enzo title: Alternative Methods of Sterilization in Dental Practices Against COVID-19 date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-291113-iizj932l.txt cache: ./cache/cord-291113-iizj932l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291113-iizj932l.txt' === file2bib.sh === id: cord-294312-ju6vuywm author: Rohde, Rodney E. title: Common Myths and Legends of Rabies date: 2019-04-19 pages: extension: .txt txt: ./txt/cord-294312-ju6vuywm.txt cache: ./cache/cord-294312-ju6vuywm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-294312-ju6vuywm.txt' === file2bib.sh === id: cord-293732-rxd1lyi7 author: Manoj, M.G. title: Potential link between compromised air quality and transmission of the novel corona virus (SARS-CoV-2) in affected areas date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-293732-rxd1lyi7.txt cache: ./cache/cord-293732-rxd1lyi7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-293732-rxd1lyi7.txt' === file2bib.sh === id: cord-295531-zojb3cew author: Huggett, Kathryn D. title: Influenza A date: 2008-01-10 pages: extension: .txt txt: ./txt/cord-295531-zojb3cew.txt cache: ./cache/cord-295531-zojb3cew.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-295531-zojb3cew.txt' === file2bib.sh === id: cord-291561-sxvgue36 author: Haixu, Liang title: Detection of 20 respiratory viruses and bacteria by influenza-like illness surveillance in Beijing, China, 2016–2018 date: 2019-11-25 pages: extension: .txt txt: ./txt/cord-291561-sxvgue36.txt cache: ./cache/cord-291561-sxvgue36.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-291561-sxvgue36.txt' === file2bib.sh === id: cord-291534-c6cjxq07 author: Gwyer Findlay, Emily title: Cationic Host Defence Peptides: Potential as Antiviral Therapeutics date: 2013-05-07 pages: extension: .txt txt: ./txt/cord-291534-c6cjxq07.txt cache: ./cache/cord-291534-c6cjxq07.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-291534-c6cjxq07.txt' === file2bib.sh === id: cord-294585-dl5v9p50 author: Klein, H. G. title: Pathogen‐reduction methods: advantages and limits date: 2009-02-13 pages: extension: .txt txt: ./txt/cord-294585-dl5v9p50.txt cache: ./cache/cord-294585-dl5v9p50.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-294585-dl5v9p50.txt' === file2bib.sh === id: cord-295873-kykyubdq author: Morikawa, Saeko title: Seasonal variations of respiratory viruses and etiology of human rhinovirus infection in children date: 2015-10-22 pages: extension: .txt txt: ./txt/cord-295873-kykyubdq.txt cache: ./cache/cord-295873-kykyubdq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295873-kykyubdq.txt' === file2bib.sh === id: cord-291063-de7v4e5s author: Moens, Ugo title: Silencing Viral MicroRNA as a Novel Antiviral Therapy? date: 2009-05-28 pages: extension: .txt txt: ./txt/cord-291063-de7v4e5s.txt cache: ./cache/cord-291063-de7v4e5s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-291063-de7v4e5s.txt' === file2bib.sh === id: cord-297494-6yxmaihl author: Katsurada, Naoko title: The impact of virus infections on pneumonia mortality is complex in adults: a prospective multicentre observational study date: 2017-12-06 pages: extension: .txt txt: ./txt/cord-297494-6yxmaihl.txt cache: ./cache/cord-297494-6yxmaihl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297494-6yxmaihl.txt' === file2bib.sh === id: cord-293472-d3iwlpsr author: Afilalo, Marc title: Evaluation and Management of Seasonal Influenza in the Emergency Department date: 2012-04-06 pages: extension: .txt txt: ./txt/cord-293472-d3iwlpsr.txt cache: ./cache/cord-293472-d3iwlpsr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293472-d3iwlpsr.txt' === file2bib.sh === id: cord-294323-mryiqmsw author: Kumar, Binod title: The emerging influenza virus threat: status and new prospects for its therapy and control date: 2018-01-10 pages: extension: .txt txt: ./txt/cord-294323-mryiqmsw.txt cache: ./cache/cord-294323-mryiqmsw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294323-mryiqmsw.txt' === file2bib.sh === id: cord-294812-nnlzwaf1 author: Desforges, Marc title: Neuroinvasive and Neurotropic Human Respiratory Coronaviruses: Potential Neurovirulent Agents in Humans date: 2014-03-12 pages: extension: .txt txt: ./txt/cord-294812-nnlzwaf1.txt cache: ./cache/cord-294812-nnlzwaf1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294812-nnlzwaf1.txt' === file2bib.sh === id: cord-298214-ivu4erpq author: Castrignano, Silvana Beres title: The metagenomic approach and causality in virology date: 2015-04-01 pages: extension: .txt txt: ./txt/cord-298214-ivu4erpq.txt cache: ./cache/cord-298214-ivu4erpq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-298214-ivu4erpq.txt' === file2bib.sh === id: cord-298905-c2uuvfm5 author: Horzinek, M. C. title: Molecular pathogenesis of virus infections date: 1987 pages: extension: .txt txt: ./txt/cord-298905-c2uuvfm5.txt cache: ./cache/cord-298905-c2uuvfm5.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-298905-c2uuvfm5.txt' === file2bib.sh === id: cord-301064-ex6qb6zj author: Elena, Santiago F. title: Editorial: A home for virology, ecology, epidemiology, and evolutionary biology date: 2015-03-26 pages: extension: .txt txt: ./txt/cord-301064-ex6qb6zj.txt cache: ./cache/cord-301064-ex6qb6zj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301064-ex6qb6zj.txt' === file2bib.sh === id: cord-290617-45be6gxe author: Poulain, Florian title: Footprint of the host restriction factors APOBEC3 on the genome of human viruses date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-290617-45be6gxe.txt cache: ./cache/cord-290617-45be6gxe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290617-45be6gxe.txt' === file2bib.sh === id: cord-300020-edolh7ww author: Nielsen, Anne Ahlmann title: Persistence of Low-Pathogenic Avian Influenza H5N7 and H7N1 Subtypes in House Flies (Diptera: Muscidae) date: 2011-05-01 pages: extension: .txt txt: ./txt/cord-300020-edolh7ww.txt cache: ./cache/cord-300020-edolh7ww.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300020-edolh7ww.txt' === file2bib.sh === id: cord-294478-3ickafd3 author: Kapil, Sanjay title: Diagnostic Investigation of Emerging Viruses of Companion Animals date: 2008-05-22 pages: extension: .txt txt: ./txt/cord-294478-3ickafd3.txt cache: ./cache/cord-294478-3ickafd3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294478-3ickafd3.txt' === file2bib.sh === id: cord-295041-5vpawtef author: Jakhmola, Shweta title: SARS-CoV-2, an Underestimated Pathogen of the Nervous System date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-295041-5vpawtef.txt cache: ./cache/cord-295041-5vpawtef.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-295041-5vpawtef.txt' === file2bib.sh === id: cord-295191-xu26mvc3 author: Avirutnan, Panisadee title: Complement and its role in protection and pathogenesis of flavivirus infections date: 2008-12-30 pages: extension: .txt txt: ./txt/cord-295191-xu26mvc3.txt cache: ./cache/cord-295191-xu26mvc3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295191-xu26mvc3.txt' === file2bib.sh === id: cord-297203-f3f31h4r author: Afrough, B. title: Emerging viruses and current strategies for vaccine intervention date: 2019-04-16 pages: extension: .txt txt: ./txt/cord-297203-f3f31h4r.txt cache: ./cache/cord-297203-f3f31h4r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-297203-f3f31h4r.txt' === file2bib.sh === id: cord-296635-8r3tm966 author: Breed, Andrew C. title: Evidence of Endemic Hendra Virus Infection in Flying-Foxes (Pteropus conspicillatus)—Implications for Disease Risk Management date: 2011-12-14 pages: extension: .txt txt: ./txt/cord-296635-8r3tm966.txt cache: ./cache/cord-296635-8r3tm966.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-296635-8r3tm966.txt' === file2bib.sh === id: cord-297834-me1ajoyb author: Schountz, Tony title: Hantavirus Immunology of Rodent Reservoirs: Current Status and Future Directions date: 2014-03-14 pages: extension: .txt txt: ./txt/cord-297834-me1ajoyb.txt cache: ./cache/cord-297834-me1ajoyb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-297834-me1ajoyb.txt' === file2bib.sh === id: cord-295433-olmein3q author: Banerjee, Arinjay title: Bats and Coronaviruses date: 2019-01-09 pages: extension: .txt txt: ./txt/cord-295433-olmein3q.txt cache: ./cache/cord-295433-olmein3q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295433-olmein3q.txt' === file2bib.sh === id: cord-287466-ag5y781z author: Cowley, J.A. title: Nidoviruses of Fish and Crustaceans date: 2016-09-09 pages: extension: .txt txt: ./txt/cord-287466-ag5y781z.txt cache: ./cache/cord-287466-ag5y781z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287466-ag5y781z.txt' === file2bib.sh === id: cord-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 2 resourceName b'cord-300711-yibdumij.txt' === file2bib.sh === id: cord-297960-4x1j0iqg author: Bösl, Korbinian title: Common Nodes of Virus–Host Interaction Revealed Through an Integrated Network Analysis date: 2019-10-04 pages: extension: .txt txt: ./txt/cord-297960-4x1j0iqg.txt cache: ./cache/cord-297960-4x1j0iqg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-297960-4x1j0iqg.txt' === file2bib.sh === id: cord-292575-vsswxwdi author: Hammou, Rahma Ait title: Chapter 7 Scientific Advances in the Diagnosis of Emerging and Reemerging Viral Human Pathogens date: 2020-12-31 pages: extension: .txt txt: ./txt/cord-292575-vsswxwdi.txt cache: ./cache/cord-292575-vsswxwdi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292575-vsswxwdi.txt' === file2bib.sh === id: cord-298489-uqrzzh0e author: Bale, James F. title: Emerging Viral Infections date: 2012-08-11 pages: extension: .txt txt: ./txt/cord-298489-uqrzzh0e.txt cache: ./cache/cord-298489-uqrzzh0e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-298489-uqrzzh0e.txt' === file2bib.sh === id: cord-298862-8bijio30 author: Eltom, Kamal H. title: Buffalopox Virus: An Emerging Virus in Livestock and Humans date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-298862-8bijio30.txt cache: ./cache/cord-298862-8bijio30.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-298862-8bijio30.txt' === file2bib.sh === id: cord-302425-aaxvlktp author: Cortey, Martí title: High levels of unreported intraspecific diversity among RNA viruses in faeces of neonatal piglets with diarrhoea date: 2019-12-05 pages: extension: .txt txt: ./txt/cord-302425-aaxvlktp.txt cache: ./cache/cord-302425-aaxvlktp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302425-aaxvlktp.txt' === file2bib.sh === id: cord-296819-gztmidn2 author: Sambri, Vittorio title: Diagnosis of West Nile Virus Human Infections: Overview and Proposal of Diagnostic Protocols Considering the Results of External Quality Assessment Studies date: 2013-09-25 pages: extension: .txt txt: ./txt/cord-296819-gztmidn2.txt cache: ./cache/cord-296819-gztmidn2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296819-gztmidn2.txt' === file2bib.sh === id: cord-302055-s155i4e9 author: Mitchell, Edith P. title: Corona Virus: Global Pandemic Causing World-Wide Shutdown date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-302055-s155i4e9.txt cache: ./cache/cord-302055-s155i4e9.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-302055-s155i4e9.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 4 resourceName b'cord-303040-ha8gufh8.txt' === file2bib.sh === id: cord-295445-f4p00yaw author: Wang, Hao title: Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments date: 2018-02-01 pages: extension: .txt txt: ./txt/cord-295445-f4p00yaw.txt cache: ./cache/cord-295445-f4p00yaw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295445-f4p00yaw.txt' === file2bib.sh === id: cord-293421-0ksn0fc7 author: Rodriguez, J. M. title: Detection of animal pathogens by using the polymerasechain reaction (PCR) date: 1997-05-31 pages: extension: .txt txt: ./txt/cord-293421-0ksn0fc7.txt cache: ./cache/cord-293421-0ksn0fc7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293421-0ksn0fc7.txt' === file2bib.sh === id: cord-302021-42vqmndl author: Stanley, Mathew title: Synthesis and inhibitory activity of sialic acid derivatives targeted at viral sialate-O-acetylesterases date: 2011-04-08 pages: extension: .txt txt: ./txt/cord-302021-42vqmndl.txt cache: ./cache/cord-302021-42vqmndl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-302021-42vqmndl.txt' === file2bib.sh === id: cord-294125-v2dr4hm0 author: Albert, Manuel title: ISG15, a Small Molecule with Huge Implications: Regulation of Mitochondrial Homeostasis date: 2018-11-13 pages: extension: .txt txt: ./txt/cord-294125-v2dr4hm0.txt cache: ./cache/cord-294125-v2dr4hm0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294125-v2dr4hm0.txt' === file2bib.sh === id: cord-300189-gsp1dozg author: Franci, Gianluigi title: Infectivity inhibition by overlapping synthetic peptides derived from the gH/gL heterodimer of herpes simplex virus type 1 date: 2017-02-14 pages: extension: .txt txt: ./txt/cord-300189-gsp1dozg.txt cache: ./cache/cord-300189-gsp1dozg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300189-gsp1dozg.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 4 resourceName b'cord-302111-kg0dmgq0.txt' === file2bib.sh === id: cord-301592-n5ns3m34 author: Ivaska, Lauri title: Aetiology of febrile pharyngitis in children: Potential of myxovirus resistance protein A (MxA) as a biomarker of viral infection date: 2017-01-07 pages: extension: .txt txt: ./txt/cord-301592-n5ns3m34.txt cache: ./cache/cord-301592-n5ns3m34.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301592-n5ns3m34.txt' === file2bib.sh === id: cord-295062-8rl4kswe author: Marsh, Mark title: Virus Entry: Open Sesame date: 2006-02-24 pages: extension: .txt txt: ./txt/cord-295062-8rl4kswe.txt cache: ./cache/cord-295062-8rl4kswe.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-295062-8rl4kswe.txt' === file2bib.sh === id: cord-296309-i1mpov7k author: Houldcroft, Charlotte J. title: Clinical and biological insights from viral genome sequencing date: 2017-01-16 pages: extension: .txt txt: ./txt/cord-296309-i1mpov7k.txt cache: ./cache/cord-296309-i1mpov7k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296309-i1mpov7k.txt' === file2bib.sh === id: cord-297131-3a9vjpvn author: Charlton Hume, Hayley K. title: Synthetic biology for bioengineering virus‐like particle vaccines date: 2018-12-31 pages: extension: .txt txt: ./txt/cord-297131-3a9vjpvn.txt cache: ./cache/cord-297131-3a9vjpvn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297131-3a9vjpvn.txt' === file2bib.sh === id: cord-300133-yc2wxgid author: Martínez, Miguel J. title: Ebola Virus Infection: Overview and Update on Prevention and Treatment date: 2015-09-12 pages: extension: .txt txt: ./txt/cord-300133-yc2wxgid.txt cache: ./cache/cord-300133-yc2wxgid.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300133-yc2wxgid.txt' === file2bib.sh === id: cord-299207-lw0cv74b author: Upadhyay, Ranjit Kumar title: Modeling the spread of bird flu and predicting outbreak diversity date: 2007-05-08 pages: extension: .txt txt: ./txt/cord-299207-lw0cv74b.txt cache: ./cache/cord-299207-lw0cv74b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299207-lw0cv74b.txt' === file2bib.sh === id: cord-302716-wfla3l20 author: Popov, Vsevolod L. title: Electron Microscopy in Discovery of Novel and Emerging Viruses from the Collection of the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA) date: 2019-05-25 pages: extension: .txt txt: ./txt/cord-302716-wfla3l20.txt cache: ./cache/cord-302716-wfla3l20.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302716-wfla3l20.txt' === file2bib.sh === id: cord-298036-2zurc60t author: Imre, Gergely title: Cell death signalling in virus infection date: 2020-09-12 pages: extension: .txt txt: ./txt/cord-298036-2zurc60t.txt cache: ./cache/cord-298036-2zurc60t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-298036-2zurc60t.txt' === file2bib.sh === id: cord-292353-z86rjwle author: Hussein, Islam T.M. title: Recent Advances in Hantavirus Molecular Biology and Disease date: 2011-04-01 pages: extension: .txt txt: ./txt/cord-292353-z86rjwle.txt cache: ./cache/cord-292353-z86rjwle.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-292353-z86rjwle.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 4 resourceName b'cord-299379-ch7a39d6.txt' === file2bib.sh === id: cord-300810-a1skdp67 author: Lafay, F. title: Spread of the CVS strain of rabies virus and of the avirulent mutant AvO1 along the olfactory pathways of the mouse after intranasal inoculation date: 1991-07-31 pages: extension: .txt txt: ./txt/cord-300810-a1skdp67.txt cache: ./cache/cord-300810-a1skdp67.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-300810-a1skdp67.txt' === file2bib.sh === id: cord-304850-9xetsc2c author: Drosten, Christian title: Virus ecology: a gap between detection and prediction date: 2013-05-22 pages: extension: .txt txt: ./txt/cord-304850-9xetsc2c.txt cache: ./cache/cord-304850-9xetsc2c.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-304850-9xetsc2c.txt' === file2bib.sh === id: cord-300837-d0a8y5qh author: Khetawat, Dimple title: A Functional Henipavirus Envelope Glycoprotein Pseudotyped Lentivirus Assay System date: 2010-11-12 pages: extension: .txt txt: ./txt/cord-300837-d0a8y5qh.txt cache: ./cache/cord-300837-d0a8y5qh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-300837-d0a8y5qh.txt' === file2bib.sh === id: cord-275795-ee7qyw5h author: Monette, Anne title: T Lymphocytes as Measurable Targets of Protection and Vaccination Against Viral Disorders date: 2018-10-24 pages: extension: .txt txt: ./txt/cord-275795-ee7qyw5h.txt cache: ./cache/cord-275795-ee7qyw5h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-275795-ee7qyw5h.txt' === file2bib.sh === id: cord-299549-bjqwwzam author: Zhang, Lei title: Against Ebola: type I interferon guard risk and mesenchymal stromal cell combat sepsis date: 2015-01-01 pages: extension: .txt txt: ./txt/cord-299549-bjqwwzam.txt cache: ./cache/cord-299549-bjqwwzam.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-299549-bjqwwzam.txt' === file2bib.sh === id: cord-302614-siyyve9e author: Shigeta, Shiro title: Anti-RNA virus activity of polyoxometalates date: 2006-05-24 pages: extension: .txt txt: ./txt/cord-302614-siyyve9e.txt cache: ./cache/cord-302614-siyyve9e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302614-siyyve9e.txt' === file2bib.sh === id: cord-303297-fiievwy7 author: Oberemok, Volodymyr V. title: SARS-CoV-2 will continue to circulate in the human population: an opinion from the point of view of the virus-host relationship date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-303297-fiievwy7.txt cache: ./cache/cord-303297-fiievwy7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303297-fiievwy7.txt' === file2bib.sh === id: cord-286719-1xjmlwqr author: Draz, Mohamed Shehata title: Applications of gold nanoparticles in virus detection date: 2018-02-15 pages: extension: .txt txt: ./txt/cord-286719-1xjmlwqr.txt cache: ./cache/cord-286719-1xjmlwqr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286719-1xjmlwqr.txt' === file2bib.sh === id: cord-303533-6s01qplg author: Neuman, Benjamin W. title: Does form meet function in the coronavirus replicative organelle? date: 2014-07-15 pages: extension: .txt txt: ./txt/cord-303533-6s01qplg.txt cache: ./cache/cord-303533-6s01qplg.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-303533-6s01qplg.txt' === file2bib.sh === id: cord-294842-aesiff1f author: Romero-Brey, Inés title: Membranous Replication Factories Induced by Plus-Strand RNA Viruses date: 2014-07-22 pages: extension: .txt txt: ./txt/cord-294842-aesiff1f.txt cache: ./cache/cord-294842-aesiff1f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294842-aesiff1f.txt' === file2bib.sh === id: cord-305302-go87uu06 author: Gessain, Antoine title: Editorial overview: Emerging viruses: interspecies transmission date: 2015-02-28 pages: extension: .txt txt: ./txt/cord-305302-go87uu06.txt cache: ./cache/cord-305302-go87uu06.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305302-go87uu06.txt' === file2bib.sh === id: cord-306983-6w2fvtfy author: Wang, Siye title: Influenza Virus—Cytokine-Protease Cycle in the Pathogenesis of Vascular Hyperpermeability in Severe Influenza date: 2010-10-01 pages: extension: .txt txt: ./txt/cord-306983-6w2fvtfy.txt cache: ./cache/cord-306983-6w2fvtfy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306983-6w2fvtfy.txt' === file2bib.sh === id: cord-298745-3rrlap70 author: Field, H. E. title: Henipaviruses: Emerging Paramyxoviruses Associated with Fruit Bats date: 2007 pages: extension: .txt txt: ./txt/cord-298745-3rrlap70.txt cache: ./cache/cord-298745-3rrlap70.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-298745-3rrlap70.txt' === file2bib.sh === id: cord-300522-okbupw61 author: Sansone, Clementina title: Marine Algal Antioxidants as Potential Vectors for Controlling Viral Diseases date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-300522-okbupw61.txt cache: ./cache/cord-300522-okbupw61.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300522-okbupw61.txt' === file2bib.sh === id: cord-298032-3zlu8g8y author: Nan, Yuchen title: Antisense Phosphorodiamidate Morpholino Oligomers as Novel Antiviral Compounds date: 2018-04-20 pages: extension: .txt txt: ./txt/cord-298032-3zlu8g8y.txt cache: ./cache/cord-298032-3zlu8g8y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-298032-3zlu8g8y.txt' === file2bib.sh === id: cord-298019-gf2asni1 author: Galdiero, Stefania title: gH625: A milestone in understanding the many roles of membranotropic peptides date: 2014-10-12 pages: extension: .txt txt: ./txt/cord-298019-gf2asni1.txt cache: ./cache/cord-298019-gf2asni1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-298019-gf2asni1.txt' === file2bib.sh === id: cord-302486-z36hcvrx author: Cobo, Fernando title: Diagnostic approaches for viruses and prions in stem cell banks date: 2006-03-30 pages: extension: .txt txt: ./txt/cord-302486-z36hcvrx.txt cache: ./cache/cord-302486-z36hcvrx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-302486-z36hcvrx.txt' === file2bib.sh === id: cord-304481-yqc8r3ll author: Luis, Angela D. title: Network analysis of host–virus communities in bats and rodents reveals determinants of cross‐species transmission date: 2015-08-24 pages: extension: .txt txt: ./txt/cord-304481-yqc8r3ll.txt cache: ./cache/cord-304481-yqc8r3ll.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-304481-yqc8r3ll.txt' === file2bib.sh === id: cord-308385-bcph664h author: Yan, Zishuo title: Modeling COVID-19 infection in a confined space date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-308385-bcph664h.txt cache: ./cache/cord-308385-bcph664h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-308385-bcph664h.txt' === file2bib.sh === id: cord-307744-wbr84taq author: Jayadevan, Rajeev title: Does a younger host make the virus weaker? Presenting a new hypothesis date: 2020-09-13 pages: extension: .txt txt: ./txt/cord-307744-wbr84taq.txt cache: ./cache/cord-307744-wbr84taq.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-307744-wbr84taq.txt' === file2bib.sh === id: cord-298051-ej8qxkce author: Louten, Jennifer title: Detection and Diagnosis of Viral Infections date: 2016-05-06 pages: extension: .txt txt: ./txt/cord-298051-ej8qxkce.txt cache: ./cache/cord-298051-ej8qxkce.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298051-ej8qxkce.txt' === file2bib.sh === id: cord-304569-o39kl5k4 author: Nguyen-Van-Tam, Jonathan S title: From the Editor's desk date: 2015-04-23 pages: extension: .txt txt: ./txt/cord-304569-o39kl5k4.txt cache: ./cache/cord-304569-o39kl5k4.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-304569-o39kl5k4.txt' === file2bib.sh === id: cord-301285-p83ondy8 author: Kautz, Tiffany F title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy date: 2018-03-06 pages: extension: .txt txt: ./txt/cord-301285-p83ondy8.txt cache: ./cache/cord-301285-p83ondy8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301285-p83ondy8.txt' === file2bib.sh === id: cord-300435-vs0ntcsb author: Katz, Al title: Heteroaggregation of an enveloped bacteriophage with colloidal sediments and effect on virus viability date: 2018-10-01 pages: extension: .txt txt: ./txt/cord-300435-vs0ntcsb.txt cache: ./cache/cord-300435-vs0ntcsb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300435-vs0ntcsb.txt' === file2bib.sh === id: cord-298733-jole21wq author: Tyrrell, D.A.J. title: A view from the common cold unit date: 1992-06-30 pages: extension: .txt txt: ./txt/cord-298733-jole21wq.txt cache: ./cache/cord-298733-jole21wq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-298733-jole21wq.txt' === file2bib.sh === id: cord-309346-4mdxe6ri author: López-Medrano, Francisco title: Virus respiratorios: los más frecuentes, los más olvidados date: 2008-02-29 pages: extension: .txt txt: ./txt/cord-309346-4mdxe6ri.txt cache: ./cache/cord-309346-4mdxe6ri.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309346-4mdxe6ri.txt' === file2bib.sh === id: cord-307893-mvl0wrsj author: Goulter-Thorsen, R.M. title: Disciplines Associated with Food Safety: Food Virology date: 2014-01-13 pages: extension: .txt txt: ./txt/cord-307893-mvl0wrsj.txt cache: ./cache/cord-307893-mvl0wrsj.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-307893-mvl0wrsj.txt' === file2bib.sh === id: cord-304807-j2k1oel2 author: Herrera-Rodriguez, José title: Inactivated or damaged? Comparing the effect of inactivation methods on influenza virions to optimize vaccine production date: 2019-03-14 pages: extension: .txt txt: ./txt/cord-304807-j2k1oel2.txt cache: ./cache/cord-304807-j2k1oel2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304807-j2k1oel2.txt' === file2bib.sh === id: cord-297790-tpjxt0w5 author: Mandl, Judith N. title: Going to Bat(s) for Studies of Disease Tolerance date: 2018-09-20 pages: extension: .txt txt: ./txt/cord-297790-tpjxt0w5.txt cache: ./cache/cord-297790-tpjxt0w5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297790-tpjxt0w5.txt' === file2bib.sh === id: cord-302529-43pd2qsp author: El Moussi, Awatef title: Virological Surveillance of Influenza Viruses during the 2008–09, 2009–10 and 2010–11 Seasons in Tunisia date: 2013-09-19 pages: extension: .txt txt: ./txt/cord-302529-43pd2qsp.txt cache: ./cache/cord-302529-43pd2qsp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302529-43pd2qsp.txt' === file2bib.sh === id: cord-303665-l57e54hu author: Lahrich, S. title: Review on the contamination of wastewater by COVID-19 virus: Impact and treatment date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-303665-l57e54hu.txt cache: ./cache/cord-303665-l57e54hu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-303665-l57e54hu.txt' === file2bib.sh === id: cord-301362-f3lp10lm author: Delgui, Laura R. title: A Novel Mechanism Underlying the Innate Immune Response Induction upon Viral-Dependent Replication of Host Cell mRNA: A Mistake of +sRNA Viruses' Replicases date: 2017-01-20 pages: extension: .txt txt: ./txt/cord-301362-f3lp10lm.txt cache: ./cache/cord-301362-f3lp10lm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-301362-f3lp10lm.txt' === file2bib.sh === id: cord-303186-2hxlx1j2 author: Won, Hokeun title: Generation and protective efficacy of a cold-adapted attenuated genotype 2b porcine epidemic diarrhea virus date: 2019-07-09 pages: extension: .txt txt: ./txt/cord-303186-2hxlx1j2.txt cache: ./cache/cord-303186-2hxlx1j2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-303186-2hxlx1j2.txt' === file2bib.sh === id: cord-305165-3twlnkac author: Bourgueil, E. title: Experimental infection of pigs with the porcine respiratory coronavirus (PRCV): measure of viral excretion date: 1992-04-30 pages: extension: .txt txt: ./txt/cord-305165-3twlnkac.txt cache: ./cache/cord-305165-3twlnkac.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-305165-3twlnkac.txt' === file2bib.sh === id: cord-298678-hjxph9jm author: Petrović, T. title: Viral Contamination of Food date: 2016-02-05 pages: extension: .txt txt: ./txt/cord-298678-hjxph9jm.txt cache: ./cache/cord-298678-hjxph9jm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-298678-hjxph9jm.txt' === file2bib.sh === id: cord-294108-uvnh0s9r author: Dube, Taru title: Repurposed Drugs, Molecular Vaccines, Immune‐Modulators, and Nanotherapeutics to Treat and Prevent COVID‐19 Associated with SARS‐CoV‐2, a Deadly Nanovector date: 2020-10-25 pages: extension: .txt txt: ./txt/cord-294108-uvnh0s9r.txt cache: ./cache/cord-294108-uvnh0s9r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294108-uvnh0s9r.txt' === file2bib.sh === id: cord-305336-wxiazglk author: Li, Ji Lian title: Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera date: 2014-01-21 pages: extension: .txt txt: ./txt/cord-305336-wxiazglk.txt cache: ./cache/cord-305336-wxiazglk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305336-wxiazglk.txt' === file2bib.sh === id: cord-302277-c66xm2n4 author: Bakaletz, Lauren O. title: Developing animal models for polymicrobial diseases date: 2004 pages: extension: .txt txt: ./txt/cord-302277-c66xm2n4.txt cache: ./cache/cord-302277-c66xm2n4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302277-c66xm2n4.txt' === file2bib.sh === id: cord-304251-dohglrm1 author: Scully, C title: Emerging and changing viral diseases in the new millennium date: 2015-08-06 pages: extension: .txt txt: ./txt/cord-304251-dohglrm1.txt cache: ./cache/cord-304251-dohglrm1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304251-dohglrm1.txt' === file2bib.sh === id: cord-305488-vk59ghjm author: Choi, Kang-Seuk title: Newcastle disease virus vectored vaccines as bivalent or antigen delivery vaccines date: 2017-07-26 pages: extension: .txt txt: ./txt/cord-305488-vk59ghjm.txt cache: ./cache/cord-305488-vk59ghjm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305488-vk59ghjm.txt' === file2bib.sh === id: cord-297662-slmlhqnb author: Yap, Sally S. L. title: Dengue Virus Glycosylation: What Do We Know? date: 2017-07-25 pages: extension: .txt txt: ./txt/cord-297662-slmlhqnb.txt cache: ./cache/cord-297662-slmlhqnb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297662-slmlhqnb.txt' === file2bib.sh === id: cord-305263-fgwf6wy3 author: Wang, Ben X. title: The yin and yang of viruses and interferons date: 2012-02-07 pages: extension: .txt txt: ./txt/cord-305263-fgwf6wy3.txt cache: ./cache/cord-305263-fgwf6wy3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305263-fgwf6wy3.txt' === file2bib.sh === id: cord-264408-vk4lt83x author: Ruiz, Sara I. title: Animal Models of Human Viral Diseases date: 2017-06-23 pages: extension: .txt txt: ./txt/cord-264408-vk4lt83x.txt cache: ./cache/cord-264408-vk4lt83x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-264408-vk4lt83x.txt' === file2bib.sh === id: cord-305742-wf6qxplf author: Gomez, Santiago A. title: Binding of SARS–CoV–2 to cell receptors: a tale of molecular evolution date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-305742-wf6qxplf.txt cache: ./cache/cord-305742-wf6qxplf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305742-wf6qxplf.txt' === file2bib.sh === id: cord-309179-5hlatbqe author: Bosch, Albert title: New tools for the study and direct surveillance of viral pathogens in water date: 2008-05-26 pages: extension: .txt txt: ./txt/cord-309179-5hlatbqe.txt cache: ./cache/cord-309179-5hlatbqe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-309179-5hlatbqe.txt' === file2bib.sh === id: cord-302047-vv5gpldi author: Willemsen, Anouk title: On the stability of sequences inserted into viral genomes date: 2019-11-14 pages: extension: .txt txt: ./txt/cord-302047-vv5gpldi.txt cache: ./cache/cord-302047-vv5gpldi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302047-vv5gpldi.txt' === file2bib.sh === id: cord-304498-ty41xob0 author: Denison, Mark R title: Coronaviruses: An RNA proofreading machine regulates replication fidelity and diversity date: 2011-03-01 pages: extension: .txt txt: ./txt/cord-304498-ty41xob0.txt cache: ./cache/cord-304498-ty41xob0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304498-ty41xob0.txt' === file2bib.sh === id: cord-309489-ubf55eux author: Carvalho, John J. title: OUR COMMON ENEMY: COMBATTING THE WORLD'S DEADLIEST VIRUSES TO ENSURE EQUITY HEALTH CARE IN DEVELOPING NATIONS date: 2009-02-19 pages: extension: .txt txt: ./txt/cord-309489-ubf55eux.txt cache: ./cache/cord-309489-ubf55eux.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309489-ubf55eux.txt' === file2bib.sh === id: cord-298033-kzdp9edn author: Domingo, Esteban title: Quasispecies dynamics in disease prevention and control date: 2019-11-08 pages: extension: .txt txt: ./txt/cord-298033-kzdp9edn.txt cache: ./cache/cord-298033-kzdp9edn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298033-kzdp9edn.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-306083-juysx6yo author: Choe, Young June title: Co-seasonality and co-detection of respiratory viruses and bacteraemia in children: a retrospective analysis date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-306083-juysx6yo.txt cache: ./cache/cord-306083-juysx6yo.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306083-juysx6yo.txt' === file2bib.sh === id: cord-304747-ojyxs3cp author: Gaynor, Anne M title: Identification of a Novel Polyomavirus from Patients with Acute Respiratory Tract Infections date: 2007-05-04 pages: extension: .txt txt: ./txt/cord-304747-ojyxs3cp.txt cache: ./cache/cord-304747-ojyxs3cp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-304747-ojyxs3cp.txt' === file2bib.sh === id: cord-310141-2jofy8fo author: Qureshi, Abid title: A review on current status of antiviral siRNA date: 2018-04-15 pages: extension: .txt txt: ./txt/cord-310141-2jofy8fo.txt cache: ./cache/cord-310141-2jofy8fo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310141-2jofy8fo.txt' === file2bib.sh === id: cord-308686-tbwecf7o author: Mortamet, G. title: Étude prospective de l’écologie virale hivernale dans un service de réanimation pédiatrique date: 2015-04-30 pages: extension: .txt txt: ./txt/cord-308686-tbwecf7o.txt cache: ./cache/cord-308686-tbwecf7o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308686-tbwecf7o.txt' === file2bib.sh === id: cord-307817-2vy28i4m author: Lou, Zhiyong title: Current progress in antiviral strategies date: 2014-01-14 pages: extension: .txt txt: ./txt/cord-307817-2vy28i4m.txt cache: ./cache/cord-307817-2vy28i4m.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-307817-2vy28i4m.txt' === file2bib.sh === id: cord-306733-df36w6l7 author: Rosales-Mendoza, Sergio title: What Does Plant-Based Vaccine Technology Offer to the Fight against COVID-19? date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-306733-df36w6l7.txt cache: ./cache/cord-306733-df36w6l7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306733-df36w6l7.txt' === file2bib.sh === id: cord-309067-aemjbkfj author: Kennedy, Melissa title: Methodology in diagnostic virology date: 2005-03-01 pages: extension: .txt txt: ./txt/cord-309067-aemjbkfj.txt cache: ./cache/cord-309067-aemjbkfj.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-309067-aemjbkfj.txt' === file2bib.sh === id: cord-298736-9bvyp21d author: Gerold, Gisa title: Decoding protein networks during virus entry by quantitative proteomics date: 2016-06-15 pages: extension: .txt txt: ./txt/cord-298736-9bvyp21d.txt cache: ./cache/cord-298736-9bvyp21d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298736-9bvyp21d.txt' === file2bib.sh === id: cord-307918-8y89p11a author: Onyango, Clayton O. title: Influenza Surveillance Among Children With Pneumonia Admitted to a District Hospital in Coastal Kenya, 2007–2010 date: 2012-12-15 pages: extension: .txt txt: ./txt/cord-307918-8y89p11a.txt cache: ./cache/cord-307918-8y89p11a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307918-8y89p11a.txt' === file2bib.sh === id: cord-307364-j86t65qu author: Uccellini, Lorenzo title: Identification of a novel nidovirus in an outbreak of fatal respiratory disease in ball pythons (Python regius) date: 2014-08-08 pages: extension: .txt txt: ./txt/cord-307364-j86t65qu.txt cache: ./cache/cord-307364-j86t65qu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307364-j86t65qu.txt' === file2bib.sh === id: cord-305807-n3fs7533 author: Ferreira, T B title: Use of adenoviral vectors as veterinary vaccines date: 2005-10-18 pages: extension: .txt txt: ./txt/cord-305807-n3fs7533.txt cache: ./cache/cord-305807-n3fs7533.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-305807-n3fs7533.txt' === file2bib.sh === id: cord-310371-pylrg91h author: Bishop, R.F. title: Enteric Viruses date: 2008-07-30 pages: extension: .txt txt: ./txt/cord-310371-pylrg91h.txt cache: ./cache/cord-310371-pylrg91h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310371-pylrg91h.txt' === file2bib.sh === id: cord-311410-lgqup9ug author: Ayers, M. title: A single tube RT-PCR assay for the detection of mosquito-borne flaviviruses date: 2006-05-02 pages: extension: .txt txt: ./txt/cord-311410-lgqup9ug.txt cache: ./cache/cord-311410-lgqup9ug.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-311410-lgqup9ug.txt' === file2bib.sh === id: cord-299786-wuve0tjz author: Anderson, Robert title: Manipulation of cell surface macromolecules by flaviviruses date: 2004-02-27 pages: extension: .txt txt: ./txt/cord-299786-wuve0tjz.txt cache: ./cache/cord-299786-wuve0tjz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-299786-wuve0tjz.txt' === file2bib.sh === id: cord-310870-w8wu8vno author: Shorten, Robert J. title: The risk of transmission of a viral haemorrhagic fever infection in a United Kingdom laboratory date: 2017-05-18 pages: extension: .txt txt: ./txt/cord-310870-w8wu8vno.txt cache: ./cache/cord-310870-w8wu8vno.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-310870-w8wu8vno.txt' === file2bib.sh === id: cord-309488-8guapzke author: Dodd, R. title: Other emerging viral pathogens date: 2006-08-15 pages: extension: .txt txt: ./txt/cord-309488-8guapzke.txt cache: ./cache/cord-309488-8guapzke.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309488-8guapzke.txt' === file2bib.sh === id: cord-309635-1tgovkr7 author: Wu, Nicholas C. title: Structural Biology of Influenza Hemagglutinin: An Amaranthine Adventure date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-309635-1tgovkr7.txt cache: ./cache/cord-309635-1tgovkr7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309635-1tgovkr7.txt' === file2bib.sh === id: cord-310171-1fmsxx2s author: Goffard, Anne title: Virus and cystic fibrosis: Rhinoviruses are associated with exacerbations in adult patients() date: 2014-02-25 pages: extension: .txt txt: ./txt/cord-310171-1fmsxx2s.txt cache: ./cache/cord-310171-1fmsxx2s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310171-1fmsxx2s.txt' === file2bib.sh === id: cord-310795-n78s0sg2 author: Brand, H. Kim title: Infection with multiple viruses is not associated with increased disease severity in children with bronchiolitis date: 2011-09-07 pages: extension: .txt txt: ./txt/cord-310795-n78s0sg2.txt cache: ./cache/cord-310795-n78s0sg2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310795-n78s0sg2.txt' === file2bib.sh === id: cord-304278-0qy1nngs author: Raj, G. Dhinakar title: Infectious bronchitis virus: immunopathogenesis of infection in the chicken date: 2007-11-12 pages: extension: .txt txt: ./txt/cord-304278-0qy1nngs.txt cache: ./cache/cord-304278-0qy1nngs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304278-0qy1nngs.txt' === file2bib.sh === id: cord-310255-aixq5mhf author: Charlton, Frank W. title: Ion Channels as Therapeutic Targets for Viral Infections: Further Discoveries and Future Perspectives date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-310255-aixq5mhf.txt cache: ./cache/cord-310255-aixq5mhf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-310255-aixq5mhf.txt' === file2bib.sh === id: cord-309048-emmtplv3 author: Lomonossoff, George P. title: TMV Particles: The Journey From Fundamental Studies to Bionanotechnology Applications date: 2018-07-26 pages: extension: .txt txt: ./txt/cord-309048-emmtplv3.txt cache: ./cache/cord-309048-emmtplv3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309048-emmtplv3.txt' === file2bib.sh === id: cord-310920-itqwhi6a author: Haddad, Christina title: Integrated Approaches to Reveal Mechanisms by which RNA Viruses Reprogram the Cellular Environment date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-310920-itqwhi6a.txt cache: ./cache/cord-310920-itqwhi6a.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-310920-itqwhi6a.txt' === file2bib.sh === id: cord-315346-ebfjba4y author: Cummings, Kristin J. title: Exposure to Influenza Virus Aerosols in the Hospital Setting: Is Routine Patient Care an Aerosol Generating Procedure? date: 2014-03-04 pages: extension: .txt txt: ./txt/cord-315346-ebfjba4y.txt cache: ./cache/cord-315346-ebfjba4y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-315346-ebfjba4y.txt' === file2bib.sh === id: cord-313356-ninzeazy author: Fiorillo, Luca title: COVID-19 Surface Persistence: A Recent Data Summary and Its Importance for Medical and Dental Settings date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-313356-ninzeazy.txt cache: ./cache/cord-313356-ninzeazy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-313356-ninzeazy.txt' === file2bib.sh === id: cord-307632-x9bxnrtn author: Wu, Zhiqiang title: Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases date: 2018-10-03 pages: extension: .txt txt: ./txt/cord-307632-x9bxnrtn.txt cache: ./cache/cord-307632-x9bxnrtn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307632-x9bxnrtn.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-310140-h7uwl0pb author: Templeton, K.E. title: A multi-centre pilot proficiency programme to assess the quality of molecular detection of respiratory viruses date: 2005-07-12 pages: extension: .txt txt: ./txt/cord-310140-h7uwl0pb.txt cache: ./cache/cord-310140-h7uwl0pb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310140-h7uwl0pb.txt' === file2bib.sh === id: cord-312964-vsrqmmv7 author: Doyle, William J. title: Prevention of otitis media caused by viral upper respiratory tract infection: Vaccines, antivirals, and other approaches date: 2003 pages: extension: .txt txt: ./txt/cord-312964-vsrqmmv7.txt cache: ./cache/cord-312964-vsrqmmv7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312964-vsrqmmv7.txt' === file2bib.sh === id: cord-316951-1swlhdz5 author: Kennedy, Melissa title: General concepts of virology date: 2005-03-01 pages: extension: .txt txt: ./txt/cord-316951-1swlhdz5.txt cache: ./cache/cord-316951-1swlhdz5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316951-1swlhdz5.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-304424-048xo7jn author: Greninger, Alexander L. title: A decade of RNA virus metagenomics is (not) enough date: 2018-01-15 pages: extension: .txt txt: ./txt/cord-304424-048xo7jn.txt cache: ./cache/cord-304424-048xo7jn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304424-048xo7jn.txt' === file2bib.sh === id: cord-311012-wyglrpqh author: Meyers, Craig title: Ethanol and Isopropanol Inactivation of Human Coronavirus on Hard Surfaces date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-311012-wyglrpqh.txt cache: ./cache/cord-311012-wyglrpqh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-311012-wyglrpqh.txt' === file2bib.sh === id: cord-308857-otsrexqu author: Goel, Saurav title: Resilient and Agile Engineering Solutions to Address Societal Challenges such as Coronavirus Pandemic date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-308857-otsrexqu.txt cache: ./cache/cord-308857-otsrexqu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308857-otsrexqu.txt' === file2bib.sh === id: cord-311908-sgdq6j6x author: Atkins, G. J. title: Transient virus infection and multiple sclerosis date: 2000-09-28 pages: extension: .txt txt: ./txt/cord-311908-sgdq6j6x.txt cache: ./cache/cord-311908-sgdq6j6x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-311908-sgdq6j6x.txt' === file2bib.sh === id: cord-314254-9ye8tfvz author: Pfaender, Stephanie title: Natural reservoirs for homologs of hepatitis C virus date: 2014-03-26 pages: extension: .txt txt: ./txt/cord-314254-9ye8tfvz.txt cache: ./cache/cord-314254-9ye8tfvz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314254-9ye8tfvz.txt' === file2bib.sh === id: cord-316295-x636ux34 author: Roth, Bernhard title: Isolation of influenza viruses in MDCK 33016PF cells and clearance of contaminating respiratory viruses date: 2012-01-11 pages: extension: .txt txt: ./txt/cord-316295-x636ux34.txt cache: ./cache/cord-316295-x636ux34.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316295-x636ux34.txt' === file2bib.sh === id: cord-311748-yr2ep7uf author: Kahyaoglu, L. N. title: 11 New approaches in microbial pathogen detection date: 2013-12-31 pages: extension: .txt txt: ./txt/cord-311748-yr2ep7uf.txt cache: ./cache/cord-311748-yr2ep7uf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-311748-yr2ep7uf.txt' === file2bib.sh === id: cord-312461-5qzpo6l1 author: Adalja, Amesh A. title: Characteristics of Microbes Most Likely to Cause Pandemics and Global Catastrophes date: 2019-08-30 pages: extension: .txt txt: ./txt/cord-312461-5qzpo6l1.txt cache: ./cache/cord-312461-5qzpo6l1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312461-5qzpo6l1.txt' === file2bib.sh === id: cord-310942-191m0e65 author: Boga, Jose Antonio title: Beneficial actions of melatonin in the management of viral infections: a new use for this “molecular handyman”? date: 2012-04-18 pages: extension: .txt txt: ./txt/cord-310942-191m0e65.txt cache: ./cache/cord-310942-191m0e65.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310942-191m0e65.txt' === file2bib.sh === id: cord-315167-ph15z424 author: Goka, E. A. title: Pan-human coronavirus and human bocavirus SYBR Green and TaqMan PCR assays; use in studying influenza A viruses co-infection and risk of hospitalization date: 2014-12-05 pages: extension: .txt txt: ./txt/cord-315167-ph15z424.txt cache: ./cache/cord-315167-ph15z424.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315167-ph15z424.txt' === file2bib.sh === id: cord-312431-de7zhswl author: Ganesh, Atheesha title: Detecting Virus‐Like Particles from the Umgeni River, South Africa date: 2013-08-30 pages: extension: .txt txt: ./txt/cord-312431-de7zhswl.txt cache: ./cache/cord-312431-de7zhswl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312431-de7zhswl.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-306948-wkisfz1m author: Han, Mingyuan title: Engineering the PRRS virus genome: Updates and perspectives date: 2014-12-05 pages: extension: .txt txt: ./txt/cord-306948-wkisfz1m.txt cache: ./cache/cord-306948-wkisfz1m.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-306948-wkisfz1m.txt' === file2bib.sh === id: cord-313598-2t40ss6h author: Ali, Mohsin title: Throat and nasal swabs for molecular detection of respiratory viruses in acute pharyngitis date: 2015-10-29 pages: extension: .txt txt: ./txt/cord-313598-2t40ss6h.txt cache: ./cache/cord-313598-2t40ss6h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313598-2t40ss6h.txt' === file2bib.sh === id: cord-315781-dejh8q22 author: Konishi, Tomokazu title: Re-evaluation of the evolution of influenza H1 viruses using direct PCA date: 2019-12-17 pages: extension: .txt txt: ./txt/cord-315781-dejh8q22.txt cache: ./cache/cord-315781-dejh8q22.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-315781-dejh8q22.txt' === file2bib.sh === id: cord-310439-z0bxsjug author: Martin, R. R. title: Pathogen-Tested Planting Material date: 2014-12-31 pages: extension: .txt txt: ./txt/cord-310439-z0bxsjug.txt cache: ./cache/cord-310439-z0bxsjug.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310439-z0bxsjug.txt' === file2bib.sh === id: cord-309381-cb80ntxs author: Nogales, Aitor title: Host Single Nucleotide Polymorphisms Modulating Influenza A Virus Disease in Humans date: 2019-09-30 pages: extension: .txt txt: ./txt/cord-309381-cb80ntxs.txt cache: ./cache/cord-309381-cb80ntxs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-309381-cb80ntxs.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 3 resourceName b'cord-314190-fvdock94.txt' === file2bib.sh === id: cord-317244-4su5on6s author: Maganga, Gael D. title: Identification of an Unclassified Paramyxovirus in Coleura afra: A Potential Case of Host Specificity date: 2014-12-31 pages: extension: .txt txt: ./txt/cord-317244-4su5on6s.txt cache: ./cache/cord-317244-4su5on6s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317244-4su5on6s.txt' === file2bib.sh === id: cord-317971-kuwargnp author: Opatz, Till title: Thoughts on What Chemists Can Contribute to Fighting SARS‐CoV‐2 – A Short Note on Hand Sanitizers, Drug Candidates and Outreach date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-317971-kuwargnp.txt cache: ./cache/cord-317971-kuwargnp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-317971-kuwargnp.txt' === file2bib.sh === id: cord-314390-q36ye9ff author: Kang, Gagandeep title: Viral Diarrhea date: 2016-10-24 pages: extension: .txt txt: ./txt/cord-314390-q36ye9ff.txt cache: ./cache/cord-314390-q36ye9ff.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314390-q36ye9ff.txt' === file2bib.sh === id: cord-314325-nquov2i0 author: Murphy, F.A. title: Epidemiology of Human and Animal Viral Diseases date: 2008-07-30 pages: extension: .txt txt: ./txt/cord-314325-nquov2i0.txt cache: ./cache/cord-314325-nquov2i0.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-314325-nquov2i0.txt' === file2bib.sh === id: cord-311823-85wj08gr author: Katze, Michael G. title: Innate immune modulation by RNA viruses: emerging insights from functional genomics date: 2008 pages: extension: .txt txt: ./txt/cord-311823-85wj08gr.txt cache: ./cache/cord-311823-85wj08gr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-311823-85wj08gr.txt' === file2bib.sh === id: cord-305327-hayhbs5u author: Gonzalez, Jean-Paul title: Global Spread of Hemorrhagic Fever Viruses: Predicting Pandemics date: 2017-09-19 pages: extension: .txt txt: ./txt/cord-305327-hayhbs5u.txt cache: ./cache/cord-305327-hayhbs5u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305327-hayhbs5u.txt' === file2bib.sh === id: cord-311382-ioemd0ij author: Tellier, Raymond title: Recognition of aerosol transmission of infectious agents: a commentary date: 2019-01-31 pages: extension: .txt txt: ./txt/cord-311382-ioemd0ij.txt cache: ./cache/cord-311382-ioemd0ij.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311382-ioemd0ij.txt' === file2bib.sh === id: cord-314201-6njwigco author: Maher-Sturgess, Sheryl L title: Universal primers that amplify RNA from all three flavivirus subgroups date: 2008-01-24 pages: extension: .txt txt: ./txt/cord-314201-6njwigco.txt cache: ./cache/cord-314201-6njwigco.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314201-6njwigco.txt' === file2bib.sh === id: cord-306424-gf0bglm0 author: Scutigliani, Enzo Maxim title: Interaction of the innate immune system with positive-strand RNA virus replication organelles date: 2017-06-27 pages: extension: .txt txt: ./txt/cord-306424-gf0bglm0.txt cache: ./cache/cord-306424-gf0bglm0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-306424-gf0bglm0.txt' === file2bib.sh === id: cord-313301-7mkadtp9 author: Duffy, Siobain title: EVOLUTION OF HOST SPECIFICITY DRIVES REPRODUCTIVE ISOLATION AMONG RNA VIRUSES date: 2007-08-23 pages: extension: .txt txt: ./txt/cord-313301-7mkadtp9.txt cache: ./cache/cord-313301-7mkadtp9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313301-7mkadtp9.txt' === file2bib.sh === id: cord-314166-79323mzd author: Vanderford, Thomas H. title: Adaptation of a Diverse Simian Immunodeficiency Virus Population to a New Host Is Revealed through a Systematic Approach to Identify Amino Acid Sites under Selection date: 2006-12-11 pages: extension: .txt txt: ./txt/cord-314166-79323mzd.txt cache: ./cache/cord-314166-79323mzd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314166-79323mzd.txt' === file2bib.sh === id: cord-313312-h607itv2 author: Mok, Darren Z. L. title: The Effects of Pre-Existing Antibodies on Live-Attenuated Viral Vaccines date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-313312-h607itv2.txt cache: ./cache/cord-313312-h607itv2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-313312-h607itv2.txt' === file2bib.sh === id: cord-317198-mean7sj9 author: Giamberardin, Heloisa I.G. title: Clinical and epidemiological features of respiratory virus infections in preschool children over two consecutive influenza seasons in southern Brazil date: 2016-02-09 pages: extension: .txt txt: ./txt/cord-317198-mean7sj9.txt cache: ./cache/cord-317198-mean7sj9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317198-mean7sj9.txt' === file2bib.sh === id: cord-316245-n6tmn4ph author: Cui, Binglin title: Viral aetiology of acute respiratory infections among children and associated meteorological factors in southern China date: 2015-03-13 pages: extension: .txt txt: ./txt/cord-316245-n6tmn4ph.txt cache: ./cache/cord-316245-n6tmn4ph.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316245-n6tmn4ph.txt' === file2bib.sh === id: cord-317851-lj07947c author: Elena, S F title: Experimental evolution of plant RNA viruses date: 2008-02-06 pages: extension: .txt txt: ./txt/cord-317851-lj07947c.txt cache: ./cache/cord-317851-lj07947c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317851-lj07947c.txt' === file2bib.sh === id: cord-317508-03u2vtzk author: Oldstone, M.B.A. title: History of Virology date: 2019-08-28 pages: extension: .txt txt: ./txt/cord-317508-03u2vtzk.txt cache: ./cache/cord-317508-03u2vtzk.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-317508-03u2vtzk.txt' === file2bib.sh === id: cord-316682-4360s2yu author: Fischer, William A. title: Personal Protective Equipment: Protecting Health Care Providers in an Ebola Outbreak date: 2015-11-01 pages: extension: .txt txt: ./txt/cord-316682-4360s2yu.txt cache: ./cache/cord-316682-4360s2yu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-316682-4360s2yu.txt' === file2bib.sh === id: cord-319208-jrxz59bb author: Ting, Chun Yi title: Are identity badges and lanyards in pediatrics potentially contaminated with viral pathogens? date: 2015-11-01 pages: extension: .txt txt: ./txt/cord-319208-jrxz59bb.txt cache: ./cache/cord-319208-jrxz59bb.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-319208-jrxz59bb.txt' === file2bib.sh === id: cord-319746-6bccxgbd author: Saxena, Latika title: Production and Characterization of Human Monoclonal Antibodies from the Cells of A(H1N1)pdm2009 Influenza Virus Infected Indian Donors date: 2015-12-31 pages: extension: .txt txt: ./txt/cord-319746-6bccxgbd.txt cache: ./cache/cord-319746-6bccxgbd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319746-6bccxgbd.txt' === file2bib.sh === id: cord-315131-4yb2b70g author: Hammerschmidt, Sven title: Threat of infection: Microbes of high pathogenic potential – strategies for detection, control and eradication date: 2005-06-28 pages: extension: .txt txt: ./txt/cord-315131-4yb2b70g.txt cache: ./cache/cord-315131-4yb2b70g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315131-4yb2b70g.txt' === file2bib.sh === id: cord-321562-hk4hzl13 author: Liu, Xuan title: Cell membrane-derived biomimetic nanodecoys for viruses date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-321562-hk4hzl13.txt cache: ./cache/cord-321562-hk4hzl13.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-321562-hk4hzl13.txt' === file2bib.sh === id: cord-322748-a5131tv9 author: Yates, Mary K. title: Flex-nucleoside analogues – Novel therapeutics against filoviruses date: 2017-06-15 pages: extension: .txt txt: ./txt/cord-322748-a5131tv9.txt cache: ./cache/cord-322748-a5131tv9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322748-a5131tv9.txt' === file2bib.sh === id: cord-318172-bdotp9ko author: Blanco, Jorge C. G. title: PROPHYLACTIC ANTIBODY TREATMENT AND INTRAMUSCULAR IMMUNIZATION REDUCE INFECTIOUS HUMAN RHINOVIRUS 16 LOAD IN THE LOWER RESPIRATORY TRACT OF CHALLENGED COTTON RATS date: 2014-01-01 pages: extension: .txt txt: ./txt/cord-318172-bdotp9ko.txt cache: ./cache/cord-318172-bdotp9ko.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-318172-bdotp9ko.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 5 resourceName b'cord-319814-tyqb473m.txt' === file2bib.sh === id: cord-316996-8yimrpaz author: Nicholls, John M. title: The use of sialidase therapy for respiratory viral infections date: 2013-04-17 pages: extension: .txt txt: ./txt/cord-316996-8yimrpaz.txt cache: ./cache/cord-316996-8yimrpaz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-316996-8yimrpaz.txt' === file2bib.sh === id: cord-309642-wwaa6ls0 author: Potgieter, Leon N.D. title: Pathogenesis of Viral Infections date: 1986-11-30 pages: extension: .txt txt: ./txt/cord-309642-wwaa6ls0.txt cache: ./cache/cord-309642-wwaa6ls0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309642-wwaa6ls0.txt' === file2bib.sh === id: cord-317412-f3ua8ks3 author: Zhang, Xing title: Characterization of the lipidomic profile of BmN cells in response to Bombyx mori cytoplasmic polyhedrosis virus infection date: 2020-08-15 pages: extension: .txt txt: ./txt/cord-317412-f3ua8ks3.txt cache: ./cache/cord-317412-f3ua8ks3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317412-f3ua8ks3.txt' === file2bib.sh === id: cord-317404-jvtozj4v author: Santos, Marfran C.D. title: Spectroscopy with computational analysis in virological studies: A decade (2006–2016) date: 2017-09-21 pages: extension: .txt txt: ./txt/cord-317404-jvtozj4v.txt cache: ./cache/cord-317404-jvtozj4v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317404-jvtozj4v.txt' === file2bib.sh === id: cord-318725-09a32vyg author: Dong, Rui title: Virus Database and Online Inquiry System Based on Natural Vectors date: 2017-12-17 pages: extension: .txt txt: ./txt/cord-318725-09a32vyg.txt cache: ./cache/cord-318725-09a32vyg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-318725-09a32vyg.txt' === file2bib.sh === id: cord-307813-elom30nx author: Yip, Tsz-Fung title: Advancements in Host-Based Interventions for Influenza Treatment date: 2018-07-10 pages: extension: .txt txt: ./txt/cord-307813-elom30nx.txt cache: ./cache/cord-307813-elom30nx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-307813-elom30nx.txt' === file2bib.sh === id: cord-316894-zhmuzv7z author: Stetzenbach, L.D. title: Airborne Infectious Microorganisms date: 2009-02-17 pages: extension: .txt txt: ./txt/cord-316894-zhmuzv7z.txt cache: ./cache/cord-316894-zhmuzv7z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-316894-zhmuzv7z.txt' === file2bib.sh === id: cord-319210-yqimufdh author: KENNEDY, P.G.E. title: On the possible viral aetiology of multiple sclerosis date: 1994-09-17 pages: extension: .txt txt: ./txt/cord-319210-yqimufdh.txt cache: ./cache/cord-319210-yqimufdh.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-319210-yqimufdh.txt' === file2bib.sh === id: cord-323333-keshu99t author: Schleis, Thomas G. title: The Process: New Methods of Purification and Viral Safety date: 2013-01-16 pages: extension: .txt txt: ./txt/cord-323333-keshu99t.txt cache: ./cache/cord-323333-keshu99t.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-323333-keshu99t.txt' === file2bib.sh === id: cord-312332-rwmuucsp author: Dicker, Kate title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-312332-rwmuucsp.txt cache: ./cache/cord-312332-rwmuucsp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312332-rwmuucsp.txt' === file2bib.sh === id: cord-308066-lrbi5198 author: Childs, James E. title: Pre-spillover Prevention of Emerging Zoonotic Diseases: What Are the Targets and What Are the Tools? date: 2007 pages: extension: .txt txt: ./txt/cord-308066-lrbi5198.txt cache: ./cache/cord-308066-lrbi5198.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-308066-lrbi5198.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 4 resourceName b'cord-321756-a7eh4dkb.txt' === file2bib.sh === id: cord-319761-bu5pzbnv author: Miller, Craig S. title: Pleiotropic mechanisms of virus survival and persistence date: 2005-07-16 pages: extension: .txt txt: ./txt/cord-319761-bu5pzbnv.txt cache: ./cache/cord-319761-bu5pzbnv.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-319761-bu5pzbnv.txt' === file2bib.sh === id: cord-320030-ojtp90na author: Montero, Antonio title: Fiebre chikungunya - Una nueva amenaza global date: 2015-08-07 pages: extension: .txt txt: ./txt/cord-320030-ojtp90na.txt cache: ./cache/cord-320030-ojtp90na.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320030-ojtp90na.txt' === file2bib.sh === id: cord-317496-6o2upns3 author: Pascual-Iglesias, Alejandro title: Recombinant Chimeric Transmissible Gastroenteritis Virus (TGEV)—Porcine Epidemic Diarrhea Virus (PEDV) Virus Provides Protection against Virulent PEDV date: 2019-07-25 pages: extension: .txt txt: ./txt/cord-317496-6o2upns3.txt cache: ./cache/cord-317496-6o2upns3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-317496-6o2upns3.txt' === file2bib.sh === id: cord-319379-qe56u93a author: Patil, Vaishali M. title: A systematic review on use of aminoquinolines for the therapeutic management of COVID-19: Efficacy, safety and clinical trials date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-319379-qe56u93a.txt cache: ./cache/cord-319379-qe56u93a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319379-qe56u93a.txt' === file2bib.sh === id: cord-318786-qd0k8174 author: Mauriz, Elba title: Recent Progress in Plasmonic Biosensing Schemes for Virus Detection date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-318786-qd0k8174.txt cache: ./cache/cord-318786-qd0k8174.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-318786-qd0k8174.txt' === file2bib.sh === id: cord-312688-12san3m7 author: Martin, Baptiste title: Filovirus proteins for antiviral drug discovery: A structure/function analysis of surface glycoproteins and virus entry date: 2016-09-14 pages: extension: .txt txt: ./txt/cord-312688-12san3m7.txt cache: ./cache/cord-312688-12san3m7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312688-12san3m7.txt' === file2bib.sh === id: cord-303265-v6ci69n0 author: Domingo, Esteban title: Introduction to virus origins and their role in biological evolution date: 2019-11-08 pages: extension: .txt txt: ./txt/cord-303265-v6ci69n0.txt cache: ./cache/cord-303265-v6ci69n0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303265-v6ci69n0.txt' === file2bib.sh === id: cord-323930-pl3qlcpo author: Sohail, Ayesha title: Forecasting the timeframe of coronavirus and human cells interaction with reverse engineering date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-323930-pl3qlcpo.txt cache: ./cache/cord-323930-pl3qlcpo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-323930-pl3qlcpo.txt' === file2bib.sh === id: cord-322082-80ym2rsq author: Monto, Arnold S title: Lessons From Influenza Pandemics of the Last 100 Years date: 2020-03-01 pages: extension: .txt txt: ./txt/cord-322082-80ym2rsq.txt cache: ./cache/cord-322082-80ym2rsq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322082-80ym2rsq.txt' === file2bib.sh === id: cord-320693-de1lmzl1 author: Hu, Han title: Antiviral activity of Piscidin 1 against pseudorabies virus both in vitro and in vivo date: 2019-07-31 pages: extension: .txt txt: ./txt/cord-320693-de1lmzl1.txt cache: ./cache/cord-320693-de1lmzl1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320693-de1lmzl1.txt' === file2bib.sh === id: cord-320935-3n157yl4 author: Kumar, Manish title: Making Waves Perspectives of Modelling and Monitoring of SARS-CoV-2 in Aquatic Environment for COVID-19 Pandemic date: 2020-09-12 pages: extension: .txt txt: ./txt/cord-320935-3n157yl4.txt cache: ./cache/cord-320935-3n157yl4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320935-3n157yl4.txt' === file2bib.sh === id: cord-321835-qn33sx8x author: Bailey, Emily S. title: A Mini Review of the Zoonotic Threat Potential of Influenza Viruses, Coronaviruses, Adenoviruses, and Enteroviruses date: 2018-04-09 pages: extension: .txt txt: ./txt/cord-321835-qn33sx8x.txt cache: ./cache/cord-321835-qn33sx8x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321835-qn33sx8x.txt' === file2bib.sh === id: cord-318686-we6pveus author: Ehlen, Lukas title: Epithelial cell lines of the cotton rat (Sigmodon hispidus) are highly susceptible in vitro models to zoonotic Bunya-, Rhabdo-, and Flaviviruses date: 2016-05-04 pages: extension: .txt txt: ./txt/cord-318686-we6pveus.txt cache: ./cache/cord-318686-we6pveus.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-318686-we6pveus.txt' === file2bib.sh === id: cord-315918-12rbbe8c author: Mukherjee, Pulok K. title: Antiviral Evaluation of Herbal Drugs date: 2019-06-21 pages: extension: .txt txt: ./txt/cord-315918-12rbbe8c.txt cache: ./cache/cord-315918-12rbbe8c.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-315918-12rbbe8c.txt' === file2bib.sh === id: cord-318495-1w74wf02 author: Vignuzzi, Marco title: Defective viral genomes are key drivers of the virus–host interaction date: 2019-06-03 pages: extension: .txt txt: ./txt/cord-318495-1w74wf02.txt cache: ./cache/cord-318495-1w74wf02.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-318495-1w74wf02.txt' === file2bib.sh === id: cord-317501-yblzopc3 author: Kuhn, Philipp title: Recombinant antibodies for diagnostics and therapy against pathogens and toxins generated by phage display date: 2016-06-21 pages: extension: .txt txt: ./txt/cord-317501-yblzopc3.txt cache: ./cache/cord-317501-yblzopc3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-317501-yblzopc3.txt' === file2bib.sh === id: cord-324280-e8mj6ecl author: Shaman, Jeffrey title: Asymptomatic Summertime Shedding of Respiratory Viruses date: 2018-04-01 pages: extension: .txt txt: ./txt/cord-324280-e8mj6ecl.txt cache: ./cache/cord-324280-e8mj6ecl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324280-e8mj6ecl.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-323700-5awng7h1 author: Goggin, Rachel K. title: Comparative Viral Sampling in the Sinonasal Passages; Different Viruses at Different Sites date: 2018-09-19 pages: extension: .txt txt: ./txt/cord-323700-5awng7h1.txt cache: ./cache/cord-323700-5awng7h1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323700-5awng7h1.txt' === file2bib.sh === id: cord-323793-c69joaqs author: Palmieri, V. title: Can graphene take part in the fight against COVID-19? date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-323793-c69joaqs.txt cache: ./cache/cord-323793-c69joaqs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323793-c69joaqs.txt' === file2bib.sh === id: cord-307899-427a7i3h author: BITTLE, JAMES L. title: Vaccines Produced by Conventional Means to Control Major Infectious Diseases of Man and Animals date: 1989-12-31 pages: extension: .txt txt: ./txt/cord-307899-427a7i3h.txt cache: ./cache/cord-307899-427a7i3h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307899-427a7i3h.txt' === file2bib.sh === id: cord-321741-aq76s37x author: Andersen, Petter I. title: Discovery and development of safe-in-man broad-spectrum antiviral agents date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-321741-aq76s37x.txt cache: ./cache/cord-321741-aq76s37x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321741-aq76s37x.txt' === file2bib.sh === id: cord-324696-htx0ul4o author: Chothe, Shubhada K. title: Avian and human influenza virus compatible sialic acid receptors in little brown bats date: 2017-04-06 pages: extension: .txt txt: ./txt/cord-324696-htx0ul4o.txt cache: ./cache/cord-324696-htx0ul4o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-324696-htx0ul4o.txt' === file2bib.sh === id: cord-322234-1zyy536y author: Lorusso, Alessio title: One-step real-time RT-PCR for pandemic influenza A virus (H1N1) 2009 matrix gene detection in swine samples date: 2009-12-17 pages: extension: .txt txt: ./txt/cord-322234-1zyy536y.txt cache: ./cache/cord-322234-1zyy536y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322234-1zyy536y.txt' === file2bib.sh === id: cord-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 4 resourceName b'cord-323009-frej2qmb.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-304343-m7tbdfri author: Khandia, Rekha title: A Comprehensive Review of Autophagy and Its Various Roles in Infectious, Non-Infectious, and Lifestyle Diseases: Current Knowledge and Prospects for Disease Prevention, Novel Drug Design, and Therapy date: 2019-07-03 pages: extension: .txt txt: ./txt/cord-304343-m7tbdfri.txt cache: ./cache/cord-304343-m7tbdfri.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-304343-m7tbdfri.txt' === file2bib.sh === id: cord-323195-buzcb8ya author: Valtonen, Maarit title: Common cold in Team Finland during 2018 Winter Olympic Games (PyeongChang): epidemiology, diagnosis including molecular point-of-care testing (POCT) and treatment date: 2019-05-29 pages: extension: .txt txt: ./txt/cord-323195-buzcb8ya.txt cache: ./cache/cord-323195-buzcb8ya.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323195-buzcb8ya.txt' === file2bib.sh === id: cord-327013-gc6o8ou3 author: Kim, Heui Man title: Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-327013-gc6o8ou3.txt cache: ./cache/cord-327013-gc6o8ou3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327013-gc6o8ou3.txt' === file2bib.sh === id: cord-326225-crtpzad7 author: Neill, John D. title: Simultaneous rapid sequencing of multiple RNA virus genomes date: 2014-06-01 pages: extension: .txt txt: ./txt/cord-326225-crtpzad7.txt cache: ./cache/cord-326225-crtpzad7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-326225-crtpzad7.txt' === file2bib.sh === id: cord-322206-roxa3ix6 author: I. Sardi, Silvia title: High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-322206-roxa3ix6.txt cache: ./cache/cord-322206-roxa3ix6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322206-roxa3ix6.txt' === file2bib.sh === id: cord-324295-9c1zxjng author: Bonilla-Aldana, D. Katterine title: Bats in Ecosystems and their Wide Spectrum of Viral Infectious Threats: SARS-CoV-2 and other emerging viruses date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-324295-9c1zxjng.txt cache: ./cache/cord-324295-9c1zxjng.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324295-9c1zxjng.txt' === file2bib.sh === id: cord-307046-ko3bdvo0 author: Vasilakis, Nikos title: Exploiting the Legacy of the Arbovirus Hunters date: 2019-05-23 pages: extension: .txt txt: ./txt/cord-307046-ko3bdvo0.txt cache: ./cache/cord-307046-ko3bdvo0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307046-ko3bdvo0.txt' === file2bib.sh === id: cord-325969-9zhmmvdg author: To, Kelvin KW title: Additional molecular testing of saliva specimens improves the detection of respiratory viruses date: 2017-06-07 pages: extension: .txt txt: ./txt/cord-325969-9zhmmvdg.txt cache: ./cache/cord-325969-9zhmmvdg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325969-9zhmmvdg.txt' === file2bib.sh === id: cord-323710-cmbg0ty8 author: Mühlebach, Michael D. title: Development of Recombinant Measles Virus-Based Vaccines date: 2016-11-26 pages: extension: .txt txt: ./txt/cord-323710-cmbg0ty8.txt cache: ./cache/cord-323710-cmbg0ty8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323710-cmbg0ty8.txt' === file2bib.sh === id: cord-325827-492xi3ee author: Evermann, J. F. title: Biological and pathological consequences of feline infectious peritonitis virus infection in the cheetah date: 1988 pages: extension: .txt txt: ./txt/cord-325827-492xi3ee.txt cache: ./cache/cord-325827-492xi3ee.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325827-492xi3ee.txt' === file2bib.sh === id: cord-323404-3mw4q7m3 author: Bomsel, Morgane title: Entry of viruses through the epithelial barrier: pathogenic trickery date: 2003 pages: extension: .txt txt: ./txt/cord-323404-3mw4q7m3.txt cache: ./cache/cord-323404-3mw4q7m3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-323404-3mw4q7m3.txt' === file2bib.sh === id: cord-325875-93krp81r author: Henao-Diaz, Alexandra title: Guidelines for oral fluid-based surveillance of viral pathogens in swine date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-325875-93krp81r.txt cache: ./cache/cord-325875-93krp81r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325875-93krp81r.txt' === file2bib.sh === id: cord-318551-c1qr27lg author: Boguszewska‐Chachulska, Anna M. title: Rna Viruses Redirect Host Factors to Better Amplify Their Genome date: 2005-12-29 pages: extension: .txt txt: ./txt/cord-318551-c1qr27lg.txt cache: ./cache/cord-318551-c1qr27lg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-318551-c1qr27lg.txt' === file2bib.sh === id: cord-321481-vrfwczve author: Watashi, Koichi title: NTCP and Beyond: Opening the Door to Unveil Hepatitis B Virus Entry date: 2014-02-19 pages: extension: .txt txt: ./txt/cord-321481-vrfwczve.txt cache: ./cache/cord-321481-vrfwczve.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-321481-vrfwczve.txt' === file2bib.sh === id: cord-317277-rr9zue4l author: Cifuentes-Munoz, Nicolas title: Viral cell-to-cell spread: Conventional and non-conventional ways date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-317277-rr9zue4l.txt cache: ./cache/cord-317277-rr9zue4l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317277-rr9zue4l.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-320015-lbr2q4qh author: Chinchar, V. Gregory title: The Molecular Biology of Frog Virus 3 and other Iridoviruses Infecting Cold-Blooded Vertebrates date: 2011-10-20 pages: extension: .txt txt: ./txt/cord-320015-lbr2q4qh.txt cache: ./cache/cord-320015-lbr2q4qh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320015-lbr2q4qh.txt' === file2bib.sh === id: cord-326719-p1ma4akz author: Enjuanes, Luis title: Virus-based vectors for gene expression in mammalian cells: Coronavirus date: 2003-12-31 pages: extension: .txt txt: ./txt/cord-326719-p1ma4akz.txt cache: ./cache/cord-326719-p1ma4akz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-326719-p1ma4akz.txt' === file2bib.sh === id: cord-320055-6ycp8m89 author: Elliot, Elisa L title: Indicator organisms for estuarine and marine waters date: 1985-07-31 pages: extension: .txt txt: ./txt/cord-320055-6ycp8m89.txt cache: ./cache/cord-320055-6ycp8m89.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320055-6ycp8m89.txt' === file2bib.sh === id: cord-325325-xw7627x9 author: Skeik, Nedaa title: Influenza viruses and the evolution of avian influenza virus H5N1 date: 2007-10-02 pages: extension: .txt txt: ./txt/cord-325325-xw7627x9.txt cache: ./cache/cord-325325-xw7627x9.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-325325-xw7627x9.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 3 resourceName b'cord-325830-mrtpihc7.txt' === file2bib.sh === id: cord-321053-lgae22f8 author: Gerold, Gisa title: Opportunities and Risks of Host-targeting Antiviral Strategies for Hepatitis C date: 2013-10-04 pages: extension: .txt txt: ./txt/cord-321053-lgae22f8.txt cache: ./cache/cord-321053-lgae22f8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321053-lgae22f8.txt' === file2bib.sh === id: cord-325280-4whzcmqv author: Takizawa, Naoki title: Current landscape and future prospects of antiviral drugs derived from microbial products date: 2017-10-11 pages: extension: .txt txt: ./txt/cord-325280-4whzcmqv.txt cache: ./cache/cord-325280-4whzcmqv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325280-4whzcmqv.txt' === file2bib.sh === id: cord-319754-5isw53wl author: Balgoma, David title: Lipidomics Issues on Human Positive ssRNA Virus Infection: An Update date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-319754-5isw53wl.txt cache: ./cache/cord-319754-5isw53wl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319754-5isw53wl.txt' === file2bib.sh === id: cord-326725-0jgw083h author: Klamroth, Robert title: Pathogen inactivation and removal methods for plasma‐derived clotting factor concentrates date: 2013-09-30 pages: extension: .txt txt: ./txt/cord-326725-0jgw083h.txt cache: ./cache/cord-326725-0jgw083h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326725-0jgw083h.txt' === file2bib.sh === id: cord-318853-mxyxwkhx author: Sallie, Richard title: Replicative homeostasis II: Influence of polymerase fidelity on RNA virus quasispecies biology: Implications for immune recognition, viral autoimmunity and other "virus receptor" diseases date: 2005-08-22 pages: extension: .txt txt: ./txt/cord-318853-mxyxwkhx.txt cache: ./cache/cord-318853-mxyxwkhx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318853-mxyxwkhx.txt' === file2bib.sh === id: cord-321112-w7x1dkds author: Zhao, Xuesen title: IFITM Genes, Variants, and Their Roles in the Control and Pathogenesis of Viral Infections date: 2019-01-08 pages: extension: .txt txt: ./txt/cord-321112-w7x1dkds.txt cache: ./cache/cord-321112-w7x1dkds.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321112-w7x1dkds.txt' === file2bib.sh === id: cord-330508-uilejxmi author: van den Hoogen, Bernadette title: Immunometabolism pathways as the basis for innovative anti-viral strategies (INITIATE): A Marie Sklodowska-Curie innovative training network date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-330508-uilejxmi.txt cache: ./cache/cord-330508-uilejxmi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330508-uilejxmi.txt' === file2bib.sh === id: cord-325925-010xj69x author: Mordecai, Gideon J title: Endangered wild salmon infected by newly discovered viruses date: 2019-09-03 pages: extension: .txt txt: ./txt/cord-325925-010xj69x.txt cache: ./cache/cord-325925-010xj69x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325925-010xj69x.txt' === file2bib.sh === id: cord-327199-ggomuomb author: Moerdyk-Schauwecker, Megan title: Cellular Proteins Associated with the Interior and Exterior of Vesicular Stomatitis Virus Virions date: 2014-08-08 pages: extension: .txt txt: ./txt/cord-327199-ggomuomb.txt cache: ./cache/cord-327199-ggomuomb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327199-ggomuomb.txt' === file2bib.sh === id: cord-325326-2bbqz4o7 author: Beitzel, Brett F. title: High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and Massively Parallel Sequencing date: 2010-10-14 pages: extension: .txt txt: ./txt/cord-325326-2bbqz4o7.txt cache: ./cache/cord-325326-2bbqz4o7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325326-2bbqz4o7.txt' === file2bib.sh === id: cord-322904-9mta0aem author: Neu, Ursula title: The Polyomaviridae: Contributions of virus structure to our understanding of virus receptors and infectious entry date: 2009-02-01 pages: extension: .txt txt: ./txt/cord-322904-9mta0aem.txt cache: ./cache/cord-322904-9mta0aem.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322904-9mta0aem.txt' === file2bib.sh === id: cord-327777-pg98zc6o author: Delogu, Mauro title: Eco-Virological Preliminary Study of Potentially Emerging Pathogens in Hedgehogs (Erinaceus europaeus) Recovered at a Wildlife Treatment and Rehabilitation Center in Northern Italy date: 2020-03-01 pages: extension: .txt txt: ./txt/cord-327777-pg98zc6o.txt cache: ./cache/cord-327777-pg98zc6o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327777-pg98zc6o.txt' === file2bib.sh === id: cord-328621-3jda0k2u author: Laporte, Manon title: Airway proteases: an emerging drug target for influenza and other respiratory virus infections date: 2017-04-14 pages: extension: .txt txt: ./txt/cord-328621-3jda0k2u.txt cache: ./cache/cord-328621-3jda0k2u.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-328621-3jda0k2u.txt' === file2bib.sh === id: cord-329902-db7hl770 author: Li, Desheng title: Influenza A(H1N1)pdm09 Virus Infection in Giant Pandas, China date: 2014-03-17 pages: extension: .txt txt: ./txt/cord-329902-db7hl770.txt cache: ./cache/cord-329902-db7hl770.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-329902-db7hl770.txt' === file2bib.sh === id: cord-325750-x7jpsnxg author: Mokili, John L title: Metagenomics and future perspectives in virus discovery date: 2012-01-20 pages: extension: .txt txt: ./txt/cord-325750-x7jpsnxg.txt cache: ./cache/cord-325750-x7jpsnxg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-325750-x7jpsnxg.txt' === file2bib.sh === id: cord-323358-05bk91lm author: Bhaskar, Sathyamoorthy title: Engineering protein nanocages as carriers for biomedical applications date: 2017-04-07 pages: extension: .txt txt: ./txt/cord-323358-05bk91lm.txt cache: ./cache/cord-323358-05bk91lm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323358-05bk91lm.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-329078-gnnis7pl author: Musella, Simona title: Identification of an indol-based derivative as potent and selective varicella zoster virus (VZV) inhibitor date: 2016-11-29 pages: extension: .txt txt: ./txt/cord-329078-gnnis7pl.txt cache: ./cache/cord-329078-gnnis7pl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-329078-gnnis7pl.txt' === file2bib.sh === id: cord-325230-3kg4oe4g author: Agol, Vadim I. title: Viral security proteins: counteracting host defences date: 2010-11-09 pages: extension: .txt txt: ./txt/cord-325230-3kg4oe4g.txt cache: ./cache/cord-325230-3kg4oe4g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325230-3kg4oe4g.txt' === file2bib.sh === id: cord-326177-zzsaf3bl author: Khatri, Mahesh title: Mesenchymal stem cell-derived extracellular vesicles attenuate influenza virus-induced acute lung injury in a pig model date: 2018-01-29 pages: extension: .txt txt: ./txt/cord-326177-zzsaf3bl.txt cache: ./cache/cord-326177-zzsaf3bl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-326177-zzsaf3bl.txt' === file2bib.sh === id: cord-329050-vzsy6xw1 author: Nabi, Ghulam title: Bats and birds as viral reservoirs: A physiological and ecological perspective date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-329050-vzsy6xw1.txt cache: ./cache/cord-329050-vzsy6xw1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-329050-vzsy6xw1.txt' === file2bib.sh === id: cord-326027-58whwspe author: Hernaez, Bruno title: Visualization of the African swine fever virus infection in living cells by incorporation into the virus particle of green fluorescent protein-p54 membrane protein chimera date: 2006-06-20 pages: extension: .txt txt: ./txt/cord-326027-58whwspe.txt cache: ./cache/cord-326027-58whwspe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326027-58whwspe.txt' === file2bib.sh === id: cord-330827-gu2mt6zp author: Shanmugaraj, Balamurugan title: Emergence of Novel Coronavirus 2019-nCoV: Need for Rapid Vaccine and Biologics Development date: 2020-02-22 pages: extension: .txt txt: ./txt/cord-330827-gu2mt6zp.txt cache: ./cache/cord-330827-gu2mt6zp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330827-gu2mt6zp.txt' === file2bib.sh === id: cord-328753-qwdxgk4z author: Lafaye, Pierre title: Use of camel single-domain antibodies for the diagnosis and treatment of zoonotic diseases date: 2018-09-25 pages: extension: .txt txt: ./txt/cord-328753-qwdxgk4z.txt cache: ./cache/cord-328753-qwdxgk4z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328753-qwdxgk4z.txt' === file2bib.sh === id: cord-329857-pcsuu597 author: Chan, Kuan Rong title: Fc receptors and their influence on efficacy of therapeutic antibodies for treatment of viral diseases date: 2015-11-02 pages: extension: .txt txt: ./txt/cord-329857-pcsuu597.txt cache: ./cache/cord-329857-pcsuu597.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-329857-pcsuu597.txt' === file2bib.sh === id: cord-329429-ur8g68vp author: Miłek, Justyna title: Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds date: 2018-12-10 pages: extension: .txt txt: ./txt/cord-329429-ur8g68vp.txt cache: ./cache/cord-329429-ur8g68vp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329429-ur8g68vp.txt' === file2bib.sh === id: cord-331217-uup16bhm author: Murphy, Frederick A. title: Adventitious Agents and Smallpox Vaccine in Strategic National Stockpile date: 2005-07-17 pages: extension: .txt txt: ./txt/cord-331217-uup16bhm.txt cache: ./cache/cord-331217-uup16bhm.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-331217-uup16bhm.txt' === file2bib.sh === id: cord-327855-txryqil7 author: Kulka, M. title: The cytopathic 18f strain of Hepatitis A virus induces RNA degradation in FrhK4 cells date: 2003 pages: extension: .txt txt: ./txt/cord-327855-txryqil7.txt cache: ./cache/cord-327855-txryqil7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327855-txryqil7.txt' === file2bib.sh === id: cord-323987-gh1m05gi author: Dziąbowska, Karolina title: Detection Methods of Human and Animal Influenza Virus—Current Trends date: 2018-10-18 pages: extension: .txt txt: ./txt/cord-323987-gh1m05gi.txt cache: ./cache/cord-323987-gh1m05gi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-323987-gh1m05gi.txt' === file2bib.sh === id: cord-326960-9phlylce author: Felberbaum, Rachael S. title: The baculovirus expression vector system: A commercial manufacturing platform for viral vaccines and gene therapy vectors date: 2015-03-20 pages: extension: .txt txt: ./txt/cord-326960-9phlylce.txt cache: ./cache/cord-326960-9phlylce.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326960-9phlylce.txt' === file2bib.sh === id: cord-329145-424vv8a8 author: Kuhn, Jens H. title: Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae date: 2012-09-23 pages: extension: .txt txt: ./txt/cord-329145-424vv8a8.txt cache: ./cache/cord-329145-424vv8a8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329145-424vv8a8.txt' === file2bib.sh === id: cord-332205-ydijp66b author: Hufsky, Franziska title: Virologists—Heroes need weapons date: 2018-02-08 pages: extension: .txt txt: ./txt/cord-332205-ydijp66b.txt cache: ./cache/cord-332205-ydijp66b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-332205-ydijp66b.txt' === file2bib.sh === id: cord-329493-ueqlhgn0 author: Stadler, Konrad title: SARS — beginning to understand a new virus date: 2003 pages: extension: .txt txt: ./txt/cord-329493-ueqlhgn0.txt cache: ./cache/cord-329493-ueqlhgn0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-329493-ueqlhgn0.txt' === file2bib.sh === id: cord-327392-9psblokc author: Srivastava, A.K. title: Potential of Graphene-based Materials to Combat COVID-19: Properties, Perspectives and Prospects date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-327392-9psblokc.txt cache: ./cache/cord-327392-9psblokc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327392-9psblokc.txt' === file2bib.sh === id: cord-332457-gan10za0 author: de Ángel Solá, David E. title: Weathering the pandemic: How the Caribbean Basin can use viral and environmental patterns to predict, prepare and respond to COVID‐19 date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-332457-gan10za0.txt cache: ./cache/cord-332457-gan10za0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332457-gan10za0.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 3 resourceName b'cord-324950-ux7shvji.txt' === file2bib.sh === id: cord-326160-mf0vh6iu author: de Wit, Emmie title: Influenza Virus A/Anhui/1/2013 (H7N9) Replicates Efficiently in the Upper and Lower Respiratory Tracts of Cynomolgus Macaques date: 2014-08-12 pages: extension: .txt txt: ./txt/cord-326160-mf0vh6iu.txt cache: ./cache/cord-326160-mf0vh6iu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-326160-mf0vh6iu.txt' === file2bib.sh === id: cord-325915-dw989txm author: Wolf, Michael W title: Downstream processing of cell culture-derived virus particles date: 2014-01-09 pages: extension: .txt txt: ./txt/cord-325915-dw989txm.txt cache: ./cache/cord-325915-dw989txm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325915-dw989txm.txt' === file2bib.sh === id: cord-330296-706hf4qw author: Romette, J. L. title: The European Virus Archive goes global: A growing resource for research date: 2018-10-31 pages: extension: .txt txt: ./txt/cord-330296-706hf4qw.txt cache: ./cache/cord-330296-706hf4qw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330296-706hf4qw.txt' === file2bib.sh === id: cord-331652-oc5s1if2 author: Trudeau, Michaela P. title: Comparison of Thermal and Non-Thermal Processing of Swine Feed and the Use of Selected Feed Additives on Inactivation of Porcine Epidemic Diarrhea Virus (PEDV) date: 2016-06-24 pages: extension: .txt txt: ./txt/cord-331652-oc5s1if2.txt cache: ./cache/cord-331652-oc5s1if2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331652-oc5s1if2.txt' === file2bib.sh === id: cord-334365-idjvbcy4 author: Gooding, J. Justin title: Virus Detection: What Were We Doing before COVID-19 Changed the World? date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-334365-idjvbcy4.txt cache: ./cache/cord-334365-idjvbcy4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-334365-idjvbcy4.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 5 resourceName b'cord-332361-pdoln3nr.txt' === file2bib.sh === id: cord-331343-qzvwwca9 author: Mason, Andrew L. title: Metagenomics and the case of the deadly hamster date: 2008-06-09 pages: extension: .txt txt: ./txt/cord-331343-qzvwwca9.txt cache: ./cache/cord-331343-qzvwwca9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331343-qzvwwca9.txt' === file2bib.sh === id: cord-325825-0lyt8gfq author: Griffiths, Samantha J. title: A Systematic Analysis of Host Factors Reveals a Med23-Interferon-λ Regulatory Axis against Herpes Simplex Virus Type 1 Replication date: 2013-08-08 pages: extension: .txt txt: ./txt/cord-325825-0lyt8gfq.txt cache: ./cache/cord-325825-0lyt8gfq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325825-0lyt8gfq.txt' === file2bib.sh === id: cord-330131-yfhrmbvx author: Danchin, Antoine title: Cytosine drives evolution of SARS‐CoV‐2 date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-330131-yfhrmbvx.txt cache: ./cache/cord-330131-yfhrmbvx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-330131-yfhrmbvx.txt' === file2bib.sh === id: cord-331584-z43ifmr3 author: Mahy, B.W.J. title: Emerging and Reemerging Virus Diseases of Vertebrates date: 2008-07-30 pages: extension: .txt txt: ./txt/cord-331584-z43ifmr3.txt cache: ./cache/cord-331584-z43ifmr3.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-331584-z43ifmr3.txt' === file2bib.sh === id: cord-327000-oyg3oyx1 author: Li, Shasha title: Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-327000-oyg3oyx1.txt cache: ./cache/cord-327000-oyg3oyx1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327000-oyg3oyx1.txt' === file2bib.sh === id: cord-331739-y1d0leic author: Kempf, Christoph title: Pathogen inactivation and removal procedures used in the production of intravenous immunoglobulins date: 2007-03-31 pages: extension: .txt txt: ./txt/cord-331739-y1d0leic.txt cache: ./cache/cord-331739-y1d0leic.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331739-y1d0leic.txt' === file2bib.sh === id: cord-332046-ihc031ly author: Li, Yan‐Chao title: Neurotropic virus tracing suggests a membranous‐coating‐mediated mechanism for transsynaptic communication date: 2013-01-01 pages: extension: .txt txt: ./txt/cord-332046-ihc031ly.txt cache: ./cache/cord-332046-ihc031ly.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-332046-ihc031ly.txt' === file2bib.sh === id: cord-334941-6uattdti author: Espmark, Åke title: Other viruses date: 2014-06-27 pages: extension: .txt txt: ./txt/cord-334941-6uattdti.txt cache: ./cache/cord-334941-6uattdti.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334941-6uattdti.txt' === file2bib.sh === id: cord-332088-5c77h0of author: Beena, V. title: Emerging horizon for bat borne viral zoonoses date: 2019-10-26 pages: extension: .txt txt: ./txt/cord-332088-5c77h0of.txt cache: ./cache/cord-332088-5c77h0of.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-332088-5c77h0of.txt' === file2bib.sh === id: cord-333043-fe24ezt6 author: Traavik, T. title: “Runde“ virus, a coronavirus-like agent associated with seabirds and ticks date: 1977 pages: extension: .txt txt: ./txt/cord-333043-fe24ezt6.txt cache: ./cache/cord-333043-fe24ezt6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333043-fe24ezt6.txt' === file2bib.sh === id: cord-332165-31tbc31x author: Rustmeier, Nils H. title: The Symmetry of Viral Sialic Acid Binding Sites—Implications for Antiviral Strategies date: 2019-10-14 pages: extension: .txt txt: ./txt/cord-332165-31tbc31x.txt cache: ./cache/cord-332165-31tbc31x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-332165-31tbc31x.txt' === file2bib.sh === id: cord-331020-lyxje82u author: M. Najimudeen, Shahnas title: Infectious Bronchitis Coronavirus Infection in Chickens: Multiple System Disease with Immune Suppression date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-331020-lyxje82u.txt cache: ./cache/cord-331020-lyxje82u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-331020-lyxje82u.txt' === file2bib.sh === id: cord-332181-k90i33gp author: Degeling, Chris title: Hendra in the news: Public policy meets public morality in times of zoonotic uncertainty date: 2012-12-29 pages: extension: .txt txt: ./txt/cord-332181-k90i33gp.txt cache: ./cache/cord-332181-k90i33gp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-332181-k90i33gp.txt' === file2bib.sh === id: cord-336212-ueh4q408 author: Koenig, Kristi L. title: Identify-Isolate-Inform: A Tool for Initial Detection and Management of Zika Virus Patients in the Emergency Department date: 2016-04-04 pages: extension: .txt txt: ./txt/cord-336212-ueh4q408.txt cache: ./cache/cord-336212-ueh4q408.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336212-ueh4q408.txt' === file2bib.sh === id: cord-323683-9h9mld6x author: Butler, M. title: Virus Removal by Disinfection of Effluents date: 2013-11-17 pages: extension: .txt txt: ./txt/cord-323683-9h9mld6x.txt cache: ./cache/cord-323683-9h9mld6x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-323683-9h9mld6x.txt' === file2bib.sh === id: cord-328252-dk54w8z9 author: Kikkert, Marjolein title: Innate Immune Evasion by Human Respiratory RNA Viruses date: 2019-10-14 pages: extension: .txt txt: ./txt/cord-328252-dk54w8z9.txt cache: ./cache/cord-328252-dk54w8z9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328252-dk54w8z9.txt' === file2bib.sh === id: cord-333853-p2kbjwpy author: Smee, Donald F. title: Therapy and Long-Term Prophylaxis of Vaccinia Virus Respiratory Infections in Mice with an Adenovirus-Vectored Interferon Alpha (mDEF201) date: 2011-10-13 pages: extension: .txt txt: ./txt/cord-333853-p2kbjwpy.txt cache: ./cache/cord-333853-p2kbjwpy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333853-p2kbjwpy.txt' === file2bib.sh === id: cord-325712-9kbnyqt3 author: Nathan, Lakshmi title: Single Virion Tracking Microscopy for the Study of Virus Entry Processes in Live Cells and Biomimetic Platforms date: 2019-07-18 pages: extension: .txt txt: ./txt/cord-325712-9kbnyqt3.txt cache: ./cache/cord-325712-9kbnyqt3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-325712-9kbnyqt3.txt' === file2bib.sh === id: cord-334771-uy3s6443 author: Rao, BL title: A large outbreak of acute encephalitis with high fatality rate in children in Andhra Pradesh, India, in 2003, associated with Chandipura virus date: 2004-09-09 pages: extension: .txt txt: ./txt/cord-334771-uy3s6443.txt cache: ./cache/cord-334771-uy3s6443.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334771-uy3s6443.txt' === file2bib.sh === id: cord-333810-57d4oopv author: Leroy, Éric Maurice title: L’Émergence du virus EBOLA chez l’homme: un long processus pas totalement élucidé date: 2015-05-31 pages: extension: .txt txt: ./txt/cord-333810-57d4oopv.txt cache: ./cache/cord-333810-57d4oopv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333810-57d4oopv.txt' === file2bib.sh === id: cord-335279-cfv18qn0 author: Paillot, Romain title: Special Issue “Equine Viruses”: Old “Friends” and New Foes? date: 2020-01-29 pages: extension: .txt txt: ./txt/cord-335279-cfv18qn0.txt cache: ./cache/cord-335279-cfv18qn0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335279-cfv18qn0.txt' === file2bib.sh === id: cord-314825-fzba05wn author: Chauhan, Ravendra P. title: A Systematic Review Analyzing the Prevalence and Circulation of Influenza Viruses in Swine Population Worldwide date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-314825-fzba05wn.txt cache: ./cache/cord-314825-fzba05wn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314825-fzba05wn.txt' === file2bib.sh === id: cord-316063-9bg2dm8e author: Morgan, Marcus title: Why meaning-making matters: the case of the UK Government’s COVID-19 response date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-316063-9bg2dm8e.txt cache: ./cache/cord-316063-9bg2dm8e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-316063-9bg2dm8e.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-336157-aqc9zrrm author: Liang, Guodong title: Factors responsible for the emergence of arboviruses; strategies, challenges and limitations for their control date: 2015-03-25 pages: extension: .txt txt: ./txt/cord-336157-aqc9zrrm.txt cache: ./cache/cord-336157-aqc9zrrm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336157-aqc9zrrm.txt' === file2bib.sh === id: cord-330647-w1bpeqzg author: Wong, Samson Sai-Yin title: Ebola virus disease in nonendemic countries date: 2015-05-31 pages: extension: .txt txt: ./txt/cord-330647-w1bpeqzg.txt cache: ./cache/cord-330647-w1bpeqzg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330647-w1bpeqzg.txt' === file2bib.sh === id: cord-327660-p1b07b4t author: Wolf, Yuri I. title: Origins and Evolution of the Global RNA Virome date: 2018-11-27 pages: extension: .txt txt: ./txt/cord-327660-p1b07b4t.txt cache: ./cache/cord-327660-p1b07b4t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327660-p1b07b4t.txt' === file2bib.sh === id: cord-324984-ojrpsdt9 author: Ji, Xingyue title: Medicinal chemistry strategies toward host targeting antiviral agents date: 2020-02-14 pages: extension: .txt txt: ./txt/cord-324984-ojrpsdt9.txt cache: ./cache/cord-324984-ojrpsdt9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-324984-ojrpsdt9.txt' === file2bib.sh === id: cord-334560-1j9zmuub author: Hunt, Catherine L. title: Filovirus Entry: A Novelty in the Viral Fusion World date: 2012-02-07 pages: extension: .txt txt: ./txt/cord-334560-1j9zmuub.txt cache: ./cache/cord-334560-1j9zmuub.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334560-1j9zmuub.txt' === file2bib.sh === id: cord-333730-qsx0m68e author: Tsai, Y. C. title: Oral disease-modifying antirheumatic drugs and immunosuppressants with antiviral potential, including SARS-CoV-2 infection: a review date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-333730-qsx0m68e.txt cache: ./cache/cord-333730-qsx0m68e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333730-qsx0m68e.txt' === file2bib.sh === id: cord-320713-b37c8aye author: Roberts, Lisa O. title: Chapter 9 Viral Strategies to Subvert the Mammalian Translation Machinery date: 2009-10-27 pages: extension: .txt txt: ./txt/cord-320713-b37c8aye.txt cache: ./cache/cord-320713-b37c8aye.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-320713-b37c8aye.txt' === file2bib.sh === id: cord-334010-gxu0refq author: Banerjee, Nilotpal title: Viral glycoproteins: biological role and application in diagnosis date: 2016-01-18 pages: extension: .txt txt: ./txt/cord-334010-gxu0refq.txt cache: ./cache/cord-334010-gxu0refq.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-334010-gxu0refq.txt' === file2bib.sh === id: cord-334082-fyxn0g3v author: O’Carroll, I.P. title: Viral Nucleic Acids date: 2015-08-20 pages: extension: .txt txt: ./txt/cord-334082-fyxn0g3v.txt cache: ./cache/cord-334082-fyxn0g3v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334082-fyxn0g3v.txt' === file2bib.sh === id: cord-333228-ejkgune0 author: Ball, Andrew S title: Chapter 1 Introduction into nanotechnology and microbiology date: 2019-12-31 pages: extension: .txt txt: ./txt/cord-333228-ejkgune0.txt cache: ./cache/cord-333228-ejkgune0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333228-ejkgune0.txt' === file2bib.sh === id: cord-331289-02411gfv author: Di Minno, Giovanni title: Current concepts in the prevention of pathogen transmission via blood/plasma-derived products for bleeding disorders() date: 2015-07-20 pages: extension: .txt txt: ./txt/cord-331289-02411gfv.txt cache: ./cache/cord-331289-02411gfv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331289-02411gfv.txt' === file2bib.sh === id: cord-331244-zaguyxm5 author: Stephenson, Iain title: Confronting the avian influenza threat: vaccine development for a potential pandemic date: 2004-07-30 pages: extension: .txt txt: ./txt/cord-331244-zaguyxm5.txt cache: ./cache/cord-331244-zaguyxm5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331244-zaguyxm5.txt' === file2bib.sh === id: cord-332632-u2ud0vmq author: Lussi, Carmela title: What can pestiviral endonucleases teach us about innate immunotolerance? date: 2016-03-17 pages: extension: .txt txt: ./txt/cord-332632-u2ud0vmq.txt cache: ./cache/cord-332632-u2ud0vmq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332632-u2ud0vmq.txt' === file2bib.sh === id: cord-336225-ijodhrwf author: Chang, Mee Soo title: Severe Fever with Thrombocytopenia Syndrome: Tick-Mediated Viral Disease date: 2013-06-03 pages: extension: .txt txt: ./txt/cord-336225-ijodhrwf.txt cache: ./cache/cord-336225-ijodhrwf.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-336225-ijodhrwf.txt' === file2bib.sh === id: cord-323311-xl2fv0qx author: Kahn, R. E. title: 6th International Conference on Emerging Zoonoses date: 2012-09-07 pages: extension: .txt txt: ./txt/cord-323311-xl2fv0qx.txt cache: ./cache/cord-323311-xl2fv0qx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-323311-xl2fv0qx.txt' === file2bib.sh === id: cord-327883-s9nbr5y8 author: nan title: Section Virology date: 1990-03-31 pages: extension: .txt txt: ./txt/cord-327883-s9nbr5y8.txt cache: ./cache/cord-327883-s9nbr5y8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327883-s9nbr5y8.txt' === file2bib.sh === id: cord-339854-scb7pz87 author: Overend, Christopher title: The synthetic futures of vesicular stomatitis virus date: 2012-07-11 pages: extension: .txt txt: ./txt/cord-339854-scb7pz87.txt cache: ./cache/cord-339854-scb7pz87.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-339854-scb7pz87.txt' === file2bib.sh === id: cord-316273-vo6j8zb0 author: Cosset, François-Loic title: Cell Entry of Enveloped Viruses date: 2011-02-08 pages: extension: .txt txt: ./txt/cord-316273-vo6j8zb0.txt cache: ./cache/cord-316273-vo6j8zb0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316273-vo6j8zb0.txt' === file2bib.sh === id: cord-332992-8rmqg4rf author: de Vries, A. A. F. title: SARS-CoV-2/COVID-19: a primer for cardiologists date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-332992-8rmqg4rf.txt cache: ./cache/cord-332992-8rmqg4rf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332992-8rmqg4rf.txt' === file2bib.sh === id: cord-333463-u7je0d1o author: Diaz-Salazar, Carlos title: Natural killer cell responses to emerging viruses of zoonotic origin date: 2020-08-09 pages: extension: .txt txt: ./txt/cord-333463-u7je0d1o.txt cache: ./cache/cord-333463-u7je0d1o.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-333463-u7je0d1o.txt' === file2bib.sh === id: cord-329527-0rlotyz3 author: Bohmwald, Karen title: Neurologic Alterations Due to Respiratory Virus Infections date: 2018-10-26 pages: extension: .txt txt: ./txt/cord-329527-0rlotyz3.txt cache: ./cache/cord-329527-0rlotyz3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329527-0rlotyz3.txt' === file2bib.sh === id: cord-336447-hpnkou41 author: Pitlik, Silvio Daniel title: COVID-19 Compared to Other Pandemic Diseases date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-336447-hpnkou41.txt cache: ./cache/cord-336447-hpnkou41.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-336447-hpnkou41.txt' === file2bib.sh === id: cord-334947-pa0p5dif author: Rozen-Gagnon, Kathryn title: Alphavirus Mutator Variants Present Host-Specific Defects and Attenuation in Mammalian and Insect Models date: 2014-01-16 pages: extension: .txt txt: ./txt/cord-334947-pa0p5dif.txt cache: ./cache/cord-334947-pa0p5dif.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-334947-pa0p5dif.txt' === file2bib.sh === id: cord-337914-1hwnxkdd author: Ehlkes, L. title: Epidemiologie des Ebolafiebers und anderer, in Deutschland seltener hochkontagiöser, lebensbedrohlicher Erkrankungen date: 2015-05-22 pages: extension: .txt txt: ./txt/cord-337914-1hwnxkdd.txt cache: ./cache/cord-337914-1hwnxkdd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337914-1hwnxkdd.txt' === file2bib.sh === id: cord-337577-dqikrmk7 author: Greenberg, Harry B. title: Vaccination against Viruses date: 2016-05-09 pages: extension: .txt txt: ./txt/cord-337577-dqikrmk7.txt cache: ./cache/cord-337577-dqikrmk7.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-337577-dqikrmk7.txt' === file2bib.sh === id: cord-336493-ggo9wsrm author: Huang, Stephen S. H. title: Immunity toward H1N1 influenza hemagglutinin of historical and contemporary strains suggests protection and vaccine failure date: 2013-04-23 pages: extension: .txt txt: ./txt/cord-336493-ggo9wsrm.txt cache: ./cache/cord-336493-ggo9wsrm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336493-ggo9wsrm.txt' === file2bib.sh === id: cord-335774-15fhg8o9 author: Mull, Nathaniel title: Ecology of Neglected Rodent-Borne American Orthohantaviruses date: 2020-04-26 pages: extension: .txt txt: ./txt/cord-335774-15fhg8o9.txt cache: ./cache/cord-335774-15fhg8o9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335774-15fhg8o9.txt' === file2bib.sh === id: cord-336045-8qcj5uiy author: Langlois, Isabelle title: Viral diseases of ferrets date: 2005-03-01 pages: extension: .txt txt: ./txt/cord-336045-8qcj5uiy.txt cache: ./cache/cord-336045-8qcj5uiy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336045-8qcj5uiy.txt' === file2bib.sh === id: cord-338081-ggw5l1qm author: Gorbalenya, Alexander E. title: Phylogeny of Viruses date: 2017-06-26 pages: extension: .txt txt: ./txt/cord-338081-ggw5l1qm.txt cache: ./cache/cord-338081-ggw5l1qm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-338081-ggw5l1qm.txt' === file2bib.sh === id: cord-337673-1nau263l author: Wu, Chang-Jer title: Antiviral applications of RNAi for coronavirus date: 2006-01-24 pages: extension: .txt txt: ./txt/cord-337673-1nau263l.txt cache: ./cache/cord-337673-1nau263l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-337673-1nau263l.txt' === file2bib.sh === id: cord-338400-30vl2hks author: Epstein, Jonathan H. title: Identification of GBV-D, a Novel GB-like Flavivirus from Old World Frugivorous Bats (Pteropus giganteus) in Bangladesh date: 2010-07-01 pages: extension: .txt txt: ./txt/cord-338400-30vl2hks.txt cache: ./cache/cord-338400-30vl2hks.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-338400-30vl2hks.txt' === file2bib.sh === id: cord-338727-1kodz527 author: Ilinskaya, O. N. title: Ribonucleases as antiviral agents date: 2014-10-11 pages: extension: .txt txt: ./txt/cord-338727-1kodz527.txt cache: ./cache/cord-338727-1kodz527.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-338727-1kodz527.txt' === file2bib.sh === id: cord-335948-qkfxfmxb author: Ampofo, William K. title: Improving influenza vaccine virus selectionReport of a WHO informal consultation held at WHO headquarters, Geneva, Switzerland, 14–16 June 2010 date: 2011-08-08 pages: extension: .txt txt: ./txt/cord-335948-qkfxfmxb.txt cache: ./cache/cord-335948-qkfxfmxb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-335948-qkfxfmxb.txt' === file2bib.sh === id: cord-338083-77re4l0w author: Bolin, Steven R. title: Origination and consequences of bovine viral diarrhea virus diversity date: 2005-03-04 pages: extension: .txt txt: ./txt/cord-338083-77re4l0w.txt cache: ./cache/cord-338083-77re4l0w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-338083-77re4l0w.txt' === file2bib.sh === id: cord-336948-8yqdhcnz author: Löhner, Rainald title: Detailed simulation of viral propagation in the built environment date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-336948-8yqdhcnz.txt cache: ./cache/cord-336948-8yqdhcnz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336948-8yqdhcnz.txt' === file2bib.sh === id: cord-334027-xhfmio7k author: Fagre, Anna C. title: Can Bats Serve as Reservoirs for Arboviruses? date: 2019-03-03 pages: extension: .txt txt: ./txt/cord-334027-xhfmio7k.txt cache: ./cache/cord-334027-xhfmio7k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-334027-xhfmio7k.txt' === file2bib.sh === id: cord-339423-5qym9dsf author: Lina, B. title: Virus émergents ou menaces à répétition date: 2005-05-31 pages: extension: .txt txt: ./txt/cord-339423-5qym9dsf.txt cache: ./cache/cord-339423-5qym9dsf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339423-5qym9dsf.txt' === file2bib.sh === id: cord-337361-salby0fu author: Bujarski, Jozef J. title: Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives date: 2013-03-26 pages: extension: .txt txt: ./txt/cord-337361-salby0fu.txt cache: ./cache/cord-337361-salby0fu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337361-salby0fu.txt' === file2bib.sh === id: cord-339744-xrit0w5i author: Feng, Bo title: Investigation of antiviral state mediated by interferon-inducible transmembrane protein 1 induced by H9N2 virus and inactivated viral particle in human endothelial cells date: 2017-11-03 pages: extension: .txt txt: ./txt/cord-339744-xrit0w5i.txt cache: ./cache/cord-339744-xrit0w5i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339744-xrit0w5i.txt' === file2bib.sh === id: cord-338804-nreqluol author: Heise, M.T. title: Viral Pathogenesis date: 2014-11-28 pages: extension: .txt txt: ./txt/cord-338804-nreqluol.txt cache: ./cache/cord-338804-nreqluol.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338804-nreqluol.txt' === file2bib.sh === id: cord-340537-pdvpmydk author: Bañon-Gonzalez, Rafael title: Autopsies of suspected SARS-CoV-2 cases date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-340537-pdvpmydk.txt cache: ./cache/cord-340537-pdvpmydk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340537-pdvpmydk.txt' === file2bib.sh === id: cord-331673-xv1tcugl author: Reina, Giacomo title: Hard Nanomaterials in Time of Viral Pandemics date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-331673-xv1tcugl.txt cache: ./cache/cord-331673-xv1tcugl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331673-xv1tcugl.txt' === file2bib.sh === id: cord-336929-2rnkotqy author: Vieira, Flávia Sarmento title: Host‐cell lipid rafts: a safe door for micro‐organisms? date: 2012-01-03 pages: extension: .txt txt: ./txt/cord-336929-2rnkotqy.txt cache: ./cache/cord-336929-2rnkotqy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336929-2rnkotqy.txt' === file2bib.sh === id: cord-342151-1e6x589e author: Talbot, Pierre J. title: Hemagglutination by Murine Hepatitis Viruses date: 2008-07-29 pages: extension: .txt txt: ./txt/cord-342151-1e6x589e.txt cache: ./cache/cord-342151-1e6x589e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342151-1e6x589e.txt' === file2bib.sh === id: cord-341303-1iayp8oa author: McINTOSH, KENNETH title: Immunofluorescence in Diagnostic Virology date: 2006-12-16 pages: extension: .txt txt: ./txt/cord-341303-1iayp8oa.txt cache: ./cache/cord-341303-1iayp8oa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341303-1iayp8oa.txt' === file2bib.sh === id: cord-339885-mpzgrogd author: Zhan, Yangqing title: Respiratory virus is a real pathogen in immunocompetent community-acquired pneumonia: comparing to influenza like illness and volunteer controls date: 2014-09-02 pages: extension: .txt txt: ./txt/cord-339885-mpzgrogd.txt cache: ./cache/cord-339885-mpzgrogd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339885-mpzgrogd.txt' === file2bib.sh === id: cord-338331-27ic5zen author: Boulagnon, Camille title: Influenza A/H1N1 (2009) Infection as a Cause of Unexpected Out‐of‐Hospital Death in the Young date: 2012-05-14 pages: extension: .txt txt: ./txt/cord-338331-27ic5zen.txt cache: ./cache/cord-338331-27ic5zen.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338331-27ic5zen.txt' === file2bib.sh === id: cord-339209-oe8onyr9 author: Vasilakis, Nikos title: Mesoniviruses are mosquito-specific viruses with extensive geographic distribution and host range date: 2014-05-20 pages: extension: .txt txt: ./txt/cord-339209-oe8onyr9.txt cache: ./cache/cord-339209-oe8onyr9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339209-oe8onyr9.txt' === file2bib.sh === id: cord-334108-4ey725dv author: Seymour, I.J. title: Foodborne viruses and fresh produce date: 2008-07-07 pages: extension: .txt txt: ./txt/cord-334108-4ey725dv.txt cache: ./cache/cord-334108-4ey725dv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-334108-4ey725dv.txt' === file2bib.sh === id: cord-337285-t6qr41wc author: Ikeda, Masanori title: Modulation of host metabolism as a target of new antivirals() date: 2007-10-10 pages: extension: .txt txt: ./txt/cord-337285-t6qr41wc.txt cache: ./cache/cord-337285-t6qr41wc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337285-t6qr41wc.txt' === file2bib.sh === id: cord-333351-homxj9uz author: Rodhain, F. title: Bats and Viruses: complex relationships date: 2015-10-10 pages: extension: .txt txt: ./txt/cord-333351-homxj9uz.txt cache: ./cache/cord-333351-homxj9uz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333351-homxj9uz.txt' === file2bib.sh === id: cord-341138-mxjsp3cm author: Denner, Joachim title: Transspecies Transmission of Gammaretroviruses and the Origin of the Gibbon Ape Leukaemia Virus (GaLV) and the Koala Retrovirus (KoRV) date: 2016-12-20 pages: extension: .txt txt: ./txt/cord-341138-mxjsp3cm.txt cache: ./cache/cord-341138-mxjsp3cm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-341138-mxjsp3cm.txt' === file2bib.sh === id: cord-340907-j9i1wlak author: Zarai, Yoram title: Evolutionary selection against short nucleotide sequences in viruses and their related hosts date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-340907-j9i1wlak.txt cache: ./cache/cord-340907-j9i1wlak.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340907-j9i1wlak.txt' === file2bib.sh === id: cord-340610-ex2yjyum author: Wang, De-Yun title: Upper Airway Stem Cells: Understanding the Nose and Role for Future Cell Therapy date: 2014-11-28 pages: extension: .txt txt: ./txt/cord-340610-ex2yjyum.txt cache: ./cache/cord-340610-ex2yjyum.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340610-ex2yjyum.txt' === file2bib.sh === id: cord-341298-mqpovrms author: Morse, S.A. title: Viruses and Bioterrorism date: 2016-10-31 pages: extension: .txt txt: ./txt/cord-341298-mqpovrms.txt cache: ./cache/cord-341298-mqpovrms.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-341298-mqpovrms.txt' === file2bib.sh === id: cord-337149-cjon7ihb author: Van Vliet, Kim M. title: The Role of the Adeno-Associated Virus Capsid in Gene Transfer date: 2008 pages: extension: .txt txt: ./txt/cord-337149-cjon7ihb.txt cache: ./cache/cord-337149-cjon7ihb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-337149-cjon7ihb.txt' === file2bib.sh === id: cord-339973-kj56zi59 author: Coleman, Kristen K. title: Bioaerosol Sampling for Respiratory Viruses in Singapore’s Mass Rapid Transit Network date: 2018-11-30 pages: extension: .txt txt: ./txt/cord-339973-kj56zi59.txt cache: ./cache/cord-339973-kj56zi59.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339973-kj56zi59.txt' === file2bib.sh === id: cord-339062-tq0f6d01 author: Weaver, Scott C. title: Transmission cycles, host range, evolution and emergence of arboviral disease date: 2004 pages: extension: .txt txt: ./txt/cord-339062-tq0f6d01.txt cache: ./cache/cord-339062-tq0f6d01.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339062-tq0f6d01.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 4 resourceName b'cord-347509-2ysw9a0a.txt' === file2bib.sh === id: cord-340042-intxyu46 author: Chaudhry, Sundas Nasir title: New insight on possible vaccine development against SARS-CoV-2 date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-340042-intxyu46.txt cache: ./cache/cord-340042-intxyu46.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340042-intxyu46.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-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-339382-ii4xurmr author: Bachofen, Claudia title: Selected Viruses Detected on and in our Food date: 2018-03-21 pages: extension: .txt txt: ./txt/cord-339382-ii4xurmr.txt cache: ./cache/cord-339382-ii4xurmr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339382-ii4xurmr.txt' === file2bib.sh === id: cord-342277-v6310fjh author: Carducci, A. title: Environmental survey to assess viral contamination of air and surfaces in hospital settings date: 2011-01-31 pages: extension: .txt txt: ./txt/cord-342277-v6310fjh.txt cache: ./cache/cord-342277-v6310fjh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342277-v6310fjh.txt' === file2bib.sh === id: cord-338737-phv12m1q author: Amor, A. title: Infecciones víricas. Clasificación. Infecciones por virus herpes date: 2006-06-30 pages: extension: .txt txt: ./txt/cord-338737-phv12m1q.txt cache: ./cache/cord-338737-phv12m1q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-338737-phv12m1q.txt' === file2bib.sh === id: cord-344009-hm36pepp author: Nathanson, N. title: Virus perpetuation in populations: biological variables that determine persistence or eradication date: 2005 pages: extension: .txt txt: ./txt/cord-344009-hm36pepp.txt cache: ./cache/cord-344009-hm36pepp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-344009-hm36pepp.txt' === file2bib.sh === id: cord-337712-ylqgraos author: Heinz, Franz X. title: Profile of SARS-CoV-2 date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-337712-ylqgraos.txt cache: ./cache/cord-337712-ylqgraos.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-337712-ylqgraos.txt' === file2bib.sh === id: cord-341923-jwckbdnb author: To, Kelvin Kai-Wang title: Pathogenesis of pandemic H1N1 2009 influenza virus infection and the implication on management date: 2010-04-28 pages: extension: .txt txt: ./txt/cord-341923-jwckbdnb.txt cache: ./cache/cord-341923-jwckbdnb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341923-jwckbdnb.txt' === file2bib.sh === id: cord-340331-51yq1rdo author: Tonelli, Michele title: Host dihydrofolate reductase (DHFR)-directed cycloguanil analogues endowed with activity against influenza virus and respiratory syncytial virus date: 2017-07-28 pages: extension: .txt txt: ./txt/cord-340331-51yq1rdo.txt cache: ./cache/cord-340331-51yq1rdo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340331-51yq1rdo.txt' === file2bib.sh === id: cord-345168-3w32v2fm author: To, Kelvin K.W. title: Viral load in patients infected with pandemic H1N1 2009 influenza A virus date: 2009-11-30 pages: extension: .txt txt: ./txt/cord-345168-3w32v2fm.txt cache: ./cache/cord-345168-3w32v2fm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345168-3w32v2fm.txt' === file2bib.sh === id: cord-336554-n8n5ii5k author: Singh, Thakur Uttam title: Drug repurposing approach to fight COVID-19 date: 2020-09-05 pages: extension: .txt txt: ./txt/cord-336554-n8n5ii5k.txt cache: ./cache/cord-336554-n8n5ii5k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336554-n8n5ii5k.txt' === file2bib.sh === id: cord-339288-y8woqsii author: Tews, Birke Andrea title: Self-Replicating RNA date: 2016-06-11 pages: extension: .txt txt: ./txt/cord-339288-y8woqsii.txt cache: ./cache/cord-339288-y8woqsii.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339288-y8woqsii.txt' === file2bib.sh === id: cord-339172-210dwhgj author: Knoops, Kèvin title: SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum date: 2008-09-16 pages: extension: .txt txt: ./txt/cord-339172-210dwhgj.txt cache: ./cache/cord-339172-210dwhgj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339172-210dwhgj.txt' === file2bib.sh === id: cord-343784-zgvxl4h3 author: Cho, Chi Hyun title: Evaluation of the AdvanSure™ real-time RT-PCR compared with culture and Seeplex RV15 for simultaneous detection of respiratory viruses date: 2014-05-31 pages: extension: .txt txt: ./txt/cord-343784-zgvxl4h3.txt cache: ./cache/cord-343784-zgvxl4h3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-343784-zgvxl4h3.txt' === file2bib.sh === id: cord-340423-f8ab7413 author: Barr, J.N. title: Genetic Instability of RNA Viruses date: 2016-09-09 pages: extension: .txt txt: ./txt/cord-340423-f8ab7413.txt cache: ./cache/cord-340423-f8ab7413.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340423-f8ab7413.txt' === file2bib.sh === id: cord-340481-i3qrxnpr author: Pozo, Francisco title: Aplicación de los métodos moleculares al diagnóstico y el estudio epidemiológico de las infecciones respiratorias causadas por virus date: 2008-07-31 pages: extension: .txt txt: ./txt/cord-340481-i3qrxnpr.txt cache: ./cache/cord-340481-i3qrxnpr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340481-i3qrxnpr.txt' === file2bib.sh === id: cord-342906-51296y8d author: Li, Zhiping title: Aerosolized avian influenza virus by laboratory manipulations date: 2012-08-06 pages: extension: .txt txt: ./txt/cord-342906-51296y8d.txt cache: ./cache/cord-342906-51296y8d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-342906-51296y8d.txt' === file2bib.sh === id: cord-342412-azkamnpa author: Ecker, David J title: The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents date: 2005-04-25 pages: extension: .txt txt: ./txt/cord-342412-azkamnpa.txt cache: ./cache/cord-342412-azkamnpa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342412-azkamnpa.txt' === file2bib.sh === id: cord-341101-5yvjbr5q author: Hashem, Anwar M. title: Therapeutic use of chloroquine and hydroxychloroquine in COVID-19 and other viral infections: A narrative review date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-341101-5yvjbr5q.txt cache: ./cache/cord-341101-5yvjbr5q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-341101-5yvjbr5q.txt' === file2bib.sh === id: cord-345157-fhmhpobi author: Qi, Dan title: Virus infection-induced host mRNA degradation and potential application of live cell imaging date: 2018-12-12 pages: extension: .txt txt: ./txt/cord-345157-fhmhpobi.txt cache: ./cache/cord-345157-fhmhpobi.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-345157-fhmhpobi.txt' === file2bib.sh === id: cord-337659-x4oywbrj author: Wilson, Brenda A. title: Global biosecurity in a complex, dynamic world date: 2008-07-31 pages: extension: .txt txt: ./txt/cord-337659-x4oywbrj.txt cache: ./cache/cord-337659-x4oywbrj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-337659-x4oywbrj.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-344576-upsc9cf8 author: Taylor-Robinson, Andrew W title: A vaccine effective against Zika virus is theoretically possible but may not be delivered anytime soon date: 2016-07-05 pages: extension: .txt txt: ./txt/cord-344576-upsc9cf8.txt cache: ./cache/cord-344576-upsc9cf8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-344576-upsc9cf8.txt' === file2bib.sh === id: cord-340503-zwdewiu1 author: Mokhtarzadeh, Ahad title: Nanomaterial-based biosensors for detection of pathogenic virus date: 2017-10-13 pages: extension: .txt txt: ./txt/cord-340503-zwdewiu1.txt cache: ./cache/cord-340503-zwdewiu1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340503-zwdewiu1.txt' === file2bib.sh === id: cord-341968-uc8i9h0m author: Izaguirre, Gonzalo title: The Proteolytic Regulation of Virus Cell Entry by Furin and Other Proprotein Convertases date: 2019-09-09 pages: extension: .txt txt: ./txt/cord-341968-uc8i9h0m.txt cache: ./cache/cord-341968-uc8i9h0m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341968-uc8i9h0m.txt' === file2bib.sh === id: cord-345359-okmkgsbr author: Ohno, Marumi title: Influenza virus infection affects insulin signaling, fatty acid-metabolizing enzyme expressions, and the tricarboxylic acid cycle in mice date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-345359-okmkgsbr.txt cache: ./cache/cord-345359-okmkgsbr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345359-okmkgsbr.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 4 resourceName b'cord-342915-r9kv67we.txt' === file2bib.sh === id: cord-344006-0iq9s94n author: Atzrodt, Cassandra L. title: A Guide to COVID‐19: a global pandemic caused by the novel coronavirus SARS‐CoV‐2 date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-344006-0iq9s94n.txt cache: ./cache/cord-344006-0iq9s94n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-344006-0iq9s94n.txt' === file2bib.sh === id: cord-344782-ond1ziu5 author: Zhang, Jing title: Identification of a novel nidovirus as a potential cause of large scale mortalities in the endangered Bellinger River snapping turtle (Myuchelys georgesi) date: 2018-10-24 pages: extension: .txt txt: ./txt/cord-344782-ond1ziu5.txt cache: ./cache/cord-344782-ond1ziu5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344782-ond1ziu5.txt' === file2bib.sh === id: cord-333655-lylt7qld author: Van Breedam, Wander title: Bitter‐sweet symphony: glycan–lectin interactions in virus biology date: 2013-12-06 pages: extension: .txt txt: ./txt/cord-333655-lylt7qld.txt cache: ./cache/cord-333655-lylt7qld.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333655-lylt7qld.txt' === file2bib.sh === id: cord-347577-p0a2rboi author: Bibby, Kyle title: Persistence of Ebola Virus in Sterilized Wastewater date: 2015-08-17 pages: extension: .txt txt: ./txt/cord-347577-p0a2rboi.txt cache: ./cache/cord-347577-p0a2rboi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-347577-p0a2rboi.txt' === file2bib.sh === id: cord-345020-ai5tib7h author: Price, O. H. title: Using routine testing data to understand circulation patterns of influenza A, respiratory syncytial virus and other respiratory viruses in Victoria, Australia date: 2019-06-17 pages: extension: .txt txt: ./txt/cord-345020-ai5tib7h.txt cache: ./cache/cord-345020-ai5tib7h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345020-ai5tib7h.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 2 resourceName b'cord-346096-aml84iv1.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 5 resourceName b'cord-346673-kyc1wks5.txt' === file2bib.sh === id: cord-344408-4ko557n1 author: Cunningham, Andrew A. title: One Health, emerging infectious diseases and wildlife: two decades of progress? date: 2017-07-19 pages: extension: .txt txt: ./txt/cord-344408-4ko557n1.txt cache: ./cache/cord-344408-4ko557n1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-344408-4ko557n1.txt' === file2bib.sh === id: cord-340194-ibli36rq author: To, Kelvin K.W. title: Ebola virus disease: a highly fatal infectious disease reemerging in West Africa date: 2014-11-29 pages: extension: .txt txt: ./txt/cord-340194-ibli36rq.txt cache: ./cache/cord-340194-ibli36rq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-340194-ibli36rq.txt' === file2bib.sh === id: cord-340629-1fle5fpz author: O’Shea, Helen title: Viruses Associated With Foodborne Infections date: 2019-05-21 pages: extension: .txt txt: ./txt/cord-340629-1fle5fpz.txt cache: ./cache/cord-340629-1fle5fpz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340629-1fle5fpz.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-343918-5yk1j4ms author: Gorbalenya, A.E. title: Phylogeny of Viruses date: 2008-07-30 pages: extension: .txt txt: ./txt/cord-343918-5yk1j4ms.txt cache: ./cache/cord-343918-5yk1j4ms.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-343918-5yk1j4ms.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 2 resourceName b'cord-346290-my8ow5ee.txt' === file2bib.sh === id: cord-341050-hnuogpqn author: Acharya, Dhiraj title: An Overview of Current Approaches Toward the Treatment and Prevention of West Nile Virus Infection date: 2016-05-18 pages: extension: .txt txt: ./txt/cord-341050-hnuogpqn.txt cache: ./cache/cord-341050-hnuogpqn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341050-hnuogpqn.txt' === file2bib.sh === id: cord-348141-eskefcwk author: Herrington, CS title: Viruses and disease: emerging concepts for prevention, diagnosis and treatment date: 2014-12-11 pages: extension: .txt txt: ./txt/cord-348141-eskefcwk.txt cache: ./cache/cord-348141-eskefcwk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348141-eskefcwk.txt' === file2bib.sh === id: cord-346904-aa88gtzr author: Bao, Y. title: Virus Classification by Pairwise Sequence Comparison (PASC) date: 2008-07-30 pages: extension: .txt txt: ./txt/cord-346904-aa88gtzr.txt cache: ./cache/cord-346904-aa88gtzr.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-346904-aa88gtzr.txt' === file2bib.sh === id: cord-348867-c0xpzd4d author: Zhai, Jun-Qiong title: First complete genome sequence of parainfluenza virus 5 isolated from lesser panda date: 2017-01-30 pages: extension: .txt txt: ./txt/cord-348867-c0xpzd4d.txt cache: ./cache/cord-348867-c0xpzd4d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348867-c0xpzd4d.txt' === file2bib.sh === id: cord-341155-3d64mso0 author: Slots, Jørgen title: Bacterial and viral pathogens in saliva: disease relationship and infectious risk date: 2010-12-07 pages: extension: .txt txt: ./txt/cord-341155-3d64mso0.txt cache: ./cache/cord-341155-3d64mso0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-341155-3d64mso0.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-346853-0c1qdjb5 author: Holmes, E. C. title: The Evolutionary Genetics of Viral Emergence date: 2007 pages: extension: .txt txt: ./txt/cord-346853-0c1qdjb5.txt cache: ./cache/cord-346853-0c1qdjb5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-346853-0c1qdjb5.txt' === file2bib.sh === id: cord-348876-v55piprx author: Zhao, Guangyu title: An M2e-based multiple antigenic peptide vaccine protects mice from lethal challenge with divergent H5N1 influenza viruses date: 2010-01-18 pages: extension: .txt txt: ./txt/cord-348876-v55piprx.txt cache: ./cache/cord-348876-v55piprx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348876-v55piprx.txt' === file2bib.sh === id: cord-343350-04e6wvov author: Liu, Haipeng title: Antiviral immunity in crustaceans date: 2009-02-15 pages: extension: .txt txt: ./txt/cord-343350-04e6wvov.txt cache: ./cache/cord-343350-04e6wvov.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-343350-04e6wvov.txt' === file2bib.sh === id: cord-342124-jdv17u86 author: Nieto‐Rabiela, Fabiola title: Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis date: 2019-06-20 pages: extension: .txt txt: ./txt/cord-342124-jdv17u86.txt cache: ./cache/cord-342124-jdv17u86.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342124-jdv17u86.txt' === file2bib.sh === id: cord-333262-xvfl7ycj author: Robson, B. title: COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles’ heel conserved region to minimize probability of escape mutations and drug resistance date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-333262-xvfl7ycj.txt cache: ./cache/cord-333262-xvfl7ycj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333262-xvfl7ycj.txt' === file2bib.sh === id: cord-339230-cc7gcy5b author: Smith, Amber M. title: Secondary Bacterial Infections in Influenza Virus Infection Pathogenesis date: 2014-07-16 pages: extension: .txt txt: ./txt/cord-339230-cc7gcy5b.txt cache: ./cache/cord-339230-cc7gcy5b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339230-cc7gcy5b.txt' === file2bib.sh === id: cord-346063-7u1a198p author: De Clercq, Erik title: Avian influenza A (H5N1) infection: targets and strategies for chemotherapeutic intervention date: 2007-05-04 pages: extension: .txt txt: ./txt/cord-346063-7u1a198p.txt cache: ./cache/cord-346063-7u1a198p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-346063-7u1a198p.txt' === file2bib.sh === id: cord-342936-43u7afl3 author: Balzarini, Jan title: Targeting the glycans of glycoproteins: a novel paradigm for antiviral therapy date: 2007 pages: extension: .txt txt: ./txt/cord-342936-43u7afl3.txt cache: ./cache/cord-342936-43u7afl3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-342936-43u7afl3.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-343690-rafvxgx1 author: Hartmann, Katrin title: Clinical Aspects of Feline Retroviruses: A Review date: 2012-10-31 pages: extension: .txt txt: ./txt/cord-343690-rafvxgx1.txt cache: ./cache/cord-343690-rafvxgx1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-343690-rafvxgx1.txt' === file2bib.sh === id: cord-348860-zaimorg0 author: Ratra, Ruchi title: Functional genomics as a tool in virus research date: 2008-06-01 pages: extension: .txt txt: ./txt/cord-348860-zaimorg0.txt cache: ./cache/cord-348860-zaimorg0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348860-zaimorg0.txt' === file2bib.sh === id: cord-335647-dhcxj7cj author: Vanderlinden, Evelien title: Emerging Antiviral Strategies to Interfere with Influenza Virus Entry date: 2013-06-25 pages: extension: .txt txt: ./txt/cord-335647-dhcxj7cj.txt cache: ./cache/cord-335647-dhcxj7cj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-335647-dhcxj7cj.txt' === file2bib.sh === id: cord-349225-504kr50e author: Alcami, Antonio title: Viral mechanisms of immune evasion date: 2000-09-01 pages: extension: .txt txt: ./txt/cord-349225-504kr50e.txt cache: ./cache/cord-349225-504kr50e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-349225-504kr50e.txt' === file2bib.sh === id: cord-344749-omzhhr0k author: Kaya, Sariye Irem title: Electrochemical virus detections with nanobiosensors date: 2020-02-14 pages: extension: .txt txt: ./txt/cord-344749-omzhhr0k.txt cache: ./cache/cord-344749-omzhhr0k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344749-omzhhr0k.txt' === file2bib.sh === id: cord-346906-1wmp43ti author: Lewandowski, Kuiama title: Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples date: 2019-12-23 pages: extension: .txt txt: ./txt/cord-346906-1wmp43ti.txt cache: ./cache/cord-346906-1wmp43ti.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346906-1wmp43ti.txt' === file2bib.sh === id: cord-345848-s84lxe6l author: Everitt, Aaron R. title: IFITM3 restricts the morbidity and mortality associated with influenza date: 2012-03-25 pages: extension: .txt txt: ./txt/cord-345848-s84lxe6l.txt cache: ./cache/cord-345848-s84lxe6l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345848-s84lxe6l.txt' === file2bib.sh === id: cord-341029-49360l2a author: Nasir, Arshan title: A phylogenomic data-driven exploration of viral origins and evolution date: 2015-09-25 pages: extension: .txt txt: ./txt/cord-341029-49360l2a.txt cache: ./cache/cord-341029-49360l2a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341029-49360l2a.txt' === file2bib.sh === id: cord-351197-xv6ymc4l author: Cibulski, Samuel title: A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-351197-xv6ymc4l.txt cache: ./cache/cord-351197-xv6ymc4l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351197-xv6ymc4l.txt' === file2bib.sh === id: cord-350467-18bvwxci author: Clark, K.J title: In vitro studies on the use of clay, clay minerals and charcoal to adsorb bovine rotavirus and bovine coronavirus date: 1998-10-01 pages: extension: .txt txt: ./txt/cord-350467-18bvwxci.txt cache: ./cache/cord-350467-18bvwxci.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350467-18bvwxci.txt' === file2bib.sh === id: cord-348161-757c51xw author: Petrosova, A. title: Development of a highly sensitive, field operable biosensor for serological studies of Ebola virus in central Africa date: 2007-03-26 pages: extension: .txt txt: ./txt/cord-348161-757c51xw.txt cache: ./cache/cord-348161-757c51xw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348161-757c51xw.txt' === file2bib.sh === id: cord-351170-belbcrcd author: Symonds, Erin M. title: Affordable Enteric Virus Detection Techniques Are Needed to Support Changing Paradigms in Water Quality Management date: 2014-10-16 pages: extension: .txt txt: ./txt/cord-351170-belbcrcd.txt cache: ./cache/cord-351170-belbcrcd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-351170-belbcrcd.txt' === file2bib.sh === id: cord-341324-f9g9gitn author: Rojas, José M. title: Viral pathogen-induced mechanisms to antagonize mammalian interferon (IFN) signaling pathway date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-341324-f9g9gitn.txt cache: ./cache/cord-341324-f9g9gitn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341324-f9g9gitn.txt' === file2bib.sh === id: cord-350235-yoy3hj3j author: Sansonetti, Philippe J title: COVID‐19, chronicle of an expected pandemic date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-350235-yoy3hj3j.txt cache: ./cache/cord-350235-yoy3hj3j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350235-yoy3hj3j.txt' === file2bib.sh === id: cord-347727-wka9q98s author: Vong, Sirenda title: Assessment of Ebola virus disease preparedness in the WHO South-East Asia Region date: 2016-12-01 pages: extension: .txt txt: ./txt/cord-347727-wka9q98s.txt cache: ./cache/cord-347727-wka9q98s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-347727-wka9q98s.txt' === file2bib.sh === id: cord-348427-worgd0xu author: Hatcher, Eneida L. title: Virus Variation Resource – improved response to emergent viral outbreaks date: 2017-01-04 pages: extension: .txt txt: ./txt/cord-348427-worgd0xu.txt cache: ./cache/cord-348427-worgd0xu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348427-worgd0xu.txt' === file2bib.sh === id: cord-339152-wfakzb6w author: Trovato, Maria title: Viral Emerging Diseases: Challenges in Developing Vaccination Strategies date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-339152-wfakzb6w.txt cache: ./cache/cord-339152-wfakzb6w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339152-wfakzb6w.txt' === file2bib.sh === id: cord-345689-5ns1onkw author: Kusters, Inca C. title: Manufacturing Vaccines for an Emerging Viral Infection–Specific Issues Associated with the Development of a Prototype SARS Vaccine date: 2009-01-30 pages: extension: .txt txt: ./txt/cord-345689-5ns1onkw.txt cache: ./cache/cord-345689-5ns1onkw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345689-5ns1onkw.txt' === file2bib.sh === id: cord-319933-yp9ofhi8 author: Ruiz, Sara I. title: Chapter 38 Animal Models of Human Viral Diseases date: 2013-12-31 pages: extension: .txt txt: ./txt/cord-319933-yp9ofhi8.txt cache: ./cache/cord-319933-yp9ofhi8.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-319933-yp9ofhi8.txt' === file2bib.sh === id: cord-351571-gwtkrt5u author: Mackay, Ian M. title: Community-Wide, Contemporaneous Circulation of a Broad Spectrum of Human Rhinoviruses in Healthy Australian Preschool-Aged Children During a 12-Month Period date: 2013-05-01 pages: extension: .txt txt: ./txt/cord-351571-gwtkrt5u.txt cache: ./cache/cord-351571-gwtkrt5u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-351571-gwtkrt5u.txt' === file2bib.sh === id: cord-330852-n7j0c4ne author: Fischer, Wolfgang B. title: Mechanism of Function of Viral Channel Proteins and Implications for Drug Development date: 2012-02-23 pages: extension: .txt txt: ./txt/cord-330852-n7j0c4ne.txt cache: ./cache/cord-330852-n7j0c4ne.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-330852-n7j0c4ne.txt' === file2bib.sh === id: cord-349249-jwvz1ux2 author: Singh, Gagandeep title: A Minimally Replicative Vaccine Protects Vaccinated Piglets Against Challenge With the Porcine Epidemic Diarrhea Virus date: 2019-10-22 pages: extension: .txt txt: ./txt/cord-349249-jwvz1ux2.txt cache: ./cache/cord-349249-jwvz1ux2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349249-jwvz1ux2.txt' === file2bib.sh === id: cord-348163-9q1rt8i7 author: Hussein, Hosni A. M. title: Beyond RGD: virus interactions with integrins date: 2015-09-01 pages: extension: .txt txt: ./txt/cord-348163-9q1rt8i7.txt cache: ./cache/cord-348163-9q1rt8i7.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-348163-9q1rt8i7.txt' === file2bib.sh === id: cord-350964-0jtfc271 author: Van Nguyen, Dung title: Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam date: 2018-02-28 pages: extension: .txt txt: ./txt/cord-350964-0jtfc271.txt cache: ./cache/cord-350964-0jtfc271.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350964-0jtfc271.txt' === file2bib.sh === id: cord-267671-ys43n672 author: Whary, Mark T. title: Biology and Diseases of Mice date: 2015-07-10 pages: extension: .txt txt: ./txt/cord-267671-ys43n672.txt cache: ./cache/cord-267671-ys43n672.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-267671-ys43n672.txt' === file2bib.sh === id: cord-344970-ud1lhkyi author: Fecchi, Katia title: Coronavirus Interplay With Lipid Rafts and Autophagy Unveils Promising Therapeutic Targets date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-344970-ud1lhkyi.txt cache: ./cache/cord-344970-ud1lhkyi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-344970-ud1lhkyi.txt' === file2bib.sh === id: cord-352054-g7q2z4l5 author: Kolivoška, Viliam title: Electrophoresis on a microfluidic chip for analysis of fluorescence‐labeled human rhinovirus date: 2007-11-15 pages: extension: .txt txt: ./txt/cord-352054-g7q2z4l5.txt cache: ./cache/cord-352054-g7q2z4l5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352054-g7q2z4l5.txt' === file2bib.sh === id: cord-353297-jizitnfl author: Meyer, R.F. title: Viruses and Bioterrorism date: 2008-07-30 pages: extension: .txt txt: ./txt/cord-353297-jizitnfl.txt cache: ./cache/cord-353297-jizitnfl.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-353297-jizitnfl.txt' === file2bib.sh === id: cord-354109-mli0c97c author: Faezi, Nasim Asadi title: Viral infections in patients with acute respiratory infection in Northwest of Iran date: 2017-01-22 pages: extension: .txt txt: ./txt/cord-354109-mli0c97c.txt cache: ./cache/cord-354109-mli0c97c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-354109-mli0c97c.txt' === file2bib.sh === id: cord-346836-6jyv0q5e author: Ikegami, Tetsuro title: The Pathogenesis of Rift Valley Fever date: 2011-05-06 pages: extension: .txt txt: ./txt/cord-346836-6jyv0q5e.txt cache: ./cache/cord-346836-6jyv0q5e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346836-6jyv0q5e.txt' === file2bib.sh === id: cord-348669-mizygp4j author: Beall, Anne title: Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A date: 2016-01-05 pages: extension: .txt txt: ./txt/cord-348669-mizygp4j.txt cache: ./cache/cord-348669-mizygp4j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348669-mizygp4j.txt' === file2bib.sh === id: cord-352619-s2x53grh author: Payne, Natalie title: Novel Circoviruses Detected in Feces of Sonoran Felids date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-352619-s2x53grh.txt cache: ./cache/cord-352619-s2x53grh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352619-s2x53grh.txt' === file2bib.sh === id: cord-347039-eap592i7 author: Lee, Seung-Hwan title: Maneuvering for advantage: the genetics of mouse susceptibility to virus infection date: 2003-08-31 pages: extension: .txt txt: ./txt/cord-347039-eap592i7.txt cache: ./cache/cord-347039-eap592i7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-347039-eap592i7.txt' === file2bib.sh === id: cord-343347-guciupc8 author: Hajj Hussein, Inaya title: Vaccines Through Centuries: Major Cornerstones of Global Health date: 2015-11-26 pages: extension: .txt txt: ./txt/cord-343347-guciupc8.txt cache: ./cache/cord-343347-guciupc8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343347-guciupc8.txt' === file2bib.sh === id: cord-350948-oog6m4h3 author: Leclercq, Loïc title: How to improve the chemical disinfection of contaminated surfaces by viruses, bacteria and fungus? date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-350948-oog6m4h3.txt cache: ./cache/cord-350948-oog6m4h3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350948-oog6m4h3.txt' === file2bib.sh === id: cord-354035-i3sl2r0k author: Wylie, Kristine M. title: The Virome of the Human Respiratory Tract date: 2016-12-10 pages: extension: .txt txt: ./txt/cord-354035-i3sl2r0k.txt cache: ./cache/cord-354035-i3sl2r0k.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-354035-i3sl2r0k.txt' === file2bib.sh === id: cord-351377-xorj8tnz author: Kao, Chi-Fei title: The Characterization of Immunoprotection Induced by a cDNA Clone Derived from the Attenuated Taiwan Porcine Epidemic Diarrhea Virus Pintung 52 Strain date: 2018-10-04 pages: extension: .txt txt: ./txt/cord-351377-xorj8tnz.txt cache: ./cache/cord-351377-xorj8tnz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351377-xorj8tnz.txt' === file2bib.sh === id: cord-336510-qzm9wgde author: Ellermann-Eriksen, Svend title: Macrophages and cytokines in the early defence against herpes simplex virus date: 2005-08-03 pages: extension: .txt txt: ./txt/cord-336510-qzm9wgde.txt cache: ./cache/cord-336510-qzm9wgde.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-336510-qzm9wgde.txt' === file2bib.sh === id: cord-355771-pxkkd3s1 author: Olagnier, David title: Oncolytic Viral Immunotherapy in the Time of COVID-19 date: 2020-11-04 pages: extension: .txt txt: ./txt/cord-355771-pxkkd3s1.txt cache: ./cache/cord-355771-pxkkd3s1.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-355771-pxkkd3s1.txt' === file2bib.sh === id: cord-356176-1nwjjgul author: Atherton, J. G. title: The effect of ascorbic acid on infection of chick-embryo ciliated tracheal organ cultures by coronavirus date: 1978 pages: extension: .txt txt: ./txt/cord-356176-1nwjjgul.txt cache: ./cache/cord-356176-1nwjjgul.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356176-1nwjjgul.txt' === file2bib.sh === id: cord-354536-c9v9kbw8 author: Han, Yan-Jie title: Advances and challenges in the prevention and treatment of COVID-19 date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-354536-c9v9kbw8.txt cache: ./cache/cord-354536-c9v9kbw8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-354536-c9v9kbw8.txt' === file2bib.sh === id: cord-351365-dc9t3vh3 author: Todt, Daniel title: Mutagenic Effects of Ribavirin on Hepatitis E Virus—Viral Extinction versus Selection of Fitness-Enhancing Mutations date: 2016-10-13 pages: extension: .txt txt: ./txt/cord-351365-dc9t3vh3.txt cache: ./cache/cord-351365-dc9t3vh3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-351365-dc9t3vh3.txt' === file2bib.sh === id: cord-349011-kxhpdvri author: Grandvaux, Nathalie title: CSV2018: The 2nd Symposium of the Canadian Society for Virology date: 2019-01-18 pages: extension: .txt txt: ./txt/cord-349011-kxhpdvri.txt cache: ./cache/cord-349011-kxhpdvri.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349011-kxhpdvri.txt' === file2bib.sh === id: cord-354151-psog34u3 author: van Asten, Liselotte title: Early occurrence of influenza A epidemics coincided with changes in occurrence of other respiratory virus infections date: 2015-12-11 pages: extension: .txt txt: ./txt/cord-354151-psog34u3.txt cache: ./cache/cord-354151-psog34u3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-354151-psog34u3.txt' === file2bib.sh === id: cord-355489-tkvfneje author: Mendez, Jairo A title: Phylogenetic history demonstrates two different lineages of dengue type 1 virus in Colombia date: 2010-09-14 pages: extension: .txt txt: ./txt/cord-355489-tkvfneje.txt cache: ./cache/cord-355489-tkvfneje.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355489-tkvfneje.txt' === file2bib.sh === id: cord-350151-s75d1hat author: Wiramus, S. title: Rianimazione e influenza grave: pandemia influenzale A (H1N1) date: 2013-04-30 pages: extension: .txt txt: ./txt/cord-350151-s75d1hat.txt cache: ./cache/cord-350151-s75d1hat.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350151-s75d1hat.txt' === file2bib.sh === id: cord-355535-01h8yyqj author: Zheng, Xue-yan title: Regional, age and respiratory-secretion-specific prevalence of respiratory viruses associated with asthma exacerbation: a literature review date: 2018-01-11 pages: extension: .txt txt: ./txt/cord-355535-01h8yyqj.txt cache: ./cache/cord-355535-01h8yyqj.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-355535-01h8yyqj.txt' === file2bib.sh === id: cord-352379-q5inrxcm author: Lai, Michael M. C. title: SARS virus: The beginning of the unraveling of a new coronavirus date: 2003-10-17 pages: extension: .txt txt: ./txt/cord-352379-q5inrxcm.txt cache: ./cache/cord-352379-q5inrxcm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352379-q5inrxcm.txt' === file2bib.sh === id: cord-352200-i05h8csb author: Xu, Yi title: Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus date: 2012-04-27 pages: extension: .txt txt: ./txt/cord-352200-i05h8csb.txt cache: ./cache/cord-352200-i05h8csb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352200-i05h8csb.txt' === file2bib.sh === id: cord-353869-l53ms3q8 author: Friesen, Robert H. E. title: New Class of Monoclonal Antibodies against Severe Influenza: Prophylactic and Therapeutic Efficacy in Ferrets date: 2010-02-08 pages: extension: .txt txt: ./txt/cord-353869-l53ms3q8.txt cache: ./cache/cord-353869-l53ms3q8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353869-l53ms3q8.txt' === file2bib.sh === id: cord-350925-1h6pbfwp author: da Silva, Priscilla Gomes title: Airborne spread of infectious SARS-CoV-2: moving forward using lessons from SARS-CoV and MERS-CoV date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-350925-1h6pbfwp.txt cache: ./cache/cord-350925-1h6pbfwp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350925-1h6pbfwp.txt' === file2bib.sh === id: cord-353509-yfkiaq80 author: Nugraha, Rhea Veda title: Traditional Herbal Medicine Candidates as Complementary Treatments for COVID-19: A Review of Their Mechanisms, Pros and Cons date: 2020-10-10 pages: extension: .txt txt: ./txt/cord-353509-yfkiaq80.txt cache: ./cache/cord-353509-yfkiaq80.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353509-yfkiaq80.txt' === file2bib.sh === id: cord-351482-hzh5tyoo author: Peng, Xinxia title: Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection date: 2011-11-15 pages: extension: .txt txt: ./txt/cord-351482-hzh5tyoo.txt cache: ./cache/cord-351482-hzh5tyoo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351482-hzh5tyoo.txt' === file2bib.sh === id: cord-355872-z6vsjmxn author: Colón-López, Daisy D. title: Emerging viral infections date: 2019-08-15 pages: extension: .txt txt: ./txt/cord-355872-z6vsjmxn.txt cache: ./cache/cord-355872-z6vsjmxn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355872-z6vsjmxn.txt' === file2bib.sh === id: cord-354848-7aakik9a author: Sayres, Lauren title: Contemporary Understanding of Ebola and Zika Virus in Pregnancy date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-354848-7aakik9a.txt cache: ./cache/cord-354848-7aakik9a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354848-7aakik9a.txt' === file2bib.sh === id: cord-344093-3bniy5b5 author: Peteranderl, Christin title: The Impact of the Interferon/TNF-Related Apoptosis-Inducing Ligand Signaling Axis on Disease Progression in Respiratory Viral Infection and Beyond date: 2017-03-22 pages: extension: .txt txt: ./txt/cord-344093-3bniy5b5.txt cache: ./cache/cord-344093-3bniy5b5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-344093-3bniy5b5.txt' === file2bib.sh === id: cord-345654-vyz6f3he author: Dennehy, John J. title: Evolutionary ecology of virus emergence date: 2016-12-30 pages: extension: .txt txt: ./txt/cord-345654-vyz6f3he.txt cache: ./cache/cord-345654-vyz6f3he.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345654-vyz6f3he.txt' === file2bib.sh === id: cord-352178-irjhmxsg author: Saxton-Shaw, Kali D. title: O'nyong nyong Virus Molecular Determinants of Unique Vector Specificity Reside in Non-Structural Protein 3 date: 2013-01-24 pages: extension: .txt txt: ./txt/cord-352178-irjhmxsg.txt cache: ./cache/cord-352178-irjhmxsg.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-352178-irjhmxsg.txt' === file2bib.sh === id: cord-353290-1wi1dhv6 author: Kustin, Talia title: Biased mutation and selection in RNA viruses date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-353290-1wi1dhv6.txt cache: ./cache/cord-353290-1wi1dhv6.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-353290-1wi1dhv6.txt' === file2bib.sh === id: cord-355181-affuyn8z author: Poggio, Claudio title: Copper-Alloy Surfaces and Cleaning Regimens against the Spread of SARS-CoV-2 in Dentistry and Orthopedics. From Fomites to Anti-Infective Nanocoatings date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-355181-affuyn8z.txt cache: ./cache/cord-355181-affuyn8z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355181-affuyn8z.txt' === file2bib.sh === id: cord-353609-no3mbg5d author: Vandegrift, Kurt J. title: An Ecological and Conservation Perspective on Advances in the Applied Virology of Zoonoses date: 2011-04-15 pages: extension: .txt txt: ./txt/cord-353609-no3mbg5d.txt cache: ./cache/cord-353609-no3mbg5d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353609-no3mbg5d.txt' === file2bib.sh === id: cord-355259-779czzzx author: Yang, Xiaoyun title: A Beneficiary Role for Neuraminidase in Influenza Virus Penetration through the Respiratory Mucus date: 2014-10-15 pages: extension: .txt txt: ./txt/cord-355259-779czzzx.txt cache: ./cache/cord-355259-779czzzx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355259-779czzzx.txt' === file2bib.sh === id: cord-355685-wgad0eoh author: Francesconi, Valeria title: Synthesis and Biological Evaluation of Novel (thio)semicarbazone-Based Benzimidazoles as Antiviral Agents against Human Respiratory Viruses date: 2020-03-25 pages: extension: .txt txt: ./txt/cord-355685-wgad0eoh.txt cache: ./cache/cord-355685-wgad0eoh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355685-wgad0eoh.txt' === file2bib.sh === id: cord-352475-cmmpy5u7 author: Pemmada, Rakesh title: Science-Based Strategies of Antiviral Coatings with Viricidal Properties for the COVID-19 Like Pandemics date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-352475-cmmpy5u7.txt cache: ./cache/cord-352475-cmmpy5u7.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-352475-cmmpy5u7.txt' === file2bib.sh === id: cord-350747-5t5xthk6 author: Gmyl, A. P. title: Diverse Mechanisms of RNA Recombination date: 2005 pages: extension: .txt txt: ./txt/cord-350747-5t5xthk6.txt cache: ./cache/cord-350747-5t5xthk6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350747-5t5xthk6.txt' === file2bib.sh === id: cord-346916-jj4l9ydl author: Girardi, Erika title: Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell date: 2020-08-23 pages: extension: .txt txt: ./txt/cord-346916-jj4l9ydl.txt cache: ./cache/cord-346916-jj4l9ydl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346916-jj4l9ydl.txt' === file2bib.sh === id: cord-350703-vrqltz3s author: nan title: ISAR News date: 2016-01-31 pages: extension: .txt txt: ./txt/cord-350703-vrqltz3s.txt cache: ./cache/cord-350703-vrqltz3s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350703-vrqltz3s.txt' === file2bib.sh === id: cord-343963-99rd3o79 author: Wong, Mun-Teng title: Emerging roles of interferon-stimulated genes in the innate immune response to hepatitis C virus infection date: 2014-12-29 pages: extension: .txt txt: ./txt/cord-343963-99rd3o79.txt cache: ./cache/cord-343963-99rd3o79.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-343963-99rd3o79.txt' === file2bib.sh === id: cord-349358-leicos9j author: Ketzinel‐Gilad, Mali title: RNA interference for antiviral therapy date: 2006-06-16 pages: extension: .txt txt: ./txt/cord-349358-leicos9j.txt cache: ./cache/cord-349358-leicos9j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-349358-leicos9j.txt' === file2bib.sh === id: cord-355906-yeaw9nr8 author: Nedjadi, Taoufik title: Tackling dengue fever: Current status and challenges date: 2015-12-09 pages: extension: .txt txt: ./txt/cord-355906-yeaw9nr8.txt cache: ./cache/cord-355906-yeaw9nr8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355906-yeaw9nr8.txt' === file2bib.sh === id: cord-355913-fhvt1ht1 author: Burrell, Christopher J. title: Virus Replication date: 2016-11-11 pages: extension: .txt txt: ./txt/cord-355913-fhvt1ht1.txt cache: ./cache/cord-355913-fhvt1ht1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355913-fhvt1ht1.txt' === file2bib.sh === id: cord-356188-rwf78stz author: Oshansky, Christine M. title: The human side of influenza date: 2012-07-01 pages: extension: .txt txt: ./txt/cord-356188-rwf78stz.txt cache: ./cache/cord-356188-rwf78stz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356188-rwf78stz.txt' === file2bib.sh === id: cord-354582-fniymnmf author: Ma, Zhiqian title: Reverse genetic systems: Rational design of coronavirus live attenuated vaccines with immune sequelae date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-354582-fniymnmf.txt cache: ./cache/cord-354582-fniymnmf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-354582-fniymnmf.txt' === file2bib.sh === id: cord-354068-4qlk6y7h author: Friedrich, Brian M. title: Potential Vaccines and Post-Exposure Treatments for Filovirus Infections date: 2012-09-21 pages: extension: .txt txt: ./txt/cord-354068-4qlk6y7h.txt cache: ./cache/cord-354068-4qlk6y7h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354068-4qlk6y7h.txt' === file2bib.sh === id: cord-021555-rrverrsj author: Delano, Margaret L. title: Biology and Diseases of Ruminants: Sheep, Goats, and Cattle date: 2007-09-02 pages: extension: .txt txt: ./txt/cord-021555-rrverrsj.txt cache: ./cache/cord-021555-rrverrsj.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-021555-rrverrsj.txt' === file2bib.sh === id: cord-340489-yo3cp5vs author: nan title: KAPITEL 13 Infektionskrankheiten date: 2008-12-31 pages: extension: .txt txt: ./txt/cord-340489-yo3cp5vs.txt cache: ./cache/cord-340489-yo3cp5vs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-340489-yo3cp5vs.txt' === file2bib.sh === id: cord-353190-7qcoxl81 author: Nicklas, Werner title: Viral Infections of Laboratory Mice date: 2012-05-17 pages: extension: .txt txt: ./txt/cord-353190-7qcoxl81.txt cache: ./cache/cord-353190-7qcoxl81.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-353190-7qcoxl81.txt' === file2bib.sh === id: cord-347710-ff64y6ef author: Wan, Qianya title: Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-347710-ff64y6ef.txt cache: ./cache/cord-347710-ff64y6ef.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-347710-ff64y6ef.txt' === file2bib.sh === id: cord-331714-2qj2rrgd author: Lvov, Dimitry Konstantinovich title: Single-Stranded RNA Viruses date: 2015-05-29 pages: extension: .txt txt: ./txt/cord-331714-2qj2rrgd.txt cache: ./cache/cord-331714-2qj2rrgd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-331714-2qj2rrgd.txt' === file2bib.sh === id: cord-001521-l36f1gp7 author: nan title: Oral and Poster Manuscripts date: 2011-04-08 pages: extension: .txt txt: ./txt/cord-001521-l36f1gp7.txt cache: ./cache/cord-001521-l36f1gp7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 19 resourceName b'cord-001521-l36f1gp7.txt' Que is empty; done keyword-virus-cord === reduce.pl bib === id = cord-001065-j4hvyyoi author = Boncristiani, Humberto F. title = In Vitro Infection of Pupae with Israeli Acute Paralysis Virus Suggests Disturbance of Transcriptional Homeostasis in Honey Bees (Apis mellifera) date = 2013-09-05 pages = extension = .txt mime = text/plain words = 6367 sentences = 326 flesch = 47 summary = title: In Vitro Infection of Pupae with Israeli Acute Paralysis Virus Suggests Disturbance of Transcriptional Homeostasis in Honey Bees (Apis mellifera) An experimental protocol to test these systems was developed, using injections of Israeli Acute Paralysis Virus (IAPV) into honey bee pupae reared ex-situ under laboratory conditions. Gene expression analyses of three separate experiments suggest IAPV disruption of transcriptional homeostasis of several fundamental cellular functions, including an up-regulation of the ribosomal biogenesis pathway. Little is known about the specific biology of the viruses in these families that infect honey bees, although they contain important bee pathogens, such as Deformed Wing Virus (DWV) and Israeli Acute Paralysis Virus (IAPV). Post-hoc tests of main treatment effects showed significantly higher gene expression in the IAPV-inoculated bees compared to the two control groups for Actin, 28S rRNA, and mGST1. The observed gene expression patterns could be due to viral manipulation of the cells to increase virus replication or present cell compensatory responses to IAPV infection. cache = ./cache/cord-001065-j4hvyyoi.txt txt = ./txt/cord-001065-j4hvyyoi.txt === reduce.pl bib === id = cord-000180-howix091 author = MacLeod, Iain J. title = Binding of Herpes Simplex Virus Type-1 Virions Leads to the Induction of Intracellular Signalling in the Absence of Virus Entry date = 2010-03-05 pages = extension = .txt mime = text/plain words = 6788 sentences = 316 flesch = 49 summary = By taking advantage of the entry-defective phenotype of glycoprotein-deficient HSV-1 virus particles, the results presented here show that binding of virions to cellular receptors on the plasma membrane is sufficient to stimulate a change in cellular gene expression. As induction of the NF-kB reporter construct occurred within one hour of inoculation with DgH virions and peaked at around two-and-a-half hours post-inoculation, then the transcripts previHFFs were stimulated with 1000 particles/cell of DgB, DgD or DgH HSV-1 for six hours and a cDNA microarray corresponding to targets of 19 signalling pathways was used to detect changes in cellular gene expression when compared to mock-infected. Real-time PCR confirmed that changes in transcription associated with the NF-kB, JAK/STAT, JAK/Src and PI3K pathways were modulated as a result of virion binding, all of which required gD on the envelope surface To demonstrate that signalling occurred at physiologically relevant multiplicities of infection, HFFs were inoculated with either 1000, 100, 10 or 1 particles per cell of entry-defective HSV-1. cache = ./cache/cord-000180-howix091.txt txt = ./txt/cord-000180-howix091.txt === reduce.pl bib === id = cord-000708-iuo2cw23 author = Lippé, Roger title = Deciphering Novel Host–Herpesvirus Interactions by Virion Proteomics date = 2012-05-28 pages = extension = .txt mime = text/plain words = 5052 sentences = 261 flesch = 43 summary = These studies include the alphaherpesvirinae herpes simplex virus type 1 (HSV-1) and pseudorabies virus (PRV; Loret et al., 2008; Kramer et al., 2011) , the betaherpesvirinae human and murine cytomegaloviruses (HCMV and MCMV, respectively; Kattenhorn et al., 2004; Varnum et al., 2004) and the gammaherpesvirinae Kaposi sarcoma herpesvirus (KSHV), gamma herpesvirus 68 (γHV68), Epstein-Barr virus (EBV), and Alcelaphine (Bortz et al., 2003; Johannsen et al., 2004; Bechtel et al., 2005; Zhu et al., 2005; Dry et al., 2008) . Cellular stress rather than stage of the cell cycle enhances the replication and plating efficiencies of herpes simplex virus type 1 ICP0-viruses Perturbation of cell cycle progression and cellular gene expression as a function of herpes simplex virus ICP0 Herpes simplex virus 1 alpha regulatory protein ICP0 interacts with and stabilizes the cell cycle regulator cyclin D3 Identification and functional evaluation of cellular and viral factors involved in the alteration of nuclear architecture during herpes simplex virus 1 infection cache = ./cache/cord-000708-iuo2cw23.txt txt = ./txt/cord-000708-iuo2cw23.txt === reduce.pl bib === id = cord-003232-nquw7qga author = Kuchipudi, Suresh V. title = Novel Flu Viruses in Bats and Cattle: “Pushing the Envelope” of Influenza Infection date = 2018-08-06 pages = extension = .txt mime = text/plain words = 3837 sentences = 214 flesch = 45 summary = This review examines the recent discovery of novel influenza viruses in bats and cattle, the evolving complexity of influenza virus host range including the ability to cross species barriers and geographic boundaries, and implications to animal and human health. In addition, we discussed the growing complexity of influenza virus-host interactions and highlighted the key research questions that need to be answered for a better understanding of the emergence of pandemic influenza viruses. Ability to infect a wide range hosts is a key contributing factor to the complex and seemingly expanding genetic diversity of IAVs. It is now well established that IAVs infect domestic pets such as dogs and cats, adding to the list of host species that could potentially expose humans to influenza viruses. Although influenza viruses infect humans and a wide range of animals and birds, cattle were never considered to be susceptible to influenza virus infection. cache = ./cache/cord-003232-nquw7qga.txt txt = ./txt/cord-003232-nquw7qga.txt === reduce.pl bib === id = cord-002274-6rddtogo author = James, Joe title = Influenza A virus PB1-F2 protein prolongs viral shedding in chickens lengthening the transmission window date = 2016-10-13 pages = extension = .txt mime = text/plain words = 6599 sentences = 311 flesch = 52 summary = Here we report that the presence of a full-length PB1-F2 protein, from a low pathogenicity H9N2 avian influenza virus, prolongs infectious virus shedding from directly inoculated chickens, thereby enhancing transmission of the virus by lengthening the transmission window to contact birds. Spillover of these viruses into domesticated poultry populations has resulted in the evolution of highly pathogenic avian influenza (HPAI) subtypes such as the Asian-lineage H5N1 which has been circulating continuously in birds since 2003 and has caused upwards of 700 human infections . To ascertain if the presence of a full-length PB1-F2 protein effected in vivo virus replication in chickens, we determined the level of infectious virus shed from both the buccal and cloacal cavities of birds inoculated with both high and low doses for 10 days following infection. We assessed viral infectivity, pathogenicity and transmissibility between chickens of isogenic viruses differing only by the presence of a full-length PB1-F2 protein. cache = ./cache/cord-002274-6rddtogo.txt txt = ./txt/cord-002274-6rddtogo.txt === reduce.pl bib === id = cord-001542-f089bs8r author = Lai, Kang Yiu title = Human Ebola virus infection in West Africa: a review of available therapeutic agents that target different steps of the life cycle of Ebola virus date = 2014-11-28 pages = extension = .txt mime = text/plain words = 11274 sentences = 604 flesch = 42 summary = These may include monoclonal antibody (mAbs)-based therapies (e.g. ZMapp), anti-sense phosphorodiamidate morpholino oligomers (PMO AVI-6002), lipid nanoparticle small interfering RNA (LNP-siRNA: TKM-Ebola), and an EBOV glycoprotein-based vaccine using live-attenuated recombinant vesicular stomatitis virus (rVSV-EBOGP) or a chimpanzee adenovirus (rChAd-EBOGP)-based vector. The GP2 of the EBOV is able to counter the interferon (IFN)-inducible antiviral protein tetherin which restricts the VP40-dependent budding of the progeny viral particles from infected cells [16] [17] [18] . Currently available therapeutic agents that are effective in targeting the EBOV infection in cell or animal studies may include convalescent plasma, favipiravir, chloroquine, amiodarone, dronedarone, verapamil, clomiphene, toremifene, IFN-β, Na + /K + exchangers, Na + /K + -ATPase pump inhibitors, and antioxidants. The anti-EBOV activity of clomiphene and toremifene is dependent not on its estrogen receptor antagonistic action but upon the ability of both drugs to induce a Niemann-Pick C-like phenotype to inhibit viral entry at late endosome. cache = ./cache/cord-001542-f089bs8r.txt txt = ./txt/cord-001542-f089bs8r.txt === reduce.pl bib === id = cord-002601-d8908t93 author = Arellano-Llamas, Rocío title = Molecular features of influenza A (H1N1)pdm09 prevalent in Mexico during winter seasons 2012-2014 date = 2017-07-10 pages = extension = .txt mime = text/plain words = 3376 sentences = 177 flesch = 51 summary = Substitutions that have been previously reported are involved in host specificity shift, viral oligomerization interfaces (VOI), binding small ligands (BSL), Ab's recognition, binding host proteins (BHP), binding nucleic acids (BNA) and antigenic drift. In this study we sequenced the entire genome of pandemic A/H1N1 strains isolated from patients in a reference Hospital in Mexico City (INER) in different years and we compared these sequences with consensus sequences in order to detect mutations that might be associated with viral evolution or might influence the antigenicity of the virus. This might also be a reflection of differences in selective pressure once the virus is in the infected host; regarding the rest of the viral genome segments, all the Mexican isolates from season 2013-2014 clustered with sequences from New York and Helsinki. In HA we observe changes that could affect immunogenicity of the influenza virus; sequences from 2015 to 2016 had additional mutations (S162N) in antigenic site (Sa) and together with the substitution I276T are defining a new clade 6B.1 [21, 22] . cache = ./cache/cord-002601-d8908t93.txt txt = ./txt/cord-002601-d8908t93.txt === reduce.pl bib === id = cord-001834-6xf4o3oy author = Sung, Pil Soo title = Interferon Response in Hepatitis C Virus (HCV) Infection: Lessons from Cell Culture Systems of HCV Infection date = 2015-10-07 pages = extension = .txt mime = text/plain words = 4039 sentences = 230 flesch = 44 summary = In HCV-infected cells, viral RNA is sensed by retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated protein 5 (MDA-5) in the cytoplasm and Toll-like receptor 3 (TLR3) in the endosome, which leads to downstream signaling that results in the induction of type III and I IFNs and other inflammatory cytokines [28, [36] [37] [38] [39] . Intracellular signals from RIG-I, MDA-5, and TLR3 are transmitted via mitochondrial antiviral signaling protein (MAVS) and Toll/IL-1 receptor domain-containing adaptor inducing IFN- (TRIF), respectively, which leads to the interferon regulatory factor-3 (IRF-3)-dependent induction of IFNs and NF-κB activation in HCV-infected cells [38, 39] . IFN-s activate the same JAK-STAT pathway as type I IFNs [48] [49] [50] , thereby inducing a similar set of ISGs. Although the exact source of IFN-s in HCV-infected liver remains to be clarified, it seems that the production of IFN-s by HCV-infected hepatocytes results in the expression of ISGs, presumably through autocrine and/or paracrine signaling via the IFN-λ receptor [28, [44] [45] [46] . HCV infection induces a unique hepatic innate immune response associated with robust production of type III interferons cache = ./cache/cord-001834-6xf4o3oy.txt txt = ./txt/cord-001834-6xf4o3oy.txt === reduce.pl bib === id = cord-003092-3owcqt3d author = Iketani, Sho title = Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation date = 2018-07-03 pages = extension = .txt mime = text/plain words = 8948 sentences = 392 flesch = 46 summary = These results utilize a method for identifying genome-wide changes associated with brief adaptation to culture to highlight the notion that even brief exposure to immortalized cells may affect key viral properties and underscore the balance of features of the HN-F complex required for fitness by circulating viruses. Deep genomic sequencing of nine sets of paired clinical samples (primary nasal swabs in viral transport medium) and culture isolates (culture harvest from zero passage virus) led to discovery of a number of HN mutations associated with rapid evolution in culture. To assess the frequency of mutations identified earlier, we also performed deep sequencing of 118 HPIV-3 clinical samples and culture isolates from the University of Washington Virology Laboratory, allowing us to confirm that the alterations associated with brief exposure to culture for viral isolation were almost entirely found in the sequences of culture isolates and found commonly within populations of viruses in those isolates. cache = ./cache/cord-003092-3owcqt3d.txt txt = ./txt/cord-003092-3owcqt3d.txt === reduce.pl bib === id = cord-003122-a3f4l6iu author = Dou, Dan title = Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement date = 2018-07-20 pages = extension = .txt mime = text/plain words = 10272 sentences = 565 flesch = 43 summary = The segmentation of the influenza genome makes these additional trafficking requirements especially challenging, as each viral RNA (vRNA) gene segment must navigate the network of cellular membrane barriers during the processes of entry and assembly. To accomplish this goal, influenza A viruses (IAVs) utilize a combination of viral and cellular mechanisms to coordinate the transport of their proteins and the eight vRNA gene segments in and out of the cell. Influenza A viruses (IAVs) and type B viruses (IBVs) contain 8, negative-sense, single-stranded viral RNA (vRNA) gene segments ( Figure 1A ) (3, 4) , which encode transcripts for 10 essential viral proteins, as well as several strain-dependent accessory proteins ( Figure 1B) . In contrast to the early steps in IAV entry, vRNP trafficking to the nucleus following the fusion event is highly dependent on the host cell machinery and transport pathways [reviewed in Ref. cache = ./cache/cord-003122-a3f4l6iu.txt txt = ./txt/cord-003122-a3f4l6iu.txt === reduce.pl bib === id = cord-002423-1u44tdrj author = Geoghegan, Jemma L. title = Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families date = 2017-02-08 pages = extension = .txt mime = text/plain words = 6186 sentences = 267 flesch = 44 summary = While this method does not explicitly model host-switching events, it does provide a simple means to compare multiple topologies of virus-host pairs, and accounts for differences in sample size and the fact that several viruses from a specific family can infect a single host species. Across the data set as a whole we found that all virus families displayed relatively large tree topological distances with nPH85 values of !0.6, suggesting that cross-species transmission is widespread, at least at the family-level (Fig 2; S3 Table) . As with the analysis of topological distances, this revealed that cross-species transmission was the most common evolutionary event in all virus families studied here, with co-divergence consistently less frequent (with the possible exception of the Hepadnaviridae-see below), and lineage duplication and extinction playing a much more minor role. To investigate the comparative prevalence of cross-species transmission among viruses we measured the congruence between virus and host phylogenetic trees using a normalized tree topological distance-based approach (nPH85, [14] ). cache = ./cache/cord-002423-1u44tdrj.txt txt = ./txt/cord-002423-1u44tdrj.txt === reduce.pl bib === id = cord-003004-iif2lnez author = Linster, Martin title = Clinical and Molecular Epidemiology of Human Parainfluenza Viruses 1–4 in Children from Viet Nam date = 2018-05-01 pages = extension = .txt mime = text/plain words = 4121 sentences = 223 flesch = 49 summary = The present study describes species-specific clinical presentation, the genetic variability and HPIV circulation in Viet Nam. The outcome of RSV infection in hospitalized children under 2 years of age presenting with acute lower respiratory infection (ALRI) in Ho Chi Minh City was described previously 17 . Samples were sourced from two previous acute respiratory infection (ARI) cohorts among in-and outpatients, that were conducted at Children's Hospital 1 and 2 in Ho Chi Minh City, Viet Nam during years 2009 and 2010. For sequencing, HPIV-positive samples were further amplified in a hemi-nested PCR approach with newly designed species-specific primers targeting overlapping regions of the viral genome (Table S2) . In this study, the median age and gender distribution of infected children and frequency of clinical presentation (fever, cough, sore throat, runny nose and nasal congestion) as well as vital signs (pulse and respiratory rate) and duration of illness at presentation were similar between HPIV species (p > 0.05). cache = ./cache/cord-003004-iif2lnez.txt txt = ./txt/cord-003004-iif2lnez.txt === reduce.pl bib === id = cord-002932-5e7xrd1y author = Watanabe, Tokiko title = Experimental infection of Cynomolgus Macaques with highly pathogenic H5N1 influenza virus through the aerosol route date = 2018-03-19 pages = extension = .txt mime = text/plain words = 4497 sentences = 212 flesch = 44 summary = In the ferret model, these studies demonstrated that the inoculation of animals with highly pathogenic avian influenza H5N1 virus via the aerosol route led to higher nasal wash virus titers, earlier onset of clinical signs, and/or a broader spectrum of disease compared with infection via intranasal inoculation despite no difference in lethality [9] [10] [11] . On day 3 post-infection, VN3040 virus was recovered from nasal swabs of two and three animals in the conventional and aerosol method groups, respectively, and the mean virus titers were comparable between the two groups. Cynomolgus macaques were inoculated with 4 ml of a 10 7 PFU/ml solution of the highly pathogenic H5N1 avian influenza virus A/Vietnam/ UT3040/2004 strain (VN3040) through the aerosol route by using the ultrasonic nebulizer NE-U17 (defined as "the aerosol method group"). In contrast, VN3040 replicated well in the right-and left-lower lung lobes of the infected animals in the conventional method group [the virus mean titers were 3.51 and 4.75 log 10 (PFU/g), respectively]. cache = ./cache/cord-002932-5e7xrd1y.txt txt = ./txt/cord-002932-5e7xrd1y.txt === reduce.pl bib === id = cord-000265-llilwq1u author = Gao, Rongbao title = A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case date = 2010-10-12 pages = extension = .txt mime = text/plain words = 4896 sentences = 253 flesch = 46 summary = Autopsy studies have shown that human highly pathogenic avian influenza virus (H5N1) can infect multiple human organs other than just the lungs, and that possible causes of organ damage are either viral replication and/or dysregulation of cytokines and chemokines. Although H5N1 virus infection of humans is primarily one of the lower respiratory tract, more recent reports suggested that influenza A H5N1 may in rare, severe cases, disseminate beyond the lungs and infect brain [26, 27] , intestines [20, 27] and lymphoid tissues [27] , and result in extra-pulmonary clinical manifestations including encephalopathy or encephalitis [15, 28] . To better understand the pathogenesis of human H5N1 virus infection, and investigate the route of virus dissemination in vivo, we report on the use of different techniques to detect virus distribution and infection of 5 organ systems in a laboratory confirmed fatal human H5N1 virus infection, and analyze the relationship between viral load in tissues and host response. cache = ./cache/cord-000265-llilwq1u.txt txt = ./txt/cord-000265-llilwq1u.txt === reduce.pl bib === id = cord-002937-7xauocti author = Huang, Chung-Guei title = A pilot study on primary cultures of human respiratory tract epithelial cells to predict patients’ responses to H7N9 infection date = 2018-02-20 pages = extension = .txt mime = text/plain words = 6238 sentences = 293 flesch = 46 summary = We aimed to investigate whether primary cultures of human respiratory tract epithelial cells are helpful to understand H7N9 virus pathogenesis and tissue tropism, and to evaluate how patient-related characteristics can affect the host's response to infection. In this scenario, primary cultures of human respiratory tract epithelial cells would be invaluable to understand H7N9 virus tissue tropism and pathogenesis, as well as to evaluate how patient-related characteristics can modulate the host's response to infection. With regard to virus tropism, viral RNA quantities were significantly higher in epithelial cells obtained from the upper anatomical locations than from the lower anatomical locations, without adjustment (P = 0.030); however, the difference lost significance after adjustment for age, sex, medical comorbidities, and obesity (P = 0.490; Figure 2B ). cache = ./cache/cord-002937-7xauocti.txt txt = ./txt/cord-002937-7xauocti.txt === reduce.pl bib === id = cord-000012-p56v8wi1 author = Bigot, Yves title = Molecular evidence for the evolution of ichnoviruses from ascoviruses by symbiogenesis date = 2008-09-18 pages = extension = .txt mime = text/plain words = 6419 sentences = 293 flesch = 44 summary = CONCLUSION: Our results provide molecular evidence supporting the origin of ichnoviruses from ascoviruses by lateral transfer of ascoviral genes into ichneumonid wasp genomes, perhaps the first example of symbiogenesis between large DNA viruses and eukaryotic organisms. With respect to both species number and mechanisms that lead to successful parasitism, endoparasitic wasps are known to inject secretions at oviposition, but only a few lineages use viruses or virus-like particles (VLPs) to evade or to suppress host defences. Extending our investigations to proteins encoded by open reading frames of certain ascoviruses and bracoviruses, hosts and bacteria, in the light of recent analyses about the involvement of the replication machinery of virus groups related to ascoviruses in lateral gene transfer [29] , we discuss the robustness and the limits of the molecular evidence supporting an ascovirus origin for ichnovirus lineages. cache = ./cache/cord-000012-p56v8wi1.txt txt = ./txt/cord-000012-p56v8wi1.txt === reduce.pl bib === id = cord-000902-ew8orn0z author = Zhao, Xiangyan title = Coevolution between simple sequence repeats (SSRs) and virus genome size date = 2012-08-30 pages = extension = .txt mime = text/plain words = 5822 sentences = 302 flesch = 53 summary = The results showed that simple sequence repeats (SSRs) is strongly, positively and significantly correlated with genome size. While, relative abundance and relative density were examined to make the SSRs comparison parallel among differently sized species genomes; principal component analysis (PCA) was designed to investigate which repeat class(es) made a greater contribution to the variance among virus species as well as the relationships between repeat classes. Therefore, the 257 genome sequences were selected as samples for the analysis of relationship between SSRs distribution and genome size in the level of the whole virus. We surveyed the distribution of different SSR classes in virus genomes to investigate the relationship between repeat classes (mono-, di-, tri-, tetra-, penta-and hexa-) and genome sequence length. Coevolution between simple sequence repeats (SSRs) and virus genome size cache = ./cache/cord-000902-ew8orn0z.txt txt = ./txt/cord-000902-ew8orn0z.txt === reduce.pl bib === id = cord-000114-f0vud3gu author = Kim, Jeong‐Ki title = Ducks: The “Trojan Horses” of H5N1 influenza date = 2009-05-31 pages = extension = .txt mime = text/plain words = 5413 sentences = 313 flesch = 51 summary = While the H5N1 HPAI viruses are 100% lethal to chickens and gallinaceous poultry, they often cause asymptomatic infection in some species of domestic and wild ducks. 37 The first indication of the spread of H5N1 HPAI viruses from domestic to wild species of aquatic birds occurred in Kowloon and Penfold Park in Hong Kong, 38 where 19 different duck species were infected. If these wild birds are migratory and experience limited morbidity, they in turn can disperse HPAI viruses widely (Figure 2) , as suggested by the high genetic similarity of HPAI isolates from Africa, Europe, and the Middle East to the Qinghai-H5N1 virus. There is consensus that the migratory waterfowl of the world (predominantly wild ducks) serve as the natural reservoirs of all influenza A viruses, which cause asymptomatic infection in these birds. 51 The continuing co-circulation of multiple subtypes of LPAI viruses in domestic poultry could explain why a small percentage of susceptible domestic species can appear healthy while shedding transmissible levels of H5N1 HPAI virus. cache = ./cache/cord-000114-f0vud3gu.txt txt = ./txt/cord-000114-f0vud3gu.txt === reduce.pl bib === id = cord-002581-r7mskri0 author = Magnani, Diogo M. title = A human inferred germline antibody binds to an immunodominant epitope and neutralizes Zika virus date = 2017-06-12 pages = extension = .txt mime = text/plain words = 5291 sentences = 313 flesch = 55 summary = title: A human inferred germline antibody binds to an immunodominant epitope and neutralizes Zika virus The isolation of neutralizing monoclonal antibodies (nmAbs) against the Zika virus (ZIKV) might lead to novel preventative strategies for infections in at-risk individuals, primarily pregnant women. Here we describe the isolation of 18 plasmablast-derived human mAbs, sorted 12 days post onset of symptoms from a ZIKV-patient in São Paulo, Brazil. Interestingly, one of these mAbs (P1F12) exhibited no nucleotide mutations when compared to its corresponding germline sequences, but still recognized a ZIKV immunodominant epitope and neutralized the virus. Virus capture assay and recombinant E protein ELISA P1F12 binding was determined by both virus capture assay (VCA) and recombinant (r)E ELISAs. The VCA plates were coated overnight with the mouse-anti-Flavivirus monoclonal antibody 4G2 (clone D1-4G2-4-15, EMD Millipore) followed by incubation with viral stocks (ZIKV or DENV). Molecular determinants of human neutralizing antibodies isolated from a patient infected with Zika virus cache = ./cache/cord-002581-r7mskri0.txt txt = ./txt/cord-002581-r7mskri0.txt === reduce.pl bib === id = cord-000539-uh3q65we author = Zhang, Yi title = Acute Respiratory Distress Syndrome Induced by a Swine 2009 H1N1 Variant in Mice date = 2012-01-03 pages = extension = .txt mime = text/plain words = 4620 sentences = 247 flesch = 51 summary = BACKGROUND: Acute respiratory distress syndrome (ARDS) induced by pandemic 2009 H1N1 influenza virus has been widely reported and was considered the main cause of death in critically ill patients with 2009 H1N1 infection. Mice infected with SD/09 virus showed typical ARDS symptoms characterized by 60% lethality on days 8–10 post-inoculation, highly edematous lungs, inflammatory cellular infiltration, alveolar and interstitial edema, lung hemorrhage, progressive and severe hypoxemia, and elevated levels of proinflammatory cytokines and chemokines. In the present mouse model, the number of leukocytes observed in the BALF of virus-infected mice significantly increased compared with the control mice on day 8 p.i. Different counts in BALF showed that the proportion of neutrophils dramatically increased. cache = ./cache/cord-000539-uh3q65we.txt txt = ./txt/cord-000539-uh3q65we.txt === reduce.pl bib === id = cord-000937-8vk89i4h author = Law, John title = Identification of Hepatotropic Viruses from Plasma Using Deep Sequencing: A Next Generation Diagnostic Tool date = 2013-04-17 pages = extension = .txt mime = text/plain words = 6644 sentences = 332 flesch = 50 summary = RNA and DNA libraries were sequenced from plasma filtrates enriched in viral particles to catalog virus populations. Seven RNA libraries (aihP01, hbvP02, hcvP02, hcvP03, hcvP05, nshP01, norP01) and seven DNA libraries (aihP01D, hbvP02D, hcvP02D, hcvP03D, hcvP05D, nshP01D, norP01D) were constructed from patients with autoimmune hepatitis (AIH), hepatitis B virus (HBV) chronic infection, hepatitis C virus (HCV) chronic infection, non-alcoholic steatohepatitis (NASH), and healthy subjects (NOR). Plasma samples were obtained from patients with autoimmune hepatitis (AIH), chronic hepatitis B virus (HBV) infection, chronic hepatitis C virus (HCV) infection, non-alcoholic steatohepatitis (NASH), and healthy subjects (NOR); each RNA library was named by diagnosis (e.g. aihP01) and a suffix 'D' was added for each DNA library (e.g. aihP01D). To a lesser extent (about one read per million), we also detected sequences resembling RNA viruses in our DNA libraries (Supplemental Tables S15-S28 ). Assembly of viral sequences was also possible for all viruses shown in Figure 2 as the most abundant virus in each library (data not shown). cache = ./cache/cord-000937-8vk89i4h.txt txt = ./txt/cord-000937-8vk89i4h.txt === reduce.pl bib === id = cord-001616-9sc2xmqr author = Erdem, Hakan title = New global viral threats date = 2015 pages = extension = .txt mime = text/plain words = 3085 sentences = 249 flesch = 58 summary = In March 2014, the Ministry of Health of Guinea reported a disease outbreak characterized by fever, severe diarrhea, vomiting, and a high case-fatality rate. 31 One avian influenza case was detected in Taiwan due to H6N1 subtype, whereas 2 of 3 H10N8 human infections observed in China were lethal. In late March 2013, novel human infections due to avian influenza A H7N9 virus were reported from China. Frequently Asked Questions on human infection caused by the avian influenza A(H7N9) virus Comparative epidemiology of human infections with avian influenza A H7N9 and H5N1 viruses in China: a populationbased study of laboratory-confirmed cases Human infections with avian influenza A(H7N9) virus Human infection with avian influenza A(H7N9) virus -update Human infection with a novel avian-origin influenza A (H7N9) virus Epidemiology of human infections with avian influenza A(H7N9) virus in China cache = ./cache/cord-001616-9sc2xmqr.txt txt = ./txt/cord-001616-9sc2xmqr.txt === reduce.pl bib === id = cord-002072-qbh728ec author = Bi, Yuhai title = A new reassortment of influenza A (H7N9) virus causing human infection in Beijing, 2014 date = 2016-05-27 pages = extension = .txt mime = text/plain words = 3096 sentences = 170 flesch = 48 summary = Genetic and phylogenetic analyses revealed that the virus belonged to a novel genotype, which probably emerged and further reassorted with other H9 or H7 viruses in poultry before transmitting to humans. The IFN-induced transmembrane protein-3 (IFITM3) C/C genotype was reported to be associated with severe clinical outcomes, as reflected by a higher viral load, more rapid progression to ARDS, higher cytokine/chemokine levels, and an increased mortality rate after H7N9 infection 22 . Although this was a severe H7N9-infected case with cytokine storm-like appearances and multiple organ failure, the patient was eventually cured after combination therapy with antivirals, mechanical ventilation, supportive nutrition and symptomatic treatment. Clinical, virological and immunological features from patients infected with re-emergent avian-origin human H7N9 influenza disease of varying severity in Guangdong province Cytokine and chemokine levels in patients infected with the novel avian influenza A (H7N9) virus in China cache = ./cache/cord-002072-qbh728ec.txt txt = ./txt/cord-002072-qbh728ec.txt === reduce.pl bib === id = cord-001676-68y733y3 author = Shoemaker, Jason E. title = An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation date = 2015-06-05 pages = extension = .txt mime = text/plain words = 10356 sentences = 460 flesch = 43 summary = After filtering transcripts for minimally confident variation (we required at least one time-matched, infected condition compared with mock-infected absolute fold change 2 and a false discovery rate [FDR]-adjusted P-value < 0.01), the log 2 of the normalized intensity of the retained transcripts (16, 063) for all 167 samples were then clustered by using the Weighted Gene Co-expression Network Analysis (WGCNA) algorithm [18] . Data corresponding to macrophage signatures in different cellular states are colored red (see S3 Table for Within the inflammation-associated modules (N1 and N2), the H5N1 virus induced the earliest gene expression changes and the highest peak expression levels, corroborating previous observations that H5N1 viruses are strong inducers of inflammatory and IFN response signaling in vivo [10, 24, 25] . We infected mice with 10 3 PFU of the H5N1 virus (a 100-fold reduced dose compared with that used in the experiments to fit the model), determined lung virus titers at the same time points used for the initial experiment (S3 Fig), and then evaluated the segmented linear model's ability to predict cytokine-associated gene expression. cache = ./cache/cord-001676-68y733y3.txt txt = ./txt/cord-001676-68y733y3.txt === reduce.pl bib === id = cord-001985-iwfidoer author = Urayama, Syun-ichi title = FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance date = 2016-02-13 pages = extension = .txt mime = text/plain words = 5007 sentences = 281 flesch = 50 summary = This method revealed a previously unidentified viral RNA diversity of more than 20 complete RNA viral genomes including dsRNA and ssRNA viruses associated with an environmental diatom colony. We herein established a novel strategy to obtain full-length RNA virus sequences with extremely high efficiency by applying a short dsRNA full-length cloning method (8) for physically fragmented dsRNAs. The improved method, named FLDS (fragmented and loop primer ligated dsRNA sequencing), was applied to a diatom colony in a tide pool and revealed previously unidentified RNA viruses. These results indicated that FLDS effectively enriched dsRNA reads, thereby allowing the retrieval of complete genome sequences including terminal regions without the requirement for the additional rapid amplification of cDNA ends (RACE). A phylogenetic analysis of RdRp in DCASSRV-2 suggested that the RNA virus was classified into the genus Mitovirus, which has a non-segmented ssRNA genome, infects the mitochondria of fungi, and lacks viral particles (Fig. S4E) . cache = ./cache/cord-001985-iwfidoer.txt txt = ./txt/cord-001985-iwfidoer.txt === reduce.pl bib === id = cord-000113-d0eur1hq author = Fooks, Anthony R. title = Emerging Technologies for the Detection of Rabies Virus: Challenges and Hopes in the 21st Century date = 2009-09-29 pages = extension = .txt mime = text/plain words = 6937 sentences = 319 flesch = 38 summary = The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. Another method for the detection of rabies virus antigen from postmortem samples is a recently developed rapid immunodiagwww.plosntds.org nostic test (RIDT) based on the principles of immunochromatography [13] . Development of RT-LAMP assays for use in diagnosis and surveillance is challenged by the considerable sequence variation observed within the rabies virus genome [44] that can frustrate specific primer design. Currently, high-throughput rabies virus molecular detection methods augment standard diagnostic tests or are in the process of development and refinement for use alone. cache = ./cache/cord-000113-d0eur1hq.txt txt = ./txt/cord-000113-d0eur1hq.txt === reduce.pl bib === id = cord-001958-2gt3fwpy author = Meseda, Clement A. title = Percutaneous Vaccination as an Effective Method of Delivery of MVA and MVA-Vectored Vaccines date = 2016-02-19 pages = extension = .txt mime = text/plain words = 8161 sentences = 361 flesch = 43 summary = Our data suggest that MVA administered by percutaneous inoculation, elicited vaccinia-specific antibody responses, and protected mice from lethal vaccinia virus challenge, at levels comparable to or better than subcutaneous or intramuscular inoculation. In the work described here, we demonstrate in mouse models that percutaneous inoculation of MVA elicited protective immune responses against lethal intranasal challenge with the Western Reserve (WR) strain of vaccinia virus, and at low doses of MVA, lower morbidity was recorded in mice that were vaccinated via the percutaneous route than in those immunized via the intramuscular or subcutaneous routes. In a preliminary experiment to investigate the utility of the percutaneous route for the delivery of MVA, we observed that MVA delivered by tail scarification, while statistically insignificant (p = 0.298), elicited a higher vaccinia-specific IgG response and protection in mice than the same dose (10 6 pfu) delivered by the intramuscular route (S1 Fig) . cache = ./cache/cord-001958-2gt3fwpy.txt txt = ./txt/cord-001958-2gt3fwpy.txt === reduce.pl bib === id = cord-001420-b4zcvd04 author = Crescenzo-Chaigne, Bernadette title = Chimeric NP Non Coding Regions between Type A and C Influenza Viruses Reveal Their Role in Translation Regulation date = 2014-09-30 pages = extension = .txt mime = text/plain words = 6267 sentences = 296 flesch = 56 summary = Interestingly, in type A influenza virus infectious context, the length of the NP segment 5′ NC region once transcribed into mRNA was found to impact its translation, and the level of produced NP protein consequently affected the level of viral genome replication. The sequence of both ends of each segment of each rescued virus was verified as described [9] , and no Influenza NP Non Coding Region Role in Translation PLOS ONE | www.plosone.org genetics, type A and type C viruses with one or both heterotypic ends. These data based on type A influenza virus NP segment showed that it is possible to obtain virus by reverse genetics when a homotypic proximal panhandle and a homotypic strength of the initial distal panhandle are maintained, and that the length of the 59 end plays an important role in the efficiency of rescue. cache = ./cache/cord-001420-b4zcvd04.txt txt = ./txt/cord-001420-b4zcvd04.txt === reduce.pl bib === id = cord-001528-33f94doo author = Fouchier, Ron A. M. title = Studies on Influenza Virus Transmission between Ferrets: the Public Health Risks Revisited date = 2015-01-23 pages = extension = .txt mime = text/plain words = 3522 sentences = 141 flesch = 40 summary = Initial calculations of the potential risks associated with research on influenza virus transmission via respiratory droplets or aerosols between ferrets (1-4) used reports on select agent theft, loss, and release collected by the U.S. Centers for Disease Control and Prevention (CDC) from 2004 to 2010 (7) to calculate the probability of occurrence of LAIs. Although these reports have limitations (1, 4, 7) , they provide the most recent account of LAIs in the United States and probably reflect the current state of the art in biosafety and biosecurity practices better than older studies on laboratory incidents (8, 9) , e.g., as a consequence of the implementation of the U.S. select agent program and best practices developed in biosafety and biosecurity in general over the last decades. cache = ./cache/cord-001528-33f94doo.txt txt = ./txt/cord-001528-33f94doo.txt === reduce.pl bib === id = cord-002136-mkl89qkt author = Nunes, Sandro F. title = An ex vivo swine tracheal organ culture for the study of influenza infection date = 2009-12-09 pages = extension = .txt mime = text/plain words = 4719 sentences = 241 flesch = 45 summary = Objectives We aimed to develop an air interface EVOC using pig tracheas in the study of influenza infection demonstrating that tracheal explants can be effectively maintained in organ culture and support productive influenza infection. 1, 3 Influenza infection in humans and pigs is primarily restricted to the upper and lower respiratory tract with viral replication occurring in the epithelial cells present on the surface of the respiratory mucosa. Ex vivo organ cultures (EVOC) of tracheal explants with an air interface system have been successfully developed and used in the study of both human and animal respiratory pathogens. To determine if the swine tracheal explants supported productive viral replication, explants were infected with 2AE5 · 10 2 pfu of swine influenza virus and maintained in organ culture for 5 days. Cultures of equine respiratory epithelial cells and organ explants as tools for the study of equine influenza virus infection cache = ./cache/cord-002136-mkl89qkt.txt txt = ./txt/cord-002136-mkl89qkt.txt === reduce.pl bib === id = cord-003523-byxuruk1 author = Fritsch, Annemarie title = Influenza C virus in pre-school children with respiratory infections: retrospective analysis of data from the national influenza surveillance system in Germany, 2012 to 2014 date = 2019-03-07 pages = extension = .txt mime = text/plain words = 4287 sentences = 211 flesch = 48 summary = title: Influenza C virus in pre-school children with respiratory infections: retrospective analysis of data from the national influenza surveillance system in Germany, 2012 to 2014 METHODS: A total of 1,588 samples from 0 to 4 year-old children presenting as outpatients with influenza-like illness (ILI) or acute respiratory infection were analysed retrospectively. In Germany, no surveillance data and no sequence information on circulating influenza C viruses have ever been reported. We furthermore sequenced the haemagglutinin esterase (HE) gene from influenza C-positive samples to phylogenetically characterise the detected viruses. To extend the basis for the co-infection data, all influenza C-positive samples were additionally tested for human parainfluenza viruses types 1-4 and coronaviruses OC43, NL63, HKU1 and 229E. Thereby, the low detection rates in the general population were confirmed, but a higher clinical impact for paediatric patients was indicated, as influenza C was described to also cause lower respiratory tract disease [6] [7] [8] [9] [10] . cache = ./cache/cord-003523-byxuruk1.txt txt = ./txt/cord-003523-byxuruk1.txt === reduce.pl bib === id = cord-001120-fxd533b4 author = Everitt, Aaron R. title = Defining the Range of Pathogens Susceptible to Ifitm3 Restriction Using a Knockout Mouse Model date = 2013-11-21 pages = extension = .txt mime = text/plain words = 4874 sentences = 252 flesch = 47 summary = We showed that Ifitm3 does not impact on the restriction or pathogenesis of bacterial (Salmonella typhimurium, Citrobacter rodentium, Mycobacterium tuberculosis) or protozoan (Plasmodium berghei) pathogens, despite in vitro evidence. Here we sought therefore to expand and define the role of Ifitm3 in pathogen restriction by assessing the susceptibility of Ifitm3-deficient (Ifitm3 -/-) mice to bacteria (Salmonella Typhimurium, Citrobacter rodentium, Mycobacterium tuberculosis), a parasite (Plasmodium berghei) and a virus (respiratory syncytial virus, RSV) to determine the specificity of this crucial antimicrobial protein. Similarly, bacterial counts revealed no significant differences between wild type and Ifitm3 -/-mice; together showing that Ifitm3 does not play a role in resistance or susceptibility to Salmonella infection. The experimental challenge revealed there to be no significant difference in phenotype seen in Ifitm3 -/-mice compared with wild type littermate controls, with both showing susceptibility to ECM ( Figure 5A ). cache = ./cache/cord-001120-fxd533b4.txt txt = ./txt/cord-001120-fxd533b4.txt === reduce.pl bib === === reduce.pl bib === id = cord-001748-7e8px4vx author = Nobach, Daniel title = Shedding of Infectious Borna Disease Virus-1 in Living Bicolored White-Toothed Shrews date = 2015-08-27 pages = extension = .txt mime = text/plain words = 4873 sentences = 249 flesch = 47 summary = The bicolored white-toothed shrew (Crocidura leucodon) has recently been identified as reservoir of the neurotropic Borna disease virus 1 (BoDV-1). In animals caught in 2013 (group 1: female #2, male #5, female #6), after an adaption phase of one month, samples of saliva, lacrimal fluid, skin surface, urine and excrements from the BoDV-1-infected shrews were taken weekly over a period of 4 weeks as necessary veterinary care. The five other shrews did not exhibit any evidence for BoDV-1-infection, neither infectious virus nor viral RNA was detected at any time point investigated. Current data from living shrews provide reliable evidence that natural BoDV-1-infection in these animals is indeed clinically inconspicuous over a long time period as already previously assumed [15, 18] despite persistent infection with shedding of infectious virus via various sites. Distribution of Borna Disease Virus Antigen and RNA in Tissues of naturally infected Bicolored White-Toothed Shrews, Crocidura leucodon, supporting their role as Reservoir Host Species cache = ./cache/cord-001748-7e8px4vx.txt txt = ./txt/cord-001748-7e8px4vx.txt === reduce.pl bib === id = cord-001142-puj74k7y author = Crescenzo-Chaigne, Bernadette title = The Panhandle Formed by Influenza A and C Virus NS Non-Coding Regions Determines NS Segment Expression date = 2013-11-21 pages = extension = .txt mime = text/plain words = 3355 sentences = 183 flesch = 55 summary = To investigate whether, or not, and how the complete NC regions of a given segment are involved in type specificity, we attempted to rescue, by reverse genetics, type A and C influenza viruses with chimeric non-coding sequences. The sole difference between 5'A/3'C(C5U) and wild-type 5'A/3'A viruses being the 3' distal extremity of the NS segment suggested that the level of NS encoded proteins (i.e. NS1 or/and NS2/NEP) was affected at early stages of infection for this virus (5'A/3'C(C5U)). The major role of the proximal panhandle in type specificity that we identified and the hypothesized involvement of the distal panhandle in transcription need to be tested on the other (2 PFU/cell), viral vRNA and mRNA levels for each segment were evaluated by specific two-step RT-qPCRs previously described [23] . cache = ./cache/cord-001142-puj74k7y.txt txt = ./txt/cord-001142-puj74k7y.txt === reduce.pl bib === === reduce.pl bib === id = cord-001974-wjf3c7a7 author = Friis-Nielsen, Jens title = Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers date = 2016-02-19 pages = extension = .txt mime = text/plain words = 5773 sentences = 348 flesch = 48 summary = Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. The datasets went through a sequential pipeline with modules (in order) of preprocessing, computational subtraction of host sequences, low-complexity sequence removal, sequence assembly, clustering, association to metadata features, and taxonomical annotation. Associations from the shortest mode tended to have higher dispersion in the range of ORs. Furthermore, one block of clustering results using global alignment mode, alignment length based on the shortest contig, and a minimum sequence identity of 90% (c09ˆaSyG1), had an overall high range of ORs as well as the highest minimum values. The clusters are significantly associated with lowest p-values to biological features and the species annotations are described by HMP. cache = ./cache/cord-001974-wjf3c7a7.txt txt = ./txt/cord-001974-wjf3c7a7.txt === reduce.pl bib === id = cord-000777-7cty5s6o author = Merten, O.-W. title = Virus contaminations of cell cultures – A biotechnological view date = 2002-01-01 pages = extension = .txt mime = text/plain words = 14936 sentences = 650 flesch = 48 summary = These may include the use of production media devoid of animal derived substances, validation of viral clearance in downstream processing or analytics for detecting adventitious viruses in cell culture and final biological product. However, the best means to increase the biological safety of the produced viral vaccines is the use of diploid or continuous cell lines, because it can be determined that such cells are free of animal derived viruses: This can be achieved by establishing master (seed stock) and working (distribution and user stocks) cell banks which have been rigorously tested and validated for the absence of microbial as well as viral contaminants (see chapter by Freshney and the section on 'Testing-virus screening in cell banks' of this article). As animal derived substances such as serum can be contaminated by adventitious viruses, γ irradition is, after routine quality control for virus detection, the best method to increase the safety of using serum in the production of animal cell culture derived biologicals. cache = ./cache/cord-000777-7cty5s6o.txt txt = ./txt/cord-000777-7cty5s6o.txt === reduce.pl bib === id = cord-000729-iq30z094 author = Marsh, Glenn A. title = Cedar Virus: A Novel Henipavirus Isolated from Australian Bats date = 2012-08-02 pages = extension = .txt mime = text/plain words = 6101 sentences = 277 flesch = 49 summary = The genome size (18,162 nt) and organization of CedPV is very similar to that of HeV and NiV; its nucleocapsid protein displays antigenic cross-reactivity with henipaviruses; and it uses the same receptor molecule (ephrinB2) for entry during infection. Preliminary challenge studies with CedPV in ferrets and guinea pigs, both susceptible to infection and disease with known henipaviruses, confirmed virus replication and production of neutralizing antibodies although clinical disease was not observed. As part of our on-going field studies on HeV genetic diversity and infection dynamics in the Queensland flying fox populations, urine samples were collected on a regular basis for PCR and virus isolation. CedPV is more closely related to HeV and NiV than henipavirus-like sequences detected in African bats [26, 32] as shown in a phylogenetic tree based on the only sequences available of a 550-nt L gene fragment (Fig. S5) . cache = ./cache/cord-000729-iq30z094.txt txt = ./txt/cord-000729-iq30z094.txt === reduce.pl bib === id = cord-000238-om92cx5q author = Ogbunugafor, C. Brandon title = On the possible role of robustness in the evolution of infectious diseases date = 2010-06-30 pages = extension = .txt mime = text/plain words = 6717 sentences = 347 flesch = 39 summary = We also draw attention to other infectious disease systems where robustness theory may prove useful for bridging evolutionary biology and biomedicine, especially the evolution of antibiotic resistance in bacteria, immune evasion by influenza, and malaria parasite infections. [14] [15] [16] In reviewing these results, we hope to highlight the importance of empirical work in RNA viruses for testing theory pertaining to robustness, as well as for better understanding the evolutionary biology and evolvability of infectious organisms in general. 1 However, theory and artificial-life data 9 support the idea that genetic robustness should be strongly favored when populations experience elevated mutation rates, suggesting that RNA viruses would be fruitful systems to explore how genetic robustness evolves. [33] [34] [35] Regardless, preliminary experiments showed that UVC exposure for periods up to 30 min greatly increased mortality in wild type phage 6 ͑Fig. 2͒, indicating that this environmental effect should produce strong selection for UVC resistance in populations of the virus. cache = ./cache/cord-000238-om92cx5q.txt txt = ./txt/cord-000238-om92cx5q.txt === reduce.pl bib === id = cord-000359-y0m1utug author = Walpita, Pramila title = Vaccine Potential of Nipah Virus-Like Particles date = 2011-04-06 pages = extension = .txt mime = text/plain words = 7808 sentences = 334 flesch = 46 summary = Co-expression of these proteins under optimized conditions resulted in quantifiable amounts of VLPs with many virus-like/vaccine desirable properties including some not previously described for VLPs of any paramyxovirus: The particles were fusogenic, inducing syncytia formation; PCR array analysis showed NiV VLP-induced activation of innate immune defense pathways; the surface structure of NiV VLPs imaged by cryoelectron microscopy was dense, ordered, and repetitive, and consistent with similarly derived structure of paramyxovirus measles virus. Plasmid-mediated expression of selected viral proteins results in the spontaneous assembly and release of VLPs. These particles make highly effective immunogens because they possess several features of the authentic virus such as their surface structure and dimensions [31, 36] . In preliminary studies it was found that co-expression of NiV G, F and M proteins in 293T cells resulted in the formation of VLPs that bud out into the transfected cell SUP and that they can be harvested, concentrated and purified as described under Methods. cache = ./cache/cord-000359-y0m1utug.txt txt = ./txt/cord-000359-y0m1utug.txt === reduce.pl bib === id = cord-002337-8v907g24 author = Lipsitch, Marc title = Viral factors in influenza pandemic risk assessment date = 2016-11-11 pages = extension = .txt mime = text/plain words = 18953 sentences = 845 flesch = 40 summary = Preference for a2,6-linked mammalian sialic acid receptors over a2,3-linked avian ones HA pH of activation HA avoids extracellular inactivation and undergoes conformational changes leading to membrane fusion at appropriate pH for human cells (5.0-5.4 or perhaps 5.5) (Russell, 2014) Polymerase complex efficiency Efficient replication in human cells (Cauldwell et al., 2014; Naffakh et al., 2008) Virus morphology Filamentous morphology associated with several adaptations to mammals (Seladi-Schulman et al., 2014; Seladi-Schulman et al., 2013; Campbell et al., 2014; Beale et al., 2014) Length of NA stalk Longer stalk of NA required to penetrate human mucus and deaggregate virions (Blumenkrantz et al., 2013) Antagonism of interferon production Species-specific binding of the NS1 protein to host factors (Rajsbaum et al., 2012) HA-NA "balance" Substrate selectivity and catalytic rate of NA are calibrated to "balance" avidity of HA for the cell-surface glycan receptor (Zanin et al., 2015; Baum and Paulson, 1991; Yen et al., 2011; Handel et al., 2014) DOI: 10.7554/eLife.18491.006 Glaser et al., 2005) ; most human H2 and H3 seasonal isolates (Connor et al., 1994; Matrosovich et al., 2000) *These anomalous results are speculated by the authors to be possibly, or even probably the result of laboratory adaptation to egg passage and may not reflect the properties of the primary isolate. cache = ./cache/cord-002337-8v907g24.txt txt = ./txt/cord-002337-8v907g24.txt === reduce.pl bib === id = cord-004477-qu2o2iu1 author = Vlasova, Anastasia N. title = Editorial: Porcine Anti-Viral Immunity date = 2020-03-06 pages = extension = .txt mime = text/plain words = 1583 sentences = 88 flesch = 45 summary = Immediately following viral infection, neonatal survival depends on innate immunity and passive protection by lactogenic immune factors such as pathogen-specific antibodies, until an adaptive immune response can develop. Wide-spread porcine reproductive and respiratory syndrome virus (PRRSV) and swine influenza virus (SIV) represent major health challenges in the large US swine production systems and possibly worldwide. In introducing the topic of anti-viral immunity, we emphasize the genetic diversity of viruses, the virus life cycle and the pathology that viral infection can cause. A more tedious procedure is to use only parts of the virus as the vaccine (subunit vaccines) that target the immune response to those viral epitopes that elicit VN antibodies. A second approach to vaccine development is use of live attenuated virus that has been genetically modified or cell culture adapted and cannot produce a disease in the host but can still replicate. cache = ./cache/cord-004477-qu2o2iu1.txt txt = ./txt/cord-004477-qu2o2iu1.txt === reduce.pl bib === id = cord-003926-ycdaw2vh author = Maslow, Joel N. title = Zika Vaccine Development—Current Progress and Challenges for the Future date = 2019-07-14 pages = extension = .txt mime = text/plain words = 3766 sentences = 189 flesch = 43 summary = Of note, the first demonstration of immunoprotection was as part of a 1953 study to define the ultrastructural characteristics of Zika virus, that found intramuscular vaccination of mice with infectious viral filtrates protected against cerebral infection [36] . In pre-clinical studies, vaccinated mice and non-human primates were shown to develop B and T-cell immune responses against the Zika virus envelope and protected against development of neurologic disease and death in immunosuppressed, interferon α, β receptor deficient (IFNAR) mice [43] . A subsequent study in non-human primates vaccinated twice at four-week intervals with alum generated binding and microneutralization antibody titers of 3.54 and 3.55 log10, respectively, and complete protection against viremia and viruria following challenge with either Brazilian or Puerto Rican strains of Zika virus [47] . Guillain-Barre Syndrome outbreak associated with Zika virus infection in French Polynesia: A case-control study cache = ./cache/cord-003926-ycdaw2vh.txt txt = ./txt/cord-003926-ycdaw2vh.txt === reduce.pl bib === id = cord-003861-qeao4ghg author = Aris-Brosou, Stéphane title = Viral Long-Term Evolutionary Strategies Favor Stability over Proliferation date = 2019-07-24 pages = extension = .txt mime = text/plain words = 4513 sentences = 209 flesch = 49 summary = To understand how these two processes affect the long-term evolution of viruses infecting humans, we comprehensively analyzed ssRNA, ssDNA, dsRNA, and dsDNA viruses, to find which virus types and which functions show evidence for episodic diversifying selection and correlated evolution. To better understand the role of correlated evolution and positive selection in the evolutionary dynamics of viruses infecting humans, we constructed a nearly exhaustive viral data set spanning all dsDNA, dsRNA, ssRNA, and ssDNA viruses deposited in GenBank (as of August 2017), and conducted an extensive survey of correlated evolution and diversifying selection in these viruses, asking more specifically about the prevalence of these two processes in each viral type, independently or jointly, with the specific hypothesis that the genes affected by both processes encode functions that are most critical to each viral life cycle. cache = ./cache/cord-003861-qeao4ghg.txt txt = ./txt/cord-003861-qeao4ghg.txt === reduce.pl bib === id = cord-002728-6oyw5sqv author = Carding, S. R. title = Review article: the human intestinal virome in health and disease date = 2017-09-04 pages = extension = .txt mime = text/plain words = 4362 sentences = 250 flesch = 40 summary = 2 With the advent of new, sequence-based technologies that do not rely on the ability to isolate viruses for their identification, it is now possible to define and characterise viruses in different environmental samples in greater detail than ever before, which has resulted in an increased interest in the role the viral assemblage of the human gut microbiota plays in health and disease. The genetic content of VLPs comprising bacteriophages (phages) that infect bacteria and archaea and, to a much lesser extent, human-, plant-, amoebae-and animal-infecting viruses found along the GI tract constitute the human intestinal virome (Figure 1 ). Analyses of metagenomic sequence data provide detailed information on phage-host and phage-phage competition within the human faecal microbiome, implying CRISPR spacers are actively and continuously acquired by prokaryotes in response to the presence of phages in the GI tract. cache = ./cache/cord-002728-6oyw5sqv.txt txt = ./txt/cord-002728-6oyw5sqv.txt === reduce.pl bib === id = cord-001207-yjaiybwf author = Sachsenröder, Jana title = The General Composition of the Faecal Virome of Pigs Depends on Age, but Not on Feeding with a Probiotic Bacterium date = 2014-02-19 pages = extension = .txt mime = text/plain words = 5919 sentences = 302 flesch = 49 summary = faecium) NCIMB 10415 on the pig faecal virome composition was analysed in a pig feeding trial with sows and their piglets, which received either the probiotic bacterium or not. RESULTS: From 8 pooled faecal samples derived from the feeding trial, DNA and RNA virus particles were prepared and subjected to process-controlled Next Generation Sequencing resulting in 390,650 sequence reads. However, it is not known so far, whether probiotic bacteria can also influence the general composition of the faecal virome, e.g. by changing the composition of the bacterial community, which represents the host population for bacteriophages, or by direct interactions with specific viruses. Faecal samples from sows and their piglets experimentally fed with or without the probiotic bacterium were analyzed using a process-controlled deep sequencing method. As the detection rate of the bacteriophages is -besides technical factors -also dependent on the amount of viruses initially present in the analyzed sample, improved deep sequencing methods enabling quantitative analyses should be developed in future for comparative virome investigations. cache = ./cache/cord-001207-yjaiybwf.txt txt = ./txt/cord-001207-yjaiybwf.txt === reduce.pl bib === id = cord-001831-3aonqyub author = Royle, Jamie title = Emerging Roles of Viroporins Encoded by DNA Viruses: Novel Targets for Antivirals? date = 2015-10-16 pages = extension = .txt mime = text/plain words = 6390 sentences = 311 flesch = 42 summary = Studies have highlighted the essential nature of a group of small, highly hydrophobic, membrane embedded, channel-forming proteins in the life cycles of a growing number of RNA viruses. This review article summarizes the recent developments in our understanding of these novel viroporins; describes their roles in the virus life cycles and in pathogenesis and speculates on their potential as targets for anti-viral therapeutic intervention. Research over recent decades has identified a group of virus-encoded proteins able to mediate the passage of ions and solutes across cellular membranes, termed viroporins [1, 2] . Due to these broad perturbations to host cell physiology, it is not surprising that viroporin function has been shown to assist in all stages of the virus life cycle including entry, membrane penetration, genome replication and virus egress [1, 2] . This review will summarize our understanding of these putative viroporins, describe their known functions and attempt to highlight how possible ion channel activity may aid the life cycles of these small DNA tumor viruses. cache = ./cache/cord-001831-3aonqyub.txt txt = ./txt/cord-001831-3aonqyub.txt === reduce.pl bib === id = cord-003993-3bozjfv7 author = Cagliani, Rachele title = Mode and tempo of human hepatitis virus evolution date = 2019-10-25 pages = extension = .txt mime = text/plain words = 7845 sentences = 400 flesch = 40 summary = Technological advances that allow throughput sequencing of viral genomes, as well as the development of computational tools to analyze such genome data, have largely expanded our knowledge on the host range and evolutionary history of human hepatitis viruses. This finding, as well as the increasing availability of the genome sequences of human-infecting viruses sampled across different geographic areas, has largely expanded our knowledge about the genetic diversity and evolutionary origin of these human pathogens. Studies that did not account for the TDRP provided estimates of the time to the most recent common ancestor (TMRCA) of HCV genotypes in a range between $200 and 1000 years ago [63, 64, 76, 87, 88] ; the origin of the horse virus was dated around 1800 CE [85] . Although several human hepatitis E cases have a zoonotic origin and orthohepeviruses A are found in diverse mammals, recent data indicated that one or more reverse zoonoses led to the emergence and radiation of HEV genotypes [121] . cache = ./cache/cord-003993-3bozjfv7.txt txt = ./txt/cord-003993-3bozjfv7.txt === reduce.pl bib === id = cord-002921-i5jxn1vj author = Morens, David M title = Pandemic Zika: A Formidable Challenge to Medicine and Public Health date = 2017-12-15 pages = extension = .txt mime = text/plain words = 1978 sentences = 104 flesch = 42 summary = Because of the pandemic's uniqueness and the insidious ability of Zika virus to harm unborn children, the pandemic has captured the attention of infectious disease researchers and practitioners of clinical and public health medicine around the world, as well as the attention of allied colleagues working in entomology, vector control, informatics, teratology, immunology, and a host of other disciplines [3] [4] [5] . Furthermore, some studies have suggested that preexisting flavivirus immunity (eg, from prior dengue virus infection) might potentiate Zika [16] via antibody-dependent infection enhancement in some circumstances [17] , while other research has countered this view [18] . As with most flaviviruses, small-animal models of Zika virus infection and disease have been problematic, but considerable progress has nonetheless been made, including important new information bearing on teratogenicity and vaccine design strategy [20] . Evolutionary enhancement of Zika virus infectivity in Aedes aegypti mosquitoes cache = ./cache/cord-002921-i5jxn1vj.txt txt = ./txt/cord-002921-i5jxn1vj.txt === reduce.pl bib === id = cord-003130-p2h8p5bm author = Lindqvist, Richard title = Tick-Borne Flaviviruses and the Type I Interferon Response date = 2018-06-21 pages = extension = .txt mime = text/plain words = 8350 sentences = 481 flesch = 48 summary = There are more than 70 viruses in the genus flavivirus, and they are transmitted by arthropods such as mosquitoes (dengue virus (DENV), Japanese encephalitis virus (JEV) and West Nile virus (WNV), yellow fever virus (YFV), and Zika virus (ZIKV) and ticks (tick-borne encephalitis virus (TBEV), Langat virus (LGTV), Kyasanur forest disease virus (KFDV), Omsk hemorrhagic fever virus (OHFV), Powassan virus (POWV), and Louping-ill virus (LIV)) [1] [2] [3] [4] [5] . Two other ISGs which have been shown to be antivirally active against TBEV are virus inhibitory protein endoplasmic reticulum associated interferon inducible (viperin) and tripartite motif-79α (TRIM79α). The role of interferon in tick-borne encephalitis virus-infected l cells. A functional toll-like receptor 3 gene (tlr3) may be a risk factor for tick-borne encephalitis virus (tbev) infection Analysis of tick-borne encephalitis virus-induced host responses in human cells of neuronal origin and interferon-mediated protection cache = ./cache/cord-003130-p2h8p5bm.txt txt = ./txt/cord-003130-p2h8p5bm.txt === reduce.pl bib === id = cord-002338-ri7v2ka3 author = Anderson, Tavis K. title = A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses date = 2016-12-14 pages = extension = .txt mime = text/plain words = 5842 sentences = 276 flesch = 42 summary = A common global nomenclature facilitates comparisons of IAVs infecting humans and pigs, within and between regions, and can provide insight into the diversity of swine H1 influenza virus and its impact on vaccine strain selection, diagnostic reagents, and test performance, thereby simplifying communication of such data. Similarly, IAV in Asia reflects the regional introduction and subsequent evolution and cocirculation of multiple genetic clades of classical-swine H1N1, avian-like H1N1, and human seasonal-like H1N1 and H1N2 viruses (6, 27, 28) . Three major first-order H1 lineages continued to circulate in pigs ( Fig. 1 ; also see Fig. S1 in the supplemental material): the 1A classical lineage, viruses related to the 1918 human influenza pandemic; the 1B human seasonal lineage, the result of multiple human-to-swine transmission episodes of human seasonal H1 strains over decades; and the 1C Eurasian avian lineage, arising from an introduction from wild birds into pigs in the 1970s. cache = ./cache/cord-002338-ri7v2ka3.txt txt = ./txt/cord-002338-ri7v2ka3.txt === reduce.pl bib === === reduce.pl bib === id = cord-002874-9rxv6fy9 author = Welch, David title = Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases date = 2018-02-09 pages = extension = .txt mime = text/plain words = 3266 sentences = 166 flesch = 47 summary = Here we applied this approach to test the efficacy of the 222-nm far-UVC light to inactivate influenza A virus (H1N1) carried by aerosols in a benchtop aerosol UV irradiation chamber, which generated aerosol droplets of sizes similar to those generated by human coughing and breathing. If these results are confirmed in other scenarios, it follows that the use of overhead low-level far-UVC light in public locations may represent a safe and efficient methodology for limiting the transmission and spread of airborne-mediated microbial diseases such as influenza and tuberculosis. In conclusion, we have shown for the first time that very low doses of far-UVC light efficiently inactivate airborne viruses carried by aerosols. If these results are confirmed in other scenarios, it follows that the use of overhead very low level far-UVC light in public locations may represent a safe and efficient methodology for limiting the transmission and spread of airborne-mediated microbial diseases. cache = ./cache/cord-002874-9rxv6fy9.txt txt = ./txt/cord-002874-9rxv6fy9.txt === reduce.pl bib === id = cord-000501-qz68gtd4 author = Greatorex, Jane S. title = Survival of Influenza A(H1N1) on Materials Found in Households: Implications for Infection Control date = 2011-11-22 pages = extension = .txt mime = text/plain words = 4311 sentences = 194 flesch = 47 summary = METHODOLOGY AND PRINCIPAL FINDINGS: Influenza A/PuertoRico/8/34 (PR8) or A/Cambridge/AHO4/2009 (pandemic H1N1) viruses were inoculated onto a wide range of surfaces used in home and work environments, then sampled at set times following incubation at stabilised temperature and humidity. The potential for transmission of influenza by indirect contact (i.e. via fomites) is linked to the ability of virus to survive in transmissible titres on commonly touched surfaces; however few data exist on this subject. We evaluate the survival of influenza A (H1N1) viruses deliberately applied to a range of commonly touched household and workplace surfaces, using RT-PCR for genome detection and culture methods to determine viability. Our data are consistent with recent findings from a study of environmental deposition of pandemic H1N1 virus in the homes of infected patients, involving our laboratory, when almost 10% of tested surfaces yielded viable virus [15] . cache = ./cache/cord-000501-qz68gtd4.txt txt = ./txt/cord-000501-qz68gtd4.txt === reduce.pl bib === id = cord-003166-k3jxvzfi author = Noh, Ji Yeong title = Isolation and characterization of novel bat paramyxovirus B16-40 potentially belonging to the proposed genus Shaanvirus date = 2018-08-22 pages = extension = .txt mime = text/plain words = 4670 sentences = 244 flesch = 51 summary = Even though the HN amino acids sequences were similar to those from viruses in the proposed genera Shaanvirus, it was also related to that of Sendai virus and human parainfluenza virus 1, which belong to a different genus, Respirovirus showing (Table 1) . In addition, among three pooled sera (two mouse sera each) against human parainfluenza virus 1 (KBPV-VR-44), one pooled serum was cross-reactive to the bat paramyxovirus B16-40 with 40 as the end-point titer for the fluorescent signal ( Table 2 , Fig. 4 ). Notably, even though the HN amino acids sequences were similar to those from viruses in the proposed genera Shaanvirus, it was also related to that of Sendai virus and human parainfluenza virus 1, which belong to a different genus, Respirovirus (Table 1) . In fact, in this study, when mouse antisera were made and tested against bat paramyxovirus B16-40 and human parainfluenza virus 1 (KBPV-VR-44), the two viruses were partially cross-reactive to each other in an indirect immunofluorescence assay. cache = ./cache/cord-003166-k3jxvzfi.txt txt = ./txt/cord-003166-k3jxvzfi.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-004280-c470nlie author = Coleman, Kristen K. title = Airborne Influenza A Virus Exposure in an Elementary School date = 2020-02-05 pages = extension = .txt mime = text/plain words = 4118 sentences = 212 flesch = 46 summary = In this study, we evaluated the use of a bioaerosol sampling method to noninvasively detect and quantify airborne influenza A virus (IAV) densities in a public elementary school. Significantly different (p = 0.049) airborne IAV densities were detected between all three indoor locations (i.e., gymnasium, classroom, and corridor) and all positive samples were collected during the last two weeks of 66 , and a 20-30% relative humidity level; Descriptive of an average elementary school student in the USA weighing ~23-32 kg with an assumed tidal volume (V T ) of 7 mL per kg of body mass. Given the high airborne IAV densities detected in the school corridor, along with elevated student contact rates, it is plausible to conclude that the school corridor is a "hotspot" for influenza virus transmission. cache = ./cache/cord-004280-c470nlie.txt txt = ./txt/cord-004280-c470nlie.txt === reduce.pl bib === id = cord-000760-4yfohp9w author = Babapoor, Sankhiros title = A Novel Vaccine Using Nanoparticle Platform to Present Immunogenic M2e against Avian Influenza Infection date = 2012-01-12 pages = extension = .txt mime = text/plain words = 6081 sentences = 327 flesch = 51 summary = Using peptide nanoparticle technology, we have designed two novel vaccine constructs representing M2e in monomeric (Mono-M2e) and tetrameric (Tetra-M2e) forms. A multiple antigenic peptide construct containing M2e (M2e-MAP) induced strong M2especific antibody titers in the serum of mice and resulted in significant protection against influenza virus challenge [13] . Chickens after each inoculation developed high levels of antibody against the injected construct and anamnestic response clearly was seen when the plates were coated with Mono-M2e and Tetra-M2e nanoparticles and M2e-GCN4 (tetrameric M2e), respectively (Table 1, Figures 7 and 8) . In the present study, protection efficiency of two different nanoparticle constructs harboring M2e was studied as possible vaccine candidates for low-pathogenicity avian influenza infection. Vaccination of chickens with recombinant Salmonella expressing M2e and CD154 epitopes increases protection and decreases viral shedding after low pathogenic avian influenza challenge cache = ./cache/cord-000760-4yfohp9w.txt txt = ./txt/cord-000760-4yfohp9w.txt === reduce.pl bib === id = cord-000050-tfcerilc author = Rao, Srinivas title = Multivalent HA DNA Vaccination Protects against Highly Pathogenic H5N1 Avian Influenza Infection in Chickens and Mice date = 2008-06-18 pages = extension = .txt mime = text/plain words = 5605 sentences = 256 flesch = 44 summary = METHODOLOGY / PRINCIPAL FINDINGS: The ability of DNA vaccines encoding hemagglutinin (HA) proteins from different HPAI H5N1 serotypes was evaluated for its ability to elicit neutralizing antibodies and to protect against homologous and heterologous HPAI H5N1 strain challenge in mice and chickens after DNA immunization by needle and syringe or with a pressure injection device. After optimization of injection conditions, alternative multivalent DNA vaccine regimens were analyzed and compared for magnitude and breadth of neutralizing antibodies, as well as protective efficacy after challenge in mouse and chicken models of HPAI H5N1 infection. The ability of chickens to generate specific antibodies was assessed with three strains that showed broad cross protection in mouse studies (A/Vietnam/1203/2004, A/Anhui/ 1/2005 and A/Indonesia/05/2005), administered individually or in combination, by different injection methods. cache = ./cache/cord-000050-tfcerilc.txt txt = ./txt/cord-000050-tfcerilc.txt === reduce.pl bib === id = cord-002407-25cawzi0 author = Nogales, Aitor title = Reverse Genetics Approaches for the Development of Influenza Vaccines date = 2016-12-22 pages = extension = .txt mime = text/plain words = 11127 sentences = 598 flesch = 41 summary = To date, three types of influenza virus vaccines are approved by the Food and Drug Administration (FDA) for human use: recombinant viral HA, inactivated virus and live-attenuated viruses [65] [66] [67] [68] [69] . Plasmid-based reverse genetics for influenza virus allows for the simultaneous expression of the viral components involved in viral genome replication and gene transcription (PB2, PB1, PA and NP) and the eight negative-stranded vRNAs in transfected susceptible cells, which together generate de novo, recombinant IAVs or IBVs (Figure 3 ) [48] . Plasmid-based reverse genetic technologies have allowed the engineering of recombinant influenza viruses that contain single or multiple mutations in the viral genome, which can be potentially implemented as novel or improved vaccine approaches. Importantly, influenza viruses generated by codon deoptimization showed similar viral replication kinetics to WT virus in MDCK cells, which is important for their effective use for vaccine production. cache = ./cache/cord-002407-25cawzi0.txt txt = ./txt/cord-002407-25cawzi0.txt === reduce.pl bib === id = cord-003216-5qioku84 author = Rehman, Zaib Ur. title = Pathobiology of Avian avulavirus 1: special focus on waterfowl date = 2018-09-19 pages = extension = .txt mime = text/plain words = 5614 sentences = 277 flesch = 41 summary = Besides the strong innate immune responses, waterfowl are generally considered long-term carrier of APMV-1 and disease outbreaks have been reported since 1997 [12] [13] [14] , and were confirmed by follow up experimental studies. Host innate immune responses of ducks infected with Newcastle disease viruses of different pathogenicities Pathotypical and genotypical characterization of strains of Newcastle disease virus isolated from outbreaks in chicken and goose flocks in some regions of China during Histopathological alterations in immune organs of chickens and ducks after experimental infection with virulent 9a5b newcastle disease virus Experimental co-infections of domestic ducks with a virulent Newcastle disease virus and low or highly pathogenic avian influenza viruses Phylogenetic diversity among low-virulence newcastle disease viruses from waterfowl and shorebirds and comparison of genotype distributions to those of poultry-origin isolates Genomic characterizations of a Newcastle disease virus isolated from ducks in live bird markets in China cache = ./cache/cord-003216-5qioku84.txt txt = ./txt/cord-003216-5qioku84.txt === reduce.pl bib === id = cord-004211-58x3nnsc author = Javelle, Emilie title = The challenging management of Rift Valley Fever in humans: literature review of the clinical disease and algorithm proposal date = 2020-01-22 pages = extension = .txt mime = text/plain words = 6929 sentences = 348 flesch = 43 summary = title: The challenging management of Rift Valley Fever in humans: literature review of the clinical disease and algorithm proposal Clinicians need to consider RVF in the differential diagnosis for febrile illnesses in a suitable context, however manifestations of RVFV in humans are varied and unspecific including hepatitis, encephalitis, hemorrhagic disease, and retinitis with potential dramatic consequences. during the major outbreak in Egypt in 1977, it is considered that less than 5% of symptomatic cases will present complications including ocular, neurologic and hemorrhagic symptoms, while favorable outcome will occur within 1 week for the others [17] . Epidemic Rift Valley fever in Saudi Arabia: a clinical study of severe illness in humans Pathologic studies on suspect animal and human cases of Rift Valley fever from an outbreak in Eastern Africa Severe human illness caused by Rift Valley Fever Virus in Mauritania cache = ./cache/cord-004211-58x3nnsc.txt txt = ./txt/cord-004211-58x3nnsc.txt === reduce.pl bib === id = cord-003880-uuuzfyjm author = Shen, Meng-xin title = Antiviral Properties of R. tanguticum Nanoparticles on Herpes Simplex Virus Type I In Vitro and In Vivo date = 2019-09-04 pages = extension = .txt mime = text/plain words = 6674 sentences = 346 flesch = 49 summary = We first conducted plaque reduction assays using HEp-2 cells to test the capacity of these nanoparticles to inactivate the HSV-1 virions and block the viral attachment and entry into cells, following the evaluation of inhibitory effect on viral replication using real-time quantitative PCR, Western blot, and immunofluorescence methods. tanguticum nanoparticles were added to HEp-2 cell monolayers at indicated time periods after HSV-1 infection (MOI = 0.01). tanguticum nanoparticles could suppress HSV-1 viral plaque formation in a dose-dependent manner ( Figure 3B ) and with the increase of drug concentrations, a noted increased antiviral activity was observed. Our previous study showed that the ethanol extracts of Rheum tanguticum, emodin inhibit the herpes simplex virus in vitro and in vivo, which the most effective dose orally administered to mice was 6.7 g/kg/day (Xiong et al., 2011) . cache = ./cache/cord-003880-uuuzfyjm.txt txt = ./txt/cord-003880-uuuzfyjm.txt === reduce.pl bib === id = cord-003482-f1uvohf0 author = Malmlov, Ashley title = Experimental Zika virus infection of Jamaican fruit bats (Artibeus jamaicensis) and possible entry of virus into brain via activated microglial cells date = 2019-02-04 pages = extension = .txt mime = text/plain words = 7503 sentences = 400 flesch = 53 summary = Quantitative probe-based reverse transcription PCR (qRT-PCR) was performed on seruminoculated Vero cell supernatants, serum, brain, lung, liver, spleen, kidney, urinary bladder, prostate and testes from bats from both studies. Brain and testicular tissues stained with both goat polyclonal goat anti-Iba1 (green) and monoclonal 4G-2 flavivirus E specific antibodies (red) showed co-localization (yellow) of ZIKV antigen in cytoplasm of activated microglial cells with their characteristic morphology in the cerebral cortex of infected bats 10 dpi in the time course study and 28 day dpi in the pilot study (Fig 9) . Two bat infection experiments were conducted in this investigation; 1) a pilot study to determine susceptibility of Jamaican fruit bats to ZIKV infection, and 2) a time course study to better understand pathophysiology and chronology of events pertaining to the dynamics of viremia, viral tropism, replication and shedding of the virus in a New World bat species. cache = ./cache/cord-003482-f1uvohf0.txt txt = ./txt/cord-003482-f1uvohf0.txt === reduce.pl bib === id = cord-003302-vxk7uqlc author = Fedson, David S title = Influenza, evolution, and the next pandemic date = 2018-10-03 pages = extension = .txt mime = text/plain words = 6378 sentences = 324 flesch = 41 summary = These studies help explain the lower mortality in children compared with adults seen in the 1918 influenza pandemic and in many other types of acute illness. They agree with Worobey et al that early life antigenic imprinting might have led to a dysregulated T-cell response that increased the risk of death following infection in 1918 with a new and antigenically dissimilar influenza virus. In trying to understand the 'mystery' of greater mortality among young adults during the 1918 pandemic, scientists have studied influenza viruses and the human response to previous infection. Considered with evidence from endotoxemic mice [28] and other studies [4] [5] [6] [7] [8] [9] , their findings suggest that the mortality impact of pandemic and seasonal influenza and other forms of acute critical illness might be reduced by treating the host response. cache = ./cache/cord-003302-vxk7uqlc.txt txt = ./txt/cord-003302-vxk7uqlc.txt === reduce.pl bib === === reduce.pl bib === id = cord-002410-2zi5iv2t author = Bruening, Janina title = The Role of Type III Interferons in Hepatitis C Virus Infection and Therapy date = 2017-02-01 pages = extension = .txt mime = text/plain words = 6696 sentences = 374 flesch = 44 summary = Among the three classes of IFNs, type III IFNs, also called IFN lambdas (IFNLs), are an essential component of the innate immune response to hepatitis C virus (HCV). Here, we will review our current knowledge on IFNL gene expression, protein properties, signaling, ISG induction, and its implications on HCV infection and treatment. Type III IFNs and ISGs are similarly inducted upon HCV infection of primary human fetal liver cells [98, 99] . In summary, expression of specific IFNL subtypes is induced in PHH and some hepatoma cell lines upon infection with HCV, resulting in limiting virus production. Viral infection and toll-like receptor agonists induce a differential expression of type I and interferons in humans plasmacytoid and monocyte-derived dendritic cells HepG2 cells mount an effective antiviral interferon-lambda based innate immune response to hepatitis C virus infection HCV infection induces a unique hepatic innate immune response associated with robust production of type III interferons cache = ./cache/cord-002410-2zi5iv2t.txt txt = ./txt/cord-002410-2zi5iv2t.txt === reduce.pl bib === id = cord-003817-k3m72uxw author = Braun, Elisabeth title = Furin‐mediated protein processing in infectious diseases and cancer date = 2019-08-05 pages = extension = .txt mime = text/plain words = 9070 sentences = 557 flesch = 41 summary = For example, avirulent Newcastle disease virus (NDV) strains harbour a monobasic cleavage site in their Fusion (F) protein and result only in local infections (mainly in the respiratory tract) since expression of the respective host proteases is limited to a few cell types. Notably, proteolytic processing of Env depends on correct N-linked glycosylation as aberrant carbohydrate side chains may result in subcellular mistrafficking or sequestration of Env. 49 Most likely, HIV-1 takes advantage of the redundancy of several proprotein convertases recognising the polybasic cleavage motif in Env. Furin, PCSK5, PCSK6 and PCSK7 have all been shown to cleave gp160 in cells, albeit with different efficiencies. 59, 60 Notably, a subset of H9N2 lowly pathogenic avian influenza A virus strains also harbour R-S-K-R↓ or R-S-R-R↓ sites that are not only cleaved by trypsin-like proteases, such as TMPRSS2 or HAT, but also by PCSKs. 61 However, their cleavage is only efficient in the presence of very high amounts of furin or upon mutation of a glycosylation site in HA. cache = ./cache/cord-003817-k3m72uxw.txt txt = ./txt/cord-003817-k3m72uxw.txt === reduce.pl bib === id = cord-003503-t6cnjwpd author = Sung, Ming-Hua title = Phylogeographic investigation of 2014 porcine epidemic diarrhea virus (PEDV) transmission in Taiwan date = 2019-03-06 pages = extension = .txt mime = text/plain words = 3362 sentences = 182 flesch = 46 summary = Acknowledging the absence of a thorough investigation at the geographic level, we used 2014 outbreak sequence information from the Taiwan government's open access databases plus GenBank records to analyze PEDV dissemination among Taiwanese pig farms. The data indicate that the 2014 Taiwan PEDV epidemic resulted from the spread of multiple strains, with strong correlations identified with pig farm numbers and sizes (measured as animal concentrations), feed mill numbers, and the number of slaughterhouses in a specifically defined geographic area. To determine specific temporal and geographic relationships associated with PEDV strain transmission, we used phylogenetic, phylodynamic and phylogeographic methods to systematically evaluate potential temporal and spatial transmission routes among Taiwanese swine farms during the 2014 outbreak. However, to date very few research efforts in Asia have utilized full genome sequencing for determining geographic structures due to the high costs and enormous amounts of computational time Phylogeographic investigation of 2014 porcine epidemic diarrhea virus transmission in Taiwan required for analyses [33, 34] . cache = ./cache/cord-003503-t6cnjwpd.txt txt = ./txt/cord-003503-t6cnjwpd.txt === reduce.pl bib === id = cord-004608-3u00cpsc author = nan title = Arboviren—durch Arthropoden übertragbare Viren: Stellungnahmen des Arbeitskreises Blut des Bundesministeriums für Gesundheit und Soziale Sicherung date = 2004 pages = extension = .txt mime = text/plain words = 2798 sentences = 356 flesch = 48 summary = Unter dem Oberbegriff Arboviren (arthropod-borne viruses) werden diejenigen Viren zusammengefasst, die sich sowohl in Arthropoden wie Mücken oder Zecken als auch in Vertebraten (Vögeln, Säugetieren) vermeh-ren. Hantaviren, die zum Genus Hantavirus der Bunyaviridae gehören, werden dagegen nicht von Arthropoden auf den Menschen übertragen, sondern durch dessen Kontakt mit Ausscheidungen der natürlichen Wirte, Mäuse und Ratten. In Deutschland spielt nach dem heutigen Wissensstand nur das Virus der Frühsommermeningoenzephalitis (FSME), das durch Zecken (Ixodes ricinus) übertragen wird, epidemiologisch eine wesentliche Rolle. Für einige Viren, wie etwa West-Nil-Virus (WNV) und St.-Louis-Enzephalitis-Virus (SLEV), wurde nachgewiesen, dass die Virusvermehrung in den Mücken abhängig ist von der durchschnittlichen Umgebungstemperatur. Für verschiedene Erreger wurde gezeigt, dass einerseits infizierte Mücken überwintern können; annahme an Krankheitsfällen bei Menschen in den USA Das Verhältnis von Infektionen zu Erkrankungen wird dabei je nach Erreger und untersuchtem Kollektiv mit 20:1 bis 1.000:1 angegeben. cache = ./cache/cord-004608-3u00cpsc.txt txt = ./txt/cord-004608-3u00cpsc.txt === reduce.pl bib === === reduce.pl bib === id = cord-004761-cgby8bhz author = Fuchs, N. title = Virus isolation and titration at 33‡ and 37‡ C date = 1975 pages = extension = .txt mime = text/plain words = 1157 sentences = 81 flesch = 52 summary = Various prototype viruses and original specimens were comparatively titrated in cell cultures at 33‡ and 37‡ C. g. Lennette and Schmidt, 1969) recommend an incubation temperature of 33 ~ rather than 37~ for the isolation of viruses from the human respiratory tract. Original specimens (stool suspensions, throat and conjunetival swabs, vesicular fluid) containing the following virus types were inoculated: adenovirus I, 2, 3, 5, 7, 8, herpesvirus hominis, poliovirus 1 and 3, coxsackievirus A9 and B5, eehovirus types 6, 9, 11, 18 and 30. To our knowledge influenza viruses are the only ones of the viruses occurring in the human respiratory tract, in which a comparative testing of original specimens (in embryonated eggs) has demonstrated the superiority of the lower temperature (Stern and Tippett, 1963) . Both temperatures appear satisfactory for vaccinia virus, herpesvirus, enteroviruses and parainfluenza viruses. cache = ./cache/cord-004761-cgby8bhz.txt txt = ./txt/cord-004761-cgby8bhz.txt === reduce.pl bib === id = cord-002076-7t4d4vvo author = Li, Yongfeng title = Applications of Replicating-Competent Reporter-Expressing Viruses in Diagnostic and Molecular Virology date = 2016-05-06 pages = extension = .txt mime = text/plain words = 4996 sentences = 229 flesch = 36 summary = Commonly used tests based on wild-type viruses, such as immunostaining, cannot meet the demands for rapid detection of viral replication, high-throughput screening for antivirals, as well as for tracking viral proteins or virus transport in real time. This article reviews the applications of RCREVs in diagnostic and molecular virology, including rapid neutralization tests, high-throughput screening systems, identification of viral receptors and virus-host interactions, dynamics of viral infections in vitro and in vivo, vaccination approaches and others. Replicating-competent reporter-expressing viruses (RCREVs) are one type of artificially modified viruses that not only retain the viral genetic characteristics but also possess the new properties of the reporter genes, which represent a useful tool for quantitative analysis of viral replication and tracking viral protein transport in both living cells and animals. cache = ./cache/cord-002076-7t4d4vvo.txt txt = ./txt/cord-002076-7t4d4vvo.txt === reduce.pl bib === id = cord-003707-fbe47bgi author = Russo, Alice G title = Novel insights into endogenous RNA viral elements in Ixodes scapularis and other arbovirus vector genomes date = 2019-06-18 pages = extension = .txt mime = text/plain words = 9010 sentences = 611 flesch = 55 summary = I. scapularis NIRVS are enriched in bunyaand orthomyxo-like sequences, reflecting that ticks are a dominant host for these virus groups. NIRVS arise from the reverse transcription of viral RNA into cDNA and its integration into the genome of a host germ cell, followed by vertical transmission to offspring (Katzourakis and Gifford 2010) . Yet recent evidence has highlighted the abundance of NIRVS in some arthropod genomes-e.g., Ae. aegypti and Ae. albopictus contain >100 NIRVS from over eight RNA virus families encompassing þssRNA, ÀssRNA, and dsRNA viral groups (Palatini et al. Using the well-studied genomes of Aedes mosquitoes to validate our analysis, we employed a bioinformatic pipeline to characterise NIRVS in seven non-Aedes arbovirus vectors that have representative genomic sequences (Table 1 and Fig. 1 ). scapularis lacked NIRVS from positive-sense RNA viruses, which comprise about one tenth of NIRVS in Aedes mosquitoes ( Fig. 3; Supplementary Table S2 ). cache = ./cache/cord-003707-fbe47bgi.txt txt = ./txt/cord-003707-fbe47bgi.txt === reduce.pl bib === id = cord-002482-2t09zqqi author = Miras, Manuel title = Non-canonical Translation in Plant RNA Viruses date = 2017-04-06 pages = extension = .txt mime = text/plain words = 13890 sentences = 732 flesch = 51 summary = Here, we review the tools utilized by positive-sense single-stranded (+ss) RNA plant viruses to initiate non-canonical translation, focusing on cis-acting sequences present in viral mRNAs. We highlight how these elements may interact with host translation factors and speculate on their contribution for achieving translational control. In this review, we describe current knowledge on the mechanisms used by positive-sense single-stranded (+ss) RNA plant viruses to initiate translation, focusing on cis-acting sequences present in viral mRNAs. We also describe other protein translation strategies used by plant viruses to optimize the usage of the coding capacity of their very compact genomes, including leaky scanning initiation, ribosomal frameshifting and stop-codon readthrough. cache = ./cache/cord-002482-2t09zqqi.txt txt = ./txt/cord-002482-2t09zqqi.txt === reduce.pl bib === id = cord-003466-599x0euj author = Nickol, Michaela E. title = A year of terror and a century of reflection: perspectives on the great influenza pandemic of 1918–1919 date = 2019-02-06 pages = extension = .txt mime = text/plain words = 5772 sentences = 283 flesch = 45 summary = MAIN TEXT: The 1918 H1N1 pandemic virus spread across Europe, North America, and Asia over a 12-month period resulting in an estimated 500 million infections and 50–100 million deaths worldwide, of which ~ 50% of these occurred within the fall of 1918 (Emerg Infect Dis 12:15-22, 2006, Bull Hist Med 76:105-115, 2002). Influenza viruses have posed a continual threat to global public health since at least as early as the Middle Ages, resulting in an estimated 3-5 million cases of severe illness and 291,243-645,832 deaths annually worldwide, according to a recent estimate [1] . To be considered a pandemic, an influenza virus must: i) spread globally from a distinct location with high rates of infectivity resulting in increased mortality; and ii) the hemagglutinin (HA) cannot be related to influenza strains circulating prior to the outbreak nor have resulted from mutation [14, 15] . cache = ./cache/cord-003466-599x0euj.txt txt = ./txt/cord-003466-599x0euj.txt === reduce.pl bib === id = cord-002933-zmx4k46v author = Stabell, Alex C title = Dengue viruses cleave STING in humans but not in nonhuman primates, their presumed natural reservoir date = 2018-03-20 pages = extension = .txt mime = text/plain words = 9265 sentences = 506 flesch = 55 summary = The dengue virus 2 (DENV2) encoded protease cleaves human STING, reducing type I interferon production and boosting viral titers in humans. We show that an 'RG' motif at positions 78/79 of STING is critical for susceptibility to cleavage, and conversion of these residues to 'RG' renders all nonhuman primate STING proteins tested, as well as mouse STING, sensitive to dengue virus proteases. Out of the entire Genbank database, along with our sequencing of STING from 16 additional primate species, we identify only a small number of apes (gorillas, orangutans, and gibbons), and three small rodent species (chinchillas, naked mole rats, and desert woodrats) as encoding a functional dengue virus cleavage determinant in STING. Further, the restoration of the 'RG' motif at positions 78/79 again renders all of these STING proteins susceptible to cleavage ( Figure 5B) , indicating that the sylvatic protease is targeting (i.e. binding or cleaving) the same cleavage determinant as the proteases from human dengue viruses. cache = ./cache/cord-002933-zmx4k46v.txt txt = ./txt/cord-002933-zmx4k46v.txt === reduce.pl bib === id = cord-003792-v48xeqdz author = Izquierdo-Suzán, Mónica title = Natural Vertical Transmission of Zika Virus in Larval Aedes aegypti Populations, Morelos, Mexico date = 2019-08-17 pages = extension = .txt mime = text/plain words = 4017 sentences = 182 flesch = 47 summary = We characterized natural vertical transmission of Zika virus in pools of Aedes aegypti larvae hatched from eggs collected in Jojutla, Morelos, Mexico. We characterized natural vertical transmission of Zika virus in pools of Aedes aegypti larvae hatched from eggs collected in Jojutla, Morelos, Mexico. Several studies carried out under laboratory conditions have demonstrated that Zika virus can infect many different Aedes mosquito species (3) ; still, the key species for the transmission of Zika virus to humans are Ae. aegypti and Ae. albopictus (4) (5) (6) . In this study, we sought to demonstrate natural vertical transmission in Ae. aegypti mosquitoes by detecting viral RNA and isolating infectious Zika virus from larvae hatched from field-collected eggs. In this work, we were also able to demonstrate the natural vertical transmission of Zika virus in Ae. aegypti mosquitoes by the successful isolation of infectious Zika virus (31N) from larvae raised from field-collected eggs. cache = ./cache/cord-003792-v48xeqdz.txt txt = ./txt/cord-003792-v48xeqdz.txt === reduce.pl bib === id = cord-003767-9xbu4hnq author = Slingenbergh, Jan title = Animal Virus Ecology and Evolution Are Shaped by the Virus Host-Body Infiltration and Colonization Pattern date = 2019-05-25 pages = extension = .txt mime = text/plain words = 6287 sentences = 311 flesch = 48 summary = The synthesis of the findings reveals a predictive virus evolution framework, based on the outerto inner-body changes in the interplay of host environment-transmission modes-organ system involvement-host cell infection cycle-virus genome. Pieced together on this basis was an outer-to inner-body line-up of viruses by organ system or combination of organ systems, guided by the one-to-four virus infiltration score, the corresponding virus organ system tropism, the matching virus transmission modes, length of the infection and shedding periods, infection severity level, and virus environmental survival rate, see Figure 3 and, also, Figure S1d . Pieced together on this basis was an outer-to inner-body line-up of viruses by organ system or combination of organ systems, guided by the one-to-four virus infiltration score, the corresponding virus organ system tropism, the matching virus transmission modes, length of the infection and shedding periods, infection severity level, and virus environmental survival rate, see Figure 3 and, also, Figure S1d . cache = ./cache/cord-003767-9xbu4hnq.txt txt = ./txt/cord-003767-9xbu4hnq.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-002757-upwe0cpj author = Sullivan, Kathleen E. title = Emerging Infections and Pertinent Infections Related to Travel for Patients with Primary Immunodeficiencies date = 2017-08-07 pages = extension = .txt mime = text/plain words = 24212 sentences = 1364 flesch = 40 summary = The first section addresses general considerations, the second section profiles specific infections organized according to mechanism of transmission, and the third section focuses on unique phenotypes and unique susceptibilities in patients with PIDDs. This review does not address most parasitic diseases. In developing countries where polio is still endemic and oral polio vaccine is essential for eradicating the disease, it is of utmost importance that all PIDD patients and family members should not receive live oral polio (OPV) because of the reported prolonged excretion of the virus for months and even years [24] . As for host factors, although severe and fatal cases have been described in healthy immunocompetent hosts [129, 130] , there is evidence to suggest that children under the age of 10 [130] and immunocompromised hosts either secondary to hematologic malignancies, immunosuppressant treatment for organ transplantation, or HIV infection are at a greater risk to develop more severe disease with higher case fatality rates [131, 132] . cache = ./cache/cord-002757-upwe0cpj.txt txt = ./txt/cord-002757-upwe0cpj.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-004751-4vl0cvyq author = Mostow, S. R. title = The behaviour in vitro of attenuated recombinant influenza viruses date = 1973 pages = extension = .txt mime = text/plain words = 2245 sentences = 132 flesch = 60 summary = Influenza strains produced by recombination and tested as possible live vaccine candidates were studied in organ cultures of trachea. Two strains which proved to be too virulent in human volunteers regularly caused damage to the ciliated epithelium and viruses grew to high titre. Attenuated influenza viruses have been produced recently by genetic recombination of avirulent laboratory-adapted strains and virulent parents (BEARE and HALL, 1971; McCAHo~ and SCHILD, 1972) . This method, which is the most rapid means of producing attenuated influenza strains to date, results in a spectrum of both attenuated and virulent clones as judged by their effects in human volunteers. The use of L-15 medium and rolling the screw-topped tubes prolonged the survival of the ciliated epithelium beyond that obtained using other standard media, and, in the conditions finally used, the human embryo trachea regularly survived for periods of 30--50 and occasionally 90 days. The recombinant viruses did not cause ciliary damage, but at 5 days the growth in ferret epithelium was similar to that in human tissue. cache = ./cache/cord-004751-4vl0cvyq.txt txt = ./txt/cord-004751-4vl0cvyq.txt === reduce.pl bib === === reduce.pl bib === id = cord-004724-llex3yed author = Dea, S. A. title = Isolation of encephalomyocarditis virus among stillborn and post-weaning pigs in Quebec date = 1991 pages = extension = .txt mime = text/plain words = 2539 sentences = 150 flesch = 45 summary = Encephalomyocarditis (EMC) virus was isolated from aborted fetuses and lungs of suckling pigs from three Quebec pig farms that experienced outbreaks of reproductive failure in sows and respiratory problems in suckling and post-weaning piglets. Encephalomyocarditis (EMC) virus was isolated from aborted fetuses and lungs of suckling pigs from three Quebec pig farms that experienced outbreaks of reproductive failure in sows and respiratory problems in suckling and post-weaning piglets. Serological evidence of EMC virus infection was reported in Canadian swine herds and associated with sudden death in young piglets and reproductive problems [20, 21] . This report describes the isolation of EMC virus from the tissues of aborted fetuses and post-weaning piglets obtained from three different farms. Necropsied fetuses did not show typical gross and microscopic heart lesions previously reported from experimental and natural infection of newborn piglets with EMC virus [12] [13] [14] . An association between encephalomyocarditis virus infection and reproductive failure in pigs cache = ./cache/cord-004724-llex3yed.txt txt = ./txt/cord-004724-llex3yed.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-004774-fvf671jn author = Kjeldsberg, Elisabeth title = Detection of astroviruses in gut contents of nude and normal mice date = 1985 pages = extension = .txt mime = text/plain words = 1607 sentences = 116 flesch = 60 summary = Gut contents of nude and normal mice were examined by electron microscopy in association with an outbreak of diarrhea in a colony of nude mice. Gut contents of nude and normal mice were examined by electron microscopy in association with an outbreak of diarrhea in a colony of nude mice. Virus-like particles with a morphology consistent with previous descriptions of astroviruses of other species were demonstrated in a high percentage of the animals. Virus-like particles with a morphology consistent with previous descriptions of astroviruses of other species were demonstrated in a high percentage of the animals. In this note we report the detection of astrovirus-like partieles in gut contents from nude mice, with and without clinical signs of illness, and from normal symptomless mice in association with an outbreak of diarrhea. The morphology of the virus-like particles detected in gut contents of nude and normal mice corresponds to the previous description of astroviruses. cache = ./cache/cord-004774-fvf671jn.txt txt = ./txt/cord-004774-fvf671jn.txt === reduce.pl bib === === reduce.pl bib === id = cord-004781-ajf9zig0 author = Ray, N. B. title = Rabies viruses infect primary cultures of murine, feline, and human microglia and astrocytes date = 2014-03-07 pages = extension = .txt mime = text/plain words = 2337 sentences = 125 flesch = 43 summary = Primary cultures of murine, feline, and human microglia and astrocytes were infected with several different rabies viruses: two unpassaged street virus isolates, a cell culture-adapted strain, and a mouse brain-passaged strain. Primary cultures of murine, feline, and human microglia and astrocytes were infected with several different rabies viruses: two unpassaged street virus isolates, a cell culture-adapted strain, and a mouse brain-passaged strain. In addition, a number of studies have reported rabies viral antigens and virions in human [1, 13, 29] and murine astrocytes [10, 18, 23] , and in murine rami®ed microglial cells [27] , begging the question of the role of these cells in viral replication and persistence, as well as pathogenesis. In the present study, as an initial step toward evaluation of the potential involvement of these glial cells in rabies virus infections, we have directly examined the ability of different rabies virus strains and isolates to infect and replicate in primary cultures of microglia and astrocytes. cache = ./cache/cord-004781-ajf9zig0.txt txt = ./txt/cord-004781-ajf9zig0.txt === reduce.pl bib === id = cord-004775-foaf3vyl author = Weiss, Marianne title = The proposed family toroviridae: Agents of enteric infections date = 1987 pages = extension = .txt mime = text/plain words = 3946 sentences = 231 flesch = 56 summary = A morphologically similar virus (Lyon 4 virus) detected in cattle in Lyon, France (6, 7) , was shown later to possess an antigenic relatedness to the Berne (BEV) and Breda (BRV) viruses. In thin sections through BEV infected cells (horse kidney, embryonic mule skin, equine dermal cells) densely staining spherical, elliptieM and elongated particles were detected (2, 9) . Thin sections through BRV infected intestinal cells of calves (10, 11, 12) showed elongated viral particles with rounded ends measuring 42 × 100.5 nm. The high molecular weight virion protein in the range of 75-100 kD of BEV is glycosylated, probably by N-linked oligosaccharides since tunicamycin, an antibiotic known to inhibit N-linked oligosaccharide synthesis, prevented the formation of infectious virus as well as appearance of the 75-100 kD band in PAGE of infected cells (20) . Evidence of a reaction of the particles in human feces with sera containing antibodies against BRV and BEV, respectively, were obtained in IEM (8), (Flewett personal communication). cache = ./cache/cord-004775-foaf3vyl.txt txt = ./txt/cord-004775-foaf3vyl.txt === reduce.pl bib === id = cord-004827-bnf3mvaf author = Desselberger, U. title = Report on an ICTV-sponsored symposium on Virus Evolution date = 2005-01-13 pages = extension = .txt mime = text/plain words = 2766 sentences = 164 flesch = 48 summary = Phylogenetic relationships have been found useful for virus identification, work on origin, speed and mechanisms of evolution, taxonomy, and the elucidation of transmission pathways (e.g. the transmission of HIV from a source to a victim [16] ). In vitro, a single round of replication of HIV-1 in T lymphocytes generated on average 9 recombination events per virus [14] . Approximately 50% of sequence changes are consistent with evolution by point mutations; other changes are due to multiple recombination events. After an introduction in which basic genetic terms were defined (mutation and mutation rate, hypermutation, recombination, reassortment, segmentation etc), the quasispecies concept was presented according to which any sample of an RNA virus represents a 'swarm' of closely related mutants. 'To maintain RNA structure, evolution selects against better alternatives elsewhere in the genome'. The aim of the talk was to show the significance of RNA structural considerations for the evolution of viruses. Plant RNA virus evolution cache = ./cache/cord-004827-bnf3mvaf.txt txt = ./txt/cord-004827-bnf3mvaf.txt === reduce.pl bib === id = cord-004830-vmka378d author = Cursiefen, Dagmar title = In vitro cultivation of cells from the chorioallantoic membrane of chick embryos date = 1975 pages = extension = .txt mime = text/plain words = 2554 sentences = 177 flesch = 57 summary = By treatment of chorioallantoic membranes from embryonated eggs with collagenase and hyaluronidase before the conventional application of trypsin cells could be grown in culture which supported growth of a large variety of myxoviruses, herpesviruses, avian reoviruses and the infectious bronchitis virus of chickens. In an attempt to plaque-purify and to quantitatc some strains of influenza viruses and of avian reoviruses we succeeded to cultivate cells from the chorioallantoic membrane of chick embryos. The following strains were tested for their ability to grow, induce a cytopathie effect and form plaques in chorioallantoic cells of the chick embryo (CAM-cells). After an incubation period of 8 to 16hrs the media were assayed for hemagglutinating activity and for infectivity by plaque tests on the same cell type used for growing the viruses, i.e. CAM cells or chick embryo fibroblasts. cache = ./cache/cord-004830-vmka378d.txt txt = ./txt/cord-004830-vmka378d.txt === reduce.pl bib === id = cord-001521-l36f1gp7 author = nan title = Oral and Poster Manuscripts date = 2011-04-08 pages = extension = .txt mime = text/plain words = 183363 sentences = 11362 flesch = 53 summary = The IC 50 values determined in functional NI assays provide valuable information for detection of resistant viruses, but should not be used to draw direct correlations with drug concentrations needed to inhibit virus replication in the infected human host, as clinical data to support such inferences are inadequate. • Standardized reagents and protocols • Choice of detection technology • Simple instrumentation requirements • High sensitivity for use with low virus concentrations • Compatibility with batch-mode processing and largescale assay throughput • Broad specificity of influenza detection • Flexibility in assay format • Additional NA assay applications -cell-based viral assays, screening for new NIs, detection of NA from other organisms Functional neuraminidase inhibition assays enable detection of any resistance mutation and are extremely important in conjunction with sequence-based screening assays for global monitoring of virus isolates for NI resistance mutations, including known and new mutations. Such new assays need to include methods to measure local antibodies and virus-specific lymphocytes, especially in the case of live attenuated influenza vaccines, because of their potential to induce such broad-based immune responses. cache = ./cache/cord-001521-l36f1gp7.txt txt = ./txt/cord-001521-l36f1gp7.txt === reduce.pl bib === id = cord-004841-wf0o3whi author = Sibalin, M. title = Herpesvirus strigis, a new avian herpesvirus: II. Biochemical and biophysical properties date = 1974 pages = extension = .txt mime = text/plain words = 1900 sentences = 154 flesch = 57 summary = Tissue cultured virus proved sensitive to ether, chloroform, 0.5 per cent trypsin, and to pH levels of 4.0 or lower. Biological properties described in a foregoing paper sustained such grouping, and indicated that the agent was a new avian herpesvirus for which the nameherpesvirus strigis was proposed. According to Table 1 , both herpesviruses tested, i.e. HSIS and IBI~, got completely inactivated by ether as well as chloroform indicating that their virions were sensitive to lipid solvents. Other authors had observed similar core structures with some of their herpesviruses (12, 20) , and also fringes on the viral envelope (3, 12, 20) , of the size recorded here for herpesvirus strigis. Based on its biological properties described in our first paper (7), which allowed to differentiate it from other herpesviruses, we proposed tISIS as a new avian virus species to be named herpesvirus strigis. cache = ./cache/cord-004841-wf0o3whi.txt txt = ./txt/cord-004841-wf0o3whi.txt === reduce.pl bib === id = cord-005876-d8sid7gd author = Varnholt, V. title = ARDS infolge schwerer RSV-Infektion Therapeutische Optionen: Therapeutische Optionen date = 1996 pages = extension = .txt mime = text/plain words = 2394 sentences = 308 flesch = 55 summary = Wir berichten im folgenden ü ber eine auffallende Hä ufung schwerster RS-Virus-Pneumonien mit konsekutivem ARDS im Winterhalbjahr 1994/1995 in unserer Klinik und den Verlauf bei den betroffenen Patienten -nach der vergeblichen Anwendung "ü blicher" Behandlungsmethoden -wä hrend der Anwendung alternativer Therapieverfahren [NO-Inhalation, Hochfrequenzoszillationsbeatmung (HFOV), extrakorporale Membranoxygenierung (ECMO)]. Respiratory syncytial virus (RSV) -ARDS -Inhaled nitric oxide (NO) -High frequency oscillatory ventilation (HFOV) -Extracorporeal membrane oxygenation (ECMO) [10] . Krankheitsverlauf bei 10 Patienten mit RSV-Pneumonie unter alternativen Therapieverfahren wurden -in den verlegenden Institutionen -in 50 % der Fä lle eingesetzt, nach Ü bernahme von uns nur noch bei 2 Kindern: Die mö gliche obstruktive Komponente einer RSV-Infektion stand bei unseren Patienten nicht im Vordergrund, ersichtlich auch an den teilweise sehr niedrigen pCO 2 -Werten. Durch den Einsatz von NO oder/und HFOV kann bei schwer verlaufenden RSV-Infektionen -wie bei anderen Formen des kindlichen Lungenversagens -eine ECMO-Therapie manchmal vermieden werden. Ob bei beatmungspflichtigen Kindern mit RSV-Pneumonie ein frü herer Einsatz von NO und/oder HFOV zu einer weiteren Senkung der Letalität fü hrt, mü ssen weitere Beobachtungen zeigen. cache = ./cache/cord-005876-d8sid7gd.txt txt = ./txt/cord-005876-d8sid7gd.txt === reduce.pl bib === id = cord-005081-kxrzv16n author = Kiselev, O. I. title = Progress in the development of pandemic influenza vaccines and their production technologies date = 2010-11-12 pages = extension = .txt mime = text/plain words = 7263 sentences = 340 flesch = 44 summary = We are using the following approaches to the development of industrial production: use of nanoparticles and nanoemulsions as functional adjuvants, construction of totally-safe strains for live attenuated influenza vaccines with deletions of molecular determinants of pathogenicity, application of protein and chemical chaperones to provide self-assembly of haemagglutinin molecules of the H1N1v-2009 virus, and impregnation of whole-virion preparations with nanoparticles to enhance antigenicity. Europe and the United States agreed to allot grants and worked out programs for developing novel technologies and vaccine preparations with improved qualities: a new generation of LAIV, that is, delNS1 vaccines with a limited replicative potential, LAIV with deletions of pathogenicity factors in genes, latest variations of subunit vaccines enhanced by adju vants, and capsid nanovaccines and nanovaccines based on inactivated viruses and virus like particles [14] . A marked breakthrough in the construction of recombinant vaccines is related to the use of insect cells and the obtaining of virus like particles (VLPs) based on baculovirus expression vectors. cache = ./cache/cord-005081-kxrzv16n.txt txt = ./txt/cord-005081-kxrzv16n.txt === reduce.pl bib === id = cord-006819-sxz1s6kz author = Daniel Givens, M. title = Infectious causes of embryonic and fetal mortality date = 2008-05-27 pages = extension = .txt mime = text/plain words = 7666 sentences = 538 flesch = 46 summary = The clinical presentations of disease due to reproductive pathogens are emphasized, with a focus on assisting development of complete lists of causes that result in abortion and infertility in these species. Fetal maceration results when abortion or parturition fails to occur following fetal death and CL regression (occasionally in bovine www.theriojournal.com Available online at www.sciencedirect.com Theriogenology 70 (2008) 270-285 Table 1 Infectious causes of infertility and abortion in domestic animals Infected animals can experience signs of infertility due to early embryonic death and abortion between 4 and 7 months of gestation. Transmission occurs via contact with materials contaminated by infected respiratory or vaginal discharges; the bacteria then spread hematogenously to the fetus. Affected animals might have no clinical signs of disease, but serve as a source of infection, or they can abort late in gestation and have stillbirths. cache = ./cache/cord-006819-sxz1s6kz.txt txt = ./txt/cord-006819-sxz1s6kz.txt === reduce.pl bib === id = cord-005281-wy0zk9p8 author = Blinov, V. M. title = Viral component of the human genome date = 2017-05-09 pages = extension = .txt mime = text/plain words = 6583 sentences = 306 flesch = 44 summary = In the human genome, this capacity is determined by the portion of chromosomal DNA, which does not contain species-specific protein-encoding sequences and, thus, can basically make a place for novel information that will be modified to reach a new balance. In fact, the scope of the described phenomena is not limited to retroviruses as such, since the ubiquity of retroviral elements in animal genomes, their activity in germline cells [31] , along with the fact that viral replication depends significantly on RNA expression, allow retroviruses to contribute in different ways to the insertion of nonretroviral genes into animal germline cells. Finally, the ability to incorporate parts of the viral genome into the chromosomal DNA of host germline cells can vary strongly among different taxonomic groups of viruses, i.e., orders, families, genera, and even species If insertions of viral sequences remain functionally active in the host cell genome, they can give rise to either proteins that function in a new environment or untranslated RNAs of different sizes. cache = ./cache/cord-005281-wy0zk9p8.txt txt = ./txt/cord-005281-wy0zk9p8.txt === reduce.pl bib === id = cord-005885-r3qtoqu1 author = Hellmich, Luisa title = Exantheme nach Auslandsreisen date = 2019-10-09 pages = extension = .txt mime = text/plain words = 2645 sentences = 362 flesch = 50 summary = Auch wenn die jährlich übermittelten Zika-Virus-Infektionen insgesamt zurückgehen (2016: 222 Fälle, 2017: 69 Fälle, 2018: 18 Fälle), ist aufgrund der häufig symptomlosen Infektion von einer beträchtlichen Dunkelziffer auszugehen (RKI [Robert Koch-Institut]) [8] . Typisch für eine Zika-Virus-Infektion ist eine meist gleichzeitig mit dem Exanthem auftretende Konjunktivitis, die im Schnitt etwas länger als das Exanthem anhält (Median 4 bis 6 Tage) [9] . Bei der Erstinfektion mit einer der 4 DENV-Typen kann sich nach einer Inkubationszeit von 4 bis 7, maximal 14 Tagen ein klassisches Dengue-Fieber mit plötzlichem (häufig biphasischem) Fieber (>38°C), einem hämmernden Retrobulbärschmerz, starken muskuloskelettalen Schmerzen ("break-bone-fever") und Konjunktivitis entwickeln. Bei der Infektion mit dem zu den Togaviridae gehörenden RNA-Virus kommt es nach einer Inkubationszeit von 3 bis 12 Tagen zu einem plötzlichen Fieberanstieg, starken Kopfschmerzen und sehr heftigen bilateralen Arthralgien (v. cache = ./cache/cord-005885-r3qtoqu1.txt txt = ./txt/cord-005885-r3qtoqu1.txt === reduce.pl bib === id = cord-005246-cskb0njm author = Ludwig, George V. title = Insect-transmitted vertebrate viruses: Flaviviridae date = 1993 pages = extension = .txt mime = text/plain words = 8060 sentences = 416 flesch = 41 summary = Additionally, these culture systems permit the study of flavivirus attachment, penetration, replication, and release from cells and have been instrumental in the production and characterization of live-attenuated vaccines. Cell culture is essential for the study of flaviviruses, and will continue to play a pivotal role in the isolation, characterization, and development of new vaccines against current and future flavivirus health threats. More recent research has shown that fusion of dengue, yellow fever, and Japanese encephalitis viruses may in fact involve fusion of virus directly to the cell's plasma membrane (52, 108) . The observation that persistent dengue virus infections can be established in a non-vector mosquito cell line associated with changes in several of the important biological characteristics, such as temperature sensitivity and antigenic structure (64) , presents the possibility that genetic selection of attenuated virus strains may be possible with insect cell lines. cache = ./cache/cord-005246-cskb0njm.txt txt = ./txt/cord-005246-cskb0njm.txt === reduce.pl bib === id = cord-005258-gps8rzb5 author = Liu, William J. title = The triphibious warfare against viruses date = 2017-12-01 pages = extension = .txt mime = text/plain words = 1616 sentences = 78 flesch = 45 summary = Different elements may drive the current trends in emerging and re-emerging infectious diseases, which are as follows: (i) the contact patterns between human beings, their commensal organisms, and wildlife reservoirs are changing due to human behaviors, (ii) the interaction between viruses and their potential hosts and vectors, such as bats and mosquitoes, may cause changes in *Corresponding author (William J. The Chinese Academy of Sciences (CAS) has been one of the backbone forces during this process and has been playing essential roles in the fight against infectious diseases since 2005, when the H5N1 sub-type, a highly pathogenic avian influenza virus (HPAI), was identified among wild birds in Qinghai Lake (Liu et al., 2005) . The majority of emerging infectious diseases in human beings are zoonotic, which indicates the fundamental role of wildlife, especially rodents and bats, as the reservoirs of emerging viruses (Olival et The surveillance of viruses among natural vectors is also an important work, considering the recent global spread of arthropod-borne viruses such as Zika virus and dengue virus. cache = ./cache/cord-005258-gps8rzb5.txt txt = ./txt/cord-005258-gps8rzb5.txt === reduce.pl bib === id = cord-006790-lye0qjw8 author = Song, R. title = Surveillance of the first case of human avian influenza A (H7N9) virus in Beijing, China date = 2013-10-16 pages = extension = .txt mime = text/plain words = 2779 sentences = 191 flesch = 58 summary = A number of specimens from the environment of this cluster and from the feces specimens tested positive for viral RNA of the H7N9 virus on the fourth day following onset of the index case's illness. A number of specimens from the environment of this cluster and from the feces specimens tested positive for viral RNA of the H7N9 virus on the fourth day following onset of the index case's illness. Fifteen hours after the fever began, the pharyngeal swab collected from the index case tested positive for the H7N9 virus by RT-time PCR. Pharyngeal swabs collected from the index case's mother tested positive for the H7N9 virus on 12 April and 14 April and were negative after 15 April. Although the family members of the index case were all exposed to asymptomatic chickens infected with H7N9 virus, they presented with distinct outcomes. cache = ./cache/cord-006790-lye0qjw8.txt txt = ./txt/cord-006790-lye0qjw8.txt === reduce.pl bib === id = cord-006997-sghhdjyi author = Rowland, M.G.M. title = Viruses and diarrhoea in West Africa and London: a collaborative study date = 1978-01-17 pages = extension = .txt mime = text/plain words = 1758 sentences = 96 flesch = 58 summary = Rotaviruses and, in some cases, adenoviruses are found on electron microscopy of faeces of a substantial proportion of children with acute diarrhoea in various parts of the world and there is evidence that these organisms can cause the disease (BISHOP et al., 1974; BRYDEN et al., 1975; MIDDLETON et al., 1974; SEXTON et al., 1974; FLEWETT et al., 1975; SCHOUB et al., 1975) . This study was undertaken to look systematically and by comparable techniques for the viral causes of childhood diarrhoea in a typical village in rural Africa and a comparison group of children and adults in north-west London. cache = ./cache/cord-006997-sghhdjyi.txt txt = ./txt/cord-006997-sghhdjyi.txt === reduce.pl bib === id = cord-006089-08g206kf author = Stevens, James title = Glycan microarray technologies: tools to survey host specificity of influenza viruses date = 2006-10-02 pages = extension = .txt mime = text/plain words = 6075 sentences = 255 flesch = 41 summary = These proteins are rich in α2-3-linked sialosides (sialylated glycans), and function to trap avian influenza viruses and prevent their attachment to epithelial cells 12 Recent studies have revealed that some human epithelial cells in the lower respiratory tract contain α2-3-linked sialic acids and can be directly infected by avian influenza viruses 10, 11, 13 . Therefore, it is clear that, although human and avian virus HAs have a primary specificity for either α2-6or α2-3-linked sialosides, each virus might use a different range of glycan receptors for cell entry, and the ability of a virus to infect a host cell might depend on features in the glycan structure, other than simply the type of sialic-acid linkage. By working together, future development of DNA and glycan microarray technologies could enable rapid assessment of emerging viruses to detect virus subtypes and receptor specificities that increase the risk to the human population, and to eliminate guesswork from sequence analyses alone. cache = ./cache/cord-006089-08g206kf.txt txt = ./txt/cord-006089-08g206kf.txt === reduce.pl bib === id = cord-004848-2cfphi88 author = Carter, M. J. title = Transcription of feline calicivirus RNA date = 1990 pages = extension = .txt mime = text/plain words = 3361 sentences = 190 flesch = 60 summary = In this way these workers have identified three intracellular RNAs (4.8, 4.2, and 2.4 kb) as well as the genome (8.2 kb) and shown that these form a nested set of 3' co-terminal molecules similar to that observed in coronavirus infected cells. We have used this to probe FCV-infected cells for the synthesis of virus specific RNA and confirm and extend the observations of Neill and Mengeling. Subcloning of the virus 3' end into a single stranded vector has allowed us to examine the occurrence of positive and negative sense RNA separately. Finally this inference was confirmed by subcloning the terminal EcoRI/PstI fragment into M13 and determining its sequence (Fig. 3a) , This showed a poly A stretch preceded by a short run ofpoly C which is exactly that structure expected for cDNA clones derived by this method from an mRNA 3' end. However, the negative strand-specific probe also showed hybridization to subgenomic messages 2-4, but this was not observed until later in infection than the detection of the positive forms of these molecules. cache = ./cache/cord-004848-2cfphi88.txt txt = ./txt/cord-004848-2cfphi88.txt === reduce.pl bib === id = cord-006129-5rog0s98 author = Hemida, Maged Gomaa title = Exploiting the Therapeutic Potential of MicroRNAs in Viral Diseases: Expectations and Limitations date = 2012-08-16 pages = extension = .txt mime = text/plain words = 7443 sentences = 508 flesch = 50 summary = [12] Answering back, certain host miRNAs alter the cell gene expression to defend the cells against the viral infection by interfering with viral proteins or other cellular factors as a type of immune response against these particular viruses. [40] These virus-encoded miRNAs play important roles in the establishment of latent infection, as well as the pathogenesis of virally induced diseases. According to the most recent studies, herpesviruses utilize their encoded miRNAs in a wide range of biologic functions, such as inhibition of apoptosis, immune evasion, control of cellular proliferation, and regulation of viral replication. [58] Downregulation of UL114 protein, using miR-UL112-1, results in inhibition of viral DNA replication and subsequently triggers the latent phase of infection, making the virus able to evade the host immune system. cache = ./cache/cord-006129-5rog0s98.txt txt = ./txt/cord-006129-5rog0s98.txt === reduce.pl bib === id = cord-004998-wuixnqy5 author = Arnold, W. title = Identic viral infections in four cases of malignant lymphoepithelioma date = 1978 pages = extension = .txt mime = text/plain words = 421 sentences = 31 flesch = 57 summary = The viral particles found in this study are not yet described in human lymphoepithelioma; they are very similar to those found in tissue culture lines derived from Burkitt's lymphoma (Epstein, 1962) and from nasopharyngeal carcinoma (De The et al., 1969) . The demonstration of herpes virus like nucleocapsids in malignant lymphoepithelioma might be of great interest because many of those patients show a changing level of EB-virus antibody titer during therapy or recurrence of the disease (Lynn et al., 1977) . This fact points at the possible role of a specific viral infection although it has to be mentioned that elevated EB-virus antibody titer is also present in mononucleosis or recurrent tonsillitis (Veltri et al., 1975) . Lymphoblastoid transformation and presence of herpes-type viral particles in a Chinese nasopharyngeal tumor cultured in vitro Prognosis of nasopharyngeal carcinoma by Epstein-Barr virus antibody titer cache = ./cache/cord-004998-wuixnqy5.txt txt = ./txt/cord-004998-wuixnqy5.txt === reduce.pl bib === id = cord-007149-m4xsx9ev author = Morahan, Pages S title = VIRUSES AND THE VERSATILE MACROPHAGE date = 1985-01-17 pages = extension = .txt mime = text/plain words = 6129 sentences = 375 flesch = 43 summary = 5S~63 Enhanced infection requires monocytes, peritoneal MuJ>or M(J>-like cell lines with Fc receptors, and non-cytophilic IgG antibody that exhibits virus serotype or cross-reactive specificity. Monocytes or M4> infected with CMV, influenza, Sendai or poliovirus have been shown to be suppressive Functions of mononuclear phagocytes that may be affected by virus infection Chemotaxis Attachment and phagocytosis of particles through nonspecific, Fc or complement receptors Intracallular oxidatrve response Lysosome-phegosome fusion Intracellular microbicidaJ activity Synthesis and/or secretion of txologicalry active molecules, e.g. prostaglandini, neutral proteases, interferon and complement Antigen presentation Regulation of immune responses, i e accessory and suppressor activity M$ activation procees for microbicidai and tumoncidal activity Antibody dependent cytotoxicrty (ADCC) by M$ Wound healing ONA synthesis and M$ proliferation in response to macrophage growth factor Mi) differentiation for certain lymphocyte responses. Antibody-mediated enhancement of dengue virus infection in mouse macrophage cell lines, Mkl and Mini (41802) cache = ./cache/cord-007149-m4xsx9ev.txt txt = ./txt/cord-007149-m4xsx9ev.txt === reduce.pl bib === id = cord-006252-cbelsymu author = Gross, Peter A. title = Current Recommendations for the Prevention and Treatment of Influenza in the Older Population date = 2012-11-18 pages = extension = .txt mime = text/plain words = 7666 sentences = 466 flesch = 49 summary = Other groups merit consideration (Recommendations of the Immunization Practices Advisory Committee 1990): (a) in the general population, anyone who wishes to reduce the chance of acquiring influenza infection; (b) anyone who provides essential community services and persons living or working in an institutional setting; (c) persons infected with HIV should be vaccinated, although they may not respond as well if their disease is far advanced; and (d) foreign travellers should be immunised when travelling to the trop-Prevention and Treatment of Influenza implication here is that B cell epitopes are intact external molecules such as haemagglutinins, while T cell epitopes appear to be linear sequences exposed by enzymatic breakdown of the original molecule. cache = ./cache/cord-006252-cbelsymu.txt txt = ./txt/cord-006252-cbelsymu.txt === reduce.pl bib === id = cord-006954-ec9x8thb author = Aznar, María title = Viral nanomechanics with a virtual atomic force microscope date = 2018-07-04 pages = extension = .txt mime = text/plain words = 9014 sentences = 433 flesch = 50 summary = Rather than focusing on a specific virus, the VAFM will be used to analyze how the mechanical response and breaking of viruses depend on different parameters controlling the effective interactions between capsid's structural units. Instead of placing the focus on the finest structural details of the nanoindentation of a specific virus, the aim is to provide a highly coarse-grained description, allowing to simulate large viruses at realistic timescales and with the advantage of being able to link the mechanical behavior to the essential physical ingredients of the interaction between capsid's structural units. Next, we will show how the elastic response of viruses depends on different physical parameters of their effective interactions, including the bending rigidity of the shell, the adsorption to the substrate, the radius of the AFM tip or the capsid shape. cache = ./cache/cord-006954-ec9x8thb.txt txt = ./txt/cord-006954-ec9x8thb.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-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-007898-nky7bo6u author = HUGHES, C.S. title = Effects of certain stress factors on the re-excretion of infectious laryngotracheitis virus from latently infected carrier birds date = 2018-09-04 pages = extension = .txt mime = text/plain words = 2227 sentences = 112 flesch = 60 summary = authors: HUGHES, C.S.; GASKELL, R.M.; JONES, R.C.; BRADBURY, J.M.; JORDAN, F.T.W. title: Effects of certain stress factors on the re-excretion of infectious laryngotracheitis virus from latently infected carrier birds Experiments were set up to assess the effects of 'natural' and 'artificial' stresses on the re-excretion of infectious laryngotracheitis (ilt) virus in latently infected chickens recovered from the acute phase of the disease. Experiments were set up to assess the effects of 'natural' and 'artificial' stresses on the re-excretion of infectious laryngotracheitis (In) virus in latently infected chickens recovered from the acute phase of the disease. It appears from these studies that the 'nat ural' stress of rehousing and, or, the addition of a contact bird, and also the onset of lay may increase the shedding rate in the ILT virus carrier. Nine of the 10 birds shed virus after onset of lay compared with only two in the three-and-a-half weeks before, and there was a highly significant increase in the overall number of virus isolations during this period. cache = ./cache/cord-007898-nky7bo6u.txt txt = ./txt/cord-007898-nky7bo6u.txt === reduce.pl bib === id = cord-007362-pjpkz6wv author = Bielefeldt-Ohmann, Helle title = The Pathologies of Bovine Viral Diarrhea Virus Infection: A Window on the Pathogenesis date = 2016-01-06 pages = extension = .txt mime = text/plain words = 9006 sentences = 442 flesch = 40 summary = Pathologic lesions caused by bovine viral diarrhea virus (BVDV) infections comprise a wide spectrum of type, degree, and, by implication, pathogenesis, including congenital defects, necrotic-erosive lesions in mucosal epithelia and skin, and reactive as well as degenerative changes in lymphoid tissues. 3, 22, 29 In PI calves, BVDV can be isolated from lung tissue, and virus antigen is widespread in bronchiolar and alveolar epithelial cells, however, without accompanying histopathologic changes (see section on persistent infection without overt clinical disease and Fig. 5 ).17 Conversely, a proportion (the size varying with study) of cattle succumbing to BRD are positive for BVDV, by virus isolation from or antigen detection in lung tissue, but the ensuing pathologic changes cannot be distinguished from those of other viral pathogens in the BRD complex (perhaps with the exception of BHV-P5), and usually are dominated by the pathology caused by the secondary bacterial agent. cache = ./cache/cord-007362-pjpkz6wv.txt txt = ./txt/cord-007362-pjpkz6wv.txt === reduce.pl bib === id = cord-006106-u5npu6ng author = Attoui, H. title = Genus Coltivirus (family Reoviridae): genomic and morphologic characterization of Old World and New World viruses date = 2002 pages = extension = .txt mime = text/plain words = 7023 sentences = 357 flesch = 51 summary = We report a genomic and morphologic study of the European Eyach (EYA) virus (genus Coltivirus, family Reoviridae) and a comparative analysis with the American Colorado tick fever (CTF) virus (the type species of the genus). These findings, together with the comparative analysis to genomes of south-east Asian isolates, support the recent classification of arboviruses with 12 segments of dsRNA within two distinct genera (genus Coltivirus and genus Seadornavirus) and raise interesting questions about the evolutionary origins of coltiviruses. Analyses of VP5 showed the presence of a potential phosphamide linkage site (amino acid 342-347 of CTF virus: LNYDKY and for EYA virus: LNYIKH) comparable to that found in the protein encoded by segment 2 of members of the genus Orthoreovirus (position 1166-1171: ANPDKF, 40). Sequence determination and analysis of the full-length genome of Colorado tick fever virus, the type species of genus Coltivirus (family Reoviridae) cache = ./cache/cord-006106-u5npu6ng.txt txt = ./txt/cord-006106-u5npu6ng.txt === reduce.pl bib === id = cord-008700-knbf8m4x author = Rodrigues, Merlyn R. title = Methods for Rapid Detection of Human Ocular Viral Infections date = 2013-10-30 pages = extension = .txt mime = text/plain words = 3011 sentences = 171 flesch = 38 summary = Simple techniques of immunofluorescence and negative stain electron microscopy are used for the rapid detection of viruses in human adenoviral, herpetic, rubella, molluscum contagiosum, and vaccinial infections. Lens aspirate from a 2-year-old patient with clinical ocular rubella was examined by immunofluorescence and negative stain electron microscopy. 10 In a recent epidemic of EKC at a Vietnamese refugee camp in Florida, adenovirus type 8 was recovered in 81% of cases cultured within two weeks of onset of infection.U Dawson et aP 2 described adenovirus-like particles in the conjunctiva of one patient and in the corneal epithelium of another by transmission electron microscopy of tissue culture preparations. In the present study, the typical virions of herpes simplex keratitis were readily identified both by immunofluorescence and by negative stain transmission electron microscopy. Herpes simplex hominis type 1 was recovered in culture and demonstrated by direct immunofluorescence and negative stain electron microscopy in three patients with herpetic dendritic keratitis. cache = ./cache/cord-008700-knbf8m4x.txt txt = ./txt/cord-008700-knbf8m4x.txt === reduce.pl bib === id = cord-006892-n2ncamqh author = Donaldson, Braeden title = Virus-like particle vaccines: immunology and formulation for clinical translation date = 2018-09-19 pages = extension = .txt mime = text/plain words = 9775 sentences = 456 flesch = 31 summary = For example, chemical conjugation of mannoside-based saccharides on the surface of Rabbit hemorrhagic disease virus (RHDV) VLP selectively targets the mannose receptor expressed on the surface of APCs, inducing increased uptake and alteration of antigen cross-presentation in murine dendritic cells [57] . While the induction of a potent humoral immune response and the subsequent production of anti-VLP antibodies is the primary desired outcome of most commercial VLP vaccines, these is increasing appreciation for the role of vaccine-induced cell-mediated immunity [123] [124] [125] . Novel Epstein-Barr virus-like particles incorporating gH/gL-EBNA1 or gB-LMP2 induce high neutralizing antibody titers and EBV-specific T-cell responses in immunized mice Induction of immune memory following administration of a prophylactic quadrivalent human papillomavirus (HPV) types 6/11/16/18 L1 virus-like particle (VLP) vaccine. Antigen incorporated in virus-like particles is delivered to specific dendritic cell subsets that induce an effective antitumor immune response in vivo cache = ./cache/cord-006892-n2ncamqh.txt txt = ./txt/cord-006892-n2ncamqh.txt === reduce.pl bib === id = cord-008454-8brxpotx author = Field, Anne M. title = Diagnostic Virology Using Electron Microscopic Techniques date = 2008-04-09 pages = extension = .txt mime = text/plain words = 18793 sentences = 981 flesch = 50 summary = The morphology of negatively stained virus particles is sufficient for grouping purposes but it is necessary to use immune electron microscopy (IEM) to differentiate morphologically identical but antigenically distinct viruses. Virus particles are sometimes present in such large numbers in clinical specimens that they can be detected directly by electron microscopy and negative staining methods in particular can be used to provide a rapid diagnosis. Immune electron microscopy on sectioned material presents considerable technical difficulties and viral content of tissue homogenates may be too low for negative stain IEM so a virus seen in the tissue cannot always be sufficiently well identified for diagnostic purposes. Similarly, thin section studies on livers of marmosets infected with hepatitis A virus showed cytoplasmic picornavirus-like particles which could be extracted for use as antigen to detect antibodies by negative stain IEM (Provost et al., 197513) and by complement fixation (Provost et al., 1975a) . cache = ./cache/cord-008454-8brxpotx.txt txt = ./txt/cord-008454-8brxpotx.txt === reduce.pl bib === id = cord-007733-zh8e76w7 author = DiMenna, Lauren J. title = Pandemic Influenza Vaccines date = 2009-06-15 pages = extension = .txt mime = text/plain words = 12728 sentences = 594 flesch = 43 summary = The efficacy of seasonal vaccines is linked to their ability to induce virus-neutralizing antibodies, which provide subtype-specific protection against influenza A viruses. Alternatively, the scientific community could step up efforts to generate a universal vaccine against influenza A viruses that provides broadly cross-reactive protection through the induction of antibodies or T cells to conserved regions of the virus. Alternatively, the scientific community could step up efforts to generate a universal vaccine against influenza A viruses that provides broadly cross-reactive protection through the induction of antibodies or T cells to conserved regions of the virus. WHO recommends three measures to lessen the impact of the next influenza virus pandemic: (1) increased surveillance to allow for the earliest possible warning that a human pandemic has started; (2) early intervention to stall global spread and prevent further adaptations; and (3) development of an effective pandemic vaccine. cache = ./cache/cord-007733-zh8e76w7.txt txt = ./txt/cord-007733-zh8e76w7.txt === reduce.pl bib === id = cord-007792-596jxrm5 author = Luo, Ming title = Influenza Virus Entry date = 2011-08-26 pages = extension = .txt mime = text/plain words = 12446 sentences = 635 flesch = 56 summary = The key player in virus entry is the surface glycoprotein HA that contains the host receptor binding site to allow the virus particle to attach to specifi c host cells, the fusion peptide that is inserted into the target cellular membrane during membrane fusion, and other structural elements that may refold during the membrane fusion process. When the HA amino acid substitutions are accumulated in the repertoire of infl uenza virus strains, they are mostly on the exposed surface of the HA glycoprotein except for the receptor binding site, the fusion peptide, and the amino acids that accommodate the fusion peptide before HA structural changes for membrane fusion (Wilson et al. The next 18 amino acids form part of the pocket that accommodates the hydrophobic fusion peptide in the metastable HA structure on the infl uenza virion prior to virus entry. cache = ./cache/cord-007792-596jxrm5.txt txt = ./txt/cord-007792-596jxrm5.txt === reduce.pl bib === id = cord-009615-xcz8m9a7 author = Stoner, Gerald L. title = Polyomavirus Models of Brain Infection and the Pathogenesis of Multiple Sclerosis date = 2008-01-28 pages = extension = .txt mime = text/plain words = 6395 sentences = 329 flesch = 44 summary = Animal models of viral demyelination and studies showing that JC virus (JCV), the polyomavirus which causes progressive multifocal leukoencephalopathy (PML), may be latent in some normal human brains suggest another possibility. It is thought that an MS virus could be one of two basic types: 1) A rare agent which infects relatively few individuals but is frequently pathogenic, or 2) A common agent which infects a majority of the population and perhaps a significant number of normal brains, but, in which the virus expression and the host response to the infection ( Immunocytochemical studies in our laboratory indicate that perivascular cellular infiltration, apparently due to immunological reactivity to SV40 antigens, occurs in this model (Fig. 1) . Thus, simian immunodeficiency virus (S1V)-infected macaques should be observed regularly for the possible occurrence of MS-like signs with demyelination attributable to mononuclear cell infiltration in response to abortively infected glial cells, rather twa-stage process of deletion and duplication known as "brain adaptation" to generate the progressive multifocal leukoencephalopathy (PML)-type viral genome capable of replicating in glial cells of the human brain. cache = ./cache/cord-009615-xcz8m9a7.txt txt = ./txt/cord-009615-xcz8m9a7.txt === reduce.pl bib === id = cord-006640-25ykas09 author = Fedson, David S. title = What treating Ebola means for pandemic influenza date = 2018-07-16 pages = extension = .txt mime = text/plain words = 5824 sentences = 278 flesch = 43 summary = Physicians should be prepared to undertake clinical trials of widely available generic drugs to determine whether they improve survival in patients with seasonal influenza, other emerging virus diseases, and other forms of acute critical illness. An experience during the recent Ebola outbreak in Sierra Leone (2014-2016) suggests that inexpensive generic drugs might be used to treat patients with pandemic influenza and other emerging virus diseases. Several new investigational treatments targeting the Ebola virus were tested in clinical trials in West Africa (Guinea, Liberia, Sierra Leone): antiviral agents, convalescent plasma, and monoclonal antibody preparations [3, 4] . The Ebola treatment experience in Sierra Leone suggests that generic drugs targeting the host response might be used to treat patients who develop severe illness due to pandemic influenza, other emerging virus diseases, and everyday diseases like seasonal influenza, bacterial sepsis, and community-acquired pneumonia [11] . cache = ./cache/cord-006640-25ykas09.txt txt = ./txt/cord-006640-25ykas09.txt === reduce.pl bib === id = cord-007575-5ekgabx5 author = Luby, James P. title = Southwestern Internal Medicine Conference: Pneumonias in Adults Due to Mycoplasma, Chlamydiae, and Viruses date = 2016-01-14 pages = extension = .txt mime = text/plain words = 11991 sentences = 735 flesch = 39 summary = Important trends and developments in the field include (1) the emergence of a Chlamydia psittaci strain (TWAR) that is passaged from human to human, causes a mycoplasma-like illness, and that is relatively resistant to erythromycin, (2) the recognition of respiratory syncytial virus as a pathogen in nursing home outbreaks and in immunosuppressed adults, (3) the continuing high lethality of fully developed influenza pneumonia, (4) the efficacy of acyclovir and adenine arabinoside in limiting the complications of varicella-zoster virus infections, and (5) the increasing frequency of pneumonia caused by cytomegalovirus and the severity of this disorder in highly immunosuppressed patients. Important trends and developments in the field include (1) the emergence of a Chlamydia psittaci strain (TWAR) that is passaged from human to human, causes a mycoplasma-like illness, and that is relatively resistant to erythromycin, (2) the recognition of respiratory syncytial virus as a pathogen in nursing home outbreaks and in immunosuppressed adults, (3) the continuing high lethality of fully developed influenza pneumonia, (4) the efficacy of acyclovir and adenine arabinoside in limiting the complications of varicella-zoster virus infections, and (5) the increasing frequency of pneumonia caused by cytomegalovirus and the severity of this disorder in highly immunosuppressed patients. cache = ./cache/cord-007575-5ekgabx5.txt txt = ./txt/cord-007575-5ekgabx5.txt === reduce.pl bib === id = cord-008013-blf57r7u author = Hartmann, K. title = Feline immunodeficiency virus infection: an overview date = 2005-03-02 pages = extension = .txt mime = text/plain words = 7164 sentences = 464 flesch = 47 summary = Acquired immune dysfunction in cats with experimentally induced feline immunodeficiency virus infection: comparison of short-term and long-term infections Programmed cell death (apoptosis) as a mechanism of cell death in peripheral blood mononuclear cells from cats infected with feline immunodeficiency virus (FIV) Journal ¢![ the American VeteHna U Medical Association hnmunization-induced decrease of the CD4+ CD8+ ratio in cats experimentally infected ~,4th feline immunodeficiency virus, l/etm4na O, Immunolo~, and hnm u nopathoh~© Effects of incidental infections and immnne activation on disease progression in experimentally feline immunodeficiency virus-infected cats Characterization of mo'rphologic changes and lymphocyte subset distribution in lymph nodes from cats with naturally acquired feline immunodeficiency virus infection Gag-and em,-specific antibodies in cats after natural and experimental infection with feline immunodeficiency virus. Effect of 3'-acido-2',3'-dideoxythymidine (AZT) on experimental feline immunodeficiency virus infection in domestic cats Progressive immune dysfunction in cats experimentally infected with feline immunodeficiency virus Pathogenesis of experimentally induced feline immunodeficiency virus infection in cats cache = ./cache/cord-008013-blf57r7u.txt txt = ./txt/cord-008013-blf57r7u.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-008556-oetrdm8g author = Kozak, Marilyn title = Regulation of Protein Synthesis in Virus-Infected Animal Cells date = 2008-03-01 pages = extension = .txt mime = text/plain words = 23945 sentences = 1270 flesch = 51 summary = One consequence of the scanning mechanism is that deleting the "ribosome binding site" (i.e., the normal initiator codon and flanking sequences) will not abolish translation; ribosomes will simply use the next AUG codon downstream, which, in some cases, has been shown to direct the synthesis of a biologically active, truncated protein (Downey et al., 1984; Halpern and Smiley, 1984; Katinka and Yaniv, 1982) . The best evidence for this is the ability of both EMC and SFV 26 S mRNA to be translated in EMC virus-infected cells, in which host translation is drastically inhibited by a mechanism that has not been difined, but that clearly does not involve cap binding protein (Mosenkis et al., 1985) . In wild-type adenovirus-infected cells, in which host protein synthesis is drastically reduced, both adenovirus and influenza virus mRNAs are translated efficiently. cache = ./cache/cord-008556-oetrdm8g.txt txt = ./txt/cord-008556-oetrdm8g.txt === reduce.pl bib === id = cord-006285-kkxdmzk9 author = Smirnova, S. S. title = Long-Term Maintenance of the Functional Changes Induced by Influenza A Virus and/or LPS in Human Endothelial ECV-304 Cell Sublines date = 2019-08-26 pages = extension = .txt mime = text/plain words = 4686 sentences = 175 flesch = 43 summary = The present work reports the comparative assessment of the functional changes which take place in human ECV-304 endothelial cell sublines obtained previously by the long-term culturing of cells after exposure to varying infectious doses (IDs) of influenza A virus, and/or bacterial lipopolysaccharide (LPS). It has been demonstrated that, in the course of long-term culturing (six passages) after exposure to pathogenic agents (influenza virus and/or LPS), endothelial cells maintain changes in their migratory activity, permeability, and expression of mRNA for cytokines TNFα and TGFβ (along with the changes in their proliferation activity, which has been demonstrated earlier). The comparative study of the human endothelial ECV-304 cell sublines carried out in the present work and in our previous work (Smirnova et al., 2018) has demonstrated that the infection of nonpermissive cells with influenza A virus (both in high and in very low doses) and exposure to LPS can change migratory, proliferation, and apoptotic activity of cells and impair cell barrier function. cache = ./cache/cord-006285-kkxdmzk9.txt txt = ./txt/cord-006285-kkxdmzk9.txt === reduce.pl bib === id = cord-007094-ur9sz21s author = Mahabir, Esther title = Rodent and Germplasm Trafficking: Risks of Microbial Contamination in a High-Tech Biomedical World date = 2008-01-01 pages = extension = .txt mime = text/plain words = 6254 sentences = 268 flesch = 39 summary = Preservation of mouse germ-plasm is achieved by cryopreservation of spermatozoa, embryos, or ovaries, and embryonic stem cells are used for the production of genetically engineered mice. In this article, we discuss regulations and practical issues in the shipping of live mice and mouse tissues, including spermatozoa, embryos, ovaries, and embryonic stem cells, and review work on microbial contamination of these biological materials. The importation paperwork for cryopreserved laboratory mouse tissues and cell lines is similar to that required for live animal importation to the United States (i.e., a pro forma invoice and declaration statements). Embryo transfer recipients in rederivation programs should be held in individually ventilated cages (IVCs 1 ) until testing shows that they are free of all unwanted microorganisms, including those listed in Appendix 3 of the Federation of Laboratory Animal Science Associations (FELASA) recommendations (Nicklas et al. Risk assessment of mouse hepatitis virus infection via in vitro fertilization and embryo transfer by the use of zona-intact and laser-microdissected oocytes cache = ./cache/cord-007094-ur9sz21s.txt txt = ./txt/cord-007094-ur9sz21s.txt === reduce.pl bib === id = cord-008149-kdlcaium author = Blacklaws, B.A. title = Emerging viruses of zoonotic and veterinary importance date = 2017-12-30 pages = extension = .txt mime = text/plain words = 690 sentences = 44 flesch = 51 summary = Emerging viruses of zoonotic and veterinary importance To enable discussion of all aspects of emerging virus infections, an Emerging Viruses meeting was held at the University of Nottingham, UK, on 27-29 July 2015. Given the success of this meeting, a second meeting was organised, now called 'Emerging Viruses of Zoonotic and Veterinary Importance', at Churchill College, Cambridge, UK, on 24-26 July 2017 to encourage discussion of emerging virus infections from a One Health perspective. This is formulated in the One Health approach to infectious disease, where the possibility of infectious agent movement between species, including human beings, is key. Whilst a major driver of emerging virus disease research is public health concern over zoonotic infections, there are also veterinary drivers for emerging viral diseases. With the accelerating changes in our world, emerging viral infections will continue to be an important issue for human and veterinary health. cache = ./cache/cord-008149-kdlcaium.txt txt = ./txt/cord-008149-kdlcaium.txt === reduce.pl bib === id = cord-007717-7x1mqqmf author = Lowen, Anice C. title = Transmission in the Guinea Pig Model date = 2014-07-08 pages = extension = .txt mime = text/plain words = 8045 sentences = 414 flesch = 46 summary = This chapter describes influenza virus infection, growth, and transmission in guinea pigs; highlights how these properties differ among influenza viruses adapted to human, swine, and avian hosts; and provides an overview of knowledge gained through the study of influenza virus transmission in the guinea pig model. By virus histochemistry, the H3N2 subtype human influenza viruses studied (Pan/99 and A/Netherlands/213/03) attached mainly to the guinea pig upper respiratory tract and the trachea, with little to no binding detected on bronchiolar and alveolar epithelia. Seasonal H3N2 viruses and 2009 H1N1 pandemic strains show similar and high efficiency of transmission in both contact and respiratory droplet models (Lowen et al. Reverse genetics-derived Pan/99 viruses with and without the NA-E119V mutation were found to transmit with equal efficiency in the guinea pig contact transmission model, as had been seen with similar isolates in the ferret model (Herlocher et al. cache = ./cache/cord-007717-7x1mqqmf.txt txt = ./txt/cord-007717-7x1mqqmf.txt === 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 === id = cord-007764-7750z41g author = Smith, M. L. title = Display of Peptides on the Surface of Tobacco Mosaic Virus Particles date = 2009 pages = extension = .txt mime = text/plain words = 7201 sentences = 336 flesch = 42 summary = In this review, we focus on the potential that tobacco mosaic virus (TMV) has as a carrier for immunogenic epitopes, and the factors that must be considered in order to bring products based on this platform to the market. There are well-established methodologies for recombinant production of VLP-epitope display systems that use self-assembling capsid proteins of several different viruses, most notably papillomaviruses, hepatitis B core and surface antigens, and various bacteriophages, including the leviviruses MS2 and Qβ. The focus of this review is on some of the practical issues that must be considered in order to bring plant-produced virus particle and VLP-based epitope display systems into commercial use. Commercial-scale biomanufacturing allows translation of the body of data providing proof of the concept that TMV can function as an effective carrier for antigenic peptides into vaccine products for human and veterinary applications (Pogue et al. cache = ./cache/cord-007764-7750z41g.txt txt = ./txt/cord-007764-7750z41g.txt === reduce.pl bib === id = cord-009504-sn00p8iw author = Taguchi, Fumihiro title = Pathogenesis of Mouse Hepatitis Virus Infection: The Role of Nasal Epithelial Cells as a Primary Target of Low‐Virulence Virus, MHV‐S date = 2013-11-14 pages = extension = .txt mime = text/plain words = 3453 sentences = 170 flesch = 54 summary = The pathogenesis of mouse hepatitis virus (MHV‐S) infection in suckling and weanling mice was comparatively studied after intranasal inoculation. In the posterior part of the brain and spinal cord, virus was detected on days 3 to 4 postinoculation when viral growth was clearly demonstrable in the liver, spleen and intestines. In weanling mice, however, neither infectious virus nor viral antigen was detected in the liver or other visceral organs, while serum neutralizing antibody became detectable on day 5 postinoculation, increasing in titer thereafter. 2A and 2B , significant viral growth was observed in the brain, spinal cord ( Fig. 2A) and head without brain (Fig. 2B) , whereas no virus was demonstrated in the spleen or liver of the infected mice with a few exceptions (not included in the figures). In 4-week-old mice, however, no or little infectious virus was detected in the liver or other visceral organs, although high titered virus demonstrable in the brain was probably disseminated from the nasal mucosa as was observed in suckling mice. cache = ./cache/cord-009504-sn00p8iw.txt txt = ./txt/cord-009504-sn00p8iw.txt === reduce.pl bib === id = cord-008686-9ybxuy00 author = Everett, Tom title = Poor transmission of seasonal cold viruses in a British Antarctic Survey base date = 2019-03-14 pages = extension = .txt mime = text/plain words = 6924 sentences = 362 flesch = 54 summary = However, in the acute infection stage respiratory viruses are generally present in relatively high copy numbers, with median values of mostly 4-8 log 10 (i.e. 10,0 0 0-10 0,0 0 0,0 0 0 copies/ml) for adeno-, corona-, hMPV, influenza, PIV and RSV, as reported in one comprehensive paediatric study. 2 A 26-year-old male ( index case of the outbreak report 2 ) from Kerala's Perambra town died undiagnosed with fever, en-cephalitis and respiratory distress in Government Medical College Kozhikode(GMCK), after being transferred from Taluk Hospital, Perambra(THP). 6 Along with the wound cleansing and post-exposure rabies immunoglobulin (RIG) and vaccination, any risk of SHBV requires that high dose acyclovir (preferably valaciclovir 1 g TDS PO; or acyclovir 800 mg 5 times daily PO, for adults) PEP for at least 14 days should be considered. After the first dengue-fever epidemic in China, which occurred in May 1978 in Foshan, Guangdong Province, there have been regional outbreaks of dengue every year and the number of cases has increased. cache = ./cache/cord-008686-9ybxuy00.txt txt = ./txt/cord-008686-9ybxuy00.txt === reduce.pl bib === id = cord-009383-ozx5u0t3 author = Sheppard, Michael title = Viral Vectors for Veterinary Vaccines date = 2007-09-28 pages = extension = .txt mime = text/plain words = 4166 sentences = 203 flesch = 43 summary = Second, genes from pathogens that encode proteins that will induce an appropriate protective immune response and can be stably integrated into the vector's genome and expressed need to be identified. The vector only expresses the antigens from the pathogen that are required to elicit a protective immune response and therefore reduces or eliminates the chance of disease by being exposed to the whole pathogen as with a killed or modified live vaccine. One of the main disadvantages of using viral vectors for vaccine delivery is that like subunit vaccines each vector can only deliver one or a relatively small number of foreign antigens to the host animal and therefore rely on those being able to elicit a completely protective immune response. Construction of a defective adenovirus vector expressing the pseudorabies virus glycoprotein gp50 and its use as a live vaccine Expression in recombinant vaccinia virus of the equine herpesvirus 1 gene encoding glycoprotein 13 and protection of immunized animals cache = ./cache/cord-009383-ozx5u0t3.txt txt = ./txt/cord-009383-ozx5u0t3.txt === reduce.pl bib === id = cord-008333-1wepke2o author = Weisz, Ora A. title = Chapter 7 Use of Recombinant Vaccinia Virus Vectors for Cell Biology date = 2008-02-28 pages = extension = .txt mime = text/plain words = 7465 sentences = 461 flesch = 56 summary = The recombinant virus is selected, expanded, and used to infect cells, which then express high levels of the foreign protein. Transfection of cells immediately after infection with a vector containing the gene of interest cloned behind a T7 promoter results in rapid and efficient expression of the encoded protein. The use of an early vaccinia promoter to drive the foreign gene is essential for cell biology applications, since the protein will be expressed before most of the cytopathic effects of the virus infection become evident. Before growing a large-scale preparation of the recombinant, we also test that the expressed protein is the correct size by immunoprecipitation from radiolabeled infected cells, followed by electrophoresis in SDS polyacrylamide gels (see Section IV,C,l). Expression is mediated by co-infecting the cells with another vaccinia virus encoding T7 RNA polymerase (vTF7-3). This chapter has discussed the preparation and use of recombinant vaccinia viruses to express proteins in mammalian cells. cache = ./cache/cord-008333-1wepke2o.txt txt = ./txt/cord-008333-1wepke2o.txt === reduce.pl bib === id = cord-007784-fq2urilg author = Elderfield, Ruth title = Influenza Pandemics date = 2011-09-22 pages = extension = .txt mime = text/plain words = 10484 sentences = 539 flesch = 51 summary = H5N1 virus has been responsible for over 500 cases of human infection and 300 deaths (as of 31st August 2010 according to the World Health Organisation avian influenza surveillance system) but thankfully has not yet reassorted with a human-adapted influenza virus, nor given rise to a pandemic outbreak [45] . For avian influenza viruses to adapt to and transmit between humans, it is now apparent that in addition to the reassortment events that occur during antigenic shift, their HA proteins must also undergo modifications that alter their fine receptor binding specificity. However, the human seasonal virus had changed so dramatically that it shared only 79% amino acids with the 1918 HA protein, and this did not allow for any antigenic cross protection for humans who had been infected with seasonal H1 in recent years against the novel 2009 pandemic strain. cache = ./cache/cord-007784-fq2urilg.txt txt = ./txt/cord-007784-fq2urilg.txt === reduce.pl bib === id = cord-007170-svsfu7fj author = Richt, J. A. title = Infection with Borna Disease Virus: Molecular and Immunobiological Characterization of the Agent date = 1992-06-17 pages = extension = .txt mime = text/plain words = 6125 sentences = 325 flesch = 42 summary = Studies on BDV may help to illuminate several important areas of neurobiology, including the mechanisms regulating the replication of a new type of RNA virus in the nuclei of neural cells, the neuroinvasiveness and neurotropism of such viruses, their T cell-mediated immunopathology, tolerance in newborn animals to persistent viral infection of the central nervous system, and behavioral diseases and eating disorders induced by such agents. Persistently infected MDCK (Madin-Darby canine kidney) cells are widely used in indirect immunofluorescence assays for the detection of BDV-specific antibodies in serum and CSF of affected animals and humans [18, 20] . The pathological changes in the brain and retina of BDVinfected animals resemble certain types of encephalitis and Most studies on the pathogenesis of BDV infection have involved experimentally inoculated Lewis rats. Although infection of newborn rats resulted in persistent viral replication in the CNS as well as in visceral organs, these animals developed no inflammatory response or signs of Borna disease. cache = ./cache/cord-007170-svsfu7fj.txt txt = ./txt/cord-007170-svsfu7fj.txt === reduce.pl bib === id = cord-008716-38sqkh9m author = Schmidt, Alexander C title = Current research on respiratory viral infections: Third International Symposium date = 2001-06-01 pages = extension = .txt mime = text/plain words = 24743 sentences = 1086 flesch = 43 summary = Renewed efforts in vaccine development against respiratory viruses began in the 1960s with the observation that infants and young children, after having recovered from respiratory tract infection with adenoviruses, shed virus from their gastrointestinal tract for an extended period of time without experiencing gastrointestinal symptoms. Earlier studies of viral pathogens in immunocompromised adults indicated that CMV, herpes simplex, influenza, parainfluenza, rhinovirus, adenovirus, enterovirus, and RSV cause lower respiratory infection (Connolly et al., 1994) . Children with RSV, adenovirus or influenza virus infections have a 30% risk of developing AOM within 2 weeks of the onset of the respiratory tract infection (Henderson et al., 1982) , and coinfection with bacteria and viruses also adversely influences the outcome of AOM. Populations at high risk for complications resulting from respiratory viral infections are now better defined and a more targeted prophylaxis is possible, be it passive prophylaxis against RSV disease with monoclonal antibody preparations or active prophylaxis with influenza-or adenovirus vaccines. cache = ./cache/cord-008716-38sqkh9m.txt txt = ./txt/cord-008716-38sqkh9m.txt === reduce.pl bib === id = cord-009820-fi54s0x7 author = Andries, K. title = Pathogenicity of Hemagglutinating Encephalomyelitis (Vomiting and Wasting Disease) Virus of Pigs, using Different Routes of Inoculation date = 2010-05-13 pages = extension = .txt mime = text/plain words = 3845 sentences = 289 flesch = 56 summary = SUMMARY: Forty‐eight pigs were inoculated by different routes with the VW 572 isolate of the hemagglutinating encephalomyelitis (vomiting and wasting disease) virus. The present studies were primarily designed to determine whether a virus isolate, obtained from pigs with the vomiting and wasting syndrome only, could produce clinical signs after inoculation by different routes. When sick, pigs were killed at time intervals varying from one to five days after the appearance of clinical signs and different tissues were collected for virus isolation. From the pigs killed at different time intervals after inoculation, the following tissues were collected for virus isolation : nasal mucosa, tonsils, lungs (apical and cardiac lobes), pyloric region of the stomach, pons and medulla combined, cerebrum, cerebellum and blood clot. Forty-eight pigs were inoculated by different routes with the VW 572 isolate of the hemagglutinating encephalomyelitis (vomiting and wasting disease) virus. cache = ./cache/cord-009820-fi54s0x7.txt txt = ./txt/cord-009820-fi54s0x7.txt === reduce.pl bib === id = cord-009589-xfdgk2j6 author = Spradbrow, P. B. title = VIRUS DISEASES OF DOMESTIC ANIMALS date = 2008-03-10 pages = extension = .txt mime = text/plain words = 926 sentences = 57 flesch = 53 summary = Viruses multiply solely from their genetic material of DNA or RNA when this is introduced into a susceptible cell and provides a code for the production of new virus genetic material and structural components. Much progress has been made towards the grouping (classifying) of related viruses by a consideration of the nature of their genetic material and of certain stable features of the infectious particle or virion. Surprisingly, many veterinary viruses that produce severe disease in conventional animals cause only mild disease in the germ-free host. In fact, the herpesvirus of feline rhinotracheitis is an unusual virus in producing a disease in germ-free animals comparable in severity with that seen naturally (Hoover et a1 1970) . group of agents, and the relative importance of the various defence mechanisms will probably vary with the nature of the infecting virus and of the host. cache = ./cache/cord-009589-xfdgk2j6.txt txt = ./txt/cord-009589-xfdgk2j6.txt === reduce.pl bib === id = cord-007710-0u5ot5h4 author = Graham, Barney S. title = Challenges and Opportunities for Respiratory Syncytial Virus Vaccines date = 2013-05-24 pages = extension = .txt mime = text/plain words = 4113 sentences = 161 flesch = 36 summary = Several technological and conceptual advances have recently occurred that make RSV vaccine development more feasible, and this collected knowledge is intended to help inform and organize the future contributions of funding agencies, scientists, regulatory agencies, and policy makers that will be needed to achieve the goal of a safe, effective, and accessible vaccine to prevent RSV-associated disease. Barik, this volume), and suggest that vaccines that elicit responses that block or avoid the immunomodulation associated with wild-type RSV infection without enhancing disease could provide more potent and durable immunity than natural infection. These include the need for improved animal models, better understanding of mucosal immunity, more definitive clinical endpoints to use in efficacy trials, alternate vaccination strategies to protect the young infant (e.g., vaccinating pregnant women) and other high risk populations for whom vaccination may have limited effectiveness, and remedies for liability concerns. cache = ./cache/cord-007710-0u5ot5h4.txt txt = ./txt/cord-007710-0u5ot5h4.txt === reduce.pl bib === id = cord-009702-02bo7pnl author = SCOTT, G. R. title = Guidelines for the Control of Equine Viral Infections date = 2010-04-23 pages = extension = .txt mime = text/plain words = 3364 sentences = 253 flesch = 53 summary = At least twenty‐eight of the fifty‐eight viruses induce clinical disease but the range of syndromes is limited; eleven provoke respiratory symptoms and eleven cause encephalitis. There is possibly one Coronavirus infecting horses; Ditchfield (1969) isolated a virus from a Thoroughbred with undifferentiated respiratory disease and found that it possessed a morphology similar to that of infectious bronchitis virus of poultry, the type-virus of the Coronavirus group. Equine infectious anaemia virus probably belongs to the Oncornavirus group, i.e. the RNA tumour viruses. Eleven of the thirty-four known vector-transmitted viruses cause disease and vaccines have been developed against six of them (Table VII) . Seventeen of the twenty known viral contagions of horses cause disease and vaccines have been developed against five of them (Table VIII ). At least twenty-eight of the fifty-eight viruses induce clinical disease but the range of syndromes is limited; eleven provoke respiratory symptoms and eleven cause encephalitis. The vector-transmitted virus diseases are best controlled by prophylactic vaccination. cache = ./cache/cord-009702-02bo7pnl.txt txt = ./txt/cord-009702-02bo7pnl.txt === reduce.pl bib === id = cord-009577-29u7pdpk author = Gonzalez‐Scarano, F. title = Molecular pathogenesis of neurotropic viral infections date = 2004-10-08 pages = extension = .txt mime = text/plain words = 6374 sentences = 294 flesch = 41 summary = To cause systemic illness, a virus must first enter the host animal, undergo primary replication at a site near its portal of entry, and then ultimately spread to distant target tissues, such as the central nervous system (CNS). An infecting animal virus faces two main blocks to penetration of the CNS or any other specific target organ: (1) a variety of barriers prevent the free access of viruses to target cells, and (2) even when these barriers are ineffective, only certain cell types will support the internalization and replication of a particular virus. Monoclonal antibody variants have been used to map the antigenic sites of the influenza hemagglutinin 122, 76, 771 and have been used successfully to define important regions of the cellular binding proteins of rabies virus, reovirus, coronaviruses, and the California serogroup-all CNS pathogens. Viruses bind to the plasma membrane of susceptible target cells through specific receptors which may be proteins (HIV), lipids (vesicular stomatitis virus), or contain sialic acid (reovirus, influenza) [21, 641. cache = ./cache/cord-009577-29u7pdpk.txt txt = ./txt/cord-009577-29u7pdpk.txt === reduce.pl bib === id = cord-007731-wu7i548j author = Sriwilaijaroen, Nongluk title = Molecular Basis of a Pandemic of Avian-Type Influenza Virus date = 2014-05-27 pages = extension = .txt mime = text/plain words = 9917 sentences = 484 flesch = 49 summary = Change in HA antigen either by accumulation of mutations in HA1 of fi ve proposed antigenic sites (based on amino acid sequence comparison among viruses isolated from different years or among variants grown in the presence of mouse monoclonal antibodies) as shown in Fig. 7c [ 56 -59 ] or by intrasubtypic reassortment between distinct clades of co-circulating infl uenza A viruses [ 35 ] is responsible for evasion of recognition by the host antibodies and thus Cleavage site 324P-X-X/R/K-X-X-R/K↓GLF X = nonbasic residue 324P-X-R/K-X-R/K-R↓GLF (due to insertion/substitution) Host proteases Extracellular tissue-restricted trypsin-like proteases Ubiquitously expressed intracellular proteases (e.g., furin and PC6) continuous circulation of the virus in host populations. However, highly mutable avian infl uenza A viruses that have sporadically continued direct transmission to and infection in humans have raised concerns for pandemic potential with unpredictable pathogenesis (depending on virus-host interactions). cache = ./cache/cord-007731-wu7i548j.txt txt = ./txt/cord-007731-wu7i548j.txt === reduce.pl bib === id = cord-009561-pg4jmvw4 author = Johnson, Richard T. title = The virology of demyelinating diseases date = 2004-10-08 pages = extension = .txt mime = text/plain words = 3602 sentences = 204 flesch = 34 summary = The possible role of a virus or viruses is supported by data that (1) a childhood exposure is involved and "viral" infections may precipitate exacerbations of disease, (2) experimental infections in animals and natural infections in humans can cause diseases with long incubation periods, remitting and relapsing courses, and demyelination, and (3) patients with multiple sclerosis have abnormal immune responses to viruses. Thud, studies of patients with multiple sclerosis consistently have shown higher levels of antibody against measles virus in serum and cerebrospinal fluid (CSF) than in controls and in some studies antibodies have been elevated to other viral agents as well (Table 2) . In studies of CSF we found no intrathecal synthesis of antibody in posuneasles encephalomyelitis to suggest antigenic stimulation Subsequently, a variety of diseases of the central and peripheral nervous system and muscle have been described as complications of HIV infection [58, 591. cache = ./cache/cord-009561-pg4jmvw4.txt txt = ./txt/cord-009561-pg4jmvw4.txt === reduce.pl bib === id = cord-007843-yqdqm4rh author = Shader, Richard I. title = Zoonotic Viruses: The Mysterious Leap From Animals to Man date = 2018-07-26 pages = extension = .txt mime = text/plain words = 980 sentences = 88 flesch = 58 summary = Nipah and Hendra viruses are both members of the Paramyxoviridae family; neither virus is known to cause disease in their host bats. Similarly, although infrequent, the H1N1 influenza virus can be transmitted from infected pigs to humans, hence its common name of swine flu. 8 Even more uncommon is for a virus to be transmitted from an infected human to an animal. In theory, infected humans could transmit the rabies virus to animals; no cases have been documented. For this issue of Clinical Therapeutics, our Infectious Diseases Topic Editor Dr Ravi Jhaveri has assembled a collection of articles entitled "Hot Topics in Viral Diseases." The collection highlights recent controversies in vaccine licensure and recommendation, as well as advances in antiviral therapies for herpesvirus, hepatitis B and C, respiratory syncytial virus, and influenza, with an emphasis on pediatric patients. A review of therapeutics in clinical development for respiratory syncytial virus and influenza in children cache = ./cache/cord-007843-yqdqm4rh.txt txt = ./txt/cord-007843-yqdqm4rh.txt === reduce.pl bib === id = cord-009836-7o6htufh author = Borrow, Persephone title = Cytotoxic T‐lymphocyte escape viral variants: how important are they in viral evasion of immune clearance in vivo? date = 2006-04-28 pages = extension = .txt mime = text/plain words = 10041 sentences = 299 flesch = 34 summary = Epitope mapping performed using the Gpl 60 sequence of the patient's autologous early HIV-1 population indicated that this response was in fact extremely focused on a single epitope encompassing Gpl60 amino acids 30-38(9), recognized in association with HLA-B44, The frequency of epitope-specific CTL was extremely high: at the earhest timepoint available for study, which may have been shghtly after the peak of the primary immune response, 1 in 1 7 peripheral blood mononuclear cells (EBMCs) were found to score as virus-specific CTL precursors by limiting dilution analysis, a technique which has recently been shown to greatly underestimate the total numher of epitope-specific T cells (55, 56) , As shown in Fig, 1 , viral variants bearing mutations in the epitopic sequence which conferred escape from recognition by epitope-specific CTL rapidly appeared in this patienc, and then increased in frequency until 164/1998 they had cotnpieteiy repiaced the transmitted virai strain. cache = ./cache/cord-009836-7o6htufh.txt txt = ./txt/cord-009836-7o6htufh.txt === reduce.pl bib === id = cord-010248-ln800g5z author = Sissons, J.G. Patrick title = Antibody-Mediated Destruction of Virus-Infected Cells date = 2008-02-29 pages = extension = .txt mime = text/plain words = 14994 sentences = 687 flesch = 44 summary = When lz5I-1abeled IgG antibody was bound to the surface of measles virus-infected cells at the start of the culture period, under the conditions described above for antigenic modulation, about 40% of the radioactivity was still cell associated at 12 hours and nearly all was protein bound Perrin and Oldstone, 1977) . Lysis by human serum of cells infected with HSV types 1 and 2, influenza A, parainfluenza 1, 2, 3, and 4, mumps, and measles viruses was dependent on the presence in serum of IgG antibody specific for the relevant virus and of complement (reviewed by Oldstone and Lampert, 1979) . The use of this system, composed of 11 highly purified complement proteins, provided conclusive evidence that the known proteins of the alternative and membrane attack pathways with IgG antibody are sufficient for lysis of the measles virus-infected cell, without other serum factors. It is apparent that considerably more surface-bound IgG is required to induce complement-dependent lysis of virus-infected cells than is required for antigenic modulation or antibody-dependent cell-mediated cytotoxicity. cache = ./cache/cord-010248-ln800g5z.txt txt = ./txt/cord-010248-ln800g5z.txt === reduce.pl bib === id = cord-007530-eyk015n3 author = Powell, H.C. title = Electron-microscopic appearance of the DA virus, a demyelinating murine virus() date = 2003-03-06 pages = extension = .txt mime = text/plain words = 2105 sentences = 100 flesch = 48 summary = cache = ./cache/cord-007530-eyk015n3.txt txt = ./txt/cord-007530-eyk015n3.txt === reduce.pl bib === id = cord-008551-yu71iewp author = Parrish, Colin R. title = Emergence, Natural History, and Variation of Canine, Mink, and Feline Parvoviruses date = 2008-04-11 pages = extension = .txt mime = text/plain words = 11842 sentences = 635 flesch = 52 summary = This chapter discusses the emergence of canine parvovirus (CPV), the evidence concerning the previous emergence of mink enteritis virus (MEV) as the cause of a new disease in minks in the 1940s, and the mechanisms that determine the host ranges and other specific properties of the viruses of cats, minks, and dogs. Feline panleukopenia virus (FPV), MEV, and CPV are classified as "host range variants." In addition to the viruses of cats, minks, and dogs, similar viruses naturally infect many species within the families Felidae, Canidae, Procyonidae, Mustelidae, and possibly the Viverridae. Feline panleukopenia virus (FPV), MEV, and CPV are classified as "host range variants." In addition to the viruses of cats, minks, and dogs, similar viruses naturally infect many species within the families Felidae, Canidae, Procyonidae, Mustelidae, and possibly the Viverridae. cache = ./cache/cord-008551-yu71iewp.txt txt = ./txt/cord-008551-yu71iewp.txt === reduce.pl bib === id = cord-009144-3slh1nbk author = Jacobs, J.W. title = RESPIRATORY SYNCYTIAL AND OTHER VIRUSES ASSOCIATED WITH RESPIRATORY DISEASE IN INFANTS date = 1971-05-01 pages = extension = .txt mime = text/plain words = 3288 sentences = 218 flesch = 60 summary = Diagnosis by virus isolation and serology was attempted in 377 cases of respiratory-tract infection in infants under one year of age admitted to hospital during two winters. THERE have been few intensive studies of respiratoryvirus infections of infants.1-5 To prevent these infections, it is necessary to know which viruses cause the most severe illness and whether maternal antibody plays any part in their prevention. We report here the results of a survey of respiratory-virus infections in infants under one year of age in hospital. In this survey, as in others, R.s. virus was the commonest cause of respiratory illness requiring admission at this age (40°0), and the illnesses were more severe than those associated with other viruses (table iv). 23 Effect of Maternal Antibody The few parainfluenza virus infections observed in this survey occurred only in infants more than four months of age. cache = ./cache/cord-009144-3slh1nbk.txt txt = ./txt/cord-009144-3slh1nbk.txt === reduce.pl bib === id = cord-010159-uo47oab1 author = Jartti, Tuomas title = Respiratory viruses and acute asthma in children date = 2007-04-02 pages = extension = .txt mime = text/plain words = 571 sentences = 41 flesch = 56 summary = title: Respiratory viruses and acute asthma in children We read with great interest the article by Khetsuriani et al 1 on the prevalence of respiratory tract viruses in children with asthma. The results of PCR analysis of combined nasopharyngeal and throat swabs for 13 different viruses were positive in 63% of patients with asthma exacerbation in the 1-year study. We disagree with the low virus detection rate reported by Khetsuriani et al 1 because many studies in wheezing children have shown virus detection rates of close to 90%. 1 Interestingly, 2 or more viruses were detected in 43% of the children compared with 7% in the study by Khetsuriani et al. Our findings suggest that nearly all exacerbations of asthma in children necessitating hospitalization are associated with viral infection. Prevalence of viral respiratory tract infections in children with asthma Human bocavirus and acute wheezing in children cache = ./cache/cord-010159-uo47oab1.txt txt = ./txt/cord-010159-uo47oab1.txt === reduce.pl bib === id = cord-009791-k09vcq96 author = Osterhaus, A. title = Antiviral Antibodies in Dogs in the Netherlands date = 2010-05-13 pages = extension = .txt mime = text/plain words = 3041 sentences = 214 flesch = 57 summary = SUMMARY: Antiviral antibodies in dogs in the Netherlands A collection of more than 700 canine sera, coming from open and closed populations and from kennels with frequent neonatal mortality, were screened for the prevalence of antibodies to canine adenoviruses, canine herpesvirus, polyoma virus, REOviruses, parainfluenza viruses, equine influenza viruses and vomiting and wasting disease virus of pigs. Sera from six animal attendants from a CP kennel, cornprizing a total of at least 170 dogs, were tested for the prevalence of HA1 antibodies to CAV,, CAV, , REOvirus types 1, 2 and 3, parainfluenzavirus types 1, 2 and 3 and VW virus. Summary Antiviral antibodies in dogs in the Netherlands A collection of more than 700 canine sera, coming from open and closed populations and from kennels with frequent neonatal mortality, were screened for the prevalence of antibodies to canine adenoviruses, canine herpesvirus, polyoma virus, REOviruses,. cache = ./cache/cord-009791-k09vcq96.txt txt = ./txt/cord-009791-k09vcq96.txt === reduce.pl bib === id = cord-010016-fs8pjy1z author = WEBB, H. E. title = CAN VIRAL ENVELOPE GLYCOLIPIDS PRODUCE AUTO‐IMMUNITY, WITH REFERENCE TO THE CNS AND MULTIPLE SCLEROSIS? date = 2008-05-12 pages = extension = .txt mime = text/plain words = 2976 sentences = 154 flesch = 47 summary = In this paper it is proposed that CNS demyelination could arise in susceptible individuals (HLA type) from an immune response to glycolipids, triggered by the carrier effect of one or more enveloped neurotropic viruses. The demyelination is dependent upon T-lymphocytes probably cytotoxic cells (Jagelman et al., 1978; Fazakerley, Amor & Webb 1983; Pathak et al., 1983) and probably results from an immune reaction against viral antigens on the surface of oligodendrocytes or myelin. Since all are budding viruses they will have a similar host derived viral envelope provided the virus replicates in the same cell type. It is an intriguing possibility that CNS demyelination in diseases such as MS, arises as a result of an auto-immune reaction against specific glycolipids, induced by the carrier effect of a budding neurotropic virus. I n this way any number of enveloped neurotropic viruses could be involved in initiating and restimulating a n autoimmune response to the same brain cell membrane specific glycolipid(s). cache = ./cache/cord-010016-fs8pjy1z.txt txt = ./txt/cord-010016-fs8pjy1z.txt === reduce.pl bib === id = cord-011917-6u0t4hy8 author = Skarlupka, Amanda L. title = Immune Imprinting in the Influenza Ferret Model date = 2020-04-08 pages = extension = .txt mime = text/plain words = 7904 sentences = 456 flesch = 37 summary = Therefore, the use of naïve ferret sera for vaccine strain selection is potentially misrepresentative of the pre-immune human population that receives each season's influenza virus vaccines, contributing to the observed VE. Unique to sequentially infected ferrets, the elicited antibody profile was broader and interacted with pandemic A(H1N1) HA compared to the single pre-immunity groups as measured with HA-specific ELISA binding. In contrast to previous reports that pre-immunity induced protection does not wane [68] , the boosts in anti-HA stalk antibodies and the cross-reactivity induced from sequential infection with antigenically distinct seasonal A(H1N1) declined over time [74] . The current pre-immunity models are moving away from investigating the differences in disease symptoms and vaccine effectiveness observed in the human population in response to the pandemic virus. Pre-immunity to a historical A(H3N2) virus helped boost the magnitude and breadth of the broadly neutralizing antibodies elicited by computationally optimized broadly reactive antigen (COBRA) immunogens compared to a naïve ferret group [37] . cache = ./cache/cord-011917-6u0t4hy8.txt txt = ./txt/cord-011917-6u0t4hy8.txt === reduce.pl bib === id = cord-010189-makhaypd author = Yamashita, Teruo title = VI, 3. Molecular biology and epidemiology of Aichi virus and other diarrhoeogenic enteroviruses date = 2004-09-14 pages = extension = .txt mime = text/plain words = 3009 sentences = 157 flesch = 50 summary = Stool samples from adult patients in six oyster-associated gastroenteritis outbreaks were examined for variation, based on their reactivity with a monoclonal antibody raised against the standard strain (A486/88) and on reverse transcription–polymerase chain reactions (RT-PCR) of three genomic regions. Aichi virus was isolated in Vero cells from 7 (12.5%) of 56 patients in 6 gastroenteritis outbreaks, 5 (0.7%) of 722 Japanese travelers returning from tours to Southeast Asian countries and complaining of gastrointestinal symptoms at the quarantine station of Nagoya International Airport in Japan, and 5(2.3%) of 222 Pakistani children with gastroenteritis (Yamashita et al., 1993; Yamashita et al., 1995) . In the ELISA, 15 (26.8%) of 56 stool samples from adult patients in six oyster-associated gastroenteritis outbreaks were found to be positive for Aichi virus. The Aichi virus RNA was detected in 54 (55%) of 99 fecal specimens from patients in 12 (32%) of 37 outbreaks of gastroenteritis in Japan. cache = ./cache/cord-010189-makhaypd.txt txt = ./txt/cord-010189-makhaypd.txt === reduce.pl bib === id = cord-008764-j9qmw4zy author = nan title = Chapter 1 The need for chemotherapy and prophylaxis against viral diseases date = 2008-05-29 pages = extension = .txt mime = text/plain words = 6399 sentences = 273 flesch = 47 summary = We shall examine the methods developed for the prevention of measles, influenza, polio and rotaviruses later on (Chapters 8, 7, 4 and 9, respectively) but it may be mentioned here that live polio vaccines used so successfully in industrialized countries are much more difficult to apply successfully in third world countries where problems of vaccine administration, heat lability control and viral interference become very important. The greatest challenges and probably the most difficult and medically important areas for prophylaxis and therapy of viral diseases are those viruses which are rapidly changing in antigenic composition and/or viruses with animal reservoirs (influenza and arboviruses) and also those forming latent infections (herpesviruses). The greatest challenges and probably the most difficult and medically important areas for prophylaxis and therapy of viral diseases are those viruses which are rapidly changing in antigenic composition and/or viruses with animal reservoirs (influenza and arboviruses) and also those forming latent infections (herpesviruses). cache = ./cache/cord-008764-j9qmw4zy.txt txt = ./txt/cord-008764-j9qmw4zy.txt === reduce.pl bib === id = cord-009846-o6wj8z6e author = Wroblewska, Zofia title = Rat tracheal organ culture supports replication of parainfluenza 1 (6/94) virus and promotes 6/94 virus rescue from latently infected human brain cells date = 2005-12-06 pages = extension = .txt mime = text/plain words = 2471 sentences = 138 flesch = 54 summary = title: Rat tracheal organ culture supports replication of parainfluenza 1 (6/94) virus and promotes 6/94 virus rescue from latently infected human brain cells For example, Cytochalasin treatment of indicator cells has been shown to enhance the rescue of 6/94 virus from latently infected human brain cells [Wroblewska et al, 19781 after cocultivation. For these reasons, we decided to study the replication of 6/94 virus in rat TOC and to determine its applicability for rescue of 6/94 virus from latently infected human brain cell cultures. The ability of rat TOC to promote 6/94 virus rescue from latently infected human brain cells is shown in Table 1 . Transfer of rat TOC that had been cocultivated with normal human brain cells to CV, cells did not result in 6/94 virus detection. TOC provides a favorable growth environment for a large number of viruses as well as a system that is capable of rescuing virus from latently infected human brain cells. cache = ./cache/cord-009846-o6wj8z6e.txt txt = ./txt/cord-009846-o6wj8z6e.txt === reduce.pl bib === id = cord-010235-hu6o1ggc author = Atmar, Robert L. title = Nonculturable agents of viral gastroenteritis date = 1997-12-01 pages = extension = .txt mime = text/plain words = 3989 sentences = 190 flesch = 43 summary = (3) provided the first clear demonstration of the causal relationship between a virus (Norwalk virus [NV] ) and gastroenteritis by using immune electron microscopy (IEM) to detect the presence of viral particles in the stools of individuals from an epidemic outbreak of gastroenteritis. This article describes the structure and genome organization of the human caliciviruses that cause gastroenteritis, the clinical and epidemiologic features of these viruses, and new methods for the laboratory diagnosis of infection with these viruses. The inability to cultivate the HuCVs and establish neutralization assays has prevented the definition of specific serotypes; however, at least five different serotypes are thought to exist based on early human cross-challenge studies and comparisons of the IEM and enzyme-linked immunosorbent assay (ELISA) reactivities of several prototype virus strains. cache = ./cache/cord-010235-hu6o1ggc.txt txt = ./txt/cord-010235-hu6o1ggc.txt === reduce.pl bib === id = cord-010188-884d196k author = Schlesinger, Sondra title = Alphaviruses — vectors for the expression of heterologous genes date = 2004-08-26 pages = extension = .txt mime = text/plain words = 3049 sentences = 140 flesch = 47 summary = Sindbis virus and Semliki Forest vires are best known as valuable models for molecular and cell biology, and it is these two viruses that are presently being developed as vectors for the expression of heterologous genes. The basic strategy for using alphaviruses as vectors for the expression of heterologous genes has been to construct cDNAs of the alphavirus genome, in which the heterologous gene is placed downstream from the promoter used to transcribe a subgenomic RNA 13 (Fig. 2a) . A second potential problem is recombination between the packaging helper virus RNA and vector RNAs. The two Sindbis RNAs can undergo recombination to produce a single molecule of RNA containing the genes that encode both the nonstructural and structural proteins m. The initial studies with Sindbis and Semliki Forest virus suggest that both viruses are promising as vectors for heterologous gene expression. cache = ./cache/cord-010188-884d196k.txt txt = ./txt/cord-010188-884d196k.txt === reduce.pl bib === id = cord-010168-aiqbqnaa author = Desselberger, Ulrich title = Classical and molecular techniques for the diagnosis of viral gastroenteritis() date = 1999-03-11 pages = extension = .txt mime = text/plain words = 3870 sentences = 223 flesch = 46 summary = The vaccine response is widened by applying a cocktail of viruses, e.g. containing a native rhesus rotavirus (RRV) of G3 type and reassortants carrying the VP7 genes of human serotypes G1, G2 and G4 in the RRV genetic background (Rennels et al., 1996) . These have been used as antigens in ELISA, and it was shown that NV or related viruses infect children worldwide in large numbers, and 60 80% of young adults have NV-reactive antibody (Gray et al., 1993) . Norwalk-like viruses are transmitted by the faeco-oral route and were found to be causative agents of various outbreaks of viral gastroenteritis occurring in recreational camps, schools and nursing homes, on cruise ships, around contaminated swimming pools, or in the community (Greenberg et al., 1981) . Sequence and genome organization of a human small, round-structured (Norwalk-like) virus cache = ./cache/cord-010168-aiqbqnaa.txt txt = ./txt/cord-010168-aiqbqnaa.txt === reduce.pl bib === id = cord-011129-btaxvmsr author = Di Paola, Nicholas title = Viral genomics in Ebola virus research date = 2020-05-04 pages = extension = .txt mime = text/plain words = 9440 sentences = 433 flesch = 37 summary = Here, we review how recent advances in genomic technologies have shaped past and current responses to outbreaks of Ebola virus disease (EVD), including insights into filovirus diversity and evolution. After this identification, considerations other than sequencing speed (for example, sequencing accuracy and processivity) become paramount in determining virus transmission networks and in detecting changes in the viral genome (between cases in the current outbreak and between the current and previous outbreaks) that could subvert MCMs. However, whereas unbiased sequencing approaches using high fidelity platforms can lead to the discovery of co-infections and reveal important clinical considerations during the treatment of patients near the point of need, targeted methods of pathogen characterization using the portable sequencing platforms iSeq 100 and MiSeq (which use bait-enrichment techniques) and MinION (which uses amplicon sequencing) can still provide useful genomic data albeit with a lower sequencing output (that is, a lower number of reads) than unbiased sequencing. cache = ./cache/cord-011129-btaxvmsr.txt txt = ./txt/cord-011129-btaxvmsr.txt === reduce.pl bib === id = cord-010273-0c56x9f5 author = Simmonds, Peter title = Virology of hepatitis C virus date = 2001-10-10 pages = extension = .txt mime = text/plain words = 7897 sentences = 337 flesch = 41 summary = 1,2 The identification of HCV led to the development of diagnostic assays for infection, based either on detection of antibody to recombinant polypeptides expressed from cloned HCV sequences or direct detection of virus ribonucleic acid (RNA) sequences by polymerase chain reaction (PCR) using primers complimentary to the HCV genome. 6 '13 Remarkably, a series of plant viruses that are structurally distinct from each of the mammalian virus groups, and with different genome organizations, have RNA-dependent RNA polymerase amino acid sequences that are perhaps more similar to those of HCV than are the flaviviruses. In contrast to the highly restricted sequence diversity of the 5'NCR and adjacent core region, the two putative envelope genes are highly divergent between different variants of HCV (Table III) 111-114 and show a three-to-four-times higher rate of sequence change with time in persistently infected patients, ll5 Because these proteins are likely to lie on the outside of the virus, they would be the principal targets of the humoral immune response to HCV elicited on infection. cache = ./cache/cord-010273-0c56x9f5.txt txt = ./txt/cord-010273-0c56x9f5.txt === reduce.pl bib === id = cord-011438-imbpgsub author = Zhang, Yun title = Host–Virus Interaction: How Host Cells Defend against Influenza A Virus Infection date = 2020-03-29 pages = extension = .txt mime = text/plain words = 9294 sentences = 567 flesch = 41 summary = Upon IAV infection, host innate immune system is triggered and activated to restrict virus replication and clear pathogens. In the current review, we present a general description on recent work regarding different host cells and molecules facilitating antiviral defenses against IAV infection and how IAVs antagonize host immune responses. Host innate immunity, including phagocytic cells, interferons (IFNs), proinflammatory cytokines, etc., applies multiple mechanisms in defending IAV infection [105] . Influenza A virus nucleoprotein induces apoptosis in human airway epithelial cells: Implications of a novel interaction between nucleoprotein and host protein Clusterin Antiviral response elicited against avian influenza virus infection following activation of toll-like receptor (TLR)7 signaling pathway is attributable to interleukin (IL)-1β production The human interferon-induced MxA protein inhibits early stages of influenza A virus infection by retaining the incoming viral genome in the cytoplasm Cell death regulation during influenza A virus infection by matrix (M1) protein: A model of viral control over the cellular survival pathway cache = ./cache/cord-011438-imbpgsub.txt txt = ./txt/cord-011438-imbpgsub.txt === reduce.pl bib === id = cord-010222-5oxie0zc author = Oldstone, Michael B.A. title = Virus-induced autoimmunity: Molecular mimicry as a route to autoimmune disease date = 2004-04-11 pages = extension = .txt mime = text/plain words = 2752 sentences = 125 flesch = 39 summary = Because the studies described above indicate that many viruses share antigenic determinants (linear or conformation) with normal host proteins, the next step was to determine experimentally whether molecular mimicry could elicit autoimmune diseases. The most likely explanation for how molecular mimicry causes disease is that an immune response against the determinant shared by host and virus takes the form of a tissue-specific attack, presumably capable of destroying cells and eventually the tissue. In any case, molecular mimicry would occur only when the virus and host determinants are sufficiently similar to induce a cross-reactive response yet different enough to break B or T-cell immunologic tolerance. Thus, the human AChR a-chain 160-167 peptide specifically cross-reacts with a shared homologous domain on herpes simplex virus glycoprotein D, residues 286-293, by binding and inhibition studies, and elicits antibodies in myasthenic patients that bind to the native AChR protein; these antibodies are capable of causing a biologic effect. cache = ./cache/cord-010222-5oxie0zc.txt txt = ./txt/cord-010222-5oxie0zc.txt === reduce.pl bib === id = cord-010343-tqqt0hj7 author = Alidjinou, Enagnon Kazali title = Resistance of Enteric Viruses on Fomites date = 2017-06-15 pages = extension = .txt mime = text/plain words = 5031 sentences = 268 flesch = 40 summary = The survival of main enteric viruses on fomites and its implication for virus transmission will be analyzed, and the major disinfection procedures and their impact will be described. Available data suggest that the majority of viruses persist longer on nonporous surfaces [7] ; however, results are sometimes conflicting, and the effect of fomite properties might also depend on the viral type. Therefore, survival and inactivation studies are commonly conducted using cultivable surrogates such as feline calicivirus (FCV) or murine norovirus (MNV) [40] . In another study conducted at room temperature, the authors demonstrated that MNV could survive for up to 28 days on 6 different surfaces and the rank order of infectivity reduction from highest to lowest was stainless steel, plastic, rubber, glass, ceramic, and wood [44] . Disinfectants are commonly used for virus inactivation, especially in the health care settings and the food industry, to prevent outbreaks due to enteric viruses. cache = ./cache/cord-010343-tqqt0hj7.txt txt = ./txt/cord-010343-tqqt0hj7.txt === reduce.pl bib === id = cord-010001-u0d5jkp1 author = KOTWAL, GIRISH J. title = Anti‐HIV, Anti‐Poxvirus, and Anti‐SARS Activity of a Nontoxic, Acidic Plant Extract from the Trifollium Species Secomet‐V/anti‐Vac Suggests That It Contains a Novel Broad‐Spectrum Antiviral date = 2006-01-22 pages = extension = .txt mime = text/plain words = 2608 sentences = 123 flesch = 51 summary = With a well-established infrastructure and the methodology to cultivate and to titer viruses accurately 6 to evaluate antiviral effects, it was possible to show that indeed a small volume of the plant extract termed Secomet-V was able to inactivate approximately 1 million virus particles of the attenuated recombinant vaccinia virus vGK5 7 in 1 minute consistently and reproducibly. Secomet-V, an extract of an African plant also found elsewhere in Asia, has been found to have potent antiviral activity against a poxvirus (vaccinia virus), rendering about 1 million particles noninfectious in 1 min with a 50th of a milliliter in in vitro assays (FIG. HIV-infected cells treated with plant extract showed no significant effect on the viral levels (TABLE 1) . There was no difference in the effectiveness of the plant extract in rendering vaccinia virus noninfectious whether it was autoclaved or not, suggesting that the bioactive agent is most likely but not necessarily a heat-stable compound and not a small peptide. cache = ./cache/cord-010001-u0d5jkp1.txt txt = ./txt/cord-010001-u0d5jkp1.txt === reduce.pl bib === id = cord-011457-hqxybv1k author = Kirui, James title = Generation and validation of a highly sensitive bioluminescent HIV-1 reporter vector that simplifies measurement of virus release date = 2020-05-19 pages = extension = .txt mime = text/plain words = 5612 sentences = 249 flesch = 46 summary = To enable simple and highly sensitive measurement of virus release from transfected cells, we generated HIV-1 reporter viruses in which Nanoluciferase (NanoLuc) was inserted between the MA and CA domains of Gag (Gag-iNanoLuc). We generated viruses using the pNL4-3 Gag-iNanoLuc vector complemented with different ratios of the WT HIV-1 molecular clone pNL4-3 and tested their infectivity by measuring the HIV-1 Tat-driven firefly luciferase activity in TZM-bl cells. These results demonstrate that the Gag-iNanoLuc vector provides a highly sensitive and quantitative tool for measuring the effects of Gag mutations, host cell restriction factors, and small-molecule inhibitors on HIV-1 particle assembly and release. The Gag-NanoLuc fusion protein is expressed in the cell and released at similar levels to WT Gag, thereby enabling simple yet highly sensitive quantification of viral gene expression and virus particle production by measurement of the NanoLuc reporter protein bioluminescent activity in the cell lysates and supernatants. cache = ./cache/cord-011457-hqxybv1k.txt txt = ./txt/cord-011457-hqxybv1k.txt === reduce.pl bib === id = cord-012582-k1mjik27 author = Gallego, Iván title = Stronger Together: Multivalent Phage Capsids Inhibit Virus Entry date = 2020-08-27 pages = extension = .txt mime = text/plain words = 1579 sentences = 95 flesch = 44 summary = This report highlights a phage capsid scaffold strategy that can be used to precisely position sialic acid moieties to inhibit influenza A virus replication. This report highlights a phage capsid scaffold strategy that can be used to precisely position sialic acid moieties to inhibit influenza A virus replication. In this work, the authors have selected the icosahedral capsid of the bacteriophage Qβ as the rigid scaffold for the attachment of the sialic acid to achieve a structurally defined presentation of the ligands that matches the binding sites of the trimeric hemagglutinin. All these findings demonstrate that these phage capsid nanoparticles can be employed as efficient inhibitors of influenza A virus and may be the first step towards the development of a new group of antivirals based on protein scaffolds for the treatment of influenza. This new approach from the Hackenberger group represents a promising example of how controlled protein assemblies can be used as precise multivalent scaffolds in the development of innovative antiviral therapeutics. cache = ./cache/cord-012582-k1mjik27.txt txt = ./txt/cord-012582-k1mjik27.txt === reduce.pl bib === id = cord-013412-gj443yei author = Lebedeva, Natalya Sh. title = The Application of Porphyrins and Their Analogues for Inactivation of Viruses date = 2020-09-23 pages = extension = .txt mime = text/plain words = 13428 sentences = 626 flesch = 46 summary = The purpose of this review paper is to summarize the main approaches developed to date in the chemical and photodynamic inactivation of human and animal viruses using porphyrins and their analogues and to analyze and discuss the information on viral targets and antiviral activity of porphyrins, chlorins, of their conjugates with organic/inorganic compounds obtained in the last 10–15 years in order to identify the most promising areas. A cationic substituent is necessary to increase the solubility of porphyrins and their analogues in aqueous media, and three nitro groups provide linking of the gp120 protein with the glycoprotein ( Figure 3 ) and thereby inhibit fusion between the virus and the cell membrane. A cationic substituent is necessary to increase the solubility of porphyrins and their analogues in aqueous media, and three nitro groups provide linking of the gp120 protein with the glycoprotein ( Figure 3 ) and thereby inhibit fusion between the virus and the cell membrane. cache = ./cache/cord-013412-gj443yei.txt txt = ./txt/cord-013412-gj443yei.txt === reduce.pl bib === id = cord-013073-siy7dvlo author = Pfäfflin, Albrecht title = Influenza virus-flow from insects to humans as causative for influenza seasonality date = 2020-10-09 pages = extension = .txt mime = text/plain words = 1845 sentences = 130 flesch = 42 summary = title: Influenza virus-flow from insects to humans as causative for influenza seasonality A model of viral flow is described and specified to explain influenza virus seasonality, which, in temperate climate, usually evolves when insects have mostly disappeared. The incidence of influenza under different circumstances e.g. temperature, humidity, or tropical conditions and different aspects like synchronicity of infections or in respect to evolutionary conditions do sustain this hypothesis if the behaviour of insects is considered. When influenza virus has reached humans and persists there, it disappears during off-season but re-emerges regularly. Seasonality of influenza is explainable using this insect-compartment model in temperate climate conditions. Associations of global weather conditions to the dynamics of seasonal influenza are found regularly, but the biological mechanism between climate variations and influenza epidemics is dubious [27] . Here, an viral-flow model contributory to explain seasonality of influenza is applied to elucidate questions and circumstances concerning influenza infections like synchronicity, environmental factors. cache = ./cache/cord-013073-siy7dvlo.txt txt = ./txt/cord-013073-siy7dvlo.txt === reduce.pl bib === id = cord-011880-qlutgfu2 author = Barberis, Abdelheq title = Full-length genome sequences of the first H9N2 avian influenza viruses isolated in the Northeast of Algeria date = 2020-07-17 pages = extension = .txt mime = text/plain words = 7502 sentences = 380 flesch = 49 summary = In addition, different studies, showed that circulating H9N2 strains have acquired affinity to mammalian like-receptors and gained high virulence and pathogenicity through substitutions in their viral proteins [13, 14] ; the most known substitutions are in the HA protein that promotes virus binding to cellular receptors. While the substitution 627 K that confers high pathogenicity, virulence and increased replication in mice [63] , was not detected in our Algerian viruses, three substitutions 318R, 590S and 661 T, associated with mammalian adaptation, were observed [71, 72] . The PB1 substitutions N105S, K577E/M and 578Q, known to be associated with increased polymerase activity, H9N2 pathogenicity in mice as well as adaptation to mammalians [61, 64, 78] , were not observed in the currently circulating Algerian strains, which however shared 105 N, 577 K and 578 K. Amino acids analysis showed that the Algerians H9N2 strains carried out different molecular markers associated with affinity to human-like receptors and increased virulence. cache = ./cache/cord-011880-qlutgfu2.txt txt = ./txt/cord-011880-qlutgfu2.txt === reduce.pl bib === id = cord-014541-2i0jga5v author = Breedlove, Byron title = The Exploding Aliveness of the World date = 2017-04-17 pages = extension = .txt mime = text/plain words = 767 sentences = 41 flesch = 54 summary = "The exploding aliveness of the world" that fuels artistic creativity also finds full expression in dynamic microscopic realms teeming with unfathomable numbers of viruses, bacteria, fungi, prions, and protozoa that lead to an incredible variety of pathologic consequences when infecting their hosts. Those influential reports-which represent the insights of Joshua Lederberg, Robert Shope, and their colleagues-from the Institute of Medicine (now National Academy of Medicine) Committee on Emerging Microbial Threats offered far-reaching recommendations and galvanized support for research and public health action to address the challenges posed by new, emerging, and reemerging infectious diseases. The time and attention given to tending to our backyard gardens, our larger communities, our public health infrastructure, and our approach to addressing emerging infections will be apparent and on display when that inevitable exploding aliveness occurs. Emerging infections: microbial threats to health in the United States cache = ./cache/cord-014541-2i0jga5v.txt txt = ./txt/cord-014541-2i0jga5v.txt === reduce.pl bib === id = cord-013176-6ckuya1w author = Ninfali, Paolino title = Antiviral Properties of Flavonoids and Delivery Strategies date = 2020-08-21 pages = extension = .txt mime = text/plain words = 8102 sentences = 372 flesch = 35 summary = Quercetin, extracted from Embelia ribes (Mirsinaceae), exhibited antiviral effects against HCV, exerted through activity inhibition of the viral protease Non-Structural protein 3 (NS3), leading to a decrease in HCV replication [36] . The natural extract of Tetrastigma hemsleyanum (Vitaceae) contains many flavonoids, including vitexin, vitexin-2-O-rhamnoside, isorhamnetin, rutin, kaempferol, astragalin, quercitrin, quercetin and iso-quercetin, which were shown to be able to exert anti-influenza virus activity, with different efficiency, through the reduction of the number of plaques induced by the influenza virus in infected Madin-Darby Canine Kidney (MDCK) cells [21] . In future perspective, this approach could be considered in order to possibly improve the antiviral activity of some flavonoids, like baicalin, that was able, like fludarabine [65] , to act against HIV-1 chronic infection of human monocytes and macrophages, inhibiting the fusion of HIV virus envelope proteins with these cells [73] . cache = ./cache/cord-013176-6ckuya1w.txt txt = ./txt/cord-013176-6ckuya1w.txt === reduce.pl bib === id = cord-014462-11ggaqf1 author = nan title = Abstracts of the Papers Presented in the XIX National Conference of Indian Virological Society, “Recent Trends in Viral Disease Problems and Management”, on 18–20 March, 2010, at S.V. University, Tirupati, Andhra Pradesh date = 2011-04-21 pages = extension = .txt mime = text/plain words = 35453 sentences = 1711 flesch = 49 summary = Molecular diagnosis based on reverse transcription (RT)-PCR s.a. one step or nested PCR, nucleic acid sequence based amplification (NASBA), or real time RT-PCR, has gradually replaced the virus isolation method as the new standard for the detection of dengue virus in acute phase serum samples. Non-genetic methods of management of these diseases include quarantine measures, eradication of infected plants and weed hosts, crop rotation, use of certified virus-free seed or planting stock and use of pesticides to control insect vector populations implicated in transmission of viruses. The results of this study indicate that NS1 antigen based ELISA test can be an useful tool to detect the dengue virus infection in patients during the early acute phase of disease since appearance of IgM antibodies usually occur after fifth day of the infection. The studies showed high level of expression in case of constructed vector as compared to infected virus for the specific protein. cache = ./cache/cord-014462-11ggaqf1.txt txt = ./txt/cord-014462-11ggaqf1.txt === reduce.pl bib === id = cord-016171-17ut32bu author = Lane, J. Michael title = Smallpox as a Weapon for Bioterrorism date = 2009 pages = extension = .txt mime = text/plain words = 8404 sentences = 512 flesch = 51 summary = Following September 11, 2001, the United States rebuilt its supplies of vaccine and Vaccinia Immune Globulin (VIG), expanded the network of laboratories capable of testing for variola virus, and engaged in a broad education campaign to help health care workers and the general public understand the disease (Centers for Disease Control and Prevention, 2003a) . Following September 11, 2001, the United States rebuilt its supplies of vaccine and Vaccinia Immune Globulin (VIG), expanded the network of laboratories capable of testing for variola virus, and engaged in a broad education campaign to help health care workers and the general public understand the disease (Centers for Disease Control and Prevention, 2003a) . If this algorithm indicates that a patient is high risk to be smallpox, local and national public health authorities should be immediately notified by telephone, and laboratory specimens taken for polymerase chain reaction (PCR), electron photomicroscopy (EM), and viral culture. cache = ./cache/cord-016171-17ut32bu.txt txt = ./txt/cord-016171-17ut32bu.txt === reduce.pl bib === id = cord-015871-1tuf4zxi author = Ergonul, Onder title = Treatment of Crimean-Congo Hemorrhagic Fever date = 2007 pages = extension = .txt mime = text/plain words = 8234 sentences = 474 flesch = 44 summary = In contrast, a dose of ribavirin at least nine times greater was required to induce a comparable inhibitory effect on the yields of Rift Valley fever virus, for which the drug has been shown to inhibit replication in monkeys and rodents [104] . However hemorrhagic fever virus infections can be approached by the following different therapeutic strategies [6] : (i) administration of high-titered neutralizing antibodies and/or (ii) treatment with antiviral drugs. In recent times, several groups have studied the antiviral activities of interferons against hemorrhagic fever viruses. Human MxA protein inhibits the replication of Crimean-Congo hemorrhagic fever virus Type I interferon inhibits Crimean-Congo hemorrhagic fever virus in human target cells Genotoxic effect of ribavirin in patients with Crimean-Congo hemorrhagic fever Ribavirin efficacy in an in vivo model of Crimean-Congo hemorrhagic fever virus (CCHF) infection Inhibition of Crimean-Congo hemorrhagic fever viral infectivity yields in vitro by ribavirin cache = ./cache/cord-015871-1tuf4zxi.txt txt = ./txt/cord-015871-1tuf4zxi.txt === reduce.pl bib === id = cord-014397-7b88ycv8 author = Gavora, JS title = Resistance of livestock to viruses: mechanisms and strategies for genetic engineering date = 1996-12-15 pages = extension = .txt mime = text/plain words = 11583 sentences = 528 flesch = 41 summary = Thus introduction of new mechanisms of disease resistance in livestock by gene transfer may be viewed as a logical continuation of the creative influence of humans on the evolution of farm animals and birds that could benefit mankind by improvements in food safety and production efficiency. As background for the discussion of the subject, the article deals briefly with coevolution of hosts and parasites and principal elements of virus-host interactions, and reviews past improvement of disease resistance in plants and livestock by conventional breeding and genetic engineering, as well as the potential 'biological cost' of genetic manipulation. Basic understanding of the parallel evolution of viruses and their hosts provides a useful starting point for the consideration of strategies for genetic engineering of new mechanisms of resistance. Genetic engineering strategies that prevent entry of viruses into host cells would be effective against all three types of viral infection. cache = ./cache/cord-014397-7b88ycv8.txt txt = ./txt/cord-014397-7b88ycv8.txt === reduce.pl bib === id = cord-014796-6rw2wk1q author = Fayyadh, Thaer Kadhim title = Simultaneous detection of multiple viruses in their co-infected cells using multicolour imaging with self-assembled quantum dot probes date = 2017-05-06 pages = extension = .txt mime = text/plain words = 4741 sentences = 239 flesch = 54 summary = title: Simultaneous detection of multiple viruses in their co-infected cells using multicolour imaging with self-assembled quantum dot probes The authors introduce a method for simultaneous imaging, detection and quantitative evaluation of multiple viruses in single cells by using multicolor quantum dot (QD) probes and in a single staining cycle. In this study, by using the multicolour QD-probes and a single staining procedure cycle, we have realized the simultaneous detection and quantitative evaluation of multiple viruses in their infected cells. As shown in Fig. 2a , there is obvious QD fluorescent signal in the cells infected with H1N1 virus incubated with fully assembly QD625-SpA-MAb as a Bone-step procedure^. As shown in Fig. 5 , by using the one-step staining procedure with a cocktail of QD625-SpA-MAb, QD525-SpA-MAb and QD705-SpA-MAb probes, the three influenza A virus subtypes H1N1, H3N2 and H9N2 were detected in the same co-infected MDCK cells with three types of corresponding QD signals (Fig. 5a) . cache = ./cache/cord-014796-6rw2wk1q.txt txt = ./txt/cord-014796-6rw2wk1q.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-012418-6ralcn8p author = Schwanke, Hella title = Of Keeping and Tipping the Balance: Host Regulation and Viral Modulation of IRF3-Dependent IFNB1 Expression date = 2020-07-07 pages = extension = .txt mime = text/plain words = 15685 sentences = 761 flesch = 38 summary = Due to its key role during the induction of the initial IFN response, the activity of the transcription factor interferon regulatory factor 3 (IRF3) is tightly regulated by the host and fiercely targeted by viral proteins at all conceivable levels. The crucial role of IRF3 and the posttranslational changes it undergoes upon viral infection were first reported more than 20 years ago: Upon stimulation, IRF3 gets phosphorylated and accumulates in the nucleus where it interacts with the coactivators CREB-binding protein (CBP)/p300 to specifically bind to virus-inducible enhancer elements and exerts transcriptional activation of the IFNB1 gene [21, [36] [37] [38] (Figure 2 ). The crucial role of IRF3 and the posttranslational changes it undergoes upon viral infection were first reported more than 20 years ago: Upon stimulation, IRF3 gets phosphorylated and accumulates in the nucleus where it interacts with the coactivators CREB-binding protein (CBP)/p300 to specifically bind to virus-inducible enhancer elements and exerts transcriptional activation of the IFNB1 gene [21, [36] [37] [38] (Figure 2 ). cache = ./cache/cord-012418-6ralcn8p.txt txt = ./txt/cord-012418-6ralcn8p.txt === reduce.pl bib === id = cord-010374-z9ygudv6 author = Siddell, S.G. title = Coronaviridae1 date = 2008-07-24 pages = extension = .txt mime = text/plain words = 1541 sentences = 111 flesch = 51 summary = The main characteristics of the member viruses are: (i) Morphological: Enveloped pleomorphic particles typically 100 nm in diameter (range 60-220 nm), bearing about 20 nm long club-shaped surface projections, (ii) Structural: A single-stranded infectious molecule of genomic RNA of about (5-7) × 10(6) molecular weight. (iv) Antigenic: 3 major antigens, each corresponding to one class of virion protein, (v) Biological: Predominantly restricted to infection of natural vertebrate hosts by horizontal transmission via the fecal/oral route. Recently, there have been reports of virus-specific RNA poly merases in coronavirus-infected cells, but the components of the enzyme have not been iden tified. UV inactivation studies in dicate that coronavirus mRNAs are not pro duced by the processing of a larger RNA, although extensive sequence homologies have been detected at the 5' ends of ail murine hepatitis virus-specific subgenomic RNAs. For murine hepatitis virus, the mRNA function of each of the subgenomic viral RNAs has been demonstrated in vitro, and the mRNAs encod ing each of the virion proteins, or its precur sors, have been identified ( fig. cache = ./cache/cord-010374-z9ygudv6.txt txt = ./txt/cord-010374-z9ygudv6.txt === reduce.pl bib === id = cord-015023-ishxfinx author = Jones, David title = Hard water date = 1995 pages = extension = .txt mime = text/plain words = 1154 sentences = 70 flesch = 57 summary = divert the search for environmental clues away from specific uncommon viruses to a broader category of events occurring early in life which are applicable to regional populations"; this comment is presumably aimed at Kurtzke and those sharing his view 3 that existing epidemiological data point to a specific infectious (presumably viral) agent as a direct cause of MS. Aircraft and rockets, for example, have to be very light but stiff structures; they also depend on liquid fuels pumped at high velocities. Many aircraft already store their fuel in compartments in their wings, and little modification should be needed to pump it to the engines through the hollow spars of the wing structure. More cunning still, its stiffness and damping could even be altered in flight by redistributing the fuel flow between different spars of the structure. cache = ./cache/cord-015023-ishxfinx.txt txt = ./txt/cord-015023-ishxfinx.txt === reduce.pl bib === id = cord-011106-h20vbmbo author = Takeda, Yohei title = Antiviral Activities of Hibiscus sabdariffa L. Tea Extract Against Human Influenza A Virus Rely Largely on Acidic pH but Partially on a Low-pH-Independent Mechanism date = 2019-10-16 pages = extension = .txt mime = text/plain words = 5362 sentences = 330 flesch = 54 summary = Here, we analyzed the antiviral activity of hibiscus (Hibiscus sabdariffa L.) tea extract against human IAV and evaluated its potential as a novel anti-IAV drug and a safe inactivating agent for whole inactivated vaccine. In addition, we assessed hibiscus tea extract's potential as a candidate for novel anti-IAV drug and as an inactivating agent for whole-virus vaccines. PR8 virus propagated in allantoic fluid was mixed with an equal amount of neutral and acidic pH PBS, Hib[crude], frHibis, or PCA. 50 μl PBS, formalin-, β-PL-, or acidic Hib[crude]-inactivated PR8 virus vaccine was intranasally administered in mice (first vaccination) under light anesthesia with isolflurane (Intervet K.K., Tokyo, Japan). The neutralized Hib[crude] in the blood loses potent anti-IAV activity due to acid, and the low-pH-independent antiviral activity is inadequate to inactivate virus in vivo. cache = ./cache/cord-011106-h20vbmbo.txt txt = ./txt/cord-011106-h20vbmbo.txt === reduce.pl bib === id = cord-015619-msicix98 author = nan title = Virus Structure & Assembly date = 2009-02-24 pages = extension = .txt mime = text/plain words = 3302 sentences = 164 flesch = 45 summary = The studies were performed with nanoindentation techniques using an Atomic Force Microscope (AFM), an approach which is becoming a standard method to measure the mechanical properties of viral particles (1, 2) . Using molecular dynamics simulations of the connector in complex with DNA, and aiming at distinguishing between these three models, we calculated mechanical properties of this system. The bacteriophage lambda is composed of an icosahedral capsid, into which a 48.5 kbp double-stranded DNA genome is packaged, and a long non-contractile tail consisting of 34 disk-like structures. The relative probabilities of fusion and endocytosis of a virus particle initially nonspecifically adsorbed on the host cell membrane are computed as functions of receptor concentration, binding strength, and number of spikes. As revealed by techniques of structural biology and single-molecule experimentation, the capsids of viruses are some of nature's best examples of highly symmetric multiscale self-assembled structures with impressive mechanical properties of strength and elasticity. cache = ./cache/cord-015619-msicix98.txt txt = ./txt/cord-015619-msicix98.txt === reduce.pl bib === id = cord-015764-ly68q5z0 author = Poissy, J. title = La modulation de la signature transcriptomique de l’hôte infecté : une nouvelle stratégie thérapeutique dans les viroses graves ? Exemple de la grippe date = 2016-04-07 pages = extension = .txt mime = text/plain words = 3985 sentences = 344 flesch = 53 summary = Une des approches possibles pour le développement de nouveaux antiviraux à plus large spectre d'action est de cibler non pas le virus, mais la cellule de l'hôte infecté, en utilisant la signature transcriptomique cellulaire de l'infection pour sélectionner et repositionner des molécules déjà sur le marché qui vont moduler ce profil transcriptomique, supposé comme étant favorable à l'infection. Les admissions en réanimation pour détresse respiratoire associée à une infection par influenza de type A sont estimées à 12/100 000 personnes.an chez l'adulte [13] . Par ailleurs, plusieurs méthodes de criblage à haut débit (petits ARN interférents [siRNA], interaction protéine-protéine) ont été menées ces dernières années et ont identifié plusieurs centaines de facteurs cellulaires impliqués dans la réplication des virus influenza et/ou la pathogenèse associée à l'infection, proposant ainsi autant de cibles thérapeutiques potentielles [43, 44] . Global host immune response: pathogenesis and transcriptional profiling of type A influenza viruses expressing the hemagglutinin and neuraminidase genes from the 1918 pandemic virus cache = ./cache/cord-015764-ly68q5z0.txt txt = ./txt/cord-015764-ly68q5z0.txt === reduce.pl bib === id = cord-016475-7ldxvbpz author = Pleschka, Stephan title = Anti-viral approaches against influenza viruses date = 2006 pages = extension = .txt mime = text/plain words = 17084 sentences = 860 flesch = 44 summary = After influenza virus infection antibodies directed against all major viral proteins can be detected in humans and the level of serum antibodies correlate with resistance to disease (Couch, 2003; Couch and Kasel, 1983; Coulter et al., 2003; Nichol et al., 1998; Potter and Oxford, 1979) . Nevertheless, IKK and NFκB might not only have anti-viral functions as two recent studies demonstrate that influenza viruses replicate much better in cells where NFκB is pre-activated (Nimmerjahn et al., 2004; Wurzer et al., 2004) . Apoptosis is mainly regarded to be a host cell defense against virus viruses (reviewed in: Julkunen et al., 2000; Ludwig et al., 2003; infections since many viruses express anti-apoptotic proteins to prevent this cellular response. Influenza virus-induced NF-kappaB-dependent gene expression is mediated by overexpression of viral proteins and involves oxidative radicals and activation of IkappaB kinase cache = ./cache/cord-016475-7ldxvbpz.txt txt = ./txt/cord-016475-7ldxvbpz.txt === reduce.pl bib === id = cord-016928-yigz9qiz author = Bhattacharyya, Sankar title = Inflammation During Virus Infection: Swings and Roundabouts date = 2019-11-05 pages = extension = .txt mime = text/plain words = 4847 sentences = 255 flesch = 42 summary = The tissue damage is caused from a combination of either direct neuronal infection which activates intrinsic apoptosis or a hyperactive inflammatory response mediated by PICs or CD8+ cytotoxic T cells (CTLs) (Wang et al. Spread through aerosols, SARS-CoV primarily infect lung cells triggering an often fatal inflammatory response clinically called acute respiratory distress syndrome (ARDS) that starts with severe hypoxia, pulmonary edema progressing to systemic inflammation, and failure of multiple organs, culminating in high rate of mortality (Peiris et al. Although evidence suggests that SARS-CoV can infect multiple cell types, lung type-II pneumocytes and ciliated epithelial cells constitute primary sites of virus replication, consequent to which these cells undergo apoptotic and/or necrotic death attracting innate immune cells and activating them to secrete PICs (Sims et al. Pro-inflammatory cytokines derived from West Nile virus (WNV)-infected SK-N-SH cells mediate neuroinflammatory markers and neuronal death cache = ./cache/cord-016928-yigz9qiz.txt txt = ./txt/cord-016928-yigz9qiz.txt === reduce.pl bib === id = cord-016796-g4kqqpy1 author = Bramhachari, Pallaval Veera title = Advanced Immunotechnological Methods for Detection and Diagnosis of Viral Infections: Current Applications and Future Challenges date = 2019-11-05 pages = extension = .txt mime = text/plain words = 5646 sentences = 305 flesch = 34 summary = As a part of modern research on immunotechniques, a diagnostic approach for chronic hepatitis C infection (CHC), detects specific antibody to HCV (anti-HCV) (indirect tests) and assays that can detect, quantify, or characterize components of HCV viral particles, viz. Nonetheless, recent studies on respiratory syncytial virus (RSV) developed Luciferase Immunoprecipitation Systems (LIPS) assay to detect IgG Antibodies against Human RSV G-Glycoprotein. Sensitive and specific detection of Crimean-Congo hemorrhagic fever virus (CCHFV) was developed employing specific IgM and IgG antibodies in human sera using recombinant CCHFV nucleoprotein as antigen in μ-capture and IgG immune complex (IC) ELISA tests (Emmerich et al. A rapid diagnostic platform for colorimetric differential detection of DENV and CHIKV viral infections was recently developed with a possibility to alter clinical diagnosis of acute febrile illnesses in resource-limited settings. This novel antibody demonstrates noteworthy specificity to identify H7N9 virus compared to homemade target-captured ELISA, qRT-PCR, and rapid influenza diagnostic test (RIDT) with high sensitivity (Chang et al. cache = ./cache/cord-016796-g4kqqpy1.txt txt = ./txt/cord-016796-g4kqqpy1.txt === reduce.pl bib === id = cord-013526-6fip93l2 author = Labadie, Thomas title = A non-enveloped arbovirus released in lysosome-derived extracellular vesicles induces super-infection exclusion date = 2020-10-19 pages = extension = .txt mime = text/plain words = 8084 sentences = 379 flesch = 51 summary = Here we used Bluetongue virus (BTV) as a model of a non-enveloped arthropod-borne virus and discovered that the majority of viruses are released in EVs. Based on the cellular proteins detected in these EVs, and use of inhibitors targeting the cellular degradation process, we demonstrated that these extracellular vesicles are derived from secretory lysosomes, in which the acidic pH is neutralized upon the infection. Virus released in secretory lysosomes infectious EVs. However, inhibition of autophagosome-lysosome fusion with chloroquine (CQ), led to a significant reduction of infectious EVs released as compared to the control ( Fig 2B) , indicating that the late steps of autophagy are necessary for infectious EVs. In addition, inhibition of MVBs regulator protein HSP90 using geldanamycin in BTV-infected cells (MOI = 10) also led to a significant reduction of infectivity measured in the EVs fraction, as compared to the control, indicating a possible role for MVBs in the release of infectious EVs. In contrast, GW4869, a drug that inhibits the release of exosomes (small vesicles~200nm) derived from MVBs, did not affect the secretion levels of EVs containing BTV ( Fig 2B) . cache = ./cache/cord-013526-6fip93l2.txt txt = ./txt/cord-013526-6fip93l2.txt === reduce.pl bib === id = cord-016663-qnp99m7o author = Taylor, Robert B. title = Medical Words Linked to Places date = 2017-02-01 pages = extension = .txt mime = text/plain words = 4835 sentences = 251 flesch = 63 summary = In addition to causing fever and malaise, when the patient is pregnant, the Zika virus may also cause birth defects, notably microcephaly (from Greek words meaning "small" and "head"). In addition to mosquito-borne infection, we now have discovered sexually transmitted Zika virus disease and continue to learn more each year. The West Nile virus is a member of the family Flaviviridae, from the Latin flavus, meaning "yellow." The family was named for the yellow fever virus, which tends to cause liver damage, giving its victims a yellow jaundiced appearance ( Fig. 5.2 ). The disease is caused by Borrelia bacteria, notably Borrelia burgdorferi, and is spread by the same vector as Nantucket fever/babesiosis: the Ixodes tick, also called the deer tick. Also sometimes called tick typhus or blue disease, Rocky Mountain spotted fever was first recognized in 1896 in the Snake River Valley in the Rocky Mountains of the Western United States. cache = ./cache/cord-016663-qnp99m7o.txt txt = ./txt/cord-016663-qnp99m7o.txt === reduce.pl bib === id = cord-016309-6mw8okmt author = Bule, Mohammed title = Antivirals: Past, Present and Future date = 2019-06-06 pages = extension = .txt mime = text/plain words = 8200 sentences = 405 flesch = 36 summary = Those included usage restricted to a single virus and specific animal species, problems with high spectrum activity and low cytotoxicity, high costs of development of new chemical compounds and absence of rapid diagnostic techniques allowing prompt use of a specific antiviral agent in the course of an acute infection (Rollinson 1992a, b) . Nevertheless, several licensed human antiviral agents are being used with cascade principle for treatment of animal diseases (e.g. acyclovir, idoxuridine and trifluridine against feline herpesvirus-1 ocular infection in cats) (Thiry et al. The discovery of PAA (Fig. 22.4) as an antiviral drug gave rise to intense research on its biological activities, which demonstrated PAA and its derivatives' ability to inhibit the replication of a number of viruses such as immunodeficiency, hepatitis and herpes viruses. To conclude with, equine herpesvirus type 1 (EHV-1) infection causes outbreak of respiratory and various neurological diseases in horses, against which acyclovir and valacyclovir are the most common drugs, but also IFN targeting IFNGR complex as a key mediator of virus-specific cellular immunity (Poelaert et al. cache = ./cache/cord-016309-6mw8okmt.txt txt = ./txt/cord-016309-6mw8okmt.txt === reduce.pl bib === id = cord-016652-x8t3lf1x author = Matthews, David title = Viruses and the Nucleolus date = 2011-05-23 pages = extension = .txt mime = text/plain words = 6630 sentences = 348 flesch = 33 summary = This process is crucial for virus biology because if the viral proteins that are required for cytoplasmic functions such as RNA synthesis and encapsidation are sequestered in the nucleolus or nucleus, then progeny virus production will be affected as has been revealed by inhibitor and genetic studies (Lee et al. Viruses may interact with the nucleolus to usurp host cell functions and recruit nucleolar proteins to facilitate virus replication. Initial studies utilising the prototype g-2 herpesvirus, herpes virus saimiri (HVS), demonstrated that the HVS nucleolar trafficking ORF57 protein induces nucleolar redistribution of the host cell human TREX proteins, which are involved in mRNA nuclear export (Boyne and Whitehouse 2006) . The localisation of porcine reproductive and respiratory syndrome virus nucleocapsid protein to the nucleolus of infected cells and identification of a potential nucleolar localization signal sequence Sequence requirements for nucleolar localization of human T cell leukemia virus type I pX protein, which regulates viral RNA processing cache = ./cache/cord-016652-x8t3lf1x.txt txt = ./txt/cord-016652-x8t3lf1x.txt === reduce.pl bib === id = cord-016798-tv2ntug6 author = Gautam, Ablesh title = Bioinformatics Applications in Advancing Animal Virus Research date = 2019-06-06 pages = extension = .txt mime = text/plain words = 6978 sentences = 405 flesch = 44 summary = The chapter further provides information on the tools that can be used to study viral epidemiology, phylogenetic analysis, structural modelling of proteins, epitope recognition and open reading frame (ORF) recognition and tools that enable to analyse host-viral interactions, gene prediction in the viral genome, etc. This chapter will introduce virologists to some of the common as well virus-specific bioinformatics tools that the researches can use to analyse viral sequence data to elucidate the viral dynamics, evolution and preventive therapeutics. Novel virus types comprise of new CDSs that are different than previously known CDSs. There are multiple databases and tools available for analysis of human viruses; however, there are still only a limited number of resources designed specifically for veterinary viruses. VIRsiRNAdb is an online curated repository that stores experimentally validated research data of siRNA and short hairpin RNA (shRNA) targeting diverse genes of 42 important human viruses, including influenza virus (Tyagi et al. cache = ./cache/cord-016798-tv2ntug6.txt txt = ./txt/cord-016798-tv2ntug6.txt === reduce.pl bib === id = cord-014908-jys1y0k9 author = Yadav, Rakesh title = Trends and Perspectives of Biosensors for Food and Environmental Virology date = 2010-05-19 pages = extension = .txt mime = text/plain words = 5113 sentences = 259 flesch = 32 summary = Unluckily, the PCR-based tools do not persistently amplify nucleic acids if viruses are found in infected food or environmental samples at critically low level. Another successful innovative biosensor with combined microfluidics and biosensing capabilities, furnish real time and automated affinity bioanalysis (e.g. for antigen-antibody assays) through surface plasmon resonance (SPR)-based original optical transduction mechanism. Since molecular recognition trait is central in the biosensing systems, all the structural components can be targeted to device a biosensor for detection of the specific virion particles present in food and environment samples. Molecular nanotechnology-based new nanostructures/nanomaterials such as aptamers are capable for developing highly specific biosensor for target elements detection. DNA-based biosensors have great applications in food and environmental analysis including determination of the pathogenic bacteria , and virus DNA sequence such as that of SARS virus (Abad-Valle et al. Quartz crystal microbalance (QCM)-based piezoelectric sensors can detect the hybridized viral DNA and also the capsid protein-ligand interactions. cache = ./cache/cord-014908-jys1y0k9.txt txt = ./txt/cord-014908-jys1y0k9.txt === reduce.pl bib === id = cord-016754-6fv8mjld author = Iturriza-Gómara, Miren title = Gastroenteric Viruses date = 2007 pages = extension = .txt mime = text/plain words = 4900 sentences = 269 flesch = 41 summary = Enzyme immunosorbent assays (EIA) and passive particle agglutination tests (PPAT), some of which are available commercially, provide sensitivity comparable to, or better than, EM for the detection of RVs, NVs, ASVs, and ADVs. More recently, molecular methods, reverse-transcription polymerase chain reaction (RT-PCR), PCR, or nucleic acid-based sequence amplification (NASBA) assays have been developed for the detection of enteric viruses. Testing for the presence of viruses in food, water, or environmental samples has only been possible since the development of very sensitive molecular methods, which include virus elution from the foodstuff, followed by concentration (36) efficient nucleic acid extraction methods for the removal of inhibitors of amplification. Multiple enteric viruses, SVs, ADVs, NVs, and RVs were detected in symptomatic patients suggesting the ingestion of fecally contaminated food or water (unpublished data). Polymerase chain reaction detection of small round-structured viruses from two related hospital outbreaks of gastroenteritis using inosine-containing primers The development of polymerase chain reaction assays for detection of small round structured and other human enteric viruses in molluscan shellfish cache = ./cache/cord-016754-6fv8mjld.txt txt = ./txt/cord-016754-6fv8mjld.txt === reduce.pl bib === id = cord-016576-1yqwci0y author = Hu, Xiaohua title = Mining Candidate Viruses as Potential Bio-terrorism Weapons from Biomedical Literature date = 2005 pages = extension = .txt mime = text/plain words = 2659 sentences = 148 flesch = 56 summary = In this paper we present a semantic-based data mining approach to identify candidate viruses as potential bio-terrorism weapons from biomedical literature. If a virus is found in the different document sets obtained by several search keywords, the virus should be considered as suspicious and treated as candidate viruses for bio-terrorism. We propose an automated, semantic-based data mining system to identify viruses that can be used as potential weapons in bio-terrorism. Following the criteria established by Geissler and the similar ideas used by Swanson [10] , in the mining procedure, we consider many important properties of the virus such as the genetic aspects of virulence; airbone transmission of viral disease; and stability of viruses in air or aerosol mixtures etc.. We introduce an automated semantic-based search system, called Combinational Search based Virus Seeker (CSbVS), to identify viruses that can be used as potential weapons in bio-terrorism. cache = ./cache/cord-016576-1yqwci0y.txt txt = ./txt/cord-016576-1yqwci0y.txt === reduce.pl bib === id = cord-016808-gy8d8285 author = Agol, Vadim I. title = The Origin and Evolution of Viruses date = 2008 pages = extension = .txt mime = text/plain words = 3255 sentences = 172 flesch = 44 summary = Modern hypotheses of viral origin are based on two major developments of the molecular biology: discovery of ribozymes (RNA-based enzymes) and formulation of the "RNA World" theory (RNA had been "invented" before proteins and DNA), on the one hand, and achievements of genomics (determination of the nucleotide sequences of a great number of cellular and viral genomes), on the other. Three distinct DNA viruses, which had infected RNA genome-containing cells, gave rise to the three distinct domains of life, bacteria, archea, and eukarya (Forterre, 2006) . To infect a human, an avian flu virus should change its receptor specificity, which depends on the interaction of viral hemagglutinin (HA) with a cellular membrane glycoprotein receptor. Such a change in the host range may be achieved by either mutations in the avian HA or acquisition by an avian virus of the HA gene from human influenza virus as a result of genetic exchange (reassortment) between these viruses during mixed infections. Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain cache = ./cache/cord-016808-gy8d8285.txt txt = ./txt/cord-016808-gy8d8285.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-017070-05vlz5dn author = Dimitrov, Dimiter S. title = Human Monoclonal Antibodies Against HIV and Emerging Viruses date = 2008 pages = extension = .txt mime = text/plain words = 6662 sentences = 299 flesch = 38 summary = These antibodies also protected uninfected animals from SARS-CoV infection, e.g., passive transfer of immune serum to naive mice prevented virus replication in the lower respiratory tract following intranasal challenge (61) . Recently, an improved method for Epstein-Barr virus transformation of human B cells has been developed based on CpG oligonucleotide (CpG 2006) that increases the B cell immortalization efficiency from 1-2% to 30-100%, and used for selection of hmAbs specific for SARS-CoV proteins (68) . We have recently identified a novel cross-reactive potent SARS-CoV-neutralizing hmAb, m396, by using a fragment containing residues 317 through 518 as a selecting antigen for panning of a large human antibody library constructed from the B lymphocytes of healthy volunteers (75) . These antibodies specific for SARS-CoV, HeV, and NiV have potential for further development into a clinically useful product for prophylaxis and perhaps treatment of the diseases caused by these infections. Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association cache = ./cache/cord-017070-05vlz5dn.txt txt = ./txt/cord-017070-05vlz5dn.txt === reduce.pl bib === id = cord-016990-ot1wi3xi author = Zaki, Sherif R. title = Viral Infections of the Lung date = 2008 pages = extension = .txt mime = text/plain words = 19585 sentences = 1132 flesch = 36 summary = 105, [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] The pathology is more prominent in larger bronchi, and inflammation may vary in intensity in individual patients, Viral inclusions cannot be identified by light microscopy (Fig, 11 .8D), Secondary bacterial infections with organisms such as Streptococcus pneumoniae (group A streptococcus [GAS]), Staphylococcus aureus, and Haemophilus influenzae may occur as a complication in about 50% to 75% of fatal cases and make it difficult to recognize the pathologic changes associated with the primary viral infec-445 tion ,190,192,193 The histopathologic features in other organs may include myocarditis, cerebral edema, rhabdomyolysis, and hemophagocytosis (Figs, 11.8H and 11.9E,F), Immunohistochemistry and ISH assays demonstrate that viral antigens and nucleic acids are usually sparse and are primarily seen in the bronchioepithelial cells of larger bronchioles (Figs. cache = ./cache/cord-016990-ot1wi3xi.txt txt = ./txt/cord-016990-ot1wi3xi.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-016538-4og05fuo author = Dolja, V. V. title = Biotechnology Applications of Grapevine Viruses date = 2017-03-30 pages = extension = .txt mime = text/plain words = 6266 sentences = 292 flesch = 44 summary = Although in theory any of the grapevine-infecting viruses can be engineered into transient gene expression or VIGS vector, in practice, only one of them, the filamentous Grapevine leafroll-associated virus-2 (GLRaV-2) from the genus Closterovirus (family Closteroviridae), was demonstrated to fulfill these roles (Dolja and Koonin 2013; Kurth et al. Among these viruses, only GLRaV-2, a closterovirus, has been so far engineered into a vector capable of systemic infection of grapevine that either produces recombinant protein or elicits VIGS response (Kurth et al. The more recently developed CTV-based gene expression vectors were shown to be not only capable of systemic infection in the natural citrus hosts but also exhibited remark-able genetic stability in regard to retention of the inserted recombinant gene, as well as VIGS capability (Dawson et al. Another candidate to be developed as a vector for protein expression and VIGS is GRSPaV, which is the only grapevine-infecting member of the genus Foveavirus that was recently characterized (Meng et al. cache = ./cache/cord-016538-4og05fuo.txt txt = ./txt/cord-016538-4og05fuo.txt === reduce.pl bib === id = cord-016995-5izyl234 author = Auewarakul, Prasert title = The Past and Present Threat of Avian Influenza in Thailand date = 2008 pages = extension = .txt mime = text/plain words = 5093 sentences = 275 flesch = 54 summary = The plan aims at effective control of avian influenza spread in animals as well as in humans for a three-year period and at efficient pandemic preparedness within one year. When this result was reported to the Ministry of Public Health, the government announced that there was a highly pathogenic avian influenza (AI) outbreak in Thailand. When this result was reported to the Ministry of Public Health, the government announced that there was a highly pathogenic avian influenza (AI) outbreak in Thailand. Although several clusters of H5N1 infections have been observed in Thailand, Vietnam, and Indonesia, it is difficult to prove human-to-human transmission, as most of these patients had exposure to poultry and it is not possible to prove whether they contracted the disease from animals or humans. The genome sequence analysis of H5N1 avian influenza A virus isolated from the outbreak among poultry populations in Thailand cache = ./cache/cord-016995-5izyl234.txt txt = ./txt/cord-016995-5izyl234.txt === reduce.pl bib === id = cord-017249-la5sum39 author = Feldblyum, Tamara V. title = Seasonal and Pandemic Influenza Surveillance and Disease Severity date = 2015-05-12 pages = extension = .txt mime = text/plain words = 11430 sentences = 516 flesch = 39 summary = With the growing focus of the US health care system on the meaningful use of electronic medical records, one of the practical applications is expanding biosurveillance and preparedness capabilities, such as surveillance of infl uenza severity and associated risk factors during seasonal epidemics and pandemics [ 18 , 22 ] . EHR-based surveillance systems such as Electronic Medical Record Support for Public Health (ESP) implemented in Ohio and Massachusetts and BioSense were successfully used for analyzing ICD-9 diagnosis codes, reporting notifi able disease cases, surveillance of ILI, identifi cation of infl uenza or upper respiratory infection risk factors among hospitalized patients, and for monitoring diabetes prevalence, risk factors, and disease severity [ 13 , 19 ] . Pregnancy has been reported as a risk factor for seasonal and pandemic infl uenza infections and severe disease outcomes using historical and current data. cache = ./cache/cord-017249-la5sum39.txt txt = ./txt/cord-017249-la5sum39.txt === reduce.pl bib === id = cord-017158-w2tlq6ho author = Moriones, Enrique title = Recombination in the TYLCV Complex: a Mechanism to Increase Genetic Diversity. Implications for Plant Resistance Development date = 2007 pages = extension = .txt mime = text/plain words = 6282 sentences = 290 flesch = 39 summary = The potential of begomoviruses to generate genetic diversity through recombination can be relevant for their ecological fitness, because greater sequence heterogeneity provides a reservoir of virus variants in the population that enables rapid adaptation to changing environmental conditions. Thus, begomoviruses like those in the Tomato yellow leaf curl virus (TYLCV) complex exploit gene flow provided by recombination as a mechanism to increase their evolutionary potential and local adaptation. Also, when region I was analyzed, phylogenetic analyses revealed that all TYLCV isolates grouped in a single clade related to Tomato yellow leaf curl Sardinia virus (TYLCSV), another species of the TYLCV complex causing the TYLCD. Tomato yellow leaf curl Sardinia virus (TYLCSV) is another monopartite begomovirus species of the TYLCV complex that comprises isolates infecting tomato in the Mediterranean Basin, both in southern Europe and northern Africa (Noris et al., 1994; . cache = ./cache/cord-017158-w2tlq6ho.txt txt = ./txt/cord-017158-w2tlq6ho.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-017429-3evwlfac author = Hubálek, Zdenek title = Vertebrates as Hosts and Reservoirs of Zoonotic Microbial Agents date = 2010-11-10 pages = extension = .txt mime = text/plain words = 4952 sentences = 630 flesch = 57 summary = VIRUSES: Lyssavirus s.s. Colonial species distributed in southern USA; roosts in caves, also mine tunnels, hollow trees, buildings, and migrates up to 70 km. Noctule Bat (Nyctalus noctula: Photo 7.12) A large Eurasian species, living in deciduous and mixed forests, and roosting in tree hollows (e.g., woodpecker holes), feeds on large insects. Extensive home range (usually up to 15 km, occasionally 160 km recorded North-American, medium-sized (about that of a small dog) species living near wooded areas, closely to streams and lakes, rock cliffs, but also in urban areas. Comparatively large (25-40 cm long plus tail 7-12 cm; weight about 1 kg) rodent, living in steppe habitat (dry upland prairies) of central and southern areas of USA, and forming extensive colonies ("towns") with deep burrows. BACTERIA: Leptospira grippotyphosa, Francisella tularensis, Borrelia burgdorferi s.s. North-Eurasian species of flying nocturnal squirrel. cache = ./cache/cord-017429-3evwlfac.txt txt = ./txt/cord-017429-3evwlfac.txt === reduce.pl bib === id = cord-017008-c7skxte0 author = Méthot, Pierre-Olivier title = Emerging Disease and the Evolution of Virulence: The Case of the 1918–1919 Influenza Pandemic date = 2014-08-22 pages = extension = .txt mime = text/plain words = 17589 sentences = 788 flesch = 49 summary = Next, we describe the biology of infl uenza viruses with a focus on the 1918-19 pandemics and we move on to the ecological-evolutionary explanations of its exceptional virulence, paying attention to the trade-off model, before turning to molecular 4 On the history, epistemology, and social aspects of the concept of emerging disease see Grmek ( 1993 ); Farmer ( 1996 ) , King ( 2004 ) ; and Weir and Mykhalovski ( 2010 ) . 6 Whereas the ecological (or exogenous) style focuses on processes (e.g. selective pressures, population density, within and between host competition, and so on) acting on the hosts and the pathogen, the molecular (or endogenous) style traces the evolutionary pathway, or patterns, of the infl uenza virus from animal(s) to man, and, by constructing molecular phylogenies, identifi es particular genes for pathogenesis and mutation sites within lineages. cache = ./cache/cord-017008-c7skxte0.txt txt = ./txt/cord-017008-c7skxte0.txt === reduce.pl bib === id = cord-017489-ftz9190a author = Richards, Guy A. title = Viruses in the Intensive Care Unit (ICU) date = 2005 pages = extension = .txt mime = text/plain words = 5792 sentences = 330 flesch = 44 summary = Pneumonia is the most common complication, which occurs in high-risk patients including those with comorbid illness such as cardiovascular or pulmonary disease, diabetes, renal failure, immunosuppression, the elderly, or residents of nursing homes. A study performed in our ICU indicates that corticosteroids may dramatically alter the course of the most severe disease and should be considered in addition to antiviral therapy along with appropriate supportive care in any previously well patient with life threatening varicella pneumonia (42). Patients with HIV or AIDS (acquired immunodeficiency syndrome) who are hospitalized with chickenpox appear to be at high risk for developing varicella pneumonia, which manifests in a similar clinical fashion to that in immunocompetent individuals. In another study of 68 adult patients admitted with measles diagnosed on clinical and serological grounds, 9 required intensive care, six mechanical ventilation for approximately 15 days, and two deaths occurred. cache = ./cache/cord-017489-ftz9190a.txt txt = ./txt/cord-017489-ftz9190a.txt === 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-017326-1caeui30 author = Seay, Montrell title = Digesting Oneself and Digesting Microbes: Autophagy as a Host Response to Viral Infection date = 2005 pages = extension = .txt mime = text/plain words = 11363 sentences = 489 flesch = 34 summary = Genetic studies in yeast and mammalian cells have also shown that the eIF2 kinase signaling pathway is required for starvation and herpes simplex virus-induced autophagy 18 . The role of some of the Atg proteins, including ones that act in the lipid kinase signaling complex and in the ubiquitin-like conjugation pathways, has been studied in plant and mammalian viral infections (see Table 1 ). Together, the studies of Sindbis virus infection in neurons overexpressing beclin 1 or in cultured cells lacking beclin 1 or atg5 demonstrate a role for mammalian autophagy genes in both restricting viral replication and in protection against virus-induced cell death. The interferon-inducible, antiviral PKR signaling pathway positively regulates autophagy, and both mammalian and plant autophagy genes restrict viral replication and protect against virus-induced cell death. The interferon-inducible, antiviral PKR signaling pathway positively regulates autophagy, and both mammalian and plant autophagy genes restrict viral replication and protect against virus-induced cell death. cache = ./cache/cord-017326-1caeui30.txt txt = ./txt/cord-017326-1caeui30.txt === reduce.pl bib === id = cord-017748-xy26tk0t author = Georgiev, Vassil St. title = Influenza date = 2009 pages = extension = .txt mime = text/plain words = 11757 sentences = 536 flesch = 39 summary = This, coupled with the difficulty to predict which subtype of avian influenza virus will cause the next human pandemic means that an ideal vaccine would elicit an immune response that protects the host from infection with a broad range of influenza viruses from the same or different subtypes (14) . Therefore, if a virus with a new HA and/or NA glycoprotein emerges in the human population, cell-mediated immunity directed against the highly conserved internal proteins could have a role in protection at the time of a pandemic (14) . Although most influenza vaccines are designed to induce HA-specific antibody responses to protect the host from infection, the biology of avian influenza viruses presents several unique challenges compared with human influenza viruses. DNA vaccines encoding the HA and NA glycoproteins of avian influenza viruses or conserved internal virus proteins, such as matrix proteins and nucleoproteins, induced protective immunity in mice and chickens (90) (91) (92) (93) . cache = ./cache/cord-017748-xy26tk0t.txt txt = ./txt/cord-017748-xy26tk0t.txt === reduce.pl bib === id = cord-017537-ztdz4a2s author = Bologna, Mauro title = Biological Agents and Bioterrorism date = 2014-09-18 pages = extension = .txt mime = text/plain words = 3324 sentences = 198 flesch = 51 summary = For this very stimulating course, I want to share with you some of my studies and even some of my scientific and phylosophical considerations on biological agents living in the environment and their relations with humans, in the very wide concepts of ecological relationships, parasitism, immunolgical defenses and infectious disease mechanisms. All these concepts must be studied and considered in the event of criminal use of biological agents (bioterrorism) aimed at harming human populations in time and in geographical space. In the light of recent concern and interest about the potential for biological terrorism (biofarware) there are several diseases and bacterial toxins that must be considered in particular, like anthrax [ 1 , 2 ] , smallpox [ 3 , 4 ] , plague [ 5 ] , botulinum toxin [ 6 ] , and tularemia [ 7 ] . cache = ./cache/cord-017537-ztdz4a2s.txt txt = ./txt/cord-017537-ztdz4a2s.txt === reduce.pl bib === id = cord-017287-70lk77zb author = Sánchez, Gloria title = Survival of Enteric Viruses in the Environment and Food date = 2016-08-26 pages = extension = .txt mime = text/plain words = 8962 sentences = 450 flesch = 44 summary = In the last decade, epidemiological reports indicate that enteric viruses, in particular human noroviruses (NoV), which cause acute gastroenteritis, and hepatitis A virus (HAV), are the leading cause of foodborne illness in developed countries (Koopmans and Duizer 2004 ; EFSA 2015 ) . While consumption of ready-to-eat foods contaminated by infected food handlers remains the major risk factor for viral foodborne outbreaks, many types of food products are being recognized as vehicles of viruses in causing gastroenteritis or hepatitis A outbreaks (Table 13 .1 ). These data suggest that temperature, and probably relative humidity, may be meaningful in the seasonal distribution of outbreaks of certain human enteric viruses (Enright 1954 ) , due to the infl uence of these factors on virus persistence. Survival of enteric viruses in the environment and different food products has been well studied employing cell-adapted virus strains. cache = ./cache/cord-017287-70lk77zb.txt txt = ./txt/cord-017287-70lk77zb.txt === reduce.pl bib === id = cord-017959-g0nf1iwm author = Lipkin, W. Ian title = Diagnosis, Discovery and Dissection of Viral Diseases date = 2014-02-27 pages = extension = .txt mime = text/plain words = 5016 sentences = 216 flesch = 37 summary = Nested PCR tests that can employ consensus or specifi c primers in two sequential amplifi cation reactions with either one (hemi-nested) or two (fully nested) primers located 3′ with respect to the fi rst primer set may both accommodate sequence variation and be more sensitive than fl uorescent or beacon-based singleplex assays. Whereas multiplex PCR systems support rapid highthroughput diagnosis with highest sensitivity for a limited number of agents, microarray-based systems provide detection of all known pathogens for which sequence information is available, but at the expense of some degree of sensitivity. Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fl uid microbead-based assay MassTag polymerasechain-reaction detection of respiratory pathogens, including a new rhinovirus genotype, that caused infl uenza-like illness in New York State during cache = ./cache/cord-017959-g0nf1iwm.txt txt = ./txt/cord-017959-g0nf1iwm.txt === reduce.pl bib === id = cord-017527-ylng1us2 author = Herman, Philippe title = Biosafety Recommendations on the Handling of Animal Cell Cultures date = 2014-11-05 pages = extension = .txt mime = text/plain words = 10237 sentences = 453 flesch = 38 summary = While biosafety recommendations (as outlined hereafter) are principally aimed at providing maximal protection of human health (including laboratory workers) and the environment, it is recognised that many of the precautionary measures will also directly benefit the quality of research activities involving animal cell cultures. The methodology of biological risk assessment of contained use activities involving pathogenic and/or genetically modified organisms (GMO) identifies and takes into account the probability of occurrence and the severity of a potential negative effect on public health (including the exposed workers) and/or the environment. The risk assessment applied to animal cell cultures relies on a thorough evaluation of both the intrinsic properties of the cell culture -including subsequent properties acquired as a result of genetic modification(s) -and the possibility that the cell culture may inadvertently be contaminated or deliberately infected with pathogenic micro-organisms. cache = ./cache/cord-017527-ylng1us2.txt txt = ./txt/cord-017527-ylng1us2.txt === reduce.pl bib === id = cord-017568-8fnr4zzv author = Wang, Lin-Fa title = Disease Outbreaks Caused by Emerging Paramyxoviruses of Bat Origin date = 2008 pages = extension = .txt mime = text/plain words = 6817 sentences = 345 flesch = 53 summary = They are Hendra virus (HeV), Nipah virus (NiV), and Menangle virus (MenV), isolated from infected horses and humans in Australia in 1994 , humans and pigs in Malaysia in 1999 , and pigs in Australia in 1997 , respectively (Chua et al., 2000 Murray et al., 1995b; Philbey et al., 1998) . In addition to the emergence of paramyxoviruses from frugivorous Pteropus bats, insectivorous Rhinolophus species have been identified as natural hosts of SARS-like viruses (Lau et al., 2005; Li et al., 2005) , and Ebola virus has been shown to have fruit bat reservoir hosts (Leroy et al., 2005) . The identification of fruit bats in the genus Pteropus as the reservoir hosts of HeV and NiV in Australia and Malaysia, respectively, prompted searches for related viruses in other nations in the region. Case-control study of risk factors for human infection with a new zoonotic paramyxovirus, Nipah virus, during a 1998-1999 outbreak of severe encephalitis in Malaysia cache = ./cache/cord-017568-8fnr4zzv.txt txt = ./txt/cord-017568-8fnr4zzv.txt === reduce.pl bib === id = cord-018164-h5k1zsyg author = Taylor, Milton W. title = What Is a Virus? date = 2014-07-22 pages = extension = .txt mime = text/plain words = 4769 sentences = 260 flesch = 60 summary = Studies of viral replication indicate that most viruses self-assemble as a result of interactions between the viral proteins to form a viral capsid that interacts with the nucleic acid to form the whole. The viral proteins are produced in one part of the cell, the replicated nucleic acid in another, and somehow they find each other, interact, and form virus particles that are expelled from the cell. Indirect contact spread includes cases where mucus from a runny nose may get onto the hands, or virus may be left on a surface such as a doorknob, telephone, or countertops, and is picked up by a second individual, who then touches his eyes or nose, resulting in infection. Vector transmission is a very common means of transmission; the best studied cases include yellow fever, dengue virus, and West Nile fever-viruses all transmitted by mosquitoes. As many as 400 million people are infected annually by dengue virus, which is caused by any one of four related viruses transmitted by mosquitoes. cache = ./cache/cord-018164-h5k1zsyg.txt txt = ./txt/cord-018164-h5k1zsyg.txt === reduce.pl bib === id = cord-017764-h1w9gbxk author = Meanwell, Nicholas A. title = The Discovery and Development of Daclatasvir: An Inhibitor of the Hepatitis C Virus NS5A Replication Complex date = 2018-06-08 pages = extension = .txt mime = text/plain words = 9250 sentences = 389 flesch = 39 summary = A groundbreaking clinical trial that combined daclatasvir (1) with the protease inhibitor asunaprevir (52) established that a chronic HCV infection could be cured with small molecule therapy in the absence of immune stimulation, setting the stage for approval of this regimen for the treatment of GT-1b-infected subjects by the Japanese health authorities on July 4, 2014. The discovery of the hepatitis C virus (HCV) nonstructural 5A (NS5A) replication complex inhibitor daclatasvir (1) began with the development of a genotype 1b (GT-1b) replicon that was implemented as a phenotypic screen using a design that conferred a stringent triaging of hit molecules [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] . A screen of compounds selected from the library of HCV NS5A inhibitors assessed in the presence of 1 using the Tyr93Asn GT-1aresistant replicon, followed by SAR optimization, identified Syn-395 (52) as a molecule capable of restoring the sensitivity of resistant virus to the inhibitory effects of 1. Discovery of daclatasvir, a pan-genotypic hepatitis C virus NS5A replication complex inhibitor with potent clinical effect cache = ./cache/cord-017764-h1w9gbxk.txt txt = ./txt/cord-017764-h1w9gbxk.txt === reduce.pl bib === id = cord-017331-ru7mvfc0 author = Samanta, Indranil title = Infectious Diseases date = 2017-02-25 pages = extension = .txt mime = text/plain words = 37735 sentences = 2273 flesch = 45 summary = The chapter includes history, etiology, susceptible hosts, transmission, pathogenesis, clinical symptoms, lesion, diagnosis, zoonosis, Treatment and control strategy of Tuberculosis, Salmonellosis, Chlamydiosis, Campylobacteriosis, Lyme disease, other bacterial infection, Newcastle disease, Avian Influenza infection, West Nile Virus infection, Usutu virus infection, Avian Borna Virus infection, Beak and feather disease, other viral infection, Toxoplasmosis, Giardiasis, Cryptosporidiosis, other parasitic infection, Cryptococcosis, Aspergillosis, Other fungal infections. Clinical samples include faeces or cloacal swabs, blood/serum of live birds and affected tissues, such as liver, spleen, heart, intestine/caeca, lung, esophagus/crop, brain and kidney in 10% buffered formalin. Non-specific clinical symptoms such as neurological signs (head between legs), depression, ruffled feathers, and standing at the bottom of the cage are observed in pet birds with AIV infection (Fig. 2.13) . The virus is detected in brain, heart, liver, kidney, lungs, and intestinal tissues of laboratory mice and naturally infected birds. cache = ./cache/cord-017331-ru7mvfc0.txt txt = ./txt/cord-017331-ru7mvfc0.txt === reduce.pl bib === id = cord-018058-n3majqes author = Modrow, Susanne title = Historical Overview date = 2013-08-12 pages = extension = .txt mime = text/plain words = 5376 sentences = 262 flesch = 46 summary = Many of the steps that characterize a viral infection were first discovered in experiments with bacterial viruses: such processes include attachment and penetration, the reproduction-cycledependent regulation of gene expression that results in early and late synthesized proteins, and lysogeny, which is associated with the existence of prophages. Besides the importance for tumour virus research, these observations aroused interest in the question concerning the basis of the high susceptibility of newborn animals to viral infections, and suggested investigations on the innate resistance of an organism to infections as well as the time and the causes of its formation. Between 1918 and 1920, a pandemic emerging viral disease, Spanish flu, claimed more than 20 million lives, i.e., more than in the First World War. After cultivation of the virus responsible in embryonated chicken eggs in 1933, their haemagglutinating properties were discovered in 1941 (i.e., their ability to agglutinate red blood cells), thereby laying the basis for the development of haemagglutination tests to detect viruses. cache = ./cache/cord-018058-n3majqes.txt txt = ./txt/cord-018058-n3majqes.txt === reduce.pl bib === id = cord-017167-8cdbcrh7 author = Ahola, Tero title = Functions of Chikungunya Virus Nonstructural Proteins date = 2016-12-03 pages = extension = .txt mime = text/plain words = 10491 sentences = 530 flesch = 49 summary = The nonstructural proteins (nsPs) of chikungunya virus (CHIKV) are expressed as one or two polyprotein precursors, which are translated directly from the viral genomic RNA. Similar to other alphaviruses, CHIKV nsPs not only perform virus RNA replication but are also crucial for other activities essential for virus infection and pathogenesis. However, recent studies of SFV P1234 processing reveal that a second mechanism, the presentation of cleavage sequences via long-range interactions between different domains of the polyprotein, Processing of CHIKV ns polyprotein P1234 and RNA synthesis. The main interaction appears to be mediated by a membrane-binding peptide located in the central part of the protein (approximately residues 244-263 in CHIKV nsP1; Fig. 2 ), which forms an amphipathic alpha helix, as characterized for the corresponding peptide from SFV (Ahola et al. However, the effects of mutations introduced into the NTPase/helicase active site were different for these viruses: in SINV such a mutation strongly reduced the nsP2-dependent degradation of Rpb1 whereas CHIKV nsP2 mostly retained its ability to block host gene expression. cache = ./cache/cord-017167-8cdbcrh7.txt txt = ./txt/cord-017167-8cdbcrh7.txt === reduce.pl bib === id = cord-018078-clxzp1ph author = Weber, Olaf title = Coronavirus infections in veterinary medicine date = 2005 pages = extension = .txt mime = text/plain words = 4430 sentences = 278 flesch = 43 summary = Some important viruses that are discussed below belong to group I and include the canine enteric coronavirus (CECoV), the transmissible gastroenteritis virus (TGEV) of swine, the porcine epidemic diarrhoea virus (PEDV), the porcine respiratory coronavirus (PRCoV) and the feline coronaviruses (FCoVs). The clinical symptoms of endemic/enzootic TGE are usually less severe in the older pigs, making a clinical differentiation between TGE and other infectious enteric diseases, like that caused by rotaviruses and/or clostridia, impossible. Bovine coronavirus (BCoV) is an important cause of neonatal calf diarrhea [33] but may also infect the respiratory tract and has been recognized as the causing agent especially for winter dysentery in adult cattle. As for other coronaviruses, seasonal changes in temperature, environmental factors but also the immune status play an important role in the transmission of the virus and the clinical outcome of the infection. Two amino acid changes at the N-terminus of transmissible gastroenteritis coronavirus spike protein result in the loss of enteric tropism cache = ./cache/cord-018078-clxzp1ph.txt txt = ./txt/cord-018078-clxzp1ph.txt === reduce.pl bib === id = cord-017752-ofzm3x3a author = nan title = Theories of Carcinogenesis date = 2007 pages = extension = .txt mime = text/plain words = 12289 sentences = 692 flesch = 47 summary = Others attributed the simplified enzyme patterns of cancerous cells to a regression of the tumor tissues to early embryonal stages of development. Viral DNA is frequently integrated into the cancer cells, but additional agents or factors may be involved at various stages of the progression to invasive carcinoma. The encounter with a family, in which many members developed breast or liver cancer, led Pierre Paul Broca to hypothesize, in 1866, that an inherited abnormality within the affected tissue caused the tumor development [Broca 1866 Theodor Boveri (1862 Boveri ( -1915 then proposed that defects in chromosomes lead to malignancy [Boveri 1914 ]. Any mutation of cancer associated genes can be handed on to following generations and predispose the affected cells to malignant transformation in the case of additional DNA damage. Further developments in tumor immunology have led to models of selection and evolution of cancer cells. cache = ./cache/cord-017752-ofzm3x3a.txt txt = ./txt/cord-017752-ofzm3x3a.txt === reduce.pl bib === id = cord-017824-0pinevfc author = Tekes, Gergely title = Vaccinia Virus-Based Reverse Genetics for Feline Coronaviruses date = 2015-09-10 pages = extension = .txt mime = text/plain words = 3190 sentences = 253 flesch = 57 summary = The main focus of this chapter is the vaccinia virus-based reverse genetic system for FCoVs. Here we present protocols for (1) the generation of a full-length cDNA clone, (2) the manipulation of the FCoV genome, and (3) the rescue of recombinant FCoVs. The establishment of a reverse genetic system for feline coronaviruses (FCoVs), which allows to modify the entire coronaviral genome, was successfully achieved for the fi rst time in 2008 [ 1 ] . Regardless of the applied strategy, viral RNA serves as a starting material for the generation of all FCoV-sequence containing plasmids (sections "First Step", 3.1.1.3, "Generation of plasmids suitable for vaccinia virus-mediated homologous recombination"). In order to integrate the full-length FCoV cDNA, fragments 1-8 are introduced via four rounds of vaccinia virus-mediated homologous recombination using GPT as a positive and a negative selection marker. cache = ./cache/cord-017824-0pinevfc.txt txt = ./txt/cord-017824-0pinevfc.txt === reduce.pl bib === id = cord-017758-zfudssm9 author = Fong, I. W. title = Emergence of New Tickborne Infections date = 2017-02-08 pages = extension = .txt mime = text/plain words = 8054 sentences = 353 flesch = 45 summary = These include new phleboviruses of the Bunyaviridae family, exemplified by severe fever with thrombocytopenia syndrome virus [SFTSV] recognized in China in 2010, and the Heartland virus, a closely related but distinct virus, presenting with similar clinical features and discovered in Missouri in 2012. Other newly recognized tickborne infections include a novel spirochete of the relapsing fever group, Borrelia miyamotoi, first reported to cause human infection in Russia in 2011 and subsequently discovered to cause clinical disease in the Netherlands, Japan, and the United States, with transmission by the black-legged deer tick Ixodes scapularis. Transmission of SFTSV is considered mainly from tick bites, but there is also evidence from multiple reports that the virus can be transmitted from human to human by direct contact with blood of infected patients [67] [68] [69] [70] [71] . Severe fever with thrombocytopenia syndrome virus in ticks collected from humans, South Korea cache = ./cache/cord-017758-zfudssm9.txt txt = ./txt/cord-017758-zfudssm9.txt === reduce.pl bib === id = cord-018364-b06084r1 author = LaBrunda, Michelle title = The Emerging Threat of Ebola date = 2019-06-07 pages = extension = .txt mime = text/plain words = 13502 sentences = 795 flesch = 57 summary = Transmission of Ebola disease is still being studied, but it is known that person-toperson contact is the most common form of spread. One study found the risk of developing EVD for healthcare workers to be 100 times that of the general community during an outbreak of Ebola in Sierra Leone [67] . After the outbreak of SARS in 2003 many countries starting using boarder screening to try to identify possibly ill people in hopes of limiting spread of infectious disease, others jumped on board after the 2009 H1N1 influenza pandemic. An article by the CDC, published around the same time as the article recommending travel restriction for high-risk individuals, concludes that border screens are expensive and not effective in preventing the spread of disease [100] . Infection Prevention and Control Recommendations for Hospitalized Patients Under Investigation (PUIs) for Ebola Virus Disease (EVD) in U cache = ./cache/cord-018364-b06084r1.txt txt = ./txt/cord-018364-b06084r1.txt === reduce.pl bib === id = cord-018040-k0h5ejjt author = Ilyinskii, P. title = Aspects of Microparticle Utilization for Potentiation of Novel Vaccines: Promises and Risks date = 2009 pages = extension = .txt mime = text/plain words = 6930 sentences = 309 flesch = 41 summary = Many recombinant vaccines against novel (HIV, HCV) or ever-changing (influenza) infectious agents require the presence of adjuvants/delivery vehicles to induce strong immune responses. Cationic and anionic polylactide co-glycolide (PLG) microparticles have been successfully used to adsorb a variety of agents, which include plasmid DNA, recombinant proteins and adjuvant active oligonucleotides and are also currently tested in several vaccine applications. The size of these vectors is generally within 10-1000 nm and it is a specific mechanism by which our immune system recognizes such particles that underlies their adjuvant potencies (in addition, many carriers protect proteins/NA from rapid degradation in vivo and release them into the organism during prolonged periods of time, which also results in higher immunogenicity). Several VLPbased vaccines have been licensed for general use, many of them against HBV, which are composed of HBV surface antigen (HBsAg), which is a main component of currently used protein-based, alum adjuvant-potentiated vaccine. cache = ./cache/cord-018040-k0h5ejjt.txt txt = ./txt/cord-018040-k0h5ejjt.txt === reduce.pl bib === id = cord-018463-a6qu0cuv author = Wimmer, Eckard title = Synthetic Biology, Dual Use Research, and Possibilities for Control date = 2018-03-23 pages = extension = .txt mime = text/plain words = 1970 sentences = 107 flesch = 48 summary = The anthrax attack coincided with the first report in 2002 of the de novo synthesis in the test tube of a pathogenic human virus, poliovirus, that was equally shocking because it indicated that dangerous infectious agents could be produced in laboratories outside of government control. These events were synchronous with the advent of a new discipline, Synthetic Biology, which was an emerging area of research that can broadly be described "as the design and construction of novel artificial biological pathways, organisms or devices, or the redesign of existing natural biological systems." The synthesis of viruses, or more broadly expressed: each experiment in Synthetic Biology, fits the definition of "Dual Use Research" – the dual use dilemma in which the same technologies can be used for the good of humans and misused for bioterrorism. cache = ./cache/cord-018463-a6qu0cuv.txt txt = ./txt/cord-018463-a6qu0cuv.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-018166-savdgy0u author = Bosch, Albert title = Survival and Transport of Enteric Viruses in the Environment date = 2006 pages = extension = .txt mime = text/plain words = 11473 sentences = 548 flesch = 38 summary = Environmental virology may be defined as the study of viruses that can be transmitted through various environments (water, sewage, soil, air, or surfaces) or food and persist enough in these vehicles to represent a health threat. Since that time, other enteric viruses responsible for gastroenteritis and hepatitis have replaced enteroviruses as the main target for detection in the environment, although the near eradication of poliomyelitis from the globe calls for exhaustive studies on the occurrence of wild-type and vaccinal-type polioviruses in environmental samples. The possibility nowadays to detect the presence of human enteric viruses in different types of water samples and foodstuff, in particular shellfish samples, should be a valuable tool in the prevention of waterborne and food-borne diseases. These data suggest that temperature, and probably relative humidity, may be meaningful in the seasonal distribution of outbreaks of certain human enteric viruses (Enright, 1954) , due to the influence of these factors on virus persistence. cache = ./cache/cord-018166-savdgy0u.txt txt = ./txt/cord-018166-savdgy0u.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-018555-3lta1tbp author = Overstreet, Robin M. title = Host–Symbiont Relationships: Understanding the Change from Guest to Pest date = 2016-01-06 pages = extension = .txt mime = text/plain words = 15626 sentences = 706 flesch = 47 summary = We provide examples involving multiple triggers for organisms associated with termites, for an endemic virus being affected by multiple factors and having multiple effects on its commercial penaeid shrimp hosts, and for contrasting variables associated with two exotic viruses in wild and cultured commercial penaeid shrimps with an emphasis on hypothesizing how the pathogenicity developed in these two viruses. Atypical temperatures, such as warm water associated with power plants, can cause infections of a specific parasite during periods when the hosts are more likely to be consumed by predators, more susceptible to disease, or more susceptible to interactions among parasites that can occur and result in unusual pathogenic conditions. The transformation triggers phenotypic and behavioral changes specifically attracting infective specimens to predatory birds in which the trematode matures considerable detail the host-symbiont relationships affecting the outcome of pathogenic viruses in populations of commercial penaeid shrimp. cache = ./cache/cord-018555-3lta1tbp.txt txt = ./txt/cord-018555-3lta1tbp.txt === reduce.pl bib === id = cord-018165-afzjx2ci author = Modrow, Susanne title = Vaccines date = 2013-08-12 pages = extension = .txt mime = text/plain words = 4013 sentences = 213 flesch = 43 summary = Live vaccines contain attenuated, replication-competent pathogens that can replicate in the vaccinated person, i.e. they are able to infect certain cells and initiate the synthesis of viral proteins and particles, but without triggering the respective clinical picture. Therefore, the immune response that is triggered by attenuated viruses is suitable to induce a long-lasting, effective protection against infections with the respective pathogen. Similarly, vaccinia viruses that were originally used to produce a protective immune response against smallpox virus induced local infections in humans, which in very rare cases had a generalized or fatal course. It is being attempted to modify well-explored, less pathogenic viruses (e.g. adenoviruses) and vaccine viruses that were used successfully in the past (usually vaccinia viruses) by using genetic engineering methods in such a way that they encode proteins of other viral species, in addition to their own gene products necessary for infection and replication (▶ Sects. cache = ./cache/cord-018165-afzjx2ci.txt txt = ./txt/cord-018165-afzjx2ci.txt === reduce.pl bib === id = cord-018265-twp33bb6 author = Becker, Pablo D. title = Community-acquired pneumonia: paving the way towards new vaccination concepts date = 2007 pages = extension = .txt mime = text/plain words = 14121 sentences = 697 flesch = 36 summary = A live vaccine based on a master virus strain developed at the Institute of Applied Microbiology (Austria) by growing wild influenza virus in Vero cells at 25°C was also demonstrated to be safe, well-tolerated and immunogenic after intranasal immunization in young adults [18]. Candidate vaccines should be able to replicate and induce a protective immune response in young infants, even in the presence of maternally acquired antibodies. This demonstrates that antibodies play a major role in protection against this disease, whereas T-cell immunity targeted to internal viral proteins appears to contribute to clearance. The second generation of PS-based conjugate vaccines stimulates stronger antibody responses, even in infants, young children and immune deficient individuals, as well as immunological memory. The resulting proteins are then used to perform immunological and/or functional studies to select the most promising candidates (e.g., able to induce the production of microbicidal or neutralizing antibodies, capacity to confer protective immunity). cache = ./cache/cord-018265-twp33bb6.txt txt = ./txt/cord-018265-twp33bb6.txt === reduce.pl bib === id = cord-018089-m94q75xn author = Mubareka, Samira title = Influenza Virus: The Biology of a Changing Virus date = 2010-06-18 pages = extension = .txt mime = text/plain words = 7034 sentences = 392 flesch = 39 summary = The genetic diversity of influenza A viruses and their capability to successfully infect an array of hosts, including avian and mammalian species, are highlighted in a discussion about host range and evolution. In contrast, avian hosts including waterfowl and domestic poultry harbor sialic acid with a2,3 linkage (SAa2,3Gal) which is distributed in the gastrointestinal tract, reflecting the fecal-oral mode of transmission of avian influenza strains in these species [23] . Specifically, changes at amino acid position 225 impart the ability of A/New York/1/18 to bind both avian and human host influenza virus receptors [26] . Since 1997, several avian influenza viruses, including H5N1, H7N2, H7N3, H7N7, H9N2, and H10N7 subtypes, have infected humans [76], though limited evidence for person to person spread exists [77, 78] . Pathology of fatal human infection associated with avian influenza A H5N1 virus cache = ./cache/cord-018089-m94q75xn.txt txt = ./txt/cord-018089-m94q75xn.txt === reduce.pl bib === id = cord-018816-v3ylisbt author = Alroy, Joseph title = Viral Pulmonary Disorders in Animals: Neoplastic and Nonneoplastic date = 2013-08-26 pages = extension = .txt mime = text/plain words = 2524 sentences = 173 flesch = 44 summary = Gross fi ndings in the lung of a nonneurological EHV-1 infection may include severe edema ( Fig. 24 .6 ) and hydrothorax. The lungs with the diffuse pattern of disease seen in monkeys (Baskin 1987 ) and sheep (Hoover and Thacker 1979 ) are heavy, wet, and consolidated. The alveolar spaces contain proteinaceous exudate with macrophages, neutrophils, and multinucleated giant cells with intranuclear basophilic inclusion bodies (Figs. In some species, such as marmosets and colobus monkeys, measles infection is more severe resulting in primary giant cell pneumonia followed by secondary bacterial bronchopneumonia (Jones et al. The presence of multinucleated giant cells containing intranuclear and intracytoplasmic eosinophilic inclusion bodies is a characteristic fi nding (Fig. 24.18 Histological findings are varied, including mild to moderate interstitial edema, mild infiltration by mononuclear cells (Fig. 24.28 ) , presence of alveolar macrophages, hemorrhagic foci, and capillary thrombosis as well as the presence of syncytial cells and eosinophilic inclusion bodies. cache = ./cache/cord-018816-v3ylisbt.txt txt = ./txt/cord-018816-v3ylisbt.txt === reduce.pl bib === id = cord-019982-hyxrgamj author = Brookfield, D.S.K. title = Viruses demonstrated in children in Tanzania: Studies in diarrhoea and measles date = 2005-04-14 pages = extension = .txt mime = text/plain words = 1906 sentences = 104 flesch = 60 summary = authors: Brookfield, D.S.K.; Cosgrove, B.P.; Bell, E.J.; Madeley, C.R. title: Viruses demonstrated in children in Tanzania: Studies in diarrhoea and measles Causes of diarrhoea with particular reference to viral agents were investigated in 123 infants and young children in Dar es Salaam, Tanzania. The pattern of virus infection causing infantile diarrhoea was similar in Dar es Salaam to other parts of the world. The present study attempted to investigate the viruses associated with diarrhoea in Dares Salaam and, since electron microscopy was considered essential, the study was limited to the number of stools that could be sent in one consignment by air to Scotland. Examination of stools from 26 cases of measles failed to implicate any particular virus as a likely cause of the associated diarrhoea. However the diarrhoea associated with measles in Tanzanian children does not appear to be caused by any of the electron microscopically detectable viruses. cache = ./cache/cord-019982-hyxrgamj.txt txt = ./txt/cord-019982-hyxrgamj.txt === reduce.pl bib === id = cord-018393-5jlqn7wq author = Finke, Ernst-Jürgen title = Bioterrorismus, infektiologische Aspekte date = 2011-12-14 pages = extension = .txt mime = text/plain words = 25008 sentences = 3876 flesch = 44 summary = Wenn sie sich jedoch verstärkt, kann man sie leicht erkennen, aber nur schwer heilen." (Nicolo Macchiavelli, 1449 -1527 Es ist wenig wahrscheinlich, dass biologische Anschläge rechtzeitig als solche erkannt werden, sofern kein automatisches Monitoring mit einem zuverlässigen Echtzeit-Nachweis von B-Agenzien existiert. B. Enzephalitiden viraler Genese sowie die Frühstadien von nvCJD und möglicherweise auch die Frühsymptomatik der Alzheimer-Krankheit; außerdem die Borreliose-Infektion (Neuroborreliose), bei der ein heterogenes Symptomenbild angenommen wird, das sich wenig mit der Ausprägung einer (BDV-spezifischen) Dysfunktion im limbischen System deckt. Unklar ist jedoch, wie häufig sich aus initial milden Infektionen der oberen Luftwege eine Bronchitis oder eine Pneumonie entwickelt und was die auslösenden Faktoren dafür sind. Beim Nachweis hoch positiver (häufig mit anderen Chlamydienspezies kreuzreagierender) Antikörper ist bei entsprechender klinischer Symptomatik die gezielte Erhebung der Anamnese hinsichtlich einer möglichen Exposition des Patienten gegenüber den natürlichen Wirten diagnostisch wegweisend. Aus Patientenseren wurden Cyclospora-spezifische Antikörper isoliert, jedoch sind die Vorgänge der Immunantwort auf Cyclospora noch nicht vollständig geklärt und ob sich eine Immunität entwickelt, ist fraglich. cache = ./cache/cord-018393-5jlqn7wq.txt txt = ./txt/cord-018393-5jlqn7wq.txt === reduce.pl bib === id = cord-018724-ss8x2g3b author = Stobbe, Anthony title = Plant Virus Diversity and Evolution date = 2016-06-22 pages = extension = .txt mime = text/plain words = 7456 sentences = 360 flesch = 47 summary = The variation we see within a single plant host has profound effects on the how the virus responds to selective pressures associated with new hosts, and factors such as the bottleneck events associated with cell-to-cell movement or vectoring. However, several forms of virus variation, such as the high mutation rates of RNA and some DNA viruses, recombination, and reassortment lead to resistance breaking (Duffy and Holmes 2008; McDonald and Linde 2002; Harrison 2002) . For example, genetic diversity (heterosis) induced tolerance to Turnip mosaic virus in wild cress (Lepidium sp.) hybrids, while plants that were selfed were more susceptable to disease, suggesting that small populations with low genetic diversity could lead to increased disease symptoms, and infection rates (Houliston et al. Genetic bottlenecks during systemic movement of Cucumber mosaic virus vary in different host plants Role of recombination in the evolution of natural populations of Cucumber mosaic virus, a tripartite RNA plant virus cache = ./cache/cord-018724-ss8x2g3b.txt txt = ./txt/cord-018724-ss8x2g3b.txt === reduce.pl bib === id = cord-018017-c8myq6bi author = Iversen, Patrick L. title = The Threat from Viruses date = 2018-09-30 pages = extension = .txt mime = text/plain words = 11563 sentences = 615 flesch = 51 summary = Numerous emerging infections caused by viral agents have imposed high impact on human survival (Table 3 .3). The apparent success of these viruses is that as they move from reservoir hosts to humans and as humans become immune to the initial infection, the population of diverse genomes offers multiple chances to adapt by finding a "fit" genome version which can propagate until the next transition requiring adaption. Human T-cell Lymphotropic Virus (HTLV-1) HTLV-1 is a single-stranded RNA retrovirus, defined by their use of reverse transcriptase, a polymerase, that makes a DNA copy of the RNA 7 kb viral genome. If we combine cardiovascular events and neoplasia caused by infection, then infectious disease is the most significant threat to human life and qualifies as the area of greatest impact. Adeno-associated Virus (AAV) is a single stranded DNA virus that infects humans but are not known to cause disease. is a 5229 base double-stranded DNA virus infecting less than 5 percent of the human population. cache = ./cache/cord-018017-c8myq6bi.txt txt = ./txt/cord-018017-c8myq6bi.txt === reduce.pl bib === id = cord-018437-yjvwa1ot author = Mitchell, Michael title = Taxonomy date = 2013-08-26 pages = extension = .txt mime = text/plain words = 9283 sentences = 561 flesch = 48 summary = Classifi cation is based on the genomic nucleic acid used by the virus (DNA or RNA), strandedness (single or double stranded), and method of replication. The nucleocapsids of some viruses are surrounded by envelopes composed of lipid bilayers and host-or viral-encoded proteins. The sequence of negative-sense ssRNA is complementary to the coding sequence for translation, so mRNA must be synthesized by RNA polymerase, typically carried within the virion, before translation into viral proteins. Among the families of viruses able to infect humans and other vertebrate hosts, there are many species that target and cause disease in the lung. The nucleocapsid is surrounded by an envelope derived from host-cell membrane and viral envelope proteins, including hepatitis B surface antigen. The genome of human parainfl uenza viruses is ~15 kb in length with an organization and six reading frames (N, P, M, F, HN, L) typical of the Paramyxoviridae (Karron and Collins 2007 ) . cache = ./cache/cord-018437-yjvwa1ot.txt txt = ./txt/cord-018437-yjvwa1ot.txt === reduce.pl bib === id = cord-020101-5rib7pe8 author = nan title = Cumulative Author Index for 2008 date = 2008-11-17 pages = extension = .txt mime = text/plain words = 2140 sentences = 126 flesch = 29 summary = Cauliflower mosaic virus gene VI product N-terminus contains regions involved in resistance-breakage, self-association and interactions with movement protein Intrahost evolution of envelope glycoprotein and OrfA sequences after experimental infection of cats with a molecular clone and a biological isolate of feline immunodeficiency virus DC-SIGN enhances infection of cells with glycosylated West Nile virus in vitro and virus replication in human dendritic cells induces production of Increase in proto-oncogene mRNA transcript levels in bovine lymphoid cells infected with a cytopathic type 2 bovine viral diarrhea virus Complete genome sequence analysis of dengue virus type 2 isolated in Modulation of hepatitis B virus replication by expression of polymerasesurface fusion protein through splicing: Implications for viral persistence Induction of apoptosis in Vero cells by Newcastle disease virus requires viral replication, de-novo protein synthesis and caspase activation Mechanisms of inhibition of HIV replication by non-nucleoside reverse transcriptase inhibitors cache = ./cache/cord-020101-5rib7pe8.txt txt = ./txt/cord-020101-5rib7pe8.txt === reduce.pl bib === id = cord-020789-slsfhrkx author = Kleines, Michael title = Virale Atemwegserkrankungen – Influenza, RSV und neue Viren date = 2017-10-27 pages = extension = .txt mime = text/plain words = 3370 sentences = 440 flesch = 44 summary = Die Bedeutung der entsprechenden Viren ließ sich nur durch die Anwendung moderner molekularer Methoden erkennen, und sie werden auch am besten durch molekulare Verfahren diagnostisch erfasst. In den letzten Jahren hat es eine Weiterentwicklung der verfügbaren Technologien (ausgehend von der für ein einzelnes Virus spezifischen Standard-PCR mit einem Zeitbedarf von 2-3 h) in 2 Richtungen gegeben: Zum einen sind nun Multiplexverfahren verfügbar, die organsystemorientiert alle relevanten Erreger für ein definiertes Krankheitsbild in einem Reaktionsansatz nachweisen können, z. Aber auch für das Management von RSV-Infektionen und Infektio-nen mit anderen respiratorischen Viren deuten sich substanzielle Fortschritte an. Letzter wichtiger Vertreter dieser Reihe, die von Subtypen mit den Hämagglutininkomponenten H5, H7 und H9 dominiert wird, ist ein Influenza-A-Virus vom Subtyp H7N9, das 2013 in China nachgewiesen wurde und eine größere Zahl humaner Infektionen verursacht hat (▶ Tab. 1). Aufgrund von eingeschränkter Sensitivität und Spezifität der Antikörpernachweisverfahren ist der positive Vorhersagewert positiver Antikörpernachweise für eine frische RSV-Infektion gering. cache = ./cache/cord-020789-slsfhrkx.txt txt = ./txt/cord-020789-slsfhrkx.txt === reduce.pl bib === id = cord-018477-hgvqd1ej author = Modrow, Susanne title = Pathogenesis date = 2013-08-12 pages = extension = .txt mime = text/plain words = 3661 sentences = 210 flesch = 51 summary = These cells are loaded with the virus particles and proteins and migrate to the immunologically active centres of the nearest lymph nodes, encountering there other immune cells such as CD4 + and CD8 + T lymphocytes, B lymphocytes and macrophages, which start to proliferate by contact with the pathogen proteins or with MHC-peptide complexes and by the influence of cytokines secreted by activated immune cells (▶ Chaps. During herpes simplex virus infections of the conjunctiva and the cornea, reactivated pathogens migrate from the ganglia of the nerve fibres into the eye, where they may spread in the epithelium of the cornea and cause inflammations. In pregnant women, haematogenously disseminated viruses such as rubella virus, cytomegalovirus and parvovirus B19 are transported via the bloodstream into the placenta and infect the endothelial cells of this organ. Other viruses, such poliovirus and tick-borne encephalitis virus, overcome the barriers probably by infection of endothelial cells, as occurs by infecting other organs (▶ Sects. cache = ./cache/cord-018477-hgvqd1ej.txt txt = ./txt/cord-018477-hgvqd1ej.txt === reduce.pl bib === id = cord-018639-0g1ov96t author = Kurpiers, Laura A. title = Bushmeat and Emerging Infectious Diseases: Lessons from Africa date = 2015-09-21 pages = extension = .txt mime = text/plain words = 14563 sentences = 713 flesch = 51 summary = Here we review the literature on bushmeat and EIDs for sub-Saharan Africa, summarizing pathogens (viruses, fungi, bacteria, helminths, protozoan, and prions) by bushmeat taxonomic group to provide for the first time a comprehensive overview of the current state of knowledge concerning zoonotic disease transmission from bushmeat into humans. In this review, we explore the links between bushmeat-related activities and EIDs in sub-Saharan Africa, where the vast majority of African emerging infectious zoonotic diseases occur (Jones et al. Although research has focused largely on mammals and, to a lesser extent, birds, theoretically any wildlife species harvested for bushmeat could be a potential source of zoonotic disease that can spillover during the hunting, butchering, and preparation process (Wolfe et al. With the increasing prevalence of zoonotic disease emergence and the associated risk for public health, we have to improve our understanding of the dynamics of spillover events of pathogens from animal to human hosts (Rostal et al. cache = ./cache/cord-018639-0g1ov96t.txt txt = ./txt/cord-018639-0g1ov96t.txt === reduce.pl bib === id = cord-018811-zhwr3h07 author = Oxford, John title = Influenza Vaccines Have a Short but Illustrious History of Dedicated Science Enabling the Rapid Global Production of A/Swine (H1N1) Vaccine in the Current Pandemic date = 2010-06-18 pages = extension = .txt mime = text/plain words = 13247 sentences = 618 flesch = 48 summary = The international investment into public health measures for a global human outbreak of avian H5N1 influenza together with a focus of swine influenza H1N1 is leading to enhanced production of conventional vaccine and to a new research searchlight on T-cell epitope vaccines, viral live-attenuated carriers of influenza proteins, and even more innovative substrates to cultivate virus, including plant cells. This was particularly well demonstrated by studies during the swine influenza campaign in the USA in 1976, when many observers reported results, which ultimately led to the recommended use in children of two doses of split-type rather than whole-virus vaccines. It has been known for many years that the serological response to inactivated vaccine depends on the previous experience of the recipient to infection by viruses of the same subtype of influenza A virus as that present in the vaccine. Comparison of inactivated vaccine A/HongKong/68 (H3N2) given intranasally or subcutaneously showed that following challenge with live virus only those who had developed a serum antibody response after vaccine by either route resisted infection. cache = ./cache/cord-018811-zhwr3h07.txt txt = ./txt/cord-018811-zhwr3h07.txt === reduce.pl bib === id = cord-020087-gs0pc6ee author = nan title = Cumulative Contents for 2010 date = 2010-11-18 pages = extension = .txt mime = text/plain words = 479 sentences = 43 flesch = 37 summary = Myristoylation of the small envelope protein of porcine reproductive and respiratory syndrome virus is non-essential for virus infectivity but promotes its growth 294 Porcine reproductive and respiratory syndrome virus (PRRSV) could be sensed by professional beta interferon-producing Hikichi (Japan) The 126-and/or 183-kDa replicases or their coding regions are responsible both for inefficient local and for systemic movements of Paprika mild mottle virus Japanese strain in tomato plants USA) Genetic control of host resistance to porcine reproductive and respiratory syndrome virus (PRRSV) infection Porcine reproductive and respiratory syndrome virus (PRRSV) in serum and oral fluid samples from individual boars: Will oral fluid replace serum for PRRSV surveillance USA) Use of a production region model to assess the efficacy of various air filtration systems for preventing airborne transmission of porcine reproductive and respiratory syndrome virus and Mycoplasma hyopneumoniae: Results from a 2-year study 177 Morrison (USA) Control and elimination of porcine reproductive and respiratory syndrome virus 185 Cumulative Author Index for cache = ./cache/cord-020087-gs0pc6ee.txt txt = ./txt/cord-020087-gs0pc6ee.txt === reduce.pl bib === id = cord-018804-wj35q88f author = Lázaro, Ester title = Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity date = 2007 pages = extension = .txt mime = text/plain words = 8510 sentences = 398 flesch = 44 summary = High error prone replication, together with the short replication times and large population sizes typical of RNA viruses, instead of being a handicap for survival provides an extraordinary evolutionary advantage by permitting the generation of a wide reservoir of mutants with different phenotypic properties [7] . However, the fact that DNA organisms, which usually live in constant environments, have evolved corrector activities, whereas RNA viruses have not, suggests that replication with high error rates is a selected character that strongly favours viral adaptation to fast changing conditions. Quasi-species replicating during a long time in a near-constant environment in the absence of large population size fluctuations can present a low rate of fixation of mutations in the consensus sequence, despite the continuous occurrence of mutants that is characteristic of the underlying dynamics of the population. The infection of a new host constitutes a sudden change in the environment in which viral replication takes place, usually with the consequence of a drastic decrease in the average fitness of the virus population, which prevents further transmission. cache = ./cache/cord-018804-wj35q88f.txt txt = ./txt/cord-018804-wj35q88f.txt === reduce.pl bib === id = cord-021034-hnw7a3a1 author = Mahony, James B. title = Negative staining in the detection of viruses in clinical specimens date = 2002-10-09 pages = extension = .txt mime = text/plain words = 4164 sentences = 297 flesch = 46 summary = In our experience the serum-in-agar (SIA) method is the most sensitive of the PAG IEM techniques for detection of rotavirus particles in clinical specimens. SPEIMDAGT employing colloidal gold-labeled secondary antibody has increased sensitivity and offers the advantage of detecting viral antigen when whole virus particles are not visible. Prior to the development of immunoassay techniques for detecting viral antigens, direct electron microscopy (DEM) with negative staining was the only method of providing a definitive diagnosis of several viral infections. We have used this method to detect rotavirus in fecal specimens (Wu et a!., 1989) (Fig. 2) Solid phase JEM Although IEM is considerably more sensitive than DEM, it is dependent upon the optimal concentrations of antibody and antigen and is susceptible to a prozone phenomenon. Development of a sensitive protein A-gold immunoelectron microscopy method for detecting viral antigens in fluid specimens cache = ./cache/cord-021034-hnw7a3a1.txt txt = ./txt/cord-021034-hnw7a3a1.txt === reduce.pl bib === id = cord-020235-stcrozdw author = nan title = Abstracts of Papers Presented at the 38th Meeting of the Deutsche Gesellschaft für Hygiene und Mikrobiologie, Virology Section, Göttingen, 5.–8.10.1981 date = 2012-03-15 pages = extension = .txt mime = text/plain words = 13494 sentences = 843 flesch = 58 summary = Hepatitis A virus (HAV) was isolated directly from human stool in diploid human fibroplasrs, Viral antigen was expressed only after 210 days of incubation of the infected cultures. Univ., 0-8700 Wiirzburg Effect of Measles (SSPE) Antiserum on Viral Surface Proteins and Hormone Receptor Activity in C6/SSPE Persistently Infected Cells BARRETT, P. Inst, of Genetics, Univ., 0-5000 Co logne Virus-Cell DNA Recombinants in Human Cells Lytically Infected by Ad2 NEUMANN, R., WEYER, U., and DOERFLER, W. In vitro, however, the gag-specific peptide sequences are cleaved off upon addition of the purified viral piS protease; in the case of the replication-defective, transforming avian sarcoma virus PRC II the cleaved nongag part has a ryrosine-phosphorylaring kinase activity similar to that described for the RSV src-gene product pp60 src . f. Virologie, Univ., D·6300 Giefen, 3 A protein of a molecular weight of about 38.000 d has been found to be phosphorylated 1 h after the onset of cell transformation by Rous sarcoma virus (RSV). cache = ./cache/cord-020235-stcrozdw.txt txt = ./txt/cord-020235-stcrozdw.txt === reduce.pl bib === id = cord-018441-r6wwpfcy author = Taylor, Milton W. title = Emerging Viruses date = 2014-07-22 pages = extension = .txt mime = text/plain words = 3674 sentences = 210 flesch = 63 summary = Most of these viruses are terrifying, and cause hemorrhagic fever, a complete destruction of the circulation system; they include Lassa fever, Nipah virus, Ebola, HIV, Severe acute respiratory syndrome (SARS), and, recently, Middle East respiratory syndrome (MERS), which is the latest in a series of "new" respiratory viruses infecting man. From 2001 to 2012 there were 280 cases of Nipah virus infections in humans, with 211 deaths-a mortality rate of 75 %. Ebola outbreaks occur with ferocity and suddenness, and with high mortality; they may originate from bats, and the virus spreads easily to a susceptible human population. Ebola is the most lethal human viral infection known, First identified in 1976 in Zaire and the Sudan, it causes hemorrhagic fever (internal bleeding) with a mortality rate of 88 %. The SARS epidemic also showed how international cooperation among health care experts can effectively contain the The virus spread from southern China to Singapore, Taiwan, the U.S. and Canada (Ontario). cache = ./cache/cord-018441-r6wwpfcy.txt txt = ./txt/cord-018441-r6wwpfcy.txt === reduce.pl bib === id = cord-021069-v9f9874x author = Morrison, Lynda A. title = Viral pathogenesis and central nervous system infection date = 2004-11-23 pages = extension = .txt mime = text/plain words = 3816 sentences = 201 flesch = 37 summary = Stages in viral pathogenesis defined as (1) virus entry, (2) spread, (3) tropism, (4) virulence and injury to the host, and (5) the outcome of infection are discussed for viral infections in general and those aspects unique to infections of the central nervous system . Stages in viral pathogenesis defined as (1) virus entry, (2) spread, (3) tropism, (4) virulence and injury to the host, and (5) the outcome of infection are discussed for viral infections in general and those aspects unique to infections of the central nervous system . Genetic determinants of disease susceptibility have been found for infection of mice with strains of most neurotropic viruses, in at least one case of coronavirus reflecting lack of a gene encoding a virus receptor protein . cache = ./cache/cord-021069-v9f9874x.txt txt = ./txt/cord-021069-v9f9874x.txt === reduce.pl bib === id = cord-020097-eh5deunk author = nan title = Cumulative Author Index for 2006 (Volumes 115–122) date = 2006-10-27 pages = extension = .txt mime = text/plain words = 1481 sentences = 87 flesch = 28 summary = Modulation of PKR activity in cells infected by bovine viral diarrhea virus Complete genome analysis of RFLP 184 isolates of porcine reproductive and respiratory syndrome virus Phylogenetic analysis of the gag region encoding the matrix protein of small ruminant lentiviruses: Comparative analysis and molecular epidemiological applications TATAbinding protein and TBP-associated factors during herpes simplex virus type 1 infection: Localization at viral DNA replication sites Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein Efficient inhibition of hepatitis B virus replication by small interfering RNAs targeted to the viral X gene in mice Preparation and characterization of a novel monoclonal antibody specific to severe acute respiratory syndrome-coronavirus nucleocapsid protein A deletion and point mutation study of the human papillomavirus type 16 major capsid gene Sequencing and comparative analysis of a pig bovine viral diarrhea virus genome Antigenic structure analysis of glycosylated protein 3 of porcine reproductive and respiratory syndrome virus cache = ./cache/cord-020097-eh5deunk.txt txt = ./txt/cord-020097-eh5deunk.txt === reduce.pl bib === id = cord-020714-h1fevqcw author = Compans, Richard W. title = Membrane Glycoproteins of Enveloped Viruses date = 2008-05-30 pages = extension = .txt mime = text/plain words = 14149 sentences = 684 flesch = 43 summary = Other advantages of enveloped viruses in studies of membrane structure and biogenesis include the ease of biosynthetic labeling of viruses grown in cell culture with specific radioactive precursors and the availability of mutants in defined gene products, some of which are proving to be useful in the analysis of viral membrane assembly. Apart from minor differences in carbohydrates of glycoproteins, virion proteins are indistinguishable when the virus is propagated in a variety of cells; therefore there appears to be little or no determining influence of viral proteins on the composition of the lipid bilayer. Based upon the estimated carbohydrate content (12,000 daltons) of the HA glycoprotein obtained by Laver (1971) and Schwarz and Klenk (1974) and the size estimates of the type I and I1 glycopeptides of influenza virus grown in MDBK cells, it was estimated that HA, contains a single type I glycopeptide whereas HA, possesses two type I and one or two type I1 oligosaccharide side-chains for the WSN strain (Nakamura and Com pans, 1978b) . cache = ./cache/cord-020714-h1fevqcw.txt txt = ./txt/cord-020714-h1fevqcw.txt === reduce.pl bib === id = cord-018706-gykw2nvt author = Yadav, Mahendra Pal title = Emerging and Transboundary Animal Viral Diseases: Perspectives and Preparedness date = 2020-02-23 pages = extension = .txt mime = text/plain words = 9686 sentences = 390 flesch = 41 summary = The factors driving the emergence of different emerging infectious disease (EID) interfaces include global travel, urbanisation and biomedical manipulations for human EIDs; agricultural intensification for domestic animal EIDs; translocation for wildlife EIDs; human encroachment, ex situ contact and ecological manipulation for wildlife–human EIDs; encroachment, new introductions and 'spill-over' and 'spill-back'; and technology and industry for domestic animal–human EIDs. The concepts of sanitary and phytosanitary (SPS) measures and biosecurity have gained recognition globally in almost all the realms of human activities, including livestock health and production management. Among the TADs having zoonotic manifestations, a number of infectious diseases, such as highly pathogenic avian influenza (HPAI), BSE (Mad cow disease caused by prion), West Nile fever, Rift Valley fever, SARS coronavirus, Hendra virus, Nipah virus, Ebola virus, Zika virus and CCHF, to name a few, adversely affecting animal and human health have been in the news in recent times (Malik and Dhama 2015; Munjal et al. cache = ./cache/cord-018706-gykw2nvt.txt txt = ./txt/cord-018706-gykw2nvt.txt === reduce.pl bib === id = cord-020969-lh2ergpm author = STRAUSS, JAMES H. title = Gene Therapy date = 2012-07-27 pages = extension = .txt mime = text/plain words = 11793 sentences = 597 flesch = 52 summary = Together with methods for cloning and manipulating viral genomes, this information has made possible the use of viruses as vectors to express foreign genes. The use of minus-strand RNA viruses as vectors was delayed because the virion RNA itself is not infectious, but recent developments has made it possible to rescue virus from cloned DNA by using coexpression of the appropriate viral proteins in a transfected cell. It is also possible to transfect cells with the E1 or E3 expression cassette together with DNA clones encoding the rest of the adenovirus genome, in which case homologous recombination results in the production of virus. Because the poliovirus replicon lacks a full complement of the structural genes (it is a suicide vector), packaging to produce particles requires infection of a cell that expresses the polioviral structural proteins by some mechanism. cache = ./cache/cord-020969-lh2ergpm.txt txt = ./txt/cord-020969-lh2ergpm.txt === reduce.pl bib === id = cord-020712-l9cn0n99 author = Ohnishi, Shun-Ichi title = Chapter 9 Fusion of Viral Envelopes with Cellular Membranes date = 2008-05-30 pages = extension = .txt mime = text/plain words = 11708 sentences = 735 flesch = 56 summary = Residues 80-100 in El and residues 100-131 in G, which have sequence homology among the strains, may be such stretches though not strongly hydrophobic (Table 262 SHUN-ICHI OHNlSHl and the putative fusogenic segment should be able to interact with the target membrane, inducing some disturbance eventually leading to fusion (Fig. Ib) . Presence of receptors for the amino-terminal segments in target membranes has been suggested from studies on inhibition of virus replication by small peptides with amino acid sequences similar to that of the viral amino terminus (Richardson et al., 1980; Richardson and Choppin, 1983) . Why is a specific amino acid sequence of F glycoprotein required for the membrane fusion reaction between envelope of HVJ (Sendai virus) and target cell membranes? pH-Dependent membrane fusion activity of a synthetic twenty amino acid peptide with the same sequence as that of the hydrophobic segment in influenza virus hemagglutinin cache = ./cache/cord-020712-l9cn0n99.txt txt = ./txt/cord-020712-l9cn0n99.txt === reduce.pl bib === id = cord-021413-1ht1xm88 author = Kraft, Lisbeth M. title = Viral Diseases of the Digestive System date = 2013-10-21 pages = extension = .txt mime = text/plain words = 14259 sentences = 882 flesch = 51 summary = Runner and Palm (1953) , studying C3H mice, indicated that there was a higher incidence of diarrhea in December/January (Kraft, 1961; Blackwell et al., 1966) , complement fixation (Wilsnack et al., 1969; Kapikian et al, 1976; Thouless et al., 1977b) , direct immunofluorescent staining or precipitin (Wilsnack et al., 1969; Spence et al., 1975; Foster α/., 1975; Peterson α/., 1976) , immune electron microscopy (Kapikian et al., 1974; Bridger and Woode, 1975) , immunoelectroosmophoresis (Tufvesson and Johnsson, 1976; Middleton et al., 1976) , enzyme-linked im munosorbent assay (ELISA) (Scherrer and Bernard, 1977; El lens etal., 1978; Yolken etal., 1978a,b,c) , radioimmunoas say (Acres and Babiuk, 1978; Kalica et al., 1977; Middleton et al., 1977) , immunodiffusion (Woode et al., 1976) , hemagglutination inhibition (Fauvel et al., 1978) , enzymelinked fluorescence assay (ELISA) (Yolken and Stopa, 1979) , an unlabeled soluble enzyme peroxidase-antiperoxidase method , plaque reduction test (Estes and Graham, 1980) , serologic trapping on antibody-coated electron microscope grids (Nicolaieff et al., 1980) , a solid phase system (SPACE, solid phase aggregation of coupled erythrocytes) for detection of rotaviruses in feces (Bradbume et al., 1979) , and immune electron microscopy with serum in agar diffusion (Lamontagne et al., 1980) . cache = ./cache/cord-021413-1ht1xm88.txt txt = ./txt/cord-021413-1ht1xm88.txt === reduce.pl bib === id = cord-021588-ec7udsmw author = Craighead, John E. title = Enteric Viral Disease date = 2007-05-09 pages = extension = .txt mime = text/plain words = 3474 sentences = 188 flesch = 45 summary = This virus and its soon-to-be-discovered close relatives (the so-called Norwalk-like viruses [NLVs]) proved to be important causes of explosive outbreaks of diarrhea in both children and adults. But, this painstaking approach has now yielded evidence to indicate that viruses of at least six families may contribute to enteric illness in children and in adult citizens whose immunity has waned (Figure 32.1, Table 32 .1). The etiological role of these viruses as a cause of intestinal disease was established by demonstrating a temporal association of naturally occurring infections (as demonstrated by stool examination using electron microscopy) with illness and by experimental induction of disease in both human volunteers and experimental animals (Hall et al, 1984) . Volunteer studies have yielded important histological and ultrastructural documentation of the profound but relatively transient changes that occur in the mucosa of the small intestine during the course of infections with NLVs (Agus ei al, 1973; Schreiber ei al, 1973 Schreiber ei al, , 1974 Dolin ei al, 1975) . cache = ./cache/cord-021588-ec7udsmw.txt txt = ./txt/cord-021588-ec7udsmw.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-019051-gtruu1op author = Weber, Olaf title = The role of viruses in the etiology and pathogenesis of common cold date = 2009-11-10 pages = extension = .txt mime = text/plain words = 12321 sentences = 734 flesch = 44 summary = Viruses with an established role in common cold are rhinoviruses, adenoviruses, parainfluenza viruses, coronaviruses and the respiratory syncytial virus, and these are reviewed in greater detail here. Therefore, the viral etiology and the role of viruses in the pathogenesis of common cold is complex and it is safe to say, not fully understood for each and every virus that is linked to respiratory tract infection. RSV infection is assumed to be frequently misdiagnosed, particularly in adults [56] , because the symptoms are similar to those caused by other respiratory viruses like influenza. Human parainfluenza viruses (HPIV) are important causes of respiratory diseases in infants and children. HMPV is thought to be the second or third cause of severe acute respiratory tract infection in children, just ranking behind RSV and influenza virus [146, 148] . Retinoic acid-inducible gene I mediates early Antiviral Response and Toll-like receptor 3 expression in respiratory syncytial virus-infected airway epithelial cells cache = ./cache/cord-019051-gtruu1op.txt txt = ./txt/cord-019051-gtruu1op.txt === reduce.pl bib === id = cord-021499-up5vftj4 author = Brayton, Cory title = Viral Infections date = 2007-09-02 pages = extension = .txt mime = text/plain words = 20925 sentences = 1063 flesch = 43 summary = Depending on inoculation route, dose, strain, and age of mice, experimental infections may result in inflammation or cytomegaly with inclusion bodies in a variety of tissues, pneumonitis, myocarditis, meningoencephalitis, or splenic necrosis in susceptible strains (National Research Council, 1991; Osborn, 1982; Percy and Barthold, 2001) . Both strains are apathogenic for adult mice, but the immunosuppressive variant is more pathogenic for neonatal mice than is MMVp. Serological surveys show that the mouse is the primary natural host (Parker et al., 1970; Smith et al., 1993b; Singleton et al., 2000) , but the virus is also infective for rats, hamsters (Garant et al., 1980; Ward and Tattersall, 1982) , and Mastomys (Haag et al., 2000) during foetal development or after parenteral inoculation. Early descriptions of naturally occurring disease may have been complicated by concurrent infections such as MHV or murine rotavirus A (MuRV-A)/epizootic diarrhoea of infant mice (EDIM) virus that contributed to the severity of the lesions especially in liver, pancreas, CNS, and intestine. cache = ./cache/cord-021499-up5vftj4.txt txt = ./txt/cord-021499-up5vftj4.txt === reduce.pl bib === id = cord-021116-rh0e4n2w author = Lippens, Ronnie title = Viral Contagion and Anti-Terrorism: Notes on Medical Emergency, Legality and Diplomacy date = 2004 pages = extension = .txt mime = text/plain words = 5100 sentences = 259 flesch = 56 summary = This paper traces the main outlines of this emerging imaginary that has left notions of Empire as spheres of integrative production firmly behind, and is now geared towards imagining Empire as a complete, organic body of free-but-organic-and-therefore-orderly flows that however needs to be kept intact by means of epidemiological interventions aimed at excluding or neutralizing viral entities. Law and diplomacy were important technologies (however repressive at times) by which nation-states as well as Empires were held together, or indeed, by which they were produced or maintained, and by which they were made to be productive. There is no need for the productive negotiations of a 'cosmopolitan globalism' either (to use Mikkel Rasmussen's words 30 ), nor for reconciliatory efforts (one does not reconcile with viruses): the sanitary exclusion of viral contagion will suffice to keep the body of today's imperial new world order healthy. cache = ./cache/cord-021116-rh0e4n2w.txt txt = ./txt/cord-021116-rh0e4n2w.txt === reduce.pl bib === id = cord-020756-d9f5fd7x author = de Jong, Menno Douwe title = Avian Influenza Viruses and Pandemic Influenza date = 2007 pages = extension = .txt mime = text/plain words = 15047 sentences = 677 flesch = 41 summary = This is illustrated by the fact that during its evolution in humans, the NA of H2N2 viruses, which were of avian origin and therefore highly specific for hydrolization of α2,3-linked sialic acids, acquired high affinity for the human α2,6-linked sialic acids (Baum and Paulson, 1991) In addition to the surface glycoproteins, laboratory experiments with reassortant viruses suggest that the genes encoding internal proteins, such as M, NP, PB1 and PB2, may also play a role in determining the host range (Almond 1977; Scholtissek et al., 1978a; Snyder et al., 1987; Subbarao et al., 1993) . By reverse genetics experiments, it has been shown that a lysine residue at position 627 (Lys627) of PB2 seems essential for high virulence and systemic replication in mice of highly pathogenic influenza H5N1 viruses responsible for the outbreak among poultry and humans in Hong Kong in 1997 (H5N1/97) (Hatta et al., 2001) . cache = ./cache/cord-020756-d9f5fd7x.txt txt = ./txt/cord-020756-d9f5fd7x.txt === reduce.pl bib === id = cord-021770-zn7na974 author = Slifka, Mark K. title = Passive Immunization date = 2017-07-17 pages = extension = .txt mime = text/plain words = 12134 sentences = 610 flesch = 31 summary = [26] [27] [28] [29] Recent studies verify these earlier results, demonstrating a 90% to 91% vaccine efficacy against whooping cough among infants younger than 2 months of nonlymphoid tissues and to penetrate mucosal sites of infection is likely to explain why it is often considered the best immunoglobulin isotype for routine passive immunization and has shown clinical benefit ranging from reduced clinical symptoms to nearly complete protection from lethal infection in a number of infectious disease models (Table 8 .3). 118 With the recent development of polyclonal and monoclonal antibodies that show protective efficacy against tularemia in animal models, [119] [120] [121] it may be possible to incorporate both passive immunotherapy and antibiotic treatment into clinical practice not only for tularemia, but for other bacterial diseases, especially in cases in which antibiotic resistance is becoming more widespread. cache = ./cache/cord-021770-zn7na974.txt txt = ./txt/cord-021770-zn7na974.txt === reduce.pl bib === id = cord-021375-lca26xum author = Voelkner, Nadine title = Riding the Shi: From Infection Barriers to the Microbial City date = 2019-08-23 pages = extension = .txt mime = text/plain words = 9599 sentences = 443 flesch = 49 summary = Taking its cue from the currently accepted germ theory of disease, such mechanisms render a global city like Hong Kong not only pervasively "on alert" and under threat of unpredictable and pathogenic viruses and other microbes, it also gives rise to a hygiene and antimicrobial politics that is never entirely able to control pathogenic circulation. Considering recent advances in gene sequencing in microbiology, through which a "vast diversity of microbial life in, on and around the human body" (Lorimer 2017, 544) has been identified as residing in complex relationality with one another, how befitting is it to fight infectious diseases by indiscriminately eliminating microbes through the use of antimicrobials and practicing urban hygiene as in the case of Hong Kong? Various scholars have noted how, much like Hong Kong in the face of SARS, global public health programs adopt an antimicrobial stance to the control and/or elimination of infectious diseases, however, which might prove to be counterproductive in securing human life (Macphail 2014; Methot and Alizon 2014; Fishel 2015 Fishel , 2017 White 2015; Hinchliffe et al. cache = ./cache/cord-021375-lca26xum.txt txt = ./txt/cord-021375-lca26xum.txt === reduce.pl bib === id = cord-021805-2j07zw6q author = Epstein, Jonathan H. title = Emerging Diseases in Bats date = 2018-09-28 pages = extension = .txt mime = text/plain words = 4160 sentences = 214 flesch = 50 summary = 6, 7 Bats have been associated with several zoonotic viruses that have recently been discovered and linked to significant human and animal disease, including severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), Ebola and Marburg viruses, and Nipah virus (NiV) 8 (see also Chapters 19, 34, and 42 ). Viral discovery has, however, significantly expanded our understanding of the phylogenetic breadth of important viral families such as filoviruses (e.g., Ebola virus), paramyxoviruses (e.g., NiV), and coronaviruses (e.g., SARS coronavirus [CoV]), which is necessary for both better understanding what makes viruses pathogenic and also for recognizing wildlife reservoirs of viral pathogens, once they do emerge, more rapidly. Data are mounting to support bats as important reservoirs compared with other mammals, and large-scale surveillance efforts like PREDICT and the recently launched Global Virome Project, a 10-year effort to identify the majority of viruses in key wildlife species in emerging disease hot spots, 73 will shed more light on the total diversity of viruses in bat species and the types of human-animal interfaces that exist in different geographic and cultural contexts. cache = ./cache/cord-021805-2j07zw6q.txt txt = ./txt/cord-021805-2j07zw6q.txt === reduce.pl bib === id = cord-021552-6jbm869r author = HURST, CHRISTON J. title = Relationship Between Humans and Their Viruses date = 2007-05-09 pages = extension = .txt mime = text/plain words = 7828 sentences = 395 flesch = 43 summary = Viral replication ~ at the individual host level, the primary tissue and organ tropisms are toward the cervix, conjunctiva, pharynx, small intestine, and urethra; the secondary tissue and organ tropisms are toward the brain, kidney, lungs, and lymph nodes; at the host population level, these viruses generally are endemic and initially acquired at a very early age, with the infections very often asymptomatic in young children. ~ral replication ~ at the individual host level, primary tissue and organ tropisms are toward the small intestine; secondary tissue and organ tropisms are toward the liver; at the host population level, these tend to be epidemic within human populations; for the hepatitis E virus it seems that acquisition occurs from swine, with the result being epidemics (often very widespread) of human disease; some acquisition from animals may come from eating infected animals; subsequent transmission of all caliciviruses within human populations is by fecally contaminated waste and thus can be very widespread. Alternate hosts: One species of viral family Hepadnaviridae (hepatitis B virus) is known to infect humans, and it seems naturally limited to humans. cache = ./cache/cord-021552-6jbm869r.txt txt = ./txt/cord-021552-6jbm869r.txt === reduce.pl bib === id = cord-022254-8y5sq72c author = Nathanson, Neal title = IMMUNOSUPPRESSION AND VIRUS INFECTION OF RODENTS date = 2012-12-02 pages = extension = .txt mime = text/plain words = 3210 sentences = 172 flesch = 35 summary = One example of specific deletion is the use of anti-mu antiserum to delete IgM bearing B cells from neonatal animals, thus blocking the B cell arm of the immune response (43-46). Complement plays an important ancillary role as a host defense, since in conjunction with specific antiviral antibody, it can lyse either virions or virus-infected cells (60). The recent development of methods for the cloning of T cells and the culture of T cell lines (88) (89) (90) (91) (92) , has made it possible to study the effect of specific T cell subsets upon virus infection (93) (94) (95) (96) . I. Comparative effectiveness of antibody and reconstitution of immune spleen cells on immunosuppressed mice Protection of mice from fatal herpes simplex virus type 1 infection by adoptive transfer of cloned virusspecific and H-2-restricted cytotoxic T lymphocytes Dual role of the immune response in street rabies virus infection of mice cache = ./cache/cord-022254-8y5sq72c.txt txt = ./txt/cord-022254-8y5sq72c.txt === reduce.pl bib === id = cord-021465-2pj26fmv author = PERDUE, MICHAEL L. title = Impact of Avian Viruses date = 2007-05-09 pages = extension = .txt mime = text/plain words = 14076 sentences = 696 flesch = 46 summary = Although there is variation in the economic or ecological impact of various viral groups from year to year and among geographic sites, the "Top Ten" list of virus groups exhibiting routine significant impact on commercial poultry worldwide (not necessarily in order of impact) are paramyxoviruses (Newcastle disease); coronaviruses (infectious bronchitis); herpesviruses (infectious laryngotracheitis; Marek's disease; duck enteritis); reoviruses (viral arthritis); picornaviruses (avian encephalomyelitis); adenoviruses (egg drop syndrome); retroviruses (lymphoid leukosis); orthomyxoviruses (avian influenza); poxviruses (fowlpox); and birnaviruses (infectious bursal disease). With the recent documented transmission of a lethal avian influenza virus from commercial poultry to humans, these ecological relationships take on new significance. Lymphomas caused by MDV and retroviruses are still the most common viral neoplastic diseases of poultry, and a recent increase in mortality and evolution of more virulent MDV strains indicates that the impact of these viruses will continue to be felt (Witter, 1996) . cache = ./cache/cord-021465-2pj26fmv.txt txt = ./txt/cord-021465-2pj26fmv.txt === reduce.pl bib === id = cord-020010-q58x6xb0 author = nan title = 19th ICAR Abstracts: date = 2006-03-13 pages = extension = .txt mime = text/plain words = 46663 sentences = 2181 flesch = 44 summary = In the present study we reported the antiviral activity of neuraminidase inhibitor oseltamivir against lethal H5N1 influenza virus infection in ferrets, an appropriate animal model that closely resembles clinical signs of human influenza. Earl Kern 1 , Kathy Keith 2 , Robert Jordan 2 , Dennis Hruby 2 , Debra Quenelle 2 1 Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL, USA; 2 SIGA Technologies, Inc., Corvallis, OR, USA Although cidofovir (CDV) has been approved as an investigational new drug for emergency treatment of smallpox, its lack of oral activity and dose limiting toxicity dictates a need for continued development of better therapeutic agents for this potential bioterror disease. The in vitro antiviral activity of one of the most selective compounds, i.e. CHI-033, was assessed by (i) MTS-based cytopathic effect assays, (ii) virus yield reduction assays, (iii) real-time quantitative PCR (RT-QPCR) and (iv) by monitoring viral antigen expression. cache = ./cache/cord-020010-q58x6xb0.txt txt = ./txt/cord-020010-q58x6xb0.txt === reduce.pl bib === id = cord-022348-w7z97wir author = Sola, Monica title = Drift and Conservatism in RNA Virus Evolution: Are They Adapting or Merely Changing? date = 2007-09-02 pages = extension = .txt mime = text/plain words = 10892 sentences = 671 flesch = 56 summary = An analysis of proteins derived from complete potyvirus genomes, positive-stranded RNA viruses, yielded highly significant linear relationships. Under the rubric replication, a virus could vary to increase its fitness, exploit different target cells or evade adaptive immune responses. For a given virus, different protein sequence sets were compared to a given reference such as RT in the case of HIV/SIV. Although these data were derived from completely sequenced primate immunodeficiency viral genomes, analyses on larger data sets, such as p17 Gag/p24 Gag or gp120/gp41, yielded relative values that differed from those given in Table 6 .1 by at most 14%. An analysis of proteins derived from complete potyvirus genomes, positive-stranded RNA viruses, yielded highly significant linear relationships (Table 6 .1). In the clear cases where genetic variation is exploited by RNA viruses, it is used to overcome barriers to transmission set up by the host population, e.g. herd immunity. cache = ./cache/cord-022348-w7z97wir.txt txt = ./txt/cord-022348-w7z97wir.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-022324-tcltmhi7 author = Barthold, Stephen W. title = MOUSE HEPATITIS VIRUS BIOLOGY AND EPIZOOTIOLOGY date = 2012-12-02 pages = extension = .txt mime = text/plain words = 5622 sentences = 320 flesch = 42 summary = Interest in MHV has evolved from a number of different perspectives, including emphasis on MHV as a model of viral hepatitis, viral encephalitis and demyelinating disease, genetic mechanisms of host resistance to viral infection, and the molecular biology of coronaviruses, using MHV as a prototype. Virus strain, passage history, dose, route of inoculation, host genotype, age, immune function and co-infection with other agents all interact to determine the ultimate expression of MHV disease. Mice of the semisusceptible C3H genotype that survive intraperitoneal inoculation of virulent MHV-3 can have persistent infections, in which virus can be recovered in low titer from liver, brain and lymphoid organs for up to 42 days (68). Therefore, when MHV initially infects a naive mouse population, neonatal mice suffer high mortality, particularly with enterotropic MHV strains (13,14). Persistent infection with mouse hepatitis virus of low virulence in nude mice Enterotropic mouse hepatitis virus infection in nude mice cache = ./cache/cord-022324-tcltmhi7.txt txt = ./txt/cord-022324-tcltmhi7.txt === reduce.pl bib === id = cord-022163-7klzsrpu author = Broder, Christopher C. title = Henipaviruses date = 2016-09-09 pages = extension = .txt mime = text/plain words = 14465 sentences = 688 flesch = 46 summary = Central pathological features of both HeV and NiV infection in humans and several susceptible animal species is a severe systemic and often fatal neurologic and/or respiratory disease (Abdullah and Tan 2014 ; Wong and Ong 2011 ; Playford et al. A new paramyxovirus was isolated and identifi ed in 1994 in an outbreak of fatal cases of respiratory disease in horses and humans in the Brisbane suburb of Hendra, Australia, and was shown to be distantly related to measles virus and other morbilliviruses (Murray et al. HeV in nature appears less transmissible and naturally acquired infections have been observed only in bats, horses, dogs and humans; however, experimentally, HeV can infect and cause disease in guinea pigs, cats, hamsters, ferrets, mice and African green monkeys (reviewed in Geisbert et al. More recently, several viral vector-based henipavirus vaccines have also been examined in animal challenge studies; these have included immunizations using the vesicular stomatitis virus based platform (VSV) expressing either the NiV G or F glycoprotein in the hamster model (DeBuysscher et al. cache = ./cache/cord-022163-7klzsrpu.txt txt = ./txt/cord-022163-7klzsrpu.txt === reduce.pl bib === id = cord-021990-a8ku5rke author = Tyring, Stephen K. title = Syndromal Tropical Dermatology date = 2016-12-02 pages = extension = .txt mime = text/plain words = 7077 sentences = 390 flesch = 46 summary = With increasing numbers of persons from industrialized, temperate countries traveling and / or working in tropical lands, there is a marked need for physicians to be able to diagnose accurately and treat tropical diseases with mucocutaneous manifestations. An example of a mosquito-borne disease that was considered primarily "tropical" in the recent past but is now relatively common in much of North America is infection with the West Nile virus (Fig. 1-3) . When one STD is confirmed, there is an increased possibility of acquisition of additional STDs. Not only is this the case because the source partner(s) may have had multiple STDs, but also because having certain STDs makes a person more susceptible to other STDs. The best example of this phenomenon is the two-to fivefold greater risk of acquiring HIV if the person with a genital ulcer disease (GUD) has sex with an HIV-positive individual. If at least 3 months separate travel from fever / rash, the following infections should be considered: bartonellosis, filariasis, gnathostomiasis, hepatitis viruses (B and C), histoplasmosis, HIV, leishmaniasis, Lyme disease, melioidosis, penicilliosis, syphilis, trypanosomiasis, and tuberculosis. cache = ./cache/cord-021990-a8ku5rke.txt txt = ./txt/cord-021990-a8ku5rke.txt === reduce.pl bib === id = cord-022674-90g0461f author = Hurst, Christon J. title = Detecting Viruses in Water date = 1989-09-01 pages = extension = .txt mime = text/plain words = 7260 sentences = 398 flesch = 39 summary = Subsequent recovery of the adsorbed viruses can occur either by dissolving the filter material, if it is composed of alginate,"" or by exposing the adsorbent to a volume of eluant that is smaller than the original water sample and facilitates a reversal of the virus adsorption process. Of the many different types and configurations of virus adsorbents, those now preferred for use in recovering viruses from large volumes of water are wound cartridge filters*' and pleated cartridge filter@ based on either glass fiber or nylon, including types that are positively charged, and columns of glass powder.26 Also of interest is the use of sheet filter material that has been modified in situ either by a precipitation of metal hydroxides within the filter ma-trix2" or by coating the filter with cationic 74 RESEARCHANDTECHNOLOGY Cultures of mammalian cells were prepared using a laminar-flow filtered air hood. cache = ./cache/cord-022674-90g0461f.txt txt = ./txt/cord-022674-90g0461f.txt === reduce.pl bib === id = cord-021555-rrverrsj author = Delano, Margaret L. title = Biology and Diseases of Ruminants: Sheep, Goats, and Cattle date = 2007-09-02 pages = extension = .txt mime = text/plain words = 71765 sentences = 5075 flesch = 49 summary = These references also provide information regarding vaccination products licensed for use in ruminants and typical herd and flock vaccination parasite control schedules ("Current Veterinary Therapy," 1986 , 1999 "Council report," 1994; "Large Animal Internal Medicine," 1996; Smith and Sherman, 1994) When designing a vaccination program during qualification of a source or at the research facility, it is important to evaluate the local disease incidence and the potential for exposure. Clinical signs in chronic cases in older animals, such as adult goats, include soft stools, weight loss, anorexia, depression, and severe diarrhea, sometimes with mucus and blood. This pathogen does present a complication due to the carrier status of some animals, the likelihood of herd outbreaks, the severity of disease in younger animals, and the morbidity, possible progression to uveitis, and time and treatment costs associated with infections. cache = ./cache/cord-021555-rrverrsj.txt txt = ./txt/cord-021555-rrverrsj.txt === reduce.pl bib === id = cord-022349-z8w1wkm8 author = Beeler, Judy A. title = Human and Animal Viruses date = 2007-09-02 pages = extension = .txt mime = text/plain words = 4584 sentences = 230 flesch = 47 summary = However, freeze-drying provided a way to maintain virally infected material over long periods of time with relative ease when compared to serial passage in a susceptible animal host. The first experiment to demonstrate that this method could provide long-term stability was reported for a bovine virus that had been freeze-dried in 1916 and was shown to be viable after being maintained at room temperature for 30 years (Fasquelle and Barbier, 1950) . In general, most viruses may be "snap frozen" in a dry ice/ethanol bath prior to storage at temperatures _<-70~ It may be preferable to freeze some viruses, such as cytomegalovirus or varicella-zoster virus, as viable infected cells. Calcium lactobionate and human serum albumin were cryoprotective for measles virus during freeze-drying (Greiff and Rightsel, 1967) , whereas cell culture medium alone was less protective. cache = ./cache/cord-022349-z8w1wkm8.txt txt = ./txt/cord-022349-z8w1wkm8.txt === reduce.pl bib === id = cord-022305-uvor9rts author = Jacoby, Robert O. title = Viral Diseases date = 2013-11-17 pages = extension = .txt mime = text/plain words = 15852 sentences = 898 flesch = 46 summary = The number of viruses known to be naturally infectious for laboratory rats is small, and most cause inapparent infections which usually are detected by serological monitoring (Table I) . Significance: Latent, vertically-transmissible agent isolated from submaxillary gland; no signs or lesions; induces HAI antibody; unre lated antigenically to rat coronaviruses or cytomegalovirus; must dif ferentiate isolates from coronaviruses, cytomegaloviruses C. Infected rats excrete virus from the respiratory tract for about 7 days, at which time anti-SDAV antibody is first detectable in serum by either NT or CF tests ( Fig. 30 and Table V) (61) . Infections of SDAV or RCV can be diagnosed on the basis of clinical signs, lesions, and serological profiles of NT and CF antibody and confirmed by isolation of the causative virus. The pathogenesis and lesions of natural and experimental Sendai virus infection have been well described for mice (2, 132, 160) , but only limited information on rats is available. cache = ./cache/cord-022305-uvor9rts.txt txt = ./txt/cord-022305-uvor9rts.txt === reduce.pl bib === id = cord-022262-ck2lhojz author = Gromeier, Matthias title = Genetics, Pathogenesis and Evolution of Picornaviruses date = 2007-09-02 pages = extension = .txt mime = text/plain words = 28035 sentences = 1423 flesch = 46 summary = The following viruses have been recognized as picornaviruses on the basis of their genome sequences and physico-chemical properties as well as the result of comparative sequence analyses (see the section on Evolution): equine rhinovirus types I and 2, Aichi virus, porcine enterovirus, avian encephalomyelitis virus, infectious flacherie virus of silkworm Clusters of enteroviruses refer to groups of enteroviruses arranged predominantly according to genotypic kinship (Hyypia et al., 1997) . Briefly, when expression vectors ( Figure 12 .6E) consisting of a gag gene (encoding p17-p24; 1161 nt) of human immunodeficiency virus that was fused to the N-terminus of the poliovirus polyprotein (Andino et al., 1994; Mueller and Wimmer, 1998) were analysed after transfection into HeLa cells, the genomes were not only found to be severely impaired in viral replication but they were also genetically unstable (Mueller and Wimmer, 1997) . cache = ./cache/cord-022262-ck2lhojz.txt txt = ./txt/cord-022262-ck2lhojz.txt === reduce.pl bib === id = cord-022196-1tionxun author = FENNER, FRANK title = The Nature and Classification of Animal Viruses date = 2013-11-17 pages = extension = .txt mime = text/plain words = 9588 sentences = 406 flesch = 46 summary = With most isometric particles and in all complex virions, the capsid encloses another protein structure containing the viral genome, called the core. All animal viruses with tubular nucleocapsids are enveloped, and in these the lipid layer from which glycoprotein peplomers project is probably applied to a protein shell (the membrane protein; see Fig. 1 -1), which may be relatively rigid, as in Rhabdovirus, or readily distorted (as in the myxoviruses) so that in negatively stained electron micrographs the virions appear to be pleomorphic. The RNA viruses that have the largest (single-stranded) genomes, those of the Leukovirus genus, also have a highly complex structure with an envelope enclosing an icosahedral capsid that, in turn, surrounds a tubular nucleocapsid. The conventional physicochemical criteria [(a) nucleic acid: type, strandedness, fragmentation, and molecular weight; (b) virion: shape, size, and symmetry] are suitable for classification at this level of family/genus, perhaps assisted by the serological cross-reactivity of "group" antigens where these have been recognized. cache = ./cache/cord-022196-1tionxun.txt txt = ./txt/cord-022196-1tionxun.txt === reduce.pl bib === id = cord-022439-8wy7rpqv author = DENMAN, A.M. title = Viral Etiology of Polymyositis/Dermatomyositis date = 2013-11-17 pages = extension = .txt mime = text/plain words = 10782 sentences = 523 flesch = 43 summary = Thus, theories based on a viral etiology must invoke a highly un usual host response to ubiquitous agents, the existence of uncommon viruses with the abil ity to provoke the disorder, or the possibility that virus infections operate synergistically with other factors. Attempted isolation Electron-microscopic studies Viral probes Antiviral antibody titers Establishing clones from infiltrating T lymphocytes and screening their antigen specificities Exploring the antigen specificities of associated autoantibodies In vitro models of virus-infected muscle cells In vivo models of experimental polymyositis ceptually. In clinical studies, EBV transformed blood lymphocytes from both normal individuals and patients with autoimmune diseases pro duced monoclonal autoantibodies reactive with antigens in multiple organs [93] . Myocarditis and PM induced by coxsackievirus infection is mediated by immunopathologic mechanisms that may continue to dam age muscle fibers long after infectious virus and even viral antigens have been eliminated. cache = ./cache/cord-022439-8wy7rpqv.txt txt = ./txt/cord-022439-8wy7rpqv.txt === reduce.pl bib === id = cord-022378-ovxmy1as author = Cook, Jane K.A. title = Coronaviridae date = 2009-05-15 pages = extension = .txt mime = text/plain words = 4034 sentences = 192 flesch = 50 summary = IBV also aff ects egg-laying performance, and renal damage associated with infectious bronchitis has become increasingly important, particularly in broilers. Economically, the most important aspects are the eff ects on egg production and quality in laying hens and production performance in broilers, where the initial respiratory infection is frequently exacerbated by secondary infections. In turkeys, coronaviruses (TCoV, also called Bluecomb disease virus and Turkey enteric coronavirus) are known to be associated with enteric disease, mortality and underperformance and to aff ect egg-laying performance in older birds. Th is is a new area of investigation and, while the coronaviruses detected in some gallinaceous and nongallinaceous birds have not so far been associated with disease, these species are potential carriers of IBV and other coronaviruses and could therefore play a role in global transmission of infection. In IBV infection of commercial layers or broiler breeders, respiratory signs may or may not be observed and the most common manifestation is the eff ect on egg production and egg quality. cache = ./cache/cord-022378-ovxmy1as.txt txt = ./txt/cord-022378-ovxmy1as.txt === reduce.pl bib === id = cord-022947-ruizhgwh author = Elliot, Elisa L title = Indicator organisms for estuarine and marine waters date = 2006-03-27 pages = extension = .txt mime = text/plain words = 10565 sentences = 551 flesch = 43 summary = These bacteria and other coliforms were used in the past as indicators of water-borne pathogens, that is, the presence of fecal contamination being correlated with the occurrence of pathogens, for which direct detection methods were not available. Total coliforms are the most universally used indicator group, but include bacteria, in addition to Escherichia coil, that are not specifically associated with fecal pollution, i.e., Klebsiella spp., Citrobacter spp., and Enterobacter spp. Finding an appropriate indicator for the presence of enteric viruses, i.e., poliovirus, coxsackievirus A, coxsackievirus B, and echovirus [50, 147] , in sea water, is a vexing problem, especially for those responsible for regulating the use of sewage-contamined sites, including fresh, estuarine, and marine water and sediment, and shellfish harvested from these waters. Correlations between the number of fecal bacterial pathogens and indicator bacteria and their respective bacteriophages in fresh and marine water have been reported [185] . cache = ./cache/cord-022947-ruizhgwh.txt txt = ./txt/cord-022947-ruizhgwh.txt === reduce.pl bib === id = cord-022399-66mzbynu author = Hopkins, Graham title = Basic microbiology date = 2009-05-15 pages = extension = .txt mime = text/plain words = 8602 sentences = 552 flesch = 52 summary = Bacteria are important because of their ubiquity -that is, their ability to infect and multiply in varied environments -and the ability of many types of bacteria to cause disease -their pathogenicity. To reduce problems caused by bacteria, it is important to understand something of their structure, growth, environmental and metabolic requirements, classification, relationship with disease and the particular problems they can cause to the eye. The result is that the cells tend to grow and divide at a slower rate but are more resistant to antibacterial chemicals, viruses (bacteriophages), phagocytes and other adverse agents. As causative organisms of disease, fungi are less important than bacteria and viruses. • Sterilization: the killing or removal of all viable organisms (including bacterial spores) from an object or pharmaceutical product by the use of chemical or physical agents. Developments have led to the introduction of agents that are more effective against the infecting organism and less toxic to the host. cache = ./cache/cord-022399-66mzbynu.txt txt = ./txt/cord-022399-66mzbynu.txt === reduce.pl bib === id = cord-023584-yaxawqhj author = Bucknall, R.A. title = The Continuing Search for Antiviral Drugs date = 2008-04-10 pages = extension = .txt mime = text/plain words = 8497 sentences = 339 flesch = 48 summary = Of course, if wide-spectrum leads appear, the choice of test virus may be irrelevant, but the antiviral compounds (as distinct from interferon inducers) known at present are characterized by their relatively limited spectrum of activity, e.g., methisazone is active only against poxviruses (Bauer and Sadler, 1960) and possibly adenoviruses (Bauer and Apostolov, 1966) ; l-aminoadamantane is active only against influenza A1 and As and not against other myxo-or paramyxoviruses (Davies et al., 1964) ; guanidine and a-hydroxybenzyl benzimidazole are active only against picornaviruses and not against other small ribonucleic acid (RNA) viruses (Eggers and Tamm, 1961) . In summary, a tissue culture screen should be able to proccss large numbers of tcst compounds, using viruses as relevant as possible to the diseases for which a drug is required, and should employ normal rather than neoplastic cells. cache = ./cache/cord-023584-yaxawqhj.txt txt = ./txt/cord-023584-yaxawqhj.txt === reduce.pl bib === id = cord-022822-7346069t author = nan title = Infections, Immunity & their Effects on Asthma date = 2006-10-02 pages = extension = .txt mime = text/plain words = 3292 sentences = 148 flesch = 30 summary = The mechanisms underlying the association between RSV bronchiolitis and the later development of wheezing are incompletely understood, though there is increasing evidence that impaired antiviral immunity is likely to play an important role in increasing susceptibility to virus infections early in life, as well as perhaps the later development of asthma [3] . Areas that particularly require attention include interplay between the innate and acquired immune responses in host defence; the role of viral persistence in development of wheezing illness and asthma; the roles of antigen presenting cells and other specific cell compartments such as epithelial cells, T cells, neutrophils, eosinophils and non T cell lymphocytes in host protection and disease severity. Further studies investigating the importance of different virus types in the association between lower respiratory infection in infancy and wheezing illness in asthma are required to clarify the relationships, including rhinovirus, human metapneumoviruses, coronaviruses and bocaviruses. cache = ./cache/cord-022822-7346069t.txt txt = ./txt/cord-022822-7346069t.txt === reduce.pl bib === id = cord-021966-5m21bsrw author = Shaw, Alan R. title = Vaccines date = 2009-05-15 pages = extension = .txt mime = text/plain words = 21170 sentences = 897 flesch = 33 summary = Because a number of proteins produced in isolation by recombinant methods have been observed to elicit lower immune responses than do natural infections or live attenuated vaccines, the development and use of adjuvants to optimize recombinant vaccine immunogenicity represent an important parallel area for future exploration. Modern molecular biology and biochemistry have provided numerous options for vaccine immunogen presentation, including recombinant proteins (and recombinant virus-like particles (VLPs)), synthetic proteins, protein-polysaccharide conjugates, and gene delivery systems (recombinant viral vectors, or DNA vaccines) >> Is the antigen of interest sufficiently immunogenic on its own, or is augmentation of the desired immune response by conjugation to a specific carrier or addition of an adjuvant necessary to elicit a sufficient and sufficiently durable immune response in individuals in the target population for vaccination? cache = ./cache/cord-021966-5m21bsrw.txt txt = ./txt/cord-021966-5m21bsrw.txt === reduce.pl bib === id = cord-023034-j8zwcfys author = Osterhaus, Albert D. M. E. title = Feline Infectious Peritonitis Virus: II. Propagation in Suckling Mouse Brain date = 2010-05-13 pages = extension = .txt mime = text/plain words = 2273 sentences = 157 flesch = 45 summary = SUMMARY: Feline infectious peritonitis (FIP) virus multiplication was demonstrated in the brains of one‐day‐old laboratory mice using direct immunofluorescence tests. In order to determine the specificity of the observed fluorescence for FIP virus, indirect IFT were carried out in parallel on poslitive mouse brain sections (homologous reaction) and on porcine kidney cells infected with TGE virus (heterologous reaction). The conclusive experiment for establishing the FIP virus specificity of the immunofluorescence in mouse brain was performed by inoculating SPF kittens with fluorescence-positive material of the 6th mouse passage (isolation series A, Table 1 ). Feline infectious peritonitis (FIP) virus multiplication was demonstrated in the brains of one-day-old laboratory mice using direct immunofluorescence tests. Specificity was assessed by virus reisolation, indirect immunofluorescence and reproduction of FIP after inoculation of SPF kittens using brain material from the 6th mouse passage. Specificity was assessed by virus reisolation, indirect immunofluorescence and reproduction of FIP after inoculation of SPF kittens using brain material from the 6th mouse passage. cache = ./cache/cord-023034-j8zwcfys.txt txt = ./txt/cord-023034-j8zwcfys.txt === reduce.pl bib === id = cord-022453-xe5v7947 author = BABIUK, L.A. title = Viral Gastroenteritis in Ruminants date = 2013-11-17 pages = extension = .txt mime = text/plain words = 4838 sentences = 253 flesch = 48 summary = Rotavirus infection is generally limited to the small intestine in calves, pigs and humans (Middleton et al., 1974; Mebus and Newman, 1977; McAdaragh et al., 1980) , but antigen can be found in the colon of lambs (Snodgrass et al., 1977) , pigs (Theil et al., 1978) and mice (Little and Shadduck, 1982) . Bovine Coronavirus diarrhea, like rotavirus diarrhea, occurs within 15-24 h p.i. Early in infection the villous epithelial cells appear morphological normal but they contain large amounts of antigen. Since diarrhea occurs before denudation and loss of enterocytes it is postulated that it is a direct result of infection of the cell and the ensuing redirection of cellular functions from absorption to virus replication. Because of the replication in lymphoid tissue this disease can be more severe, especially in small animals, than other viral infections, because of interference with immune responses and damage to the crypts. cache = ./cache/cord-022453-xe5v7947.txt txt = ./txt/cord-022453-xe5v7947.txt === reduce.pl bib === id = cord-023608-w2g7v7g1 author = nan title = ISAR News date = 2017-10-20 pages = extension = .txt mime = text/plain words = 6059 sentences = 284 flesch = 48 summary = ICAR retains its flavor and personality, providing an interdisciplinary forum at which investigators involved in basic, translational, and clinical research worldwide meet to review recent developments in all areas of antiviral research, drug and vaccine development. Additionally, satellite activities such as the Women in Science Roundtable, the Career Development Panel and the New Member and First Time Attendee luncheon (The Happy Hour) provided an opportunity to discuss other issues of relevance. With so many different competing conferences and meetings to attend and a long economic crisis of which scientific research did not escape, ISAR has gone through great financial efforts to continue supporting the participation of students, postdocs and young investigators. The TCFF Awards support the professional development of women with potential to make significant contributions to the field of Antiviral Research by providing funds to attend a conference, visit another laboratory, take a course, or acquire specialized training. cache = ./cache/cord-023608-w2g7v7g1.txt txt = ./txt/cord-023608-w2g7v7g1.txt === reduce.pl bib === id = cord-022354-aqtceqqo author = HUNTER, ERIC title = Membrane Insertion and Transport of Viral Glycoproteins: A Mutational Analysis date = 2012-12-02 pages = extension = .txt mime = text/plain words = 17747 sentences = 697 flesch = 44 summary = second apolar region in gp 37 consists of a 27 amino acid long stretch of hydrophobic residues near the carboxy terminus that functions during translation to stop the movement of the protein into the lumen of the rough endoplasmic reticulum (RER) and to anchor the complex in the membrane. In order to examine the role of the signal peptide in RSV glycoprotein biosynthesis we constructed a series of deletion mutations within the 5' coding region of the env gene using the double-stranded exonuclease BaBl. Oligonucleotide linkers of the sequence CATCGATG were ligated to the ends of the truncated molecules to introduce a unique restriction endonuclease cleavage site and to replace the deleted in-frame AUG. We found that replacement of the nonconserved region of the cytoplasmic domain with a longer unrelated sequence of amino acids from SV40 vector sequences (mutant Cl) did not alter the rate of transport to the Golgi apparatus nor the appearance of the glycoprotein on the cell surface. cache = ./cache/cord-022354-aqtceqqo.txt txt = ./txt/cord-022354-aqtceqqo.txt === reduce.pl bib === id = cord-023092-unjv71qv author = Horzinek, Prof. Dr Marian C. title = Feline leukaemia prophylaxis date = 2008-04-10 pages = extension = .txt mime = text/plain words = 2407 sentences = 140 flesch = 50 summary = The humoral immune response against FeLV is directed mainly against the viral surface structure gp70/85 and against the so-called 'feline oncornavirus-associated membrane antigen' (FOCMA). The numerous experiments to develop an efficient vaccine against FeLV infection have recently shown their first success: in the U.S.A. a preparation is presently being marketed for use by the small animal practitioner. (1) cells (virus-producing, live or inactivated) (2) virus (live or inactivated) (3) split products (viral or cellular surface structures; gp7O/gp85, FOCMA) (4) synthetic antigens ( 5 ) products obtained by genetic engineering (antigens from pro-or eukaryotic Each of the above-mentioned strategies has been followed with varying success, cells after cloning of the respective viral genes) and the hope for the future is directed towards development of synthetic and genetically engineered vaccines. Vaccination against feline leukaemia virus using a cell membrane antigen system Feline leukemia virus envelope glycoprotein vaccine: preparation and evaluation of immunizing potency in guinea pig and cat cache = ./cache/cord-023092-unjv71qv.txt txt = ./txt/cord-023092-unjv71qv.txt === reduce.pl bib === id = cord-022128-r8el8nqm author = Domingo, Esteban title = Molecular basis of genetic variation of viruses: error-prone replication date = 2019-11-08 pages = extension = .txt mime = text/plain words = 17663 sentences = 798 flesch = 39 summary = In the case of viral genomes, mutations can result from different mechanisms: (i) template miscopying (direct incorporation of an incorrect nucleotide); (ii) primer-template misalignments that include miscoding followed by realignment, and misalignment of the template relative to the growing chain (polymerase "slippage" or "stuttering"); (iii) activity of cellular enzymes (i.e., deaminases), or (iv) chemical damage to the viral nucleic acids (deamination, depurination, depyrimidination, reactions with oxygen radicals, direct and indirect effects of ionizing radiation, photochemical reactions, etc.) (Naegeli, 1997; Bloomfield et al., 2000; Friedberg et al., 2006) . In addition to the general environmental and sequence context consequences for templatecopying fidelity that may affect any genome type, mutation rates for DNA viruses will also be influenced by: (i) whether the DNA polymerase that catalyzes viral DNA synthesis includes or lacks a functional proofreading-repair activity. cache = ./cache/cord-022128-r8el8nqm.txt txt = ./txt/cord-022128-r8el8nqm.txt === reduce.pl bib === id = cord-022383-pz0htccp author = Kohn, Dennis F. title = Biology and Diseases of Rats date = 2013-11-17 pages = extension = .txt mime = text/plain words = 20181 sentences = 1195 flesch = 50 summary = The severity and prevalence of clinical disease within an infected colony are associated with environmental conditions that induce stress (e.g., experimental manipulation, overcrowding, fluctuations in ambient temperature and humid ity, and copathogens). Salmonellosis, which was once a major cause of disease in laboratory rat and mouse colonies, is rarely reported in either species today. Mycoplasma pulmonis recently has become recognized as an important pathogen in the female genital tract of rats, and thus is being treated here as a distinct disease rather than as a sequella to MRM. Sendai virus commonly infects laboratory rats, but its clinical significance is less than in mice. Infection is usually diagnosed retrospectively in rats, where pulmonary lesions are observed following seroconversion to PVM in the absence of other respiratory pathogens. This disease, which occurs more fre quently in females, has been reported in numerous strains of rats. cache = ./cache/cord-022383-pz0htccp.txt txt = ./txt/cord-022383-pz0htccp.txt === reduce.pl bib === id = cord-022393-s26d54ew author = E. Newcomer, Christian title = Zoonoses and Other Human Health Hazards date = 2007-09-02 pages = extension = .txt mime = text/plain words = 17040 sentences = 872 flesch = 42 summary = Wild caught mice that are maintained in naturalistic housing environments in the laboratory, laboratory mice that have contact with wild or feral mice, and mice kept as pets in the home environment are examples of animal management conditions that would be conducive to the expression and transmission of zoonotic diseases and other mouse-associated implications in the New World serocomplex group are present among the wild rodents endemic to the United States such as Neotoma spp. Many published reports of human LCM infection are associated with laboratory animal and pet contact, particularly mice and hamsters, and these studies now span many decades (Armstrong and Lillie 1934; Bowen et al. The apparent ease with which LCMV is transmitted to humans also occurs in a variety of other laboratory animal species; hamsters, guinea pigs, swine, dogs, and nonhuman primates, especially callitrichids, which readily sustain natural infections. akari infections depend on the prevention of wild mice and the mite vector from entering laboratory animal facilities and human dwellings. cache = ./cache/cord-022393-s26d54ew.txt txt = ./txt/cord-022393-s26d54ew.txt === reduce.pl bib === id = cord-023200-3caevjvh author = Falanga, Annarita title = Membranotropic peptides mediating viral entry date = 2018-02-13 pages = extension = .txt mime = text/plain words = 6062 sentences = 270 flesch = 41 summary = The discovery of short, membrane interacting, amphipathic or hydrophobic sequences (known as membranotropic peptides) in both enveloped and non‐enveloped viruses suggests that these small peptides are strongly involved in breaching the host membrane and in the delivery of the viral genome into the host cell. [3, 4] The molecular details of the interactions at the interface of virus and cell surfaces are quite complex and highly variable, but there is a common idea that only a limited number of pathways allowing viruses to reach the sites of penetration exist, with enveloped and non-enveloped viruses presenting different and unrelated processes, but with general principles driving all fusion events. [16, 17] Viral fusion proteins undergo significant rearrangements from the pre-fusion to the post-fusion conformations which are triggered by either receptor binding, proteolytic cleavage or low endosomal pH, and eventually determine the exposure of previously sequestered hydrophobic peptides, loops, or patches, able to interact with and destabilize one or both the opposing membranes. cache = ./cache/cord-023200-3caevjvh.txt txt = ./txt/cord-023200-3caevjvh.txt === reduce.pl bib === id = cord-022830-tvt58gtn author = Li, Dan title = Fate of Foodborne Viruses in the “Farm to Fork” Chain of Fresh Produce date = 2015-10-08 pages = extension = .txt mime = text/plain words = 12200 sentences = 520 flesch = 44 summary = In order to supply a basis to identify possible prevention and control strategies, this review intends to demonstrate the fate of foodborne viruses in the farm to fork chain of fresh produce, which include the introduction routes (contamination sources), the viral survival abilities at different stages, and the reactions of foodborne viruses towards the treatments used in food processing of fresh produce. In order to determine a basis to identify possible prevention and control efforts, this article reviewed the transmission routes and viral persistence of foodborne viruses (mainly NoVs and HAV) during the farm-to-fork chain of fresh produce, as well as the effect of treatments used in food processing of fresh produce on viruses. In this section the effect of radiation, both nonionizing and ionizing radiation, and high-pressure processing (HPP) will be discussed as nonthermal inactivation treatment options for enteric viruses in fresh produce. cache = ./cache/cord-022830-tvt58gtn.txt txt = ./txt/cord-022830-tvt58gtn.txt === reduce.pl bib === id = cord-025181-eg108wcd author = Zheng, Zhihang title = Establishment of Murine Infection Models with Biological Clones of Dengue Viruses Derived from a Single Clinical Viral Isolate date = 2020-05-25 pages = extension = .txt mime = text/plain words = 5919 sentences = 340 flesch = 59 summary = In this study, with biologically cloned viruses from a single clinical isolate, we have established two mouse models of DENV infection, one is severe lethal infection in immunocompromised mice, and the other resembles self-limited disease manifestations in Balb/c mice with transient blockage of type I IFN responses. Further, we compared the infectivity of these two viral variants in a self-limited infection model, in which type I IFN receptor of wild-type Balb/c mice had been transiently blocked before infection, and found only the virus strain exhibiting larger plaque size caused infectious viral particles in sera. We have recently developed a ZIKV infection model in Balb/c mice with transient blockage of type I IFN Fig. 2 Phylogenetic analysis of DENV-2 1D4-5-SP and DENV-2 8H2-7-LP with representative serotype-2 dengue viruses of different genotypes isolated from different geographical regions. cache = ./cache/cord-025181-eg108wcd.txt txt = ./txt/cord-025181-eg108wcd.txt === reduce.pl bib === id = cord-022980-tkii8se4 author = nan title = Diarrhea date = 2008-03-05 pages = extension = .txt mime = text/plain words = 303 sentences = 19 flesch = 52 summary = Nevertheless, until recently gastro-enteritis provided a poor hunting ground for virologists for, although such viruses as adenoviruses, echoviruses and Coxsackie viruses could be isolated from the stools of patients with acute gastro-enteritis, they could often be recovered with almost equal frequency from those without diarrhoeal disease, particularly in developing countries. However, the examination of negatively stained faecal preparations from patients witb gastro-enteritis by electron microscopy has resulted in the discovery of many viruses, some of which, for example, rotaviruses and such parovirus-like viruses as the Norwalk agent, are undoubtedly the cause of acute gastroenteritis. In general, in vitro cultivation of viruses causing gastroenteritis in humans is either not possible or extremely difficult and of little value for routine diagnostic purposes but, since they are often excreted in very high titres, they may be detected without difficulty by electron microscopic examination of faecal extracts,-Banatvala jE: Viruses and Diarrhoes, Trans R Soc Trop Med Hyg 73: 503, 1979. cache = ./cache/cord-022980-tkii8se4.txt txt = ./txt/cord-022980-tkii8se4.txt === reduce.pl bib === id = cord-022960-u4s23x1r author = Pihlstrom, Bruce Lee title = Selections from the current literature date = 2020-04-17 pages = extension = .txt mime = text/plain words = 1107 sentences = 63 flesch = 54 summary = In the context of the novel coronavirus pandemic, the authors reviewed relevant literature about the virus and made recommendations for controlling its transmission in dental offices. 2 In light of these reports, the authors noted that dental patients and personnel can be exposed to this virus because of face-to-face communication with patients, frequent exposure to saliva, blood, and aerosols, and by handling sharp instruments. They also noted that the virus could be spread by direct or indirect contact with human fluids, patient materials, contaminated dental instruments, and environmental surfaces. [3] [4] Because of the likelihood of 2019-nCoV transmission in the dental office, the authors made several recommendations to help mitigate the spread of the virus in this setting. This is an important study because as the authors noted, it may explain why this virus appears to persist in the environment and is more transmissible than other coronaviruses. cache = ./cache/cord-022960-u4s23x1r.txt txt = ./txt/cord-022960-u4s23x1r.txt === reduce.pl bib === id = cord-023622-tul7bonh author = nan title = Rotaviruses of Man and Animals date = 1975-02-01 pages = extension = .txt mime = text/plain words = 1952 sentences = 100 flesch = 51 summary = Certainly bacterial pathogens may cause both sporadic and epidemic gastroenteritis in children, but they cannot be isolated in up to 75% of cases.2, 3 Whilst it is true that some investigations suggest that enteroviruses or adenoviruses may occasionally cause localised outbreaks of gastroenteritis,4-7 others have shown that these viruses may be detected almost as frequently in controls as among patients. Employing negativestaining techniques on fsecal extracts, FLEWETT and his colleagues found similar particles in children with gastroenteritis in Birmingham 13; indeed, if virologists had only looked at such simply prepared specimens, there is no technical reason why these viruses could not have been detected, say, 15 years ago. Thus, existing evidence suggests that rotaviruses are the most important cause of infantile gastroenteritis throughout the world, but as yet only a limited number of specimens have been examined from those tropical areas where mortality-rates are particularly high. cache = ./cache/cord-023622-tul7bonh.txt txt = ./txt/cord-023622-tul7bonh.txt === reduce.pl bib === id = cord-023678-9q68ftr9 author = Hierholzer, J.C. title = Virus isolation and quantitation date = 2007-09-02 pages = extension = .txt mime = text/plain words = 7674 sentences = 425 flesch = 61 summary = The method conserves the virus and viral antigens, because the supernatant fluid is decanted from the cell culture into a sterile tube at the end of the incubation period (7-10 days); the monolayer is washed twice with 2-3 ml of plain Hanks Balanced Salt Solution (HBSS) at room temperature; 1 ml of fresh HBSS followed by 0.2 ml of 0.4% mammalian erythrocyte suspension from the appropriate species is added to the monolayer; the tube is incubated stationary with the fluid covering the monolayer; and the test is read 3 times at 20-min intervals by agitating the tube in a sideways motion and then observing the monolayer at 40-100x magnification to see if the erythrocytes are firmly attached to the cultured cells or are floating free in the fluid (see Fig. 15 .4). cache = ./cache/cord-023678-9q68ftr9.txt txt = ./txt/cord-023678-9q68ftr9.txt === reduce.pl bib === id = cord-023564-kpqvyxxe author = nan title = Viral gastroenteritis: Causes, pathophysiology, immunology, treatment, and epidemiology date = 2004-09-14 pages = extension = .txt mime = text/plain words = 2512 sentences = 145 flesch = 45 summary = This chapter discusses the causes, pathophysiology, immunology, treatment, and epidemiology of viral gastroenteritis. Infection with gastroenteritis agents can be asymptomatic or can be followed by mild or severe disease, including vomiting or diarrhea or both, and can be fatal because of severe dehydration. Infection with gastroenteritis agents can be asymptomatic, or be followed by mild or severe disease including vomiting or diarrhoea or both, and can be fatal as a consequence of severe dehydration. The main diarrhoeogenic agents comprise four virus families: rotaviruses, enteric adenoviruses, human caliciviruses (Norwalk-and Sapporo-like viruses, now termed noro-and sapoviruses) and astroviruses, and cause diarrhoea at frequencies of 20-30%, 5%, 5-10%, and 5%, respectively. By contrast, epidemic disease is found in all ages, mainly caused by Norwalk-and Sapporo-like viruses (human caliciviruses), rotaviruses of group B (in China), and sometimes astroviruses. Systemic and intestinal antibody secreting cell responses and correlates of protective immunity to human rotaviruses in a gnotobiotic pigs model of disease cache = ./cache/cord-023564-kpqvyxxe.txt txt = ./txt/cord-023564-kpqvyxxe.txt === reduce.pl bib === id = cord-023740-g84fa45m author = Oldstone, Michael B.A. title = Mimicry by Virus of Host Molecules: Implications for Autoimmune Disease date = 2014-06-27 pages = extension = .txt mime = text/plain words = 2498 sentences = 117 flesch = 41 summary = Monoclonal antibodies against 11 different viruses including DNA and RNA viruses known to cause human infection from the herpes virus group, vaccinia virus, myxoviruses, paramyxoviruses, arenaviruses, flaviviruses, alphaviruses, rhabdovirus, and coronaviruses cross-react with host cell determinants expressed on uninfected tissues. other examples (reviewed in Oldstone and Notkins, 1986 ) suggest a mechanism whereby immune reactants directed against a viral or microbial component may cross-react with a host component and generate autoimmune disease. Since, on the basis of antibody cross-reactivity, many viruses share antigenic sites with normal host cell components, the next step was to look for crossreactive capability in eliciting autoimmunity and related disease. The most likely mechanism by which molecular mimicry would cause disease is by eliciting an immune response against a determinant shared between the host and the virus to bring forth a tissue-specific immune response, presumably capable of destroying cells and eventually the tissue. cache = ./cache/cord-023740-g84fa45m.txt txt = ./txt/cord-023740-g84fa45m.txt === reduce.pl bib === id = cord-026641-eemp6b5j author = Kabiljo, Julijan title = From threat to cure: understanding of virus-induced cell death leads to highly immunogenic oncolytic influenza viruses date = 2020-06-11 pages = extension = .txt mime = text/plain words = 6689 sentences = 373 flesch = 37 summary = In the absence of NS1 apoptosis appears to be induced through the viral-RNA-mediated induction of retinoic acidinducible gene I (RIG-I) and interferon (IFN) signaling including protein kinase R (PKR) and eukaryotic initiation factor 2 alpha (eIF2α) activation and subsequent block of translation [39] [40] [41] . Another study screened a variety of wild-type influenza A viruses for their infectivity in pancreatic carcinoma cell lines and showed oncolytic effectiveness in a mouse model of human pancreatic cancer 67 . expressed a recombinant humanized cytotoxic T-lymphocyte-associated protein 4 (CTLA4) immune checkpoint inhibiting antibody from two different RNA fragments of the influenza A virus genome in order to enhance its anti-cancer effectiveness in a murine B16 melanoma model 96 . Further effects of oncolytic influenza A viruses on the cancer-immune microenvironment shown in murine models include activation of NK-cells and macrophage polarization towards immuno-stimulatory M1 phenotypes 66, 114 . cache = ./cache/cord-026641-eemp6b5j.txt txt = ./txt/cord-026641-eemp6b5j.txt === reduce.pl bib === id = cord-023831-93xqrblk author = Rosenberg, Helene F. title = Pneumonia Virus of Mice (PVM): Exploring Novel Therapeutic Options In a Severe Respiratory Disease Model date = 2010-03-30 pages = extension = .txt mime = text/plain words = 3599 sentences = 160 flesch = 35 summary = Our laboratories have pioneered the use of the PVM model for the study of human clinical disease, which has provided important insights into the role of the inflammatory response in the pathogenesis of severe respiratory virus infection. Our laboratories have pioneered the use of the PVM model for the study of human clinical disease, which has provided important insights into the role of the inflammatory response in the pathogenesis of severe respiratory virus infection. With these factors in mind, around 1997, we began our collaborative exploration of the pneumonia virus of mice (PVM) pathogen for the study of respiratory virus replication and the ensuing inflammatory response within a natural, evolutionarily relevant host-pathogen relationship. In a study performed using young adult (eight-12 weeks) through aged (up to 78 weeks), but otherwise immunologically naïve mice, we observed no change in the kinetics of PVM replication, but diminished local production of several proinflammatory mediators, including MIP-1a, MCP-1, and IFN-g, along with diminished recruitment of granulocytes to the lung tissue [35] . cache = ./cache/cord-023831-93xqrblk.txt txt = ./txt/cord-023831-93xqrblk.txt === reduce.pl bib === id = cord-022252-9yiuuye3 author = Mims, Cedric A. title = Mechanisms of Cell and Tissue Damage date = 2013-11-17 pages = extension = .txt mime = text/plain words = 28864 sentences = 1432 flesch = 48 summary = A few viruses are remarkable because they cause no pathological changes at all in the cell, even during a productive infection in which infectious virus particles are produced. Primary consideration will be given to those substances which are produced under ecologically significant conditions (i.e. in the natural host or relevant animal model) and cause (also in biologically relevant systems) damage to cells or tissues thereby contributing to disease. Here we consider toxins which act on extracellular substances and are responsible for many of the main features of the diseases caused by the infecting organism. Circulating immune complexes are also deposited in the walls of small blood vessels in the skin and elsewhere, where they may induce inflammatory changes.* The prodromal rashes seen in exanthematous virus infections and in hepatitis B are probably caused in this way. cache = ./cache/cord-022252-9yiuuye3.txt txt = ./txt/cord-022252-9yiuuye3.txt === reduce.pl bib === id = cord-023293-te0n2vvp author = Carter, M. J. title = Caliciviruses date = 2005-10-18 pages = extension = .txt mime = text/plain words = 5075 sentences = 307 flesch = 55 summary = Antibodies to SMSV were also found in some land animals including potential scavengers such as foxes, and the virus was also obtained from a fish preyed on by sealions thus raising the possibility that SMSV could be transmitted through food.' SMSV is serologically distinct from vesicular exanthema of swine virus (VESV), but the viruses are clearly related by RNA homology, and are also similar in terms of the cells in which the virus can replicate in culture. These include the small round structured viruses (SRSV) which are also associated with diarrhoea, and the virus causing enterically transmitted non-A, non-B hepatitis now termed hepatitis E virus (HEV). Most of the increases in serum titre took place between the ages of 14-36 months.23 Broadly similar results were obtained in studies performed in Ecuador and the phi lip pine^.^^^^^ Volunteers infected with Norwalk virus commonly develop vomiting and diarrhoea, often associated with headache and abdominal discomfort.26 Illness generally lasts 24-48 hours. cache = ./cache/cord-023293-te0n2vvp.txt txt = ./txt/cord-023293-te0n2vvp.txt === reduce.pl bib === id = cord-026130-ki7bn67o author = Sharma, Anand Kumar title = Novel Coronavirus Disease (COVID-19) date = 2020-06-05 pages = extension = .txt mime = text/plain words = 5073 sentences = 330 flesch = 57 summary = In humans, coronaviruses cause respiratory tract infections that are typically mild, such as some cases of the common cold (among other possible causes, predominantly rhinoviruses), though rarer forms such as Middle East Respiratory Syndrome (MERS), Severe Acute Respiratory Syndrome (SARS), and COVID-19 can be lethal [4] . Based on currently available information and clinical expertise, older adults of over 60 years and people of any age who have serious underlying medical conditions (comorbidities) might be at higher risk of developing the severe disease with SARS-CoV-2, which may even lead to death. As of April 22, 2020, more than 2.5 million people all over the world have tested positive for COVID19 countries including India have evaluated the pandemic situation and have taken the "extraordinary measures" of complete lockdown to contain the virus. cache = ./cache/cord-026130-ki7bn67o.txt txt = ./txt/cord-026130-ki7bn67o.txt === reduce.pl bib === id = cord-025995-nxeg03xj author = Gerba, Charles P. title = Pathogen Removal from Wastewater during Groundwater Recharge date = 2013-11-17 pages = extension = .txt mime = text/plain words = 10527 sentences = 533 flesch = 53 summary = Studies indicate that bacteria and viruses are not removed effectively from wastewaters during primary treatment [19] ; removal of viruses during secondary treatment (active sludge) is dependent largely on virus adsorption to solids. [40] with cores of sandy forest soil receiving poliovirus in sewage effluent at various pH levels between 5.5 and 9.0, virus retention was best at pH 5.5, and the release and migration of retained viruses by subsequent distilled water applications was lower from the cores that re ceived sewage effluent having lower pH values. [57] on virus survival and movement in a rapid-infiltration system for wastewater, the rate of inactivation of indigenous viruses was greater in the fall than in the winter, possibly due in part to the effects of higher temperatures in the former season. cache = ./cache/cord-025995-nxeg03xj.txt txt = ./txt/cord-025995-nxeg03xj.txt === reduce.pl bib === id = cord-023488-jf2xl3vl author = Le Duc, James W. title = Emerging Viral Diseases: Why We Need to Worry about Bats, Camels, and Airplanes date = 2016-02-12 pages = extension = .txt mime = text/plain words = 9385 sentences = 464 flesch = 49 summary = On occasion, a virus that is already widespread in a population can emerge as a cause of epidemic or endemic disease, due to an increase in the ratio of cases to infections. Although many zoonotic viruses can be transmitted to humans on occasion, their relative ability to spread from human to human determines whether or not they emerge as significant new virus diseases of mankind (Table 2 ). In the history of modern virology (the last 50 years) there are very few documented instances where zoonotic viruses have established themselves in the human population and emerged as new viral diseases of mankind (Table 2 ). Rarely, as in the case of HIV, SARS coronavirus, and Ebola filovirus, a zoonotic virus becomes established in humans, causing a disease that is truly new to the human species. cache = ./cache/cord-023488-jf2xl3vl.txt txt = ./txt/cord-023488-jf2xl3vl.txt === reduce.pl bib === id = cord-023721-e0zp2gux author = Meissner, H. Cody title = Bronchiolitis date = 2013-02-10 pages = extension = .txt mime = text/plain words = 5111 sentences = 278 flesch = 34 summary = Bronchiolitis may be defined as an episode of obstructive lower airway disease precipitated by a viral infection in infants younger than 24 months of age. Monthly administration of monoclonal antiF anti body (palivizumab) throughout the RSV season reduces the inci dence of hospitalization due to RSV infection in infants with bronchopulmonary dysplasia, congenital heart disease, and pre maturity by about 50% (see Chapter 225, Respiratory Syncytial Virus). Early trials indicated that ribavirin therapy was associated with modest improvement in clinical scores, oxygenation, and duration of mechanical ventilation for infants with severe bron chiolitis due to RSV infection. Duration of hospitalization in previously well infants with respiratory syncytial virus infection Ribavirin aerosol treatment of bronchiolitis associated with respiratory syncytial virus infection in infants Intravenous immunoglobulin treatment of respiratory syncytial virus infections in infants and young children Respiratory syncytial virus immune globulin treatment of RSV lower respiratory tract infection in previously healthy children cache = ./cache/cord-023721-e0zp2gux.txt txt = ./txt/cord-023721-e0zp2gux.txt === reduce.pl bib === id = cord-024188-d7tnku8z author = Nissen, Michael D. title = Respiratory Infections date = 2010-03-27 pages = extension = .txt mime = text/plain words = 5267 sentences = 249 flesch = 39 summary = For example, recent findings from the New Vaccine Surveillance Network in the United States show that despite respiratory syncytial virus (RSV), parainfluenza viruses (PIVs), and human coronaviruses (HCoVs) all being common in early childhood; RSV and PIVs are more common causes of hospital admission with acute febrile and respiratory illness than HCoVs [33, 41] . A review of healthy adult human volunteer studies showed that viral shedding increased sharply between 0.5 and 1 day after influenza virus challenge, peaking on day two; shedding can be detected 24 to 28 h before clinical onset, and has a mean duration of 4.8 days; two-thirds of subjects had symptomatic infection, and total symptom scores peaked on day three [11] . Infections due to common viruses that result in disease severe enough to warrant laboratory testing, notification, or hospitalisation occur in the young, the very old, or both, such as with RSV and influenza [9, 14] . cache = ./cache/cord-024188-d7tnku8z.txt txt = ./txt/cord-024188-d7tnku8z.txt === reduce.pl bib === id = cord-023726-2fduzqyb author = STRAUSS, JAMES H. title = The Structure of Viruses date = 2012-07-27 pages = extension = .txt mime = text/plain words = 10614 sentences = 633 flesch = 57 summary = Also shown for each family is the presence or absence of an envelope in the virion, the triangulation number (defined later) if the virus is icosahedral, the morphology of the nucleocapsid or core, and figure numbers where the structures of members of a family are illustrated. Structural studies of viruses have shown that the capsid proteins that form the virions of many plant and animal icosahedral viruses have a common fold. The largest particle is the nucleocapsid of herpes simplex virus, which is 1250 Å in diameter and has T=16 symmetry (the virion is enveloped but only the nucleocapsid is regular FIGURE 2.5 Gallery of three-dimensional reconstructions of icosahedral viruses from cryoelectron micrographs. For most RNA viruses, nucleocapsids can be recognized as distinct structures within the infected cell and can be isolated from virions by treatment with detergents that dissolve the envelope. cache = ./cache/cord-023726-2fduzqyb.txt txt = ./txt/cord-023726-2fduzqyb.txt === reduce.pl bib === id = cord-023731-jqgervt7 author = FENNER, FRANK title = Laboratory Diagnosis of Viral Diseases date = 2014-06-27 pages = extension = .txt mime = text/plain words = 6992 sentences = 320 flesch = 39 summary = Having allocated it to a particular family (e.g., Adenoviridae), one can then go on to determine the species or serotype (e.g., canine Immunodiffusion Antibody neutralizes infectivity of virion; inhibits cytopathology, reduces plaques, or protects animals Antibody inhibits viral hemagglutination Antigen-antibody complex binds complement, which is thereafter unavailable for the lysis of hemolysissensitized sheep red blood cells Antibody-aggregated virions are visible by electron microscopy Antibody labeled with fluorochrome binds to intracellular antigen; fluoresces by UV microscopy Peroxidase-labeled antibody binds to intracellular antigen; colored precipitate forms on adding substrate Enzyme-labeled antibody (or antigen) binds to antigen (or antibody); substrate changes color Radiolabeled antibody (or antigen) binds to antigen (or antibody), e.g., attached to solid phase Antibodies and soluble antigens produce visible lines of precipitate in a gel adenovirus 1) by more discriminating serological procedures. cache = ./cache/cord-023731-jqgervt7.txt txt = ./txt/cord-023731-jqgervt7.txt === reduce.pl bib === id = cord-027654-k0uby99n author = Nabel, Gary J. title = The development of gene-based vectors for immunization date = 2020-06-22 pages = extension = .txt mime = text/plain words = 6550 sentences = 321 flesch = 37 summary = The advantages of their ability to induce cellular immunity, immunogenicity, safety, mode of antigen presentation, and other attractive features are countered by limitations in knowledge about clinical effi cacy, production methodologies, DNA vaccination as the initial vaccine constituent and replication-defective viral vectors, including modifi ed vaccinia Ankara virus (MVA), 21,28 rAd 22,23,27,29 or proteins to boost the initial response. 31, 32 In addition, the development of improved enhancer/ promoter regions can allow for even higher expression 5 and these vaccines have advanced into multiple human Phase I studies, alone or in combination with other gene-based vectors. Depending on their ability to target antigen presenting cells, ability to develop packaging lines, inherent immunogenicity of both the vector and insert, and other factors (Table 62 -2), these viral vectors are helping to improve vaccine effi cacy in a variety of infectious disease models. Comparative immunogenicity in rhesus monkeys of DNA plasmid, recombinant vaccinia virus, and replication-defective adenovirus vectors expressing a human immunodefi ciency virus type 1 gag gene cache = ./cache/cord-027654-k0uby99n.txt txt = ./txt/cord-027654-k0uby99n.txt === reduce.pl bib === id = cord-023724-5at0rhqk author = Cann, Alan J. title = Infection date = 2015-07-24 pages = extension = .txt mime = text/plain words = 14979 sentences = 755 flesch = 48 summary = The problems plant viruses face in initiating infections of host cells have already been described (Chapter 4), as has the fact that no known plant virus employs a specific cellular receptor of the types that animal and bacterial viruses use to attach to cells. There are probably many different mechanisms involved in systemic resistance, but in general terms there is a tendency of these processes to increase local necrosis when substances such as proteases and peroxidases are produced by the plant to destroy the virus and to prevent its spread and subsequent systemic infection. Virus-resistant plants have been created by the production of transgenic plants expressing recombinant virus proteins or nucleic acids which interfere with virus replication without producing the pathogenic consequences of infection, for example: I Virus coat proteins, which have a variety of complex effects, including inhibition of virus uncoating and interference of expression of the virus at the level of RNA ("gene silencing" by "untranslatable" RNAs), I Intact or partial virus replicases which interfere with genome replication, I Antisense RNAs, I Defective virus genomes, I Satellite sequences (see Chapter 8), I Catalytic RNA sequences (ribozymes), I Modified movement proteins. cache = ./cache/cord-023724-5at0rhqk.txt txt = ./txt/cord-023724-5at0rhqk.txt === reduce.pl bib === id = cord-023925-qrr7jcwe author = Verhoef, Jan title = A8 Immune response in human pathology: Infections caused by bacteria, viruses, fungi, and parasites date = 2011-07-12 pages = extension = .txt mime = text/plain words = 5499 sentences = 282 flesch = 42 summary = 128 Immune response in human pathology: infections caused by bacteria, viruses, fungi, and parasites Micro-organisms that succeed in penetrating the first line of defence are ingested, killed, and degraded by phagocytic cells [polymorphonuclear leukocytes (PMN) or neutrophils, monocytes, and macrophages], which are attracted to a microbial infection through chemotaxis. Intracellular signalling involves several kinases depending on 132 Immune response in human pathology: infections caused by bacteria, viruses, fungi, and parasites Genotypical characteristics: chromosomal DNA fragment analysis, nucleic acid sequence analysis, probes Phenotypical characteristics: morphology, biotyping, serotyping, antibiotic resistance Analytical characteristics: cell-wall analysis, lipid and protein analysis, enzyme typing (catalase) Gram staining positive or negative Aerobic, anaerobic: Fermentation of different sugars Naming and classification of viruses according to: Structure: size, morphology (naked, enveloped), nucleic acid (RNA, DNA) Molecular aspects: mode of replication, assembly and budding Disease: encephalitis, hepatitis Means of transmission: droplets, water, blood, insects Host range: animal, plant, bacteria Classification of fungi according to: Structure: macroscopic morphology of hyphae (mycelium); microscopic morphology of hyphae, conidophores and conidia (spores); and shape and size Cell features: nucleus, cytosol, plasmalemma (cell membrane which contains cholesterol), physiology, staining properties Sexual characteristics: sexual and /or asexual reproduction, extended dikaryotic phase, basidium formation Genotypical characteristics: chromosomal DNA fragment analysis, nucleic acid sequence analysis, probes cache = ./cache/cord-023925-qrr7jcwe.txt txt = ./txt/cord-023925-qrr7jcwe.txt === reduce.pl bib === id = cord-027752-xcpv9k22 author = Bresalier, Michael title = Uses of a Pandemic: Forging the Identities of Influenza and Virus Research in Interwar Britain date = 2011-12-15 pages = extension = .txt mime = text/plain words = 10132 sentences = 753 flesch = 56 summary = In May 1922, Walter Morley Fletcher, Secretary of the Medical Research Council (MRC), organized a secret meeting of pathologists at the War Office to outline a new scheme of research on 'diseases probably caused by filter-passing organisms.' 1 Created in 1913, the MRC had used the war to apply laboratory science to military medicine. The pandemic had ignited interest in the nature of filterable viruses, however, the way forward was unclear, as Fletcher observed: 'The chief problem which the investigator of [filterable viruses] meets is the difficulty of proceeding by sound experimental methods.' 3 The purported influenza agent was one of a group of pathogens that could not be seen with light microscopes or studied by the culture methods that had been so successful with bacteria. 11 Especially important were military pathology investigations, supported by the War Office and MRC, into the bacteriology of the pandemic and, in due course, into the role of a 'filterable virus'. cache = ./cache/cord-027752-xcpv9k22.txt txt = ./txt/cord-027752-xcpv9k22.txt === reduce.pl bib === id = cord-031840-k9l91unc author = Lu, Li title = Forum: COVID-19 Dispatches date = 2020-09-11 pages = extension = .txt mime = text/plain words = 15686 sentences = 686 flesch = 53 summary = With death count worldwide reaching 586,000 merely 7 months after its first outbreak in China in late December 2019 and 13.6 million cases reported in 188 countries and territories as of July 2020, this ongoing pandemic has spread far beyond domain of world health problem to become an unprecedented challenge facing humanity at every level. On one hand, the eagerness to build solidarity with East Asian countries represented by Japan and South Korea might be a strategy to react to the racialization of COVID-19 as a "Chinese virus" and the demonization of China as a "public enemy" and "trouble maker" in the Euro-American political and media agenda (Viala-Gaudefroy & Lindaman, 2020). On the other hand, the rise of this East Asian imaginary centering around China's historical and cultural bonds with Japan and South Korea has far-reaching implications for China's geopolitical strategies beyond the COVID-19 pandemic and the realm of public health. cache = ./cache/cord-031840-k9l91unc.txt txt = ./txt/cord-031840-k9l91unc.txt === reduce.pl bib === id = cord-023705-3q9yr6np author = FENNER, FRANK title = Viral Replication date = 2014-06-27 pages = extension = .txt mime = text/plain words = 8331 sentences = 424 flesch = 51 summary = Many important biochemical phenomena such as the splicing and other types of posttranscriptional processing of RNA, the posttranslational cleavage and glycosylation of proteins, the replication of RNA, reverse transcription, integration, and the transposition of viral genes and cellular oncogenes were first elucidated by virologists and have general application in cell biology. Many important biochemical phenomena, such as splicing and other types of posttranscriptional processing of RNA, posttranslational cleavage and glycosylation of proteins, replica tion of RNA, reverse transcription, integration, and transposition of viral genes and cellular oncogenes, were first elucidated by virologists and have general application in cell biology. The proteins translated from the early transcripts of DNA viruses include enzymes and other proteins required for the replication of viral nucleic acid, as well as proteins that suppress host cell RNA and protein synthesis. cache = ./cache/cord-023705-3q9yr6np.txt txt = ./txt/cord-023705-3q9yr6np.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-025704-icedihm2 author = Pawestri, Hana A. title = Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008–2015 date = 2020-06-01 pages = extension = .txt mime = text/plain words = 6529 sentences = 323 flesch = 43 summary = Since the initial detection in 2003, Indonesia has reported 200 human cases of highly pathogenic avian influenza H5N1 (HPAI H5N1), associated with an exceptionally high case fatality rate (84%) compared to other geographical regions affected by other genetic clades of the virus. Sequencing data contain valuable information about viral genetic characteristics, including presence of known human adaptive markers, resistance against available antiviral drugs or other changes that can explain the high and rising mortality, while antigenic characterization will help assess the potential protection of pre-pandemic vaccines. Amino acid sequences were analyzed to identify substitutions potentially linked to human adaptation, virulence, antiviral resistance and antigenic properties as listed in the CDC H5N1 Genetic Change Inventory [37] . Although some genetic diversity was observed in the polymerase genes, well-known substitutions such as PB2-E627K and PB2-D701N, which are often selected upon infection of humans and affects the virulence of avian influenza viruses such as H5N1 [12, 66, 67, 79] , were not commonly found in the new samples. cache = ./cache/cord-025704-icedihm2.txt txt = ./txt/cord-025704-icedihm2.txt === reduce.pl bib === id = cord-023143-fcno330z author = nan title = Molecular aspects of viral immunity date = 2004-02-19 pages = extension = .txt mime = text/plain words = 43425 sentences = 2056 flesch = 47 summary = Based on a variety of experimental evidence, it is clear that demyelination induced in SJUJ mice by infection with the BeAn strain of TMEV is a Thl-mediated event: (a) disease induction is suppressed in T cell-deprived mice and by in vivo treatment with anti-I-A and anti-CD4 antibodies; (b) disease susceptibility correlates temporally with the development of TMEV-specific, MHC-class Il-restricted DTH responses and with a predominance of anti-viral lgG2a antibody; (c) activated (Le., lL-2RC) T cells infiltrating the CNS are exclusively of the CD4+ phenotype, and (d) proinflammatory cytokines (IFNq and TNF-p) are predominantly produced in the CNS. These results have important implications for a possible viral trigger in MS as they indicate that chronic demyelination in TMEV-infected mice is initiated in the absence of demonstrable neuroantigen-specific autoimmune responses and are consistent with a model wherein early myelin damage is mediated via primarily by mononuclear phagocytes recruited to the CNS and activated by pro-inflammatory cytokines produced by TMEV-specific Thl cells. cache = ./cache/cord-023143-fcno330z.txt txt = ./txt/cord-023143-fcno330z.txt === reduce.pl bib === id = cord-029419-b0w9nomq author = Matthews, Adam title = Review of Mark Honigsbaum (2020). The Pandemic Century—A History of Global Contagion from the Spanish Flu to Covid-19: Cambridge, MA: Penguin. 321 pp. ISBN 9780753558287 date = 2020-07-20 pages = extension = .txt mime = text/plain words = 3955 sentences = 186 flesch = 54 summary = Honigsbaum surveys with biological detail the genealogy and history of influenza, the plague, Parrot Fever, Legionnaires Disease, Aids, SARS, Ebola, Zika and Covid-19. Honigsbaum describes ecological disruption amplifying the mutation and spread of a virus which had existed in its natural environment for centuries. From a postdigital perspective, the ten cases detailed by Honigsbaum in The Pandemic Century (2020) show how digital and wider technologies are not separate from the natural and social world. The questions then, which The Pandemic Century (Honigsbaum 2020) illustrates is whether to take a posthuman perspective and pull back from technological and human development and reduce ecological disruption and work with the natural environment as equals or to push on unabated with technological developments to go beyond what has been done already to 'fix' ourselves and the planet, including new viral outbreaks. cache = ./cache/cord-029419-b0w9nomq.txt txt = ./txt/cord-029419-b0w9nomq.txt === reduce.pl bib === id = cord-026340-2nf97zvc author = Singh, Ranjana title = Chloroquine: A Potential Drug in the COVID-19 Scenario date = 2020-06-07 pages = extension = .txt mime = text/plain words = 7542 sentences = 412 flesch = 55 summary = In this review article, we have systematically searched for details of COVID-19 pandemic till May 2020 and assembled few data pertaining to (i) Corona viruses; (ii) SARS-CoV2, the virus that causes COVID-19' and (iii) How chloroquine and hydroxychloroquine mediates anti-viral effect in both prophylactic and therapeutic setting. The Corona Study Group (CSG) of the International Committee on Taxonomy of Viruses (ICTV) after assessing the etiological agent named it SARS-CoV2 (Severe Acute Respiratory Syndrome Corona Virus2) and the disease outbreak as COVID-19 (Corona Virus Disease-Year of Identification). During COVID-19, SARS-CoV2 S-protein binds to host cell's receptor ACE2 (Belouzard et al. As for the case of SARS-CoV, it was shown that the binding specificity of virus to host cell was due to 3 prime amino acid residues in S1 protein at positions 360, 479, and 487. cache = ./cache/cord-026340-2nf97zvc.txt txt = ./txt/cord-026340-2nf97zvc.txt === reduce.pl bib === id = cord-030961-5gzc7193 author = Wang, Jiajun title = Adhesive contact between cylindrical (Ebola) and spherical (SARS-CoV-2) viral particles and a cell membrane date = 2020-08-28 pages = extension = .txt mime = text/plain words = 4335 sentences = 260 flesch = 55 summary = In the limit where bending dominates, for sufficiently large values of normalized bending stiffness, there is no adhesion between viral particles and the cell membrane without applied force. In this work, we create a continuum model for the small-deflection adhesive contact mechanics of virus particle attachment onto the host cell membrane in terms of the principal biophysical properties of the virus, membrane, and their interaction. These results also help to retrieve conditions for lack of adhesion, pull-off force, and contact area between the virus particle and cell membrane. We now describe in outline the continuum models for adhesive contact between the virus and cell membrane, driven by adhesion and external displacement or force, and resisted by tension and elastic bending. In our models, the parameters that govern the adhesive contact mechanics are (more in Table 1 ) bending rigid κ, tension σ, adhesion free energy per receptor β, binding receptor density ρ, and the radius of the virus, R. cache = ./cache/cord-030961-5gzc7193.txt txt = ./txt/cord-030961-5gzc7193.txt === reduce.pl bib === id = cord-103135-nly9vojr author = Fletcher, Nicola F. title = A novel antiviral formulation inhibits a range of enveloped viruses date = 2020-03-30 pages = extension = .txt mime = text/plain words = 6468 sentences = 329 flesch = 47 summary = ViroSAL had no effect on the infectivity of a non-enveloped virus, norovirus, which is in agreement with previous studies demonstrating that free fatty acids are ineffective against nonenveloped viruses (Thormar et al., 1987 , Kohn et al., 1980 . In this study, ViroSAL at the indicated concentrations was mixed with an equal volume of viral inoculum (MeV:original TCID50 = 4.48 7 /mL, HSV-1: 100 PFU/mL, EBV: MOI=10, Zika: MOI=10, Orf: 4 PFU/mL) or pseudoviruses bearing VSV, Ebola, Lassa or SARS-CoV-1 envelope glycoproteins, and incubated at room temperature for 2 minutes. Virus/ViroSAL or control treated virus was inoculated onto appropriate target cells and incubated for 48h at 37°C, then fixed and infection enumerated, or, for pseudovirus assays, lysed and luciferase activity quantified as previously described (Fletcher et al., 2015) . Milk-based free fatty acids, as well as fatty acid emulsions, have been shown to inhibit infection of Vero cells with VSV and HSV-1, with no antiviral effect on poliovirus, a non-enveloped virus (Thormar et al., 1987) . cache = ./cache/cord-103135-nly9vojr.txt txt = ./txt/cord-103135-nly9vojr.txt === reduce.pl bib === id = cord-027473-8zerjwa0 author = Roos, Yrjö H. title = Water and Pathogenic Viruses Inactivation—Food Engineering Perspectives date = 2020-06-20 pages = extension = .txt mime = text/plain words = 9805 sentences = 515 flesch = 43 summary = The large number of virus species, differences in spreading, likelihood of foodborne infections, unknown infective doses, and difficulties of infective virus quantification are often limiting experimental approaches to establish accurate data required for detailed understanding of virions' stability and inactivation kinetics in various foods. The stability of enteric viruses, human norovirus (HuNoV), and hepatitis A (HAV) virions in food materials and their resistance against inactivation in traditional food processing and preservation is well recognized. The small size, concentration, and a tiny infective dose of virions besides the need of host cells for reproduction of viral material result in challenges in studies analyzing virus survival and infectiousness in food, water, and the environment [60] . Here, we summarize studies reporting on virus survival and degradation kinetics with critical evaluation of the importance of known data to understanding losses of virus infectivity in normal circumstances, and particularly as affected by water from a food engineering and safety perspective. cache = ./cache/cord-027473-8zerjwa0.txt txt = ./txt/cord-027473-8zerjwa0.txt === reduce.pl bib === id = cord-102704-wfuzk2dp author = Meza, Diana K. title = Predicting the presence and titer of rabies virus neutralizing antibodies from low-volume serum samples in low-containment facilities date = 2020-04-30 pages = extension = .txt mime = text/plain words = 3183 sentences = 192 flesch = 43 summary = Despite small conflicts, titer predictions were correlated across tests repeated on different dates both for dog samples (r = 0.93), and for a second dataset of sera from wild common vampire bats (r = 0.72, N = 41), indicating repeatability. The pmRFFIT enables high-throughput detection of rabies virus neutralizing antibodies in low-biocontainment settings and is suited to studies in wild or captive animals where large serum volumes cannot be obtained. The binomial and log-normal models fit to 193 this data subset included only the fixed effect of the virus-infected N2A cell counts, but the random 194 effects were identical to those explained above (i.e. test date and field). A final distinction is that 316 instead of scoring microscope field or wells as virus positive or negative, the pmRFFIT predicts 317 serological status and RVNA titer from infected cell counts in a single serum dilution using statistical 318 cache = ./cache/cord-102704-wfuzk2dp.txt txt = ./txt/cord-102704-wfuzk2dp.txt === reduce.pl bib === id = cord-030279-pv770doe author = Novossiolova, Tatyana title = Twenty-first Century Governance Challenges in the Life Sciences date = 2016-11-29 pages = extension = .txt mime = text/plain words = 15222 sentences = 743 flesch = 42 summary = From 'dual-use life science research of concern' through the rise of amateur biology to the advent of personalised medicine, the chapter exposes the limitations of the existing governance mechanisms in accommodating the multifaceted ethical, social, security, and legal concerns arising from cutting-edge scientific and technological developments. Indeed, rapid advances in the field have produced a knowledge base and set of tools and techniques that enable biological processes to be understood, manipulated and controlled to an extent never possible before 5 ; they have found various applications in numerous spheres of life, generating enormous benefits and offering bright prospects for human betterment; and they have come to be regarded as a key driver of economic development with potential to close the gap between resource-rich and resource-poor countries. cache = ./cache/cord-030279-pv770doe.txt txt = ./txt/cord-030279-pv770doe.txt === reduce.pl bib === id = cord-102862-oq54sfx6 author = Dastjerdi, Akbar M. title = Characterisation of the bovine enteric calici-like virus, Newbury agent 1 date = 2000-11-01 pages = extension = .txt mime = text/plain words = 3180 sentences = 172 flesch = 55 summary = A single capsid protein of 49.4 kDa was detected by Western blotting in purified NA1 preparations prepared from post-infection but not pre-infection faecal samples and with postbut not pre-infection sera. Calici-like virus particles were identi¢ed in faecal samples by electron microscopy but no other viruses were seen. Western blotting analysis of NA1 virions puri¢ed from faeces by CsCl density gradient centrifugation demonstrated the presence of a single protein band in each of ¢ve separate preparations from the day 2 p.i. faecal sample from calf 1424 (Fig. 4a, track 2) . The speci¢city of the protein band was con¢rmed by examination of day 0 versus day 2 p.i. faecal samples, staining with pre-and postinoculation antisera and association with the presence of virus particles in CsCl gradients. Capsid diversity in small round-structured viruses : molecular characterization of an antigenically distinct human enteric calicivirus cache = ./cache/cord-102862-oq54sfx6.txt txt = ./txt/cord-102862-oq54sfx6.txt === reduce.pl bib === id = cord-030028-s6sxi8uj author = Rubio, Luis title = Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution date = 2020-07-17 pages = extension = .txt mime = text/plain words = 14687 sentences = 698 flesch = 40 summary = This technique has been used to differentiate isolates of some plant viruses, such as prunus necrotic ringspot virus (PNRSV), TYLCV and CTV (Gillings et al., 1993; Hammond et al., 1998; Font et al., 2007) ; iii) Single-strand conformation polymorphism (SSCP) analysis is based on electrophoresis of denatured dsDNA in non-denaturing gels so migration of single-stranded DNA depends on its conformation determined by its nucleotide sequence and the electrophoretic conditions. This technique followed by sequencing of the different haplotypes detected has been used to evaluate the genetic variation of some plant viruses, such as cucumber mosaic virus (CMV), citrus psorosis virus (CPsV) and CTV (Rubio et al., 1996; Rubio et al., 1999; Vives et al., 2002; Lin et al., 2003; Martıń et al., 2006) . Procedures to detect and identify various viruses or virus strains in a single assay simultaneously reduce time and cost of the analysis (see Pallaś et al., 2018 for a comprehensive review), and are especially suitable for evaluating mixed infections in individual plants. cache = ./cache/cord-030028-s6sxi8uj.txt txt = ./txt/cord-030028-s6sxi8uj.txt === reduce.pl bib === id = cord-035163-tqh5wv12 author = Ijaz, M. Khalid title = Combating SARS-CoV-2: leveraging microbicidal experiences with other emerging/re-emerging viruses date = 2020-09-08 pages = extension = .txt mime = text/plain words = 6841 sentences = 345 flesch = 46 summary = In the present review, we suggest that approaches for infection prevention and control (IPAC) for SARS-CoV-2 and future emerging/re-emerging viruses can be invoked based on pre-existing data on microbicidal and hygiene effectiveness for related and unrelated enveloped viruses. These therefore included coronaviruses, Lassa virus, SFTSV, Hantaan virus, MERS-CoV, SARS-CoV, SARS-CoV-2, Ebola virus, influenza H5N1, Nipah virus, EV-D68, particle size, reservoir species, tissue tropism, mode of transmission, transmissibility, virus shedding, minimal infectious dose, infectious dose 50 , mortality, survival on surfaces, persistence on surfaces, stability on surfaces, survival in aerosols, persistence in aerosols, stability in aerosols, microbicidal efficacy, virucidal efficacy, disinfectant efficacy, antiseptic efficacy, emerging/re-emerging enveloped viruses, UVC susceptibility, zoonoses, and personal hygiene for SARS-CoV-2. As mentioned in Table 2 , the most common modes of transmission for the emerging/ re-emerging viruses discussed in this review are contact with infected bodily secretions/ excretions and contaminated fomites, especially high-touch environmental surfaces (HITES), and inhalation of respiratory droplets/aerosols containing infectious virus (Fig. 1) . cache = ./cache/cord-035163-tqh5wv12.txt txt = ./txt/cord-035163-tqh5wv12.txt === reduce.pl bib === id = cord-076082-4kpkhz0o author = Lam, Tommy Tsan-Yuk title = Evolutionary and Transmission Dynamics of Reassortant H5N1 Influenza Virus in Indonesia date = 2008-08-22 pages = extension = .txt mime = text/plain words = 6973 sentences = 312 flesch = 44 summary = The H5N1 highly pathogenic avian influenza (HPAI) virus was originally isolated from a farmed goose in Guangdong province of China in 1996 [1] , and soon spread to live-poultry markets in Hong Kong [2] , resulting in 18 cases of human infection in 1997, 6 of which were fatal [3, 4] . We found previously unrecognized phylogenetic discordance between gene trees involving human and cat isolates (n = 25, denoted in red in Figures 1, S1-S3)-the main focus of our study-suggesting that they are reassortant viruses descending from group 2 and 3 lineages. To further investigate the putative reassortant human and cat viruses, a selected dataset (n = 24) of manually concatenated full genomes (Figure 2A ; see Methods) of Indonesian H5N1 HPAI viruses were analyzed using more sophisticated analysis methods, including similarity plots, bootscan analyses and GARD analyses (genetic algorithm for recombination detection). cache = ./cache/cord-076082-4kpkhz0o.txt txt = ./txt/cord-076082-4kpkhz0o.txt === reduce.pl bib === id = cord-048368-wm4c7rk6 author = Evseenko, Vasily A title = Experimental infection of H5N1 HPAI in BALB/c mice date = 2007-07-27 pages = extension = .txt mime = text/plain words = 2880 sentences = 202 flesch = 55 summary = Serological analysis showed wide cross-reactivity of this virus with sera produced to H5N1 HPAI viruses isolated earlier in South-East Asia. Earlier HPAI viruses were investigated in mice [4, 5] and murine models were successively used for reverse genetics made influenza vaccines [6] . Sequence comparison of the NA protein of A/duck/Tuva/01/06 aligned with the NA of N2 subtype of A/Wuhan/359/95 (H3N2) influenza virus showed phenotype potentially sensitive to neuraminidase inhibitors. Despite powerful anti-influenza virus effects of TNF-α in lung tissue, as it was described previously [28] , we consider that elevated production of the cytokines seems to be crucial in the pathogenesis of HPAI infection. Summing up, in our study BALB/c mice infected with HPAI, strain A/duck/Tuva/01/06, appeared to be able to produce the innate immune response, which culminated to the development of shock and subsequent multiple organ failure. cache = ./cache/cord-048368-wm4c7rk6.txt txt = ./txt/cord-048368-wm4c7rk6.txt === reduce.pl bib === id = cord-103688-n7hzpbyf author = Wang, Lina title = VirusDIP: Virus Data Integration Platform date = 2020-06-09 pages = extension = .txt mime = text/plain words = 1286 sentences = 81 flesch = 47 summary = Results To facilitate virus research and promote the global sharing of virus data, we present here VirusDIP, a one-stop service platform for archive, integration, access, analysis of virus data. It accepts the submission of viral sequence data from all over the world and currently integrates data resources from the National GeneBank Database (CNGBdb), Global initiative on sharing all influenza data (GISAID), and National Center for Biotechnology Information (NCBI). Moreover, based on the comprehensive data resources, BLAST sequence alignment tool and multi-party security computing tools are deployed for multi-sequence alignment, phylogenetic tree building and global trusted sharing. For data compatibility, the virus data standard integrates the virus and pathogen sample data standard of The International Nucleotide Sequence Database Collaboration (INSDC) (Karsch-Mizrachi et al., 2018) , the hCoV-19 data standard of GISAID, and the sample data standard of COVID-19 Genomics UK (COG-UK) Consortium. VirusDIP is committed to building a comprehensive virus data platform for archive, integration, access, and analysis. cache = ./cache/cord-103688-n7hzpbyf.txt txt = ./txt/cord-103688-n7hzpbyf.txt === reduce.pl bib === id = cord-102908-sr7j8z9c author = Mersmann, Sophia F. title = Learning to count: determining the stoichiometry of bio-molecular complexes using fluorescence microscopy and statistical modelling date = 2020-07-24 pages = extension = .txt mime = text/plain words = 5244 sentences = 260 flesch = 42 summary = We used differential binary labelling and statistical modelling to extract estimates of stoichiometry, our strategy is outlined in Figure 1 ; note that this approach can be generalised to apply to many other multi-component systems (i.e. how many protein x are found in assembly y?). As described above, our experimental design utilizes antibody labelled with spectrally distinct dyes allowing binary scoring of individual virus particles as positive if they interact with at least one Ab B molecule ( Figure 1 ). We have demonstrated quantitative analysis of 9C12 interaction with individual Adv particles ( Figure 3) ; we have confirmed that differential labelling of antibody does not bias binding ( Figure 4A & B) ; and that we could detect single molecules of 9C12 Biotin allowing discrimination of positive and negative AdV-9C12 complexes ( Figure 4C & D). However, using stoichiometric estimates to calibrate fluorescent data revealed population heterogeneity with a small proportion of virus particles binding ∼200 antibody molecules. cache = ./cache/cord-102908-sr7j8z9c.txt txt = ./txt/cord-102908-sr7j8z9c.txt === reduce.pl bib === id = cord-102383-m5ahicqb author = Romano, Alessandra title = Energy dynamics for systemic configurations of virus-host co-evolution date = 2020-05-15 pages = extension = .txt mime = text/plain words = 3776 sentences = 190 flesch = 43 summary = A systems-thinking representation, based on stock-flow diagramming of virus-host interaction at the cellular level, is used here for the first time to simulate the system energy dynamics. A systems-thinking representation, based on stock-flow diagramming of virus-host interaction at the cellular level, is used here for the first time to simulate the system energy dynamics. A systems-thinking representation, based on stock-flow diagramming of virus-host interaction at the cellular level, is used here for the first time to simulate the system energy dynamics. Viral load and early addressing (in the first two days from infection) of leverage points are the most effective strategies on stock dynamics to minimize virion assembly and preserve host-cell bioenergetics. Viral load and early addressing (in the first two days from infection) of leverage points are the most effective strategies on stock dynamics to minimize virion assembly and preserve host-cell bioenergetics. cache = ./cache/cord-102383-m5ahicqb.txt txt = ./txt/cord-102383-m5ahicqb.txt === reduce.pl bib === id = cord-104286-5yw4zwo4 author = Doane, F. W. title = Virus morphology as an aid for rapid diagnosis. date = 1980 pages = extension = .txt mime = text/plain words = 2206 sentences = 138 flesch = 39 summary = A specimen is inoculated into a host system (tissue culture, eggs, animals), and subsequent detection and identification of an isolated virus depends on indicators such as cytopathic effect, hemagglutinin, complement fixation, etc. The following brief review will examine some of the ways in which virus morphology can serve as an important aid for rapid virus diagnosis, some of the limitations of this approach, and current and future developments in electron microscopy relating to diagnostic virology. The same results can be obtained within one hour if one uses immunoelectron microscopy (IEM), by which the virusantiserum mixtures are negatively stained and examined on an EM specimen grid. A major advantage of using electron microscopy for rapid virus diagnosis is that one can actually see the virus and identify it by its morphology. Hepatitis A: detection by immune electron microscopy of a virus-like antigen associated with acute illness cache = ./cache/cord-104286-5yw4zwo4.txt txt = ./txt/cord-104286-5yw4zwo4.txt === reduce.pl bib === id = cord-035015-slgywe0c author = Nunn, Alistair V. W. title = SARS-CoV-2 and mitochondrial health: implications of lifestyle and ageing date = 2020-11-09 pages = extension = .txt mime = text/plain words = 14660 sentences = 715 flesch = 36 summary = Data is now showing that COVID-19 patients do have populations of T-cells displaying mitochondrial dysfunction, as well as altered mitochondrial markers in monocyteshinting that immune-metabolic phenotyping could be used to understand disease pathogenesis and possible treatments; this could include targeting mitochondria [32] . The underlying aetiology for "inflammaging" has long thought to be associated with mitochondrial dysfunction as suggested by Nick Lane in 2003 in his "double agent" theory [5] , and is now receiving renewed interest, for instance, in how decreasing mitochondrial function can reduce T-cell function and enhance immune senescence, as mitochondria are pivotal in metabolic reprogramming towards the Warburg effect [40] . Furthermore, as evidence indicates that many viruses, which most likely include SARs-CoV-2, modulate bioenergetics and redox in both the immune system and other cells they infect to enhance their own replication, they could potentially induce excessive stress in these systems if their mitochondria are already sub-optimally functional. cache = ./cache/cord-035015-slgywe0c.txt txt = ./txt/cord-035015-slgywe0c.txt === reduce.pl bib === id = cord-214795-8jweuq50 author = Mongia, Aanchal title = DeepVir -- Graphical Deep Matrix Factorization for"In Silico"Antiviral Repositioning: Application to COVID-19 date = 2020-09-22 pages = extension = .txt mime = text/plain words = 6420 sentences = 369 flesch = 47 summary = Results on our curated RNA drug virus association (DVA) dataset shows that the proposed approach excels over state-of-the-art graph regularized matrix completion techniques. It shows how the matrix completion framework can be used to computationally predict the drugs that could be effective against SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the virus responsible for the ongoing pandemic, COVID-19 (COrona VIrus Disease-2019). In this present work, we propose to solve the problem of drug-virus association prediction via graph regularized deep matrix factorization. Among all the methodologies compared in [52] , graph regularized matrix factorization based technique (GRMF) provided the best results for the validation setting where drugs are predicted for novel viruses. In our proposed technique, multi-graph regularization is incorporated in the deep matrix factorization formulation with the aim to incorporate the metadata associated with the drugs and viruses in the form of similarity information as shown below: cache = ./cache/cord-214795-8jweuq50.txt txt = ./txt/cord-214795-8jweuq50.txt === reduce.pl bib === id = cord-203232-1nnqx1g9 author = Canturk, Semih title = Machine-Learning Driven Drug Repurposing for COVID-19 date = 2020-06-25 pages = extension = .txt mime = text/plain words = 5023 sentences = 257 flesch = 52 summary = Using the National Center for Biotechnology Information virus protein database and the DrugVirus database, which provides a comprehensive report of broad-spectrum antiviral agents (BSAAs) and viruses they inhibit, we trained ANN models with virus protein sequences as inputs and antiviral agents deemed safe-in-humans as outputs. Using sequences for SARS-CoV-2 (the coronavirus that causes COVID-19) as inputs to the trained models produces outputs of tentative safe-in-human antiviral candidates for treating COVID-19. For Experiment II, we split the data on virus species, meaning the models were forced to predict drugs for a species that it was not trained on, and have to detect peptide substructures in the amino-acid sequences to suggest drugs. In post-processing, we applied a threshold to the sigmoid function outputs of the neural network, where we assigned each drug a probability of being a potential antiviral for a given amino acid sequence. cache = ./cache/cord-203232-1nnqx1g9.txt txt = ./txt/cord-203232-1nnqx1g9.txt === reduce.pl bib === id = cord-161674-nk0wie0w author = Liu, Zhi title = Implications of the virus-encoded miRNA and host miRNA in the pathogenicity of SARS-CoV-2 date = 2020-04-10 pages = extension = .txt mime = text/plain words = 5137 sentences = 304 flesch = 54 summary = Our results implicated that the immune response and cytoskeleton organization are two of the most notable biological processes regulated by the infection-modulated miRNAs. Impressively, we found hsa-miR-4661-3p was predicted to target the S gene of SARS-CoV-2, and a virus-encoded miRNA MR147-3p could enhance the expression of TMPRSS2 with the function of strengthening SARS-CoV-2 infection in the gut. In the gut, 54 genes were predicted to be enhanced by 34 miRNAs. The most notable target of the virus miRNA is TMPRSS2, which is reported to enhance SARS-CoV-2 infection together with ACE2 48 In the liver, the virus miRNA mainly regulates genes involved in the function of actin filament severing and regulation of cellular protein metabolic process ( Figure 3E ). There were more than human 800 genes were predicted to be regulated by these miRNA (Figure 4A) , and a notable enrichment at the immune system process was observed There were 27 SARS-CoV-2 encoded miRNA that can target the virus genome ( Figure 5A ). cache = ./cache/cord-161674-nk0wie0w.txt txt = ./txt/cord-161674-nk0wie0w.txt === reduce.pl bib === id = cord-048466-fj9l8che author = Bragstad, Karoline title = The evolution of human influenza A viruses from 1999 to 2006: A complete genome study date = 2008-03-07 pages = extension = .txt mime = text/plain words = 5357 sentences = 322 flesch = 53 summary = BACKGROUND: Knowledge about the complete genome constellation of seasonal influenza A viruses from different countries is valuable for monitoring and understanding of the evolution and migration of strains. The influenza virus evades host immunity by accumulation of point mutations (drift) in the major surface glycoproteins, haemagglutinin (HA) and neuraminidase (NA) or by reassortment of segments from different viruses co-infecting the same cell leading to a new stain with a HA (and NA) not seen in the population before (shift). The A/Fujian/411/02(H3N2)-like clinical Danish viruses had several substitutions in HA at sites that might influence the virus' capability for egg growth [10, 37] . Substitutions at antigenic site B and the predicted N-glycosylation at position 144 in HA antigenic site A together with a stronger NA might have contributed to the increased infectivity of the reassorted Fujian-like viruses of the 2003-2004 season, causing an epidemic in Denmark. Positive selection on the H3 hemagglutinin gene of human influenza virus A cache = ./cache/cord-048466-fj9l8che.txt txt = ./txt/cord-048466-fj9l8che.txt === reduce.pl bib === id = cord-171099-d0qr84xg author = Buehler, Markus J. title = Nanomechanical sonification of the 2019-nCoV coronavirus spike protein through a materiomusical approach date = 2020-03-30 pages = extension = .txt mime = text/plain words = 4509 sentences = 205 flesch = 46 summary = Presenting musical encoding in two versions one in the amino-acid scale and one based on equal temperament tuning the method allows for expressing protein structures in audible space, offering novel avenues to represent, analyze and design architectural features across lengthand time-scales. We further report a hierarchical frequency spectrum analysis of five distinct protein structures, which offer insights into how genetic mutations, and the binding of the virus spike protein to the human ACE2 cell receptor directly influence the audio. What you hear is a multi-layered algorithmic composition featuring both the vibrational spectrum of the entire protein (expressed in sound and rhythmic elements), the sequence and folding of amino acids that compose the virus spike structure, as well as interwoven melodiesforming counterpoint music -reflecting the complex hierarchical intersecting geometry of the protein. cache = ./cache/cord-171099-d0qr84xg.txt txt = ./txt/cord-171099-d0qr84xg.txt === reduce.pl bib === id = cord-104317-t30dg6oj author = Parker, Michael T. title = An Ecological Framework of the Human Virome Provides Classification of Current Knowledge and Identifies Areas of Forthcoming Discovery date = 2016-09-30 pages = extension = .txt mime = text/plain words = 7986 sentences = 408 flesch = 40 summary = However, the obvious importance of viruses in the composition of all biomes has not (yet) been met with an appropriate fervor for the characterization of the viral REVIEW Recent advances in sequencing technologies have opened the door for the classification of the human virome. The discovery of intimate interactions of viruses with humans, like the role of endogenous retrovirus (ERV †) syncytins in placentation [27] , are categorically dissimilar to the classical view of viruses only as parasites and brings to issue how scientists are approaching the study of the virome. The application of this scaffold will not only deepen the understanding of known virus-host interactions in the ecological context of the virome, but will also identify logical next steps and gaps in current knowledge that are tantalizing areas for future exploration. Additionally, further characterization of the human virome is likely to uncover more viruses that persistently infect humans [31] , and such discoveries could pave the way for the treatment of diseases of currently unknown etiology. cache = ./cache/cord-104317-t30dg6oj.txt txt = ./txt/cord-104317-t30dg6oj.txt === reduce.pl bib === id = cord-252456-971d0sir author = Hemida, Maged Gomaa title = The SARS-CoV-2 outbreak from a one health perspective date = 2020-03-16 pages = extension = .txt mime = text/plain words = 4824 sentences = 244 flesch = 55 summary = The SARS-CoV-2 is a new human coronavirus candidate recently detected in China that is now reported in people on inhabited continents. Currently, the case fatality rate is relatively low (⁓3.6%) compared to infections with severe acute respiratory syndrome coronavirus (SARS-CoV, (10%) and MERS-CoV (32%) [11] . Based on the previous emergence history of SARS-CoV, the presence of a large number of mammals and birds overcrowded in one place may give a chance for pathogens, particularly those with RNA genomes such as coronaviruses and influenza viruses, to emerge. Based on the previous experience from the other emerging diseases, particularly SARS-CoV and influenza viruses, avoiding the mixing of various species of animals, birds, and mammals, is highly suggested [51, 65, 66] . The process of decontamination of the virus-contaminated surfaces by the appropriate disinfectants or virucidal agents was successful in case of other respiratory viruses such as SARS-CoV and avian influenza [59] . cache = ./cache/cord-252456-971d0sir.txt txt = ./txt/cord-252456-971d0sir.txt === reduce.pl bib === id = cord-102905-rlee32x7 author = Leis, Jonathan title = Ilaprazole and other novel prazole-based compounds that bind Tsg101 inhibit viral budding of HSV-1/2 and HIV from cells date = 2020-05-04 pages = extension = .txt mime = text/plain words = 5755 sentences = 297 flesch = 51 summary = In this report we show that tenatoprazole and a related prazole drug, ilaprazole, effectively block infectious Herpes Simplex Virus (HSV)-1/2 release from Vero cells in culture. Our results indicate that prazole-based compounds may represent a class of drugs with potential to be broad-spectrum antiviral agents against multiple enveloped viruses, by interrupting cellular Tsg101 interaction with maturing virus, thus blocking the budding process that releases particles from the cell. Tenatoprazole and esomeprazole were shown to quantitatively inhibit the release of infectious HIV-1 from 293T cells in culture, and it was suggested that these effects may be mediated via changes in viral interaction with Tsg101, a key component of the cellular ESCRT complex (5, 33) . Given multiple reports suggesting that herpes viruses also use cellular ESCRT proteins in their replication process (20) (21) (22) (23) we tested if the Tsg101-binding prazole drugs, which blocked budding of HIV-1, would also block the release of herpes viruses from cells. cache = ./cache/cord-102905-rlee32x7.txt txt = ./txt/cord-102905-rlee32x7.txt === reduce.pl bib === id = cord-102898-eyyd7ent author = Rizvi, Vaseef A. title = Translation regulation of Japanese encephalitis virus revealed by ribosome profiling date = 2020-07-17 pages = extension = .txt mime = text/plain words = 3048 sentences = 159 flesch = 44 summary = Using ribosome profiling, we identify multiple mechanisms including frameshifting, tRNA dysregulation and alternate translation initiation sites that regulate viral protein synthesis. downstream polyprotein, 2) Significant modulation in levels of a distinct subset of ribosome-bound tRNAs 48 that cannot be explained by virtue of codon usage and 3) Translation from an upstream ORF (uORF) using 49 a non-canonical initiation codon in the 5 UTR region of JEV. However, these sites do not represent commonly associated Studies on RNA viruses have suggested adaptations in codon usage of viral genes to the host translation [30] . Interestingly, JEV infection appears to stimulate 251 expression from UUG start site by almost 67% suggesting viral or virus-induced host trans-regulatory factors 252 promoting uORF translation (Fig.4D) . We also identify a subset of ribosome associated 286 tRNAs whose levels are modulated globally upon JEV infection (Fig.3) . cache = ./cache/cord-102898-eyyd7ent.txt txt = ./txt/cord-102898-eyyd7ent.txt === reduce.pl bib === id = cord-245161-xbw72k4m author = Castano, Nicolas title = Fomite transmission and disinfection strategies for SARS-CoV-2 and related viruses date = 2020-05-23 pages = extension = .txt mime = text/plain words = 11558 sentences = 720 flesch = 44 summary = Contaminated objects or surfaces, referred to as fomites, play a critical role in the spread of viruses, including SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Elucidating the physicochemical processes and surface science underlying the adsorption and transfer of virus between surfaces, as well as their inactivation, are important in understanding how the disease is transmitted, and in developing effective interception strategies. Three primary transmission routes have been found to contribute to the spread of respiratory viruses (e.g., SARS-CoV-1 and -2, measles, HCoV, rhinovirus, and influenza virus) ( Figure 1A ): 1) direct contact between individuals, 2) indirect contact via contaminated objects (fomites), 3) airborne transmission via droplets and aerosols. A study on SARS-CoV-2 infected patients in isolation rooms showed contamination of high-contact surfaces such as doorknobs and bedrails, as well as air outlet fans which indicated virus transfer from aerosols to a surface. cache = ./cache/cord-245161-xbw72k4m.txt txt = ./txt/cord-245161-xbw72k4m.txt === 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-252397-qlu7dilh author = Johnson, Reed F. title = Intratracheal exposure of common marmosets to MERS-CoV Jordan-n3/2012 or MERS-CoV EMC/2012 isolates does not result in lethal disease date = 2015-11-01 pages = extension = .txt mime = text/plain words = 5024 sentences = 255 flesch = 49 summary = Results from a natural history study of MERS-CoV-infected rhesus monkeys indicated that intratracheal inoculation induced a non-lethal disease with limited pathology observed in recovering animals at 28 days post-inoculation and infectious virus could be recovered from lung but not other tissues assayed (Yao et al., 2014) . One subject in the MERS-EMC inoculated group appeared to develop a secondary infection observed by CT that increased to study end, day 25 post-exposure. With the use of CT, we observed that IT inoculation of common marmosets with MERS-JOR or MERS-EMC isolates resulted in a non-lethal disease characterized by limited clinical signs and moderate consolidative lung pathology that did not completely resolve by study end. In this experiment, we sought to determine if there were virus specific differences in disease progression following intratracheal inoculation of common marmosets with Middle Eastern Respiratory Syndrome Coronavirus, commonly known as MERS-CoV, with two common laboratory viral isolates (MERS-EMC and MERS-Jordan). cache = ./cache/cord-252397-qlu7dilh.txt txt = ./txt/cord-252397-qlu7dilh.txt === reduce.pl bib === id = cord-253594-9gbo8viu author = Konieczny, Leszek title = The COVID-19 Puzzle date = 2020-05-31 pages = extension = .txt mime = text/plain words = 1366 sentences = 90 flesch = 49 summary = From the epidemiological perspective, an important factor affecting the spread of the virus is the proximity between infection targets. The bacterial genome includes a repository of viral genetic sequences -effectively a "catalogue" of known viruses. Its effects appear to depend on the carrier's age: many people, particularly young ones, remain asymptomatic, while older individuals frequently develop serious -even life-threateningsymptoms. Variable susceptibility to infection may be a consequence of the general state of health, which, of course, depends on the individual's age and co-morbidities -particularly metabolic ones (e.g. diabetes). Since the virus preferentially attacks the lungs, we can point to tobacco smoking as a factor, which promotes infection by damaging lung tissue. One mechanism which exhibits clear susceptibility to external disruption (including the presence of unusual substances) is protein folding. Genetic polymorphism undoubtedly results in individual variability, including well-known differences in alcohol tolerance. cache = ./cache/cord-253594-9gbo8viu.txt txt = ./txt/cord-253594-9gbo8viu.txt === reduce.pl bib === id = cord-212761-4bwatc2r author = Contoyiannis, Y. title = On the effectiveness of imposing restrictive measures in a graded Self-Organized Criticality epidemic spread model The case of COVID-19 date = 2020-04-01 pages = extension = .txt mime = text/plain words = 4323 sentences = 194 flesch = 50 summary = title: On the effectiveness of imposing restrictive measures in a graded Self-Organized Criticality epidemic spread model The case of COVID-19 However, it is revealed that very close to the critical point, the critical slowing-down (CSD) phenomenon, introduced by the theory of critical phenomena, emerges, leading to a tremendous increase of both the percentage of active carriers and the duration of the epidemic. As expected from the theory of critical phenomena, in the case of initial virus densities ρ below the critical value, time durations of the epidemic spread become significantly small. As already discussed, the proposed self-organized model seems to demonstrate a noteworthy behavior for a virus density equal to its critical value ρc, due to the CSD phenomenon, further leading to spectacularly increased relaxation times (high durations of the epidemic). cache = ./cache/cord-212761-4bwatc2r.txt txt = ./txt/cord-212761-4bwatc2r.txt === reduce.pl bib === id = cord-252466-usrpodjx author = Yun, Nadezhda E. title = Pathogenesis of Lassa Fever date = 2012-10-09 pages = extension = .txt mime = text/plain words = 5668 sentences = 290 flesch = 40 summary = Apparently, failure to develop the cellular immune response that would control dissemination of LASV, which is indicated by high serum virus titers, combined with disseminated replication in tissues and absence of neutralizing antibodies, leads to the development of fatal Lassa fever [64] . Downregulation of immune responses caused by LASV infection demonstrated in vitro is also in agreement with the results of clinical observations showing that fatal outcome of Lassa fever correlates with low levels or absence of interleukin (IL) 8 and IFN inducible protein 10 (IP-10) in circulation [70] . These data indicate that T cells are essential for rapid resolution of LASV infection; however, if the host fails to control virus replication due to inadequate activation of the immune system, T lymphocytes may play a key role in Lassa fever pathogenesis. cache = ./cache/cord-252466-usrpodjx.txt txt = ./txt/cord-252466-usrpodjx.txt === reduce.pl bib === id = cord-253143-73dsc6q3 author = Tang, Julian W. title = Emerging, Novel, and Known Influenza Virus Infections in Humans date = 2010-08-02 pages = extension = .txt mime = text/plain words = 5007 sentences = 248 flesch = 45 summary = Nevertheless, the plethora of epidemiologic, diagnostic, mathematical and phylogenetic modeling, and investigative methodologies developed since the severe acute respiratory syndrome outbreak of 2003 and the subsequent sporadic human cases of avian influenza have been applied effectively and rapidly to the emergence of this novel pandemic virus. 3 In addition, sporadic, generally mild (although there has been at least 1 recorded death because of H7N7) human infections resulting from occasional bird-to-human transmissions, with low pathogenic avian influenza strains (eg, subtypes H9N2, H7N7, H7N2, and H7N3) have been ongoing since 1997, when heightened surveillance for avian influenza viruses began (Fig. 2) . Analyses of the viruses that caused the 1957 and 1968 influenza pandemics therefore proved that zoonotic transmissions of influenza viruses (ie, from animals to man) with gene reassortment were capable of generating antigenically new influenza strains, novel to human immunity, with significant effects on the public health. cache = ./cache/cord-253143-73dsc6q3.txt txt = ./txt/cord-253143-73dsc6q3.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-254200-9bpdfxrt author = Barin, F. title = La sécurité virale des médicaments d’origine biologique date = 2008-06-30 pages = extension = .txt mime = text/plain words = 6497 sentences = 560 flesch = 61 summary = Résumé Les crises sanitaires survenues dans les années 1980 ont dramatiquement contribué à la prise de conscience des risques iatrogènes liés aux médicaments d'origine biologique et, ainsi, au développement du concept de sécurité virale de ces médicaments, qu'ils soient d'origine humaine, avec notamment les médicaments dérivés du sang (MDS), animale ou issus des biotechnologies (produits par des cellules eucaryotes). La sécurité virale des médicaments repose sur trois éléments : la qualité de la matière première, le procédé de fabrication qui inclue des étapes aptes à éliminer ou à inactiver les virus et, éventuellement, les contrôles des produits intermédiaires ou finis. L'objectif des études de validation virale est de fournir des éléments tangibles, concrets, démontrant que telle ou telle étape permet effectivement d'éliminer ou d'inactiver tel ou tel type de virus, susceptible de contaminer spécifiquement la matière première (par exemple, VIH, VHC ou parvovirus B19 pour le plasma) ou représentatif de familles non encore impliquées dans des contaminations liées aux produits sanguins. cache = ./cache/cord-254200-9bpdfxrt.txt txt = ./txt/cord-254200-9bpdfxrt.txt === reduce.pl bib === id = cord-252725-e3pazjdi author = Khalil, Ayman title = The upshot of Polyphenolic compounds on immunity amid COVID-19 pandemic and other emerging communicable diseases: An appraisal date = 2020-10-15 pages = extension = .txt mime = text/plain words = 8759 sentences = 338 flesch = 30 summary = In fact, several studies and clinical trials increasingly proved the role of polyphenols in controlling numerous human pathogens including SARS and MERS, which are quite similar to COVID-19 through the enhancement of host immune response against viral infections by different biological mechanisms. Actually, data indicated that activation of the nuclear factor (NF)-κB transcription factor (NF-κB) signaling pathway represents a major contribution to the inflammation induced post SARS-CoV infection and that NF-κB inhibitors are promising antiviral drugs against infections caused by the virus and potentially other pathogenic human coronaviruses [8] . Moreover, it was found to reduce the reactive oxygenated species (ROS) produced during viral infection and subsequently decrease pro-inflammatory markers such as IL-8, TNF-α, IL-1β and IL-6 [25] and increases anti-inflammatory cytokines such as IL-10 [35] , indicating that it has clear antiviral effects on several respiratory and common cold viruses through its ability to reduce virus imputation, replication and viral load in vitro, as well as lung inflammation and airways hyper-responsiveness in vivo [29] . cache = ./cache/cord-252725-e3pazjdi.txt txt = ./txt/cord-252725-e3pazjdi.txt === reduce.pl bib === id = cord-253705-utp8po48 author = Sriwilaijaroen, Nongluk title = Sialoglycovirology of Lectins: Sialyl Glycan Binding of Enveloped and Non-enveloped Viruses date = 2020-04-19 pages = extension = .txt mime = text/plain words = 20192 sentences = 863 flesch = 46 summary = While HEF glycoproteins of influenza C and D viruses attach to 9-O-acetyl-Neu5Accarrying sugar chains found in the respiratory tract of animals [31] as a receptor determinant for infection in cattle and pigs (only C virus has been detected in humans), HAs of influenza A (Fig. 3a) and B viruses recognize α2-6Neu5Ac-carrying sugar chains and Fig. 3 (continued) σ1 containing a Sia-binding site in its body) interacts with a sialoglycan on a glycoprotein/ glycolipid (a brown dash), which is anchored to the host cell membrane. Variants with the HE gene, which have become circulating strains, could be explained by the finding that the HE protein increases the efficiency of production of infectious virus [78] possibly by acting as a lectin for enhancing viral binding and as an enzyme that destroys receptors by de-O-acetylation (esterase) for enhancing release of trapped virions from the host mucosa and of budding virions from infected cells. cache = ./cache/cord-253705-utp8po48.txt txt = ./txt/cord-253705-utp8po48.txt === reduce.pl bib === id = cord-252769-fe50u028 author = Mendes, J. Pinto title = Infecção na modulaçâo da asma 1 1 Trabalho apresentado no XXIII Congresso de Pneumologia da SPP – Guarda, Novembro 2007 / Paper presented at the XXIII Congresso de Pneumologia da SPP / PSP Pulmonology Congress, Guarda, November 2007 date = 2008-10-31 pages = extension = .txt mime = text/plain words = 14003 sentences = 964 flesch = 56 summary = Animal research is difficult to extrapolate to man but suggests RSV can induce allergic sensitisation 28 , increase bronchial and interleukin (IL)-13 hyperresponsiveness, and rão, na maioria dos casos, consequências remotas, embora algumas vezes descrevam sibilâncias que irão desaparecer aos 3 -5 anos e só raramente se prolongam, instalando -se ou não uma asma. This phenomenon has been put to the test in inhalatory challenge tests which could bring on asthma episodes or exacerbations in children and adults 82, 102 , but, to test this seeming paradox, it is not necessary to resort to these arguments as in a German study 82 , the degree of early life exposure to domestic endotoxins was in direct correla-Infecção na modulaçâo da asma J Pinto Mendes fende um efeito daquelas células na supressão simultânea das respostas Th 1 e Th 2 . cache = ./cache/cord-252769-fe50u028.txt txt = ./txt/cord-252769-fe50u028.txt === reduce.pl bib === id = cord-232446-vvb2ffhv author = Mongia, Aanchal title = A computational approach to aid clinicians in selecting anti-viral drugs for COVID-19 trials date = 2020-07-03 pages = extension = .txt mime = text/plain words = 7123 sentences = 382 flesch = 47 summary = In view to assist acceleration of this process (by pruning down the search space), we create and share a publicly available DVA database, along with a number of matrix completion techniques (mentioned above) for drug-virus association prediction. Such a computational approach requires the chemical structure of the drugs and, in case of graph-regularized matrix completion techniques, the genome of the viruses, or existing associations otherwise. A clear observation from the experiments is that the graph regularized-based matrix completion algorithms that incorporate the similarity information associated with the drugs and viruses, perform fairly well giving an AUC greater or equal than 0.83 in CV1. It can be noted that the standard matrix completion methods, which do not take into account the metadata, fail to learn from the association data giving a near-random performance as far as the prediction on novel viruses is concerned, depicting how very important the similarity information is. cache = ./cache/cord-232446-vvb2ffhv.txt txt = ./txt/cord-232446-vvb2ffhv.txt === reduce.pl bib === id = cord-252871-qfrpuy3t author = Nasir, Arshan title = Investigating the Concept and Origin of Viruses date = 2020-11-03 pages = extension = .txt mime = text/plain words = 5153 sentences = 298 flesch = 46 summary = We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution. We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution. In turn, the origin of archaeoviruses from Archaea, bacterioviruses from Bacteria, and eukaryoviruses from Eukarya also seems less likely as these viruses share several conserved protein folds involved in virion synthesis and other functions, indicating that they may have evolved prior to the diversification of LUCA into modern cells. cache = ./cache/cord-252871-qfrpuy3t.txt txt = ./txt/cord-252871-qfrpuy3t.txt === reduce.pl bib === id = cord-253466-7gpije5d author = Netherton, Christopher title = A Guide to Viral Inclusions, Membrane Rearrangements, Factories, and Viroplasm Produced During Virus Replication date = 2007-08-31 pages = extension = .txt mime = text/plain words = 26372 sentences = 1363 flesch = 45 summary = Significantly, Poliovirus infection causes enrichment of GEFs in membranes containing replicase proteins, and this would provide a mechanism for increasing levels of Arf1-GTP at sites of virus replication. There is evidence that Tobacco mosaic virus also uses the ER as a site of replication because the replicase enzyme and viral RNA are located on the ER of infected cells, and infection causes major changes in ER morphology (Reichel and Beachy, 1998) , including ER aggregation and formation of lamella structures. Even though these viruses infect a diverse range of hosts from different phyla, including vertebrates [poxviruses, African swine fever virus (ASFV)], arthropods (entomopox, ASFV, chloriridoviruses), amphibians and fish (Ranavirus, Megalocytivirus, and Lymphocystivirus genera of the Iridoviridae family), marine algae (phycodnaviruses), and protozoa (mimivirus), they all generate cytoplasmic factories as major sites of virus assembly and replication (illustrated in Fig. 4 ). Formation of DNA replication structures in herpes virus-infected cells requires a viral DNA binding protein cache = ./cache/cord-253466-7gpije5d.txt txt = ./txt/cord-253466-7gpije5d.txt === reduce.pl bib === id = cord-254932-b447w202 author = Panda, Aruna title = Role of fusion protein cleavage site in the virulence of Newcastle disease virus date = 2003-11-18 pages = extension = .txt mime = text/plain words = 5550 sentences = 259 flesch = 53 summary = The genetic stability of the mutations introduced into the genome of LaSota V.F. virus was determined by sequence analysis of the RT-PCR fragment that covered the region of the F protein cleavage site of the mutant virus that was passed five times in 9-day-old chicken embryos, and also from the mutant virus that was passaged once in chicken brains. These results demonstrated that the efficiency of cleavage of the F protein plays an important role if the NDV is delivered directly into the brains of chicks, but there could be other viral factors that probably affect peripheral replication, viremia, or entry into the central nervous system. These results demonstrated that the efficiency of cleavage of the F protein plays an important role if the NDV is delivered directly into the brains of chicks, but there could be other viral factors that probably affect peripheral replication, viremia, or entry into the central nervous system. cache = ./cache/cord-254932-b447w202.txt txt = ./txt/cord-254932-b447w202.txt === reduce.pl bib === id = cord-252147-bvtchcbt author = Domingo-Espín, Joan title = Engineered Biological Entities for Drug Delivery and Gene Therapy: Protein Nanoparticles date = 2011-11-15 pages = extension = .txt mime = text/plain words = 17193 sentences = 888 flesch = 39 summary = Modular protein engineering, virus-like particles (VLPs), and other self-assembling entities are envisioned as modulatable novel protein nanoparticles able to include many desirable properties in the correct delivery of drugs and nucleic acids. 120 Modular fusion proteins that combine distinct functions required for cell type-specific uptake and intracellular delivery of DNA or drugs present an attractive approach for the development of self-assembling vectors for targeted gene or drug delivery. 215, 216 Although VLP-based vaccines have been primarily developed for their use against the corresponding virus, in the last decades genetic engineering or chemical modifications have been applied in order to generate chimeric VLPs. Thus, on the one hand, commonly short heterologous peptide epitopes or full proteins that are unable to form VLPs or that are unsafe for vaccination have been presented on surface-exposed loops or fused to N-or C-exposed termini of structural viral capsid proteins on VLPs. 154, 161, 210 Different HPV, 217-219 HBV, 220,221 parvovirus, 222, 223 and chimeric polyoma VLPs have been engineered 170, 175 and tested for different applications including vaccination against viral or bacterial diseases, against virus-induced tumors, and more recently, for immunotherapy of nonviral cancer. cache = ./cache/cord-252147-bvtchcbt.txt txt = ./txt/cord-252147-bvtchcbt.txt === reduce.pl bib === id = cord-254090-x8tnweih author = Yang, Szu-Chi title = Efficient Structure Resonance Energy Transfer from Microwaves to Confined Acoustic Vibrations in Viruses date = 2015-12-09 pages = extension = .txt mime = text/plain words = 6073 sentences = 302 flesch = 53 summary = It is interesting to notice that the required threshold electric field magnitudes at the resonant frequency (86.9 V/m) to fracture H3N2 viruses as shown in Fig. 3 (c) are within the IEEE Microwave Safety Standard (106 V/m), indicating high SRET efficiency, even though the quality factor of the H3N2 virus is low. To further investigate the efficiency of this SRET effect from microwave to virus and the threshold effect, we further measured the inactivation ratio of H3N2 virus with different power densities at the resonant frequency ~8 GHz of the confined acoustic dipolar mode. Second, at the resonant frequency, we do observe H3N2 virus inactivation by illuminating 82 W/m 2 (lower than the IEEE safety standard in public space) 8 GHz microwaves on our viral solution, corresponding to an average 87 V/m electric field intensity inside the solution, confirming that our proposed simple model to estimate the field threshold (86.9 V/m) to structurally fracture the virus is quantitatively correct, especially combining the observed threshold effect as discussed above. cache = ./cache/cord-254090-x8tnweih.txt txt = ./txt/cord-254090-x8tnweih.txt === reduce.pl bib === id = cord-255075-6azu6k3h author = Zhuang, Jianjian title = Advanced “lab-on-a-chip” to detect viruses – Current challenges and future perspectives date = 2020-05-12 pages = extension = .txt mime = text/plain words = 3141 sentences = 230 flesch = 49 summary = Multiplexed efficient on-chip sample preparation 613 and sensitive amplification-free detection of Ebola virus A bead-based 689 immunofluorescence-assay on a microfluidic dielectrophoresis platform for rapid dengue virus 690 detection Fast and Parallel Detection of Four Ebola Virus Species on a Microfluidic-Chip-Based Portable 770 An integrated self-driven microfluidic device for rapid 781 detection of the influenza A (H1N1) virus by reverse transcription loop-mediated isothermal 782 amplification Paper-based RNA detection and 785 multiplexed analysis for Ebola virus diagnostics Multiplex microfluidic paper-based 805 immunoassay for the diagnosis of hepatitis C virus infection Simultaneous and automated detection of influenza A virus hemagglutinin H7 and H9 based on 965 magnetism and size mediated microfluidic chip A 1026 point of care platform based on microfluidic chip for nucleic acid extraction in less than 1 minute D: Schematic of a 1149 paper-based chip for the detection of HIV developed by Li et al. cache = ./cache/cord-255075-6azu6k3h.txt txt = ./txt/cord-255075-6azu6k3h.txt === reduce.pl bib === id = cord-254592-wa5il5go author = Brierley, Liam title = Tissue tropism and transmission ecology predict virulence of human RNA viruses date = 2019-11-26 pages = extension = .txt mime = text/plain words = 5887 sentences = 269 flesch = 37 summary = To quantify the effects of the most informative risk factors, averaged partial dependence was extracted from the random forests, describing the marginal predicted probabilities of severe virulence associated with each virus trait (Fig 4, S2 Table) . Predicted probability of classifying virulence as 'severe' for each of the most informative risk factors in random forest models applied to all known human RNA viruses and zoonotic viruses only (primary tissue tropism, any known neural tropism, any known renal tropism, level of human-to-human transmissibility, primary transmission route, and any known vector-borne transmission). In both classification tree and random forest models, viruses were more likely to be predicted to cause severe disease if they caused systemic infections, had neural or renal tropism, transmitted via direct contact or respiratory routes, or had limited capability to transmit between humans (0 < R 0 � 1). cache = ./cache/cord-254592-wa5il5go.txt txt = ./txt/cord-254592-wa5il5go.txt === reduce.pl bib === id = cord-255026-fdp6mies author = Belák, Sándor title = Molecular diagnosis of viral diseases, present trends and future aspects: A view from the OIE Collaborating Centre for the Application of Polymerase Chain Reaction Methods for Diagnosis of Viral Diseases in Veterinary Medicine date = 2007-07-26 pages = extension = .txt mime = text/plain words = 5342 sentences = 225 flesch = 40 summary = The experiences of an OIE-Collaborating Centre and of two EU project consortia are summarised on the diagnostic application of gel-based PCR, general PCR systems, phylogeny, molecular epidemiology, real-time PCR (TaqMan, Molecular Beacons, Primer-Probe Energy Transfer), amplification without thermocycling (Invader), multiplex PCR, nucleic acid extraction and pipetting robotics, automation and quality control, including internal controls. cache = ./cache/cord-255026-fdp6mies.txt txt = ./txt/cord-255026-fdp6mies.txt === reduce.pl bib === id = cord-255479-yd5cbwnx author = Vu, David M. title = Chikungunya Virus date = 2017-06-30 pages = extension = .txt mime = text/plain words = 4097 sentences = 232 flesch = 45 summary = Anti-CHIKV antibodies directed against the envelope protein that neutralize the virus in vitro also protect neonatal mice from lethal CHIKV infection in vivo, suggesting that these proteins may be important antigenic lethal targets for development of naturally acquired, or vaccine-elicited protection. Stedman, who reported this "anomalous disease" called "dandy fever" by local residents, noted that the illness "attacked almost every individual in the town," had "extremely low mortality," and was associated with "pains in the joints for weeks after recovery from the acute stage," which were key differences between the 1827 and 1828 West Indies epidemic and previous descriptions of a "break-bone fever" (referring to modern-day dengue fever). For diagnostic confirmation of current and recent infection, a molecular test (typically polymerase chain reaction [PCR]) for the virus and an assay for the presence of specific IgM antibody are required. cache = ./cache/cord-255479-yd5cbwnx.txt txt = ./txt/cord-255479-yd5cbwnx.txt === reduce.pl bib === id = cord-254527-zddwajzg author = Junter, Guy-Alain title = Polysaccharide-based chromatographic adsorbents for virus purification and viral clearance date = 2020-01-13 pages = extension = .txt mime = text/plain words = 16940 sentences = 907 flesch = 42 summary = Table 2 gathers a variety of packed-bed column chromatography procedures applied to viral particle purification in which the stationary phase consists of AG -essentially Sepharose® ("Separation-Pharmacia-AG"; GE Healthcare, Chicago, Ill.) (Seph) -or CELe.g., Cellufine™ (JNC Corporation, Tokyo, Japan) -gel beads, modified to fulfill varying separation modes, i.e., ion exchange, size exclusion and affinity (Table 3 [77] [78] [79] [80] [81] ). For instance, the purification process for Nuwiq®, a recombinant coagulation factor VIII (a blood-clotting protein whose deficiency is associated with hemophilia A) patented by Octapharma AG (Lachen, Switzerland) [195] , includes solvent/detergent (S/D) treatment, Planova NF, and five chromatography steps using PS-based stationary phases, i.e., MMC (Capto MMC), CEC (SP Seph FF), AFC (VIIISelect, a Capto matrix with factor VIIIselective ligand), AEC (Q Seph FF) and SEC (Superdex 200). cache = ./cache/cord-254527-zddwajzg.txt txt = ./txt/cord-254527-zddwajzg.txt === reduce.pl bib === id = cord-253825-d9borky8 author = Blaising, Julie title = Arbidol as a broad-spectrum antiviral: An update date = 2014-04-24 pages = extension = .txt mime = text/plain words = 8757 sentences = 431 flesch = 44 summary = ARB has been shown to display antiviral in vitro and/or in vivo activity against a number of enveloped or non-enveloped RNA or DNA viruses, including influenza viruses A, B and C , respiratory syncytial virus, SARS-CoV, adenovirus, parainfluenza type 5, poliovirus 1, rhinovirus 14, coxsackievirus B5, hantaan virus, Chikungunya virus, HBV and HCV [reviewed in Boriskin et al. Shi and coworkers showed a greater inhibitory effect on influenza A H1N1 when ARB was added before infection or when it was pre-incubated with the virus (Shi et al., 2007) , suggesting that membrane impregnation and/or metabolites could underlie ARB antiviral activity (see Section 6.). Recently, Tannock and coworkers reported a potent antiviral activity of ARB on several virus families responsible of respiratory infections in animals and humans, in particular on influenza A H3N2 (IC50 12 lM), and the non-enveloped Picornaviridae poliovirus 1 and rhinovirus 14 (Brooks et al., 2012 ; see also Brooks et al., 2004) . cache = ./cache/cord-253825-d9borky8.txt txt = ./txt/cord-253825-d9borky8.txt === reduce.pl bib === id = cord-254194-962vynwk author = Galdiero, Stefania title = Silver Nanoparticles as Potential Antiviral Agents date = 2011-10-24 pages = extension = .txt mime = text/plain words = 10034 sentences = 447 flesch = 38 summary = Silver nanoparticles have mainly been studied for their antimicrobial potential against bacteria, but have also proven to be active against several types of viruses including human imunodeficiency virus, hepatitis B virus, herpes simplex virus, respiratory syncytial virus, and monkey pox virus. Theoretically, any metal could be analysed for antiviral activity, however, little effort has been done to determine the interactions of metal nanoparticles with viruses, and only recently some studies have emerged showing that metal nanoparticles can be effective antiviral agents against HIV-1 [37] [38] [39] [40] , hepatitis B virus [41] , respiratory syncytial virus [42] , herpes simplex virus type 1 [43, 44] , monkeypox virus [45] , influenza virus [46] and Tacaribe virus [47] . cache = ./cache/cord-254194-962vynwk.txt txt = ./txt/cord-254194-962vynwk.txt === reduce.pl bib === id = cord-252974-pwx27kdi author = Fornek, Jamie L. title = Use of Functional Genomics to Understand Influenza–Host Interactions date = 2007-08-31 pages = extension = .txt mime = text/plain words = 6755 sentences = 331 flesch = 42 summary = We will explore increasingly complex models for studying influenza-host interactions using functional genomics, including cell culture systems, murine models of infection, and nonhuman primates (Fig. 1) . These studies, led by John Kash, revealed that genes related to various immune cells, notably NK cells, neutrophils, macrophages, and T helper 1 (Th1) cells, were upregulated in mice infected with the fully reconstructed 1918 virus as early as 1 day postinfection. To expand upon the above study, we have also employed functional genomics to assess the effect of influenza infection on the early innate immune response in the lungs of pigtailed macaques, how genes related to this response were regulated over time, and whether gene expression signatures of infection could also be detected in the blood. Global host immune response: Pathogenesis and transcriptional profiling of type A influenza viruses expressing the hemagglutinin and neuraminidase genes from the 1918 pandemic virus cache = ./cache/cord-252974-pwx27kdi.txt txt = ./txt/cord-252974-pwx27kdi.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 2708 sentences = 161 flesch = 44 summary = 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. e clinical presentation depends on the specific causative agent but typically includes fever and lower respiratory tract symptoms, such as tachypnoea, nonproductive cough, wheeze, and increased breath sound [7, 8] . In the present study, we used the xTAG RVP FAST assay to identify the viruses causing RI in children and the relationship between specific viruses and clinical outcome. We enrolled 194 pediatric infants (2-24 months old) who had lower respiratory tract infections and were treated at the Vietnam National Children's Hospital. Bronchiolitis was the most common clinical characteristic of lower respiratory tract infection at the Vietnam National Children's Hospital. cache = ./cache/cord-255623-qdpdsye9.txt txt = ./txt/cord-255623-qdpdsye9.txt === reduce.pl bib === id = cord-255137-utg8k7qs author = Yinda, Claude Kwe title = Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses date = 2019-01-23 pages = extension = .txt mime = text/plain words = 9528 sentences = 861 flesch = 51 summary = Previously, we identified a plethora of known and novel eukaryotic viruses in Cameroonian fruit bats using a viral metagenomics approach, including viruses known to cause gastroenteritis in humans (sapovirus, sapelovirus, and rotaviruses A and H) and Astroviridae (Mamastrovirus), Calciviridae (Sapovirus), Picornaviridae (Parechovirus), and Reoviridae (Rotavirus), viral families known to cause gastroenteritis in humans, were identified in both bat and human pools from the same region. In this study, we focused on viruses from which near-complete genomes were obtained, particularly those that are known to cause viral gastroenteritis (belonging to the Astroviridae, Caliciviridae [norovirus and sapovirus] , Picornaviridae [enterovirus, parechovirus, cosavirus] , Parvoviridae, Reoviridae, and Adenoviridae [human mastadenovirus]). Recently, we thoroughly investigated the gut virome of fruit bats from Cameroon (20) (21) (22) (23) 63) and showed the presence of many novel and divergent eukaryotic viral families, including viruses known to cause gastroenteritis in humans. cache = ./cache/cord-255137-utg8k7qs.txt txt = ./txt/cord-255137-utg8k7qs.txt === reduce.pl bib === id = cord-254963-cnvxlv6h author = Paskey, Adrian C. title = Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples date = 2019-02-26 pages = extension = .txt mime = text/plain words = 6201 sentences = 267 flesch = 45 summary = In order to test this newly expanded probe panel and to specifically assess the effect of hybridization-based viral enrichment on the sensitivity of HTS for detection of a single virus within a complex environmental sample, commercial bat guano was spiked with increasing concentrations of Influenza virus (IFV). As expected, a dose-dependent effect in the proportion of sequencing reads derived from IFV was observed as the number of spiked genome copies increased ( Fig. 1a and Additional file 1: Table S1 ), in both the unbiased shotgun sequence data as well as the virus enriched sequence data. Such limitations have been of particular concern for U.S. Department of Defense (DoD) laboratories tasked with biosurveillance and biodefense activities in regions with limited material resources and human We demonstrate here that hybridization-based viral target enrichment yields robust coverage of small genomes from clinical samples, even yielding full-length, deeply covered genomes at concentrations whereby Fig. 3 Detection of close relative viruses irrespective of extensive multiplexing. cache = ./cache/cord-254963-cnvxlv6h.txt txt = ./txt/cord-254963-cnvxlv6h.txt === reduce.pl bib === id = cord-252048-ftbjsoup author = McKinley, Enid T. title = Attenuated live vaccine usage affects accurate measures of virus diversity and mutation rates in avian coronavirus infectious bronchitis virus date = 2011-04-22 pages = extension = .txt mime = text/plain words = 6380 sentences = 309 flesch = 55 summary = The full-length genomes of 11 infectious bronchitis virus (IBV) field isolates from three different types of the virus; Massachusetts (Mass), Connecticut (Conn) and California (CAL) isolated over a 41, 25 and 8 year period respectively, were sequenced and analyzed to determine the mutation rates and level of polymorphisms across the genome. The genetic data also identified a recombinant IBV isolate with 7 breakpoints distributed across the entire genome suggesting that viruses within the same serotype can have a high degree of genetic variability outside of the spike gene. The objective of this study was to determine the levels of polymorphism across the entire genome of IBV isolates with similar spike genes and to examine the mutation rates for viruses with and without vaccine selection pressure. cache = ./cache/cord-252048-ftbjsoup.txt txt = ./txt/cord-252048-ftbjsoup.txt === reduce.pl bib === id = cord-254100-u6x5zd4i author = Taliansky, M.E. title = Involvement of the Plant Nucleolus in Virus and Viroid Infections: Parallels with Animal Pathosystems date = 2010-10-15 pages = extension = .txt mime = text/plain words = 13988 sentences = 662 flesch = 40 summary = An increasing number of reports reveal that similar to the proteins of animal viruses, many plant virus proteins localize in the nucleolus to divert host nucleolar proteins from their natural functions in order to exert novel role(s) in the virus infection cycle. An increasing number of reports reveal that similar to the proteins of animal viruses, many plant virus proteins localize in the nucleolus to divert host nucleolar proteins from their natural functions in order to exert novel role(s) in the virus infection cycle. As their name suggests, MPs are involved in virus spread in infected plants, and the potential role of fibrillarin in this process will be discussed in Section IV.B. The multifunctional PVA (potato virus A)-encoded viral genomelinked protein (VPg) is also able to interact with fibrillarin (Rajamäki and Bonfiglioli et al. cache = ./cache/cord-254100-u6x5zd4i.txt txt = ./txt/cord-254100-u6x5zd4i.txt === reduce.pl bib === id = cord-254890-4ynsgu6c author = Heldens, J.G.M. title = Veterinary vaccine development from an industrial perspective date = 2008-03-03 pages = extension = .txt mime = text/plain words = 9217 sentences = 443 flesch = 39 summary = Live vaccine: Low passage lot for safety (GLP) on target species including pregnant animals in case indication is required High passage lot for efficacy: Onset of immunity and duration of immunity Inactivated vaccine: High passage lot for safety (GLP) and efficacy Licensing batches (10% commercial scale, GMP) -Consistency of production, process validation -Transfer of production process and control tests to manufacturing departments and quality control departments -Stability studies on antigen and final product in final container Field studies (GCP) -Safety -Efficacy derived from treated animals from which food is derived, and the consumer. The likely approach to develop vaccines would be, first, the cloning and site directed mutagenesis to turn the HA-gene into a non-pathogenic form, and, second, the production of so-called high growth re-assortants producing considerable amounts of the new HA protein, which is, among others, the protective antigen in influenza virus. cache = ./cache/cord-254890-4ynsgu6c.txt txt = ./txt/cord-254890-4ynsgu6c.txt === reduce.pl bib === id = cord-255096-27dfbhsl author = Sweet, Michael J. title = Reprint of ‘Diseases in marine invertebrates associated with mariculture and commercial fisheries’ date = 2016-06-19 pages = extension = .txt mime = text/plain words = 18108 sentences = 1017 flesch = 52 summary = Interestingly, although there are countless examples of the spread of disease usually associated with transportation of specific infected hosts for development of aquaculture practices, this process appears to be continuing with no real sign of effective management and mitigation strategies being implicated. In this review, we are not listing all known diseases for the three main commercially important phyla/ sub-phyla and/or class (echinoderms, crustaceans and molluscs), but instead focus on those which likely pose a major threat and/or are infecting large populations of both wild and farmed organisms around the world. Hosts affected: Again, this disease predominantly occurs during the auricularia stages of development of many different sea cucumber species, with mortality being recorded as high as 90% in certain cases (Zhang et al., 2010) . Furthermore, diseases caused by Platyhelminthiasis have been shown to infect both aestivated juveniles (larger than 1 cm) and adults of many different sea cucumber species. cache = ./cache/cord-255096-27dfbhsl.txt txt = ./txt/cord-255096-27dfbhsl.txt === reduce.pl bib === id = cord-255217-l2ak5ygj author = Eccles, Ronald title = Why is temperature sensitivity important for the success of common respiratory viruses? date = 2020-08-10 pages = extension = .txt mime = text/plain words = 3861 sentences = 200 flesch = 40 summary = 34 It has been known for some time that human influenza viruses vary in their temperature sensitivity with those adapted to the cooler human airway causing mild disease and those adapted to higher temperatures causing more serious lower respiratory tract infections. 44, 45 The common cold syndrome is a mild disease because the respiratory viruses have a permissive temperature sensitivity close to that found in the human upper airways 30 C-34 C and a restrictive temperature sensitivity that conThe acquisition of temperature sensitivity is key to the success of a respiratory virus and this is well illustrated with emerging avian influenza H5N1. The temperature sensitivity of respiratory viruses should be considered as an important factor in determining their success as parasites of the human airway. Journal of clinical virology: the official publication of the Pan American Society for Clinical Virology cache = ./cache/cord-255217-l2ak5ygj.txt txt = ./txt/cord-255217-l2ak5ygj.txt === reduce.pl bib === id = cord-257064-iafm3pcc author = Kint, Joeri title = Quantification of Infectious Bronchitis Coronavirus by Titration In Vitro and In Ovo date = 2014-12-18 pages = extension = .txt mime = text/plain words = 1809 sentences = 156 flesch = 63 summary = During a titration assay, tissue cultures or embryonated eggs are incubated with tenfold serial dilutions of a virus containing sample and several days later the cytopathic effect is scored. The virus titer is defined as the reciprocal of the dilution at which 50 % of the inoculated embryos or tissue cultures show CPE. Passaging of IBV in either embryonated eggs or primary cell cultures leads to attenuation of the virus in vivo [10] [11] [12] . IBV strains which have been adapted to grow in cultures of primary chicken cells can be titrated on these cells using either the TCID 50 method or plaque titration. Virus titers in the original sample, expressed as 10 log EID 50 /ml are calculated using the method described by Spearman and Kaerber [6, 7] , using the following formula: Plaque formation by infectious bronchitis virus in chicken embryo kidney cell cultures Growth kinetics of embryo-and organ-culture adapted Beaudette strain of infectious bronchitis virus in embryonated chicken eggs cache = ./cache/cord-257064-iafm3pcc.txt txt = ./txt/cord-257064-iafm3pcc.txt === reduce.pl bib === id = cord-256325-q70rky3r author = Stewart, Cameron R. title = A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease date = 2017-07-04 pages = extension = .txt mime = text/plain words = 8310 sentences = 409 flesch = 43 summary = title: A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease Here we largely focus on findings from two recent RNAi screens to identify protein-coding genes and host-encoded microRNAs impacting the henipavirus infection cycle in human cells. X-ray data have suggested that the methylation of rRNA requires the formation of this complex with involvement of four fibrillarin molecules interacting with different regions of the target rRNAs. The yeast equivalent of fibrillarin, NOP1, has been more extensively studied than the human counterpart but fibrillarin is a well-conserved protein in most organisms, reinforcing the notion that all post-transcriptional processes involving fibrillarin such as chemical modification (methylation) of rRNA, pre-rRNA cleavage and ribosome assembly are essential for proper cellular functioning (Rodriguez-Corona et al. Deffrasnes and colleagues showed that siRNA-mediated knockdown of fibrillarin expression dramatically reduced HeV protein production and viral genome replication but did not impact viral fusion, and that fibrillarin catalytic activity was essential to henipavirus infection. cache = ./cache/cord-256325-q70rky3r.txt txt = ./txt/cord-256325-q70rky3r.txt === reduce.pl bib === id = cord-255697-trig04hd author = Cheng, Vincent Chi-Chung title = Viral Infections, an Overview with a Focus on Prevention of Transmission date = 2016-10-24 pages = extension = .txt mime = text/plain words = 6422 sentences = 301 flesch = 42 summary = Hand hygiene is always the core component of infection control measures in both community and hospitals to prevent the transmission of influenza A virus. Wearing face masks by either the index case as source control or the health-care workers as contacts has shown to be equally effective in the control of nosocomial transmission of pandemic influenza A H1N1 (Cheng et al., 2010) . Timely implementation of infection control measures by single room isolation of index case with strict contact precautions significantly reduced the incidence of hospital-acquired norovirus infection from 131 (baseline) to 16 cases per 1000 potentially infectious patient-days (P < 0.001) (Cheng et al., 2011) . When there is no highly effective antiviral for the treatment of a severe viral illness, especially in patients at the extremes of age or with medical comorbidities, and infection control measures are difficult to implement or comply with, vaccination is the final option to prevent massive outbreaks. cache = ./cache/cord-255697-trig04hd.txt txt = ./txt/cord-255697-trig04hd.txt === reduce.pl bib === id = cord-256837-100ir651 author = Smith, Steven B. title = Identification of Common Biological Pathways and Drug Targets Across Multiple Respiratory Viruses Based on Human Host Gene Expression Analysis date = 2012-03-14 pages = extension = .txt mime = text/plain words = 8447 sentences = 415 flesch = 38 summary = Several recent studies have generated multiple mRNA microarray gene expression datasets derived from experiments involving the infection of human cell-lines or animal models with one or more of the major respiratory viruses [21] [22] [23] . Through a systematic analysis of these respiratory virus-human host gene expression datasets, we determined common sets of genes and pathways involved in host responses to viral infections. A total of seven different respiratory viruses were analyzed, represented by fifteen unique Gene Expression Omnibus (GEO) datasets (indicated by GEO Series or GSE accession numbers), nine different human cell types, and seven different array platforms for a total of 28 unique comparisons. This assumption is based on the occurrence of genes that are differentially expressed in infection models for at least five of the seven respiratory viruses, have involvement in a number of relevant pathways related to host immune response, and encode for known drug targets. cache = ./cache/cord-256837-100ir651.txt txt = ./txt/cord-256837-100ir651.txt === reduce.pl bib === id = cord-256510-orr2roxz author = de Castro, Isabel Fernández title = Virus factories: biogenesis and structural design date = 2012-10-04 pages = extension = .txt mime = text/plain words = 5188 sentences = 259 flesch = 43 summary = For example, transmission electron microscopy (TEM) of cells infected with coxsackievirus showed intracellular organized lattices (Fig. 1E) , very similar to those assembled by the viral RNA polymerase in vitro (Kemball et al., 2010) close relationship between self-interaction and replication activity is reported for viral polymerases of other viruses such as FHV (Dye et al., 2005) , hepatitis C virus (Qin et al., 2002) and RUBV (Risco et al., 2012) . For viral genome replication, the virus first assembles cytoplasmic mini-nuclei with attached mitochondria (Tolonen et al., 2001) ; virus morphogenesis then starts an aggresome-like structure (Risco et al., 2002) , where immature viruses assemble using an atypical membrane remodelling mechanism that has been characterized by ET (Chlanda et al., 2009) . Although we are beginning to understand how replication organelles are assembled, information is still limited about how cell organelles are recruited, about the mechanisms of macromolecular transport between compartments, and about the signals that regulate the major structural changes in the factory during distinct stages in the virus life cycle. cache = ./cache/cord-256510-orr2roxz.txt txt = ./txt/cord-256510-orr2roxz.txt === reduce.pl bib === id = cord-257569-36qx1sy9 author = Hanada, Kousuke title = A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes date = 2004-06-17 pages = extension = .txt mime = text/plain words = 3460 sentences = 156 flesch = 43 summary = title: A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes In conclusion, the variation of mutation rates for RNA viruses is caused by different replication frequencies, which are affected strongly by the infection and transmission modes. First, we estimated the rates of synonymous substitution for 46 different species of RNA viruses except Puumala virus, human T-lymphotropic virus 1 (HTLV-1) and GB virus C/hepatitis G virus (HGV), using the time-serial sample data. This indicated that the transmission mode affected the replication frequency and that differences in the replication frequencies contributed to the variation of the rate of synonymous substitution for RNA viruses. Moreover, in the present study, we proved that the variation in the synonymous substitution rates among RNA viruses was caused by variation of the replication frequency, and that differences in the infection and transmission modes affected the variation of replication frequencies. cache = ./cache/cord-257569-36qx1sy9.txt txt = ./txt/cord-257569-36qx1sy9.txt === reduce.pl bib === id = cord-255181-du6rqc6i author = Louz, Derrick title = Cross‐species transfer of viruses: implications for the use of viral vectors in biomedical research, gene therapy and as live‐virus vaccines date = 2005-06-29 pages = extension = .txt mime = text/plain words = 8017 sentences = 425 flesch = 42 summary = This review addresses a number of potential risk factors and their implications for activities with viral vectors from the perspective of cross‐species transfer of viruses in nature, with emphasis on the occurrence of host‐range mutants resulting from either cell culture or tropism engineering. The HIV virus and contemporary human influenza viruses are prominent examples of viruses that have crossed the species barrier and established themselves permanently in the human population without further dependence on the presence of the original animal host reservoir. The emergence of HIV exemplifies how multiple independent cross-species transmissions of simian viruses that are not associated with disease in their natural hosts eventually resulted in the establishment of two types of HIV in the human population. The following examples demonstrate that upon persistent infection and passage in cell culture, cross-species transmissibility may be promoted by selection of virus variants with an altered host range. Adaptation in cell culture may result in changes in receptor specificity and tropism, and leads to the emergence of host-range mutant viruses. cache = ./cache/cord-255181-du6rqc6i.txt txt = ./txt/cord-255181-du6rqc6i.txt === reduce.pl bib === id = cord-255690-xc4bxin4 author = Rolain, Jean-Marc title = Recycling of chloroquine and its hydroxyl analogue to face bacterial, fungal and viral infections in the 21st century date = 2007-07-16 pages = extension = .txt mime = text/plain words = 7020 sentences = 351 flesch = 39 summary = Here we review available in vitro and in vivo data on the effects of CQ/HCQ on bacterial, fungal and viral infections, with the concept that manipulation of the intracellular pH in cells and modification of glycosylation of proteins by lysosomotropic agents instead of antimicrobial compounds is a powerful approach as new therapeutic strategies for the prevention and therapeutic management of several infectious diseases, including some of great public health concern worldwide. Coxiella burnetii [5, 13] Histoplasma capsulatum [24] HIV [2, [29] [30] [31] [32] ] Tropheryma whipplei [7, 8] Cryptococcus neoformans [15, 25] SARS-CoV [33, 34] Legionella pneumophila [11] Paracoccidioides brasiliensis [26] Influenza viruses [35] [36] [37] [38] Francisella tularensis [12] Penicillium marneffei [15, 27] Flavivirus, including yellow fever virus [39] Mycobacterium tuberculosis [14] Aspergillus fumigatus [28] Rubella virus [ tetracycline and quinolone regimen for at least 4 years, with a high percentage of relapses [6] . cache = ./cache/cord-255690-xc4bxin4.txt txt = ./txt/cord-255690-xc4bxin4.txt === reduce.pl bib === id = cord-257019-lj1yzjn0 author = ter MEULEN, V. title = Mechanisms and Consequences of Virus Persistence in the Human Nervous System date = 2006-12-16 pages = extension = .txt mime = text/plain words = 5189 sentences = 304 flesch = 44 summary = Virus penetration may result in acute encephalitis, but occasionally a persistent infection is established that leads to a fatal slowly progressing disease, subacute sclerosing panencephalitis (SSPE). However, virus expression may sometimes be rescued from this infected tissue by co-cultivation procedure^.'^ These experiments have therefore confirmed that measles virus is the etiological agent of SSPE and also indicated that virus persistence may be based on some defect in the virus maturation process that could involve some form of host effect. The case of PRP is an exception; infectious virus may be isolated directly despite a strong antibody response in both serum and CSF.M Similarly, the cell-mediated immune system does not show any specific deficien~y.*~.~' However, the site of rubella virus antigen expression has not yet been identified during this disease process. Similarly, chronic echovirus infection is associated with immune deficiency, and although inflammatory processes are observed in extraneural tissue, it seems unlikely that C N S damage is largely caused by virus-mediated cell destruction. cache = ./cache/cord-257019-lj1yzjn0.txt txt = ./txt/cord-257019-lj1yzjn0.txt === reduce.pl bib === id = cord-256917-6h1ip37z author = Habibi-Yangjeh, Aziz title = Review on heterogeneous photocatalytic disinfection of waterborne, airborne, and foodborne viruses: Can we win against pathogenic viruses? date = 2020-07-15 pages = extension = .txt mime = text/plain words = 4781 sentences = 262 flesch = 32 summary = suggested three mechanisms for viral disinfection in photocatalytic processes, which include physical damage of viruses, metal ion toxicity obtained from metal-including photocatalysts, and chemical oxidation by ROS generated over the photocatalysts [5] . Therefore, by considering the actual state of the review, this study focuses on a survey of the photocatalytic inactivation of waterborne, airborne, and foodborne viruses using semiconductor-assisted photocatalysis and the perspective of this important research field to tackle issues related to the spread of different viruses worldwide. In a research conducted by Kim and Jang [18] , the photocatalytic processes were investigated by V-UV with short illumination times to simultaneously disinfect MS2 as an airborne virus (nearly 90% disinfection efficiency at a VUV illumination time of 0.009 s) and remove the produced ozone toward an air inactivation system. After designing and fabricating more efficient photocatalysts, these photoactive materials could be used for inactivation of waterborne viruses in water decontamination plants and fabrication of more effective filters to disinfect airborne viruses. cache = ./cache/cord-256917-6h1ip37z.txt txt = ./txt/cord-256917-6h1ip37z.txt === reduce.pl bib === id = cord-255339-oudj079q author = Al-Tayib, Omar A. title = An Overview of the Most Significant Zoonotic Viral Pathogens Transmitted from Animal to Human in Saudi Arabia date = 2019-02-22 pages = extension = .txt mime = text/plain words = 15843 sentences = 712 flesch = 46 summary = The most important zoonotic viral diseases of which eight were diagnosed (in dead or diseased animals or through antibody detection) on the Arabian Peninsula over the last years include rabies, Middle East Respiratory Syndrome (MERS-CoV), influenza virus (IFV), Alkhurma hemorrhagic fever, Crimean-Congo hemorrhagic fever (CCHF), Rift Valley fever (RVF), West Nile fever (WNV), and dengue fever virus. The same WHO epidemiological data suggest that in these 22 countries including Saudi Arabia, in recent years, there has been report of steadily increasing number of sporadic human cases, incidence, and outbreaks of the virus [122] . Surprisingly, the current review showed that during an outbreak, each of these eight most zoonotic viruses (rabies, MERS-CoV, influenza, AHFV, CCHFV, RVFV, DHFV, and WNV) which occurred and/or cases confirmed in Saudi Arabia particularly from (Jeddah and/or Makkah) areas with at least one or all of these eight zoonotic viral pathogenic diseases [33, 44, 46, 78, [96] [97] [98] [99] 121, 130, 156, 171] . cache = ./cache/cord-255339-oudj079q.txt txt = ./txt/cord-255339-oudj079q.txt === reduce.pl bib === id = cord-255734-038xu4hq author = Taylor, Deborah R. title = Obstacles and advances in SARS vaccine development date = 2006-02-13 pages = extension = .txt mime = text/plain words = 5334 sentences = 263 flesch = 44 summary = 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. Spike-specific monoclonal and polyclonal antibodies that neutralize the virus have been developed [51, 52] and passive transfer of immune serum into naive mice protected them from infection with SARS-CoV [18] . Mice immunized with a plasmid containing the S protein produced anti-SARS-CoV IgG [64] and developed neutralizing antibodies and a T-cell mediated response resulting in a six-fold reduction in viral titer in the lungs [65] . Inactivation of the coronavirus that induces severe acute respiratory syndrome, SARS-CoV Severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice Immunization with modified vaccinia virus Ankara-based recombinant vaccine against severe acute respiratory syndrome is associated with enhanced hepatitis in ferrets cache = ./cache/cord-255734-038xu4hq.txt txt = ./txt/cord-255734-038xu4hq.txt === reduce.pl bib === id = cord-256036-gd53s4dv author = Sandmann, Lisa title = Barriers of hepatitis C virus interspecies transmission date = 2013-01-01 pages = extension = .txt mime = text/plain words = 7894 sentences = 373 flesch = 40 summary = In contrast to human hepatocytes, murine cells do not support HCV entry thereby creating a first and important barrier for a broader host tropism of the virus. Utilizing blocking antibodies specific to CD81 or the viral envelope protein E2, expression of entry factor mutants and mice with a targeted disruption of the SCARB1 gene validated uptake of HCV into murine hepatocytes in an HCV glycoprotein-mediated fashion. Taking advantage of the high mutational plasticity of HCV, three adaptive mutations in the viral glycoproteins E1 and E2 were identified that allowed the virus to enter cells expressing human SCARB1, CLDN1, OCLN and mouse CD81. Recently, a genetically humanized mouse model was constructed utilizing cell culture produced recombinant hepatitis C virus to activate a cellular encoded reporter (Dorner et al., 2011, in press ). Human occludin is a hepatitis C virus entry factor required for infection of mouse cells A humanized mouse model to study Hepatitis C virus infection, immune response, and liver disease cache = ./cache/cord-256036-gd53s4dv.txt txt = ./txt/cord-256036-gd53s4dv.txt === reduce.pl bib === id = cord-256370-cz88t29n author = Jansen van Vuren, Petrus title = Isolation of a Novel Fusogenic Orthoreovirus from Eucampsipoda africana Bat Flies in South Africa date = 2016-02-29 pages = extension = .txt mime = text/plain words = 5529 sentences = 263 flesch = 49 summary = This is the first report on isolation of an orthoreovirus from an arthropod host associated with bats, and phylogenetic and sequence data suggests that MAHLV constitutes a new species within the Orthoreovirus genus. Maximum Likelihood trees were prepared using amino acid sequences of all open reading frames from all segments, showing the placement of Mahlapitsi virus (MAHLV) in the Orthoreovirus genus relative to other viruses in this genus for which sequence is available on Genbank. A Maximum Likelihood tree, constructed with nucleic acid sequence data for the RNA-dependent RNA polymerase (RdRp) encoding segments of representative viruses from the different genera within Reoviridae (Figure 7) shows the placement of both isolates amongst other orthoreoviruses in the family. Maximum Likelihood trees were prepared using the deduced amino acid sequences from the open reading frames (ORF's) of all the virus' segments and those of other viruses in the Orthoreovirus genus (Figures 8-10) . cache = ./cache/cord-256370-cz88t29n.txt txt = ./txt/cord-256370-cz88t29n.txt === reduce.pl bib === id = cord-257321-l1swyr6g author = Chen, Lihong title = DRodVir: A resource for exploring the virome diversity in rodents date = 2017-05-20 pages = extension = .txt mime = text/plain words = 3249 sentences = 161 flesch = 45 summary = The database currently covers 7690 sequences from 5491 rodent-associated mammal viruses of 26 viral families detected from 194 rodent species in 93 countries worldwide. As a data application example, we further compared the current status of rodent-associated viruses with bat-associated viruses to highlight the necessity for including additional host species and geographic regions in future investigations, which will help us achieve a better understanding of the virome diversities in the two major reservoirs of emerging zoonotic infectious diseases. To facilitate online data analysis, two visualization tools are integrated into the result table: i) a statistical pie chart is available with a single click on the column title of virus family, rodent species/family, sample type and sampling country (Fig. 2B) ; ii) a global map with indicative markers is provided for the column of sampling country to better illustrate the geographic distribution of the rodent-associated viruses (http://www.mgc.ac. cache = ./cache/cord-257321-l1swyr6g.txt txt = ./txt/cord-257321-l1swyr6g.txt === reduce.pl bib === id = cord-258489-pyfc7jde author = Lico, Chiara title = Viral vectors for production of recombinant proteins in plants date = 2008-03-10 pages = extension = .txt mime = text/plain words = 11091 sentences = 527 flesch = 39 summary = In this review, we will focus on transient production strategies using plant viral expression systems, with a particular focus on the variety of proteins produced, and their applications. The unique properties of viruses such as ease of manipulation, high level amplification, site specific recombination, strong infectivity, enhanced translation and compact and repetitive morphological structure have enabled their broad application, from basic research to product development, including the generation of robust expression systems. From the discovery of viruses in 1898 (tobacco mosaic virus, TMV) (Bos, 1999) , to the first demonstration of RNAs role in virus replication by turnip yellow mosaic virus (TYMV) (Matthews, 1989) , to the very recent discovery of gene silencing and its implication in host response to infection, gene regulation and transgene expression (Baulcombe, 1999; Lu et al., 2003; Waterhouse and Helliwell, 2003) , plant virology has played a crucial role in the understanding of the most fundamental concepts of modern biology. Thanks to the recent improvements of viral-based vectors, mAbs have been produced with transient expression systems to quickly achieve much higher production levels along with other complex proteins. cache = ./cache/cord-258489-pyfc7jde.txt txt = ./txt/cord-258489-pyfc7jde.txt === 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-257163-hodykbcb author = Sanz, Ivan title = Viral Etiology of Chronic Obstructive Pulmonary Disease Exacerbations during the A/H1N1pdm09 Pandemic and Postpandemic Period date = 2015-05-07 pages = extension = .txt mime = text/plain words = 3825 sentences = 176 flesch = 44 summary = During the study period (2009–2012), respiratory viruses were identified in 48.7% of samples, and the proportion of viral detections in AE-COPD was higher in patients aged 30–64 years than ≥65 years. Studies conducted before emergence of the pandemic H1N1pdm09 strain showed that half of all AE-COPD cases were associated with viral infections and that picornaviruses (especially human rhinovirus and enterovirus (HREV)) were the dominant viral pathogens diagnosed in these patients [15, 16] . The aim of this study is to describe the etiological characteristics of respiratory viruses linked to COPD exacerbations after a singular pandemic period caused by a new influenza virus. We used the OR to analyze the probability of detection of viral categories (ORP, HREV, any influenza virus, and RSV) as well as viral coinfections in AE-COPD patients among different demographic and epidemiological characteristics such as gender, age groups, and the different periods analyzed. cache = ./cache/cord-257163-hodykbcb.txt txt = ./txt/cord-257163-hodykbcb.txt === reduce.pl bib === id = cord-259505-7hiss0j3 author = Kong, Qingming title = Proteomic analysis of purified coronavirus infectious bronchitis virus particles date = 2010-06-09 pages = extension = .txt mime = text/plain words = 6907 sentences = 355 flesch = 44 summary = It is an important prerequisite for the functional studies to know the protein composition of the purified viral particles, as it allows the analysis of specific proteins and their roles during the virus life cycle, resulting in better understanding of the infection process and the pathogenesis of viruses. To date, there have been no reports about TENP associated with virus, but it's an enriched and abundant protein identified in purified infectious bronchitis particles which suggests to us that it may be a requisite host protein in IBV life cycles. The present study 1) provides the first proteomic analysis of infectious bronchitis particles, 2) establishes the most comprehensive proteomic index of IBV and 3) shows that most of the virion incorporated host proteins have central roles in virus life cycle. cache = ./cache/cord-259505-7hiss0j3.txt txt = ./txt/cord-259505-7hiss0j3.txt === 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-257255-n5o368ih author = Barker, J. title = Spread and prevention of some common viral infections in community facilities and domestic homes date = 2001-12-21 pages = extension = .txt mime = text/plain words = 9238 sentences = 459 flesch = 48 summary = Amongst health care professionals there is growing awareness that improved standards of hand, surface and air hygiene in community settings could do much to prevent the spread of viral infections within these environments. In a preschool daycare centre, respiratory and gastrointestinal infections decreased following implementation of measures which included reinforcing existing handwashing procedures and education of staff and families on issues of infection control including environmental surface cleaning and disinfection and disinfection of toys (Krilov et al. Nevertheless, overall, there is convincing circumstantial evidence to suggest that improved standards of hygiene can have a signi®cant impact in reducing the rates of respiratory, intestinal and other viral infections in childcare facilities, domestic homes, hospitals and adult care centres and the circulation of infections between these communities. Potential role of hands in the spread of respiratory viral infections Ð studies with human parain¯uenza virus 3 and rhinovirus 14 cache = ./cache/cord-257255-n5o368ih.txt txt = ./txt/cord-257255-n5o368ih.txt === reduce.pl bib === id = cord-258333-jmk8hdk2 author = Sivier, V title = Place des viroses respiratoires dans les hyperthermies de sujets âgés hospitalisés au cours d’une saison hivernale date = 2001-12-10 pages = extension = .txt mime = text/plain words = 2657 sentences = 232 flesch = 59 summary = Sur les 129 malades ayant présenté une hyperthermie, 12 décès ont été observés, soit un taux de mortalité de 9,3 % : un décès dans le groupe « virose respiratoire » par surinfection bactérienne pulmonaire, sept décès dans le groupe « infection respiratoire non virale » (un choc septique, cinq décompensations respiratoires aiguës, une décompensation cardiaque aiguë) et quatre décès dans le groupe « autre » (deux cancers en phase terminale, un accident vasculaire cérébral et une cause indéterminée). L'épidémie nosocomiale de virus respiratoire syncytial est survenue dans un service de long séjour avec des locaux communs et exigus, chez des patients porteurs de multiples maladies et souvent déments. En conclusion, les infections respiratoires, qu'elles soient virales, bactériennes ou non documentées, apparaissent comme la principale cause d'hyperthermie chez le sujet âgé institutionnalisé pendant la saison hivernale et sont à l'origine de nombreuses complications, voire de décès. cache = ./cache/cord-258333-jmk8hdk2.txt txt = ./txt/cord-258333-jmk8hdk2.txt === reduce.pl bib === id = cord-257553-479x7av6 author = Kortepeter, Mark G. title = Health Care Workers and Researchers Traveling to Developing-World Clinical Settings: Disease Transmission Risk and Mitigation date = 2010-12-01 pages = extension = .txt mime = text/plain words = 3967 sentences = 217 flesch = 39 summary = title: Health Care Workers and Researchers Traveling to Developing-World Clinical Settings: Disease Transmission Risk and Mitigation This review provides practical advice for this special population of travelers, targeted to specific health care-related risks (needlestick, hemorrhagic fever viruses, severe viral respiratory disease, and tuberculosis), with suggestions for risk mitigation. Although no prophylaxis for hepatitis C virus (HCV) exposure exists, the needlestick transmission risk is lower (1.8%), and up to 20% of transmitted infections resolve spontaneously. The Centers for Disease Control and Prevention (CDC) recommends a 3-drug PEP regimen if the source patient is known to be infected with HIV and the source device is a hollow-bore needle or has visible blood contamination. During the pandemic, transmission to HCWs occurred after close, unprotected contact with symptomatic persons and was significantly mitigated once infection-control precautions were implemented; the degree of risk was related to the type and intensity of exposure (endotracheal intubation was significantly associated with contracting SARS) [27, 28] . cache = ./cache/cord-257553-479x7av6.txt txt = ./txt/cord-257553-479x7av6.txt === reduce.pl bib === id = cord-259458-o2yts5pq author = O’Grady, Kerry‐Ann F. title = Successful application of a simple specimen transport method for the conduct of respiratory virus surveillance in remote Indigenous communities in Australia date = 2011-03-21 pages = extension = .txt mime = text/plain words = 3636 sentences = 176 flesch = 49 summary = This study assessed the sensitivity of a simple method for transporting respiratory samples from a remote setting for viral PCR compared with frozen specimens. To inform the design of surveillance and intervention studies addressing respiratory infections in remote communities, we compared the sensitivity of a simple, cost-efficient method for transporting respiratory samples from a remote setting for viral real-time PCR with transport using frozen specimens. Given the sensitivity and specificity of real-time PCR diagnosis, we considered a specimen from either nostril positive for any virus to represent a true-positive, similar to previous studies (Lambert et al. Determining the aetiology and burden of viral respiratory infections in remote communities has to date been limited by the inability to store and transport clinical specimens requiring freezing ⁄ refrigeration to urban laboratories. We propose that this method, combining standard clinic refrigeration and weekly surface mailing of specimens combined with real-time PCR, can be used for viral respiratory research in remote locations. cache = ./cache/cord-259458-o2yts5pq.txt txt = ./txt/cord-259458-o2yts5pq.txt === reduce.pl bib === id = cord-259627-8stewshp author = Huang, Qing title = Inactivation of dengue virus by methylene blue/narrow bandwidth light system date = 2004-12-02 pages = extension = .txt mime = text/plain words = 2690 sentences = 132 flesch = 47 summary = Because photodynamic virus inactivation with methylene blue (MB)/light system has proven effective in blood banking, MB was selected as a photosensitizing agent, dengue virus as a model virus for enveloped RNA viruses, and an in-house fabricated narrow bandwidth light system overlapping the absorption spectrum of MB as the light source. Results showed that the concentration of MB working solution, illumination intensity of light source, illumination distance and time were four key factors affecting efficiency of virus inactivation using the MB/narrow bandwidth light system. The results indicate that MB concentration, illumination time and distance are three key factors affecting efficiency of virus inactivation when the illumination intensity of the light source was held constant. MB working concentration and illumination intensity, time and distance are the four key factors affecting the inactivation efficiency of the MB/narrow bandwidth light system. cache = ./cache/cord-259627-8stewshp.txt txt = ./txt/cord-259627-8stewshp.txt === reduce.pl bib === id = cord-256615-gvq8uyfk author = Rosenberg, Ronald title = Detecting the emergence of novel, zoonotic viruses pathogenic to humans date = 2014-11-22 pages = extension = .txt mime = text/plain words = 6688 sentences = 306 flesch = 45 summary = RNA viruses, with their high potential for mutation and epidemic spread, are the most common class of pathogens found as new causes of human illness. An analysis of virus discovery indicates that the small number of novel viruses discovered annually is an artifact of inadequate surveillance in tropical and subtropical countries, where even established endemic pathogens are often misdiagnosed. Many of the emerging viruses of the future are already infecting humans but remain to be uncovered by a strategy of disease surveillance in selected populations. Despite the differences in clinical presentation and geographical location, these three pathogens share three characteristics: all were unknown before found infecting humans, all are RNA viruses, and all have proven or putative non-human, animal sources. A single subtropical bat species hardly represents all mammal species and indeed many viruses are known to infect more than one species; they tested for only 9 of the 25 virus families pathogenic to humans. cache = ./cache/cord-256615-gvq8uyfk.txt txt = ./txt/cord-256615-gvq8uyfk.txt === reduce.pl bib === id = cord-259233-smmhhroe author = de Armas‐Rillo, Laura title = Membrane dynamics associated with viral infection date = 2016-01-28 pages = extension = .txt mime = text/plain words = 7086 sentences = 374 flesch = 40 summary = Several RNA viruses induce the formation of these autophagosome-like vesicles (also referred to as DMVs) to enhance viral replication and non-lytic egression, such as poliovirus and CVB3, HIV-1 and HCV. Indeed, autophagosome-like vesicles may represent a trafficking pathway for these viruses, connecting to multivesicular bodies (MVBs), and assuring virus assembly and budding at the cell surface while protecting them from intrinsic antiviral factors and immune responses. Trogocytosis involves the exchange of cell surface membrane patches that may contain receptor clusters associated to viral particles, while exosomes are vesicles formed from MVBs that could participate in viral infection and spreading between cells of the Alphavirus group of this family [12] , couple their RNA synthesis to endosome and lysosome membranes modified by the association of virus specific components. It remains unclear how proteins from distinct viruses and host cells use the same intracellular membrane compartments or events (e.g. autophagy) to achieve viral replication, without affecting important cellular processes. cache = ./cache/cord-259233-smmhhroe.txt txt = ./txt/cord-259233-smmhhroe.txt === reduce.pl bib === id = cord-260420-4s7akmdp author = Mubareka, Samira title = Bioaerosols and Transmission, a Diverse and Growing Community of Practice date = 2019-02-21 pages = extension = .txt mime = text/plain words = 4020 sentences = 206 flesch = 29 summary = There is a need to enhance the knowledge translation for researchers, stakeholders, and private partners to support a growing network of individuals and agencies to achieve common goals to mitigate interand intra-species pathogen transmission via bioaerosols. New developments have enabled progress in this domain, and one of the major turning points has been the recognition that cross-disciplinary collaborations across spheres of human and animal health, microbiology, biophysics, engineering, aerobiology, infection control, public health, occupational health, and industrial hygiene are essential. There is a need to enhance the knowledge translation for researchers, stakeholders, and private partners to support a growing network of individuals and agencies to achieve common goals to mitigate inter-and intra-species pathogen transmission via bioaerosols. A network approach has proven successful in other cross-disciplinary fields, including One Health and eco-health whereby wildlife, computational and evolutionary biologists, microbiologists, virologists, epidemiologists, ecologists, environmental scientists, climatologists, and human, animal, and public health practitioners are collaborating to address challenges in zoonotic diseases research and control (17, 18) . cache = ./cache/cord-260420-4s7akmdp.txt txt = ./txt/cord-260420-4s7akmdp.txt === reduce.pl bib === id = cord-259927-xh9cw9ao author = Papadopoulos, Nikolaos G. title = Promising approaches for the treatment and prevention of viral respiratory illnesses date = 2017-07-21 pages = extension = .txt mime = text/plain words = 7342 sentences = 400 flesch = 34 summary = 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. Here we provide an overview of the options and highlight some of the most promising approaches in vRTI treatment, including symptomatic medication, immunomodulatory drugs, antiviral agents, and natural products, as well as in vRTI prevention, ranging from vaccines to immunostimulators and public health policies. Early in vivo evidence suggested that azithromycin has anti-inflammatory and antiviral effects through induction of interferon-stimulated gene mRNA expression and reduced viral replication and release in patients with asthma and chronic obstructive lung disease. mAb therapies to viral infections, such as EBV (rituximab) or RSV (palivizumab), provide passive immunization and are licensed, whereas similar agents targeting influenza and other viruses are in preclinical development. cache = ./cache/cord-259927-xh9cw9ao.txt txt = ./txt/cord-259927-xh9cw9ao.txt === reduce.pl bib === id = cord-257665-12gyrmh2 author = Liu, Shan-Lu title = Emerging Viruses without Borders: The Wuhan Coronavirus date = 2020-01-22 pages = extension = .txt mime = text/plain words = 790 sentences = 48 flesch = 56 summary = We applaud the rapid release to the public of the genome sequence of the new virus by Chinese virologists, but we also believe that increased transparency on disease reporting and data sharing with international colleagues are crucial for curbing the spread of this newly emerging virus to other parts of the world. We applaud the rapid release to the public of the genome sequence of the new virus by Chinese virologists, but we also believe that increased transparency on disease reporting and data sharing with international colleagues are crucial for curbing the spread of this newly emerging virus to other parts of the world. We applaud the rapid release to the public of the genome sequence of the new virus by Chinese virologists [3] , as this represents an important first step in curbing the spread of the new virus to other parts of the world. cache = ./cache/cord-257665-12gyrmh2.txt txt = ./txt/cord-257665-12gyrmh2.txt === reduce.pl bib === id = cord-258027-f3rr5el1 author = Østby, Anne‐Cathrine title = Respiratory virology and microbiology in intensive care units: a prospective cohort study date = 2013-05-18 pages = extension = .txt mime = text/plain words = 5259 sentences = 268 flesch = 38 summary = Our aim was to determine the frequency of 12 common respiratory viruses in patients admitted to intensive care units with respiratory symptoms, evaluate the clinical characteristics and to compare the results to routine microbiological diagnostics. The information included the following: age, gender, underlying comorbidity, use of immunosuppressant drugs, respiratory symptoms, diagnoses on admission, diagnoses on discharge, length of hospital stay, ICU stay and intubation, Simplified Acute Physiology Score II (SAPS II)scores, administration of antibiotics, non-invasive ventilation, chest x-ray, laboratory analyses and results of the physical examination, which included temperature, saturation, stethoscopic findings and clinical signs of respiratory infection or distress. Viruses -Of the 122 patients included in the study group, 19 (16%) were positive for a virus, of which the most frequently detected were influenza A (n = 9) and RSV (n = 3, Fig. 2 ). cache = ./cache/cord-258027-f3rr5el1.txt txt = ./txt/cord-258027-f3rr5el1.txt === 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 === id = cord-258389-1u05w7r4 author = Verma, Anju title = Animal tissue culture principles and applications date = 2020-06-26 pages = extension = .txt mime = text/plain words = 12098 sentences = 740 flesch = 49 summary = The development of basic culture media has enabled scientists to work with a wide variety of cells under controlled conditions; this has played an important role in advancing our understanding of cell growth and differentiation, identification of growth factors, and understanding of mechanisms underlying the normal functions of various cell types. Many animal cells can be induced to grow outside of their organ or tissue of origin under defined conditions when supplemented with a medium containing nutrients and growth factors. With advancements in animal cell culture technology, a number of cell lines have evolved and are used for vaccine production, therapeutic proteins, pharmaceutical agents, and anticancerous agents. The animal cell culture can be grown for a wide variety of cell-based assays to investigate morphology, protein expression, cell growth, differentiation, apoptosis, and toxicity in different environments. cache = ./cache/cord-258389-1u05w7r4.txt txt = ./txt/cord-258389-1u05w7r4.txt === reduce.pl bib === id = cord-257008-7q5s1vu1 author = Sharma, Virender K. title = Environmental chemistry is most relevant to study coronavirus pandemics date = 2020-05-20 pages = extension = .txt mime = text/plain words = 1326 sentences = 85 flesch = 42 summary = In the environment, SARS-CoV-2 may survive in the air, on the surfaces, in water and wastewater (Qu et al. Systematically designed experiments will help us gain insight into the virus survival on various surfaces, thus minimizing the exposure of the novel coronavirus to the humans. During wastewater treatment, oxidants and disinfectants can inactivate enveloped viruses (Manoli et al. Research on enveloped-virus transmission and on the treatment of wastewater must include a wide range of enveloped viruses. The recommendation of using oxidants and disinfectants to inactivate SARS-CoV-2 must be experimentally based, which includes testing dose demand and contact time under the environmental conditions at which the virus would be presented. Overall, research in environmental chemistry is disclosing unique knowledge that may help to understand the behavior of viruses and other microbial pathogens in the environment. An imperative need for research on the role of environmental factors in transmission of novel coronavirus (COVID-19) cache = ./cache/cord-257008-7q5s1vu1.txt txt = ./txt/cord-257008-7q5s1vu1.txt === reduce.pl bib === id = cord-260554-nao59qx4 author = Wargo, Andrew R title = Viral fitness: definitions, measurement, and current insights date = 2012-09-15 pages = extension = .txt mime = text/plain words = 2898 sentences = 134 flesch = 38 summary = Important recent trends include increasing use of in vivo systems to assess vertebrate virus fitness, and a broadening of research beyond replicative fitness to also investigate transmission fitness and epidemiologic fitness. The majority of viral fitness study systems are based on RNA viruses, and the highest numbers of publications in recent years involves human pathogens associated with major disease emergence events, such as human immunodeficiency virus-1 (HIV-1), influenza virus, and dengue virus (DENV). In many cases the ultimate goal of replicative and transmission fitness studies is to understand the epidemiology 540 Virus evolution and population level processes governing viral evolution, emergence, and displacement in the field. For vertebrate viruses the recent increase of in vivo virus fitness research is encouraging, but the majority of studies still remain in vitro. cache = ./cache/cord-260554-nao59qx4.txt txt = ./txt/cord-260554-nao59qx4.txt === reduce.pl bib === id = cord-257652-ndt8f812 author = Zhang, Yong-Zhen title = The diversity, evolution and origins of vertebrate RNA viruses date = 2018-08-13 pages = extension = .txt mime = text/plain words = 4249 sentences = 171 flesch = 40 summary = In addition, despite frequent cross-species transmission, the RNA viruses in vertebrates generally follow the evolutionary history of their hosts, which began in the oceans and then moved to terrestrial habitats over timescales covering hundreds of millions of years. In addition, despite frequent cross-species transmission, the RNA viruses in vertebrates generally follow the evolutionary history of their hosts, which began in the oceans and then moved to terrestrial habitats over timescales covering hundreds of millions of years. However, following the extensive use of PCR and the Sanger sequencing methods for virus identification over the past decade, the number of RNA viruses sampled from lower vertebrates has steadily increased [28] , with notable examples being arenavirus and paramyxoviruses in reptiles [29] , and novirhabdoviruses and other RNA viruses from fish [30] , although these numbers were still very limited compared to the viruses described in birds and mammals. cache = ./cache/cord-257652-ndt8f812.txt txt = ./txt/cord-257652-ndt8f812.txt === reduce.pl bib === id = cord-261417-4pf5nsw2 author = Harwig, Alex title = The Battle of RNA Synthesis: Virus versus Host date = 2017-10-21 pages = extension = .txt mime = text/plain words = 7864 sentences = 443 flesch = 53 summary = Why the virus prefers to use these snRNAs as targets has yet to be experimentally established, but it has been proposed that the selective de-capping of U1 and U2 RNAs in combination with the binding of the viral NS1 protein to U6 snRNA may serve to inhibit host pre-mRNA splicing [66] . The folding of the TAR hairpin is key to the regulation of HIV-1 transcription [94] as it is used as a scaffold to recruit essential transcription factors, including the 86-101 amino acid (aa) viral trans-activator protein (Tat) [83] ( Figure 3C ). Interestingly, the human T-lymphotropic virus type 1 transcriptional activator Tax also utilizes P-TEFb for viral transcription and displaces P-TEFb from 7SK snRNP through binding CycT1 [101, 102] , suggesting that P-TEFb liberation from 7SK snRNP could be a common theme developed by different viruses to support their replication in host cells. cache = ./cache/cord-261417-4pf5nsw2.txt txt = ./txt/cord-261417-4pf5nsw2.txt === reduce.pl bib === id = cord-260705-huyyw5z6 author = Moshe, Adi title = Virus-Induced Aggregates in Infected Cells date = 2012-10-17 pages = extension = .txt mime = text/plain words = 5063 sentences = 265 flesch = 39 summary = During infection, many viruses induce cellular remodeling, resulting in the formation of insoluble aggregates/inclusions, usually containing viral structural proteins. The aggregates are utilized by viruses to house a large complex of proteins of both viral and host origin to promote virus replication, translation, intraand intercellular transportation. In plant cells, both RNA and DNA viruses are associated with large inclusions detected in the cytoplasm and nucleus, however, their role in virus propagation or oppositely in virus restraint is less investigated than in infected mammalian cells. In general, mammalian and plant viruses make use of aggregates as scaffolds for anchoring the replication complex, increasing the local concentration of viral and host components required for replication and assembly, and shielding the process of replication from host defense. cache = ./cache/cord-260705-huyyw5z6.txt txt = ./txt/cord-260705-huyyw5z6.txt === reduce.pl bib === id = cord-260168-rb7j94dh author = Gu, Jiang title = H5N1 infection of the respiratory tract and beyond: a molecular pathology study date = 2007-09-27 pages = extension = .txt mime = text/plain words = 6291 sentences = 369 flesch = 51 summary = Negative controls also included an unrelated antisense probe against the fragment of the polymerase gene (R1AB) of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV), 20 as well as H5N1 in-situ hybridisation probes to tissues (including lung and tracheal) obtained from seven adults who died from infectious lung diseases other than H5N1 infl uenza (four, SARS; one, purulent bronchitis; two, pneumonia), one adult who died from a non-infectious disease (gastric ulcer), one pregnant woman who died from an amniotic embolism, and one aborted fetus. Presence of viral sequences and antigens in the CNS is consistent with the recent isolation of H5N1 virus from cerebrospinal fl uid of a boy who died from encephalitis 6 with neurological symptoms commonly seen in patients with H5N1 infl uenza (Gao Zh, unpublished), including the two cases in this study. cache = ./cache/cord-260168-rb7j94dh.txt txt = ./txt/cord-260168-rb7j94dh.txt === reduce.pl bib === id = cord-262722-cz3ce29n author = Kuzmanovic, Deborah A. title = A novel application of small-angle scattering techniques: Quality assurance testing of virus quantification technology date = 2008-03-31 pages = extension = .txt mime = text/plain words = 5479 sentences = 271 flesch = 50 summary = Abstract Small-angle scattering (SAS) techniques, like small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS), were used to measure and thus to validate the accuracy of a novel technology for virus sizing and concentration determination. Additionally, scattering methods such as classical light scattering, small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) have also been employed to measure the concentration of samples when the molecular weight of the virus is known (Guinier, 1939; Guinier and Fournet, 1955; Jacrot and Zaccai, 1981; Koch et al., 2003) . The primary goal of this study is to explore the utility of using small-angle scattering (SAS) techniques, such as SAXS and SANS, as a general approach to the evaluation and quality assurance testing of virus characterization technology, using the integrated virus detection system (IVDS) instrument as a test technology. Specifically, it was determined using SAXS and SANS that the virus sizing and concentration technology, IVDS, can accurately measure the size of synthetic latex microspheres. cache = ./cache/cord-262722-cz3ce29n.txt txt = ./txt/cord-262722-cz3ce29n.txt === reduce.pl bib === id = cord-261160-g92zhv19 author = Rowland, Raymond R.R title = Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero date = 2003-10-30 pages = extension = .txt mime = text/plain words = 6383 sentences = 322 flesch = 48 summary = title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero Even though PRRSV-specific antibody appears as early as 5 days post-infection and is followed by serum neutralizing activity and cell-mediated immunity Molitor, 1997, 1999; Rowland et al., 1999 Rowland et al., , 2001 persistently infected pigs can continue to shed virus. The purpose of this study was to further understand persistent infection in congenitally infected pigs by characterizing the course of clinical disease, sites of virus replication and the capacity to transmit virus in a group of pigs exposed to PRRSV in utero. Analysis of virus and antibody in blood and/or umbilical cords from the 28 live neonates showed that at least 20 or 74% were virus isolation (VI) or RT-PCR positive for PRRSV at the time of farrowing indicating that in utero infection was successful. cache = ./cache/cord-261160-g92zhv19.txt txt = ./txt/cord-261160-g92zhv19.txt === reduce.pl bib === id = cord-260147-w19hl2vs author = Gröner, Albrecht title = Effective inactivation of a wide range of viruses by pasteurization date = 2017-11-16 pages = extension = .txt mime = text/plain words = 4285 sentences = 204 flesch = 33 summary = STUDY DESIGN AND METHODS: The virus inactivation kinetics of pasteurization for a broad range of viruses were evaluated in the relevant intermediates from more than 15 different plasma manufacturing processes. The first reliable virus inactivation method, pasteurization (heat treatment in aqueous solution at 608C for 10 hr), to effectively inactivate HBV and HCV (at that time called non-A/non-B hepatitis virus) in coagulation factor concentrates was studied and implemented at Behringwerke (a predecessor company of CSL Behring) in the late 1970s and early 1980s by employing suitable stabilizers and conditions to permit pasteurization without modifying the product, for example, formation of neoantigens or activated factors. 11, 12 Virus validation guidelines were ultimately developed and issued by the European authorities, requiring manufacturers to carry out studies to demonstrate the capacity, reliability, and effectiveness of the manufacturing processes to inactivate and/or remove viruses potentially present in the starting material (plasma pool for fractionation). cache = ./cache/cord-260147-w19hl2vs.txt txt = ./txt/cord-260147-w19hl2vs.txt === reduce.pl bib === id = cord-258783-ev0h95b9 author = Kapil, Sanjay title = Canine Distemper Spillover in Domestic Dogs from Urban Wildlife date = 2011-11-30 pages = extension = .txt mime = text/plain words = 7346 sentences = 390 flesch = 42 summary = Canine distemper virus (CDV) causes a major disease of domestic dogs that develops as a serious systemic infection in unvaccinated or improperly vaccinated dogs. 68 In addition to domestic dogs, urban wildlife in the United States such as raccoons, foxes, and skunks may play a role in direct transmission of distemper to large felids and other carnivores in zoos, wildlife parks, circuses, and captive breeding facilities. Canine distemper is a highly contagious disease of domestic dogs that also infects multiple wildlife hosts, some that serve as secondary or amplifying reservoirs of the virus. Because canine distemper is an RNA virus, a potential for emergence of antigenic variants exists, particularly in situations where wildlife that are infected with a strain of CDV that has adapted to that host spills back to domestic dogs. Introduction of novel canine distemper viruses in improperly vaccinated dog populations with insufficient immunity can cause new outbreaks of CDV. cache = ./cache/cord-258783-ev0h95b9.txt txt = ./txt/cord-258783-ev0h95b9.txt === reduce.pl bib === id = cord-260014-q5sug7uu author = Szűcs, Zsolt title = Reprogramming of the Antibacterial Drug Vancomycin Results in Potent Antiviral Agents Devoid of Antibacterial Activity date = 2020-06-29 pages = extension = .txt mime = text/plain words = 5179 sentences = 333 flesch = 51 summary = We prepared six vancomycin aglycone hexapeptide derivatives with the aim of obtaining compounds having anti-influenza virus but no antibacterial activity. On the other hand, this result is in line with our previous findings on ristocetin and teicoplanin aglycone derivatives, indicating that even minor structural differences in the peptide core can lead to significantly different anti-influenza virus activity [27] . On the other hand, this result is in line with our previous findings on ristocetin and teicoplanin aglycone derivatives, indicating that even minor structural differences in the peptide core can lead to significantly different anti-influenza virus activity [27] . Hence, we established, by virus yield assays, that compound 6 suppresses the replication of influenza virus and coronavirus, and for the other viruses, activity was indicated by the protection against viral CPE. Diazo transfer-click reaction route to new, lipophilic teicoplanin and ristocetin aglycon derivatives with high antibacterial and anti-influenza virus activity: An aggregation and receptor binding study cache = ./cache/cord-260014-q5sug7uu.txt txt = ./txt/cord-260014-q5sug7uu.txt === reduce.pl bib === id = cord-260956-w6wxsg4p author = Dimitrov, Kiril M. title = Newcastle disease vaccines—A solved problem or a continuous challenge? date = 2017-07-31 pages = extension = .txt mime = text/plain words = 10563 sentences = 423 flesch = 39 summary = When administered correctly to healthy birds, ND vaccines formulated with NDV of low virulence or viral-vectored vaccines that express the NDV fusion protein are able to prevent clinical disease and mortality in chickens upon infection with virulent NDV. Characterization of live LaSota vaccine strain-induced protection in chickens upon early challenge with a virulent Newcastle disease virus of heterologous genotype Protection from clinical disease against three highly virulent strains of Newcastle disease virus after in ovo application of an antibody-antigen complex vaccine in maternal antibodypositive chickens Antigenic differences among Newcastle disease virus strains of different genotypes used in vaccine formulation affect viral shedding after a virulent challenge Level of protection of chickens against highly pathogenic H5 avian influenza virus with Newcastle disease virus based live attenuated vector vaccine depends on homology of H5 sequence between vaccine and challenge virus cache = ./cache/cord-260956-w6wxsg4p.txt txt = ./txt/cord-260956-w6wxsg4p.txt === reduce.pl bib === id = cord-258626-p469ysi8 author = Davis-Wurzler, Gina M. title = 2013 Update on Current Vaccination Strategies in Puppies and Kittens date = 2014-02-26 pages = extension = .txt mime = text/plain words = 10938 sentences = 543 flesch = 43 summary = Criteria for assigning vaccines into these categories, and a third category, "generally not recommended," are based on: (1) morbidity and mortality associated with the specific disease (does the organism cause serious illness or does it cause a mild, transient disease that may pose only minimal risk to the individual or population?); (2) the prevalence and/or incidence rate of the disease (although a specific disease may not commonly be seen, the organism is ubiquitous in the environment and therefore poses risk to the individual or population); (3) the risk of the individual for exposure to the disease (indoor-only animal vs free-roaming individual, regional variations of occurrence); (4) the efficacy of the vaccine (does the vaccine prevent infection or simply ameliorate some signs or length of disease?); (5) the risks associated with administering the vaccine (are the risks associated with that vaccine greater than the risk of the disease?); (6) the potential for zoonotic disease; (7) the route of infection or transmissibility. 9, 13 The current recommendation is to use the CAV-II modified live virus product, as it stimulates the immune system to protect against both CAV-I and CAV-II, without the associated adverse reaction caused by the type I vaccine. cache = ./cache/cord-258626-p469ysi8.txt txt = ./txt/cord-258626-p469ysi8.txt === reduce.pl bib === id = cord-259260-qcfgigga author = Ibrahim, Ibrahim M. title = GRP78: A cell's response to stress date = 2019-06-01 pages = extension = .txt mime = text/plain words = 6837 sentences = 393 flesch = 50 summary = GRP78 expression is increased in cases of ER stressors like when the cell is abridged from sugar, treated with reagents that inhibit the process of protein glycosylation or disturb the intercellular calcium storage [5] . In the standard conditions of balance in the cell (homeostasis) GRP78 is bounded in an inactive form to Activating transcription factor 6 (ATF6), protein kinase RNA-like endoplasmic reticulum kinase (PERK), and Inositol-requiring enzyme 1 (IRE1) which are UPR transmembrane stress sensors. According to the ligand or the peptide that bind to CS-GRP78, it will be activated in a defined signaling pathway that affects Besides, if the cell is cancerous, CS GRP78 will induce resistance to chemotherapy. Glucose regulated protein 78 (GRP78) inhibits apoptosis and attentinutes chemosensitivity of gemcitabine in breast cancer cell via AKT/mitochondrial apoptotic pathway De-regulation of GRP stress protein expression in human breast cancer cell lines Kringle 5 of human plasminogen induces apoptosis of endothelial and tumor cells through surface-expressed glucose-regulated protein 78 cache = ./cache/cord-259260-qcfgigga.txt txt = ./txt/cord-259260-qcfgigga.txt === reduce.pl bib === id = cord-259235-p0yj9qug author = de Lamballerie, Xavier title = Diagnostic et traitement des viroses émergentes : comment aller de l’avant ? date = 2016-12-31 pages = extension = .txt mime = text/plain words = 1633 sentences = 178 flesch = 60 summary = (ii) l'émergence dans une population donnée d'un pathogène déjà impliqué en pathologie humaine dans un contexte épidémiologique différent (on parle ici plus proprement de pathologie « ré-émergente » et l'arrivée des virus Chikungunya [2] ou Zika [3] dans le Nouveau Monde constituent des exemples récents ayant provoqué des épidémies massives) ; À titre d'exemple, le seul arbovirus dont la circulation avait été prouvée en République du Congo jusqu'à une période récente était le virus de la fièvre jaune, alors qu'une simple étude de séroprévalence a permis de préciser l'importance de la circulation de la dengue, du chikungunya, de la fièvre de la vallée du Rift, de la fièvre de West Nile (Dr. Nanikaly Moyen, données personnelles Un cas particulier de thérapeutique antivirale applicable aux infections émergentes et ré-émergentes est constitué par la sérothérapie au sens large qui inclut l'usage d'immunoglobulines humaines ou animales (ces dernières pouvant être « humanisées ») monoclonales ou polyclonales [19] . cache = ./cache/cord-259235-p0yj9qug.txt txt = ./txt/cord-259235-p0yj9qug.txt === reduce.pl bib === id = cord-260496-s2ba7uy3 author = Moncany, Maurice L.J. title = Identification of conserved lentiviral sequences as landmarks of genomic flexibility date = 2006-08-08 pages = extension = .txt mime = text/plain words = 5991 sentences = 296 flesch = 51 summary = Comparison of entire genomes, including 237 human, simian and non-primate mammal lentiviruses and 103 negative control viruses, led to identify 28 Conserved Lentiviral Sequences (CLSs). Immunodeficiency lentiviral genomes correspond to 171 human viruses (155 HIV-1s and 16 HIV-2s), 33 simian viruses (3 CPZ, 9 AGM, 8 Macaque, 2 Mandrill, 10 Sooty Mangabey, 1 Sykes' monkey viruses) and 33 non-primate mammal viruses (2 bovine, 2 caprine, 11 equine, 9 feline, 3 ovine and 6 ovine/caprine viruses). From the particular organization of the HIV-1 and HIV-2 ( Fig. 1) , AGM and macaque (Fig. 2) , CPZ, feline, equine and D-particle-forming viruses (Fig. 3) and that of sooty mangabey, mandrill and other non-primate lentiviruses (supplementary data), it appears that a given CLS occupied on the viral genome a specific position that was roughly conserved in the different viral families. cache = ./cache/cord-260496-s2ba7uy3.txt txt = ./txt/cord-260496-s2ba7uy3.txt === reduce.pl bib === id = cord-260708-l9w5jhsw author = Lasecka, Lidia title = The molecular biology of nairoviruses, an emerging group of tick-borne arboviruses date = 2013-12-11 pages = extension = .txt mime = text/plain words = 10690 sentences = 446 flesch = 46 summary = The nairoviruses are a rapidly emerging group of tick-borne bunyaviruses that includes pathogens of humans (Crimean-Congo hemorrhagic fever virus [CCHFV]) and livestock (Nairobi sheep disease virus [NSDV], also known as Ganjam virus), as well as a large number of viruses for which the normal vertebrate host has not been established. As several potential cysteine-protease-like cleavage sites have been identified in the L protein sequence of nairoviruses [94] and some viral proteins containing an OTU-like protease domain have also been shown to undergo autoproteolytic cleavage to generate multiple mature proteins, e.g., the replicase of BlScV [98] , it has been suggested that the L proteins of nairoviruses may also be autoproteolytically cleaved into an active RNA polymerase and protein(s) with additional function [85] . Role of actin filaments in targeting of Crimean Congo hemorrhagic fever virus nucleocapsid protein to perinuclear regions of mammalian cells Structural analysis of a viral ovarian tumor domain protease from the Crimean-Congo hemorrhagic fever virus in complex with covalently bonded ubiquitin Induction of caspase activation and cleavage of the viral nucleocapsid protein in different cell types during Crimean-Congo hemorrhagic fever virus infection cache = ./cache/cord-260708-l9w5jhsw.txt txt = ./txt/cord-260708-l9w5jhsw.txt === reduce.pl bib === id = cord-263017-rh86g4jk author = Wigginton, Krista Rule title = Virus disinfection mechanisms: the role of virus composition, structure, and function date = 2011-12-09 pages = extension = .txt mime = text/plain words = 3710 sentences = 186 flesch = 34 summary = Non-culturable virus disinfection kinetics must be either determined with human charge studies or predicted using surrogate viruses that can be cultured in vitro but that differ in composition, structure, and function. Coupling structure and composition information aids in our understanding of virus reactivity X-ray crystal structures have been published for numerous enteric viruses [25,26 ,27] and with these reports have come a windfall of valuable information including the location and orientation of capsid protein residues. Specific questions include: 1) Which virus protein residues are involved with fundamental functions and how do these vary amongst different strains and species; 2) What specific chemical modifications take place in the genome and capsid during disinfection and what effects do these modifications have on virus structure and function; 3) How similar are disinfectant-induced modifications amongst various enteric viruses? cache = ./cache/cord-263017-rh86g4jk.txt txt = ./txt/cord-263017-rh86g4jk.txt === reduce.pl bib === id = cord-261961-u4d0vvmq author = St-Germain, Jonathan R. title = A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research date = 2020-08-28 pages = extension = .txt mime = text/plain words = 2735 sentences = 147 flesch = 41 summary = To this end, we conducted a mass spectrometry-based characterization of the SARS-CoV-2 virion and infected cell lysates, identifying 189 unique high-confidence virus tryptic peptides derived from 17 different virus proteins, to create a high quality resource for use in targeted proteomics approaches. The resulting viral tryptic peptides were identified using nanoflow liquid chromatography -tandem mass spectrometry (LC-MS/MS; Fig 1A, Together, these data confirm and expand upon previous proteomic analyses of SARS-CoV-2 virions, infected cells 4, 7-11 and patient samples [12] [13] [14] , and provide a library of high quality virus peptide spectra covering 17 virus proteins that can be used for the creation of peptide spectral libraries and targeted proteomics approaches. To this end, we also undertook an analysis of SARS-CoV-2 virions and infected Vero cell lsyates using data-dependent acquisition tandem mass spectrometry, and identified 189 unique tryptic peptides, assigned to 17 different virus proteins. cache = ./cache/cord-261961-u4d0vvmq.txt txt = ./txt/cord-261961-u4d0vvmq.txt === reduce.pl bib === id = cord-262776-6k7tcgfs author = Burnouf, Thierry title = Assessment of the viral safety of antivenoms fractionated from equine plasma date = 2004-09-30 pages = extension = .txt mime = text/plain words = 8211 sentences = 417 flesch = 43 summary = Analysis of production parameters indicate that acid pH treatments and caprylic acid precipitations, which have been validated for the manufacture of some human IgG products, appear to provide the best potential for viral inactivation of antivenoms. Among those, caprylic acid and low pH treatments, both of which are commonly used also for the purification of antivenom IgG, have been shown to contribute to the viral safety of human plasma IgG products as described below. It should be kept in mind that treatment of whole plasma or crude fractions, as is the case for equine antivenoms production, may lead to lower rate and kinetics of viral inactivation, due to the high endogenous lipid content, as found in a study that evaluated the virucidal effect of sodium oleate [85] . However, a comparison with validated manufacturing processes used for human IgG clearly indicates that at least two widely used antivenom production steps, caprylic acid treatment and low-pH incubation, are likely to contribute in a robust manner to viral safety, at least against enveloped viruses. cache = ./cache/cord-262776-6k7tcgfs.txt txt = ./txt/cord-262776-6k7tcgfs.txt === reduce.pl bib === id = cord-263245-2qub96mz author = Singh, D. title = Alcohol-based hand sanitisers as first line of defence against SARS-CoV-2: a review of biology, chemistry and formulations date = 2020-09-29 pages = extension = .txt mime = text/plain words = 4779 sentences = 234 flesch = 41 summary = This review summarises the studies on alcohol-based hand sanitisers and their disinfectant activity against SARS-CoV-2 and related viruses. The literature shows that the type and concentration of alcohol, formulation and nature of product, presence of excipients, applied volume, contact time and viral contamination load are critical factors that determine the effectiveness of hand sanitisers. When soap and water are not available, the Food and Drug Administration (FDA) recommends sanitising of non-visibly soiled hands with an alcoholbased agent containing 80% v/v ethanol or 75% v/v isopropanol [4] . This review assesses available information on the composition, formulation and effectiveness of alcohol-based hand disinfection products with specific reference to their activity against SARS-CoV-2. Alcohol-based hand rubs in the form of foam, rinse and gel did not differ significantly in trials of antimicrobial activity but the application volume and drying time had a profound effect on their efficacy [54] . cache = ./cache/cord-263245-2qub96mz.txt txt = ./txt/cord-263245-2qub96mz.txt === reduce.pl bib === id = cord-262752-bwofzbwa author = Li, Qianqian title = Current status on the development of pseudoviruses for enveloped viruses date = 2017-12-07 pages = extension = .txt mime = text/plain words = 3268 sentences = 179 flesch = 37 summary = Early work by Witte and colleagues showed that when they used VSV to infect the cells in which MLV is packaged, they were able to harvest pseudovirus for use in neutralization antibody assays. Development of in vitro and in vivo rabies virus neutralization assays based on a high-titer pseudovirus system Development of a pseudotyped-lentiviral-vector-based neutralization assay for chikungunya virus infection Second generation of pseudotype-based serum neutralization assay for Nipah virus antibodies: sensitive and high-throughput analysis utilizing secreted alkaline phosphatase Use of vesicular stomatitis virus pseudotypes bearing Hantaan or Seoul virus envelope proteins in a rapid and safe neutralization test A neutralization test for specific detection of Nipah virus antibodies using pseudotyped vesicular stomatitis virus expressing green fluorescent protein Truncation of the human immunodeficiency virus-type-2 envelope glycoprotein allows efficient pseudotyping of murine leukemia virus retroviral vector particles Cholesterol supplementation during production increases the infectivity of retroviral and Lentiviral vectors pseudotyped with the vesicular stomatitis virus glycoprotein (VSV-G) cache = ./cache/cord-262752-bwofzbwa.txt txt = ./txt/cord-262752-bwofzbwa.txt === reduce.pl bib === id = cord-260690-h5pjv2dw author = Druce, Julian title = Laboratory diagnosis and surveillance of human respiratory viruses by PCR in Victoria, Australia, 2002–2003 date = 2004-11-12 pages = extension = .txt mime = text/plain words = 3803 sentences = 201 flesch = 45 summary = A total of 333 additional respiratory specimens, including 20 from asymptomatic laboratory staff was used to validate the PCR assays for influenza A virus (H1 and H3 subtypes), influenza B virus, RSV, parainfluenza viruses (at least one of types 1-3), picornaviruses (a mixture of enteroviruses and rhinoviruses), and adenoviruses (each of different serotype) (Table III) . The process included the design and evaluation of primers; optimization of nucleic acid extraction conditions; establishment of optimum PCR amplification conditions; evaluation of applicable specimen types; determination of assay sensitivity compared to conventional assays; specificity testing using clinical material likely to be negative (including asymptomatic staff volunteers); or material previously shown to be positive for respiratory viruses by conventional assays or by sequencing of an amplified product where no other confirmatory method was available. cache = ./cache/cord-260690-h5pjv2dw.txt txt = ./txt/cord-260690-h5pjv2dw.txt === reduce.pl bib === id = cord-262748-v4xue7ha author = Xu, Yongtao title = Identification of Peptide Inhibitors of Enveloped Viruses Using Support Vector Machine date = 2015-12-04 pages = extension = .txt mime = text/plain words = 4636 sentences = 253 flesch = 40 summary = Here we developed a support vector machine model using sequence-based statistical scores of self-derived peptide inhibitors as input features to correlate with their activities. The predictive support vector machine model for selfderived peptides of envelope proteins would be useful in development of antiviral peptide inhibitors targeting the virus fusion process. In view of the important role of E proteins in virus fusion process and common mechanism of action of self-derived peptides, we developed a SVM model to predict the antiviral activities of self-derived peptides using sequence-based statistical scores as input features. Because similar sequences are often associated with similar structure and function, the sequence-based property AVPalign would account for the activities of the self-derived peptide inhibitors which regulate the virus fusion by mimicking the binding to E proteins. The prominent performance of EAPscoring model indicates the sequence-based stability feature of self-derived peptides may reflect their potential of binding to E proteins so as to regulate the virus entry process. cache = ./cache/cord-262748-v4xue7ha.txt txt = ./txt/cord-262748-v4xue7ha.txt === reduce.pl bib === id = cord-261241-eqf6ame6 author = van Beek, Josine title = Influenza-like Illness Incidence Is Not Reduced by Influenza Vaccination in a Cohort of Older Adults, Despite Effectively Reducing Laboratory-Confirmed Influenza Virus Infections date = 2017-08-15 pages = extension = .txt mime = text/plain words = 4445 sentences = 243 flesch = 49 summary = The aim of this prospective observational study was to determine the relative contribution of influenza virus and other respiratory pathogens to ILI in older adults (aged ≥60 years) in 2 consecutive seasons in the Netherlands. In 60.8% (2011-2012) and 44.7% (2012-2013) of ILI samples, potential pathogens other than influenza virus were detected (Figure 3 ; Supplementary Table 1 ). Coronaviruses of all 4 common human subtypes (18.2% in 2011-2012 and 11.3% in 2012-2013), human metapneumovirus (hMPV) (20.3% and 3.6%), rhinoviruses (8.4% and 21.1%), respiratory syncytial virus (RSV) (4.9% and 6.5%), and parainfluenza viruses (2.8% and 5.1%) were detected in >5% of the ILI samples in at least 1 season. In this study in a cohort of community-dwelling older adults in the Netherlands, we show that influenza virus was present in 18.9% and 34.2% of ILI cases in 2 consecutive seasons and that influenza vaccination significantly reduced laboratory-confirmed influenza virus infection. Effectiveness of seasonal influenza vaccine in community-dwelling elderly people: a meta-analysis of test-negative design case-control studies cache = ./cache/cord-261241-eqf6ame6.txt txt = ./txt/cord-261241-eqf6ame6.txt === reduce.pl bib === id = cord-263165-bv4dh9eu author = Möstl, Karin title = Coronaviridae, pathogenetic and clinical aspects: An update date = 1990-12-31 pages = extension = .txt mime = text/plain words = 4906 sentences = 331 flesch = 45 summary = The recent detection of previously unknown coronaviruses or mutants, like the "Porcine Epidemic Diarrhea"-virus (PEDV) and the TGE-like "Porcine Respiratory Coronavirus" (PRCV) on one hand and new knowledge about pathogenetic mechanisms, for example in FIPV-infections, on the other hand are the basis for this review article. For diagnosis TGEV antigen can be detected by immunofluorescence in the small intestine of piglets at an early stage of disease, by virus isolation in tissue culture or by ELISA. As it causes a respiratory infection and does not replicate in the enteric tract, it was named "Respiratory Variant" of TGEV [16] and recently "Porcine respiratory coronavirus". Pedersen [51] assumed that not only the properties of the infecting virus strain were responsible for the outcome of the disease, but that also the immunologic situation of the host and the type and degree of developing immunity may be of great importance. Natural infection with the Porcine Respiratory Coronavirus induces protective lactogenic immunity against Transmissible Gastroenteritis cache = ./cache/cord-263165-bv4dh9eu.txt txt = ./txt/cord-263165-bv4dh9eu.txt === reduce.pl bib === id = cord-263315-g7os15m1 author = Martins-da-Silva, Andrea title = Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response date = 2018-01-18 pages = extension = .txt mime = text/plain words = 6975 sentences = 460 flesch = 48 summary = title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response The two most abundant secreted peptides at 24 h in the dsRNA-transfected group were phospholipid scramblase, an interferon-inducible protein that mediates antiviral activity, and forskolin-binding protein (FKBP), a member of the immunophilin family, which mediates the effect of immunosuppressive drugs. In human and mouse plasmacytoid dendritic cells (pDCs), which are professional interferon-producing cells specialized in recognizing viral RNA and DNA through the endosomal Toll-like receptors (TLRs) TLR7 and TLR9, respectively, PLSCR1 was described as a TLR9-binding protein that plays a significant role in type-1 interferon responses in pDCs by regulating TLR9 expression and trafficking [57] . Binding of FKBP51 to TRAF proteins facilitates the type-I interferon response induced by dsRNA transfection or Newcastle disease virus (NDV) infection in murine fibroblasts. Binding of FKBP51 to TRAF proteins facilitates the type-I interferon response induced by dsRNA transfection or Newcastle disease virus (NDV) infection in murine fibroblasts. cache = ./cache/cord-263315-g7os15m1.txt txt = ./txt/cord-263315-g7os15m1.txt === reduce.pl bib === id = cord-264291-0czphube author = Varfolomeev, S. D. title = Kinetic model of development of acute viral infection in the human body. Critical conditions, control mechanisms, “thermoheliox” date = 2020-07-20 pages = extension = .txt mime = text/plain words = 3008 sentences = 174 flesch = 50 summary = A kinetic model of the development of acute viral infection is proposed and the dynamic behavior of key variables, including the concentrations of viral particles, infected cells, and pathogenic microorganisms, is described. The most important parameters determining the process dynamics are the concentration of the infecting viral agent, the concentration of pathogenic microfl ora, which develops symbiotrophically on the aff ected cells, and physical conditions of the process such as temperature and pH of the medium. Quite a few publications of the last decade describe modeling of the dynamics of viral growth in the body, taking account of the production of pathogenic microfl ora and human immune system response. Most of mathematical models describe the incubation, the viral growth, activation of the immune system, and treatment of infection, but they do not consider the causes for collapse of the system, that is, molecular causes for the death of an organism related to the disease. cache = ./cache/cord-264291-0czphube.txt txt = ./txt/cord-264291-0czphube.txt === reduce.pl bib === id = cord-262514-1e2bc0bi author = Harrison, Alyne K title = Visceral target organs in systemic St. Louis encephalitis virus infection of hamsters date = 1982-12-31 pages = extension = .txt mime = text/plain words = 3177 sentences = 169 flesch = 45 summary = SLE virus causes a widespread infection in suckling mice and hamsters when it is inoculated by a peripheral route and involves numerous organs and tissues in addition to the CNS, the principal target when the virus is injected intracerebrally. Light microscopic observations were of little help in identifying major extraneural target organs and tissues in the clinically ill and moribund hamsters, but frozen-section immunofluorescence of all organ systems indicated significant virus growth in the pancreas, adrenal gland, small intestine, heart, skeletal muscle, and kidney. Immunofluorescence studies of mice experimentally infected with tick-borne encephalitis virus indicated that, in addition to the CNS, the peripheral nervous system, the special sensory nerve cells of the retina and olfactory mucosa, the secretory glands, the tubular epithelium of the kidney, and both striated and smooth muscle tissue were affected (Albrecht, 1960) . cache = ./cache/cord-262514-1e2bc0bi.txt txt = ./txt/cord-262514-1e2bc0bi.txt === reduce.pl bib === id = cord-263157-8jin6oru author = Martínez, Miguel Angel title = Progress in the Therapeutic Applications of siRNAs Against HIV-1 date = 2008-10-13 pages = extension = .txt mime = text/plain words = 9234 sentences = 466 flesch = 45 summary = Recent advances regarding the utility of RNA-mediated interference (RNAi) to specifically inhibit HIV-1 replication have opened new possibilities for the development of gene-based therapies against HIV-1 infection. Importantly, this study made the extraordinary demonstration that cell transfection of synthetic 21 base pairs (bp) short interfering RNA (siRNA) duplexes can mediate RNAi in a sequence-specific manner; this finding enabled the specific regulation of gene expression in a variety of biological systems, including diseased cells. Soon after the demonstration that synthetic siRNAs were able to induce the RNAi mechanism in mammalian cells (15) , several studies reported that HIV-1 gene expression and replication ex vivo could be inhibited by virus-specific synthetic siR-NAs (16 22) or expressed siRNAs (16, 18) that were targeted to early or late phases of virus replication. To counteract this strategic weakness, co-expression of multiple siRNAs or shRNAs that target conserved RNA sequences could reduce the emergence of single siRNA-resistant virus with a comparable effect to that achieved by the multiple anti-HIV drug combination approach employed by HAART. cache = ./cache/cord-263157-8jin6oru.txt txt = ./txt/cord-263157-8jin6oru.txt === reduce.pl bib === id = cord-261171-iknoqb4d author = Roingeard, Philippe title = Viral detection by electron microscopy: past, present and future date = 2012-01-09 pages = extension = .txt mime = text/plain words = 4446 sentences = 227 flesch = 44 summary = In research, new imaging techniques for fluorescence light microscopy have supplanted TEM, making it possible to study live cells and dynamic interactions between viruses and the cellular machinery. This large diversity of viruses potentially involved in human gastroenteritis contributed to the use of TEM on negatively stained samples for routine diagnosis by this rapid 'catch-all' method in clinical virology ( Figures 2C and 2D ). The new techniques, which can be used on living cells, make it possible to follow the fate of individual viral particles and to monitor dynamic interactions between viruses and cellular structures, making it possible to study steps in infection that could previously not be observed. HIV morphogenesis also provides a remarkable example of intensive research into virus-host cell interactions, for which the debate concerning the Figure 6 Budding of HCV Ultrastructural analysis of cells producing the HCV core protein shows that this protein self-assembles into HCV-like particles (arrows) at convoluted and electron-dense ER membranes surrounding the lipid droplets (LD) present in the perinuclear area. cache = ./cache/cord-261171-iknoqb4d.txt txt = ./txt/cord-261171-iknoqb4d.txt === reduce.pl bib === id = cord-264264-7j3xirfg author = TüRsen, Ümit title = CORONAVIRUS‐DAYS IN DERMATOLOGY date = 2020-04-15 pages = extension = .txt mime = text/plain words = 2144 sentences = 128 flesch = 49 summary = Soap works better than alcohol and disinfectants at destroying the structure of viruses. Soap dissolves the fat membrane, and the virus falls apart like a house of cards and "dies," or rather, it becomes inactive as viruses aren't really alive. Apart from alcohol and soap, antibacterial agents in those products don't affect the virus structure much. However, it was observed that washing hands with soap is better than using alcohol-based disinfectants in removing the noroviruses, rhinovirus and H1N1 influenza virus from hands (Tuladhar 2015, Kopra 2012, Grayson 2009 ). Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial Efficacy of soap and water and alcohol-based hand-rub preparations against live H1N1 influenza virus on the hands of human volunteers Single treatment with ethanol hand rub is ineffective against human rhinovirus--hand washing with soap and water removes the virus efficiently cache = ./cache/cord-264264-7j3xirfg.txt txt = ./txt/cord-264264-7j3xirfg.txt === 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-263484-afcgqjwq author = Ladner, Jason T. title = Precision epidemiology for infectious disease control date = 2019-02-06 pages = extension = .txt mime = text/plain words = 3990 sentences = 179 flesch = 29 summary = With sufficient sampling, relevant metadata (such as location and date) and an appropriate statistical framework, pathogen genomes can reveal patterns of epidemic transmission at a fine-scale resolution, thus enabling the design of targeted interventions that are more precise than those based on traditional epidemiological data alone. Through near-real-time genome sequencing and public data deposition of clinical, environmental, and foodrelated bacterial isolates, this network is streamlining the process of recognizing, investigating, and reducing the impact of foodborne disease outbreaks 42, 43 . This includes changes to research practice regarding the benefits for rapid and open sharing of data and results as well as a focus on building capacity for sequencing and analysis within public health agencies and the regions most severely impacted by infectious disease 57, 58 . One important approach to accelerating responses in the future is to build genome sequencing and analysis capabilities within public health agencies and hospitals as well as in developing countries disproportionately impacted by infectious disease outbreaks. cache = ./cache/cord-263484-afcgqjwq.txt txt = ./txt/cord-263484-afcgqjwq.txt === reduce.pl bib === id = cord-263868-ewnf96cz author = Srivastava, Mayank title = Chemical proteomics tracks virus entry and uncovers NCAM1 as Zika virus receptor date = 2020-08-04 pages = extension = .txt mime = text/plain words = 7614 sentences = 429 flesch = 52 summary = ZIKV was labeled on its surface with a chemical probe, which carries a photocrosslinker to covalently link virus-interacting proteins in living cells on UV exposure at different time points, and a biotin tag for subsequent enrichment and mass spectrometric identification of the receptor or other host proteins critical for virus internalization. We used the labeled ZIKV to infect Vero cells and interacting proteins were crosslinked at fixed time points to identify the virus-host factors and elucidate the virus entry mechanism (Fig. 1c) . To further investigate whether the strategy was also capable of correlating spatial information with the virus crosslinked proteins, we performed the STRING analysis to determine whether there is statistical overrepresentation of specific genes or proteins in the sample at specific time points and identify proteins specific at the attachment or cellular entry stages ( Supplementary Fig. 6 ). cache = ./cache/cord-263868-ewnf96cz.txt txt = ./txt/cord-263868-ewnf96cz.txt === reduce.pl bib === id = cord-263764-2ewz8ok4 author = Kutter, Jasmin S title = Transmission routes of respiratory viruses among humans date = 2018-01-17 pages = extension = .txt mime = text/plain words = 4392 sentences = 242 flesch = 40 summary = 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. Our observations underscore the urgent need for new knowledge on respiratory virus transmission routes and the implementation of this knowledge in infection control guidelines to advance intervention strategies for currently circulating and newly emerging viruses and to improve public health. Increasing numbers of studies focused on the detection and quantification of influenza viruses contained in droplets and aerosols expelled into the air through breathing, sneezing and coughing of infected individuals The SARS outbreak was primarily linked to healthcare settings, with 49% of the cases linked to hospitals [71] , most probably caused by aerosol-generating procedures on severely ill patients [72, 73] . cache = ./cache/cord-263764-2ewz8ok4.txt txt = ./txt/cord-263764-2ewz8ok4.txt === reduce.pl bib === id = cord-263785-0iift8zy author = Zhang, Xiaorong title = Evaluation of the reproductive system development and egg-laying performance of hens infected with TW I-type infectious bronchitis virus date = 2020-07-31 pages = extension = .txt mime = text/plain words = 3690 sentences = 171 flesch = 50 summary = title: Evaluation of the reproductive system development and egg-laying performance of hens infected with TW I-type infectious bronchitis virus Our findings suggest that TW I-type IBV is deadly to chickens and could cause permanent damage to the oviduct, resulting in the poor laying performance of female survivors and decreasing the breeding value and welfare of the infected flock. In this study, the pathogenicity of TW I-type IBV was evaluated by examining clinical symptoms, mortality rates, virus shedding, lesions, and laying performance in terms of egg quantity and quality in infected chickens. The pathogenicity of TW I-type IBV in the early stage post-infection was evaluated via the clinical symptoms, pathological lesions, and virus shedding from trachea and cloaca. Abbreviations IBV: infectious bronchitis virus; SPF: specific-pathogen-free; dpi: days post infection; RT-qPCR: reverse transcription-quantitative polymerase chain reaction. cache = ./cache/cord-263785-0iift8zy.txt txt = ./txt/cord-263785-0iift8zy.txt === reduce.pl bib === id = cord-264794-bgygebgx author = Lundgren, A.-L. title = Feline non-suppurative meningoencephalomyelitis. A clinical and pathological study date = 1992-11-30 pages = extension = .txt mime = text/plain words = 4861 sentences = 288 flesch = 48 summary = It has been argued that the syndrome may include several aetiologically unrelated conditions affecting the central nervous system of cats, e.g. toxoplasmosis (Hirth and Nielsen, 1969) and the cerebral form of feline infectious peritonitis (Slauson and Finn, 1972; Kornegay, 1978) . Histopathological examination revealed throughout the central nervous system a non-suppurative inflammation characterized by perivascular mononuclear cuffing, presence of inflammatory nodules and neuronal degeneration in all cats. Neuropathological examination of the cats of the present study showed a marked inflammatory reaction in the cerebral leptomeninges as well as in the grey matter of the brain and spinal cord. Neither the serological results nor the clinical and histopathological findings in the cats with staggering disease indicate a FeLV infection. Feline immunodeficiency virus (FIV) has emerged as an important cause of neurological disease in cats (Dow, Poss and Hoover, 1990; Sparger, 1991) , often in association with clinical syndromes typical of an immunodeficient state (chronic stomatitis, enteritis, dermatitis, etc). cache = ./cache/cord-264794-bgygebgx.txt txt = ./txt/cord-264794-bgygebgx.txt === reduce.pl bib === id = cord-263619-p17oomzn author = Moss, William J. title = Measles date = 2009-01-30 pages = extension = .txt mime = text/plain words = 9541 sentences = 457 flesch = 41 summary = Although providing passive immunity to young infants, maternally acquired antibodies can interfere with the immune responses to the attenuated measles vaccine by inhibiting replication of vaccine virus. Women with vaccine-induced immunity tend to have lower antimeasles virus antibody titers than women with naturally acquired immunity, and their children may be susceptible to measles at an earlier age. The cumulative distribution can reach 50% by 1 year of age, with a significant proportion of children acquiring measles virus infection before 9 months, the age of routine vaccination. Infants and younger children, although susceptible if not protected by immunization, are not exposed to measles virus at a rate sufficient to cause a large disease burden in this age group. The only documented case of disease induced by vaccine virus in an HIV-infected person was in a 20-year-old man who died 15 months after receiving his second dose of measles vaccine ( Angel et al., 1998 ) . cache = ./cache/cord-263619-p17oomzn.txt txt = ./txt/cord-263619-p17oomzn.txt === reduce.pl bib === id = cord-264350-4zxp3uae author = Kelley, James L. title = Chapter 12. Antiviral Agents date = 1984-12-31 pages = extension = .txt mime = text/plain words = 2520 sentences = 167 flesch = 46 summary = The focus of this year's chapter is on agents with activity A brief update of this year's advances More comprehensive reviews dealing VIRAL RESPIRATORY DISEASE RNA viruses are the major causative factors of the various forms of acute respiratory disease .8 respiratory tract are probably the most common cause of symptomatic human infections. Ribavirin (l-~-~-ribofuranosyl-1,2,~-triazole-3-carboxamide) -This nucleoside has activity against a broad range of DNA and RNA viruses in An tissue culture and in animal model systems.2 analysis of the status of ribavirin 3) as an is still unresolved but may involve guanosine nucleotides and inhibition of inosine monophosphate dehydrogenase.Z6 In a clinical trial against influenza A, oral ribavirin failed to alter clinical signs and symptoms of the disease.2 However, it OR OR has recently been reported to have a therapeutic effect against both influenza A and influenza B virus infections when administered to patients by inhalation of small-particle aerosol through a face m a s k . cache = ./cache/cord-264350-4zxp3uae.txt txt = ./txt/cord-264350-4zxp3uae.txt === reduce.pl bib === id = cord-264308-y6xuxj16 author = Liu, Rui title = Mouse lung slices: An ex vivo model for the evaluation of antiviral and anti-inflammatory agents against influenza viruses date = 2015-05-26 pages = extension = .txt mime = text/plain words = 7663 sentences = 403 flesch = 55 summary = In this study, we established an ex vivo model using mouse lung slices to evaluate both antiviral and anti-inflammatory agents against influenza virus infection. Our results suggested that mouse lung slices provide a robust, convenient and cost-efficient model for the assessment of both antiviral and anti-inflammatory agents against influenza virus infection in one assay. Our results showed that the lung slice model provides a robust, convenient and cost-economical method for the screening and evaluation of both antiviral and anti-inflammatory agents against influenza virus infection in one assay. To meet the goal of this study in the establishment of an ex vivo mouse slice model for the screening and evaluation of both antiviral and anti-inflammatory drugs against influenza infection in one assay, ensuring that the ex vivo model has similar patterns in influenza-induced cytokine and chemokine responses is critical. cache = ./cache/cord-264308-y6xuxj16.txt txt = ./txt/cord-264308-y6xuxj16.txt === reduce.pl bib === id = cord-264884-ydkigome author = Villarreal, Luis P. title = The Widespread Evolutionary Significance of Viruses date = 2008-07-05 pages = extension = .txt mime = text/plain words = 23138 sentences = 1203 flesch = 47 summary = For example, common structural motifs from phage to eukaryotic DNA viruses (T4 and herpesvirus) suggest very ancient links in virus evolution that span all domains of life (see below). On an evolutionary time-scale, the majority of viral lineages tend to exist as species-specifi c persistent (aka temperate, latent, and chronic) infections in which individual hosts will be colonized by mostly silent (asymptomatic) viruses for the duration of their life . It has distinct genetic, fi tness, and evolutionary characteristics that require intimate, host (tissue)-specifi c viral strategies and precise gene functions to attain stable maintenance in the presence of immunity and to allow biologically controlled reactivation. Thus, the phycodnaviruses appear to represent a basal but diverse viral lineage that has both acute and persistent lifestyle and have some clear relationships to most large eukaryotic DNA viruses and many phage. cache = ./cache/cord-264884-ydkigome.txt txt = ./txt/cord-264884-ydkigome.txt === reduce.pl bib === id = cord-264699-l8db5gll author = Kino, Tomoshige title = Virus-mediated modulation of the host endocrine signaling systems: clinical implications date = 2007-06-30 pages = extension = .txt mime = text/plain words = 4723 sentences = 226 flesch = 33 summary = For example, HIV-1-encoded gp120 molecules, which are located on the surface of the viral particle and have a major role in the entry of viruses into target cells, demonstrate amino acid sequence similarity to the growth hormone-releasing hormone (GHRH) receptor of the host and suppress the activation of this receptor by GHRH. In addition to their extracellular actions, many viral molecules act inside infected cells to modulate intracellular host signaling systems, including transcriptional regulation of target genes by hormones. In agreement with these findings, one of the HIV-1 proteins, Vpr, which is a 96-amino acid virion-associated accessory protein that has multiple functions (including influencing transcriptional activity and arresting the cell cycle), increases the effects of GR stimulation by several fold, functioning as a nuclear receptor coactivator in cooperation with a host cell coactivator complex containing p300 or its homolog CREB-binding protein (CBP) [29] [30] [31] [32] . cache = ./cache/cord-264699-l8db5gll.txt txt = ./txt/cord-264699-l8db5gll.txt === reduce.pl bib === id = cord-266138-yibbiiij author = Wege, Helmut title = Immunopathological aspects of coronavirus infections date = 1995 pages = extension = .txt mime = text/plain words = 6899 sentences = 398 flesch = 37 summary = Murine coronaviruses (mouse hepatitis virus, MHV) can spread inapparently or may hide as persistent infections that modulate the immune response [38, 100] . Suppression of immune response induction in Peyer's patch lymphoid cells from mice infected with mouse hepatitis virus Infection of BALB/cByJ mice with the JHM strain of mouse hepatitis virus alters in vitro splenic T cell proliferation and cytokine production Interaction of immune and central nervous systems: contribution of anti-viral Thy-1 + cells to demyelination induced by coronavirus JHM Impaired T and B cell subpopulations involved in a chronic disease induced by mouse hepatitis virus type 3 Identification of antigenic sites mediating antibody-dependent enhancement of feline infectious peritonitis virus infectivity The pathogenic role of virus-specific antibody-secreting cells in the central nervous system of rats with different susceptibility to coronavirus-induced demyelinating encephalitis Demyelination induced by murine hepatitis virus JHM strain (MHV-4) is immunologically mediated cache = ./cache/cord-266138-yibbiiij.txt txt = ./txt/cord-266138-yibbiiij.txt === reduce.pl bib === id = cord-264406-s5c0grz0 author = Miró-Cañís, Sílvia title = Multiplex PCR reveals that viruses are more frequent than bacteria in children with cystic fibrosis date = 2016-11-13 pages = extension = .txt mime = text/plain words = 2084 sentences = 128 flesch = 47 summary = Bacterial infections are very frequent in children with cystic fibrosis, but because rapid Methods: for screening for the wide variety of potentially involved viruses were unavailable until recently, the frequency of viral presence is unknown. Bacterial infections are very frequent in children with cystic fibrosis, but because rapid Methods: for screening for the wide variety of potentially involved viruses were unavailable until recently, the frequency of viral presence is unknown. Study design: In this 2-year prospective study, we obtained paired nasopharyngeal-swab and sputum specimens from children with cystic fibrosis during clinical respiratory examinations separated by at least 14 days. Study design: In this 2-year prospective study, we obtained paired nasopharyngeal-swab and sputum specimens from children with cystic fibrosis during clinical respiratory examinations separated by at least 14 days. This study aimed to evaluate the frequency viruses and bacteria in respiratory specimens and to clarify the incidence and characteristics (seasonality and age of patients) of different viruses in children with cystic fibrosis. cache = ./cache/cord-264406-s5c0grz0.txt txt = ./txt/cord-264406-s5c0grz0.txt === reduce.pl bib === id = cord-266136-81sx505i author = Freymuth, F. title = Les virus des bronchiolites aiguës date = 2010-06-16 pages = extension = .txt mime = text/plain words = 3458 sentences = 336 flesch = 66 summary = In Normandy (France), human respiratory syncytial virus (hRSV) was detected in 64.1% of acute bronchiolitis in hospitalized children, rhinovirus in 26.8%, human metapneumovirus (hMPV) in 7.6%, and parainfluenza virus (PIV) in 3.4%. Une étude américaine a estimé à 18 % la fréquence des infections à hRSV chez les enfants de moins de 5 ans atteints d'une infection respiratoire aiguë ; 20 % de ces infections conduisant à une hospitalisation, 18 % à une consultation dans un service d'urgence pédiatrique et 15 % à la visite d'un médecin [7] . Une étude caennaise a été menée entre septembre 1998 et octobre 2000 chez 211 enfants hospitalisés pour une infection respiratoire aiguë dans laquelle seul un rhinovirus était détecté dans les voies respiratoires, alors que la recherche des virus influenza, PIV, hRSV, adénovirus était négative [31] . cache = ./cache/cord-266136-81sx505i.txt txt = ./txt/cord-266136-81sx505i.txt === reduce.pl bib === id = cord-264916-c4n0kyog author = Zimmerman, Keith title = Natural protection of ocular surface from viral infections – a hypothesis date = 2020-07-09 pages = extension = .txt mime = text/plain words = 4671 sentences = 225 flesch = 46 summary = A pandemic outbreak of a viral respiratory infection (COVID-19) caused by a coronavirus (SARS-CoV-2) prompted a multitude of research focused on various aspects of this disease. In this work, we discuss the significance of natural protective factors related to anatomical and physiological properties of the eyes and preventing the deposition of large number of virus-loaded particles on the ocular surface. Specifically, we advance the hypothesis that the standing potential of the eye plays an important role in repelling aerosol particles (microdroplets) from the surface of the eye and discuss factors associated with this hypothesis, possible ways to test it and its implications in terms of prevention of ocular infections. This hypothesis could be tested by measuring the electrical charge of bioaerosol generated by normal breathing in healthy subjects and in patients with viral infections caused by different viruses, causing respiratory infections or with suspected aerosol transmission pathway. cache = ./cache/cord-264916-c4n0kyog.txt txt = ./txt/cord-264916-c4n0kyog.txt === reduce.pl bib === id = cord-265751-q1ecpfyg author = Shahani, Lokesh title = Antiviral therapy for respiratory viral infections in immunocompromised patients date = 2017-01-16 pages = extension = .txt mime = text/plain words = 10657 sentences = 523 flesch = 34 summary = â�¢ High prevalence of M2 inhibitors resistance detected in influenza A (H3N2) and 2009 H1N1 virus strains preclude their use for prophylaxis or empiric treatment of seasonal influenza â�¢ Neuraminidase inhibitors are the first line agents for treatment of Influenza and treatment is most likely to provide the most benefit when initiated within the first 48 h of illness â�¢ Zanamivir is currently the therapy of choice for the treatment of oseltamivir-resistant influenza infection â�¢ An immunodeficiency scoring index for RSV, that accounts for the number of risk factors, can be used to identify HSCT recipients who are at high risk for progression to RSV LRTI and RSV associated mortality â�¢ Ribavirin-based therapy (alone or in combination with immunomodulators) can be effective in preventing progression from URTI to LRTI and may improve mortality in highly immunosuppressed adult HSCT recipients â�¢ The safety and efficacy of DAS181 in immunocompromised patients with PIV pneumonia, is currently being studied in an ongoing phase 2 double-blind, placebo-controlled trial. cache = ./cache/cord-265751-q1ecpfyg.txt txt = ./txt/cord-265751-q1ecpfyg.txt === reduce.pl bib === id = cord-265461-hj2b1wc4 author = Decroly, Etienne title = Biochemical principles and inhibitors to interfere with viral capping pathways date = 2017-05-18 pages = extension = .txt mime = text/plain words = 5089 sentences = 262 flesch = 46 summary = Some virus families code for two different MTase domains carrying a cap-binding site (e.g., poxviruses [11] , coronaviruses [ Structure of inhibitors targeting enzymes involved in viral RNA capping pathways. Cap analogues exemplified here with m7 GTP, and several inhibitors of cap-binding protein have been identified through X-ray structure analysis of the influenza virus PB2-CBD in complex with the corresponding ligands. The X-ray structure of influenza A or B virus PB2 in complex with m7 GTP [49, 50] reveals a conserved cap-recognition mechanism in which the methylated guanosine is stacked between two aromatic residues similar to its binding mode with the eukaryotic initiation factor (eIF4E). However, the past research decade has a contrario unveiled that RNA capping is essential for virus replication, and is in fact a most interesting target for the design of potent antivirals due to two main reasons: (i) incomplete/inhibited RNA capping triggers a potent host immune response adding up to direct inhibition of viral gene expression, and (ii) structural and functional studies of viral capping enzymes have revealed a profound uniqueness of the viral enzymes involved, which shows promises to achieve high drug selectivity. cache = ./cache/cord-265461-hj2b1wc4.txt txt = ./txt/cord-265461-hj2b1wc4.txt === reduce.pl bib === id = cord-265681-ab8j4o1u author = Boroomand, Zahra title = Pathogenesis and Tissue Distribution of Avian Infectious Bronchitis Virus Isolate IRFIBV32 (793/B Serotype) in Experimentally Infected Broiler Chickens date = 2012-04-01 pages = extension = .txt mime = text/plain words = 3553 sentences = 219 flesch = 53 summary = title: Pathogenesis and Tissue Distribution of Avian Infectious Bronchitis Virus Isolate IRFIBV32 (793/B Serotype) in Experimentally Infected Broiler Chickens The aim of this study was to investigate the distribution of avian infectious bronchitis virus isolate IRFIBV32 (793/B serotype) in experimentally infected chicken. Data indicated that the number of infected chickens and viral RNA detection from tissues was reduced with increasing antibody titer on day 20 PI. Gross lesions were recorded, and their trachea, lungs, kidneys, caecal tonsil, testes, and oviduct were aseptically collected for virus detection using RT-PCR assay ( Table 1) . In this study, the pathogenesis of the infectious bronchitis virus isolate IRFIBV32 which was recently isolated in Iran [12] , tissue tropism, and dissemination of the virus throughout the body were evaluated following intranasal (IN) inoculation of commercial broiler chickens by RT-PCR. Immunohistochemistry for detection of avian infectious bronchitis virus strain M41 in the proventriculus and nervous system of experimentally infected chicken embryos cache = ./cache/cord-265681-ab8j4o1u.txt txt = ./txt/cord-265681-ab8j4o1u.txt === reduce.pl bib === id = cord-267326-355q6k6k author = Gu, Xiaoqiong title = Geospatial distribution of viromes in tropical freshwater ecosystems date = 2018-06-15 pages = extension = .txt mime = text/plain words = 8426 sentences = 424 flesch = 44 summary = This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems. However, up till now, studies of land use impacts on the virome community in freshwater ecosystems are still limited as they mainly rely on traditional methodology (culture-based method or qPCR/RT-qPCR), which focuses on limited human virus targets without considering the whole picture of the viral community in the water environment (Corsi et al., 2014; Lenaker et al., 2017) . Thus, the objectives of this study were to: 1) investigate the overall virome distribution and diversity in diverse freshwater ecosystems (reservoirs/tributaries) in a tropical environment, 2) compare the virome community based on the different land use patterns, 3) assess the extent of human-related pathogenic viruses in surface waters, especially emerging zoonotic and human-related viruses, which may have been undetected before. cache = ./cache/cord-267326-355q6k6k.txt txt = ./txt/cord-267326-355q6k6k.txt === reduce.pl bib === id = cord-266985-9qwttt2y author = Gale, P. title = Applications of omics approaches to the development of microbiological risk assessment using RNA virus dose–response models as a case study date = 2014-11-04 pages = extension = .txt mime = text/plain words = 8073 sentences = 341 flesch = 43 summary = At present, the great strength of gene sequence data appears to be in giving information on the distribution and proportion of susceptible genotypes (for example due to the presence of the appropriate pathogen‐binding receptor) in the host population rather than in predicting specificities from the amino acid sequences concurrently obtained. The nature of the mutant spectrum in RNA viruses greatly complicates the application of omics approaches to the development of mechanistic dose–response models and prevents prediction of risks of disease progression (given infection has occurred) at the level of the individual host. The binding of NoV capsid protein to its HBGA receptor Table 1 Breakdown of the initial infection process into four steps for building a mechanistic dose-response relationship for RNA viruses through the oral route: information needs Host glycans play a central role in the pathogen infection process including binding of virus to specific receptors in steps 1 and 2 and also in the immune system. cache = ./cache/cord-266985-9qwttt2y.txt txt = ./txt/cord-266985-9qwttt2y.txt === reduce.pl bib === id = cord-264408-vk4lt83x author = Ruiz, Sara I. title = Animal Models of Human Viral Diseases date = 2017-06-23 pages = extension = .txt mime = text/plain words = 34464 sentences = 1865 flesch = 47 summary = Well-developed animal models are necessary to understand disease progression, pathogenesis, and immunologic responses to viral infections in humans. NHPs including marmosets, cotton-top tamarins, and rhesus macaques infected with Norwalk virus are monitored for the extent of viral shedding; however, no clinical disease is observed in these models. Intracerebral and IN routes of infection resulted in a fatal disease that was highly dependent on dose while intradermal (ID) and subQ inoculations caused only 50% fatality in mice regardless of the amount of virus (liu et al., 1970) . Ferrets infected with Hendra or Nipah virus display the same clinical disease as seen in the hamster model and human cases (Bossart et al., 2009; Pallister et al., 2011) . Characterization studies with IFNAr −/− mice challenged with different routes (IP, IN, IM, and subQ) showed that CCHFV causes acute disease with high viral loads, pathology in liver and lymphoid tissues, increased proinflammatory response, severe thrombocytopenia, coagulopathy, and death, all of which are characteristics of human disease . cache = ./cache/cord-264408-vk4lt83x.txt txt = ./txt/cord-264408-vk4lt83x.txt === reduce.pl bib === id = cord-265642-7mu530yp author = Syomin, B. V. title = Virus-Like Particles as an Instrument of Vaccine Production date = 2019-06-17 pages = extension = .txt mime = text/plain words = 7107 sentences = 325 flesch = 41 summary = Using protein expression systems it is possible to produce virus-like particles (VLPs), which are made up of monomers, which are able to multimerize into VLPs, and display the antigenic determinants of target pathogens on their surface. For example, in different laboratories different eukaryotic systems for viral protein expression, including plant cells, are used to produce VLPs which are used for vaccination against the hepatitis C virus (HCV) [36] . Antigen of the duck hepatitis A virus produced in the baculovirus expression system assembles into VLPs immediately in the cultured Spodoptera frugiperda (sf9) cells, while immunization of ducklings with the obtained VLPs induces a high level humoral immune response and protects them from developing the disease [46] . Expression vectors for foreign protein production in plants have been developed based on plant viruses, which allows obtaining plant-producing recombinant viruses or VLPs displaying the target antigen on their surface [101, 102] . cache = ./cache/cord-265642-7mu530yp.txt txt = ./txt/cord-265642-7mu530yp.txt === 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-267003-k7eo2c26 author = Hendaus, Mohamed A title = Virus-induced secondary bacterial infection: a concise review date = 2015-08-24 pages = extension = .txt mime = text/plain words = 3468 sentences = 238 flesch = 36 summary = 7 The human body is usually capable of eliminating respiratory viral infections with no sequelae; however, in some cases, viruses bypass the immune response of the airways, causing conceivable severe respiratory diseases. 49, 50 virus effect on the immune system Post-viral sustained desensitization of lung sentinel cells to TLR signals may be one possible contributor to the common secondary bacterial pneumonia associated with viral infection. Hendaus et al human-alveolar basal-epithelial cells) during a respiratory viral infection by increasing the expression of ICAM-1. It has been recommended that treatment or prevention of a viral disease may be a superior method for diminishing 62 It has also been published that live attenuated influenza vaccine is effective in reducing the incidence of all-cause AOM [86] [87] [88] and pneumonia 89 compared to placebo in children. Effects of rhinovirus infection on the adherence of Streptococcus pneumoniae to cultured human airway epithelial cells cache = ./cache/cord-267003-k7eo2c26.txt txt = ./txt/cord-267003-k7eo2c26.txt === reduce.pl bib === id = cord-267134-5gz2dotn author = Sallenave, Jean-Michel title = Innate Immune Signaling and Proteolytic Pathways in the Resolution or Exacerbation of SARS-CoV-2 in Covid-19: Key Therapeutic Targets? date = 2020-05-28 pages = extension = .txt mime = text/plain words = 5347 sentences = 239 flesch = 39 summary = The first anatomical/histological reports from the lungs of severely SARS-CoV-2-affected patients experiencing acute respiratory disease syndrome (ARDS) revealed excessive inflammatory activation and destruction of the bronchial and alveolar epithelium, features already observed during the first SARS pandemics in 2003 (3, 4). The following sections will give an overview of the molecular and cellular mechanisms underpinning SARS-CoV virus infections and how lung and systemic host innate immune responses affect survival either positively, through downregulating the initial viral load, or negatively, by triggering uncontrolled inflammation. Regarding the lung, the differentiated Calu-3 cell line [when cultured at the air-liquid interface (ALI)] is the model of choice: in that set-up, SARS-CoV infection triggered an inflammatory response characterized by increased production of interleukin (IL)-6, IL-8, gamma interferon (IFN-γ), inducible protein 10 (IP-10), and activation of the transcription factor NF-κB (56) . Innate immune response of human alveolar type II cells infected with severe acute respiratory syndrome-coronavirus cache = ./cache/cord-267134-5gz2dotn.txt txt = ./txt/cord-267134-5gz2dotn.txt === reduce.pl bib === id = cord-267194-i6vetquk author = Carman, William F. title = The pathogens date = 2007-10-31 pages = extension = .txt mime = text/plain words = 4498 sentences = 247 flesch = 57 summary = In a number of occasions, patients can have a severe lower respiratory tract infection, with no bacteriological cause and the only pathogen found is rhinovirus. hMPV causes both upper and lower tract infections and the signs and symptoms are very similar to those caused by RSV ranging from mild rhinorrhea associated with common colds to severe cough, wheezing, bronchiolitis and pneumonia (Konig et al., 2004; Van den Hoogen et al., 2001) . Although the main clinical symptoms are those of severe respiratory tract disease, the virus also infected other organs. NL63 is predominantly a common cold virus like OC43 and 229E that can cause lower respiratory tract disease in young children, the elderly and immunocompromised patients. HBoV has been associated with both upper and lower tract infections with prevalences ranging from 1% to 19%, with most reports indicating prevalences in the range of 3−6% in hospitalized children <5 years with ARI. cache = ./cache/cord-267194-i6vetquk.txt txt = ./txt/cord-267194-i6vetquk.txt === reduce.pl bib === id = cord-268999-6748c617 author = Gibson, Kristen E title = Viral pathogens in water: occurrence, public health impact, and available control strategies date = 2014-01-14 pages = extension = .txt mime = text/plain words = 4052 sentences = 197 flesch = 41 summary = Although there have been advances in both drinking water treatment technologies and source water protection strategies, waterborne disease outbreaks (WBDOs) due to viral pathogens still occur each year worldwide. Although there have been advances in both drinking water treatment technologies and source water protection strategies, waterborne disease outbreaks (WBDOs) due to viral pathogens still occur each year worldwide. The current review ( Figure 1 ) focuses on (1) the occurrence of viral pathogens of primary concern in various water sources; (2) virus-related WBDOS by water type reported worldwide over the past decade (from approximately 2000 to 2012); and (3) DW treatment options for the inactivation or removal of viruses. This paucity of available data for viruses in DW can most likely be attributed to the need for very large volumes (>100 to 6000 L) of water to be concentrated followed by subsequent recovery and detection of virus targets -a process that is challenging often Viral pathogens in water Gibson 51 Treatment options specific to removal/inactivation of viruses: -Many options available though implementation varies worldwide due to availability of technology. cache = ./cache/cord-268999-6748c617.txt txt = ./txt/cord-268999-6748c617.txt === reduce.pl bib === id = cord-266199-smlq11y9 author = Dhakal, Santosh title = Nanoparticle-based vaccine development and evaluation against viral infections in pigs date = 2019-11-06 pages = extension = .txt mime = text/plain words = 7647 sentences = 414 flesch = 38 summary = The economic burden caused by virus infections such as Porcine Reproductive and Respiratory Syndrome Virus, Swine influenza virus, Porcine Epidemic Diarrhea Virus, Porcine Circovirus 2, Foot and Mouth Disease Virus and many others are associated with severe morbidity, mortality, loss of production, trade restrictions and investments in control and prevention practices. Likewise, DCs targeted chitosan NPs loading plasmid DNA encoding nucleocapsid protein of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) induced better nucleocapsid protein-specific mucosal IgA antibody response compared to soluble unentrapped antigens after nasal immunization in mice [57] . In this review, only studies conducted in pigs related to the development and evaluation of NPs-based vaccine candidates by using virus-like particles (VLPs), biodegradable polymers, polysaccharides and liposomes against porcine viral infections are included (Table 3) . Chitosan-based NPs are used in pigs to deliver adjuvants such as bee venom and plasmid encoding porcine IL-2 and IL-4/IL-6 genes, which improved induction of better virus-specific immune responses of respective vaccines against PRRSV and PCV2 [103, 104] . cache = ./cache/cord-266199-smlq11y9.txt txt = ./txt/cord-266199-smlq11y9.txt === reduce.pl bib === id = cord-267831-uu883ofc author = Kang, Yuan-Lin title = Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2 date = 2020-06-15 pages = extension = .txt mime = text/plain words = 1257 sentences = 80 flesch = 44 summary = We describe here potent inhibitory effects on content release and infection by chimeric VSV containing the envelope proteins of Zaire ebolavirus (VSV-ZEBOV) or SARS-CoV-2 (VSV-SARS-CoV-2) elicited by Apilimod and Vacuolin-1, small molecule inhibitors of the main endosomal Phosphatidylinositol-3-Phosphate/Phosphatidylinositol 5-Kinase, PIKfyve. 143 All of these viruses require low pH to trigger viral membrane fusion with the endosomal 144 membranes, and as expected, infection was fully blocked by Bafilomycin A1, which 145 inhibits the vacuolar type H + -ATPase (V-ATPase) acidification activity (Fig. 1C) . Mammalian cell morphology and 671 endocytic membrane homeostasis require enzymatically active phosphoinositide 672 5-kinase PIKfyve The phosphatidylinositol-3-phosphate 5-kinase inhibitor 710 apilimod blocks filoviral entry and infection A transmembrane serine protease is linked to the severe 735 acute respiratory syndrome coronavirus receptor and activates virus entry Characterization of severe acute respiratory syndrome-744 associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry cache = ./cache/cord-267831-uu883ofc.txt txt = ./txt/cord-267831-uu883ofc.txt === reduce.pl bib === id = cord-267140-vdcf6vok author = Trudel, M. title = Purification of infectious rubella virus by gel filtration on sepharose 2B compared to gradient centrifugation in sucrose, sodium metrizoate and metrizamide date = 1981-02-28 pages = extension = .txt mime = text/plain words = 1718 sentences = 105 flesch = 45 summary = title: Purification of infectious rubella virus by gel filtration on sepharose 2B compared to gradient centrifugation in sucrose, sodium metrizoate and metrizamide Yields were lower in sucrose and metrizamide, while sodium metrizoate reduced the infectivity of the virus below detectable levels. This report describes the application of Sepharose 2B gel fitration for the purification of infectious rubella virus in comparison to centrifugation on sucrose, metrizamide and sodium metrizoate. Aliquots of 5 ml of viruses were purified by two cycles of density gradient centrifugation in sucrose, metrizoic acid (sodium salt) or metrizamide (Sigma Chemical Co., St. Louis, MO). Density gradient centrifugation of rubella virus on sucrose, metrizamide or sodium a Virus (5 ml, 65,566 HAU and 109*6TCID,,) was purified by ultracentrifugation or chromatography as described in Material and methods. Purification of rubella virus yielded similar results in sucrose and metrizamide but the infectivity was reduced to undetectable levels in sodium metrizoate. cache = ./cache/cord-267140-vdcf6vok.txt txt = ./txt/cord-267140-vdcf6vok.txt === reduce.pl bib === id = cord-269324-zh1a3gwh author = Mubareka, Samira title = Human Genes and Influenza date = 2008-01-01 pages = extension = .txt mime = text/plain words = 1822 sentences = 93 flesch = 36 summary = Specific genes responsible for the host immune response have been invoked as major determinants of the clinical course of HIV-associated disease and hepatitis B and C virus infections [2, 3] . Clinical and animal studies indicate that cytokine dysregulation is associated with acute respiratory distress syndrome and death among hosts infected with avian influenza virus (H5N1) [4 -6] . TLR4 has been implicated in the innate immune response to respiratory syncytial virus (RSV) infection, and polymorphisms in the TLR4 gene have been associated with severe bronchiolitis in RSV-infected infants, although the significance of the Asp299Gly polymorphism appears to be a matter of ongoing debate [9 -12] . All of these genes would be excellent candidates for an analysis to iden-tify determinants of severity of disease after influenza virus infection. Association between common Toll-like receptor 4 mutations and severe respiratory syncytial virus disease Association between mannose-binding lectin gene polymorphisms and susceptibility to severe acute respiratory syndrome coronavirus infection cache = ./cache/cord-269324-zh1a3gwh.txt txt = ./txt/cord-269324-zh1a3gwh.txt === reduce.pl bib === id = cord-269623-9pxdeva3 author = Nicholson, Karl G title = Influenza date = 2003-11-22 pages = extension = .txt mime = text/plain words = 9797 sentences = 506 flesch = 43 summary = The contrast between recent cases of H5N1 infection, associated with high mortality, and the typically mild, self-limiting nature of human infections with avian H7N7 and H9N2 influenza shows the gaps in our understanding of molecular correlates of pathogenicity and underlines the need for continuing international research into pandemic influenza. We gave priority to randomised controlled trials when available, to larger studies, articles published in high-impact journals that have a wide readership, and the systematic review and economic decision modelling, for the prevention and treatment of influenza, commissioned by the Health Technology Assessment Programme on behalf of the National Institute of Clinical Excellence. A meta-analysis of reports published before 2001 showed that vaccination reduces numbers of cases of influenza-like illness by 35%, hospital admissions for pneumonia and influenza by 47%, and all-cause mortality by 50%. cache = ./cache/cord-269623-9pxdeva3.txt txt = ./txt/cord-269623-9pxdeva3.txt === reduce.pl bib === id = cord-268501-z4oztgi0 author = Palatnik-de-Sousa, Clarisa B. title = What Would Jenner and Pasteur Have Done About COVID-19 Coronavirus? The Urges of a Vaccinologist date = 2020-08-26 pages = extension = .txt mime = text/plain words = 6331 sentences = 280 flesch = 46 summary = In fact, by May 11th, 2020 seven vaccines had already entered Phase I clinical trials: (1) encapsulated mRNA encoding protein S (Moderna and NIAID, USA); (2) Adenovirus expressing protein S (Cansino Biologics, China); (3) DCs modified with lentivirus expressing several proteins and CTLs (Shenzen Geno-Immune Medical, China); (4) an APC modified with lentivirus expressing several viral proteins (35); (5) Inno 4800, SARS CoV2 DNA Injection (Innovio, USA); (6) ChAdOx1 vaccine from the Jenner Institute, Oxford University, (UK) which is a genetically modified Adenovirus expressing Coronavirus proteins (39) , and is also being tested in a Phase II trial; and finally (7) the whole inactivated coronavirus with Alum by Sinovac, China (40) . Furthermore, in vaccinated monkeys, seven days after infection, the Sinovac inactivated vaccine at 6 µg/dose induced high titers of IgG antibodies directed against the S, RBD and lower levels of anti-N protein antibodies, high titers of virus neutralizing antibodies with no detected antibodydependent enhancement of disease (ADE) (40) . cache = ./cache/cord-268501-z4oztgi0.txt txt = ./txt/cord-268501-z4oztgi0.txt === reduce.pl bib === id = cord-266762-z08rn959 author = Rouse, Barry T. title = 25 Host Defenses to Viruses date = 2019-12-31 pages = extension = .txt mime = text/plain words = 7272 sentences = 388 flesch = 45 summary = authors: Rouse, Barry T.; Mueller, Scott N. However, broadly neutralizing antiviral antibodies have the potential to be effective therapies against many different human infections, including HIV, influenza viruses, and Ebola virus. Initiation of adaptive immunity is closely dependent on early innate mechanisms that activate antigen-presenting cells (APCs), principally subsets of DCs. APCs and lymphocytes are drawn into lymphoid tissues by chemokine and cytokine signals and are retained there for a few days to facilitate effective intercellular interactions. 19 T-cell immunity against a particular virus involves both CD4 + and CD8 + T-cell subsets that recognize peptides derived from viral antigens bound to surface MHC proteins (class II and class I, respectively) (Chapters 5, 6). Immune responses against virus-infected cells often result in tissue damage, especially if cell killing is involved or if there is extensive recruitment and activation of inflammatory cell types, such as macrophages and sometimes neutrophils. cache = ./cache/cord-266762-z08rn959.txt txt = ./txt/cord-266762-z08rn959.txt === reduce.pl bib === id = cord-269519-8hr8wyrr author = Hirotsu, Yosuke title = Analysis of Covid-19 and non-Covid-19 viruses, including influenza viruses, to determine the influence of intensive preventive measures in Japan date = 2020-07-07 pages = extension = .txt mime = text/plain words = 1599 sentences = 113 flesch = 54 summary = Other viruses in addition to SARS-CoV-2 cause cold-like symptoms and spread in the winter. However, the extent to which SARS-CoV-2, influenza viruses and other causative viruses have prevailed since implementing preventive measures is unclear. RESULTS: FilmArray Respiratory Panel analysis detected at least one virus in 32 of 191 patients with cold-like symptoms (21%). RT-PCR analysis detected SARS-CoV-2 (4.2%, n=8) in patients who were not infected with the aforementioned respiratory viruses. This epidemiologic study shows the infectability of each virus after implementing social preventive measures against SARS-CoV-2. The respiratory panel detected that 17% of the cohort (32/191 patients) were infected with causative viruses. At the start of the coronavirus epidemic, the infectivity of SARS-CoV-2 was unknown compared to that of influenza viruses. This study evaluated the differences in infectivity between SARS-CoV-2 and influenza viruses. The This study showed that taking stringent measures may prevent influenza viruses, which have more strongly affected human life for a longer time. cache = ./cache/cord-269519-8hr8wyrr.txt txt = ./txt/cord-269519-8hr8wyrr.txt === reduce.pl bib === id = cord-269975-1ebmq7t8 author = Duplantier, Allen J. title = Combating biothreat pathogens: ongoing efforts for countermeasure development and unique challenges date = 2020-05-27 pages = extension = .txt mime = text/plain words = 12963 sentences = 580 flesch = 32 summary = None of the filoviruses or henipaviruses has any FDA-approved therapeutics or vaccines available for prevention or treatment of human disease, and while ribavirin is sometimes used to treat Lassa fever, it is not a terribly effective drug against this viral infection [28] . Many of the therapeutics that are in different stages of either preclinical or clinical development for select biothreat pathogens include small molecule antivirals (Tables 7.3 and 7.4), antibody (or antibody cocktails) against viruses or bacteria/virulence factors (Table 7 .5), and combination drug therapy (Table 7 .6). Although no FDA-approved HDT therapies are yet available for treating infectious diseases, we have summarized in this section the antimicrobial Primary screening of small molecule chemical libraries in the phenotypic HCI assay will identify compounds that inhibit pathogen infection as well as those that may contribute to cellular toxicity. cache = ./cache/cord-269975-1ebmq7t8.txt txt = ./txt/cord-269975-1ebmq7t8.txt === reduce.pl bib === id = cord-267261-8z4aqfff author = Su, John R. title = Emerging viral infections date = 2005-03-01 pages = extension = .txt mime = text/plain words = 6882 sentences = 400 flesch = 45 summary = In 1999, a similar outbreak in pigs caused an outbreak of human encephalitis in Malaysia with a case-fatality rate approaching 40% [70] ; the causative agent was identified as a distinct but Hendra-like virus later named Nipah virus (NiV) [70] . In November 2002, cases of a new pulmonary disease, later named severe acute respiratory syndrome (SARS), were noted in the Guandong Province of China. In humans, about 20% of cases of infection with WNV lead to clinical disease, typically after an incubation period of 2 to 6 days. Virological features and clinical manifestations associated with human metapneumovirus: a new paramyxovirus responsible for acute respiratory-tract infections in all age groups Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome Detection of Severe Acute Respiratory Syndrome coronavirus in blood of infected patients cache = ./cache/cord-267261-8z4aqfff.txt txt = ./txt/cord-267261-8z4aqfff.txt === reduce.pl bib === id = cord-267567-w39f584z author = Pombo, Joao Palma title = Perturbation of Intracellular Cholesterol and Fatty Acid Homeostasis During Flavivirus Infections date = 2018-06-04 pages = extension = .txt mime = text/plain words = 4034 sentences = 217 flesch = 32 summary = Upon flavivirus infections, these are significantly altered: on the one hand, these viruses can co-opt lipid metabolic pathways to generate ATP to facilitate replication, or to synthesize membrane components to generate replication sites; on the other hand, more recent evidence suggests counter strategies employed by host cells, which actively modulate several of these networks in response to infection, enhancing interferon signaling by doing so, and thus creating an antiviral environment. In this review, we discuss recent data on mechanisms of alteration of lipid metabolic pathways during infection by flaviviruses, with a focus on cholesterol and fatty acid biosynthesis, which can be manipulated by the invading viruses to support replication, but can also be modulated by the host immune system itself, as a means to fight infection. cache = ./cache/cord-267567-w39f584z.txt txt = ./txt/cord-267567-w39f584z.txt === reduce.pl bib === id = cord-268417-6eyetb5i author = Mandel, Benjamin title = Neutralization of Animal Viruses date = 1978-12-31 pages = extension = .txt mime = text/plain words = 23012 sentences = 1239 flesch = 43 summary = Somewhat earlier, Morgan (1945'1 had reported that discrepancies in the quantitative aspects of the neutralization of WEE virus by immune rabbit sera were related to the use of fresh or heated serum, and that the addition of complement to the latter tended to eliminate the discrepancies. Further studies (Radwan et al., 1973) showed that the addition of complement to virus complexed with dependent antibody eventually resulted in lysis of the viral membrane. It was also shown (Yoshino and Taniguchi, 1966 ) that antibodies induced in guinea pigs by immunization, and in humans following herpes infection, were initially dependent and later independent of complement for neutralizing activity. A relevant observation has been made in several studies; neutralization of infectious virus-antibody complexes by antiglobulin also shows a single-hit mechanism, and at a rate that exceeds the rate of the homotypic reaction. cache = ./cache/cord-268417-6eyetb5i.txt txt = ./txt/cord-268417-6eyetb5i.txt === reduce.pl bib === id = cord-267733-fuz8r3vj author = Al Ali, Sally title = Use of Reporter Genes in the Generation of Vaccinia Virus-Derived Vectors date = 2016-05-21 pages = extension = .txt mime = text/plain words = 7966 sentences = 392 flesch = 41 summary = This broad host range allows infection of cell lines with recombinant viruses for large-scale expression of heterologous proteins, which reduces its cost This broad host range allows infection of cell lines with recombinant viruses for large-scale expression of heterologous proteins, which reduces its cost in comparison to other production systems [21, 24] . This reporter gene system has been widely used in transgenic plants, and it has also been successfully used in mammalian cells for VACV recombinant virus selection [54] . Reporter-gene assays have helped the pox virologists in basic research, for example for the study of the location, structure and function of many VACV proteins during the infection cycle and their interaction with proteins of the host cell [44, 70] . The main limitation of using VACV as a vector is the short-term gene expression, since it is a lytic virus killing the infected cells. Insertion sites for recombinant vaccinia virus construction: Effects on expression of a foreign protein cache = ./cache/cord-267733-fuz8r3vj.txt txt = ./txt/cord-267733-fuz8r3vj.txt === reduce.pl bib === id = cord-268788-jcu3pasy author = Thor, Sharmi W. title = Recombination in Avian Gamma-Coronavirus Infectious Bronchitis Virus date = 2011-09-23 pages = extension = .txt mime = text/plain words = 4426 sentences = 219 flesch = 49 summary = In this study, the full-length genomes of eight avian gamma-coronavirus infectious bronchitis virus (IBV) isolates were sequenced and along with other full-length IBV genomes available from GenBank were analyzed for recombination. In this study we sequenced and analyzed the entire genome of eight IBV strains that represent different serotypes that have not been previously sequenced, and we compared these sequences with other gamma-coronavirus full-length genome sequences available in GenBank for evidence of recombination [16] . A phylogenetic compatibility matrix constructed at the 70% bootstrap level for 250 bp sequence fragments at 100 bp intervals also showed that recombination breakpoints were distributed throughout the IBV genomes (data not shown). Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus Complete genome sequence and recombination analysis of infectious bronchitis virus attenuated vaccine strain H120 cache = ./cache/cord-268788-jcu3pasy.txt txt = ./txt/cord-268788-jcu3pasy.txt === reduce.pl bib === id = cord-268593-rvxxv1dn author = Wang, Mingyang title = Hemagglutinin-esterase-fusion (HEF) protein of influenza C virus date = 2015-07-28 pages = extension = .txt mime = text/plain words = 10152 sentences = 468 flesch = 50 summary = Influenza C virus is unique since it contains only one spike protein, the hemagglutinin-esterase-fusion glycoprotein HEF that possesses receptor binding, receptor destroying and membrane fusion activities, thus combining the functions of Hemagglutinin (HA) and Neuraminidase (NA) of influenza A and B viruses. While influenza A and B virus contain the two glycoproteins Hemagglutinin (HA) and Neuraminidase (NA) inserted into the viral membrane, influenza C virus possesses only one spike designated Hemagglutinin-Esterase-Fusion (HEF) protein which combines the functions of both HA and NA (Herrler et al., 1988a; Herrler and Klenk, 1991) . Although there is only 12% amino acid identity between HA and HEF, the overall structure of both molecules as well as folds of individual segments are quite similar, except an additional bulge, which is located at the lower part of the globular domain and contains the esterase region that is not present in HA (Fig. 3) . cache = ./cache/cord-268593-rvxxv1dn.txt txt = ./txt/cord-268593-rvxxv1dn.txt === reduce.pl bib === id = cord-269193-a647hwu9 author = Lin, Debby A. title = Evolutionary relatedness of the predicted gene product of RNA segment 2 of the Tick-Borne Dhori virus and the PB1 polymerase gene of influenza viruses date = 1991-05-31 pages = extension = .txt mime = text/plain words = 2946 sentences = 152 flesch = 57 summary = Abstract The complete nucleotide sequence of the second largest RNA segment of Dhori/India/1313/61 virus was determined and the deduced amino acid sequence was compared with the polymerase (P) proteins of influenza A, B, and C viruses. The viral RNAs have been shown to encode information in the negative-sense (Clerx et al., 1983; Fuller et al., 1987; Freedman-Faulstich and Fuller, 1990) and it was previously shown that the Dhori nucleoprotein (encoded by RNA segment 5) shares conserved amino acid sequences with the influenza A, B, and C virus nucleoproteins (Fuller et al., 1987) . The PBl polymerase proteins are the most highly conserved among the proteins of the influenza A, B, and C viruses (Yamashita et a/,, 1989 ) and they are most likely required for nucleotide addition during viral RNA synthesis (Braam et al., 1983) . cache = ./cache/cord-269193-a647hwu9.txt txt = ./txt/cord-269193-a647hwu9.txt === reduce.pl bib === id = cord-270243-moxleyjg author = Cholleti, Harindranath title = Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique date = 2018-05-28 pages = extension = .txt mime = text/plain words = 3245 sentences = 190 flesch = 50 summary = Conclusions: In summary, this study has identified a highly divergent virus with in the Orthomyxoviridae family associated with Rhipicephalus ticks from Mozambique. Different studies have shown that viral pathogens, such as Thogoto viruses, Wad Medani virus, Nairobi sheep disease virus, Crimean-Congo hemorrhagic fever virus, African swine fever virus and Tick-borne encephalitis virus [1, [6] [7] [8] , can be found in Rhipicephalus ticks. Numerous studies have used metagenomics to explore viral communities in different arthropod species and have in these identified viruses associated with a broad range of animals, plants and insects. However, the identified ORFs exhibit high genetic diversity to known quaranjavirus genomes, with an amino acid identity of only 32-55%, indicating that these represent novel viral sequences belonging to the Quaranjavirus genus. The parvovirus sequences identified in the current study had closest similarity to non-structural protein 1 of different densoviruses, which were shown previously to integrate into tick genomes such as in Ixodes, Amblyomma and Rhipicephalus genera [28, 29] . cache = ./cache/cord-270243-moxleyjg.txt txt = ./txt/cord-270243-moxleyjg.txt === reduce.pl bib === id = cord-270772-zshjrc87 author = To, Kelvin Kai-Wang title = Host genes and influenza pathogenesis in humans: an emerging paradigm date = 2015-06-14 pages = extension = .txt mime = text/plain words = 4110 sentences = 228 flesch = 35 summary = The emergence of the pandemic influenza virus A(H1N1)pdm09 in 2009 and avian influenza virus A(H7N9) in 2013 provided unique opportunities for assessing genetic predispositions to severe disease because many patients did not have any underlying risk factor or neutralizing antibody against these agents, in contrast to seasonal influenza viruses. Integration of knowledge from genetic and phenotypic studies is essential to identify important gene targets for treatment and prevention of influenza virus infection. Specific amino acid changes in the viral proteins have been associated with increased disease severity in humans or adaptation of avian influenza viruses in humans [13] . High-throughput screening platforms have allowed researchers to systematically screen a large number of genes associated with influenza virus infection in vitro, in animals or in humans. 9 Host genetic determinants of influenza virus disease severity identified in humans. Surfactant protein A genetic variants associate with severe respiratory insufficiency in pandemic influenza A virus infection This study incorporated in vitro, animal and human data to prioritize genes for future research on genetic susceptibility to severe influenza cache = ./cache/cord-270772-zshjrc87.txt txt = ./txt/cord-270772-zshjrc87.txt === reduce.pl bib === id = cord-271709-5frm3dnb author = Arden, Katherine E. title = Genotypic diversity, circulation patterns and co-detections among rhinoviruses in Queensland, 2001 date = 2019-11-04 pages = extension = .txt mime = text/plain words = 3918 sentences = 218 flesch = 48 summary = We aimed to estimate the spectrum of RV genotypes, species seasonality and RV involvement in co-detections in Queensland using a convenience collection of airway sample extracts from patients with suspected respiratory infections, collected during 2001 and tested using molecular tools expected to account for all RV species. Extracts had been previously tested by PQ using direct or culture-amplified direct fluorescent assay to detect respiratory syncytial virus (RSV), adenoviruses (AdV), parainfluenza viruses (PIVs) and influenza viruses A and B (IFAV, IFBV) [9] . Positive correlations included RV with RSV; EV with RSV; AdV with PIVs; HMPV with IFAV, HCoV-OC43, HCoV-NL63 and PIV RVs were detected in all seasons, but a bimodal distribution was evident with peaks in spring (36.5 % of all picornaviruses) and autumn (35.8%) and a trough in winter (13.2 %; summer extract numbers were low, so prevalence was difficult to determine; Fig. 2 ). cache = ./cache/cord-271709-5frm3dnb.txt txt = ./txt/cord-271709-5frm3dnb.txt === reduce.pl bib === id = cord-271105-eyigl0wz author = Ionidis, Georgios title = Development and virucidal activity of a novel alcohol-based hand disinfectant supplemented with urea and citric acid date = 2016-02-11 pages = extension = .txt mime = text/plain words = 4990 sentences = 252 flesch = 48 summary = Under the Guideline of Deutsche Vereinigung zur Bekämpfung der Viruskrankeiten e.V. and the Robert Koch-Institute (DVV/RKI Guideline) [22] , disinfectants achieving at least 4 log 10 titer reduction factor (RF of 4) against vaccinia virus and bovine viral diarrhea virus (BVDV) are active against all enveloped viruses (limited spectrum virucidal) [23, 24] . The different formulations of the new hand rub based on ethanol, citric acid and urea were screened undiluted (80.0 % due to the addition of test virus suspension and interfering substance) against PV, AdV and polyomavirus SV40 as non-enveloped test viruses of the Guideline of DVV/RKI in the presence of FCS with a fixed exposure time of 60 s. Consequently, the formulation with the sufficient virucidal activity containing 69.39 % w/w ethanol, 3.69 % w/w 2-propanol, 2.0 % urea and 2.0 % citric acid was tested against several non-enveloped (MNV, AdV, PV, polyomavirus SV40) and enveloped viruses (BVDV, vaccinia virus strain Elstree) in the presence or absence of FCS according to Guideline of DVV/RK or in clean conditions according to EN 14476. cache = ./cache/cord-271105-eyigl0wz.txt txt = ./txt/cord-271105-eyigl0wz.txt === reduce.pl bib === id = cord-270911-z637eh2z author = Zhou, Jie title = Differentiated human airway organoids to assess infectivity of emerging influenza virus date = 2018-06-26 pages = extension = .txt mime = text/plain words = 5003 sentences = 274 flesch = 47 summary = title: Differentiated human airway organoids to assess infectivity of emerging influenza virus airway organoid | proximal differentiation | influenza virus | infectivity I nfluenza A viruses (IAVs) can infect a diversity of avian and mammalian species, including humans, and have the remarkable capacity to evolve and adapt to new hosts (1) . Current in vitro models for studying influenza infection in the human respiratory tract involve shortterm cultures of human lung explants and primary airway epithelial cells. We chose to compare the infectivity of H7N2 with that of H7N9/Ah in the PD organoids as a proof of concept, to verify that the differentiated AOs can indeed simulate human airway epithelium in the context of influenza virus infection. Fig. 4 shows that viral loads in the cell lysate and medium of H7N9/ Ah-infected organoids increased gradually after inoculation; the viral titer increased more than 3 log 10 units within 24 h, indicating a robust viral replication. cache = ./cache/cord-270911-z637eh2z.txt txt = ./txt/cord-270911-z637eh2z.txt === reduce.pl bib === id = cord-270091-sqrh8ylt author = Cohen, Pascal title = Vascularites associées aux infections virales date = 2004-11-30 pages = extension = .txt mime = text/plain words = 6087 sentences = 531 flesch = 43 summary = Résumé Des virus, causes de vascularites Si la plupart des vascularites systémiques sont de cause inconnue, la responsabilité d'une infection virale a été démontrée de façon formelle pour certaines d'entre elles, un traitement spécifique pouvant les guérir définitivement. Cryoglobulinemia related to the hepatitis C virus (HCV) The clinical manifestations are those of systemic vasculitis with particular tropism for the skin (involvement generally inaugural and almost constant), peripheral nerves and the glomerula. Des virus, causes de vascularites Si la plupart des vascularites systémiques sont de cause inconnue, la responsabilité d'une infection virale a été démontrée de façon formelle pour certaines d'entre elles, un traitement spécifique pouvant les guérir définitivement. L'infection à HTLV1 est rarement compliquée de vascularite ;cette dernière a un tropisme neurologique central 181 192, 193 qui fut le premier à décrire la responsabilité liée à l'hépatite B au cours de la périartérite noueuse 194 , nous décidâmes d'inclure dans un protocole prospectif tous les patients atteints de PAN HBV+ et de traiter les patients par une combinaison d'antiviraux et d'échanges plasmatiques 195 . cache = ./cache/cord-270091-sqrh8ylt.txt txt = ./txt/cord-270091-sqrh8ylt.txt === reduce.pl bib === id = cord-268645-5op2m7pu author = Wu, Zhiqiang title = Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases date = 2015-08-11 pages = extension = .txt mime = text/plain words = 5949 sentences = 277 flesch = 49 summary = However, the understanding of the viral population and the ecological diversity residing in bat populations is unclear, which complicates the determination of the origins of certain EIDs. Here, using bats as a typical wildlife reservoir model, virome analysis was conducted based on pharyngeal and anal swab samples of 4440 bat individuals of 40 major bat species throughout China. Based on the partial genomic sequences of the viruses obtained by the assembly, we designed specific nested primers for PCR or reverse trancriptase-PCR to screen for each virus in individual samples from each bat species (the primer sequences for each virus are available in Supplementary Table S2 ). The diverse BtCoVs were grouped into several novel evolutionary clades that significantly differed from those of all known αand β-CoVs, providing additional evidence to support investigations of the evolution of bat-originated CoVs. With regard to BtParaVs, a previous study has revealed that bats host major mammalian ParaVs in the genera Rubulavirus, Morbillivirus, Henipavirus and the subfamily Pneumovirinae (Drexler et al., 2012) . cache = ./cache/cord-268645-5op2m7pu.txt txt = ./txt/cord-268645-5op2m7pu.txt === reduce.pl bib === id = cord-270161-vaejyy4i author = Reicks, Darwin L. title = Effective biosecurity to protect North American studs and clients from emerging infectious disease date = 2019-10-01 pages = extension = .txt mime = text/plain words = 5263 sentences = 253 flesch = 53 summary = Circumstances in North America in the period of 1999–2004 resulted in numerous PRRS virus (Porcine Reproductive and Respiratory Syndrome) negative boar studs becoming infected and disseminating virus to sow farms. Cleary defined physical barriers for people and animal entry and exit, sanitization and/or down time on incoming supplies, risk mitigation and testing of feed ingredients, and filtration have been keys to changing the incidence of emerging infectious disease introduction into boar studs. Biosecurity measures to prevent PRRS (Porcine Reproductive and Respiratory Syndrome) virus transfer among farms has largely influenced the biosecurity practices of boar studs in North America and worldwide. The purpose of this paper is to review practical effective biosecurity procedures that have made an impact in reducing the risk of emerging infectious disease entering boar studs and infecting sow farms through semen. Air filtration can be an effective way to prevent aerosol transmission of important swine viral diseases that can spread from the boars through the semen and infect sow farms. cache = ./cache/cord-270161-vaejyy4i.txt txt = ./txt/cord-270161-vaejyy4i.txt === reduce.pl bib === id = cord-269126-d81z6t0a author = Jayaseelan, Vijayashree Priyadharsini title = Repurposing calcium channel blockers as antiviral drugs date = 2020-08-19 pages = extension = .txt mime = text/plain words = 1141 sentences = 68 flesch = 45 summary = As convincing reports on calcium channel blockers mediated increase in ACE2 expression has not been documented so far, these drugs can be a safe alternative for treating CoVID patients with hypertension. Host cells are found to modulate calcium signalling in response to viral infection and the viruses in-turn harness this environment for their own survival and propagation. Interestingly, in an attempt made to identify genetic variants associated with susceptibility to neuro-invasive disease caused by West Nile virus, CASNA1H (Calcium Voltage-Gated Channel Subunit Alpha1 H) achieved a genome-wide significance implying the fact that ionchannels could be as important as other immuno-modulatory proteins controlling host response to viral infections (Long et al. Extensive research on existing calcium channel blockers intended for use as anti-hypertensives might as well aid in repurposing these drugs into the anti-viral regimen. Host calcium channels and pumps in viral infections Calcium ions directly interact with the Ebola virus fusion peptide to promote structure-function changes that enhance infection cache = ./cache/cord-269126-d81z6t0a.txt txt = ./txt/cord-269126-d81z6t0a.txt === reduce.pl bib === id = cord-271171-tohbzenc author = Bhola, J. title = Corona Epidemic in Indian context: Predictive Mathematical Modelling date = 2020-04-07 pages = extension = .txt mime = text/plain words = 3810 sentences = 217 flesch = 56 summary = Scientists also believe that peri-domestic mammals may also serve as For long, human viruses have not been considered severe pathogens as infected people develop flu like symptoms and then get cured on their own as innate immune system triggers antibody formation that provides resistance against the diseases (Chiu, 2013; Kistler et al., 2007; Wrammert et al., 2008) . https://doi.org/10.1101/2020.04.03.20047175 doi: medRxiv preprint Figure 2 From what is known about corona viruses, it is evident that the per capita rate of increase in the number of infectives is directly proportional to the number of susceptible in the vicinity of an infective and hence, the total intake in the first compartment looks like (kS)I ; where k signifies the rate of transmission indicated by the average number of people who will catch the virus from one infected person. cache = ./cache/cord-271171-tohbzenc.txt txt = ./txt/cord-271171-tohbzenc.txt === reduce.pl bib === id = cord-268540-wrjzr3ws author = Park, You Jeong title = Fighting the War Against COVID-19 via Cell-Based Regenerative Medicine: Lessons Learned from 1918 Spanish Flu and Other Previous Pandemics date = 2020-08-13 pages = extension = .txt mime = text/plain words = 16363 sentences = 868 flesch = 45 summary = A potential target for drug development for COVID-19 also involves inhibition of ACE2, the host cell receptor for the S protein of SARS-CoV-2 that is primed by TMPRSS2 protease and may prevent the entry of the virus. As previously described, the intermolecular interaction between the viral SP and human ACE2 Phase II CAStem cells will be intravenously injected into patients with or without acute respiratory distress syndrome (ARDS) induced by COVID-19. Phase II Patients with acute respiratory distress syndrome caused by COVID-19 will be treated with intravenous UC-MSCs at a dose 1 million xKg. Patient improvement will be evaluated over three weeks, along with the assessment of the immune profile, investigating the stem cells' effect on the cytokine storm. The similarities in systemic multi-organ complications between H7N9 and Sars-Cov-2 infections, along with direct evidence of the benefits of MSCs transplantation for COVID-19, further supports the potential of stem cells as an effective treatment [138] . cache = ./cache/cord-268540-wrjzr3ws.txt txt = ./txt/cord-268540-wrjzr3ws.txt === reduce.pl bib === id = cord-267671-ys43n672 author = Whary, Mark T. title = Biology and Diseases of Mice date = 2015-07-10 pages = extension = .txt mime = text/plain words = 63666 sentences = 3678 flesch = 40 summary = Clinical Signs MCMV causes subclinical infection in adult immunocompetent mice, but experimental inoculation of neonates can cause lethal disease due to multisystemic necrosis and inflammation. Diagnosis Because infected mice do not manifest signs or lesions and the virus is very difficult to propagate in cell culture, detection and diagnosis rely on serology and molecular methods. Differential Diagnosis Reovirus infection must be differentiated from other diarrheal diseases of infant mice, including those caused by mouse coronaviruses, EDIM virus, Salmonella spp., or Clostridium piliforme. Epizootiology EDIM virus appears to be infectious only for mice and occurs episodically in mouse colonies, and infection is probably widespread geographically (Livingston and Riley, 2003; Pritchett-Corning LABORATORY ANIMAL MEDICINE et al., 2009) . Sentinel mouse surveillance, using soiled bedding, is an effective strategy for detecting MNV (Manuel et al., 2008) Differential Diagnosis The mild change in fecal consistency associated with MNV in adult mice may mimic rotavirus, coronavirus, Helicobacter spp., Citrobacter rodentium, or other enteric diseases. cache = ./cache/cord-267671-ys43n672.txt txt = ./txt/cord-267671-ys43n672.txt === reduce.pl bib === id = cord-270803-jtv5jmkn author = Wang, Lin-Fa title = Mass extinctions, biodiversity and mitochondrial function: are bats ‘special’ as reservoirs for emerging viruses? date = 2011-11-09 pages = extension = .txt mime = text/plain words = 5612 sentences = 256 flesch = 47 summary = This has been due to a combination of factors including the emergence of highly virulent zoonotic pathogens, such as Hendra, Nipah, SARS and Ebola viruses, and the high rate of detection of a large number of previously unknown viral sequences in bat specimens. This has been due to a combination of factors including the emergence of highly virulent zoonotic pathogens, such as Hendra, Nipah, SARS and Ebola viruses, and the high rate of detection of a large number of previously unknown viral sequences in bat specimens. Bats (order Chiroptera), one of the most abundant, diverse and geographically dispersed vertebrates on earth, have recently been shown to be reservoir hosts of a number of emerging viruses responsible for severe disease outbreaks in humans and livestock [1 ,2,3]. cache = ./cache/cord-270803-jtv5jmkn.txt txt = ./txt/cord-270803-jtv5jmkn.txt === reduce.pl bib === id = cord-271692-60nlid3c author = Guo, Wen-Ping title = Phylogeny and Origins of Hantaviruses Harbored by Bats, Insectivores, and Rodents date = 2013-02-07 pages = extension = .txt mime = text/plain words = 6203 sentences = 305 flesch = 51 summary = Notably, the phylogenetic histories of the viruses are not always congruent with those of their hosts, suggesting that cross-species transmission has played a major role during hantavirus evolution and at all taxonomic levels, although we also noted some evidence for virus-host co-divergence. Our phylogenetic analysis also suggests that hantaviruses might have first appeared in Chiroptera (bats) or Soricomorpha (moles and shrews), before emerging in rodent species. An evolutionary analysis of all known hantaviruses including the novel viruses described here reveals the existence of four distinct phylogenetic groups of viruses that infect a range of mammalian hosts, and which have sometimes exchanged genes through segment reassortment. Irrespective of this history of reassortment it is clear that there have been multiple cross-species transmission events in the evolutionary history of the hantaviruses with, for example, those viruses sampled Soricomorpha forming a paraphyletic group, as do those from bats shown in the L tree. cache = ./cache/cord-271692-60nlid3c.txt txt = ./txt/cord-271692-60nlid3c.txt === reduce.pl bib === id = cord-271927-u8p6c9w4 author = Stefanacci, Richard G. title = Learnings to Operate LTC Better from the COVID-19 Crisis date = 2020-09-07 pages = extension = .txt mime = text/plain words = 3454 sentences = 167 flesch = 57 summary = But the indirect impact of COVID and LTC residents from social isolation causing weight loss, falls, delirium, dementia and depression as well as staff burn out will likely cause early deaths that may be even more significant. And what I mean by that it's an opportunity to do things you think you could not do before.‖ This COVID-19 is a serious crisis that we should not let go to waste but rather use as an opportunity operate differently around improving socialization, senses and staff support. For residents of health care facilities and staff the COVID-19 pandemic has added to our existing burden of daily stressors. As we navigate the COVID-19 pandemic, the need or deprescribing and optimizing medication management is more critical than it has ever been as reducing medications will potentially reduce opportunities for transmission of the virus between staff and residents. cache = ./cache/cord-271927-u8p6c9w4.txt txt = ./txt/cord-271927-u8p6c9w4.txt === reduce.pl bib === id = cord-270940-acwkh6ed author = Kallio-Kokko, Hannimari title = Viral zoonoses in Europe date = 2005-06-29 pages = extension = .txt mime = text/plain words = 14695 sentences = 733 flesch = 46 summary = Recently, during an outbreak in Finland in 2002, the causative agent of Pogosta disease was isolated for the first time in Europe from skin biopsies and a blood sample of patients [115] ; the virus strains were most closely related to SINV strains isolated from mosquitoes in Sweden and Russia 20 years previously. The genus Nairovirus (family Bunyaviridae) is composed of 34 predominantly tick-borne viruses that have been divided into seven serogroups [154] including several associated with severe human and livestock diseases (especially Crimean-Congo hemorrhagic fever virus (CCHFV) and Nairobi sheep disease virus). Rift Valley fever virus (RVFV), which is the type species of the genus and is transmitted by mosquitoes, causing an influenza-like disease that affects domestic animals and humans. cache = ./cache/cord-270940-acwkh6ed.txt txt = ./txt/cord-270940-acwkh6ed.txt === reduce.pl bib === id = cord-272052-8vvpm4tx author = Hartmann, Katrin title = Clinical aspects of feline immunodeficiency and feline leukemia virus infection date = 2011-10-15 pages = extension = .txt mime = text/plain words = 9582 sentences = 444 flesch = 35 summary = In a survey study of 826 naturally FIV-infected cats examined at North American Veterinary Teaching Hospitals, the most common disease syndromes were stomatitis, neoplasia (especially lymphoma and cutaneous squamous cell carcinoma), ocular inflammation (uveitis and chorioretinitis), anemia and leukopenia, opportunistic infections, renal insufficiency, lower urinary tract disease, and endocrinopathies such as hyperthyroidism and diabetes mellitus (Levy, 2000a) . Causes of CD4 + cell loss include decreased production secondary to bone marrow or thymic infection, lysis of infected cells induced by FIV itself (cytopathic effects), destruction of virus-infected cells by the immune system, or death by apoptosis (cell death that follows receipt of a membrane signal initiating a series of programmed intracellular events) (Bishop et al., 1993; Ohno et al., 1993 Ohno et al., , 1994 Johnson et al., 1996; Guiot et al., 1997a,b; Mizuno et al., 1997; Mortola et al., 1998a,b; Piedimonte et al., 1999; Mizuno et al., 2001 Mizuno et al., , 2003b Tompkins et al., 2002) . cache = ./cache/cord-272052-8vvpm4tx.txt txt = ./txt/cord-272052-8vvpm4tx.txt === 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-270335-8vqi9c68 author = Seifert, Stephanie N title = Rousettus aegyptiacus Bats Do Not Support Productive Nipah Virus Replication date = 2019-11-04 pages = extension = .txt mime = text/plain words = 3272 sentences = 155 flesch = 47 summary = Nipah virus is capable of infecting a broad range of hosts including humans, pigs, ferrets, dogs, cats, hamsters, and at least 2 genera of bats. Studies of wild caught Pteropus spp suggest potential for viral recrudescence [16, 23] ; however, the hypothesis that NiV may persist in an individual bat and re-emerge under times of stress has yet to be confirmed experimentally. In contrast, the Egyptian fruit bat (EFB), Rousettus aegyptiacus, belongs to the same taxonomic family as Pteropus spp, Pteropodidae, and has been successfully used to model Marburg virus transmission [24, 25] and serological cross-reactivity after filovirus challenge [26] . Previous studies have demonstrated that EFB cells are permissive to Ebola virus, but experimentally challenged bats did not shed virus or support productive replication [38, 39] despite compatibility between the Ebola virus glycoprotein and the host receptor, NPC1 [40] . cache = ./cache/cord-270335-8vqi9c68.txt txt = ./txt/cord-270335-8vqi9c68.txt === reduce.pl bib === id = cord-272405-jmwn8pdn author = Parvez, Mohammad K. title = Evolution and Emergence of Pathogenic Viruses: Past, Present, and Future date = 2017-08-04 pages = extension = .txt mime = text/plain words = 4192 sentences = 210 flesch = 43 summary = Despite substantial advancements in the understanding of the biology of pathogens, the breakthroughs in prevention, and their effects on public health and the global economy, the emergence of novel pandemic viruses remains an enduring puzzle. This review presents an update on the knowledge of important emerging/re-emerging viral infections worldwide, discussing their possible origin, evolution, natural reservoirs, human adaptations, and risk factors ( Fig. 1 ). To understand this further, a recently isolated HEV genotype 3 from a chronic hepatitis E patient containing a recombinant virus-host RNA genome was shown to infect cultured human, pig, and deer hepatocytes [39] . The field of phylodynamics, combining a modeling framework for host, epidemiological, and molecular data, especially for RNA viruses, shows particular promise for Parvez understanding the patterns of viral evolution during epidemics [40, 41] . Despite landmark advances in understanding the nature and biology of many pathogenic viruses, there is limited knowledge on emerging novel viruses, their potential reservoirs, and their modes of transmission. cache = ./cache/cord-272405-jmwn8pdn.txt txt = ./txt/cord-272405-jmwn8pdn.txt === reduce.pl bib === id = cord-272099-26nhza2s author = IKEDA, KEIKO title = Survival of influenza A virus on contaminated student clothing date = 2015-02-09 pages = extension = .txt mime = text/plain words = 2903 sentences = 137 flesch = 49 summary = The amount of infectious virus recovered from the nine types of clothing decreased with time and was shown to differ widely between clothing samples, when the contaminated clothing samples were maintained in uncovered glass Petri dishes in a safety cabinet under air blowing. At the indicated time points after virus deposition, one piece of the contaminated cloth was transferred into a glass test tube, immediately followed by the addition of 1,000 µl ice-cold Dulbecco's phosphate-buffered saline (PBS) without Ca 2+ and Mg 2+ , but containing 0.1% BSA. After leaving for 20 min in air, the cloths were transferred to glass test tubes, the contaminated virus was extracted with PBS containing 0.1% BSA by vigorous mixing with a Vortex mixer, and the amount of infectious virus recovered in the extract was measured. These observations support the importance of water in the deposit for the maintenance of the infectivity and transmissibility of influenza virus on contaminated clothes. cache = ./cache/cord-272099-26nhza2s.txt txt = ./txt/cord-272099-26nhza2s.txt === reduce.pl bib === id = cord-273343-als886fe author = McClenahan, Shasta D. title = Discovery of a Bovine Enterovirus in Alpaca date = 2013-08-12 pages = extension = .txt mime = text/plain words = 4596 sentences = 214 flesch = 51 summary = A cytopathic virus was isolated using Madin-Darby bovine kidney (MDBK) cells from lung tissue of alpaca that died of a severe respiratory infection. To identify the virus, the infected cell culture supernatant was enriched for virus particles and a generic, PCR-based method was used to amplify potential viral sequences. The new alpaca virus sequence was most similar to recently designated Enterovirus species F, previously bovine enterovirus (BEVs), viruses that are globally prevalent in cattle, although they appear not to cause significant disease. Analysis of the full polyprotein and the individual capsid, 2A protease, 3C protease, and polymerase proteins of the alpaca-infecting virus relative to sequences of other representative enteroviruses from bovine EV-E (BEV-A serotypes 1-4) and EV-F (BEV-B serotypes 1-4), and sequences from three unclassified EV-F viruses [16] , two from bovine sources (AY724744 and AY724745) [20] , and one from a capped langur (JX538037) [21] , possum, porcine (PEV), and human (HEV) hosts. cache = ./cache/cord-273343-als886fe.txt txt = ./txt/cord-273343-als886fe.txt === reduce.pl bib === id = cord-271568-qgpi2kcs author = Jackwood, M.W. title = Avian coronavirus infectious bronchitis virus susceptibility to botanical oleoresins and essential oils in vitro and in vivo date = 2010-01-21 pages = extension = .txt mime = text/plain words = 7596 sentences = 351 flesch = 57 summary = Genomic diversity and the Abbreviations: CPE, cytopathic effects; EID50, 50% embryo infectious dose; ELISA, enzyme linked immunosorbent assay; HMA, hexamethylene amiloride; IBV, infectious bronchitis virus; MHV, mouse hepatitis virus; PBS, phosphate buffered saline; RFLP, restriction fragment length polymorphism; RT-PCR, reverse transcriptasepolymerase chain reaction; SARS-CoV, Severe Acute Respiratory Syndrome virus; SPF, specific pathogen free; TCID50, 50% tissue culture infectious dose. Clinical signs were observed in all of the Mass41 virus challenged groups of birds regardless of treatment but in the intranasal and spray treated groups, fewer birds had signs and the signs were milder, as reflected by lower average scores (Table 1) . Virus was detected in 1 of 5 vaccinated birds in the treated group at 7 days post-vaccination Table 3 Experiment 4: clinical signs a in broiler chickens challenged with IBV at various times after treatment with QR448(a) at 1 day of age. cache = ./cache/cord-271568-qgpi2kcs.txt txt = ./txt/cord-271568-qgpi2kcs.txt === reduce.pl bib === id = cord-272829-i4jh6bcn author = ZANETTI, A. R. title = Emerging and re‐emerging infections at the turn of the millennium date = 2010-01-04 pages = extension = .txt mime = text/plain words = 4100 sentences = 180 flesch = 50 summary = Globalization changes promote the emergence of new infections and pandemics; international deliveries and travelling facilitate the dissemination of infectious agents; man‐induced environmental changes create new opportunities for contacts between species, leading to infections in aberrant hosts, including man; global warming enables insects, a major vector of pathogens, to thrive in more countries. What is more, a number of other factors promote not only the dissemination but also the emergence of new infectious diseases: intensive farming and breeding associated with crowding promote the development of foci of infection; global warming has modified the climate, making insects, a major vector of pathogens, able to thrive in countries where the climate was previously hostile; the exploitation of natural resources has produced environmental changes that create opportunities for new contacts between species leading to emergence of infections in new hosts. cache = ./cache/cord-272829-i4jh6bcn.txt txt = ./txt/cord-272829-i4jh6bcn.txt === reduce.pl bib === id = cord-269426-82g5eiyg author = Holman, David H. title = Viral Vectors date = 2009-01-30 pages = extension = .txt mime = text/plain words = 8734 sentences = 420 flesch = 40 summary = Abstract Traditional vaccine development platforms such as live-attenuated virus, killed virus, or recombinant subunit-based vaccines are often effective in eliciting long-term immunity to a number of infectious human pathogens. Finally, it is suggested that vaccination by alternate routes of administration (such as oral or intranasal) rather than injection can overcome pre-existing vector immunity ( Appaiahgari et al., 2006 ; Xiang et al., 2003 ) , which is supported by data from a human clinical trial ( Van Kampen et al., 2005 Lusky et al., 1998 ; Moorhead et al., 1999 ) or the E4 region ( Dedieu et al., 1997 ; Gao et al., 1996 ) of the Ad genome, which reduced or eliminated the expression of E2 or E4 proteins. High-level primary CD8( ϩ ) T-cell response to human immunodeficiency virus type 1 gag and env generated by vaccination with recombinant vesicular stomatitis viruses cache = ./cache/cord-269426-82g5eiyg.txt txt = ./txt/cord-269426-82g5eiyg.txt === reduce.pl bib === id = cord-271172-y48dovux author = Potter, Christopher William title = Chapter 25 Respiratory tract viruses date = 1998-12-31 pages = extension = .txt mime = text/plain words = 8618 sentences = 346 flesch = 37 summary = Adenoviruses, spread by droplet infection, impinge on epithelial cells in the pharynx or in the lower respiratory tract to enter and kill cells by a combination of inhibition of cellular metabolism, virus replication and the toxic effects of the penton: the results are extensive desquamation of affected areas, causing sore throat, necrotizing bronchitis, bronchiolitis and interstitial pneumonia. 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. 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. cache = ./cache/cord-271172-y48dovux.txt txt = ./txt/cord-271172-y48dovux.txt === reduce.pl bib === id = cord-271076-436nxsua author = Paul-Pierre, Pastoret title = Emerging diseases, zoonoses and vaccines to control them date = 2009-10-30 pages = extension = .txt mime = text/plain words = 3723 sentences = 173 flesch = 43 summary = In Northern America, the spectacular spread of West Nile virus infection, another vector transmitted disease, in humans and horses, was rapidly followed by the development of several vaccines, including a DNA-based vaccine for horses. To prevent Nipah virus (Henipavirus) infection in pigs a vaccine has recently been developed but, unfortunately, in countries like Bangladesh, humans are directly infected by the reservoir, a fruit bat species. The changes following globalisation, climatic change [6, 7] , and the opening of previously closed ecosystems, have considerably modified the pattern of endemic (or enzootic) infections/diseases, and contributed to the emergence of new agents that are pathogenic for humans and domestic animals. It is even more true when facing a really emerging disease that moreover is zoonotic such as Nipah virus infection [27] for which no vaccine was available yet, because the causative agent was previously unknown; the only solution is once again to kill and destroy the infected and in-contact animals. cache = ./cache/cord-271076-436nxsua.txt txt = ./txt/cord-271076-436nxsua.txt === reduce.pl bib === id = cord-271313-h9v0nmx5 author = Bagust, T. J. title = A REVIEW OF VIRAL INFECTIONS OF HORSES date = 2008-03-10 pages = extension = .txt mime = text/plain words = 2275 sentences = 128 flesch = 53 summary = In Australia, extensive investigation of respiratory diseases seen in horses in Victoria and Queensland have shown that equine herpesvirus type 1 (rhinopneumonitis) is the most common aetiological agent (Duxbury and Oxer 1968; Bagust and Pascoe 1968, 1970) . These clinical signs may be produced by any of several groups of viruses (Studdert 1967) , including equine herpesvirus type 1 (previously called equine influenza virus, then *This is the third article in a series of reviews on viral diseases of animals. Virus diseases of the skin of horses in Australia have not been investigated in detail, but there is ample clinical evidence for the occurrence of equine cutaneous papillomatosis (warts), caused by a host-specific papovavirus and appearing approximately 2 -3 months after infection. Equine viral arteritis has not been detected in Australian horses, but the disease is important in that clinical signs of acute infection (fever, depression, ocular and nasal discharges, oedema of the eyelids, limbs and abdomen, coughing and difficulty in breathing, colic, enteritis, jaundice, abortion) could be confused with infection by several viruses previously discussed. cache = ./cache/cord-271313-h9v0nmx5.txt txt = ./txt/cord-271313-h9v0nmx5.txt === reduce.pl bib === id = cord-273372-69rlh9or author = Litterman, Nadia title = Small molecules with antiviral activity against the Ebola virus date = 2015-02-09 pages = extension = .txt mime = text/plain words = 3257 sentences = 157 flesch = 48 summary = In addition we propose that a collaborative database for sharing such published and novel information on small molecules is needed for the research community studying the Ebola virus. We have found that indeed there is much prior knowledge regarding small molecules that have been shown to be active against the Ebola virus in vitro or in animal models 10-13 , including a number of FDA-approved drugs 14-16 . Medicinal chemistry analysis of small molecules active against the Ebola virus We have recently described an expert's medicinal chemistry 26 analysis of the over 320 NIH probe compounds using public and commercial sources of chemical structures and the issues related to doing this type of analysis 27 . By organizing the data on small molecules tested against the Ebola virus similarly in a central database and using machine learning models based on public data may help identify additional compounds for testing. cache = ./cache/cord-273372-69rlh9or.txt txt = ./txt/cord-273372-69rlh9or.txt === reduce.pl bib === id = cord-271884-86yl9ren author = Traavik, T. title = Development of a modified immunoelectroosmophoresis method for Uukuniemi and Runde virus serology date = 1977 pages = extension = .txt mime = text/plain words = 3120 sentences = 239 flesch = 56 summary = In search for a suitable method for sero-ecological screenings for arboviruses in Norway, efforts were undertaken to make the immunoelectroosmophoresis technique more sensitive than here to fare in detection of antibodies. The isolation of Uukuniemi (UUK) group viruses and a new coronavirus-like agent, Runde virus, from Norwegian Ixodes ticks (19, 21, 22, 23) , were intended to be followed up promptly by sero-ecological surveys by a standard haemagglutination inhibition test (HAI). B y using a gel composed of 0.4 per cent agar and 0.6 per cent agarose, and concentrated B H K antigens, results comparable to the H A I titers were obtained for the reference sera with all the viruses tested. Provided the opportunity to concentrate the antigen, the modifications used in this work to obtain a sensitive I E O P for antibody detection might prove valuable also with other viruses. cache = ./cache/cord-271884-86yl9ren.txt txt = ./txt/cord-271884-86yl9ren.txt === reduce.pl bib === id = cord-270670-cubh9jxc author = Domingo, E. title = Viruses as Quasispecies: Biological Implications date = 2006 pages = extension = .txt mime = text/plain words = 10489 sentences = 453 flesch = 39 summary = a Upon infection with an RNA virus (even with a single particle, as depicted here, enlarged about 10 6 times), viral replication leads to a mutant spectrum of related genomes, termed viral quasispecies. As further discussed in the text, in real infections multiple mutant spectra that can amount to a large number of replicating (or potentially replicating) genomes (up to 10 9 or even 10 12 per infected individual) provide highly dynamic mutant repertoire viral yields in cell culture, have been immensely powerful in characterizing the population dynamics of RNA viruses (see references in the reviews by Domingo and Holland 1997; Quiñones-Mateu and Arts 2002; Novella 2003; and the chapters by Quiñones-Mateu and Arts and Escarmís et al., this volume) . Despite these limitations, determination of nucleotide sequence heterogeneities in virus populations using correct reagents and adequate controls has consistently documented that most RNA viruses (and also some DNA viruses) consist of complex mutant spectra, with an average number of 1-100 mutations per genome (Sect. cache = ./cache/cord-270670-cubh9jxc.txt txt = ./txt/cord-270670-cubh9jxc.txt === reduce.pl bib === id = cord-274765-3wzht843 author = Kweon, Chang-Hee title = Derivation of attenuated porcine epidemic diarrhea virus (PEDV) as vaccine candidate date = 1999-06-04 pages = extension = .txt mime = text/plain words = 2518 sentences = 133 flesch = 55 summary = The field isolate of porcine epidemic diarrhea virus (PEDV) was serially passaged in Vero cells. The cell passaged PEDV, designated KPEDV-9, was tested for its pathogenicity in the neonatal pigs, immunogenicity and safety in the pregnant sows. The results of this study supported that the attenuated virus derived from serial passage could be applied as vaccine for protecting suckling piglets against PEDV infection. In this study, we investigated the attenuation of PEDV through serial passages in Vero cell cultures and its prophylactic eect in pregnant sows. Nevertheless, when compared with the wild PEDV, the animals inoculated with the high passage level of virus did not show any severe signs of diarrhea or death in piglets, supporting attenuation. Development of an Elispot for the detection of antibody secreting cells against the porcine epidemic diarrhea virus (PEDV) in dierent tissues cache = ./cache/cord-274765-3wzht843.txt txt = ./txt/cord-274765-3wzht843.txt === reduce.pl bib === id = cord-272981-8gahvdt0 author = Wege, Helmut title = Relapsing subacute demyelinating encephalomyelitis in rats during the course of coronavirus JHM infection date = 1984-08-31 pages = extension = .txt mime = text/plain words = 3725 sentences = 295 flesch = 57 summary = These results demonstrate that mutants of JHM virus can induce a relapsing demyelinating disease process, associated with a persistent infection, which possesses some similarities to chronic experimental allergic encephalomyelitis. It has been shown that an autoimmune reaction against CNS tissue can lead to 6hronic relapsing demyelination as seen in chronic experimental allergic encephalomyelitis (EAE) whereas the role of a virus infection in the induction of such a condition has not so far been directly demonstrated (McFarlin et al. After virus infection in rats inflammatory disseminating CNS lesions of marked demyelination develop accompanied by clinical signs of a subacute disease after varying incubation times. The induction of a progressive demyelinating, or relapsing demyelinating, disease process, in JHM virus-infected rats has ~me parallels to chronic EAE, an animal model based on sensitation ~8ainst CNS tissue extracts or myelin basic protein (McFarlin et al. cache = ./cache/cord-272981-8gahvdt0.txt txt = ./txt/cord-272981-8gahvdt0.txt === reduce.pl bib === id = cord-271650-biq0chyn author = Torres, Juan M title = Safety evaluation of a recombinant myxoma-RHDV virus inducing horizontal transmissible protection against myxomatosis and rabbit haemorrhagic disease date = 2000-09-15 pages = extension = .txt mime = text/plain words = 4589 sentences = 226 flesch = 45 summary = title: Safety evaluation of a recombinant myxoma-RHDV virus inducing horizontal transmissible protection against myxomatosis and rabbit haemorrhagic disease Safety evaluation of a recombinant myxoma-RHDV virus inducing horizontal transmissible protection against myxomatosis and rabbit haemorrhagic disease In order to protect wild rabbits against both myxomatosis and RHD, we constructed a recombinant virus based on the naturally attenuated MV ®eld strain 6918 [24] , that expressed the RHDV VP60 protein [25] . Groups of eight wild rabbits (2 month old, weighing around 0.8 kg) free from MV and RHDV antibodies, were inoculated at the back by intradermic (i.d.) or subcutaneous (s.c.) route with dierent doses of the vaccine (10 4 , 10 5 , 10 6 pfu of 6918VP60-T2 recombinant virus). Treated rabbits were inoculated (by s.c or i.d. route) with 10 4 pfu of 6918VP60-T2 virus, and clinical signs due to virus infection were compared with those induced in control rabbits, which were vaccinated but not treated with prednisolone (Fig 2, Table 3 ). cache = ./cache/cord-271650-biq0chyn.txt txt = ./txt/cord-271650-biq0chyn.txt === reduce.pl bib === id = cord-275013-na6319rg author = Singh, Indra P. title = Innate defences against viraemia date = 2000-11-23 pages = extension = .txt mime = text/plain words = 3294 sentences = 168 flesch = 42 summary = Recently, two naturally occurring nonspecific broad‐spectrum antiviral agents, University of Texas Inhibitor β (UTIβ) glycoprotein and high density lipoprotein, have been described in human serum. In this review, we emphasise the properties of broadly active antiviral molecules in human serum and explore the possibility that they can be important as natural defence mechanisms. Based on this protection and other correlations, the authors suggested a natural defensive role for this broadly antiviral inhibitor that is present widely and in high concentration in tissues and extracellular¯uid of human nervous system [25] . The mechanisms of action of these inhibitors are competitive inhibition of virus attachment to cells and neutralisation of viral infectivity by a mechanism unlike classical antibody because complement is not needed for their activity. These observations point to a relationship in vivo between the level of serum inhibitors and in¯uenza virus multiplication and thus support the notion that the narrowly active, nonspeci®c viral inhibitors can be a factor in innate resistance to speci®c viruses. cache = ./cache/cord-275013-na6319rg.txt txt = ./txt/cord-275013-na6319rg.txt === reduce.pl bib === id = cord-274112-6t0wpiqy author = Webby, RJ title = Responsiveness to a pandemic alert: use of reverse genetics for rapid development of influenza vaccines date = 2004-04-03 pages = extension = .txt mime = text/plain words = 4199 sentences = 206 flesch = 48 summary = INTERPRETATION: The ability to produce a candidate reference virus in such a short period of time sets a new standard for rapid response to emerging infectious disease threats and clearly shows the usefulness of reverse genetics for influenza vaccine development. The agent must be handled only under conditions of at least biosafety level 3 (BSL3), and it can kill fertilised chicken eggs, the standard medium for the reassortment and Responsiveness to a pandemic alert: use of reverse genetics for rapid development of influenza vaccines propagation of influenza virus before its inactivation and formulation for use in vaccines. The vaccine-candidate reference virus stock described in this report has been produced entirely on a cell substrate licensed for the manufacture of human vaccine, and as such, is-to our knowledge-the first reverse genetically derived influenza vaccine suitable for testing in clinical trials. Recombinant influenza A virus vaccines for the pathogenic human A/Hong Kong/97 (H5N1) viruses cache = ./cache/cord-274112-6t0wpiqy.txt txt = ./txt/cord-274112-6t0wpiqy.txt === reduce.pl bib === id = cord-271790-3s8o774l author = Pinto Mendes, J. title = The role of infection in asthma date = 2008-10-31 pages = extension = .txt mime = text/plain words = 13929 sentences = 956 flesch = 56 summary = Animal research is difficult to extrapolate to man but suggests RSV can induce allergic sensitisation 28 , increase bronchial and interleukin (IL)-13 hyperresponsiveness, and rão, na maioria dos casos, consequências remotas, embora algumas vezes descrevam sibilâncias que irão desaparecer aos 3 -5 anos e só raramente se prolongam, instalando -se ou não uma asma. If viral infection in acute asthma, particularly RV -the most studied -is associated with neutrophilic inflammation, cellular lysis and production of interferons (IFNs) 46 and if the environment is rich in IL-4, the production of IL-5, RANTES (Regulated upon Activated T cell Expressed and Selected), eotaxin, eosinophilic infiltration and IgE production 47 generally occur. While children at risk at allergic asthma have long been told to avoid contact with these animals, it is concluded that prolonged early life exposure to Feld-1 induces a form of immune tolerance specific to that allergen 89 . cache = ./cache/cord-271790-3s8o774l.txt txt = ./txt/cord-271790-3s8o774l.txt === reduce.pl bib === id = cord-274306-cxvnv8dy author = Chastel, C. title = Émergence de virus nouveaux en Asie : les changements climatiques sont-ils en cause ? date = 2004-11-30 pages = extension = .txt mime = text/plain words = 4564 sentences = 448 flesch = 70 summary = L'Asie, en particulier la Chine et le Sud-est asiatique, a également connu l'émergence de viroses humaines graves, telles que la dengue hémorragique (les Philippines, 1954) ou plusieurs pandémies grippales, la grippe asiatique (N2H2) en 1957, la grippe de Hong-Kong (H3N2) en 1968, et la grippe russe (H1N1) en 1977. Mais, c'est surtout au cours des dix dernières années que les émergences virales s'y sont multipliées avec l'apparition de la fièvre hémorragique à virus Alkhurma en Arabie Saoudite (1995), de la grippe aviaire H5N1 à Hong-Kong, en 1997, de l'encéphalite à virus Nipah en Malaisie, en 1998, et surtout du SRAS, en Chine du sud en 2002. Depuis l'extermination des porcs infectés, on a plus signalé de cas d'encéphalite à virus Nipah, mais il convient de rester vigilant car les roussettes et les porcs sont très nombreux dans tout le Sud-est asiatique. cache = ./cache/cord-274306-cxvnv8dy.txt txt = ./txt/cord-274306-cxvnv8dy.txt === reduce.pl bib === id = cord-273019-hbpfz8rt author = Glingston, R. Sahaya title = Organelle dynamics and viral infections: at cross roads date = 2018-06-25 pages = extension = .txt mime = text/plain words = 9513 sentences = 486 flesch = 35 summary = Studies on the herpes simplex virus-1 (HSV-1) infection on Vero, BHK-21 and PtK 2 cells reported transportation of viral tegument-capsid by dynein to the cytoplasmic side of NPC [22, 23] . In order to construct these compartments, viruses alter host's fatty acid metabolism, induce rearrangement of the membrane constituents and also recruit cellular machinery to produce proteins essential for its replication [59, 60] . Upregulation of mitophagy and degradation of the mitochondrial antiviral signalling protein (MAVS) in order to attenuate the antiviral immune response in non-small cell lung cancer (NSCLC) cells was reported upon measles virus infection [83] . The expression of matrix protein (M) of human parainfluenza virus type 3 (HPIV3) in HEK293T and HeLa cells was reported to induce mitophagy resulting in the suppression of type1 interferon response [84] . Many viruses or viral proteins are reported to localize to peroxisomes and/or exploit their functions to facilitate their replication in the host cells [108] . cache = ./cache/cord-273019-hbpfz8rt.txt txt = ./txt/cord-273019-hbpfz8rt.txt === reduce.pl bib === id = cord-271091-ffn59sgf author = Galao, Rui P title = Saccharomyces cerevisiae: a versatile eukaryotic system in virology date = 2007-10-10 pages = extension = .txt mime = text/plain words = 6539 sentences = 318 flesch = 42 summary = These include the analysis of the function of individual proteins from important pathogenic viruses, the elucidation of key processes in viral replication through the development of systems that allow the replication of higher eukayotic viruses in yeast, and the use of yeast in antiviral drug development and vaccine production. Although the expression of viral proteins in yeast not always necessarily reflects their role in higher eukaryotes, here we selected some examples in which the analysis in yeast of their effect on highly conserved cellular processes such as cell cycle control, apoptosis or mRNA degradation have contributed to the current understanding of the pathogenesis of important viral pathogens such as HIV-1 and HCV. The identification of the host factors involved in viral RNA replication is a priority area of research in virology because it can provide new targets for antiviral drug development. cache = ./cache/cord-271091-ffn59sgf.txt txt = ./txt/cord-271091-ffn59sgf.txt === reduce.pl bib === id = cord-275602-cog4nma0 author = Watkins, Kevin title = Emerging Infectious Diseases: a Review date = 2018-06-22 pages = extension = .txt mime = text/plain words = 4672 sentences = 278 flesch = 49 summary = SUMMARY: In addition to the aforementioned pathogens, the Severe Acute Respiratory Syndrome, Middle East Respiratory Syndrome, Nipah virus, New Delhi metallo-ß-lactamase-1 Enterobacteriaceae, Rift Valley Fever virus, and Crimean-Congo Hemorrhagic Fever virus are reviewed. In 1992, an expert committee that produced the Institute of Medicine report on emerging infections defined them as "new, reemerging, or drug-resistant infections whose incidence in humans has increased within the past two decades or whose incidence threatens to increase in the near future." Additionally, six major contributors to these diseases were presented and included changes in human demographics and behavior, advances in technology and changes in industry practices, economic development and changes in land-use patterns, dramatic increases in volume and speed of international travel and commerce, microbial adaptation and change, and breakdown of public health capacity [1] . The World Health Organization has prioritized a number of infectious diseases as requiring urgent need for research and development given the concern for potential of severe outbreaks. cache = ./cache/cord-275602-cog4nma0.txt txt = ./txt/cord-275602-cog4nma0.txt === reduce.pl bib === id = cord-272066-f6q6q3io author = Shim, Byoung-Shik title = Sublingual Delivery of Vaccines for the Induction of Mucosal Immunity date = 2013-06-30 pages = extension = .txt mime = text/plain words = 2763 sentences = 114 flesch = 20 summary = These studies have successfully demonstrated the safety and efficacy of sublingual immunization in inducing antigen-specific systemic and mucosal immune responses and protection against pathogen challenges. Taken together, these studies recognized the sublingual mucosa as a potential route of vaccine delivery, which promotes the induction broadly distributed humoral and cell-mediated immune response in systemic lymphoid tissues as well as various mucosal compartments, to offer protection against pathogens that possess tropism for mucosal epithelia. In one study, a recombinant influenza virus M2 protein-based subunit vaccine containing three tandem copies of the M2e (3M2eC) was expressed in Escherichia coli, and the protective efficacy of parenteral and sublingual immunizations was compared (7) . Sublingual sHA1 immunization induced neutralizing antibody responses in the serum and in the respiratory mucosa and provided complete protection against a lethal challenge with pandemic H1N1 influenza A/CA/04/09 virus. In this report, sublingual administration of rADV-S in mice induced SARS virus-specific neutralizing antibody response in the serum and secretory IgA response in the respiratory mucosa. cache = ./cache/cord-272066-f6q6q3io.txt txt = ./txt/cord-272066-f6q6q3io.txt === reduce.pl bib === id = cord-274643-vjb2yt93 author = Kang, G. title = Viral Diarrhea date = 2008-08-26 pages = extension = .txt mime = text/plain words = 5682 sentences = 282 flesch = 39 summary = Of the 'non-group A' rotaviruses, group B rotavirus has been identified in epidemic outbreaks of severe diarrhea in adults in China and in symptomatic infections in children. Between 20% and 50% of cases of gastroenteritis caused by rotavirus in hospitals are considered to be of nosocomial origin, and nosocomial viral enteric infections have been documented in up to 6% of children admitted for more than 72 hours in both developed and developing countries. Rotaviruses induce a clinical illness characterized by vomiting, diarrhea, abdominal discomfort, fever, and dehydration (or a combination of some of these symptoms) that occurs primarily in infants and young children and may lead to hospitalization for rehydration therapy. Studies in adult volunteers indicate that people with detectable levels of antibodies do not develop the illness, although epidemiological observations suggest that human astrovirus infections do not induce heterotypic immunity, as an episode of astrovirus diarrhea is not associated with a reduced incidence of a subsequent episode. cache = ./cache/cord-274643-vjb2yt93.txt txt = ./txt/cord-274643-vjb2yt93.txt === reduce.pl bib === id = cord-271122-3fsl5589 author = Wathes, D. Claire title = Importance of Viral Disease in Dairy Cow Fertility date = 2019-07-24 pages = extension = .txt mime = text/plain words = 7111 sentences = 346 flesch = 44 summary = Acute infection with non-cytopathic bovine viral diarrhea virus (BVDV) in mid-gestation increases abortion rates or causes the birth of persistently infected calves. In cultured bovine endometrial cells, experimental infection with ncp BVDV inhibited a variety of immune pathways normally activated in response to a challenge with bacterial lipopolysaccharide (LPS), including downregulation of many interferon-stimulated genes (ISGs), which are an important part of uterine defense mechanisms [40, 41] . Establishment of persistent infection with non-cytopathic bovine viral diarrhoea virus in cattle is associated with a failure to induce type I interferon A field investigation of the effects of bovine viral diarrhea virus infection around the time of insemination on the reproductive performance of cattle The effect of infection with bovine viral diarrhea virus on the fertility of Swiss dairy cattle Embryos produced from fertilization with bovine viral diarrhea virus (BVDV)-infected semen and the risk of disease transmission to embryo transfer (ET) recipients and offspring cache = ./cache/cord-271122-3fsl5589.txt txt = ./txt/cord-271122-3fsl5589.txt === reduce.pl bib === id = cord-273326-gmw8gl2r author = Saiz, Juan-Carlos title = Host-Directed Antivirals: A Realistic Alternative to Fight Zika Virus date = 2018-08-24 pages = extension = .txt mime = text/plain words = 7111 sentences = 293 flesch = 34 summary = In this line, and contrary to above mentioned report [73] , CQ, an FDA-approved anti-inflammatory 4-aminoquinoline and an autophagy inhibitor widely used as an anti-malaria drug that is administered to pregnant women at risk of exposure to Plasmodium parasites, was shown to have anti-ZIKV activity in different cell types (Vero cells, human brain microvascular endothelial cells (hBMECs), and human neural stem cells (NSCs)), affecting early stages of the viral life cycle, possibly by raising the endosomal pH and inhibiting the fusion of the envelope protein to the endosomal membrane [74, 75] . Similarly, by using a drug repurposing screening of over 6000 molecules, it was found that emricasan, a pan-caspase inhibitor that restrains ZIKV-induced increases in caspase-3 activity and is currently in phase 2 clinical trials in chronic hepatitis C virus (HCV)-infected patients, protected human cortical neural progenitor cells (NPC) in both monolayer and three-dimensional organoid cultures, showing neuroprotective activity without suppression of viral replication [82] . cache = ./cache/cord-273326-gmw8gl2r.txt txt = ./txt/cord-273326-gmw8gl2r.txt === reduce.pl bib === id = cord-273708-2q64at3z author = Annunziata, Giuseppe title = May Polyphenols Have a Role Against Coronavirus Infection? An Overview of in vitro Evidence date = 2020-05-15 pages = extension = .txt mime = text/plain words = 3067 sentences = 148 flesch = 34 summary = In this context, a great interest has been focused on resveratrol (RSV), whose antiviral mechanisms of actions are mainly attributable to its ability to inhibit the viral replication via (i) inhibition of immediate-early virus protein expression (i.e., ICP-4 and−27), (ii) inhibition of the NFκB signaling pathway, and (iii) activation of the AMPK/Sirt1 axis in the host cell (14) . The present mini-review aimed to report the few promising evidence regarding the potential anti-coronavirus activity of polyphenols, which may serve to drive the research toward the development of novel strategies to counteract the SARS-CoV2 pandemic. Studies available in the literature agree in establishing that the reduction of virus titer and the inhibition of nucleocapsid protein expression are their main general mechanisms of action at the base of this promising effect of polyphenols. cache = ./cache/cord-273708-2q64at3z.txt txt = ./txt/cord-273708-2q64at3z.txt === reduce.pl bib === id = cord-276006-mjjnkqv6 author = Jarach, Natanel title = Polymers in the Medical Antiviral Front-Line date = 2020-07-31 pages = extension = .txt mime = text/plain words = 12573 sentences = 738 flesch = 41 summary = Those anions show antiviral properties by affecting Larson studied modified PEI composed of N,N-Dodecylmethyl-PEI that exhibited antiviral effect on HSV-1 and HSV-2 viruses (see also Figure 6 ) [98] , influenza A virus [99] and on poliovirus and rotavirus [100] . Larson studied modified PEI composed of N,N-Dodecylmethyl-PEI that exhibited antiviral effect on HSV-1 and HSV-2 viruses (see also Figure 6 ) [98] , influenza A virus [99] and on poliovirus and rotavirus [100] . Xiao and Xue examined the antiviral effect of quaternary pyridinium containing co-polymers on several Influenza viruses (A, PR8, 8, 34) , as demonstrated in Figure 11 [35]. Xiao and Xue examined the antiviral effect of quaternary pyridinium containing co-polymers on several Influenza viruses (A, PR8, 8, 34) , as demonstrated in Figure 11 [35]. cache = ./cache/cord-276006-mjjnkqv6.txt txt = ./txt/cord-276006-mjjnkqv6.txt === reduce.pl bib === id = cord-273777-qb0vp9gr author = Happel, Anna-Ursula title = The Vaginal Virome—Balancing Female Genital Tract Bacteriome, Mucosal Immunity, and Sexual and Reproductive Health Outcomes? date = 2020-07-30 pages = extension = .txt mime = text/plain words = 6250 sentences = 279 flesch = 30 summary = A range of vaginal DNA viruses infecting eukaryote cells have been identified by shotgun metagenomics of vaginal samples from generally healthy, asymptomatic women of reproductive age participating in the Human Microbiome Project (HMP) [9] , including double-stranded (ds) DNA (families Adenoviridae, Herpesviridae, Papillomaviridae and Polyomaviridae) and single-stranded (ss) DNA viruses (families Anelloviridae) ( Table 1 and Figure 1 ). Although prokaryotic-infecting viruses, from now on referred to as bacteriophages, are estimated to be amongst the most abundant living entities on Earth [24] and are thought to play an important role in shaping the bacterial microbiota and associated health outcomes in the human gut [5, [25] [26] [27] , oral cavity [28, 29] , skin [30, 31] and lungs [32] , their role in the lower reproductive tract is understudied. Observational studies have shown that the acquisition and transmission of viral sexually transmitted infections (STIs), including HSV-2, HPV and HIV, are more common in women with high diversity, nonoptimal vaginal bacterial microbiota [42] [43] [44] . cache = ./cache/cord-273777-qb0vp9gr.txt txt = ./txt/cord-273777-qb0vp9gr.txt === reduce.pl bib === id = cord-276348-vr5fit8r author = Ogra, Pearay L. title = Respiratory syncytial virus: The virus, the disease and the immune response date = 2004-01-31 pages = extension = .txt mime = text/plain words = 4788 sentences = 282 flesch = 44 summary = 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. 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. Children at increased risk from RSV infection include young infants with prematurity, bronchopulmonary dysplasia, congenital heart disease, congenital or acquired immunodeficiency, subjects with hematologic malignancies, patients with bone-marrow or organ transplants, and cystic fibrosis. 6 It is important to recognise that virtually all children who get infected with RSV develop virus-specific IgE homocytotropic antibody in the respiratory tract. cache = ./cache/cord-276348-vr5fit8r.txt txt = ./txt/cord-276348-vr5fit8r.txt === reduce.pl bib === id = cord-276193-cngz535o author = Volz, A. title = Modified Vaccinia Virus Ankara: History, Value in Basic Research, and Current Perspectives for Vaccine Development date = 2016-08-01 pages = extension = .txt mime = text/plain words = 17857 sentences = 787 flesch = 36 summary = Safety tested Modified Vaccinia virus Ankara (MVA) is licensed as third-generation vaccine against smallpox and serves as a potent vector system for development of new candidate vaccines against infectious diseases and cancer. Immunizations with this MVA deletion mutant led to significantly enhanced virus-specific CD8+ T-cell responses and increased protective capacity against lethal challenge infection with virulent VACV strain Western Reserve (WR) . Upon prime-boost vaccinations in BALB/c mice, all four MVA-WNV candidate vaccines elicited circulating serum antibodies binding to recombinant WNV-E protein and neutralizing WNV in tissue culture infections In addition, immunizations in HLA-A2.1-/HLA-DR1-transgenic H-2 class I-/class II-knockout mice efficiently induced WNV-E-specific CD8+ T-cell responses. At the moment, recombinant MVA viruses expressing various heterologous antigens are among the most promising vector candidates to develop innovative vaccination strategies to protect against complex infections such as AIDS, tuberculosis, or malaria, or against rare but threatening emerging diseases. cache = ./cache/cord-276193-cngz535o.txt txt = ./txt/cord-276193-cngz535o.txt === reduce.pl bib === id = cord-276585-m1dkkbq7 author = Pulliam, Juliet R. C. title = Viral Host Jumps: Moving toward a Predictive Framework date = 2008-02-13 pages = extension = .txt mime = text/plain words = 6920 sentences = 349 flesch = 41 summary = Focusing on the appearance of viral pathogens in new host species, I outline a framework that uses specific molecular characteristics to rank virus families by their expected a priori ability to complete each of three steps in the emergence process (encounter, infection, and propagation). This approach yields predictions consistent with empirical observations regarding the ability of specific viral families to infect novel host species but highlights the need for consideration of other factors, such as the ecology of host interactions and the determinants of cellular susceptibility and permissivity to specific virus groups, when trying to predict the frequency with which a virus will encounter a novel host species or the probability of propagation within a novel host species once infection has occurred. Although he makes no attempt to quantitatively determine the relative frequency of emergence for different types of pathogens, Burke claims that recent pandemics in humans and wildlife have mostly been caused by RNA viruses, citing multiple examples (influenza A, HIV-1, enteroviruses 70 and 71, human T-cell lymphoma virus, three paramyxoviruses, porcine respiratory coronavirus, and a calicivirus that causes hemorrhagic disease in rabbits). cache = ./cache/cord-276585-m1dkkbq7.txt txt = ./txt/cord-276585-m1dkkbq7.txt === reduce.pl bib === id = cord-275719-ru33ubss author = Roingeard, Philippe title = Virus detection by transmission electron microscopy: Still useful for diagnosis and a plus for biosafety date = 2018-11-09 pages = extension = .txt mime = text/plain words = 2555 sentences = 146 flesch = 44 summary = Despite the lack of established methods of biological sample preparation for transmission electron microscopy (TEM) at this time, Helmut Ruska was able to characterize the morphology of several viruses and he developed a rough viral classification based on the size and shape of the viral particles. 4 TEM was rapidly adopted for its first major use in clinical virology: the differential diagnosis of smallpox, caused by the variola virus Abbreviations: ELISA, enzyme-linked immunosorbent assay; EM, electron microscopy; EMEA, European Medicines Agency; FDA, Food and Drug Administration; FPERT, fluorescent product-enhanced reverse transcription; LCMV, lymphocytic choriomeningitis virus; PCR, polymerase chain reaction; SARS, severe acute respiratory syndrome; SFTS, severe fever with thrombocytopenia syndrome; TEM, transmission electron microscopy from the poxvirus family, and chickenpox, caused by the varicellazoster virus of the herpes family, based on investigations of fluid samples from the vesicles on the patients' skin. Detection of retrovirus-like particles by transmission electron microscopy (TEM) with negative staining in bulk harvests of rodent cells used for the production of biological products. cache = ./cache/cord-275719-ru33ubss.txt txt = ./txt/cord-275719-ru33ubss.txt === reduce.pl bib === id = cord-276212-ys5njiw0 author = Wei, L. title = Burden, seasonal pattern and symptomatology of acute respiratory illnesses with different viral aetiologies in children presenting at outpatient clinics in Hong Kong date = 2015-05-30 pages = extension = .txt mime = text/plain words = 2860 sentences = 117 flesch = 40 summary = authors: Wei, L.; Chan, K.-H.; Ip, D.K.M.; Fang, V.J.; Fung, R.O.P.; Leung, G.M.; Peiris, M.J.S.; Cowling, B.J. title: Burden, seasonal pattern and symptomatology of acute respiratory illnesses with different viral aetiologies in children presenting at outpatient clinics in Hong Kong In this study, we aimed to investigate the burden of ARIs caused by different respiratory viral pathogens among children aged 15 years in a community outpatient setting, to describe their seasonal patterns of occurrence, and to characterize their clinical characteristics at presentation. The specimens were tested for eight common respiratory viruses (including types and subtypes), namely IFVA (subtypes H1 and H3), influenza virus B (IFVB), RSV (subtypes A and B), PIV (types 1-4), metapneumovirus (MPV), enterovirus (EnV)/RhV, AdV, bocavirus (BoV), and coronavirus (CoV) (types NL63, HKU1, 229E, and OC43), with the xTAG RVP FAST version 2.0 multiplex assay (Luminex Molecular Diagnostics, Toronto, Ontario, Canada), and this was followed by product detection and identification with a Luminex suspension microarray [7] . cache = ./cache/cord-276212-ys5njiw0.txt txt = ./txt/cord-276212-ys5njiw0.txt === reduce.pl bib === id = cord-276009-p98wjtjb author = Iyer, Arun V. title = Recombinant vesicular stomatitis virus-based west Nile vaccine elicits strong humoral and cellular immune responses and protects mice against lethal challenge with the virulent west Nile virus strain LSU-AR01 date = 2009-02-05 pages = extension = .txt mime = text/plain words = 7538 sentences = 406 flesch = 45 summary = title: Recombinant vesicular stomatitis virus-based west Nile vaccine elicits strong humoral and cellular immune responses and protects mice against lethal challenge with the virulent west Nile virus strain LSU-AR01 These results suggest that VSV-vectored vaccines administered intranasally can efficiently induce protective humoral and cellular immune responses against WNV infections. The salient features of this vaccine study are: (1) A prime-boost intranasal vaccination approach with recombinant VSVs expressing the WNV E glycoprotein produced robust CD8 + IFN␥ + T cell responses; (2) This vaccine approach produced strong neutralizing titers against the WNV; (3) Vaccinated mice were protected against lethal challenge and they were free of neuronal necrosis, while unvaccinated mice There was no statistically significant difference observed between these two groups. These results suggest that a prime-boost VSV-vectored intranasal vaccine approach induces strong humoral and cellular immune responses that protect mice against WNV-induced neuronal necrosis. cache = ./cache/cord-276009-p98wjtjb.txt txt = ./txt/cord-276009-p98wjtjb.txt === reduce.pl bib === id = cord-276052-gk6n8slx author = Yadav, Pragya title = Isolation of Tioman virus from Pteropus giganteus bat in North-East region of India date = 2016-09-09 pages = extension = .txt mime = text/plain words = 3005 sentences = 164 flesch = 51 summary = During the survey for Nipah virus among bats at North-East region of India; Tioman virus (TioV), a new member of the Paramyxoviridae family was isolated from tissues of Pteropus giganteus bats for the first time in India. While investigating NiV in urine samples of giant fruit bats of the Pteropus genus on Tioman Island, Malaysia, in 2001, researchers isolated a novel virus which was placed in the Rubulavirus genus of the Paramyxoviridae family. In order to study susceptibility of different vertebrate cells to TioV, the infectious virus titer was determined by estimating 50% tissue culture infective dose (TCID 50 ) using Reed and Muench method (Reed and Muench, 1938) . Negative contrast electron microscopy of the cell supernatant of Vero CCL-81 infected with virus isolate showed the presence of virus particles with the typical paramyxovirus morphology. TioV isolated from kidney tissue homogenate of bat showed a titer of 10 4.61 /100 μL by TCID 50 in Vero CCL-81 cell line. cache = ./cache/cord-276052-gk6n8slx.txt txt = ./txt/cord-276052-gk6n8slx.txt === reduce.pl bib === id = cord-276715-d1nh2dvb author = Raha, Syamal title = Is Copper beneficial for COVID-19 patients? date = 2020-05-05 pages = extension = .txt mime = text/plain words = 1610 sentences = 103 flesch = 50 summary = Besides, Cu can kill several infectious viruses such as bronchitis virus, poliovirus, human immunodeficiency virus type 1(HIV-1), other enveloped or nonenveloped, singleor double-stranded DNA and RNA viruses. Based on available data, we hypothesize that enrichment of plasma copper levels will boost both the innate and adaptive immunity in people. Copper exposure to human coronavirus 229E destroyed the viral genomes and irreversibly affected virus morphology, including disintegration of envelope and dispersal of surface spikes [16] . Copper deficiency could lead a decreased number of circulatory blood cells with a greater susceptibility towards infection in older people In a study of 11 men on a low-Cu diet (0.66 mg Cu/day for 24 days and 0.38 mg/day for another 40 days) showed a decreased proliferation response of their white blood cells when presented with an immune challenge in cell culture [33] . Thujaplicin-copper chelates inhibit replication of human influenza viruses Effects of low-copper diets on human immune response cache = ./cache/cord-276715-d1nh2dvb.txt txt = ./txt/cord-276715-d1nh2dvb.txt === reduce.pl bib === id = cord-275821-yu39aw54 author = Ciminski, Kevin title = Novel insights into bat influenza A viruses date = 2017-09-14 pages = extension = .txt mime = text/plain words = 5218 sentences = 259 flesch = 44 summary = Although there is a certain degree of functional compatibility between bat and conventional influenza A virus proteins, there are striking differences, including receptor usage, polarity of infection and reassortment potential. In addition, as the bat IAV non-structural protein 1 (NS1) was previously shown to share the dsRNA-binding property and IFN-suppression characteristics of conventional IAV NS1s [38] , an infectious recombinant PR8 virus encoding the NS1 but not NEP gene of HL17NL10 could be generated [39] . The vRNA packaging signals and the NP proteins of The exchange of genomic segments is known to take place in cells co-infected with different conventional IAV subtypes. Likewise, based on experiments with chimeric bat influenza viruses, genomic reassortment is believed to occur in cells co-infected with the known bat IAV subtypes. cache = ./cache/cord-275821-yu39aw54.txt txt = ./txt/cord-275821-yu39aw54.txt === reduce.pl bib === id = cord-275795-ee7qyw5h author = Monette, Anne title = T Lymphocytes as Measurable Targets of Protection and Vaccination Against Viral Disorders date = 2018-10-24 pages = extension = .txt mime = text/plain words = 28265 sentences = 1205 flesch = 38 summary = We focus on immunity generated against both natural infection and vaccination, where a steady shift in conferred vaccination immunogenicity is observed from quantifying activated and proliferating, long-lived effector memory T cell subsets, as the prominent biomarkers of long-term immunity against viruses and their associated disorders causing high morbidity and mortality rates. Since that time, the occurrence of epidemics and outbreaks are now at lower risk, following the introduction of massive vaccination programs able to induce immune system targeting of viruses causing severe disorders affecting distinct geographical locations, and with many epidemiological reports demonstrating long-term efficacy of viral control of non-naïve populations. This approach is being developed to use virus-infected cell-killing antibodies that produce an antiviral environment; these termed antibody-dependent cellular cytotoxicity (ADCC)-mediating antibodies, which are predicted to link innate and adaptive immune responses, and is becoming possible due to new technologies for rapid isolation and characterization of monoclonal antibodies targeting conserved regions of influenza virus, reviewed in Jegaskanda et al. cache = ./cache/cord-275795-ee7qyw5h.txt txt = ./txt/cord-275795-ee7qyw5h.txt === reduce.pl bib === id = cord-275570-i9fw0afj author = Lau, Susanna K. P. title = Molecular Research on Emerging Viruses: Evolution, Diagnostics, Pathogenesis, and Therapeutics date = 2018-01-30 pages = extension = .txt mime = text/plain words = 1475 sentences = 84 flesch = 42 summary = The recent epidemics caused by Zika virus and Middle East respiratory syndrome coronavirus (MERS-CoV) clearly illustrate the ability of emerging viruses to pose huge public health problems within a short time. In this special issue, "Molecular Research on Emerging Viruses: Evolution, Diagnostics, Pathogenesis, and Therapeutics", insights into advances and discoveries in understanding the different aspects of various emerging viruses are given by eight original studies and four review articles. Three articles focus on arthropod-borne viruses (arboviruses) which are important emerging pathogens having caused various epidemics in recent years. In the systematic review and meta-analysis study by Coelho et al., the prevalence of microcephaly in infants born to Zika virus-infected women among all pregnancies was estimated [6] , which may contribute to the understanding of the public health impact of this emerging arbovirus. Two articles report on the virus-host interaction during porcine reproductive and respiratory syndrome virus (PRRSV) infection which causes severe losses in the swine industry worldwide. cache = ./cache/cord-275570-i9fw0afj.txt txt = ./txt/cord-275570-i9fw0afj.txt === reduce.pl bib === id = cord-274080-884x48on author = Rumlová, Michaela title = In vitro methods for testing antiviral drugs date = 2018-06-30 pages = extension = .txt mime = text/plain words = 17989 sentences = 941 flesch = 41 summary = For the majority of animal viruses, the activation of these fusion or penetration mechanisms occurs through conformational changes and structural rearrangements in viral surface proteins and/or the whole virion shell that may destabilize the capsid core. D: Three mechanisms (I.-III.) of DNA viruses replication are shown: (I): Following entry and uncoating, the DNA genome is transported to the nucleus; products of early genes (regulatory proteins, transcription factors) regulate the synthesis of viral enzymes (e.g. DNA polymerase) required for genome replication; expression of late genes encoding structural capsid proteins in the cytosol, they are then transported into nucleus where packaging and pre-assembly take place; preassembled procapsids exit the nucleus and leave the cell (e.g. Herpesviruses). Here, we provide an overview of in vitro methods, including cell-based assays, that may be suitable for screening of antivirotics that interfere with the key steps of viral life cycles and target either virus or cell-encoded proteins required for the infectivity. cache = ./cache/cord-274080-884x48on.txt txt = ./txt/cord-274080-884x48on.txt === reduce.pl bib === id = cord-277107-gs7j6fxo author = Yamin, Mohammad title = Counting the cost of COVID-19 date = 2020-05-13 pages = extension = .txt mime = text/plain words = 4178 sentences = 236 flesch = 64 summary = Coronavirus disease 2019 (COVID-19) is the name given by the World Health Organization (WHO) to the highly contagious and infectious disease caused by the Novel Corona Virus or SARS-CoV-2, which was first reported on 31 December 2019 in Wuhan city of the capital of China's Hubei province. In recent years we have witnessed an increased growth and spread of communicable and highly contagious viruses and diseases like EBOLA [3] , HIV Aids [4] , Swine Influenza (H1N1, H1N2) [5] , various strands of Flu [6] , Severe Acute Respiratory Syndrome (SARS) [7] and Middle Eastern Respiratory Syndrome (MERS) [8] in Africa, the Middle East and several other parts of the world. The coronavirus disease COVID-19 is a highly transmittable and pathogenic viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ( Fig. 1) , which is resulting in a heavy toll on people's lives and colossal economic damage. cache = ./cache/cord-277107-gs7j6fxo.txt txt = ./txt/cord-277107-gs7j6fxo.txt === reduce.pl bib === id = cord-277392-s0bldxg9 author = Cann, Alan J. title = Replication date = 2012-02-29 pages = extension = .txt mime = text/plain words = 7934 sentences = 376 flesch = 49 summary = This simple step is the key to the entire experiment, because it effectively synchronizes the infection of the cells and allows the subsequent phases of replication in a population of individual cells and virus particles to be viewed as if they were a single interaction (in much the same way that molecular cloning of nucleic acids allows analysis of populations of nucleic acid molecules as single species). (At the time, it was generally believed that proteins, which consist of a much more complex mixture of more than 20 different amino acids, were the carriers of the genes and that DNA was probably a structural component of cells and viruses.) Together, these two experiments illustrate the essential processes of virus replication. n Fusion of the virus envelope (so this is only applicable to enveloped viruses) with the cell membrane, either directly at the cell surface or following endocytosis in a cytoplasmic vesicle (Figure 4.12) , which requires the presence of a specific fusion protein in the virus envelopedfor example, influenza hemagglutinin or retrovirus transmembrane (TM) glycoproteins. cache = ./cache/cord-277392-s0bldxg9.txt txt = ./txt/cord-277392-s0bldxg9.txt === reduce.pl bib === id = cord-276583-j8bf0eme author = Ghalyanchi Langeroudi, Arash title = Full-length characterization and phylogenetic analysis of hemagglutinin gene of H9N2 virus isolated from broilers in Iran during 1998–2007 date = 2012-01-21 pages = extension = .txt mime = text/plain words = 5360 sentences = 266 flesch = 53 summary = The results showed that all nine representative H9N2 isolates belong to low pathogenic AIVs since none of the amino acid sequences at the cleavage site of the HA of the isolates possessed the basic motif required for highly pathogenic viruses (R-X-R/K-R). Amino acid sequences at the cleavage site of the HA of the isolates possessed -P-A-R-S-S-R-G-L-motif, except for two isolated: TH85 (A to T) and Fig. 1 Phylogenetic relationships of HA genes of representative influenza A viruses isolated in Iran, Middle Eastern, Eurasian countries, and USA. In the present study, seven from nine H9N2 Iranian isolates possessed amino acid 226-L (numbered according to H3) at the receptor binding site, indicating its potential to infect humans. Sequence and phylogenetic analysis of the haemagglutinin genes of H9N2 avian influenza viruses isolated from commercial chickens in Iran Sequence analysis and phylogenetic study of hemagglutinin Gene of H9N2 subtype of avian influenza virus isolated during 1998-2002 in Iran cache = ./cache/cord-276583-j8bf0eme.txt txt = ./txt/cord-276583-j8bf0eme.txt === reduce.pl bib === id = cord-278093-0twnkv93 author = Perveen, Shagufta title = Coronavirus nCOVID-19: A Pandemic Disease and the Saudi precautions date = 2020-06-18 pages = extension = .txt mime = text/plain words = 3149 sentences = 162 flesch = 56 summary = Recently a novel coronavirus (nCOVID-19) has first emerged in China, causing multiple symptoms in humans and closely related to those caused by SARS (Severe Acute Respiratory Syndrome) and MERS (Middle East Respiratory Syndrome). In these circumstances, rapid reviews which recommended by WHO (World Health Organization), and these recommendations are very significant, helpful and cover current data with different preventive measures developed by the Saudi CDC (Saudi Centre for Disease Prevention and Control). Taking into consideration the preventive measures by pharmacists as part of health care professions, however, the number of infected people, especially those with close contact with nCOVID-19 patients, are rise day by day and currently seems unstoppable. In comparison to other members of coronaviruses ,which cause humans respiratory infections, SARS-CoV (first then it has spread to 216 different countries and territories all over the world, and it seems more deadly. cache = ./cache/cord-278093-0twnkv93.txt txt = ./txt/cord-278093-0twnkv93.txt === reduce.pl bib === id = cord-277327-il8uaavn author = Couch, MD, Robert B. title = Respiratory Viral Infections in Immunocompetent and Immunocompromised Persons date = 1997-03-17 pages = extension = .txt mime = text/plain words = 3712 sentences = 207 flesch = 33 summary = 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. The frequencies of pneumonia and death associated with a documented infection among immunocompromised adult leukemia and bone marrow transplant patients hospitalized at MDACC are shown in Table VII . Although overall frequencies of pneumonia and death appear similar for each virus, analysis of patterns of occurrences suggested a greater severity for RSV infection after bone marrow transplantation or chemotherapy than for the other viruses. Thus, the immune deficiencies described for immunocompromised persons can account for a high frequency of viral respiratory infections as well as an increased severity of illness and a significant risk of death. Combination therapy with aerosolized ribavirin and intravenous immunoglobulin for respiratory syncytial virus disease in adult bone marrow transplant recipients cache = ./cache/cord-277327-il8uaavn.txt txt = ./txt/cord-277327-il8uaavn.txt === reduce.pl bib === id = cord-275683-1qj9ri18 author = Roux, Simon title = Metagenomics in Virology date = 2019-06-12 pages = extension = .txt mime = text/plain words = 5891 sentences = 225 flesch = 37 summary = Against the background of an extensive viral diversity revealed by metagenomics across many environments, new sequence assembly approaches that reconstruct complete genome sequences from metagenomes have recently revealed surprisingly cosmopolitan viruses in specific ecological niches. However, these techniques can only detect previously known viruses, and often require Box 1 Use of complementary methods to target different types of viruses A number of approaches have been developed to specifically select and survey the genetic material contained by virus particles in a given sample. Virus sequences obtained from "bulk" metagenomes will typically reflect viruses infecting their host cell at the time of sampling, either actively replicating or not, while viromes enables a deeper and more focused exploration of the virus diversity in a specific site or sample. With viral metagenomics being applied to a larger set of samples and environments, and with bioinformatic analyses including genome assembly and interpretation constantly improving, novel groups of dominant and widespread viruses may thus be progressively revealed across many environments. cache = ./cache/cord-275683-1qj9ri18.txt txt = ./txt/cord-275683-1qj9ri18.txt === reduce.pl bib === id = cord-277010-2iecsho0 author = Wen, Xiaohong title = Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study date = 2019-01-08 pages = extension = .txt mime = text/plain words = 3100 sentences = 153 flesch = 47 summary = title: Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study Similarly, the positive rate of cases with a single virus infection was highest in the young children (65.5%) and lowest in adults of 18-60 years of age (38.5%). The proportion of respiratory viruses notably differed across different age groups; the virus positive rate was the highest in young children under 5 years but was lowest in adults (18~60 years) in this study. Therefore, all positive RhV and/or EV specimens and 10 FluA virus specimens with random selection were identified Table 2 Age distribution of viruses from outpatients with ARIs ARIs, acute respiratory infections by sequencing assay, respectively, and among them, four RhV positive and 3 EV positive specimens were not sequenced due to low viral load in the specimens. In summary, this study provides important epidemiologic data regarding the clinical characteristics, viral spectrum, age distribution and seasonality of viruses in outpatients with ARIs in Huzhou, China. cache = ./cache/cord-277010-2iecsho0.txt txt = ./txt/cord-277010-2iecsho0.txt === reduce.pl bib === id = cord-276039-nqqwnmwc author = Rua, Rejane title = Origin, evolution and innate immune control of simian foamy viruses in humans date = 2015-02-17 pages = extension = .txt mime = text/plain words = 4070 sentences = 229 flesch = 52 summary = In this review, we present current data on the discovery, cross-species transmission, and molecular evolution of SFV in human populations initially infected and thus at risk for zoonotic emergence. In this brief review, we will present the current available data on the discovery, cross-species transmission and molecular evolution of the simian foamy viruses (SFV) present in different human populations at risk for zoonotic emergence. They were mostly hunters who reported direct contacts with blood and/or body fluids from wild NHPs. We extended such studies into different areas and populations of this Central African country and found the presence of SFV infection in at least 50 persons [12 ] . Origin, evolution and innate immune control of simian foamy viruses in humans Rua and Gessain 51 Table 1 SFV tropism and viral load in the blood of SFV-infected humans and NHPs. The proportion of SFV DNA positive samples among leukocyte populations in SFV-infected NHP and SFVinfected humans is indicated. cache = ./cache/cord-276039-nqqwnmwc.txt txt = ./txt/cord-276039-nqqwnmwc.txt === reduce.pl bib === id = cord-278250-dwok857k author = Li, Heng title = The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites date = 2019-08-19 pages = extension = .txt mime = text/plain words = 7452 sentences = 379 flesch = 44 summary = We performed metagenomic sequencing of fecal samples to detect the bacterial microbiome and virome composition of healthy one-year-old rhesus monkeys housed at the IMBCAMS (Fig. 1) . We comprehensively analyzed the interactions among the gut virome, bacterial microbiome and metabolomes based on the above results there were noticeable differences in bacterial β-diversity between control and experimental animals, as determined using principal component analysis (PCA), and the results showed good repeatability within a single group (Additional file 2: Figure S2F ). Briefly, the fecal virome composition was noticeably altered after depletion of the bacterial microbiome, and the abundances of many DNA viruses, bacteriophages and RNA viruses in the gut were clearly decreased. As expected, the whole gut bacterial microbiome, including gram-positive and gram-negative bacteria (Additional file 2: Figure S2E ), was depleted after treatment with the antibiotic cocktail, except for Escherichia-Shigella species belonging to Proteobacteria, which were resistant to the cocktail. cache = ./cache/cord-278250-dwok857k.txt txt = ./txt/cord-278250-dwok857k.txt === reduce.pl bib === id = cord-275538-c44gmu22 author = Davis-Wurzler, Gina M. title = Current Vaccination Strategies in Puppies and Kittens date = 2006-03-24 pages = extension = .txt mime = text/plain words = 10385 sentences = 472 flesch = 41 summary = The current recommendation is to use the CAV-II MLV because it stimulates the immune system to protect against CAV-I and CAV-II without the associated adverse reaction caused by the type I vaccine [4, 14, 20] . There is a killed vaccine available; however, vaccination against this agent is typically not recommended, because most animals are not at risk to contract the parasite, the vaccine does not prevent infection (it may ameliorate clinical signs and decrease cyst shedding), and the disease is readily amenable to therapy (fenbendazole, albendazole, and metronidazole are off-label uses but commonly accepted as standard of care). Because the vaccine does not fully prevent infection and carries an association with adverse events that may be greater than the actual disease, routine vaccination of household pets with this product is generally not recommended. cache = ./cache/cord-275538-c44gmu22.txt txt = ./txt/cord-275538-c44gmu22.txt === reduce.pl bib === id = cord-277400-w7mvk3x4 author = Nasir, Arshan title = Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification date = 2017-03-10 pages = extension = .txt mime = text/plain words = 7527 sentences = 398 flesch = 47 summary = While the member viruses within a lineage exhibit strong 3D structural similarities in capsid/coat fold architectures (or principles in constructing a functional virion) regardless of the viral replicon (i.e., DNA or RNA) and/or infected host type, the lineages however are believed to be unrelated to each other indicating the polyphyletic origin of viruses (Bamford, 2003) . The b.121 fold in the SCOP hierarchy includes 7 children FSFs (that are not necessarily related in evolution according to SCOP definitions): (i) "PHM/PNGase F" FSF (b.121.1) involved in oxidation-reduction metabolic processes (not detected in any of our sampled viral proteomes), (ii) "Group II dsDNA viruses VP" FSF (b.121.2), which is the "double β-barrel" fold signature of the PRD1/Adenovirus-like lineage (read below), (iii) "Nucleoplasmin-like core domain" FSF (b.121.3) involved in the assembly of nucleosomes in cells, and (iv-vii) FSFs b.121.4, b.121.5, b.121.6, and b.121.7 (Figure 1 ) that define the picornavirus-like lineage and are individually described below. cache = ./cache/cord-277400-w7mvk3x4.txt txt = ./txt/cord-277400-w7mvk3x4.txt === reduce.pl bib === id = cord-278099-ypov9ha3 author = Kumar, Surender title = Molecular characterization of a novel cryptic virus infecting pigeonpea plants date = 2017-08-03 pages = extension = .txt mime = text/plain words = 11403 sentences = 622 flesch = 55 summary = The four dsRNAs eluted from the agarose gel were purified and have been used as templates for RT-PCR amplification employed in SISPA to generate fulllength cDNAs. It is of interest to examine if ArCV-1 RNA dependent RNA polymerase (RdRp) structurally resembles the known RdRp of the dsRNA bacteriophage Փ-6, reovirus, or with other viruses like calciviruses and picornaviruses [12] [13] [14] [15] [16] . We report here the results of elaborated computer-assisted analysis of ArCV-1 replicase which revealed the presence of conserved sequence motifs (A to G) present in the fingers and palm subdomains of the polymerase that are shared in most of the RdRps. Interestingly, ArCV-1 replicase has more structural resemblances with several members of ssRNA (+) mono-partite Picornaviruses (viral replication by primer-dependent initiation), than the de novo dsRNA bacteriophage Փ-6 and reovirus polymerases. Possible functions of the residues of the A to G motifs described for identical RdRps was conserved with respect to the ArCV-1 3Dpol structure and was discussed in structural analysis of ArCVTable 1 ) and the 3' terminus contained the sequence "GCA CCCATATTC". cache = ./cache/cord-278099-ypov9ha3.txt txt = ./txt/cord-278099-ypov9ha3.txt === reduce.pl bib === id = cord-277641-nb1p1akx author = Shaw, D. M. title = Invisible Enemies: Coronavirus and Other Hidden Threats date = 2020-08-25 pages = extension = .txt mime = text/plain words = 2734 sentences = 117 flesch = 62 summary = Fourth, I go on to explore the underlying structural weaknesses and disparities in society that have been exposed by the virus but previously remained unconsidered for so long that they too have become camouflaged, even if their effects are all too apparent; like the virus, neoliberal capitalism is an invisible enemy that has made prisoners of us all. Only by rendering the rest of humanity morally visible to ourselves can we overcome capitalism and stop treating other people as invisible enemies. Socio-economic inequalities existed for centuries before coronavirus came along, but the crisis exposes the invisible enemy that underlies all our lives. The essential flaw of capitalism is that it forces us to treat other people as invisible enemies against whom we are always competing, day in, day out, in a battle to the death. But despite the necessity of physical distancing, coronavirus has reduced our moral distance from the people we share our planet with, revealing them to be not invisible enemies but friends in need. cache = ./cache/cord-277641-nb1p1akx.txt txt = ./txt/cord-277641-nb1p1akx.txt === reduce.pl bib === id = cord-276506-dj7dyo0x author = Coria, M. F. title = Protective effect of an inactivated avian coronavirus vaccine administered by aerosol date = 1973 pages = extension = .txt mime = text/plain words = 1796 sentences = 116 flesch = 51 summary = Chickens administered 2 doses of the inactivated Connecticut strain (IBV-46) vaccine by aerosol at 3-week intervals had significant levels of virus-neutralizing antibodies and were resistant to infection by the Massachusetts strain (IBV-41) as determined by virus isolation attempts. Immunity to avian infectious bronchitis (AIB), a highly contagious viral infection of the respiratory tract of chickens has been studied using live and inactivated virus vaccirres (6) . However, more recent evidence shows that a BPL-inactivated AIB virus vaccine administered by an aerosol and concurrent subcutaneous inoculation induced significant levels of VN antibodies and afforded a good degree of protection against infection (4) . Immunization of the human respiratory tract with inactivated influenza A2 I-IongKong virus (13) and rhinovirus type 13 (ii), administered by an aerosol, indicates that a significant protective effect was observed when compared to individuals vaccinated by subcutaneous or intra-muscular routes. The immune response to BPL-inactivated AIB virus vaccines administered by an aerosol, as determined by PI~-NI's, virus isolation (VI) and respiratory signs are shm~a~ in Table 1 . cache = ./cache/cord-276506-dj7dyo0x.txt txt = ./txt/cord-276506-dj7dyo0x.txt === reduce.pl bib === id = cord-278456-gsv6dh36 author = Qureshi, Abid title = AVCpred: an integrated web server for prediction and design of antiviral compounds date = 2016-09-09 pages = extension = .txt mime = text/plain words = 3465 sentences = 211 flesch = 49 summary = In this study, we have developed quantitative structure–activity relationship (QSAR)‐based models for predicting antiviral compounds (AVCs) against deadly viruses like human immunodeficiency virus (HIV), hepatitis C virus (HCV), hepatitis B virus (HBV), human herpesvirus (HHV) and 26 others using publicly available experimental data from the ChEMBL bioactivity database. We have integrated these models in the AVCpred web server, which will be helpful for virtual screening of AVCs and designing new compounds to target the viruses. The QSAR models have been integrated into a freely available and easy to use web server, 'AVCpred', where users can predict the antiviral potential of their query molecules against the different viruses in terms of percent inhibition value. In this study, we developed virus specific as well as general prediction models to identify the likelihood of a compound being antiviral using selected chemical attributes of experimentally validated AVCs. PaDEL, an open-source software, was used to calculate molecular descriptors and fingerprints. cache = ./cache/cord-278456-gsv6dh36.txt txt = ./txt/cord-278456-gsv6dh36.txt === reduce.pl bib === id = cord-277309-kelebqr6 author = Wang, Lin-Fa title = Viruses in bats and potential spillover to animals and humans date = 2019-01-18 pages = extension = .txt mime = text/plain words = 6080 sentences = 299 flesch = 49 summary = While it is not easy to assess the spillover potential of many SARS-CoV related bat CoVs due to unsuccessful attempts to isolate the viruses, it should be noted that a 'consensus' virus constructed via reverse genetics pointed to a high probability of human infection [19] . Further study is required to determine the true zoonotic potential of SADS-CoV and closely related bat CoVs. For unknown reasons, despite of the wide presence of CoVs in bats of different locations and species with relative high viral genome levels, multiple attempts by different international groups to isolate bat CoVs have been largely unsuccessful. The genetic and functional Viruses in bats and potential spillover to animals and humans Wang and Anderson 81 Aside from MenPV and TioPV, other paramyxoviruses from the genus Rubulavirus have been isolated from or detected in bats without evidence of zoonotic transmission. cache = ./cache/cord-277309-kelebqr6.txt txt = ./txt/cord-277309-kelebqr6.txt === reduce.pl bib === id = cord-276616-odmnvv7m author = Darcel, C. title = Reflections on scrapie and related disorders, with consideration of the possibility of a viral aetiology date = 1995 pages = extension = .txt mime = text/plain words = 10478 sentences = 494 flesch = 48 summary = Conclusions drawn from the vaccination trials and transmission experiments were that ~crapie, given by subcutaneous inoculation, had a latent period of 2 years and longer; that the infective agent was resistant to 0.35% formalin; that the disease appeared more quickly and in a higher percentage of recipients following intracerebral than following~subcutaneous injection; and that the causative agent was probably a filtrable virus. There are many difficulties in studying either the natural or experimentally induced diseases: the animals involved, the incubation period required for the emergence of the disease, the innate resistance of a proportion of the population seen as an expression of genetic influences, the differing behaviour of strains of agents isolated from a given species, the symptomatology, the pathology, the uncertain nature of the agent and its means of transmission, the perceived 'lack' of an immunological response or changes in the immune system, and the biological hazards involved in conducting experiments. cache = ./cache/cord-276616-odmnvv7m.txt txt = ./txt/cord-276616-odmnvv7m.txt === reduce.pl bib === id = cord-278635-vwdxr1bl author = Świętoń, Edyta title = Low pathogenic avian influenza virus isolates with different levels of defective genome segments vary in pathogenicity and transmission efficiency date = 2020-08-28 pages = extension = .txt mime = text/plain words = 5432 sentences = 295 flesch = 48 summary = In the present study we compared the clinical outcome, mortality and transmission in chickens and turkeys infected with the same infectious doses of H7N7 low pathogenic avian influenza virus containing different levels of defective gene segments (95/95(DVG-high) and 95/95(DVG-low)). Virions containing highly deleted forms of genome segments (defective viral genes-DVGs) are able to replicate only in the presence and at the expense of fully infectious virus, hence the term "defective interfering particles" (DIPs) [4] . To evaluate the effect of DIPs on the course of infection with low pathogenic avian influenza virus (LPAIV), a comparison of pathogenicity of two virus stocks of H7N7 LPAIV with different levels of defective genomes was performed in turkeys and chickens. Infected birds received the same infectious dose of the virus but with different amount of DVGs. The semiquantitative analysis of defective particles was done by a combination of RT-PCR, real time RT-PCR and whole genome sequencing and indicated significantly higher amount of truncated gene segments in 95/95(DVG-high). cache = ./cache/cord-278635-vwdxr1bl.txt txt = ./txt/cord-278635-vwdxr1bl.txt === reduce.pl bib === id = cord-277970-sb1wjd3b author = Kang, Qianli title = Screening for Anti-Influenza Actives of Prefractionated Traditional Chinese Medicines date = 2020-10-14 pages = extension = .txt mime = text/plain words = 2817 sentences = 165 flesch = 43 summary = It's therefore of great value to discover novel antivirals from TCMs. In this paper, One hundred medicinal plants which have been included in TCM prescriptions for antiviral treatment were selected and prefractionated into 5 fractions each by sequentially using cyclohexane, dichloromethane, ethyl acetate, n-butanol, and water. As a result, ten TCM fractions were identified to have antiviral potency against IAV, deserving further analysis for novel anti-influenza lead drugs. To this end, 100 medicinal plants which have been recorded as antiviral formula compositions were fractionated with cyclohexane, dichloromethane, ethyl acetate, n-butanol, and water sequentially, generating a library consisting of 500 prefractionated TCM extracts (Figure 1, Table S1 ). By using a HTS approach based on recombinant reporter influenza PR8-PB2-Gluc virus, the antiviral activity of each fraction against IAV was evaluated, and 10 simplified extracts were identified as anti-influenza actives ( Figure 3 ). cache = ./cache/cord-277970-sb1wjd3b.txt txt = ./txt/cord-277970-sb1wjd3b.txt === reduce.pl bib === id = cord-278465-tjjkz16y author = Wille, Michelle title = Urbanization and the dynamics of RNA viruses in Mallards (Anas platyrhynchos) date = 2017-03-18 pages = extension = .txt mime = text/plain words = 5890 sentences = 307 flesch = 52 summary = Recent studies have been instrumental in starting to describe dynamics and ecology of AMPV-1 and CoV in wild birds; 9-12% of migrating Mallards have CoV infections, compared to a lower prevalence (2%) of AMPV-1 towards the end of the migratory season in Sweden (Tolf et al., 2013b; Wille et al., 2015) . In context of IAV, and to a lesser degree CoV and APMV-1, an assessment of virus prevalence and diversity in an urban population will further allow us to assess if dynamics in wild birds are reflected in an urban setting. In comparing prevalence [Sept-Dec] between our urban dataset and a wild bird dataset from southern Sweden using the same qPCR methods (Wille et al., 2015) , autumnal prevalence for IAV (p b 0.0010) and CoV (p b 0.0010) is significantly different, where prevalence for both these viruses is lower in urban Mallards (Fig. 2) . cache = ./cache/cord-278465-tjjkz16y.txt txt = ./txt/cord-278465-tjjkz16y.txt === reduce.pl bib === id = cord-276364-zyw5aukk author = Wong, Ho Him title = Manipulation of autophagy by (+) RNA viruses date = 2019-08-08 pages = extension = .txt mime = text/plain words = 6884 sentences = 360 flesch = 33 summary = Over the past few decades, a growing body of research has defined the critical role of this pathway in facilitating infection by numerous +RNA RNA viruses, including poliovirus (PV) [7, 8] , Coxsackievirus B3 (CVB3) [9, 10] , CVB4 [11] , Enterovirus 71 (EV71) [12] , Human rhinovirus (HRV) [13] , Foot-and-mouth disease virus (FMDV) [14] , encephalomyocarditis virus (EMCV) [15] , Dengue virus (DENV) [16, 17] , Zika virus (ZIKV) [18, 19] , Hepatitis C virus (HCV) [20] , Mouse hepatitic virus (MHV), Newcastle disease virus (NDV) [21] , Severe and acute respiratory syndrome coronavirus (SARS-CoV) [22] , Chikungunya virus (ChikV) [23] , and Japanese encephalitis virus (JEV) [24] . Delineating the process of viral assembly from replication is technically challenging, especially since both processes would very likely Induces formation of autophagosome-like double-membrane liposomes [112] Summary of Interactions between proteins from positive strand RNA viruses and host autophagy machinery. cache = ./cache/cord-276364-zyw5aukk.txt txt = ./txt/cord-276364-zyw5aukk.txt === reduce.pl bib === id = cord-279694-25rblhwb author = Mahy, B.W.J title = Emerging and Reemerging Virus Diseases of Vertebrates date = 2014-11-28 pages = extension = .txt mime = text/plain words = 4322 sentences = 177 flesch = 50 summary = Although it is still important to isolate viruses in cell culture for their complete characterization, it is now possible directly to detect viruses in diseased tissues by PCR, then, by sequencing the amplicon, to determine whether a new virus has emerged to cause the disease. For example, when hantavirus pulmonary syndrome, caused by a bunyavirus of rodents, Sin Nombre virus, was initially detected in 1993 in the Four Corners region of Western USA, it was found that rodents inside a house where people had been infected carried a virus identical in sequence to virus isolated from human cases. Then, in 1993, a new hantavirus emerged in the Four Corners region of Southwestern USA as the cause of a severe acute respiratory disease syndrome, with a fatality rate close to 40%, and named Sin Nombre virus. It will be important in the future to detect new viruses before they can emerge to cause disease in the population. cache = ./cache/cord-279694-25rblhwb.txt txt = ./txt/cord-279694-25rblhwb.txt === reduce.pl bib === id = cord-279798-b5tduubu author = Sano, Daisuke title = Risk management of viral infectious diseases in wastewater reclamation and reuse: Review date = 2016-03-14 pages = extension = .txt mime = text/plain words = 7986 sentences = 341 flesch = 38 summary = The objectives of this review were to calculate representative values of virus removal efficiency in wastewater treatment units based on published datasets, and to identify research topics that should be further addressed for improving implementation of the multiple-barrier system. In this review article, current guidelines for designing wastewater reclamation and reuse systems from the viewpoint of virus risk management are overviewed, and the efficiency of virus removal from wastewater by currently employed wastewater treatment units are shown by the results of meta-analysis. The United States Environmental Protection Agency (USEPA) (2012) guideline explicitly notes that setting a tolerable virus concentration in reclaimed wastewater (virus limit) is not recommended for the following reasons: 1) viruses are well reduced by appropriate wastewater treatments, 2) identification and enumeration of viruses is time-and labor-consuming, 3) detection of infectious viruses in water is further labor-and time-consuming, 4) molecular-based virus detection does not always indicate the presence of infectious viruses, and 5) waterborne viral infections due to reclaimed water have not been documented. cache = ./cache/cord-279798-b5tduubu.txt txt = ./txt/cord-279798-b5tduubu.txt === reduce.pl bib === id = cord-276908-9jthjf24 author = Gupta, Akanksha title = COVID‐19: Emergence of Infectious Diseases, Nanotechnology Aspects, Challenges, and Future Perspectives date = 2020-07-06 pages = extension = .txt mime = text/plain words = 5174 sentences = 385 flesch = 57 summary = In last two decades, entire world faced three major outbreaks of coronaviruses like Severe Acute respiratory syndrome (SARS), middle east respiratory syndrome (MERS) and novel coronavirus disease i.e., COVID-19. Previously, CoV causes an epidemic of SARS in humans and infected thousands viruses belong to family Coronaviridae, which shows crown-like appearances under an electron microscope. A recent study published, relied on this approach, using the predicted structure of all SARS-CoV-2 proteins based on their homology with other known coronavirus protein structures, and identified several compounds with potential antiviral activity. [39, 77] A biological preparation provides active acquired immunity against particular infectious disease like COVID19 [51, 68] 5 Shenzhen, China SARS-CoV, NL63, HKU1 The organosulfur in the essential garlic oil inhibit the ACE2 (host-receptor site of the virus) and main protease of the virus as well as to treat the infection due to SARS-CoV-2. cache = ./cache/cord-276908-9jthjf24.txt txt = ./txt/cord-276908-9jthjf24.txt === reduce.pl bib === id = cord-278973-82n0d1dh author = Li, Zhijie title = Characterization and pathogenicity of a novel mammalian orthoreovirus from wild short-nosed fruit bats date = 2016-05-31 pages = extension = .txt mime = text/plain words = 3737 sentences = 207 flesch = 53 summary = This study describes the isolation, molecular characterization and analysis of pathogenicity of MRV variant B/03 from wild short-nosed fruit bats. BALB/c mice experimentally infected with B/03 virus by intranasal inoculation developed severe respiratory distress with tissue damage and inflammation. MRV isolates were obtained from hosts with or without clinical signs of disease, and the virus can infect a broad range of mammals (Dermody et al., 2013) . In this study, we report the characterization of a novel MRV strain (called "B/03") isolated from healthy, wild shortnosed fruit bats in Guangdong province, China. In this study, one strain of MRV, B/03, was isolated by in vitro cell culture from thirty wild short-nosed fruit bat samples from Shaoguan city of China's Guangdong province. Based on sequence comparison and phylogenetic analysis, we conclude that the B/03 isolate is a novel type 1 bat orthoreovirus, and it might have originated from gene segment mixing during infection with more than one MRV strain in nature. cache = ./cache/cord-278973-82n0d1dh.txt txt = ./txt/cord-278973-82n0d1dh.txt === reduce.pl bib === id = cord-279617-xuzu55cg author = Tuladhar, E. title = Thermal stability of structurally different viruses with proven or potential relevance to food safety date = 2012-03-30 pages = extension = .txt mime = text/plain words = 4595 sentences = 278 flesch = 54 summary = Methods and Results: Suspensions with poliovirus Sabin1, adenovirus type5, parechovirus1, human norovirus (NoV) GII.4, murine NoV (MNV1) and human influenza A (H1N1) viruses were heated at 56 and 73°C. The viral stocks titres used were as follows: poliovirus Sabin 1: 6AE3 · 10 8 50% Tissue Culture Infective Dose (TCID 50 ) ml )1 (1AE6 · 10 10 PCR unit (PCRU) ml )1 ), adenovirus type 5: 6AE3 · 10 7 TCID 50 ml )1 (3AE2 · 10 9 PCRU ml )1 ), parechovirus 1: 1AE3 · 10 8 TCID 50 ml )1 (2AE0 · 10 9 PCRU ml )1 ), influenza A (H1N1) virus: 1AE3 · 10 6 TCID 50 ml )1 (1AE5 · 10 8 PCRU ml )1 ), MNV1: 1AE7 · 10 7 PFU ml )1 (5AE0 · 10 8 PCRU ml )1 ) and human NoV GII.4 was at a concentration of 1 · 10 8 PCRU ml )1 . cache = ./cache/cord-279617-xuzu55cg.txt txt = ./txt/cord-279617-xuzu55cg.txt === reduce.pl bib === id = cord-277417-f71jwdzj author = Geoghegan, Jemma L. title = The phylogenomics of evolving virus virulence date = 2018-10-10 pages = extension = .txt mime = text/plain words = 10443 sentences = 468 flesch = 44 summary = Our current understanding of virulence evolution is based on insights drawn from two perspectives that have developed largely independently: long-standing evolutionary theory based on limited real data examples that often lack a genomic basis, and experimental studies of virulence-determining mutations using cell culture or animal models. Such a phylogenomic approach to studying virulence evolution is timely because of the rapidity with which virus genome sequence data are now being generated, including during ongoing disease outbreaks of emerging viruses [19] [20] [21] , and because of the development of new phylogeny-based methods for studying and visualizing genomic data [22] [23] [24] . For example, the repeated evolution of the same amino acid changes following the cross-species transmission of avian influenza virus to humans strongly suggests that they directly affect host range 66 , and a similar approach has been used to elucidate the nature of the evolutionary arms race between viruses and their hosts 67, 68 . cache = ./cache/cord-277417-f71jwdzj.txt txt = ./txt/cord-277417-f71jwdzj.txt === reduce.pl bib === id = cord-278482-j5zlismf author = Taylor, Raymond title = BCX4430 – A broad-spectrum antiviral adenosine nucleoside analog under development for the treatment of Ebola virus disease date = 2016-06-30 pages = extension = .txt mime = text/plain words = 2543 sentences = 131 flesch = 47 summary = Summary The adenosine nucleoside analog BCX4430 is a direct-acting antiviral drug under investigation for the treatment of serious and life-threatening infections from highly pathogenic viruses, such as the Ebola virus. The adenosine nucleoside analog BCX4430 is a direct-acting antiviral drug under investigation for the treatment of serious and life-threatening infections from highly pathogenic viruses, such as the Ebola virus. In a study in cynomolgus macaques infected with MARV [5] , 0/6 controls survived compared to 17/18 animals treated with a 15 mg/kg BD dose of The maximum viral load, as measured by quantitation of viral RNA copies in the peripheral blood, was reduced by ∼600-fold (geometric mean 0.008 × 10 9 compared to 4.79 × 10 9 copies/mL, p < 0.0005). The slope of the relationship of the dose of BCX4430 to both antiviral effect and survival in nonclinical models of lethal viral infections is steep. cache = ./cache/cord-278482-j5zlismf.txt txt = ./txt/cord-278482-j5zlismf.txt === reduce.pl bib === id = cord-280854-cxpgwwjd author = Kumarasamy, Dhanabal title = Synthesis and in vitro antiviral evaluation of 4-substituted 3,4-dihydropyrimidinones date = 2017-01-15 pages = extension = .txt mime = text/plain words = 1649 sentences = 99 flesch = 53 summary = The compounds were evaluated in vitro for their antiviral activity against a broad range of DNA and RNA viruses, along with assessment for potential cytotoxicity in diverse mammalian cell lines. The compounds were evaluated in vitro for their antiviral activity against a broad range of DNA and RNA viruses, along with assessment for potential cytotoxicity in diverse mammalian cell lines. The present work was aimed to synthesize 4-substituted 3,4-dihydropyrimidin-2(1H)-ones using various aromatic and aliphatic aldehydes and evaluate their antiviral activity against a broad range of DNA and RNA viruses, along with their cytotoxicity assessment in diverse mammalian cell lines. The antiviral activities and cytotoxicity of the synthesized compounds (4a-m and 5) were determined in CPE reduction assays with a broad and diverse panel of DNA and RNA viruses and using relevant mammalian cell lines. Compound 4m was found to be a selective and potent inhibitor of Punta Toro virus (PTV), a member of the family Bunyaviridae and the genus Phlebovirus. cache = ./cache/cord-280854-cxpgwwjd.txt txt = ./txt/cord-280854-cxpgwwjd.txt === reduce.pl bib === id = cord-280987-uhxk5b1b author = Turtle, L. title = Encephalitis, Viral date = 2014-05-01 pages = extension = .txt mime = text/plain words = 2266 sentences = 120 flesch = 33 summary = Encephalitis is inflammation and swelling of the brain, often caused by an acute viral infection, or a paraor postinfectious phenomenon known as acute disseminated encephalomyelitis (ADEM). The term includes both viral infections of the brain with predominantly gray matter disease and acute disseminated encephalomyelitis (ADEM), an immune-mediated demyelinating disease. Clinically, acute viral encephalitis and ADEM usually manifest with fever, severe headache, neck stiffness, alterations of consciousness, focal neurological signs, and often seizures, especially in children. Once permissive host cells are infected in the subcutaneous tissue, the mucous membranes, or the hematopoietic system (particularly macrophages), viruses replicate usually locally before there is invasion of the central nervous system (CNS). Enteroviruses and mumps virus infect primarily meningeal and ependymal cells; therefore, they usually cause benign meningitis and only rarely are associated with encephalitis. On rare occasions when arboviruses infect the brain, they usually cause encephalitis with a significant death rate; thus, these viruses are not highly neuroinvasive but are highly neurotropic (and neuronotropic) and neurovirulent. cache = ./cache/cord-280987-uhxk5b1b.txt txt = ./txt/cord-280987-uhxk5b1b.txt === reduce.pl bib === id = cord-280048-b4dz1lnn author = Domingo, Esteban title = Viral quasispecies date = 2019-10-17 pages = extension = .txt mime = text/plain words = 7955 sentences = 411 flesch = 36 summary = Research on quasispecies has proceeded through several theoretical and experimental avenues that include continuing studies on evolutionary optimization and the origin of life, RNA-RNA interactions and replicator networks, the error threshold in variable fitness landscapes, consideration of chemical mutagenesis and proofreading mechanisms, evolution of tumor cells, bacterial populations or stem cells, chromosomal instability, drug resistance, and conformation distributions in prions (a class of proteins with conformation-dependent pathogenic potential; in this case the quasispecies is defined by a distribution of conformations) [16, 20] . Adaptability of RNA viruses is linked to parameters that facilitate exploration of sequence space: genome size (1.8 to 33 Kb), population size (variable but that can attain an impressive 10 12 individual genomes in an infected host at a given time), replication rate, mutation rate, fecundity (yield of viral particles per cell), and number of mutations required for a phenotypic change (surprisingly low for several relevant traits) (see [49] ). cache = ./cache/cord-280048-b4dz1lnn.txt txt = ./txt/cord-280048-b4dz1lnn.txt === reduce.pl bib === id = cord-279557-hk77e3pp author = Drosten, Christian title = Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection date = 2013-06-17 pages = extension = .txt mime = text/plain words = 4214 sentences = 243 flesch = 55 summary = BACKGROUND: The Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging virus involved in cases and case clusters of severe acute respiratory infection in the Arabian Peninsula, Tunisia, Morocco, France, Italy, Germany, and the UK. [4] [5] [6] Here, we provide a full description of a fatal case of MERS-CoV infection imported to Munich, Germany, from Abu Dhabi, including a chronological profi le of virus concentrations in diverse body compartments. We subjected all available MERS-CoV genome sequences to phylogenetic analysis, including a correlation and regression analysis of known dates of virus isolation versus tree branch lengths (fi gure 3). Without quantitative laboratory data from well documented cases of MERS-CoV infection, most considerations had been made on the basis of an assumed analogy to severe acute respiratory syndrome (SARS). The recorded viral load profi le, with highest RNA concentrations in bronchoalveolar lavage and tracheobronchial aspirates, confi rms suggestions made in another report about the preferential use of lower-respiratory-tract samples for virus diagnostic tests. cache = ./cache/cord-279557-hk77e3pp.txt txt = ./txt/cord-279557-hk77e3pp.txt === reduce.pl bib === id = cord-280391-5kiu2pb6 author = Akinloye, Oluwabukola M. title = Specific Viruses Detected in Nigerian Children in Association with Acute Respiratory Disease date = 2011-10-11 pages = extension = .txt mime = text/plain words = 2499 sentences = 126 flesch = 48 summary = Adenoviruses, coronaviruses, human enteroviruses (HEV), human rhinoviruses (HRV), influenza viruses, parainfluenza viruses (PIV), and respiratory syncytial viruses (RSV) are well-known causes of acute respiratory tract infections (ARTI) in both industrialized and developing countries. Moreover, different viruses, including influenza viruses and RSV, are also frequently detected in samples obtained from patients with lower respiratory tract infection (LRTI), either alone or together with pathogenic bacteria. While the overall proportion of virus-positive specimens was similar in children aged under or over two years, as well as in the group with unrecorded age, all adenovirus, influenza virus A, RSV, and all but one HBoV and "true HEV" detections were in the youngest age group (Table 1) . This study revealed that all major respiratory virus groups tested for can be detected in Nigerian children with respiratory tract infection. Rhinoviruses and parainfluenza viruses were the most prevalent virus groups while influenza A and B viruses, as well RSV were rarely detected, possibly due to low season of these viruses during the time of sample collection. cache = ./cache/cord-280391-5kiu2pb6.txt txt = ./txt/cord-280391-5kiu2pb6.txt === reduce.pl bib === id = cord-278913-u6vihq3u author = Allam, Zaheer title = The Rise of Machine Intelligence in the COVID-19 Pandemic and Its Impact on Health Policy date = 2020-07-24 pages = extension = .txt mime = text/plain words = 5397 sentences = 214 flesch = 51 summary = For instance, despite the challenges raised earlier, some startup companies were able to use the available data from social media, airline ticketing, and medical institutions to identify that the world is experiencing a new virus outbreak days before those in medical fraternity had made similar findings (Gaille, 2019) . According to Niiler (2020) , BlueDot, whose profile is shared in the following, was able to employ the services of AIdriven algorithms, to analyze data gathered from sources such as new reports, air ticketing, and animal disease outbreaks to predict that the world is facing a new type of virus outbreak. In the recent case of COVID-19, Metabiota was in the forefront to analyze the outbreak, and during the analysis of the data, some even sourced from social media, the company was able to predict which neighboring countries were at high risk of being the next target of the virus spread, more so because the panic in Wuhan had stated to trigger some fear, forcing people to flee. cache = ./cache/cord-278913-u6vihq3u.txt txt = ./txt/cord-278913-u6vihq3u.txt === reduce.pl bib === id = cord-278876-il7g78w1 author = Akkina, Ramesh title = 2016 International meeting of the Global Virus Network date = 2017-03-16 pages = extension = .txt mime = text/plain words = 7538 sentences = 315 flesch = 35 summary = This report highlights the accomplishments of GVN researchers in many priority areas of medical virology, including the current Zika epidemic, infections by human papillomavirus, influenza, Ebola, Lassa, dengue, HIV, hepatitis C, and chikungunya viruses, and the development of improved diagnostics and new vaccines. This meeting report highlights accomplishments of GVN researchers in many priority areas of human virology, including the current Zika epidemic, infections by human papillomavirus, influenza, Ebola, Lassa, dengue, HIV, hepatitis C and chikungunya viruses, and the development of improved diagnostics and new vaccines. The main objectives of the meeting were to present and discuss current findings in medical virology, including advances in research on HIV vaccines and other important retroviruses; provide a framework to encourage collaborations among world experts; and address the GVN's annual strategy for continued development. Hideki Hasegawa, a GVN center director at the National Institute of Infectious Diseases in Tokyo, explained that secretory IgA antibodies on mucosal surfaces play an important role in protection against influenza virus infection. cache = ./cache/cord-278876-il7g78w1.txt txt = ./txt/cord-278876-il7g78w1.txt === reduce.pl bib === id = cord-280986-i27mge10 author = Mallia, Patrick title = How Viral Infections Cause Exacerbation of Airway Diseases date = 2017-01-25 pages = extension = .txt mime = text/plain words = 4238 sentences = 199 flesch = 34 summary = Exacerbations are associated with increased airway inflammation in patients with both asthma and COPD, but many questions remain unanswered regarding the key inflammatory cells and mediators involved. 24, 25 In the lower respiratory tract, increases in Il-6, IL-8, and the chemokine regulated on activation, normal T-cell expressed and secreted (RANTES) have been documented in the sputum of asthmatic patients after experimental rhinovirus infection, 10, 26 and IL-8 has been detected in the sputum of children with naturally occurring exacerbations. A recent study 10 in patients with naturally occurring virusassociated asthma exacerbations found increased levels of IL-10 messenger RNA in the sputum of asthmatic patients compared to virus-infected healthy subjects, but no differences in the level of RANTES or IL-8 between the two groups. Studies 38 of airway inflammation in stable patients with COPD have shown that the disease is characterized by pulmonary infiltration of macrophages, neutrophils, and CD8ϩ T lymphocytes, together with increased expression of cytokines, chemokines, and adhesion molecules. cache = ./cache/cord-280986-i27mge10.txt txt = ./txt/cord-280986-i27mge10.txt === reduce.pl bib === id = cord-278479-vl296i1b author = Samuel, Arthur S title = Experimental infection of hamsters with avian paramyxovirus serotypes 1 to 9 date = 2011-02-23 pages = extension = .txt mime = text/plain words = 6316 sentences = 335 flesch = 46 summary = In this study, groups of hamsters were infected with a prototype strain of each APMV serotype by the intranasal route and monitored for virus replication, clinical symptoms, histopathology, and seroconversion. Our results showed that each of the APMV serotypes replicated in hamsters without causing adverse clinical signs of illness, although histopathologic evidence of disease was observed in some cases, and also induced high neutralizing antibody titers. Necropsies were performed immediately postmortem and the following tissue samples were collected for immunohistochemistry (IHC), histopathology, and virus isolation: brain, nasal turbinates, lung, spleen, kidney and small intestine. Deparaffinized sections of the virus-infected and uninfected control tissue (brain, lungs, nasal turbinates, small intestine, kidney, and spleen) were immunostained using polyclonal antisera against the N protein of the homologous APMV serotypes. In animals infected with any of the other APMV serotypes, virus-specific antigens were detected on 3 dpi in the lungs and nasal turbinates (Figure 3 ). cache = ./cache/cord-278479-vl296i1b.txt txt = ./txt/cord-278479-vl296i1b.txt === reduce.pl bib === id = cord-281332-5mddyv0n author = Wilson, Michael R. title = A novel cause of chronic viral meningoencephalitis: Cache Valley virus date = 2017-07-25 pages = extension = .txt mime = text/plain words = 4008 sentences = 232 flesch = 42 summary = Interpretation: Cache Valley virus, a mosquito-borne orthobunyavirus, has only been identified in 3 immunocompetent North American patients with acute neuroinvasive disease. This report demonstrates that metagenomic next generation sequencing allows for unbiased pathogen identification, the early detection of emerging viruses as they spread to new locales, and the discovery of novel disease phenotypes. This report demonstrates that metagenomic next generation sequencing allows for unbiased pathogen identification, the early detection of emerging viruses as they spread to new locales, and the discovery of novel disease phenotypes. Here, we report the effective deployment of metagenomic next generation sequencing (mNGS) to diagnose Cache Valley virus (CVV), a mosquito-borne orthobunyavirus, 4 in an Australian patient with a primary immunodeficiency suffering from chronic meningoencephalitis. 41 Because CVV is rarely identified as a cause of human disease and has not been reported in Australia previously, there are no traditional candidate-based diagnostic tests for this virus available in Australia. cache = ./cache/cord-281332-5mddyv0n.txt txt = ./txt/cord-281332-5mddyv0n.txt === reduce.pl bib === id = cord-278511-je1509ar author = Wang, David title = 5 challenges in understanding the role of the virome in health and disease date = 2020-03-26 pages = extension = .txt mime = text/plain words = 2166 sentences = 107 flesch = 38 summary = An even more significant problem is that in most virome studies, more than 50% of the sequences in virus-enriched preparations have no detectable sequence similarity to any known reference sequences; these unalignable sequences are referred to as viral "dark matter" [8] and may include novel, highly divergent viruses that are unrecognizable. To illustrate this point, the United States National Institutes of Health (NIH) virology study sections address only "non-bacteriophage viral genetics, infection and replication, cellular and host responses to viral infections, and mechanisms of viral disease pathogenesis." Thus, there is a great need to bring these disparate communities together in order to collectively attack questions associated with the virome, especially as more complex trans-kingdom interactions are identified linking phages, bacteria, eukaryotic viruses, and eukaryotic cells. With new cell-culture systems and animal models for novel viruses, there will ideally be studies that attribute causal roles for some of the associations. cache = ./cache/cord-278511-je1509ar.txt txt = ./txt/cord-278511-je1509ar.txt === reduce.pl bib === id = cord-280429-4fota9rl author = Medvedev, Kirill E. title = Functional and evolutionary analysis of viral proteins containing a Rossmann‐like fold date = 2018-06-13 pages = extension = .txt mime = text/plain words = 7468 sentences = 465 flesch = 49 summary = 10 However, structural analyses of virion architecture and coat protein topology have revealed unexpected similarities, not visible in sequence comparisons, suggesting a common origin for viruses that infect hosts residing in different domains of life. In this current work, we provide functional and evolutionary analysis of viral proteins containing a Rossmann-like fold that can be found in the Evolutionary Classification of protein Domains (ECOD) database developed in our lab. The structures represented gene products from 21 viral taxonomical families with host ranges from all kingdoms of life (http://prodata.swmed.edu/rossmann_fold/viruses/). Our analysis detected 14 different bacterial virus structure topology types defined by ECOD T-groups that contain a Rossmann-like fold (Fig. 2, 12 topology groups shown). Like the bacterial and eukaryotic branches in the tree of life, the Archea are host to a multitude of Functional and Evolutionary Analysis of Viral Proteins viruses. 61 Among viral protein structures containing the minimal Rossmann fold, 14 protein families are known helicases (http://prodata.swmed.edu/ross-mann_fold/viruses/). cache = ./cache/cord-280429-4fota9rl.txt txt = ./txt/cord-280429-4fota9rl.txt === reduce.pl bib === id = cord-278684-txlvla0j author = Gonzalez–Dunia, Daniel title = Borna Disease Virus and the Brain date = 1998-01-30 pages = extension = .txt mime = text/plain words = 13952 sentences = 784 flesch = 43 summary = The BDV paradigm is amenable to study virus–cell interactions in the CNS that can lead to neurodevelopmental abnormalities, immune-mediated damage, as well as alterations in cell differentiated functions that affect brain homeostasis. Evidence provided by epidemiological and clinical data, together with virological studies, have led to the hypothesis that chronic viral infections of the CNS contribute to human mental disorders of unknown etiology. Therefore, neuronal damage seen in BD appears to be mediated by the cytotoxic activity of CD8 ϩ T-cells present in the brain parenchyma of BDV-infected rats. Studies on PTI-NB rats may provide valuable information regarding the contribution of CNS resident cells to disturbances in cytokine gene expression caused by BDV. Borna disease virus replicates in astrocytes, Schwann cells and ependymal cells in persistently infected rats: Location of viral genomic and messenger RNAs by in situ hybridization Expression of tissue factor is increased in astrocytes within the central nervous system during persistent infection with Borna disease virus cache = ./cache/cord-278684-txlvla0j.txt txt = ./txt/cord-278684-txlvla0j.txt === reduce.pl bib === id = cord-280427-smqc23vr author = Singla, Rubal title = Human animal interface of SARS-CoV-2 (COVID-19) transmission: a critical appraisal of scientific evidence date = 2020-09-14 pages = extension = .txt mime = text/plain words = 7194 sentences = 381 flesch = 58 summary = The various evidence from the past clearly suggest that the evolution of the virus in both reservoir and intermediate animal hosts needs to be explored to better evaluate the emergence of SARS-CoV-2 in humans. The qPCR and virus titration test conducted on the various isolated organs of the ferrets on day 4 post inoculation detected infectious virus in the nasal turbinate, soft palate and tonsils of ferrets indicating the possible replication of the virus in the upper respiratory tract of the ferrets while no infection was found in other organs such as trachea, lung, heart, spleen, kidneys, pancreas, small intestine, brain and liver of the ferrets (Kim et al. This study results stipulate ferret to have high susceptibility for the SARS-CoV-2 and this infectious virus sheds by multiple routes of body discharge specimens such as urine and faeces of the infected ferrets which serve as a potential source of viral transmission to close contact. cache = ./cache/cord-280427-smqc23vr.txt txt = ./txt/cord-280427-smqc23vr.txt === reduce.pl bib === id = cord-279691-v5kpmk0b author = Hagemeijer, Marne C. title = Biogenesis and Dynamics of the Coronavirus Replicative Structures date = 2012-11-21 pages = extension = .txt mime = text/plain words = 9036 sentences = 483 flesch = 43 summary = Upon infection, coronaviruses extensively rearrange cellular membranes into organelle-like replicative structures that consist of double-membrane vesicles and convoluted membranes to which the nonstructural proteins involved in RNA synthesis localize. This review will summarize the current knowledge on the biogenesis of the replicative structures, the membrane anchoring of the replication-transcription complexes, and the location of viral RNA synthesis, with particular focus on the dynamics of the coronavirus replicative structures and individual replication-associated proteins. A distinctive common feature of +RNA viruses is the replication of their genomes in the cytoplasm of the host cell in association with rearranged cellular membranes that are remodeled into organelle-like membranous structures to which the viral replication-transcription complexes (RTCs) localize. The first detectable membrane rearrangements in CoV-infected cells are 200 to 350 nm organelle-like structures that have been described for both MHV [47, 62] and the SARS-CoV [5, 63] and consist of spherical vesicles containing double lipid bilayers, termed DMVs ( Figure 2 ). cache = ./cache/cord-279691-v5kpmk0b.txt txt = ./txt/cord-279691-v5kpmk0b.txt === reduce.pl bib === id = cord-280130-ewqe9edq author = Weber, Friedemann title = Viral suppression of the interferon system date = 2007-01-27 pages = extension = .txt mime = text/plain words = 4298 sentences = 224 flesch = 39 summary = In most nucleated body cells, viral infections activate transcription of the ''classic'' IFN-b gene [1] by a signaling chain which is initiated by the RNA sensors RIG-I and MDA-5, which in turn act trough the adaptor IPS-1 and the kinases TBK-1 and IKK-3 to activate the transcription factor IRF-3 (see reviews by P. Many RNA and DNA viruses therefore express proteins which bind this key molecule to avoid both IFN induction and activation of dsRNA-dependent antiviral enzymes [7, 8] . Binding of the influenza virus NS1 protein to double-stranded RNA inhibits the activation of the protein kinase that phosphorylates the elF-2 translation initiation factor Ebola virus VP35 protein binds double-stranded RNA and inhibits alpha/beta interferon production induced by RIG-I signaling Double-stranded RNA binding of influenza B virus nonstructural NS1 protein inhibits protein kinase R but is not essential to antagonize production of alpha/beta interferon cache = ./cache/cord-280130-ewqe9edq.txt txt = ./txt/cord-280130-ewqe9edq.txt === reduce.pl bib === id = cord-282628-6uoberfu author = Tiwari, Bhagyashree title = Future impacts and trends in treatment of hospital wastewater date = 2020-05-01 pages = extension = .txt mime = text/plain words = 5920 sentences = 286 flesch = 35 summary = The causative agent of most emerging infectious diseases is viruses; every year approximately more than two novel viral pathogens are identified, which can cause illness in a human. Factors for emergence include natural process (evolution of pathogen), infectious agents transfer from vertebrate to mammals, antimicrobial resistance (AMR), and climate change. The factors responsible for the emergence of infectious diseases such as (1) the evolution of new strain, (2) the introduction of a host to enzootic, (3) translocation of infected wildlife, (4) farming practices, and (5) others were provided. Due to emergence of antibiotic-resistant pathogens and unavoidable use of antibiotics, concomitant environmental perturbation caused by climate change might make the earth is not suitable for humans and other livings. Increasing resistance to antibiotics and the emergence of "superbugs" that are resistant to drugs of last resort have highlighted the great need for alternative treatments of bacterial disease. Furthermore, development of drug-resistant organisms and increased pathogen survival rate, only raising panic about the human, animal, and environmental health. cache = ./cache/cord-282628-6uoberfu.txt txt = ./txt/cord-282628-6uoberfu.txt === reduce.pl bib === id = cord-280564-kgoczioe author = Conceição-Neto, Nádia title = Identification of an enterovirus recombinant with a torovirus-like gene insertion during a diarrhea outbreak in fattening pigs date = 2017-09-08 pages = extension = .txt mime = text/plain words = 6204 sentences = 339 flesch = 54 summary = title: Identification of an enterovirus recombinant with a torovirus-like gene insertion during a diarrhea outbreak in fattening pigs In the sample, we observed the presence of a small Torovirus contig of 256 bp, which was included in the phylogenetic tree (Fig. 1A , Torovirus/BEL/2015), showing very low similarity with the gene insertion found in the recombinant virus. The enterovirus genome region before the torovirus insertion (VP1-VP4, 2 A, 2B, and 2 C) showed its highest similarity on the amino-acid level (94.5%) with EVG/Porcine/USA/Texas1/ 2014 (Fig. 1C) . In addition to confirming the presence of the enterovirus-torovirus recombinant using Sanger sequencing, we used proteomics to infer whether the protein of the insertion could be found in the sample. Taking the metagenomics data, the Sanger sequence confirmation and the proteomics results all together we can conclude that this recombinant virus is present in the sample and that the inserted protein is being expressed. cache = ./cache/cord-280564-kgoczioe.txt txt = ./txt/cord-280564-kgoczioe.txt === reduce.pl bib === id = cord-281061-uoszpnst author = Watanabe, Yohei title = A novel immunochromatographic system for easy-to-use detection of group 1 avian influenza viruses with acquired human-type receptor binding specificity date = 2015-03-15 pages = extension = .txt mime = text/plain words = 4300 sentences = 188 flesch = 54 summary = A biotinylated anti-hemagglutinin antibody that bound a broad range of group 1 influenza A viruses and latex-conjugated α2,3 (blue) and α2,6 (red) sialylglycopolymers were used in an immunochromatographic strip test, with avidin and lectin immobilized on a nitrocellulose membrane at test and control lines, respectively. The strip test could detect the receptor binding specificity of a wide range of influenza viruses, as well as small increases in the binding affinity of variant H5N1 viruses to α2,6 sialylglycans at viral titers >128 hemagglutination units. In conclusion, the immunochromatographic strip test developed in this study should be useful for monitoring potential changes in the receptor binding specificity of group 1 influenza A viruses in the field. In this study, we developed a new easy-to-use immunochoromatographic strip test to detect the emergence of AI viruses with increased human-type receptor specificity and confirmed the applicability of this test using AI viruses isolated in several different geographic areas. cache = ./cache/cord-281061-uoszpnst.txt txt = ./txt/cord-281061-uoszpnst.txt === reduce.pl bib === id = cord-279849-zzkliu76 author = DaPalma, T. title = A systematic approach to virus–virus interactions date = 2010-01-20 pages = extension = .txt mime = text/plain words = 8230 sentences = 366 flesch = 36 summary = Therefore, in this review we identify known and potential types of virus-virus interactions (VVIs) and organize them into three categories: (1) direct interactions of viral genes or gene products, (2) indirect interactions that result from alterations in the host environment, and (3) a subset of indirect interactions called immunological interactions, unique to organisms equipped with an adaptive immune system. One of the first helper-dependent viruses described was bacteriophage P4, a bacteria-infecting virus that is able to replicate its own genome, but requires the presence of a coinfecting bacteriophage, such as P2, to provide capsid components and cell lysis (Shore et al., 1978; Six and Klug, 1973) . While direct binding and activation of viral transactivating proteins to heterologous viral promoters has been documented, more common are reports of viral infections inducing increased expression or activation of cellular transcription factors, which then act on promoters of coinfecting viruses. Human cytomegalovirus TRS1 and IRS1 gene products block the double-stranded-RNA-activated host protein shutoff response induced by herpes simplex virus type 1 infection cache = ./cache/cord-279849-zzkliu76.txt txt = ./txt/cord-279849-zzkliu76.txt === reduce.pl bib === id = cord-280878-1kt51viz author = To, Janet title = Targeting the Channel Activity of Viroporins date = 2016-01-07 pages = extension = .txt mime = text/plain words = 15297 sentences = 701 flesch = 47 summary = For other viroporins, these studies are still mostly in their infancy, although a highresolution structure of the hepatitis C virus (HCV) p7 protein has been recently described (Ouyang et al., 2013) that may be useful for the rational design of p7 channel inhibitors in the future. Structure and ion channel activity of the human respiratory syncytial virus (hRSV) small hydrophobic protein transmembrane domain The small hydrophobic protein of the human respiratory syncytial virus forms pentameric ion channels NMR structure and ion channel activity of the p7 protein from hepatitis C virus Influenza B virus BM2 protein has ion channel activity that conducts protons across membranes Identification of an ion channel activity of the Vpu transmembrane domain and its involvement in the regulation of virus release from HIV-1-infected cells Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus cache = ./cache/cord-280878-1kt51viz.txt txt = ./txt/cord-280878-1kt51viz.txt === reduce.pl bib === id = cord-281593-bq12grqo author = Liu, Zheng title = Transmission Electron Microscopy Studies of Cellular Responses to Entry of Virions: One Kind of Natural Nanobiomaterial date = 2012-04-11 pages = extension = .txt mime = text/plain words = 2043 sentences = 112 flesch = 49 summary = For this paper, we chose Bombyx mori cypovirus 1 (BmCPV-1) interactions with midgut cells from silkworm, and severe acute respiratory syndrome (SARS) associated coronavirus interactions with Vero E6 cells, as examples to demonstrate the response of eukaryotic cells to two different types of virus from our previous studies. In this paper, we discuss our previous studies on Bombyx mori cypovirus 1 (BmCPV-1) interactions with midgut cells from silkworm, and severe acute respiratory syndrome (SARS) associated coronavirus interactions with Vero E6 cells as examples to demonstrate the response of eukaryotic cells to two different types of viruses [11, 12] . It could be seen with ultrathin sectioning and electron microscopy that the virions first attached themselves to the surface of host cell, then their envelopes fused with the cell membrane, and the whole nucleocapsids entered the cell. cache = ./cache/cord-281593-bq12grqo.txt txt = ./txt/cord-281593-bq12grqo.txt === reduce.pl bib === id = cord-281158-vjh9z7l4 author = Storch, Gregory A title = Respiratory Viruses in Babies: Important Insights From Down Under date = 2018-02-01 pages = extension = .txt mime = text/plain words = 1578 sentences = 69 flesch = 44 summary = Impressive study attributes include large size, community base, enrollment from birth, scheduled frequent longitudinal sampling with or without illness, high percentage of specimen acquisition rate, even enrollment of subjects throughout the year to account for virus seasonality, and testing of samples with an extensive panel of real-time polymerase chain reaction (PCR) assays. This intensive prospective study of respiratory viruses in infants finds that human rhinovirus (HRV) is by far the most frequent virus detected in the infant respiratory tract. Of the 152 infants followed, 81% experienced a first infection with HRV by 6 months of age, compared to 8.5% for RSV, and 0.7%-9.4% for the other respiratory viruses. Timing of first respiratory virus detection in infants: a community-based birth cohort study Viral etiology of acute respiratory infections with cough in infancy: a community-based birth cohort study Etiology of acute respiratory infections in infants: a prospective birth cohort study cache = ./cache/cord-281158-vjh9z7l4.txt txt = ./txt/cord-281158-vjh9z7l4.txt === reduce.pl bib === id = cord-282344-o1rkx2z4 author = Kim, Seung Won title = Effects of humidity and other factors on the generation and sampling of a coronavirus aerosol date = 2007-07-25 pages = extension = .txt mime = text/plain words = 5076 sentences = 277 flesch = 54 summary = The airborne viruses were collected on heating, ventilating, and air conditioning (HVAC) filters in an experimental apparatus and also sampled upstream of these test filters using AGI-30 and BioSampler impinger samplers. To study the effects of relative humidity (RH) on TGEV collection by the filters and samplers, the virus was nebulized into air at 30, 50, 70, and 90% RH. To measure the degree to which the nebulizers generated airborne viruses that could be sampled and remain viable, aerosolization efficiency, g A , was calculated in the same way as Adams et al. The recovery of TGEV from the test filter can be calculated in two ways: (1) relative to the airborne virus concentration, R a , and (2) relative to the nebulizer suspension concentration, R n . TGEV was nebulized, then sampled using AGI-30 impingers and BioSamplers, and finally collected on an HVAC test filter to measure the effects of nebulization stress and the recovery of viable virus from the filter. cache = ./cache/cord-282344-o1rkx2z4.txt txt = ./txt/cord-282344-o1rkx2z4.txt === reduce.pl bib === id = cord-280781-u3wd27rn author = Stohlman, S. A. title = Stability of neurotropic mouse hepatitis virus (JHM strain) during chronic infection of neuroblastoma cells date = 1978 pages = extension = .txt mime = text/plain words = 3509 sentences = 184 flesch = 50 summary = title: Stability of neurotropic mouse hepatitis virus (JHM strain) during chronic infection of neuroblastoma cells A line of mouse neuroblastoma cells which was chronically infected with the neurotropic strain (JHM) of MHV, a member of the coronavirus group, was established. The addition of low concentration antiviral antibody modulated the infection to a carrier culture with viral antigen in the cytoplasm of the cells, but no infectious virus was produced, and the cells lacked both surface viral antigen and CPE. Following incubation at room temperature for 30 minutes in the presence of anti-JHM hyperimmune aseitie fluid (50 per cent plaque reduction neutralization titer = 1/1~00), serial dilutions were plated on the indicator monolayers and fixed with 0.5 ml of DMEM plus 5 per cent FBS containing 0.6 per cent agarose. Figure 3 shows that following the initial passage in the presence of antibody, there was an increase in both the supernatant and cell associated virus titer, which rapidly declined until after 4 serial passages no infectious virus was detectable. cache = ./cache/cord-280781-u3wd27rn.txt txt = ./txt/cord-280781-u3wd27rn.txt === reduce.pl bib === id = cord-283405-aozxvxxs author = Vermillion, Meghan S. title = Pregnancy and infection: using disease pathogenesis to inform vaccine strategy date = 2018-02-01 pages = extension = .txt mime = text/plain words = 8428 sentences = 431 flesch = 33 summary = Pregnant women, unborn fetuses, and neonates represent three populations of high-risk individuals that can all be simultaneously protected from vaccine-preventable infectious disease with strategic maternal immunization protocols. Third are neonatal and infant infections, which are not considered to pose significant risk to pregnant women or unborn fetuses, but can cause severe, and sometimes fatal disease in neonates and infants that lack protective maternal immunity following birth. Studies in pregnant nonhuman primates have been instrumental for the identification of CD4 + T cell responses as critical for early control of CMV infection and transmission during pregnancy, 100 and studies in guinea pigs have demonstrated that a single-cycle infectious CMV vaccine induces immune responses similar to natural infection and protects against congenital infection. 125 Vaccine candidates have been developed using diverse platforms, including DNA, mRNA, and purified inactivated and live-attenuated virus, many of which have been tested in non-pregnant mouse and nonhuman primate models for their ability to generate immune responses that mimic responses to natural infection and protected against ZIKV challenge. cache = ./cache/cord-283405-aozxvxxs.txt txt = ./txt/cord-283405-aozxvxxs.txt === reduce.pl bib === id = cord-283641-2u16otbf author = Vainionpää, R. title = Diagnostic Techniques: Serological and Molecular Approaches date = 2015-03-06 pages = extension = .txt mime = text/plain words = 4400 sentences = 222 flesch = 40 summary = For diagnostic purposes the following approaches can be used: demonstration of presence of infectious virus or its structural components directly from a patient's specimens or investigation of specific antibody response in serum specimens. Glossary EIA Enzyme immunoassays are methods used to estimate virus-specific IgG and IgM antibodies or virus antigens by enzyme-labeled conjugates. Nucleic acid testing has become the main approach for the demonstration of the presence of virus while cultivation is used by fewer specialized laboratories and antigen detection methods have moved to the point of care. Diagnostic applications of the measurement of the avidity of IgG antibodies against specific antigens have been developed to help distinguish serological responses due to acute infections from those of chronic or past infections. In immunofluorescence tests, cells from a clinical specimen are fixed on a glass slide and viral antigens present in the cells are detected by fluorescein-labeled virus-specific antibodies. cache = ./cache/cord-283641-2u16otbf.txt txt = ./txt/cord-283641-2u16otbf.txt === reduce.pl bib === id = cord-279418-3r1ijafm author = Nevers, Quentin title = Negri bodies and other virus membrane-less replication compartments() date = 2020-08-21 pages = extension = .txt mime = text/plain words = 6437 sentences = 406 flesch = 44 summary = We particularly examine the interplay between viral factories and the cellular innate immune response, of which several components also form membrane-less condensates in infected cells. With the rapid identification of cellular membraneless compartments and proteins that undergo LLPS in vitro, a major challenge in the field is to demonstrate unambiguously that a specific structure is indeed a phase-separated liquid body in the cellular context. Until now, only a few specific cellular factors, which directly interact with viral proteins such as the nucleoproteins and phosphoproteins of MNV, have been shown to concentrate in these structures. Upon Infection, Cellular WD Repeat-Containing Protein 5 (WDR5) Localizes to Cytoplasmic Inclusion Bodies and Enhances Measles Virus Replication The Ebola Virus Nucleoprotein Recruits the Nuclear RNA Export Factor NXF1 into Inclusion Bodies to Facilitate Viral Protein Expression The Cellular Protein CAD is Recruited into Ebola Virus Inclusion Bodies by the Nucleoprotein NP to Facilitate Genome Replication and Transcription cache = ./cache/cord-279418-3r1ijafm.txt txt = ./txt/cord-279418-3r1ijafm.txt === reduce.pl bib === id = cord-281429-6lv3di4x author = García-Nicolás, Obdulio title = Targeting of the Nasal Mucosa by Japanese Encephalitis Virus for Non-Vector-Borne Transmission date = 2018-11-27 pages = extension = .txt mime = text/plain words = 7414 sentences = 396 flesch = 49 summary = Using nasal mucosal tissue explants and primary porcine nasal epithelial cells (NEC) at the air-liquid interface (ALI) and macrophages as ex vivo and in vitro models, we determined that the nasal epithelium could represent the route of entry and exit for JEV in pigs. Porcine NEC at the ALI exposed to with JEV resulted in apical and basolateral virus shedding and release of monocyte recruiting chemokines, indicating infection and replication in macrophages. Using nasal mucosa tissue explants and three-dimensional porcine nasal epithelial cells cultures and macrophages as ex vivo and in vitro models, we determined that the nasal epithelium could be a route of entry as well as exit for the virus. In fact, our data demonstrate that JEV has the ability of infecting apically, resulting in both apical and basolateral virus shedding in swine nasal epithelial cells and indicating that the porcine nasal mucosa could represent a gateway for JEV entry and exit in pigs. cache = ./cache/cord-281429-6lv3di4x.txt txt = ./txt/cord-281429-6lv3di4x.txt === reduce.pl bib === id = cord-284523-lknyehsa author = da Mata, Élida Cleyse Gomes title = Antiviral activity of animal venom peptides and related compounds date = 2017-01-06 pages = extension = .txt mime = text/plain words = 7073 sentences = 347 flesch = 43 summary = This review provides a panorama of peptides described from animal venoms that present antiviral activity, thereby reinforcing them as important tools for the development of new therapeutic drugs. Synthetic hybrid peptides, namely cecropin A (1-8)-magainin 2 (1-12), exhibited potent antiviral activity by a mechanism mainly based on the compound hydrophobicity and α-helical content, inhibiting the virushost cell fusion [85] (Table 2) . Other peptides from marine sponges that inhibit HIV-1 entry into host cells are: callipeltin A, isolated from sponges of the genus Callipelta, which displayed antiviral activity with a high selectivity index (29) between the virus and host cells (SI ratio 50% cytotoxic dose [CD 50 ]/ED 50 ) [109] ; celebesides A-C from Siliquariaspongia mirabilis [108] ; neamphamide A, from Neamphius huxleyi, a compound with structural similarities to callipeptins and papuamides that exhibited low toxicity to host cells and a selectivity index above 10 [110] ; and microspinosamide, isolated from Sidonops microspinosa [111] . cache = ./cache/cord-284523-lknyehsa.txt txt = ./txt/cord-284523-lknyehsa.txt === reduce.pl bib === id = cord-282204-j1slaefb author = Silva, José V.J. title = A scoping review of Chikungunya virus infection: epidemiology, clinical characteristics, viral co-circulation complications, and control date = 2018-12-31 pages = extension = .txt mime = text/plain words = 8010 sentences = 464 flesch = 43 summary = de; Oliveira, Renato A.S.; Durães-Carvalho, Ricardo; Lopes, Thaísa R.R.; Silva, Daisy E.A.; Gil, Laura H.V.G. title: A scoping review of Chikungunya virus infection: epidemiology, clinical characteristics, viral co-circulation complications, and control Laboratory tests for specific diagnosis of CHIKV infection are based on virus isolation, viral RNA detection and serology (Johnson et al., 2016) . Anti-CHIKV candidates that have been already tested in humans and/or animals include inactivated-, attenuated-, virus like particle-(VLP), DNA-and chimeric vaccines (Eckels et al., 1970; Levitt et al., 1986; Muthumani et al., 2008; Wang et al., 2008; Tiwari et al., 2009; Sharma et al., 2012 Akahata et al., 2010 Plante et al., 2011; Wang et al., 2011; Gorchakov et al., 2012; Brandler et al., 2013; Chang et al., 2014; García-Arriaza et al., 2014; Tretyakova et al., 2014; van den Doel et al., 2014; Erasmus et al., 2017) . cache = ./cache/cord-282204-j1slaefb.txt txt = ./txt/cord-282204-j1slaefb.txt === reduce.pl bib === id = cord-281844-c0uhcatg author = Costa, Lusmaia D.C. title = Exacerbation of asthma and airway infection: is the virus the villain? date = 2014-12-31 pages = extension = .txt mime = text/plain words = 6547 sentences = 351 flesch = 45 summary = Abstract Objective To review the available literature on the association between acute viral respiratory tract infection and the onset of asthma exacerbations, identifying the most prevalent viruses, detection methods, as well as preventive and therapeutic aspects. Studies using reverse transcriptase polymerase chain reaction (RT-PCR) as the detection technique, isolated or combined with traditional methods, observed positivity for respiratory viruses in up to 92.2% of episodes of acute asthma exacerbation in children. Several authors have performed studies aiming to detect viruses in respiratory secretions of exacerbated asthma patients, showing a prevalence of viral identification that varies with several factors, such as patient age, time of the year, method of sample collection, and method of viral detection. The use of viral detection techniques with high sensitivity and specificity has increased the identification of some respiratory viruses in children with asthma exacerbation. cache = ./cache/cord-281844-c0uhcatg.txt txt = ./txt/cord-281844-c0uhcatg.txt === reduce.pl bib === id = cord-284880-xsh3wkqy author = Bandaly, Victor title = The Fate of Mengovirus on Fiberglass Filter of Air Handling Units date = 2017-06-28 pages = extension = .txt mime = text/plain words = 4703 sentences = 257 flesch = 58 summary = The aim of this work is to study the characterization of viral bioaerosols in indoor environments and to understand the fate of mengovirus eukaryote RNA virus on glass fiber filter F7 used in AHU. Regarding the virus infectivity on the filter under a constant air flow, mengovirus was remained infectious during 10 h after aerosolization. From an average of 4.43 9 10 8 PFU L -1 of initial solution of virus aerosolized, 3.43 9 10 2 PFU cm -2 of infectious mengovirus was detected after 25 min of air flow. With a continuous air flow in the system, the persistence of mengovirus was assessed at different times and showed infectivity on the filter up to 10 h after aerosolization (Fig. 7) . Thus, time has an effect on the infectivity of the virus; this study showed that, with a continuous air flow in the cache = ./cache/cord-284880-xsh3wkqy.txt txt = ./txt/cord-284880-xsh3wkqy.txt === reduce.pl bib === id = cord-282343-cko4curf author = Cheng, Han title = A parallel genome-wide RNAi screening strategy to identify host proteins important for entry of Marburg virus and H5N1 influenza virus date = 2015-11-24 pages = extension = .txt mime = text/plain words = 5071 sentences = 278 flesch = 56 summary = RESULTS: The parallel nature of the strategy allows us to easily identify the host factors for a specific virus with a greatly reduced number of false positives in the initial screen, which is one of the major problems with high throughput screening. This strategy was used for an RNAi screen to identify host proteins specific for the entry process of Marburg virus (MARV) or avian influenza virus H5N1 (AIV), demonstrating the utility of this approach. The key feature of the protocol is that AIV and siRNA showing low signals in assay plates of both viruses is regarded as a "shared" hit by the two viruses MARV pseudovirions were used in parallel in the RNAi screen which allowed us to reduce the number of false positives and to quickly identify Marburg-specific and flu-specific host factors (which will be further discussed below). cache = ./cache/cord-282343-cko4curf.txt txt = ./txt/cord-282343-cko4curf.txt === reduce.pl bib === id = cord-281281-knelqmzx author = Villas-Boas, Gustavo R. title = The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents date = 2020-09-07 pages = extension = .txt mime = text/plain words = 15780 sentences = 708 flesch = 42 summary = The use of bioinformatics and other computational tools in addition to molecular modeling has helped researchers from different areas in the search for strategies for diagnosing viral infection, in the development of vaccines for its prevention, as well as in the discovery of new anti-SARS-CoV-2 agents. In the context of COVID-19, this characteristic was important for a better understanding of the origin of SARS-CoV-2 from the comparative analysis of genomic data of the new virus with others from the same family, suggesting its origin from natural selection, with modifications in its spike protein, more specifically in the host receptor binding domain, which may have enhanced its interaction and recognition by the human cell [83, 91] . The contributions of bioinformatics and molecular modeling in elucidating essential targets for the planning and development of new drugs, and the analysis of already known compounds, support the search for safer and more effective treatments against SARS-CoV-2 infection. cache = ./cache/cord-281281-knelqmzx.txt txt = ./txt/cord-281281-knelqmzx.txt === reduce.pl bib === id = cord-285462-9i61rsei author = Almomani, Hesham title = L'ampleur de la réaction des gens aux rumeurs et aux fausses nouvelles à la lumière de la crise du virus Corona date = 2020-06-25 pages = extension = .txt mime = text/plain words = 3633 sentences = 160 flesch = 50 summary = In addition to the concerns that the World Health Organization fears about the Corona virus epidemic, the combination of false information and rumors also contributes to exaggerating the epidemiological situation and the difficulty of combating it, because most users and pioneers of social media are at their best in tracking fake sources and competing to spread misinformation [24, 25] . As the situation worsens and the number of concerns increases, the state of suspicion will increase among the general public, thus spreading false information and rumors greatly [17] , in addition to the presence of free times due to curfews, spacing, and social closures, which will make the situation more anxious and thus persistent and pervasive misinformation [38] , especially with the ease of finding fake news and information about the Corona virus [14] . cache = ./cache/cord-285462-9i61rsei.txt txt = ./txt/cord-285462-9i61rsei.txt === reduce.pl bib === id = cord-285148-bch7814v author = Singanayagam, Aran title = Viruses exacerbating chronic pulmonary disease: the role of immune modulation date = 2012-03-15 pages = extension = .txt mime = text/plain words = 7923 sentences = 393 flesch = 35 summary = However in vitro RV infection of epithelial cells from COPD patients resulted in higher virus load and increased inflammatory mediators, but no differences in interferon production compared to cells from control subjects [87] . List of abbreviations ATF: activating transcription factor; BAL: bronchoalveolar lavage; CF: cystic fibrosis; CFTR: cystic fibrosis transmembrane regulator; COPD: chronic obstructive pulmonary disease; ENA-78: epithelial-derived neutrophilactivating peptide 78; ICAM-1: intercellular adhesion molecule; IFN-α: interferon-alpha; IFN-β: interferon-beta; IFN-λ: interferon-lambda; IFN-γ: interferon-gamma; IL: interleukin; IP-10: IFN-γ-induced protein-10; IRF: interferon regulatory factor; ISG: interferon stimulated genes; MDA-5: melanoma differentiation-associated protein-5; NF-κB: nuclear factor-kappa B; NO: nitric oxide; NOS2: nitric oxide synthase 2; PCR: polymerase chain reaction; PEF: peak expiratory flow; PIV: parainfluenza virus; RANTES: regulated on activation: normal T-cell expressed and secreted; RIG-I: retinoic acid inducible gene I; RSV: respiratory syncytial virus; RV: rhinovirus; SLPI: secretory leukoprotease inhibitor; SOCS: suppressor of cytokine signaling family; Th1/2: T helper 1/2; TLR: toll-like receptors; TNF-α: tumor necrosis factor-alpha -1. cache = ./cache/cord-285148-bch7814v.txt txt = ./txt/cord-285148-bch7814v.txt === reduce.pl bib === id = cord-283880-lrrkuist author = Kumar, Arvind title = Evolution of selective-sequencing approaches for virus discovery and virome analysis date = 2017-07-15 pages = extension = .txt mime = text/plain words = 5934 sentences = 286 flesch = 38 summary = Use of sequence dependent (i.e; generic PCR assays and microarray) and sequence independent (i.e; single primer amplification (SISPA) and random priming) approaches for nucleic acid amplification combined with Sanger sequencing or HTS allowed the rapid identification of new viruses after 1980 (Bishop-Lilly et al., 2010; Chang et al., 1994; Day et al., 2010; Grard et al., 2012; Kapoor et al., 2015; Ladner et al., 2016; Linnen et al., 1996; Matsui et al., 1991; Mokili et al., 2012; Muerhoff et al., 1997; Nichol et al., 1993; Qin et al., 2014; Quan et al., 2010; Simons et al., 1995b) (Fig. 1) . For the virome analysis of clinical samples with an abundance of host cells, like blood or tissues, pre-extraction based enrichment is not appropriate as the virus genome itself can be present in its non-capsidated or transcribed form. In positive selection methods, samples are enriched for viral nucleic acids directly using probes targeting the viruses like in PCR assays, microarray or virus capture (in solution based hybridization) approaches. cache = ./cache/cord-283880-lrrkuist.txt txt = ./txt/cord-283880-lrrkuist.txt === reduce.pl bib === id = cord-285367-jxlt0gby author = Johnson, Richard T. title = Emerging Issues in Neurovirology: New Viruses, Diagnostic Tools, and Therapeutics date = 2008-08-31 pages = extension = .txt mime = text/plain words = 3296 sentences = 158 flesch = 41 summary = In the current era of escalating globalization with rapid transport, changing climate, and an ever growing human population with associated changes in lifestyle, poverty, and war, the emergence of new neurologic infections is accelerated. In the 1960s and 1970s, this emergence was foreshadowed by the appearance of new recombinant (duck-human) influenza viruses, legionnaires' disease, toxic shock syndrome, Lyme disease, and the neurovirulent La Crosse strains of California encephalitis virus. Some have been due to the evolution of more virulent agents (eg, enterovirus 71, chikunqunya virus, and drug-resistant microbes), some to geographic relocation of agents (eg, Dengue type 3 in Sri Lanka and West Nile virus in North America), and some to contact with animals and crossing of species barriers (eg, bovine spongiform encephalopathy, variant Creutzfeldt-Jakob disease, Nipah virus, and the severe acute respiratory syndrome [SARS] virus). cache = ./cache/cord-285367-jxlt0gby.txt txt = ./txt/cord-285367-jxlt0gby.txt === reduce.pl bib === id = cord-284941-wfn0pnev author = Samal, S.K. title = Paramyxoviruses of Animals date = 2008-07-30 pages = extension = .txt mime = text/plain words = 4948 sentences = 251 flesch = 41 summary = The members of this virus family are enveloped and have genomes consisting of a single segment of negative-sense RNA that contains 6–10 genes encoding up to 12 proteins. The family Paramyxoviridae contains a large number of viruses of animals (Table 1) , including a number of major animal pathogens (such as Newcastle disease virus (NDV), canine distemper virus, and rinderpest virus), zoonotic pathogens (such as Hendra and Nipah viruses), and a number of somewhat obscure viruses whose natural histories are poorly understood. A number of animal paramyxoviruses have been recovered from cDNAs using reverse genetics, including simian virus 5, NDV, bovine parainfluenza virus 3, Sendai virus, canine distemper virus, rinderpest virus, bovine respiratory syncytial virus, and avian metapneumovirus. Infection occurs by several different routes, including aerosols (NDV, bovine respiratory syncytial virus, avian metapneumovirus) and contaminated feed and water (Newcastle disease, canine distemper, and rinderpest viruses). cache = ./cache/cord-284941-wfn0pnev.txt txt = ./txt/cord-284941-wfn0pnev.txt === reduce.pl bib === id = cord-285856-0sw3wt1i author = Naesens, Lieve title = Anti-influenza virus activity and structure–activity relationship of aglycoristocetin derivatives with cyclobutenedione carrying hydrophobic chains date = 2009-02-05 pages = extension = .txt mime = text/plain words = 2963 sentences = 149 flesch = 38 summary = We here report on the chemical synthesis, anti-influenza virus activity and structure-activity relationship of novel glycopeptide compounds carrying a hydrophobic side chain on an aglycoristocetin backbone ( Fig. 1) . b HPLC conditions: instrument: Waters 600 with UV230nm detection; column: Lichrospher RP-8 (4 mm × 250 mm; 10 m); injection volume: 20 l (corresponding to 2 g compound); solvents: Table 2 , several asymmetric squaric diamides derived from aglycoristocetin exerted marked activity against influenza virus, the most potent compounds being the phenylbenzyl derivative 8e [average antiviral EC 50 : 0.4 M; selectivity index (SI), defined as the ratio of MCC to EC 50 : 50]; the hexanol deriva-tive 8a (EC 50 : 1 M; SI: 14) and the naphthyl derivative 8f (EC 50 : 1.4 M; SI: 10). With regard to the antiviral mode of action, time-of-addition studies suggested that 8e blocks the viral entry process, since optimal anti-influenza virus activity was obtained when the compound was added to MDCK cells 30 min prior to or simultaneously with virus infection. cache = ./cache/cord-285856-0sw3wt1i.txt txt = ./txt/cord-285856-0sw3wt1i.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-290034-4b0mshqa author = Le, Yen H. title = Virus detections among patients with severe acute respiratory illness, Northern Vietnam date = 2020-05-12 pages = extension = .txt mime = text/plain words = 2833 sentences = 145 flesch = 43 summary = To examine evidence for select viral infections among patients with SARI in northern Vietnam, we studied 348 nasopharyngeal samples from military and civilian patients admitted to 4 hospitals in the greater Hanoi area from 2017–2019. Initial screening for human respiratory viral pathogens was performed in Hanoi, Vietnam at the National Institute of Hygiene and Epidemiology (NIHE) or the Military Institute of Preventative Medicine (MIPM), and an aliquot was shipped to Duke-NUS Medical School in Singapore for validation. There was one case of co-infection with enterovirus and coronavirus 229E including a female military hospital patient 28 years of age. Additionally, our results display enterovirus, adenovirus and coronavirus infections among the SARI cases, suggesting that cities in northern Vietnam could benefit also from local surveillance of non-influenza respiratory viruses. cache = ./cache/cord-290034-4b0mshqa.txt txt = ./txt/cord-290034-4b0mshqa.txt === reduce.pl bib === id = cord-285330-td4vr0zv author = Mohammadi, Ali title = Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus date = 2015-11-12 pages = extension = .txt mime = text/plain words = 3157 sentences = 180 flesch = 56 summary = title: Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus An Iranian isolate of avian infectious bronchitis virus IRFIBV32 was quantified in experimentally infected broilers using real-time reverse transcriptase polymerase chain reaction and histopathological changes was investigated. In this study, we identified IBV load in different tissues of experimentally infected broilers to clarify the replication strength of IRFIBV32 Isolate at intervals post challenge. Gross lesions were recorded and their trachea, lungs, kidneys, caecal tonsils, testes and ovaries were aseptically collected separately for the virus detection, titration and histopathological evaluations. We detected the viral RNA in the caecal tonsils of infected chicken from 1 to 20 dpi and the maximal loads of the virus were on 5 dpi. Pathogenesis and tissue distribution of avian infectious bronchitis virus isolate IRFIBV32 (793/b serotype) in experimentally infected broiler chickens Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens cache = ./cache/cord-285330-td4vr0zv.txt txt = ./txt/cord-285330-td4vr0zv.txt === reduce.pl bib === id = cord-282742-eyukbot7 author = Diosa-Toro, Mayra title = Arthropod-Borne Flaviviruses and RNA Interference: Seeking New Approaches for Antiviral Therapy date = 2013-02-20 pages = extension = .txt mime = text/plain words = 6493 sentences = 364 flesch = 48 summary = Geiss, Pierson, and Diamond (2005) observed that siRNAs targeting the C gene had no effect on virus replication when transfected into cells 10 h after WNV infection using lipid-based reagents. In addition, no significant reduction in viral protein or RNA levels was seen in WNV replicon-expressing cells transfected with siRNAs targeting the NS3 gene using lipid-based reagents. Also, a recent report showed that siRNA toward the TNF-a gene reduced cytokine response in DENV-infected DCs, highlighting the potential of targeted RNAi-based approaches to simultaneously decrease viral replication and the detrimental host immune response (Subramanya et al., 2010) . In addition, it has been shown that WNV (Chotkowski et al., 2008) and DENV (Mukherjee & Hanley, 2010) infection (Mukherjee & Hanley, 2010) of Drosophila cell lines induce functional virus-specific siRNAs that promote a protective RNAi response. So far we have described the antiviral effect of the RNAi mechanism induced by exogenous delivery of siRNA or precursors, and how cellular miRNA can target sequences artificially introduced within the genome of flaviviruses. cache = ./cache/cord-282742-eyukbot7.txt txt = ./txt/cord-282742-eyukbot7.txt === reduce.pl bib === id = cord-286137-4cbh3u3z author = Honce, Rebekah title = They are what you eat: Shaping of viral populations through nutrition and consequences for virulence date = 2020-08-13 pages = extension = .txt mime = text/plain words = 1928 sentences = 119 flesch = 33 summary = In mineral-and vitamin-deficient mice, genetic mutations arise in coxsackie B and influenza virus populations that promote virulence even in well-nourished hosts [36] [37] [38] [39] [40] . Experimental evolution of CA/09 virus through two models of murine obesity resulted in a viral population displaying increased virulence upon inoculation of a wild-type host. Interestingly, arbovirus-infected obese or protein-deficient mice showed higher morbidity but lower viral diversity, and both malnourished models transmitted virus less efficiently, highlighting that the effects of nutrition may vary based on the natural life cycles of viral families [42] . In our studies with influenza virus, we linked the emergence of a more diverse and virulent viral population with blunted interferon responses in obese hosts. Interferon treatment of obese mice restricted the emergence of a diverse quasispecies and attenuated the virulence of the resulting viral population, strengthening the claim that a robust innate immune response restricts subsequent infection severity, possibly through reduced viral replication and acquisition of a genetically diverse viral population [8, 20, 41] . cache = ./cache/cord-286137-4cbh3u3z.txt txt = ./txt/cord-286137-4cbh3u3z.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-283756-ycjzitlk author = Simons, Robin R. L. title = Potential for Introduction of Bat-Borne Zoonotic Viruses into the EU: A Review date = 2014-05-16 pages = extension = .txt mime = text/plain words = 14415 sentences = 605 flesch = 53 summary = Bat-borne viruses can pose a serious threat to human health, with examples including Nipah virus (NiV) in Bangladesh and Malaysia, and Marburg virus (MARV) in Africa. In assessing the risks of introduction of these bat-borne zoonotic viruses to the EU, it is important to consider the location and range of bat species known to be susceptible to infection, together with the virus prevalence, seasonality of viral pulses, duration of infection and titre of virus in different bat tissues. Bats are known to have varying degrees of contact with domestic animals and commercial food crops [20, 21] , in particular contact of Pteropus giganteus bats with date palm sap producing trees in Bangladesh is considered a risk factor for human NiV infection [22] . It can be seen that while recent human infections of both NiV and MARV appear to be limited in geographical range (the red areas in Figure 2 ), there are a number of countries where bats have been identified as having the virus, but no human infection has been reported. cache = ./cache/cord-283756-ycjzitlk.txt txt = ./txt/cord-283756-ycjzitlk.txt === reduce.pl bib === id = cord-286708-igu984oc author = Chua, Kaw Bing title = Identification and Characterization of a New Orthoreovirus from Patients with Acute Respiratory Infections date = 2008-11-25 pages = extension = .txt mime = text/plain words = 4359 sentences = 219 flesch = 53 summary = Recently, our group reported the isolation of the Melaka virus from a patient with acute respiratory disease and provided data suggesting that this new orthoreovirus is capable of human-to-human transmission and is probably of bat origin. Here we report yet another Melaka-like reovirus (named Kampar virus) isolated from the throat swab of a 54 year old male patient in Kampar, Perak, Malaysia who was suffering from high fever, acute respiratory disease and vomiting at the time of virus isolation. Here, we report the discovery and characterization of Kampar virus (KamV), the fourth member in the NBV species group and its isolation from a human patient with fever and acute respiratory illness. Due to the similar CPE morphology ( Figure 1 ) and cell line susceptibility patterns between KamV and the recently discovered Melaka virus (MelV), which also causes acute respiratory diseases in humans [5] , immunofluorescent antibody testing was conducted to examine cross reactivity. cache = ./cache/cord-286708-igu984oc.txt txt = ./txt/cord-286708-igu984oc.txt === reduce.pl bib === id = cord-286219-qcx5ehnh author = Calistri, Arianna title = The Ubiquitin-Conjugating System: Multiple Roles in Viral Replication and Infection date = 2014-05-06 pages = extension = .txt mime = text/plain words = 10182 sentences = 498 flesch = 41 summary = In this review we will present several examples of the complex interplay that links viruses and the ubiquitin conjugation machinery, with a special focus on the mechanisms evolved by the human immunodeficiency virus to escape from cellular restriction factors and to exit from infected cells. Furthermore, small DNA viruses with known oncogenic activity, such as the human papillomavirus (HPV), adenoviruses and polyomaviruses, take control of the cell cycle by usurping specific cellular Ub ligase complexes to target crucial cell cycle regulators such as p53 and the protein of the retinoblastoma (pRB) for degradation [58] . In addition to this important function, which is likely required for proper trafficking and maturation of the viral envelope glycoproteins, Vpu has been more recently characterized for yet another crucial role, connected with the ability of the virus to evade a specific IFN-1 induced antiviral factor: the B cell stromal factor 2 (BST-2) or tetherin. cache = ./cache/cord-286219-qcx5ehnh.txt txt = ./txt/cord-286219-qcx5ehnh.txt === reduce.pl bib === id = cord-283964-k3hy2ewx author = Chan, Jasper Fuk-Woo title = Cross-species transmission and emergence of novel viruses from birds date = 2015-01-31 pages = extension = .txt mime = text/plain words = 2810 sentences = 147 flesch = 38 summary = Birds may act as a vehicle for vector dissemination, an amplifying host in bird-vector-bird cycles, or the gene source of emerging viruses in cross-species virus transmission ( Figure 1) Sixteen of 18 hemagglutinin (HA) subtypes and nine of 11 neuraminidase (NA) subtypes of influenza viruses can be found in birds, especially waterfowl and shorebirds [2 ] . A study using influenza viruses generated with gene segments originating from circulating avian influenza viruses and the 1918 pandemic A(H1N1) virus showed that substitutions in the HA, PB2 and PA are important for virulence and efficient transmission in ferrets [35] . Human infections with the emerging avian influenza A H7N9 virus from wet market poultry: clinical analysis and characterisation of viral genome A novel psittacine adenovirus identified during an outbreak of avian chlamydiosis and human psittacosis: zoonosis associated with virus-bacterium coinfection in birds cache = ./cache/cord-283964-k3hy2ewx.txt txt = ./txt/cord-283964-k3hy2ewx.txt === reduce.pl bib === id = cord-288703-wdh1jiry author = Ishtiaq, Farah title = A Call to Introduce Structured Zika Surveillance in India date = 2017-11-15 pages = extension = .txt mime = text/plain words = 3042 sentences = 149 flesch = 47 summary = India has the climatic conditions conducive to year-round transmission of Zika virus, and a structured disease surveillance program should be implemented to prevent an outbreak. Farah Ishtiaq 1, * India has the climatic conditions conducive to year-round transmission of Zika virus, and a structured disease surveillance program should be implemented to prevent an outbreak. In fact, India is an ideal place to explore the coevolutionary dynamics of this host-parasite system because of several factors: (i) the high volume of human movements [5] , (ii) the apparent immunity to Zika from circulating strains of the virus [1] , and (iii) the possibility of transmission in less immunocompetent hosts, such as pregnant women and the elderly viii , and (iv) adults with a prior history of malaria or dengue infections, which may help facilitate transmission and pathogenesis of Zika, potentially resulting in a positive feedback loop [12] . cache = ./cache/cord-288703-wdh1jiry.txt txt = ./txt/cord-288703-wdh1jiry.txt === reduce.pl bib === id = cord-286298-pn9nwl64 author = Helmy, Yosra A. title = The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control date = 2020-04-24 pages = extension = .txt mime = text/plain words = 9290 sentences = 516 flesch = 51 summary = Another group of researchers reported that the virus originated from bats based on the genome sequence of SARS-CoV-2, which is 96% identical to bat coronavirus RaTG13. These factors include, but are not limited to: (1) travel to or contact with individuals who have recently visited Wuhan, China, or other places experiencing an outbreak; (2) close contact with persons who are diagnosed positive for the disease, such as healthcare workers caring for patients with SARS-CoV-2; (3) contact with droplets and secretions (produced by sneezing or coughing) from an infected person and eating or handling wild animals native to China such as bats. These factors include, but are not limited to: (1) travel to or contact with individuals who have recently visited Wuhan, China, or other places experiencing an outbreak; (2) close contact with persons who are diagnosed positive for the disease, such as healthcare workers caring for patients with SARS-CoV-2; (3) contact with droplets and secretions (produced by sneezing or coughing) from an infected person and eating or handling wild animals native to China such as bats. cache = ./cache/cord-286298-pn9nwl64.txt txt = ./txt/cord-286298-pn9nwl64.txt === reduce.pl bib === id = cord-285935-5rsk6g7l author = Kinast, Volker title = Hepatitis E Virus Drug Development date = 2019-05-28 pages = extension = .txt mime = text/plain words = 6638 sentences = 364 flesch = 46 summary = Cyclic peptides (CP) that had been developed to abrogate interaction of p6Gag and TSG101 and inhibited viral release of HIV Virus like particles (VLPs) [76] were tested for their activity against HEV [77] . The compounds RBV and mycophenolic acid (MPA), both of which target enzymes involved in nucleotide synthesis, are either already used as treatment against HEV or have been reported for their potential to inhibit the virus. So far, the antiviral activity against HEV of only four drugs (Sofosbuvir, pegIFN-α, Ribavirin and silvestrol) was approved in experimental settings beyond in vitro cell culture systems. Sofosbuvir Inhibits Hepatitis E Virus Replication In Vitro and Results in an Additive Effect When Combined With Ribavirin Sofosbuvir shows antiviral activity in a patient with chronic hepatitis E virus infection Zinc Salts Block Hepatitis E Virus Replication by Inhibiting the Activity of Viral RNA-Dependent RNA Polymerase The natural compound silvestrol inhibits hepatitis E virus (HEV) replication in vitro and in vivo cache = ./cache/cord-285935-5rsk6g7l.txt txt = ./txt/cord-285935-5rsk6g7l.txt === reduce.pl bib === id = cord-284156-btb4oodz author = Liu, Yiliu title = Host and Viral Modulation of RIG-I-Mediated Antiviral Immunity date = 2017-01-03 pages = extension = .txt mime = text/plain words = 7021 sentences = 397 flesch = 38 summary = Retinoic acid-inducible gene-I (RIG-I) is critical in triggering antiviral and inflammatory responses for the control of viral replication in response to cytoplasmic virus-specific RNA structures. They function as cytoplasmic sensors for the recognition of a variety of RNA viruses and subsequent activation of downstream signaling to drive type I IFN production and antiviral gene expressions. (c) Interactions between RIG-I-TRIM25 complex and 14-3-3ϵ promote RIG-I translocation to mitochondrial mitochondrial antiviral signaling protein (MAVS) for downstream signaling, leading to interferon production. Protein purification and mass spectrometry analysis identified that phosphorylation of Thr170 in the CARDs antagonizes RIG-I signaling by inhibiting TRIM25-mediated Lys172 ubiquitination and MAVS binding (68) . Ebola virus VP35 protein binds double-stranded RNA and inhibits alpha/beta interferon production induced by RIG-I signaling Inhibition of dengue and chikungunya virus infections by RIG-I-mediated type I interferon-independent stimulation of the innate antiviral response cache = ./cache/cord-284156-btb4oodz.txt txt = ./txt/cord-284156-btb4oodz.txt === reduce.pl bib === id = cord-287286-4l963z2q author = Green, Victoria A. title = Molecular mechanisms of viral infection and propagation: An overview of the second Advanced Summer School in Africa date = 2010-07-28 pages = extension = .txt mime = text/plain words = 7368 sentences = 363 flesch = 43 summary = The main themes of discussion at the summer school were: 1) why viral infection can lead to cancer; 2) how a greater understanding of the mechanisms underpinning human immunodeficiency virus (HIV) propagation can inform new antiviral strategies; 3) the abilities of viruses to evade the immune system and the obstacles to the development of effective vaccines; and, 4) the potential afforded by viruses as research tools. The import of the host, including an ability to regulate viral gene expression in different tissues and to mount an effective immune response, is becoming increasingly apparent in determining the molecular basis of HPV-associated tumor progression. Advantages CoVs possess over other viruses as expression vectors include: 1) the possibility of spike protein manipulation, to engineer virus tropism (88, 89) ; 2) the replication of the RNA genome in the cytoplasm, side-stepping potential problems associated with integration (90); 3) the existence of nonpathogenic strains that infect a wide range of species of health and economic importance; 4) the ability to carry large genomes (27-30 kb) , which could favor the introduction of extensive foreign genes (91); and 5) the availability of cDNA clones derived from infectious strains (92, 93) . cache = ./cache/cord-287286-4l963z2q.txt txt = ./txt/cord-287286-4l963z2q.txt === reduce.pl bib === id = cord-288111-0ufc54kw author = ter MEULEN, VOLKER title = Autoimmune Reactions Against Myelin Basic Protein Induced by Corona and Measles Viruses date = 2006-12-17 pages = extension = .txt mime = text/plain words = 2851 sentences = 153 flesch = 37 summary = What apparently happens is that the viruses themselves induce Ia expression on the astrocytes, enabling these cells to present the viral antigens to the lymphocytes and allowing the host to mount an effective immune response to control the infection. However, in extremely high constitutive levels of class I1 expression on astrocytes, an inappropriate or excessive presentation of self-antigens and viral antigens may develop, similar to that in autoimmune processes directed against the thyroid gland.'" This mechanism could well play a role in the JHM-and measles-virus-induced CNS disease in Lewis rats, because as recently shown by us," these hyperexpressions of Ia molecules on astrocytes after contact with gamma-interferon or viral particles are genetically regulated. JHM and measles virus infections in rats are models of a persistent viral infection of the CNS with and without demyelination, associated with a cell-mediated immune reaction to MBP. cache = ./cache/cord-288111-0ufc54kw.txt txt = ./txt/cord-288111-0ufc54kw.txt === reduce.pl bib === id = cord-288348-b10e023s author = Estes, Mary Kolb title = Epidemic viral gastroenteritis date = 1979-06-30 pages = extension = .txt mime = text/plain words = 4523 sentences = 232 flesch = 39 summary = Of the many viruses identified in stools, only two groups have met the criteria as definite etiologic agents of epidemic gastroenteritis in human subjects: rotaviruses and the small 27 nm agents [Norwalk-like agents) ( of investigations which began with an epidemic of gastroenteritis occurring in the newborn in the Baltimore-Washington area in the fall of 1941. Rotaviruses have been established as enteritis viruses by isolation and purification from stools of subjects suffering from gastroenteritis, and by induction of disease and seroconversion in both animals and volunteer subjects with purified preparations, Epidemiologic studies on the prevalence of rotavirus infections have shown these ubiquitous agents to be a major cause of gastroenteritis in children. Local immune factors, such as secretory immunoglobulin A or interferon, may therefore be important in protection against rotavirus infection, Alternatively, reinfection in the presence of circulating antibody could reflect the presence of multiple serotypes of virus [37] ; at least four agents in human subjects have been characterized to date [38-411. cache = ./cache/cord-288348-b10e023s.txt txt = ./txt/cord-288348-b10e023s.txt === reduce.pl bib === id = cord-284479-75zgljet author = García-Serradilla, Moisés title = Drug repurposing for new, efficient, broad spectrum antivirals date = 2019-04-15 pages = extension = .txt mime = text/plain words = 7574 sentences = 416 flesch = 43 summary = Thus, the antiviral activity of cyclosporine A (CsA) and some of its nonimmunosuppressive analogs against these viruses has been shown to be related to its ability to bind cellular cyclophilins and inhibiting the interaction with the viral proteins (Bienkowska-Haba et al., 2009; Bose et al., 2003; Damaso and Moussatche, 1998; Franke et al., 1994; Kaul et al., 2009; Nakagawa et al., 2004; Thali et al., 1994; Wainberg et al., 1988; Yang et al., 2008) . CsA has also been reported to inhibit the propagation of several strains of influenza A virus in cell cultures blocking a late step of the replication cycle by mechanisms that might implicate CypA-dependent and -independent pathways (Hamamoto et al., 2013; Liu et al., 2012a; Ma et al., 2016) . Therefore, further studies are needed to better understand the mode of action of AgNPs, their cell specificity and toxicological issues in order to generate new and more effective compounds as well as the use in combination with other drugs in the treatment of different viral diseases. cache = ./cache/cord-284479-75zgljet.txt txt = ./txt/cord-284479-75zgljet.txt === reduce.pl bib === id = cord-286719-1xjmlwqr author = Draz, Mohamed Shehata title = Applications of gold nanoparticles in virus detection date = 2018-02-15 pages = extension = .txt mime = text/plain words = 18990 sentences = 901 flesch = 37 summary = The developed AuNP-based detection techniques are reported for various groups of clinically relevant viruses with a special focus on the applied types of bio-AuNP hybrid structures, virus detection targets, and assay modalities and formats. These techniques represent the majority of molecular techniques applied in virus detection and include various types of target amplification techniques (e.g., PCR, loop-mediated isothermal amplification (LAMP), transcription-mediated amplification, and nucleic acid sequence-based amplification), signal amplification techniques (e.g., branched DNA and hybrid capture), and probe amplification techniques (e.g., ligase chain reaction and strand-displacement amplification). [70] developed an impedimetric electrochemical assay for the detection of AIV M gene sequences based on measuring changes in the impedimetric behavior of the electrode when the target DNA hybridizes with the capture DNA probes immobilized onto its surface and is subsequently labeled by AuNPs via streptavidin/ biotin interaction (Fig. 12C) . cache = ./cache/cord-286719-1xjmlwqr.txt txt = ./txt/cord-286719-1xjmlwqr.txt === reduce.pl bib === id = cord-287348-00yaxpkp author = Martinez, Maria Jose Abad title = Antiviral Activities of Polysaccharides from Natural Sources date = 2005-12-31 pages = extension = .txt mime = text/plain words = 7003 sentences = 323 flesch = 41 summary = Although many compounds with potent antiviral activity in cell cultures and in experimental animals have been detected, at present only several molecules and a-interferon have been approved by the health authorities for therapy of viral infections in humans. Furthermore, several soluble derivatized dextrans with different percentages of carbomethyl, benzylamide and sulphonate/sulphate groups were also evaluated for possible inhibitory effects on HIV-1 infection, and from the results obtained, their use as anti-HIV therapeutic agents can be proposed [56] . Carrageenans and fucoidan are sulphated PS extracted from red seaweed and brown algae, which have shown potent inhibitory activity against different viruses including HIV. These compounds act as potent inhibitors of different enveloped viruses, including members of Herpesviridae, and their activity is linked to the anionic features of the molecule which hinder the attachment of viral particles to host cells. cache = ./cache/cord-287348-00yaxpkp.txt txt = ./txt/cord-287348-00yaxpkp.txt === reduce.pl bib === id = cord-287711-gw8mgg4m author = Junter, Guy-Alain title = Cellulose-based virus-retentive filters: a review date = 2017-06-01 pages = extension = .txt mime = text/plain words = 11711 sentences = 582 flesch = 40 summary = Data from spiking studies quantifying the viral filtration performance of cellulosic filters are detailed, i.e., first, the virus reduction capacity of regenerated cellulose hollow fiber filters in the manufacturing process of blood products and, second, the efficiency of virus recovery/concentration from water samples by the viradel (virus adsorption–elution) method using charge modified, electropositive cellulosic filters or conventional electronegative cellulose ester microfilters. Data from spiking studies quantifying the viral filtration performance of cellulosic filters are detailed, i.e., first, the virus reduction capacity of regenerated cellulose hollow fiber filters in the manufacturing process of blood products and, second, the efficiency of virus recovery/concentration from water samples by the viradel (virus adsorption-elution) method using charge modified, electropositive cellulosic filters or conventional electronegative cellulose ester microfilters. cache = ./cache/cord-287711-gw8mgg4m.txt txt = ./txt/cord-287711-gw8mgg4m.txt === reduce.pl bib === id = cord-288372-48wao8a0 author = Dia, Ndongo title = Respiratory viruses associated with patients older than 50 years presenting with ILI in Senegal, 2009 to 2011 date = 2014-04-08 pages = extension = .txt mime = text/plain words = 3873 sentences = 215 flesch = 55 summary = The main aim of this study was to determine the prevalence and the diversity of respiratory viruses associated with ILI cases in adults over 50 years old in Senegal. Viral aetiology, prevalence and diversity data in people with influenza like illness (ILI) and/or acute respiratory illness (ARI) in Africa, (especially in West Africa), are scarce and often limited to the influenza viruses' infection. For example in the United States alone, up to 40% of non-pneumonic lower respiratory illnesses in the elderly have been associated with respiratory viral infection [10] , and an estimated 54,000 deaths annually have been attributed to the influenza and respiratory syncytial viruses (RSV) [11] . The present study is the first description of the etiology of respiratory viruses associated with patients with ILI in a cohort of elderly people in the West African context. cache = ./cache/cord-288372-48wao8a0.txt txt = ./txt/cord-288372-48wao8a0.txt === reduce.pl bib === id = cord-287337-2ljbsia2 author = Ludwig, Christine title = Virus-like particles—universal molecular toolboxes date = 2008-01-04 pages = extension = .txt mime = text/plain words = 5065 sentences = 205 flesch = 33 summary = It is noteworthy that VLPs assembled from HPV major capsid protein L1 in yeast were capable of inducing protective immune responses against HPV subtypes 16 and 18 causing cervical cancer in humans, thus resulting in a safe, well tolerated and highly immunogenic vaccine that received approval for marketing in 2006 [13] . Since particulate antigens had been demonstrated to induce better cellular and humoral immune responses than soluble antigens, the detection that HIV-1 Pr55Gag polyprotein self-assembles into particulate spheres provided a new rationale for generating a Gag-based VLP vaccine [15, 16] . The authors demonstrated efficient expression of murine leukemia virus (MLV) Gag-Env VLPs from plasmid DNA in vitro and used these plasmo-retroVLPs to induce strong specific CTL responses towards displayed T cell epitopes, protecting mice from lethal virus challenge. [52] have formerly shown that virosome-mediated targeting of mumps virus DNA to APCs induces specific CTL responses suggesting efficient expression and presentation of the encoded mumps antigens. DNA vaccines encoding retrovirusbased virus-like particles induce efficient immune responses without adjuvant cache = ./cache/cord-287337-2ljbsia2.txt txt = ./txt/cord-287337-2ljbsia2.txt === reduce.pl bib === id = cord-288238-36hiiw91 author = Keshavarz, Mohsen title = Metabolic host response and therapeutic approaches to influenza infection date = 2020-03-05 pages = extension = .txt mime = text/plain words = 8134 sentences = 425 flesch = 32 summary = It is also reported that influenza infection significantly increases ROS production by inducing Nox4, and the proliferation of this virus in lung epithelial cells is dependent on redox-sensitive pathways activated by Nox4-derived ROS [16] . IFN can also exert its function on metabolic changes by producing several mediators including indoleamine-2,3-dioxygenase (IDO) and nitric oxide (NO), both of which appear to have either an inducible or an inhibitory role in viral replication [33] . In addition, increased temperature of cells during infection (which could be the result of virus replication and fever) causes heat stress which in turn can considerably downregulate carnitine palmitoyltransferase II (CPT II) activity and reduce the β-oxidation and ATP levels in fibroblasts of influenza-associated encephalopathy patients and healthy volunteers [110] . Through enhancing the activity of the mTORC1 complex, the influenza virus strengthens several metabolic pathways, including glycolysis, glutaminolysis, pentose phosphate, and fatty acid synthesis, to provide more ATP and structural materials for viral replication. cache = ./cache/cord-288238-36hiiw91.txt txt = ./txt/cord-288238-36hiiw91.txt === reduce.pl bib === id = cord-288231-vg8bwed9 author = Haagmans, Bart L. title = The Application of Genomics to Emerging Zoonotic Viral Diseases date = 2009-10-26 pages = extension = .txt mime = text/plain words = 3406 sentences = 146 flesch = 35 summary = Other viruses, such as influenza A viruses and severe acute respiratory syndrome coronavirus (SARS-CoV), may need multiple genetic changes to adapt successfully to humans as a new host species; these changes might include differential receptor usage, enhanced replication, evasion of innate and adaptive host immune defenses, and/or increased efficiency of transmission. New molecular techniques such as high-throughput sequencing, mRNA expression profiling, and array-based single nucleotide polymorphism (SNP) analysis provide ways to rapidly identify emerging pathogens (Nipah virus and SARS-CoV, for example) and to analyze the diversity of their genomes as well as the host responses against them. After introduction of a new influenza A virus from an avian or porcine reservoir into the human species, viral genomics studies are essential to identify critical mutations that enable the circulating virus to spread efficiently, interact with different receptors, and cause disease in the new host. cache = ./cache/cord-288231-vg8bwed9.txt txt = ./txt/cord-288231-vg8bwed9.txt === reduce.pl bib === id = cord-287554-2lqy2ix9 author = Amarelle, Luciano title = Tratamiento antigripal: fármacos actualmente utilizados y nuevos agentes en desarrollo date = 2017-01-31 pages = extension = .txt mime = text/plain words = 5858 sentences = 471 flesch = 46 summary = El tratamiento disponible con fármacos antivirales, de ser administrado de forma precoz, puede reducir el riesgo de complicaciones severas; sin embargo, muchos tipos de virus desarrollan resistencia a fármacos, reduciendo su efectividad, por lo que ha habido un gran interés en los últimos años en el desarrollo de nuevas opciones terapéuticas para combatir la enfermedad. La estructura del virus influenza A consta de una envoltura lipídica que proviene de la célula huésped y lleva ancladas las glucoproteínas hemaglutinina (HA) y neuraminidasa (NA), antígenos de superficie usados para clasificar a los virus (por ejemplo, H1N1, H3N2, H5N1). Se ha demostrado que posee actividad antiviral en diferentes tiempos del ciclo del virus: en fases tempranas inhibe la transcripción de ARN viral y la síntesis proteica, y en fases tardías bloquea el tráfico citoplasmático de las nuevas ribonucleoproteínas 71 . Por ejemplo, se ha demostrado que los inhibidores de la Na,K-ATPasa poseen actividad antiviral frente a distintos tipos de virus ADN y ARN. cache = ./cache/cord-287554-2lqy2ix9.txt txt = ./txt/cord-287554-2lqy2ix9.txt === reduce.pl bib === id = cord-286559-y8z0pwgn author = Ding, Nai-Zheng title = A permanent host shift of rabies virus from Chiroptera to Carnivora associated with recombination date = 2017-03-21 pages = extension = .txt mime = text/plain words = 4244 sentences = 211 flesch = 45 summary = Bat virus host shifts have resulted in the emergence of several serious diseases in humans and animals, such as SARS 1 , Ebola 2 , and rabies 3 viruses. Interestingly, although evolutionary analyses have demonstrated that bat-to-carnivore host-shifting viruses accumulate few adaptive mutations 4, 6, 11 , in none of these examples did bat RABV establish permanent transmission cycles in the new host species 7 . The second permanent host shift appears to have occurred in North America, producing a lineage including two variants, raccoon rabies virus (RRV) and south-central skunk variant (SCSKV). Since bat RABVs are potentially able to infect carnivore species 6, 11, 14, 45 , we also propose that recombination may function as the third and fourth stages of establishment of a permanent host shift by significantly enhancing the adaptability of a bat virus in terrestrial mammals. cache = ./cache/cord-286559-y8z0pwgn.txt txt = ./txt/cord-286559-y8z0pwgn.txt === reduce.pl bib === id = cord-287151-4hlvrfeh author = Steinmann, J title = Surrogate viruses for testing virucidal efficacy of chemical disinfectants date = 2004-04-30 pages = extension = .txt mime = text/plain words = 2911 sentences = 173 flesch = 43 summary = Abstract Since important agents of viral nosocomial infections like hepatitis B and C viruses and norovirus do not replicate sufficiently in cell culture systems, disinfectants with suspected efficacy against these viruses must be evaluated by different methods. Besides molecular approaches and indirect tests, the use of surrogate viruses with similar biophysical properties and genomic structure allows the assessment of virucidal efficacy of chemical disinfectants in quantitative suspension tests. By including these viruses in inactivation experiments, valuable data from suspension tests can be derived on the virucidal efficacy of chemical disinfectants. Besides the viruses mentioned in the guidelines, there are other important pathogens such as Hepatitis B virus (HBV), Hepatitis C virus (HCV) and norovirus which cause nosocomial infections but cannot be propagated sufficiently by cell culture techniques. Inactivation of hepatitis B virus in plasma by hospital in-use chemical disinfectant assessed by a modified HepG2 cell culture cache = ./cache/cord-287151-4hlvrfeh.txt txt = ./txt/cord-287151-4hlvrfeh.txt === reduce.pl bib === id = cord-287466-ag5y781z author = Cowley, J.A. title = Nidoviruses of Fish and Crustaceans date = 2016-09-09 pages = extension = .txt mime = text/plain words = 17715 sentences = 760 flesch = 47 summary = As evidenced by the presence of genomic-length and sgmRNA-length replicativeintermediate double-stranded (ds)RNAs in shrimp cells infected with gill-associated virus (GAV) (Cowley et al., 2002a) , the type species okavirus (Cowley et al., 2012) , it is speculated that transcription termination of the antisense RNAs might occur at precise positions, resulting in common 3′-termini, and that these then act directly as promoters for transcription initiation of the genomic and sgmRNAs. In all other nidoviruses, however, and for the longest of the sgmRNAs transcribed by toroviruses, the (−) and (+) strand sgmRNAs are transcribed using a far more complex discontinuous process involving the splicing of a common "anti-leader" sequence derived from the genome 5′-terminus to each (−) strand sgmRNA that then acts as a universal promoter for transcribing each (+) strand sgmRNA (Pasternak et al., 2006; Sawicki et al., 2007; Smits et al., 2005; van Vliet et al., 2002) . Nidoviruses of aquatic species include the rod-shaped okaviruses GAV and yellow head virus (YHV) that primarily infect Penaeid shrimp (Longyant et al., 2005; Flegel, 2012; Flegel et al., 1997a; Cowley et al., 2000a Cowley et al., , 2002a Cowley and Walker, 2002; Sittidilokratna et al., 2008) and a morphologically similar virus with a ~22 kb ssRNA genome detected in diseased Chinese mitten crabs (Zhang and Bonami, 2007) . cache = ./cache/cord-287466-ag5y781z.txt txt = ./txt/cord-287466-ag5y781z.txt === reduce.pl bib === id = cord-285547-7m3dh8hu author = Nomura, Naoki title = Characterization of avian influenza viruses isolated from domestic ducks in Vietnam in 2009 and 2010 date = 2011-11-09 pages = extension = .txt mime = text/plain words = 3271 sentences = 154 flesch = 51 summary = In the present study, a surveillance of avian influenza was carried out in Vietnam in domestic ducks and wild birds in 2009 and 2010, and the isolates were antigenically and phylogenetically analyzed and their pathogenicity in birds and mammals was assessed. One hundred tracheal and cloacal swab samples that were viral gene positive from 600 domestic ducks and 207 wild birds (night heron, Nycticorax nycticorax; grey heron, Ardea cinerea; purple heron, Ardea purpurea; chinese pond heron, Ardeola bacchus; chinese egret, Egretta eulophotes; little egret, Egretta garzetta; intermediate egret, Egretta intermedia; cormorant, Phalacrocorax carbo; little cormorant, Microcarbo niger; Japanese bush warbler, Cettia diphone; black-browed reed warbler, Acrocephalus bistrigiceps; olive bulbul, Iole virescens; black capped kingfisher, Halcyon pileata; collared kingfisher, Halcyon chloris; racket tailed treepie, Crypsirina temia; oriental magpie robin, Copsychus saularis; tiger shrike, Lanius tigrinus; yellow bittern, Ixobrychus sinensis; indian cuckoo, Cuculus micropterus; common koel, Eudynamys scolopacea; and black collared starling, Sturnus nigricollis) in April 2009 and March 2010 in southern Vietnam were inoculated into the allantoic cavities of 10-day-old embryonated chicken eggs. cache = ./cache/cord-285547-7m3dh8hu.txt txt = ./txt/cord-285547-7m3dh8hu.txt === reduce.pl bib === id = cord-288879-rj03dsib author = Schein, Catherine H. title = Polyglutamine Repeats in Viruses date = 2018-09-04 pages = extension = .txt mime = text/plain words = 6195 sentences = 301 flesch = 45 summary = While the mechanisms for the function and toxicity of extended polyQ segments (or the nucleic regions that encode them) in eukaryotic proteins continue to be actively studied [16] , there has been little exploration of their occurrence and possible roles, even in neurovirulent viruses. At the start of this work, the ViPR database [29] , which allows rapid access to the published sequences of over 75,000 viral genomes or genome segments, was used to determine which RNA and DNA viruses contain polyQ repeats. As discussed below, the longest repeats were found in DNA virus proteins that function in enhancing transmissibility (cowpox ATI) or contribute to viral latency (herpes viruses). Under growth conditions allowing the virus to resume lytic growth, where the enzyme activity is required to ensure efficient replication, the region Fig. 2 Soluble polyQ segments (of cell or viral origin) may prevent beclin-1-induced autophagy, which depends on the DNA binding ability of the polyQ segment of wt-ataxin-3 (based on [2, 67] ). cache = ./cache/cord-288879-rj03dsib.txt txt = ./txt/cord-288879-rj03dsib.txt === reduce.pl bib === id = cord-286741-h3oix9zc author = Park, Mee Sook title = Animal models for the risk assessment of viral pandemic potential date = 2020-04-22 pages = extension = .txt mime = text/plain words = 9619 sentences = 484 flesch = 46 summary = Focusing on the pandemic potential of viral infectious diseases, we suggest what should be assessed to prevent global catastrophes from influenza virus, Middle East respiratory syndrome coronavirus, dengue and Zika viruses. When a virus with a nonhuman origin HA and an efficient human transmissibility gets transmitted from the adaptation host swine to human (4), a pandemic might ensue (5) of IAVs, avian and swine species should be considered the natural reservoir animals, and in case of MERS-CoVs, bats and dromedary camels [32, 87, 90] . In addition to NHP and hDPP4-mouse models, rabbits might be a good candidate for MERS-CoV transmission experiments due to its camel-like receptor distribution in the upper respiratory tract (Table 2 ) [142, 150] . Human-like symptoms of MERS-CoV infection have not been reproduced in other animals than hDPP4-mice and NHPs. Starting from the distinct receptor specificities of the HA proteins between avian and human IAVs, host restriction determinants of IAVs have been documented [56] . cache = ./cache/cord-286741-h3oix9zc.txt txt = ./txt/cord-286741-h3oix9zc.txt === reduce.pl bib === id = cord-287770-oxfnt2n4 author = Caricati, C. P. title = Safety of snake antivenom immunoglobulins: Efficacy of viral inactivation in a complete downstream process date = 2013-06-27 pages = extension = .txt mime = text/plain words = 4776 sentences = 304 flesch = 48 summary = title: Safety of snake antivenom immunoglobulins: Efficacy of viral inactivation in a complete downstream process In this article, we used a wide panel of viruses to assess viral removal/inactivation of our downstream process for Snake Antivenom Immunoglobulin (SAI). Among the steps analyzed in the process, phenol addition was the most effective one, followed by heat, caprylic acid, and pepsin. The main steps are cited in sequential order (a) ammonium sulfate precipitation of immunoglobulins, (b) pepsin digestion to obtain F(ab')2 fragments, (c) caprylic acid precipitation of nonimmunoglobulin proteins, (d) heat treatment, (e) ammonium sulfate precipitation of F(ab')2 fragments, (f) tangential filtration, (g) ion-exchange chromatography, (h) tangential filtration, and (i) phenol addition. 34 We found no reports using both viruses as models for viral inactivation concerning the described purification steps. 52, 55 Phenol inactivated both viruses, which indicates that it might also be an effective preservative for human-derived immunoglobulins, when it comes to viral safety. cache = ./cache/cord-287770-oxfnt2n4.txt txt = ./txt/cord-287770-oxfnt2n4.txt === reduce.pl bib === id = cord-288945-c9ow1q5c author = Spengler, Ulrich title = Liver Disease Associated with Non-Hepatitis Viruses date = 2019-11-01 pages = extension = .txt mime = text/plain words = 7425 sentences = 443 flesch = 39 summary = Although exotic diseases, in particular viral hemorrhagic fevers are a severe threat in certain regions of the world, liver disease due to exotic infections such as Ebola virus, Rift valley fever or Lassa fever have been reported only sporadically but do not represent a frequent health problem in returning travelers. Clinically more severe diseases, for example, dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS) can follow from secondary infection with dengue virus of different serotype. Herpes simplex virus (HSV), varizella zoster virus (VZV), Epstein-Barr virus (EBV), cytomegalovirus (CMV) and Human Herpesvirus type 6 or 7 (HHV6, HHV7) can directly affect the liver and are infections in the human population usually acquired during childhood or adolescence. In patients with severe immunodeficiency lymphomatoid granulomatosis is a further unusual complication of Epstein-Barr virus infection leading to granuloma formation in multiple organs including the liver, which may require interferon-alpha antiviral therapy (Wilson et al., 1996) . cache = ./cache/cord-288945-c9ow1q5c.txt txt = ./txt/cord-288945-c9ow1q5c.txt === reduce.pl bib === id = cord-287851-9p0dr7rl author = Fedson, David S title = Confronting an influenza pandemic with inexpensive generic agents: can it be done? date = 2008-09-30 pages = extension = .txt mime = text/plain words = 4878 sentences = 277 flesch = 46 summary = The investigators commented that because of the functional redundancy of many cytokines and chemokines, deleting more than one of these genes might have had a greater (presumably more adverse) eff ect on the course of disease, and concluded that mice are suitable for evaluating agents that "modulate the infl ammatory response induced by H5N1 viruses, either alone or in combination with antiviral therapy". 18 More recently, a study of acute infl uenza pneumonia showed that compared with normal mice, Toll-like receptor (TLR) 3 knockout mice had reduced levels of several proinfl ammatory cytokines and chemokines and high pulmonary virus titres, yet mortality was unexpectedly low. For reasons of global public health it is crucially important for investigators to undertake experimental studies to determine whether these or other generic agents (or several of them in combination) could be eff ective in treating H5N1 and other potentially pandemic infl uenza virus infections. cache = ./cache/cord-287851-9p0dr7rl.txt txt = ./txt/cord-287851-9p0dr7rl.txt === reduce.pl bib === id = cord-288930-h13cxuh3 author = Lim, Faye J title = Viral Etiology and the Impact of Codetection in Young Children Presenting With Influenza-Like Illness date = 2016-07-20 pages = extension = .txt mime = text/plain words = 3429 sentences = 179 flesch = 42 summary = METHODS: Children aged 6 to 59 months who presented to a tertiary pediatric hospital between influenza seasons 2008 and 2012 with fever and acute respiratory symptoms were enrolled, and nasal samples were collected. We compared demographics, presenting symptoms, and clinical outcomes of children with a single-virus infection and those in whom 2 or more viruses were detected (virus-virus codetection). With this study, we describe the virology of ARTI in children aged 6 months to 4 years who presented to a tertiary pediatric hospital in Australia with influenza-like illness during influenza season. We conclude that the impact of virus-virus codetection on disease severity in children who present with influenza-like illness is likely to be limited to those infected with specific pathogen pairs. Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children cache = ./cache/cord-288930-h13cxuh3.txt txt = ./txt/cord-288930-h13cxuh3.txt === reduce.pl bib === id = cord-289360-h6wvx7gw author = Imperiale, Michael J. title = The Importance of Virology at a Time of Great Need and Great Jeopardy date = 2015-03-10 pages = extension = .txt mime = text/plain words = 1290 sentences = 59 flesch = 51 summary = journal: mBio Viruses account for up to 20% of all human cancers, and although a large percentage of new human papillomavirus (HPV) and HBV infections can now be prevented by vaccination, many are already infected, and the vaccines are not being used to their full potential. The tremendous reduction in mortality from such diseases as variola, measles, and rubella came about only because the causative viruses were identified, cultivated, attenuated, and made into effective vaccines by biomedical research. While we scientists cannot directly control funding or regulations, we can take charge of some aspects of the research enterprise in a way to ensure that it continues to benefit society. This requires engaging our elected officials both directly and indirectly by continuing to educate them and the public at large about the importance of fundamental research in infectious diseases. cache = ./cache/cord-289360-h6wvx7gw.txt txt = ./txt/cord-289360-h6wvx7gw.txt === reduce.pl bib === id = cord-288734-xinkqs6u author = Muñoz-Fontela, César title = Ebola Virus Disease in Humans: Pathophysiology and Immunity date = 2017-03-30 pages = extension = .txt mime = text/plain words = 9957 sentences = 451 flesch = 44 summary = Discovered in 1976 during the first documented outbreak of Ebola virus disease (EVD) in the town of Yambuku in northern Zaire (today Democratic Republic of the Congo), EBOV has since caused sporadic human disease outbreaks of varying magnitude in Equatorial African countries (Sanchez et al. Antigen-presenting cells are a putative initial target of EBOV infection and previous research in animal models of disease has indicated that dendritic cells (DCs) and macrophages are early and preferred targets of EBOV and support virus replication (Geisbert et al. Clinical presentation, biochemical, and haematological parameters and their association with outcome in patients with Ebola virus disease: an observational cohort study Sequence-based human leukocyte antigen-B typing of patients infected with Ebola virus in Uganda in 2000: identification of alleles associated with fatal and nonfatal disease outcomes cache = ./cache/cord-288734-xinkqs6u.txt txt = ./txt/cord-288734-xinkqs6u.txt === reduce.pl bib === id = cord-289593-81vu2kbu author = de Blic, J. title = Interactions micro-organismes et voies aériennes distales : spécificités pédiatriques date = 2017-03-03 pages = extension = .txt mime = text/plain words = 5325 sentences = 526 flesch = 65 summary = Les relations entre bronchiolites virales et asthme, la place des virus à tropisme respiratoire dans l'histoire naturelle de l'asthme ont fait l'objet de nombreuses études, d'abord concentrées sur le virus respiratoire syncytial humain (hVRS) et plus récemment sur le rhinovirus humain (hRV). D'autres IAV aviaires ont pu contaminer l'homme ces dernières années, mais c'est du porc en 2009 qu'une pandémie grippale a éclos avec un virus influenza A triple réassortant (H 1 N 1pdm09 ), heureusement d'une pathogénicité moindre que celle imaginée lors des premières transmissions au Mexique puis de son expansion pandémique dans l'hémisphère sud [3] . En effet, à partir de la cohorte Childhood Origins of ASThma (COAST) constituée de 285 nouveau-nés, ayant au moins un parent atopique (1 Prick test positif) et/ou asthmatique, les auteurs ont évalué la prévalence des manifestations sifflantes dans les 6 premières années de la vie, en regard des antécédents de bronchiolite à VRS et à hRV [17, 28] . cache = ./cache/cord-289593-81vu2kbu.txt txt = ./txt/cord-289593-81vu2kbu.txt === reduce.pl bib === id = cord-290481-i2ppvsh5 author = Dolja, Valerian V. title = Comparative and functional genomics of closteroviruses date = 2006-03-09 pages = extension = .txt mime = text/plain words = 9298 sentences = 455 flesch = 47 summary = It was concluded that, at least in part, viral pathogenicity is due to interference of silencing suppressors with developmental function of plant small RNAs. Despite their mechanistic similarity, p21 and p19 appear to be structurally and evolutionarily unrelated and neither has detectable homologues outside the respective virus genera (Vargason et al., 2003; Ye and Patel, 2005) . Although Citrus tristeza virus (CTV) encodes p20, a p21like suppressor of RNA silencing, screening of the CTV genome revealed an additional suppressor, p23, that has no homologues in other closteroviruses (Fig. 2) (Lu et al., 2004) . A comparison of TMV and BYV, which both evolved from the alphavirus-like ancestors, shows that the large part of the ∼9 kb genomic surplus of BYV is dedicated to facilitating the synthesis of the virion RNA and multiple sgRNAs. The rest of the surplus was invested in the formation of the complex virion tail that empowers virus transport within and transmission between the host plants and in suppression of RNA silencing (Fig. 1) . cache = ./cache/cord-290481-i2ppvsh5.txt txt = ./txt/cord-290481-i2ppvsh5.txt === reduce.pl bib === id = cord-289406-54vyzxjf author = Edwards, Suzanne title = An Experimental Model for Myocarditis and Congestive Heart Failure after Rabbit Coronavirus Infection date = 1992-01-17 pages = extension = .txt mime = text/plain words = 3503 sentences = 217 flesch = 48 summary = In a model for virus-induced myocarditis and congestive heart failure, rabbit coronavirus infection was divided into acute (days 2–5) and subacute (days 6–12) phases on the basis of day of death and pathologic findings. Both Coxsackie Band encephalomyocarditis virus infections in mice may progress to myocarditis and congestive heart failure, and some survi-vors may progress to a dilated cardiomyopathy later in life [5, [14] [15] [16] . Rabbits that died on days 10-12 had pleural effusion, pulmonary edema, ascites, enlarged hearts, dilated right and left ventricular cavities, and congestion in the lungs and liver. It seems likely that pleural effusion disease virus infection also results in a significant percentage of animals dying from heart failure, since degeneration and necrosis of myocytes, pulmonary edema, pleural effusion, dilated ventricles, and congestion of the lungs, liver, and spleen are common [18, 26] . cache = ./cache/cord-289406-54vyzxjf.txt txt = ./txt/cord-289406-54vyzxjf.txt === reduce.pl bib === id = cord-290385-0smnl70i author = Chan, Jasper F.W. title = Zika fever and congenital Zika syndrome: An unexpected emerging arboviral disease date = 2016-03-03 pages = extension = .txt mime = text/plain words = 8256 sentences = 479 flesch = 45 summary = Unlike its mosquito-borne relatives, such as dengue, West Nile, and Japanese encephalitis viruses, which can cause severe human diseases, Zika virus (ZIKV) has emerged from obscurity by its association with a suspected "congenital Zika syndrome", while causing asymptomatic or mild exanthematous febrile infections which are dengueor rubella-like in infected individuals. ZIKV RNA could be detected in breast milk and saliva of infected women, although replicative virus particles have not been demonstrated 78, 79 Perinatal transmission of other arboviruses, including DENV, CHIKV, WNV, and YFV, has also been reported. 115,120 74/ 8750 (0.8%) patients with suspected ZIKV infection in the French Polynesia outbreak developed neurological syndromes after presenting with a Zika fever-like illness. Zika fever-related death appears to be extremely rare but a number of probable cases have been reported, especially among immunocompromised patients and neonates with suspected congenital ZIKV infection. cache = ./cache/cord-290385-0smnl70i.txt txt = ./txt/cord-290385-0smnl70i.txt === reduce.pl bib === id = cord-290231-4m9lj0uq author = Guirakhoo, Farshad title = The Murray Valley encephalitis virus prM protein confers acid resistance to virus particles and alters the expression of epitopes within the R2 domain of E glycoprotein date = 1992-12-31 pages = extension = .txt mime = text/plain words = 5738 sentences = 261 flesch = 48 summary = Abstract To study the role of the precursor to the membrane protein (prM) in flavivirus maturation, we inhibited the proteolytic processing of the Murray Valley encephalitis (MVE) virus prM to membrane protein in infected cells by adding the acidotropic agent ammonium chloride late in the virus replication cycle. By using monoclonal antibodies (MAbs) and protease maps, we previously demonstrated that the E glycoprotein of tick-borne encephalitis (TBE) virus undergoes an irreversible conformational change, predominantly in the epitopes of domain A, at mildly acidic pH . To understand the role of prM protein in virus maturation and its interaction with the E glycoprotein, we investigated the effect that ammonium chloride had on MVE viruses grown in C6/36 mosquito cells. The reactivities of MAbs defining nine distinct epitopes on the MVE E glycoprotein were compared on M-and prMcontaining viruses using supernatants of ammonium chloride-treated or untreated virus-infected C6/36 cells. cache = ./cache/cord-290231-4m9lj0uq.txt txt = ./txt/cord-290231-4m9lj0uq.txt === reduce.pl bib === id = cord-290556-x7t7zqjd author = Middleton, Peter J title = Viruses that multiply in the gut and cause endemic and epidemic gastroenteritis date = 1996-08-31 pages = extension = .txt mime = text/plain words = 3932 sentences = 261 flesch = 47 summary = Objective: To nominate the various viral agents that cause enteritis, discuss the pathogenesis, clinical features, epidemiology and diagnostic procedures employed. Results: The viruses causing gastroenteritis include: Rotaviruses; Adenoviruses-especially Ad 31, Ad 40 and Ad 41; members of the Caliciviridae, e.g. Norwalk virus, Hawaii virus, Snow Mountain virus, Taunton virus, Southampton virus, Toronto virus (formerly mini-reovirus) and others; Astrovirus; Coronavirus; Torovirus; Cytomegalovirus (CMV) and possibly Picobirnavirus. Rotavirus eventually became established as the leading worldwide cause of serious viral enteritis in infants and young children. Antigens or virions that form the basis of these serological tests may be obtained by purification procedures on infected stools; by cell culture cultivation, e.g. adenovirus, rotavirus and, in the case of Norwalk virus (NV), by self-assembled recombinant NV (rNV) particles expressed in a baculovirus system (Jiang et al., 1990 (Jiang et al., , 1993 . Enteric viruses and diarrhea in HIV-infected patients cache = ./cache/cord-290556-x7t7zqjd.txt txt = ./txt/cord-290556-x7t7zqjd.txt === reduce.pl bib === id = cord-290133-4ou7ubb4 author = Weiss, Martin M. title = Rethinking Smallpox date = 2004-12-01 pages = extension = .txt mime = text/plain words = 3976 sentences = 244 flesch = 51 summary = The last recorded death due to smallpox, according to World Health Organization investigators, was likely associated with virus that had been transmitted by aerosol [16] . Such observations-along with the long incubation period of smallpox (mean, 12-14 days; range, 7-21 days)suggest that there would be adequate time to vaccinate the public and prevent a more widespread outbreak. Nonetheless, these masks, if distributed to the public, could prove to be critical for the control of a smallpox epidemic that was overwhelming our health care system, and they might also prove to be effective in limiting contagion of smaller viruses, such as influenza virus (either natural virus, as in 1918, or engineered virus [61] ). Because of the possibility of an attack involving bioengineered smallpox virus that is resistant to the current vaccine, methisazone should be reexamined, and research should be continued on other antiviral agents. cache = ./cache/cord-290133-4ou7ubb4.txt txt = ./txt/cord-290133-4ou7ubb4.txt === reduce.pl bib === id = cord-289093-si8btsab author = Beard, Philippa M. title = A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference date = 2014-06-05 pages = extension = .txt mime = text/plain words = 6578 sentences = 310 flesch = 49 summary = To explore these interactions a functional high throughput small interfering RNA (siRNA) screen targeting 6719 druggable cellular genes was undertaken to identify host factors (HF) influencing the replication and spread of an eGFP-tagged VACV. Multiple components of the AMPK complex were found to act as pro-viral HFs, while several septins, a group of highly conserved GTP binding proteins with a role in sequestering intracellular bacteria, were identified as strong anti-viral VACV HFs. This screen has identified novel and previously unexplored roles for cellular factors in poxvirus replication. The methodology in the previously published VACV screens varied considerably; Mercer et al [32] measured the growth of a thymidine-kinase-deficient VACV (strain Western Reserve) after only 8 h of infection, thereby identifying cellular proteins involved in the initial stages of virus replication but excluding analysis of viral spread. cache = ./cache/cord-289093-si8btsab.txt txt = ./txt/cord-289093-si8btsab.txt === reduce.pl bib === id = cord-291294-w5ecsht4 author = Foulongne, V. title = Le bocavirus humain (HBoV) date = 2008-03-17 pages = extension = .txt mime = text/plain words = 2784 sentences = 259 flesch = 62 summary = Dans le domaine des infections respiratoires, le recourt extensif à la biologie moléculaire a également apporté des progrès très significatifs, avec les découvertes respectives depuis 2001 du metapneumovirus humain (HMPV) [3] , du SARS-Co [4, 5] , des nouveaux coronavirus humains HCoV-NL63 et HCoV-HKU1 [6] [7] [8] et du bocavirus humain (HBoV) [9] . Des observations récentes en microscopie électronique, conduites sur des prélèvements respiratoires dans lesquels l'ADN du virus avait pu être détecté, ont confirmé que le bocavirus humain présentait toutes les caractéristiques structurales des Parvoviridae. Cette prévalence place le HBoV selon les études et les régions au deuxième ou troisième rang des agents viraux détectés dans ces prélèvements, derrière le virus respiratoire syncytial mais à une fréquence comparable avec les rhinovirus ou le HMPV. Enfin, certaines études décrivent une phase virémique chez quelques patients, notamment en phase aiguë de l'infection, [35] suggérant que le HBoV puisse induire des infection systémiques comme cela est d'ailleurs observé avec les autres parvovirus [35, 36] . cache = ./cache/cord-291294-w5ecsht4.txt txt = ./txt/cord-291294-w5ecsht4.txt === reduce.pl bib === id = cord-290352-0pc5eji4 author = de Jong, Menno D. title = Avian influenza A (H5N1) date = 2005-10-06 pages = extension = .txt mime = text/plain words = 9156 sentences = 412 flesch = 41 summary = Since their reemergence in 2003, highly pathogenic avian influenza A (H5N1) viruses have reached endemic levels among poultry in several southeast Asian countries and have caused a still increasing number of more than 100 reported human infections with high mortality. However, occurrences of direct bird-to-human transmission of avian influenza viruses have increasingly been reported in recent years, culminating in the ongoing outbreak of influenza A (H5N1) among poultry in several Asian countries with associated human infections. The "Asian influenza" pandemic of 1957 was caused by an H2N2 virus that had acquired three genes (H2, N2, and PB1) from avian viruses infecting wild ducks, in a backbone of the circulating H1N1 human influenza strain. Furthermore, these infections were associated with severe hemorrhagic pneumonia and the induction of high levels of macrophage-derived cytokines and chemokines, strikingly reminiscent of clinical observations in humans during the Spanish flu pandemic, as well as of recent in vitro and in vivo observations of infections with highly pathogenic avian influenza H5N1 viruses (Cheung et al., 2002; Oxford, 2000; Peiris et al., 2004; To et al., 2001) . cache = ./cache/cord-290352-0pc5eji4.txt txt = ./txt/cord-290352-0pc5eji4.txt === reduce.pl bib === id = cord-290282-oxyzndsj author = Ortego, Javier title = Transmissible gastroenteritis coronavirus gene 7 is not essential but influences in vivo virus replication and virulence date = 2003-03-30 pages = extension = .txt mime = text/plain words = 4287 sentences = 215 flesch = 53 summary = Transmissible gastroenteritis coronavirus (TGEV) contains eight overlapping genes that are expressed from a 3′-coterminal nested set of leader-containing mRNAs. To facilitate the genetic manipulation of the viral genome, genes were separated by duplication of transcription regulating sequences (TRSs) and introduction of unique restriction endonuclease sites at the 5′ end of each gene using an infectious cDNA clone. All the rTGEV viruses conserved the modifications engineered in the cDNAs (data not shown), indicating that the ORF separation and the insertion of unique endonuclease restriction sites between genes were stably maintained in the rTGEV genomes. Interestingly, analysis of viral growth in the gut of infected piglets showed a 100-to 5000-fold reduction of recombinant viruses containing one or more restriction sites in relation to the rTGEV-wt virus ( Fig. 5D and E) . cache = ./cache/cord-290282-oxyzndsj.txt txt = ./txt/cord-290282-oxyzndsj.txt === reduce.pl bib === id = cord-289017-vwye3pk9 author = Comach, Guillermo title = Sentinel Surveillance of Influenza-Like Illness in Two Hospitals in Maracay, Venezuela: 2006–2010 date = 2012-09-11 pages = extension = .txt mime = text/plain words = 6262 sentences = 301 flesch = 47 summary = CONCLUSIONS/SIGNIFICANCE: Influenza viruses were the most commonly detected viral organisms among patients with acute febrile respiratory illnesses presenting at two hospitals in Maracay, Venezuela. Recent prospective studies, which utilized more sensitive methods for detecting respiratory viruses such as multiplex polymerase chain reaction (PCR), have similarly demonstrated that the highest rates of viral respiratory infection occur among children and the frequency of infection tends to decrease with age due to increasing acquired immunity [8] . On the other hand, the percentage of influenza viruses (not including pH1N1) detected in our study during a similar period of time, but in different years accounted for the significant differences found in both studies: a) the collection, preservation and further processing of respiratory samples, and b) the type of cells and IFA reagents used for virus isolation and identification. In contrast, a prospective study of ILI among Brazilian adults, which utilized viral isolation and RT-PCR testing on respiratory samples, detected rhinoviruses in 19.6% of patients [14] . cache = ./cache/cord-289017-vwye3pk9.txt txt = ./txt/cord-289017-vwye3pk9.txt === reduce.pl bib === id = cord-290432-4dli5emd author = O’Grady, Kerry-Ann F. title = Upper airway viruses and bacteria in urban Aboriginal and Torres Strait Islander children in Brisbane, Australia: a cross-sectional study date = 2017-04-04 pages = extension = .txt mime = text/plain words = 3764 sentences = 184 flesch = 44 summary = We aimed to describe the prevalence of upper airway viruses and bacteria in symptomatic and asymptomatic urban-based Australian Indigenous children aged less than 5 years. METHODS: A cross-sectional analysis of data collected at baseline in an ongoing prospective cohort study of urban Aboriginal and Torres Strait Islander children registered with a primary health care service in the northern suburbs of Brisbane, Australia. Thus, in 164 urban-based Indigenous children presenting to an urban primary health care service, we described the prevalence of upper airway respiratory viruses and bacteria. We analysed data from a cohort of urban Aboriginal and Torres Strait Islander children aged less than 5 years collected at time of enrolment into a prospective study of ARIwC. In a study of upper airway viruses and bacteria in Central Australian Aboriginal children hospitalised for pneumonia [8] , a population with high rates of hospitalised lower ARI [15] and nasal colonisation [16] , the [8] . cache = ./cache/cord-290432-4dli5emd.txt txt = ./txt/cord-290432-4dli5emd.txt === reduce.pl bib === id = cord-291707-dzmvjh7j author = Tupper, G. T. title = Antigenic and biological diversity of feline coronaviruses: feline infectious peritonitis and feline enteritis virus date = 1987 pages = extension = .txt mime = text/plain words = 2789 sentences = 179 flesch = 60 summary = FIPV grows to higher titer, forms larger plaques and switches off host cell protein synthesis more effectively than FECV. It was reported that both virus strains produce relatively large plaques in cell culture and grew to fairly high titers (1) . This indicated the differences were consistent and were not due to maturation artitSct. There was a cell protein band just above the nucleoprotein of the FECV 79-1683 of the radiolabelled virus. The FIPV strains produced larger plaques in CrFK cells and half a log higher titer of virus than the FECV strain. Host cell protein synthesis was also shut offby infection with murine coronavirus and different strains vary in the extent to which they do it, (25) . In this study, all 3 st, ruetural polypeptides appeared synchronously in cells infected with FIPV or FECV strains. Viral protein synthesis in mouse hepatitis virus strain A 59-infected cells: effect oftunieamyein cache = ./cache/cord-291707-dzmvjh7j.txt txt = ./txt/cord-291707-dzmvjh7j.txt === reduce.pl bib === id = cord-290149-eed4v2jl author = ODEND'HAL, STEWART title = Porcine Hemagglutinating Encephalomyelitis Virus date = 2012-12-02 pages = extension = .txt mime = text/plain words = 221 sentences = 24 flesch = 32 summary = key: cord-290149-eed4v2jl title: Porcine Hemagglutinating Encephalomyelitis Virus This chapter provides an overview of the classification, description, hosts, key developments, diagnostic techniques, and diagnostic reagents for porcine hemagglutinating encephalomyelitis virus. Porcine hemagglutinating encephalomyelitis virus causes two distinct syndromes; one is known as vomiting and wasting disease, and the other involves encephalomyelitis. The hosts of porcine hemagglutinating encephalomyelitis virus are pigs. Vomiting and wasting disease and encephalomyelitis were initially reported as two separate diseases in Canada in the late 1950s. Porcine hemagglutinating encephalomyelitis virus was isolated in 1962, and the common etiology of the two syndromes was shown in 1969. The diagnostic techniques for porcine hemagglutinating encephalomyelitis virus are virus neutralisation (VN) and agar gel immunodiffusion (AGID). To day in Canada the virus is endemic and antibodies can be demonstrated, but the disease syndrome is no longer evident (5). cache = ./cache/cord-290149-eed4v2jl.txt txt = ./txt/cord-290149-eed4v2jl.txt === reduce.pl bib === id = cord-290851-1e5e033r author = Gerlier, Denis title = Emerging zoonotic viruses: new lessons on receptor and entry mechanisms date = 2011-06-12 pages = extension = .txt mime = text/plain words = 2742 sentences = 153 flesch = 45 summary = Here I review the receptors and mode of entry of three emerging zoonotic viruses, responsible for rare but deadly diseases, whose natural reservoir is the bat: severe acute respiratory syndrome coronavirus (SARS-CoV), Hendra (HeV), Nipah (NiV), Ebola (EboV), and Marburg (MarV) viruses. S mediates binding to the cellular receptor Angiotensin Converting Enzyme 2 (ACE2) [4 ] , and ensures the viral-cell membrane fusion that allows virus entry. The EboV (and MarV) entry process lasts for about 1 h [94, 95] and can be schematized as follows ( Figure 3) : Firstly, (i) EboV attaches to the cells via the GP1/GP2 interaction with DC-SIGN/R and/or LECStin and is (ii) immediately internalized by constitutive and/or virus-contact-induced macropinocytosis. Cell adhesion promotes ebola virus envelope glycoprotein-mediated binding and infection cache = ./cache/cord-290851-1e5e033r.txt txt = ./txt/cord-290851-1e5e033r.txt === reduce.pl bib === id = cord-290509-56pfww0l author = Fleet, Graham H title = Foodborne viral illness - status in Australia date = 2000-07-25 pages = extension = .txt mime = text/plain words = 4915 sentences = 281 flesch = 50 summary = Norwalk-like virus contamination of oysters and orange juice, and hepatitis A virus contamination of oysters have been responsible for large outbreaks of foodborne viral disease in Australia. However, 1973, and were found in the faeces and duodenal genuine interest in food or waterborne viral diseases mucosal epithelial cells of children who had been did not develop in Australia until 1978 when oysters hospitalised with acute, non-bacterial gastroenteritis were found to be responsible for a very large (Bishop et al., 1974) . Oysters harvested Victoria, by examining for the virus in faecal specifrom an estuary in northern NSW and supposedly mens that had been submitted for suspected viral depurated were suspected of causing an outbreak of gastroenteritis over the period 1980-1996. A recent report has suggested that Norwalk virus was not detected in the juice but the outbreak and Norwalk-like viruses probably account for the terminated when the juice was withdrawn from the greatest incidence of foodborne disease in Australia market. cache = ./cache/cord-290509-56pfww0l.txt txt = ./txt/cord-290509-56pfww0l.txt === reduce.pl bib === id = cord-290855-6umgvt28 author = Ma, Li title = Antiviral Effects of Plant-Derived Essential Oils and Their Components: An Updated Review date = 2020-06-05 pages = extension = .txt mime = text/plain words = 5620 sentences = 303 flesch = 42 summary = Previous studies have demonstrated essential oils to be excellent candidates to treat antiviral-resistant infection associated with their chemical complexity which confers broad-spectrum mechanisms of action and non-specific antiviral properties. This review provides an up-to-date overview of the antiviral efficacy of essential oils from a wide range of plant species and their characteristic components, as well as their overall mechanisms of action, focusing on the last decade. Virucidal effects of EOs extracted from numerous aromatic and herbal plants are also well documented on a variety of viruses, such as IFV, HSV, HIV, yellow fever virus, and avian influenza, etc. Essential oils from Star Anise, Australian tea tree, oregano, Eucalyptus caesia, to name a few, have been demonstrated to exhibit high anti-HSV-1 activities in vitro (Table 1 ). cache = ./cache/cord-290855-6umgvt28.txt txt = ./txt/cord-290855-6umgvt28.txt === reduce.pl bib === id = cord-290539-8ak2tths author = Cagno, Valeria title = Novel broad spectrum virucidal molecules against enveloped viruses date = 2018-12-07 pages = extension = .txt mime = text/plain words = 5524 sentences = 276 flesch = 51 summary = To further elucidate the mechanism of action we performed a virucidal assay in which 9d was incubated with the virus at 10 μM 5μM or 1μM concentration for different times (Fig 6A) or for 1h with serial dilutions of compound ( Fig 6B) ; subsequently, the mixture was titrated on cells and the viral titer was evaluated at dilutions at which the compound concentration was known not to be active in plaquing efficiency assays. The irreversibility of the mechanism was also tested with an assay in which the compound was incubated with the virus for 1h and subsequently the mixture has been diluted in drug free medium for additional 1, 2, 3 or 4 hours before the addition on cells (S2 Fig) . cache = ./cache/cord-290539-8ak2tths.txt txt = ./txt/cord-290539-8ak2tths.txt === reduce.pl bib === id = cord-291860-dw1sfzqx author = van Boheemen, Sander title = Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients date = 2019-12-16 pages = extension = .txt mime = text/plain words = 5398 sentences = 276 flesch = 40 summary = Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. Clinical sensitivity was analyzed using the optimized procedure, which in short consisted of total nucleic acid extraction, including internal controls (1:100 dilution); the adapted New England Biolabs Next library preparation protocol, including fragmentation with zinc, for combined RNA and DNA detection (see Library Preparation); and sequencing of 10 million reads (Illumina NextSeq 500). The Centrifuge default settings, with NCBI's nucleotide database and assignment of sequence reads to a maximum of five labels per sequence, resulted in various spurious classifications ( Figure 4) [eg, Lassa virus ( Figure 5 ), evidently highly unlikely to be present in patient samples from the Netherlands with respiratory complaints]. cache = ./cache/cord-291860-dw1sfzqx.txt txt = ./txt/cord-291860-dw1sfzqx.txt === reduce.pl bib === id = cord-290617-45be6gxe author = Poulain, Florian title = Footprint of the host restriction factors APOBEC3 on the genome of human viruses date = 2020-08-14 pages = extension = .txt mime = text/plain words = 10515 sentences = 610 flesch = 56 summary = Certain viruses actively encode viral proteins antagonizing the APOBEC3s, others passively face the APOBEC3 selection pressure thanks to a depleted genome for APOBEC3-targeted motifs. By breaking down the human viruses into their respective Baltimore's group (S3 Fig), we observed that NTC depletion is not present in reverse transcribing nor in negative sense single strand RNA viruses. We also observed a mild general NCC depletion in single strand DNA and double strand RNA viruses, justifying further investigation for a possible A3G-induced footprint (S1 Fig). In order to identify A3-footprinted viruses, we detailed the NTC and NNGANN ratios for 870 human viral species (Fig 4A) . B. The observed/expected ratios of TC dinucleotide at various codon positions and on both strands (i.e. NNTCNN, TCN, NTC, GAN, NGA and NNGANN) were calculated for the putative A3-footprinted viral species and depicted by a heatmap. cache = ./cache/cord-290617-45be6gxe.txt txt = ./txt/cord-290617-45be6gxe.txt === reduce.pl bib === id = cord-290540-r0d6oaez author = Rottier, Peter J.M. title = The molecular dynamics of feline coronaviruses date = 1999-09-01 pages = extension = .txt mime = text/plain words = 3820 sentences = 200 flesch = 56 summary = Special attention is given to the genetic dynamics of the viruses as these now allow us to begin to understand the origin of the different phenotypes, in particular the genesis of virulence during persistent infection. The conclusion from these experiments is that feline coronaviruses may persist in the lower intestinal tract where the virus continues to replicate at low levels. Conceivably, the persisting virus confers to its host resistance against superinfection by the closely related feline coronaviruses, which were infecting the other cats. The idea was that'feline enteric coronaviruses' are indeed restricted in tropism, while'FIP viruses' would cross the epithelium, infect macrophages and go systemically. The result of all these studies is that generally there is no protection when an antibody response to the spike protein is induced there is rather an enhancement of the infection, with an'early death' phenomenon. Detection of feline coronavirus RNA in feces, tissues and body fluids of naturally infected cats by reverse transcriptase PCR cache = ./cache/cord-290540-r0d6oaez.txt txt = ./txt/cord-290540-r0d6oaez.txt === reduce.pl bib === id = cord-291816-d4j8samu author = Diniz Beduschi Travassos Alves, Christian title = Mamastrovirus 5 detected in a crab-eating fox (Cerdocyon thous): Expanding wildlife host range of astroviruses date = 2018-08-15 pages = extension = .txt mime = text/plain words = 4285 sentences = 270 flesch = 47 summary = Herein, we describe the genomic characterization of a MAstV5 (strain crab-eating fox/2016/BRA) identified in a wild canid (Cerdocyon thous) diagnosed with canine distemper virus (CDV) as causa mortis. The present report is the first evidence of MAstV5 infection in an animal species other than the dog and highlights a possible natural astrovirus spillover between domestic and wild canids. The data presented herein shows two important findings: (i) it is the crab-eating fox/BRA/2016 strain was likely derived from the canine host, and (ii) the extra intestinal MAstV5 presence. The sequence for the ribosomal frameshift site between ORF1a and ORF1b, which is conserved in the Astrovirudae family members [38] , is present in the crab-eating fox/2016/BRA nearly full genome (Fig. 2) . The crab-eating fox/2016/BRA nearly full genome, as expected, grouped in the MAstV5 cluster with all other characterized canine astroviruses. cache = ./cache/cord-291816-d4j8samu.txt txt = ./txt/cord-291816-d4j8samu.txt === reduce.pl bib === id = cord-291534-c6cjxq07 author = Gwyer Findlay, Emily title = Cationic Host Defence Peptides: Potential as Antiviral Therapeutics date = 2013-05-07 pages = extension = .txt mime = text/plain words = 8778 sentences = 410 flesch = 39 summary = In addition, various a-defensins are described as having additional, non-microbicidal properties, including chemotaxis for effector cells of the innate and adaptive immune systems [24, 25] , inhibition of macrophage pro-inflammatory cytokines [26] , modulation of the intestinal microbiome [27] and the formation of protective peptide nanonets [28] . In particular, it demonstrated direct antiviral activity of HNP1 against HSV-1 in a temperature-and pH-dependent manner, inhibited by serum, but interestingly less sensitive to the inhibitory effects of cations than the more broadly studied antibacterial properties. Thus, although b-defensins can inhibit influenza virus infectivity (albeit less potently than the a-defensins or LL-37) [89] , immunomodulatory properties, perhaps also including up-regulation of IAV uptake by neutrophils [84] , may prove to be key to their protective function against this virus in vivo and future therapeutic developments. Both rhesus h-defensins and retrocyclins (including RTD3, RC1 and RC2) have been found to inhibit HSV-1 and HSV-2 infection of human cervical epithelial cell lines following pre-incubation of virus and peptide [66] . cache = ./cache/cord-291534-c6cjxq07.txt txt = ./txt/cord-291534-c6cjxq07.txt === reduce.pl bib === id = cord-290548-0wezrr1b author = Watanabe, Tokiko title = Villains or heroes? The raison d'être of viruses date = 2020-02-19 pages = extension = .txt mime = text/plain words = 2919 sentences = 171 flesch = 42 summary = For example, Ebola virus disease and acquired immunodeficiency syndrome emerged in 1976 and 1981, respectively, 5-9 and more recently, severe acute respiratory syndrome (SARS), highly pathogenic avian influenza viruses and Middle East respiratory syndrome (MERS) have appeared in human society. In traditional virology, most viruses found in humans are considered to be pathogenic to their hosts; however, recent studies have shown that there are some viruses that have symbiotic relationships with their hosts and do not cause disease. 44 In the last a few decades, emerging infectious diseases caused by newly identified viruses, such as Ebola virus, 5-8 SARS and MERS coronaviruses, [10] [11] [12] human immunodeficiency virus (HIV), 9 Nipah virus and Hendra virus, [45] [46] [47] [48] have appeared in human society. To date, the PREDICT programme has found over 1100 viruses in animals and humans, including a new Ebola virus and MERSand SARS-like coronaviruses. cache = ./cache/cord-290548-0wezrr1b.txt txt = ./txt/cord-290548-0wezrr1b.txt === reduce.pl bib === id = cord-291561-sxvgue36 author = Haixu, Liang title = Detection of 20 respiratory viruses and bacteria by influenza-like illness surveillance in Beijing, China, 2016–2018 date = 2019-11-25 pages = extension = .txt mime = text/plain words = 10271 sentences = 543 flesch = 50 summary = A full genome phylogenetic analysis of this 2019-nCoV indicates that it is closely related to bat SARS-like CoV ( Fig. 1 ) , compatible with a zoonotic origin for this virus, similar to SARS-CoV and MERS-CoV. 3 5 This study aim to assess the genetic diversity and potential role of genetic recombination in the evolutionary dynamics of FRCoVs. Genetic analyses were conducted with five complete genomes and 160 gene sequences of FRCoVs downloaded from the NIAID Virus Pathogen Database and Analysis Resource. 3 Ten years after the SARS, MERS emerged in 2012, have caused 2494 human infections with 858 deaths (as of November 2019) and remains a disease of global, and particularly Middle Eastern, public health concern. Relatively low detection rates have even been reported in studies conducted in other geographical areas, such as Gansu Province in China, 6 The discrepancies in the influenza detection rates among patients with ILI from different areas highlighted the geographical differences in virus burdens. cache = ./cache/cord-291561-sxvgue36.txt txt = ./txt/cord-291561-sxvgue36.txt === reduce.pl bib === id = cord-291156-zxg3dsm3 author = Bernasconi, Anna title = Empowering Virus Sequences Research through Conceptual Modeling date = 2020-05-01 pages = extension = .txt mime = text/plain words = 4600 sentences = 206 flesch = 38 summary = We hereby present the Viral Conceptual Model (VCM), centered on the virus sequence and described from four perspectives: biological (virus type and hosts/sample), analytical (annotations and variants), organizational (sequencing project) and technical (experimental technology). -We propose a new Viral Conceptual Model (VCM), a general conceptual model for describing viral sequences, organized along specific dimensions that highlight a conceptual schema similar to GCM [6] ; -Focusing on SARS-CoV2, we show how VCM can be profitably linked to a phenotype database with information on COVID-19 infected patients; -We provide a list of interesting queries replicating newly released literature on infectious diseases; these can be easily performed on VCM. Some interesting portals have become interfaces to GISAID data with particular focuses: NextStrain [18] overviews emergent viral outbreaks based on the visualization of sequence data integrated with geographic information, serology, and host species; CoV-GLUE, 9 part of the GLUE suite [38] , contains a database of replacements, insertions and deletions observed in sequences sampled from the pandemic. cache = ./cache/cord-291156-zxg3dsm3.txt txt = ./txt/cord-291156-zxg3dsm3.txt === reduce.pl bib === id = cord-290993-bsnja161 author = McAuliffe, Josephine title = Replication of SARS coronavirus administered into the respiratory tract of African Green, rhesus and cynomolgus monkeys date = 2004-12-05 pages = extension = .txt mime = text/plain words = 4548 sentences = 203 flesch = 52 summary = Serologic evidence of infection, defined as a four-fold rise in Nt Ab titer, was observed in 4 of 4 rhesus, 3 of 4 cynomolgus, and 4 of 4 AGMs. Although the study described above indicated that all three species of monkeys were infected with SARS-CoV, there were significant discrepancies between our findings and published reports of cynomolgus macaques infected with SARS-CoV; Kuiken et al. Mean titers of virus (expressed as log 10 TCID 50 /ml of sample; y axis) detected on indicated days (x axis) in the upper respiratory tract (left panels, A, C, and E, closed symbols) and lower respiratory tract (right panels, B, D, and F, open symbols) of rhesus (panels A and B, x, w), cynomolgus (panels C and D, E, 4), and African Green (panels E and F, n, 5) monkeys following intranasal and intratracheal administration of 10 6 TCID 50 of SARS-CoV. cache = ./cache/cord-290993-bsnja161.txt txt = ./txt/cord-290993-bsnja161.txt === reduce.pl bib === id = cord-292075-t9z7zqz4 author = Gessain, Antoine title = Mécanismes d’émergence virale et transmission interespèces : l’exemple des rétrovirus Foamy simiens chezl’Homme en Afrique Centrale date = 2013-12-31 pages = extension = .txt mime = text/plain words = 2159 sentences = 133 flesch = 52 summary = After reviewing the current available data on the discovery, cross-species transmission from monkeys and apes to humans of the simian foamy retroviruses, we will report the results of our study. These populations are living nearby the habitats of several monkeys and apes, often naturally infected by different retroviruses including SIV, STLV and simian foamy virus. These populations are living nearby the habitats of several monkeys and apes, often naturally infected by different retroviruses including SIV, STLV and simian foamy virus. After reviewing the current available data on the discovery, cross-species transmission from monkeys and apes to humans of the simian foamy INTRODUCTION L'espèce humaine est en contact permanent avec l'environnement qui contient une multitude d'agents infectieux (virus, bactéries, parasites, champignons). Cross-species transmission of simian retroviruses, how and why they could lead to the emergence of new diseases in the human population Two distinct variants of simian foamy virus in naturally infected mandrills (Mandrillus sphinx) and cross-species transmission to humans cache = ./cache/cord-292075-t9z7zqz4.txt txt = ./txt/cord-292075-t9z7zqz4.txt === reduce.pl bib === id = cord-293375-qcy56ui7 author = Strauss, Ellen G. title = Identification of the active site residues in the nsP2 proteinase of sindbis virus date = 1992-12-31 pages = extension = .txt mime = text/plain words = 5192 sentences = 265 flesch = 56 summary = coma-, nepo-, and potyviruses; coronaviruses; and flaviviruses (and their proposed relatives pestiviruses and hepatitis C virus.) Originally these domains were predicted to have proteolytic activity based on the presence of certain conserved amino acid residues and on the basis of protein-modeling studies (Bazan and Fletterick, 1989; Boege et a/., 1981; Gorbalenya et al., 1989; Hahn eta/., 1985) . Furthermore, we present data to show that none of the asparagine residues in the proteinase domain of Sindbis nsP2 that are conserved among alphaviruses are absolutely required for proteolytic activity, but that Trp-559, adjacent to His-558, is essential for function. We also examined the effect of changing Cys-525, one of the two remaining conserved cysteine residues in the C-terminal half of nsP2, to serine or arginine, as well as changing Ser-535, which is found in a domain of limited similarity to the active site serine of serine proteinases, to threonine. cache = ./cache/cord-293375-qcy56ui7.txt txt = ./txt/cord-293375-qcy56ui7.txt === reduce.pl bib === id = cord-293472-d3iwlpsr author = Afilalo, Marc title = Evaluation and Management of Seasonal Influenza in the Emergency Department date = 2012-04-06 pages = extension = .txt mime = text/plain words = 9919 sentences = 516 flesch = 38 summary = During influenza season (testing should be done in the following persons if the result will influence clinical management) Outpatient immunocompetent persons of any age at high risk of developing influenza complications (eg, hospitalization or death) presenting with acute febrile respiratory symptoms 5 days or less after illness onset (when virus is usually being shed) Outpatient immunocompromised persons of any age presenting with febrile respiratory symptoms, irrespective of time since illness onset (because immunocompromised persons can shed influenza viruses for weeks to months) Hospitalized persons of any age (immunocompetent or immunocompromised) with fever and respiratory symptoms, including those with a diagnosis of community-acquired pneumonia, irrespective of time since illness onset Elderly persons and infants presenting with suspected sepsis or fever of unknown origin, irrespective of time since illness onset Children with fever and respiratory symptoms presenting for medical evaluation, irrespective of time since illness onset Persons of any age who develop fever and respiratory symptoms after hospital admission, irrespective of time since illness onset Immunocompetent persons with acute febrile respiratory symptoms who are not at high risk of developing complications secondary to influenza infection may be tested for purposes of obtaining local surveillance data cache = ./cache/cord-293472-d3iwlpsr.txt txt = ./txt/cord-293472-d3iwlpsr.txt === reduce.pl bib === id = cord-293975-np9xdag5 author = Barnett, E. M. title = Two neurotropic viruses, herpes simplex virus type 1 and mouse hepatitis virus, spread along different neural pathways from the main olfactory bulb date = 1993-12-31 pages = extension = .txt mime = text/plain words = 8286 sentences = 435 flesch = 46 summary = The data also demonstrate that two viruses can enter the brain via the olfactory system and localize to different structures, suggesting that neurological diseases involving disparate regions of the brain could be caused by different viruses, even if entry occurred at a common A number of viruses have been shown to spread transneuronally into and throughout the rodent CNS following intranasal inoculation, including herpes simplex virus type 1 (HSV-I)," vesicular stomatitis virus,43 Borna disease virus," mouse hepatitis virus (MHV),-pseudorabies viru? Abbreviafions: HSV-1, hernes simplex virus, type 1; LC, locus coeruleus; MHV'-JHM, -mouse hepatitis virus, strain JHM; MOB, main olfactorv bulb; PFU, plaque forming unit; p.i. post-inoculation; TH, tyrosine hydroxylase; TH + , tyrosine hydroxylase immunoreactive; TH -, tyrosine hydroxylase immunonegative; VTA, ventral tegmental area; WGA-HRP, wheatgerm agglutinin-horseradish peroxidase. cache = ./cache/cord-293975-np9xdag5.txt txt = ./txt/cord-293975-np9xdag5.txt === reduce.pl bib === id = cord-292830-gcfx1095 author = Ianevski, Aleksandr title = Novel activities of safe-in-human broad-spectrum antiviral agents date = 2018-04-23 pages = extension = .txt mime = text/plain words = 5511 sentences = 298 flesch = 45 summary = Here, we reviewed all approved, investigational and experimental antiviral agents, which are safe in man, and identified 59 compounds that target at least three viral diseases. Here, we hypothesised that some of the identified safe-in-human BSAs could possess novel antiviral activities and, therefore, could be used for treatment of many different viral infections. Fig. 1 shows BSAs and other approved antiviral drugs linked to viral and host targets through viruses they inhibit. Thus, we tested several known BSA agents against (−)ssRNA, (+) ssRNA, ssRNA-RT and dsDNA viruses and identified novel activities for dalbavancin against EV1, ezetimibe against ZIKV and HIV-1, as well as azacitidine, cyclosporine, minocycline, oritavancin and ritonavir against RVFV. We identified novel antiviral activities for dalbavancin (against EV1), ezetimibe (against HIV-1 and ZIKV), azacitidine, cyclosporine, minocycline, oritavancin and ritonavir (against RVFV) (Fig. 4) . cache = ./cache/cord-292830-gcfx1095.txt txt = ./txt/cord-292830-gcfx1095.txt === reduce.pl bib === id = cord-292643-n6xp5mlz author = Hall, Richard J. title = Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery date = 2013-09-13 pages = extension = .txt mime = text/plain words = 4803 sentences = 219 flesch = 44 summary = The relative abundance of a virus (or viral nucleic acid) in a sample, compared to that of other organisms such as bacteria or host cells (or their genomes), is a critical factor for the discovery of viruses when using metagenomics. A study on human liver tissue compared enrichment techniques of freeze-thaw, centrifugation and nuclease-treatment for the detection of Hepatitis C Virus using both Roche 454 and Illumina high-throughput sequencing platforms (Daly et al., 2011) . After an initial 10 min reverse transcription step at 45 • C and 10 min denaturation Table 1 Virus enrichment process prior to sequencing in metagenomic studies on human and animal samples. This artificial sample represents a starting point to evaluate simple and rapid viral enrichment methods for use in virus metagenomics studies that seek to detect a virus that is causing disease in humans or animals. cache = ./cache/cord-292643-n6xp5mlz.txt txt = ./txt/cord-292643-n6xp5mlz.txt === reduce.pl bib === id = cord-292286-ygomb3oi author = Zakaryan, Hovakim title = Flavonoids: promising natural compounds against viral infections date = 2017-05-25 pages = extension = .txt mime = text/plain words = 6064 sentences = 327 flesch = 37 summary = Flavonoids are widely distributed as secondary metabolites produced by plants and play important roles in plant physiology, having a variety of potential biological benefits such as antioxidant, anti-inflammatory, anticancer, antibacterial, antifungal and antiviral activity. The antiviral activity of flavones is known from the 1990s, when it was showed that the simultaneous application of apigenin with acyclovir resulted in an enhanced antiviral effect on herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) in cell culture [92] . Besides these DNA viruses, apigenin was found to exert antiviral effect against African swine fever virus (ASFV), by suppressing the viral protein synthesis and reducing the ASFV yield by 3 log [46]. Besides these viruses, EGCG has been found to exert antiviral activity against HCV by preventing the attachment of the virus to the cell surface and suppressing RNA replication steps [8, 15] . Antiviral activity of baicalin against influenza A (H1N1/ H3N2) virus in cell culture and in mice and its inhibition of neuraminidase cache = ./cache/cord-292286-ygomb3oi.txt txt = ./txt/cord-292286-ygomb3oi.txt === reduce.pl bib === id = cord-291113-iizj932l author = Cumbo, Enzo title = Alternative Methods of Sterilization in Dental Practices Against COVID-19 date = 2020-08-08 pages = extension = .txt mime = text/plain words = 7441 sentences = 273 flesch = 40 summary = It is time to consider a dental practice quite similar to a hospital surgery room, where particular attention should be paid to problems related to the spread of infections caused by air and surface contaminations, especially a time when viruses such as SARS-CoV-2 have emerged as an important public health problem due to their ability to spread through close person-to-person contact. Ultraviolet light has proven effective against corona viruses and, therefore, could be used against COVID-19 both in the case of bioaerosols and in the sterilization of contaminated environmental surfaces in which this microorganism is present-in particular, on products of unstable composition that cannot be treated by conventional means [62, 63] . Now that the risk of spreading COVID-19 is very high, it is necessary to pay particular attention to all the sterilization procedures that should be reviewed, improved, and perhaps used in combinations to obtain a final result that aims to complete the sterilization of all structures present in the operating room, including air, which for some dangerous diseases, such as SARS-CoV-2, is the transmission route. cache = ./cache/cord-291113-iizj932l.txt txt = ./txt/cord-291113-iizj932l.txt === reduce.pl bib === id = cord-292353-z86rjwle author = Hussein, Islam T.M. title = Recent Advances in Hantavirus Molecular Biology and Disease date = 2011-04-01 pages = extension = .txt mime = text/plain words = 13579 sentences = 708 flesch = 47 summary = Hantaviruses pose a serious threat to human health because their infection causes two highly fatal diseases, hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS). The sequences at both the 3 0 and 5 0 termini of each RNA segment are complementary forming ''panhandle'' structures that are specifically recognized by the N protein and were shown to be important for viral transcription and replication. Further studies revealed that cellular 5 0capped mRNA oligoribonucleotides are rescued by N in virus-infected cells and stored in P-bodies for the later use as primers by the viral RdRp during transcription initiation . The UTRs are encapsidated by nucleocapsid protein and associate with RdRp both in the host cells and in the virion, and only these nucleocapsids are believed to be functional templates for mRNA synthesis and RNA replication by the viral RdRp. c. cache = ./cache/cord-292353-z86rjwle.txt txt = ./txt/cord-292353-z86rjwle.txt === reduce.pl bib === id = cord-291946-kq0rsuxj author = Etienne, Lucie title = The Mongoose, the Pheasant, the Pox, and the Retrovirus date = 2013-08-27 pages = extension = .txt mime = text/plain words = 2911 sentences = 132 flesch = 46 summary = The genomes of two species of mongooses and an egg-laying mammal called an echidna show that a virus currently present in poultry, the reticuloendotheliosis virus (REV), is actually of ancient exotic mammalian origin. The genomes of two species of mongooses and an egg-laying mammal called an echidna show that a virus currently present in poultry, the reticuloendotheliosis virus (REV), is actually of ancient exotic mammalian origin. Although REV may still exist somewhere in a mammalian host, its modern form links an 8 million-year-old infection of the ancestor of a mongoose to a virus that now is circulating in wild birds through malaria studies in the mid-20 th century. Although REV may still exist somewhere in a mammalian host, its modern form links an 8 million-year-old infection of the ancestor of a mongoose to a virus that now is circulating in wild birds through malaria studies in the mid-20 th century. cache = ./cache/cord-291946-kq0rsuxj.txt txt = ./txt/cord-291946-kq0rsuxj.txt === reduce.pl bib === id = cord-291063-de7v4e5s author = Moens, Ugo title = Silencing Viral MicroRNA as a Novel Antiviral Therapy? date = 2009-05-28 pages = extension = .txt mime = text/plain words = 9122 sentences = 526 flesch = 49 summary = The expressions of EBV-encoded miRNAs in clinical samples and computational analysis to predict putative targets were applied to unravel the biological functions of EBV miRNAs. These approaches showed that the miR-BARTs are abundantly expressed in latently infected epithelial cells, nasopharyngeal carcinomas, EBV-associated gastric carcinoma cell lines and tissues, Burkitt's lymphomas latency type I, EBV positive primary effusion lymphomas, and diffuse large B-cell lymphomas, but at a significantly lower level in B cells. However, computational alignment of the potential HIV-1 miRNAs with specific human T-cell mRNAs identified potential cellular targets including genes encoding CD4, CD28 and interleukin-2, IL-3, and IL-12 [119] . The idea of targeting viral transcripts is not new, and RNA interference has been demonstrated to efficiently mediate inhibition of replication of human pathogenic viruses such as HIV-1, HCV, dengue virus, severe acute respiratory syndrome (SARS) coronavirus, poliovirus, human rhinovirus, influenza A virus, hepatitis D virus, HBV, HSV-1, HPV, JCV, EBV, and CMV in cell culture (reviewed in [12] ). cache = ./cache/cord-291063-de7v4e5s.txt txt = ./txt/cord-291063-de7v4e5s.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 4930 sentences = 240 flesch = 45 summary = Influenza viruses are one of the main causative agents of ARIs worldwide; however, many other respiratory viruses for which insufficient epidemiological information is available can also cause ARIs. Studies performed at the international level have frequently identified human respiratory syncytial virus (HRSV), human parainfluenza virus (HPIV), influenza virus (flu), human mastadenovirus (HMdV), rhinovirus (RV), and enterovirus (EV) and less frequently identified human metapneumovirus (HMPV), primate bocaparvovirus (PBpV), and human coronavirus (HCoV) [12] . Therefore, the objective of this study was to determine the viral aetiology of these infections and to analyse the behaviour of non-influenza respiratory viruses in the Mexican population. The importance of the differential diagnosis of other respiratory viruses in samples with negative influenza results becomes apparent when we observe the prevalence of the three main viruses identified in this study as well as their associations with severe cases and deaths, especially in the child population. cache = ./cache/cord-294568-12eyo13f.txt txt = ./txt/cord-294568-12eyo13f.txt === reduce.pl bib === id = cord-297339-et2305rz author = Lauber, Chris title = Genetics-Based Classification of Filoviruses Calls for Expanded Sampling of Genomic Sequences date = 2012-08-31 pages = extension = .txt mime = text/plain words = 4480 sentences = 235 flesch = 46 summary = In DEmARC, virus clusters are delimited objectively by devising a universal family-wide threshold on intra-cluster genetic divergence of viruses that is specific for each level of the classification. Based on our experience with other virus families, we conclude that the current sampling of filovirus genomic sequences needs to be considerably expanded in order to resolve these uncertainties in the framework of genetics-based classification. The DEmARC specifics include (i) the use of pairwise evolutionary distances (PEDs) instead of uncorrected p-distances, and (ii) a quantitative method to devise taxon levels and associated PED thresholds for virus clustering in a systematic and family-wide manner. The first selected threshold (PED of 0.120) results in seven clusters ( Figure 1B ) that match the official or tentative ICTV species of the family Filoviridae. In the high-sampling case of picornaviruses, no PED values with zero frequency are observed which suggests that the current sampling of filovirus genome sequences may strongly underestimate the natural genetic diversity in the family. cache = ./cache/cord-297339-et2305rz.txt txt = ./txt/cord-297339-et2305rz.txt === reduce.pl bib === id = cord-292416-3hhi4wps author = Sarid, Ronit title = Investigating an Emerging Virus During a Sudden Pandemic Outbreak date = 2020-07-31 pages = extension = .txt mime = text/plain words = 4869 sentences = 230 flesch = 41 summary = Five years later, in 2020, when the World Health Organization declared the coronavirus disease 2019 (COVID-19)-caused by the newly emerging SARS-CoV-2 virus-to be a pandemic, this talk was widely acknowledged to be almost prophetic. 24, 25 All four reportedly mild pathogenic coronaviruses are associated with 10%-30% of cases of the common cold, 26 -28 yet they have the potential to cause severe lower respiratory tract infection in infants, in the elderly, and in patients with other underlying illness, 29 while hCoV-OC43, like SARS-CoV-2, has been associated with neurologic dysfunction as well. Development of animal models for SARS-CoV-2 infection is vital in providing comprehensive understanding of the pathogenic mechanisms involved but may also serve for screening anti-viral drugs and vaccines. Accordingly, transfusion of convalescent plasma is likely to be beneficial to SARS-CoV-2, 45 ,46 yet its effect on virus shedding and disease outcome must be evaluated when given to healthy individuals and patients at different stages and severity of the disease. cache = ./cache/cord-292416-3hhi4wps.txt txt = ./txt/cord-292416-3hhi4wps.txt === reduce.pl bib === id = cord-292657-gq3965se author = Das, Piyanki title = Decoding the global outbreak of COVID-19: the nature is behind the scene date = 2020-06-22 pages = extension = .txt mime = text/plain words = 5030 sentences = 221 flesch = 43 summary = The rapid evolving nature by changing host body environment and extreme environmental stability, collectively makes SARS-CoV-2 into an extremely virulent genetic variant. Thus both the host body or internal environment and the external environment performs equally as a source, responsible for shaping the genetic evolution of the SARS-CoV-2 towards theCOVID-19 disease fitness in nature in a pandemic form. The probable line of development for such pandemic outcomes happened by continuous evolutionary procedure within different species or host environment exposure, by mutation during replication or genetic recombination between two different viral species and ultimate adaptation to a susceptible host by natural selection of the new version of the viable pathogen resulting infection [7, 8] . Then genetically close different subtypes of SARS-CoV-2 develops unique spike protein receptor binding domain with high degree of receptor binding property to human cells and adapt itself to fit the character inside the host body. cache = ./cache/cord-292657-gq3965se.txt txt = ./txt/cord-292657-gq3965se.txt === reduce.pl bib === id = cord-293540-45awgabp author = Drancourt, Michel title = Point-of-care testing for community-acquired pneumonia date = 2013-07-23 pages = extension = .txt mime = text/plain words = 1697 sentences = 97 flesch = 50 summary = The rate and timing of pandemic A H1N1 virus infections might have revealed the diff erences in H7N9 disease outcome, by contrast with historical infections with seasonal infl uenza A H3N2 viruses. To avoid this delay, we introduced point-of-care (POC) microbiology laboratories near emergency departments where patients with community-acquired pneumonia are seen fi rst. However, it should be noted that not all pathogens that can cause community-acquired pneumonia can be detected by POC tests, and molecular tests for Staphylococus aureus have not been approved by the US Food and Drug Administration (FDA) or the European Conformity (CE). 9 This new capacity of POC tests increases the number of diagnoses 11 and underscores that community-acquired pneumonia can result from co-infection with several pathogens, 10 which will challenge common notions about causation and management. Furthermore, detection by POC testing of an abnormal increase in group A streptococci might suggest co-infection with infl uenza. cache = ./cache/cord-293540-45awgabp.txt txt = ./txt/cord-293540-45awgabp.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-295792-hajvtzj9 author = Álvez, Fernando title = SARS-CoV2 coronavirus: So far polite with children. Debatable immunological and non-immunological evidence date = 2020-07-03 pages = extension = .txt mime = text/plain words = 4504 sentences = 196 flesch = 46 summary = In short, the purpose of this first defensive barrier for early control during the incubation period and the first symptoms of SAR-CoV2 infection is to inhibit viral replication, promote elimination of the virus, induce tissue repair and trigger a specific adaptive immune response (AIR) (12) . Furthermore, this enzyme also plays an important role in the immune response, especially in inflammation, and is involved in the defensive mechanisms of the lung -protecting it from severe injury induced by respiratory viruses (11, 18) . However, serological studies evaluating the immune response to respiratory infections including CovH have shown steadily increasing seroprevalence of antibodies to CovH in both children and young adults, as well as cross-reactivity, such as between antibodies to the previous SARS-CoV and CovH (25) (26) . Cell Responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-Infected mice cache = ./cache/cord-295792-hajvtzj9.txt txt = ./txt/cord-295792-hajvtzj9.txt === reduce.pl bib === id = cord-295640-mhfu0e9r author = Wang, Wenling title = Improving Cross-Protection against Influenza Virus Using Recombinant Vaccinia Vaccine Expressing NP and M2 Ectodomain Tandem Repeats date = 2019-06-25 pages = extension = .txt mime = text/plain words = 4793 sentences = 305 flesch = 51 summary = Therefore, the cross-protection potentially correlates with both NP and M2e-specific humoral and cellular immune responses induced by RVJ-4M2eNP, which expresses a fusion antigen of full-length NP preceded by four M2e repeats. Previously, we expressed a fusion protein of NP and M2e (NM2e) in Escherichia coli and showed that immunization with NM2e formulated with aluminum hydroxide gel protected mice from a lethal challenge with heterologous influenza virus . BALB/c mice were immunized with the recombinant viruses to measure NP-and M2e-specific humoral and cellular immune responses as well as protective effect against lethal challenge with a heterologous influenza virus. Mice immunized with the recombinant vaccinia virus RVJ-NPM2e and RVJ-M2eNP showed strong antibody responses against NP, with lower titers of antibodies against M2e (Fig. 3A) . The recombinant vaccinia virus expressing 4M2e and full-length NP fusion antigen induced strong cross-protection (92%) against a lethal heterosubtypic PR8 challenge at 20 MLD 50 and thus regarded as the optimal one among the four constructs. cache = ./cache/cord-295640-mhfu0e9r.txt txt = ./txt/cord-295640-mhfu0e9r.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-294323-mryiqmsw author = Kumar, Binod title = The emerging influenza virus threat: status and new prospects for its therapy and control date = 2018-01-10 pages = extension = .txt mime = text/plain words = 8201 sentences = 390 flesch = 43 summary = The wide range of hosts provides influenza A viruses greater chances of genetic re-assortment, leading to the emergence of zoonotic strains and occasional pandemics that have a severe impact on human life. Here, we primarily discuss the pathogenesis of influenza virus type A, its epidemiology, pandemic potential, current status of antiviral drugs and vaccines, and ways to effectively manage the disease during a crisis. A genetic shift occurs when two or more different influenza virus strains infect the same cell in a host, leading to recombination of genetic materials, an event that occasionally generates a new strain with a novel combination of hemagglutinin and neuraminidase. The antiviral drugs currently available against influenza viruses are adamantane derivatives (amantadine and rimantadine) and neuraminidase (NA) inhibitors (zanamivir, oseltamivir and peramivir). Due to the increasing burden of vaccine formulations and cases of antiviral-drug-resistant influenza virus isolates turning up every year, it has become necessary to search for alternatives to the current treatment and prevention strategies. cache = ./cache/cord-294323-mryiqmsw.txt txt = ./txt/cord-294323-mryiqmsw.txt === reduce.pl bib === id = cord-293097-poh1y6o7 author = V, Antony Aroul Raj title = The contribution of dry indoor built environment on the spread of Coronavirus: Data from various Indian states date = 2020-07-02 pages = extension = .txt mime = text/plain words = 3072 sentences = 139 flesch = 53 summary = This concept is assessed using four major parameters such as population density, climate severity, the volume of indoor spaces, and air-conditioning usage which affect the infection spread and mortality using the data available for various states of India. Hence the major objective of the present work is to propose the mechanism of virus spread under various climates and the indoor environment conditions maintained through the existing theory of respiratory droplet drying. Further, it is aimed to perform a statistical study on the dependence of mortality and infection in the Indian States with respect to four major parameters such as population density, climate severity, volume of indoor spaces, and air-conditioning usage based on monthly data for March and April. In an environment with low humidity and low temperature, due to combined high heat and mass transfer potential leads to fast drying and size reduction of the respiratory droplets and the virus is almost active in all the locations. cache = ./cache/cord-293097-poh1y6o7.txt txt = ./txt/cord-293097-poh1y6o7.txt === reduce.pl bib === id = cord-294478-3ickafd3 author = Kapil, Sanjay title = Diagnostic Investigation of Emerging Viruses of Companion Animals date = 2008-05-22 pages = extension = .txt mime = text/plain words = 7330 sentences = 328 flesch = 38 summary = Variants of a known virus that has gained enhanced virulence or that is able to infect completely vaccinated animals A known virus that has reappeared in the population after a decline in incidence Novel or previously unidentified viral agents detected for the first time because of improved diagnostic capabilities ''Mystery diseases'' with large numbers of naive animals involved that are caused by previously uncharacterized viruses Spread of an emerging virus among small companion animals is multifactorial and includes animal health and sanitation practices; migration of a pathogen from a wild reservoir to domestic animals because of changes in populations, trade, climate, land use, and the introduction of invasive species (eg, plant, animal, insect); and, finally, globalization, as was the case with West Nile virus (WNV). Detecting emerging viral diseases of companion animals requires interaction and discussion among clinicians, pathologists, and virologists, and practicing small animal veterinarians must stay engaged in communication with these specialists through their state diagnostic laboratories or nearby colleges of veterinary medicine. cache = ./cache/cord-294478-3ickafd3.txt txt = ./txt/cord-294478-3ickafd3.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-292575-vsswxwdi author = Hammou, Rahma Ait title = Chapter 7 Scientific Advances in the Diagnosis of Emerging and Reemerging Viral Human Pathogens date = 2020-12-31 pages = extension = .txt mime = text/plain words = 8496 sentences = 402 flesch = 39 summary = It is in this context that this chapter aims to discuss the various scientific advances, particularly molecular, in terms of diagnosis of these diseases; the new discoveries in the role of nanotechnologies and nanobiosensors; and also the implication of biomarkers, especially microRNAs (miRNAs), since it was reported that a single miRNA has the ultimate capacity to target multiple genes simultaneously. The availability of nucleic acidÀbased technology, such as real-time PCR, along with conventional staining and culture methods and immunoassays, can provide laboratories of many sizes with a comprehensive and responsible approach for the detection of both commonly encountered and emerging or reemerging pathogens. As is the case for SARS, agents of bioterrorism, and the other pathogens, rapid diagnostic methods, such as real-time PCR, and microarray will likely play a major role in the early and sensitive detection of emerging and reemerging infectious diseases encountered in the future. cache = ./cache/cord-292575-vsswxwdi.txt txt = ./txt/cord-292575-vsswxwdi.txt === reduce.pl bib === id = cord-294842-aesiff1f author = Romero-Brey, Inés title = Membranous Replication Factories Induced by Plus-Strand RNA Viruses date = 2014-07-22 pages = extension = .txt mime = text/plain words = 11038 sentences = 520 flesch = 40 summary = Three-dimensional reconstructions of the WNV KUN replication sites revealed an intimate association of the rough ER (rER) with the bounding membrane of the VPs [20] (Figure 2B ), resembling the vesicles observed in DENV-infected cells. In cells infected with TBEV, one of the most important tick-transmitted viruses in Europe and Asia, virus particles and membrane-connected vesicles were also observed inside the ER [25] , similar to what was described for DENV and WNV KUN . Importantly, pulse-radiolabeling experiments localized sites of active RNA replication to the outer surface of single-membrane tubules [71] and isolation of the membranous replication factories and their subsequent visualization by EM revealed that they form rosette-like structures composed of virus-induced cytoplasmic vesicles [124] . Formation of plant RNA virus replication complexes on membranes: Role of an endoplasmic reticulum-targeted viral protein cache = ./cache/cord-294842-aesiff1f.txt txt = ./txt/cord-294842-aesiff1f.txt === reduce.pl bib === id = cord-294312-ju6vuywm author = Rohde, Rodney E. title = Common Myths and Legends of Rabies date = 2019-04-19 pages = extension = .txt mime = text/plain words = 4488 sentences = 281 flesch = 60 summary = While in fact, today's treatment regimen is typically only four vaccinations (five for immunocompromised individuals) in the arm, plus a dose of humane rabies immune globulin (HRIG). A viral disease of the central nervous system, rabies transmits between animals, including humans, when saliva containing the virus enters an opening in the skin. Usually, the rabies virus enters through the bite of a rabid animal, but transmission can also occur when infected saliva enters through mucous membranes or a break in the skin. According to the Centers for Disease Control and Prevention (CDC), the first clinical signs and symptoms of rabies may be very similar to those of the flu including general weakness or discomfort, fever, or headache. For the rabies virus to get to the salivary glands, it has to travel first from the site of entry (usually a bite wound) through the animal's nervous system, then to the brain. cache = ./cache/cord-294312-ju6vuywm.txt txt = ./txt/cord-294312-ju6vuywm.txt === reduce.pl bib === id = cord-293387-0m1ngob3 author = Wood, A. title = The action of three antiseptics/disinfectants against enveloped and non-enveloped viruses date = 1998-04-30 pages = extension = .txt mime = text/plain words = 2917 sentences = 141 flesch = 45 summary = Four antiseptic/disinfectant solutions with chloroxylenol, benzalkonium chloride, cetrimide/ chlorhexidme and povidone-iodine were also assessed for antiviral effect against human immunodeficiency virus in the presence of whole human blood. Four antiseptic/disinfectant solutions with chloroxylenol, benzalkonium chloride, cetrimide/ chlorhexidine and povidone-iodine were also assessed for antiviral effect against human immunodeficiency virus in the presence of whole human blood. Virucidal activity of the antiseptic/disinfectants in the presence of albumin/ yeast extract The virucidal activity of Dettol, Dettol Hospital Concentrate and Savlon was compared to that of water of standard hardness against all the test viruses. The exception was Dettol Hospital Concentrate (active agent benzalkonium chloride) which was effective in the inactivation of the non-enveloped human coxsackie virus with a reduction of >5 log,,, after the 1 min timepoint. In conclusion, the solutions tested at their recommended concentrations for antiseptic use were very effective in inactivating the non-enveloped viruses, human immunodeficiency virus type 1 and herpes simplex virus type 1 in the presence of significant levels of organic soil. cache = ./cache/cord-293387-0m1ngob3.txt txt = ./txt/cord-293387-0m1ngob3.txt === reduce.pl bib === id = cord-293421-0ksn0fc7 author = Rodriguez, J. M. title = Detection of animal pathogens by using the polymerasechain reaction (PCR) date = 1997-05-31 pages = extension = .txt mime = text/plain words = 9106 sentences = 559 flesch = 49 summary = Summary The polymerase chain reaction (PCR) is a nucleic acid-based technique that enables the rapid and sensitive detection of specific micro-organisms. Althougla PCR has some shortcomings, such as the problems caused by contaminants and inhibitors or the lack of suitable sequences for designing specific primers, the outstanding research effort focused on tiffs technique, together with the remarkable development of molecular biology have minimized the deficiencies and allowed its increased general use as a diagnostic tool. Sensitive studies using reference strains of BVDV fi-om persistently infected carriers have shown that reverse transo-iption (RT)-PCR has greater sensitivity than other tests, including enzyme-linked immunosorbent assay (ELISA) (Horner el aL, 1995) ; unfortunately, cost currently makes this technique unsuitahle for large-scale testing but it should be valuahle as a coniirmatm T test in cases where ELISA resuhs are in the 'suspicious range' or where the viral titre is low, such as in batches of foetal bovine serum. Comparison of polymerase chain reaction and virus isolation for detection of epizootic hemorrhagic disease in clinical samples from naturally infected deer cache = ./cache/cord-293421-0ksn0fc7.txt txt = ./txt/cord-293421-0ksn0fc7.txt === reduce.pl bib === id = cord-296935-y77c4ro4 author = Couch, Robert B. title = Prior Infections With Seasonal Influenza A/H1N1 Virus Reduced the Illness Severity and Epidemic Intensity of Pandemic H1N1 Influenza in Healthy Adults date = 2011-11-10 pages = extension = .txt mime = text/plain words = 3992 sentences = 205 flesch = 48 summary = Serum antibody to the pH1N1 and seasonal A/H1N1 viruses was measured in 579 healthy adults at enrollment (fall 2009) and after surveillance for illness (spring 2010). Preexisting antibody to pH1N1 virus, responses to a single vaccine dose, a low infection-to-illness ratio, and a short duration of illness and virus shedding among those with influenza indicated presence of considerable preexisting immunity to pH1N1 in the population. To assess the clinical and epidemiological impact of pH1N1 infections and to identify immunologic factors correlating with infections and illnesses, we conducted a prospective study of influenza in a young adult population. Occurrences of pH1N1 influenza infections and illnesses in relation to serum HAI antibody titer at enrollment are shown in Table 2 . When the retrospectively identified moderate to severe ARIs with a significant antibody response were included, the inverse correlation between baseline titer and frequency of pH1N1 infection and illness was significant (v 2 for trend, P 5 .01). cache = ./cache/cord-296935-y77c4ro4.txt txt = ./txt/cord-296935-y77c4ro4.txt === reduce.pl bib === id = cord-294125-v2dr4hm0 author = Albert, Manuel title = ISG15, a Small Molecule with Huge Implications: Regulation of Mitochondrial Homeostasis date = 2018-11-13 pages = extension = .txt mime = text/plain words = 8040 sentences = 444 flesch = 33 summary = Finally, based on our recent observations, we discuss the essential functions of mitochondria in the antiviral response and examine the role of ISG15 in the regulation of mitochondrial processes, specifically OXPHOS and mitophagy. Binding to IFNARs leads to the activation of the Janus kinase-signal transducer and activator of transcription proteins (JAK-STAT) signaling pathway and the formation of the interferon-stimulated gene factor 3 (ISGF3) complex, with the subsequent expression of IFN-stimulated genes [3] that establish an antiviral state and play important roles in determining the host innate and adaptive immune responses [4] . In the following sections, we discuss the antiviral mechanisms mediated by ISGylation of both viral and cellular proteins, with a focus on mitochondrial proteins, as we recently showed that ISG15 modulates essential mitochondrial metabolic processes such as respiration and mitophagy in macrophages, with important implications for innate immune responses [29] . cache = ./cache/cord-294125-v2dr4hm0.txt txt = ./txt/cord-294125-v2dr4hm0.txt === reduce.pl bib === id = cord-294812-nnlzwaf1 author = Desforges, Marc title = Neuroinvasive and Neurotropic Human Respiratory Coronaviruses: Potential Neurovirulent Agents in Humans date = 2014-03-12 pages = extension = .txt mime = text/plain words = 7096 sentences = 318 flesch = 36 summary = However, in some circumstances, viruses can avoid the immune response and cause more severe respiratory diseases [1] or even spread to other tissues, including the central nervous system (CNS), where they could induce other types of pathologies [7] . Coronaviruses, a family of enveloped positive-stranded RNA viruses with a characteristic crown-shaped appearance, are widespread in nature and can infect several different species [44] , in which they cause mainly respiratory and enteric pathologies, with neurotropic and neuroinvasive properties in various hosts including humans, cats, pigs, rodents, and fowl [45] [46] [47] [48] . Furthermore, we have shown that these viruses are able to establish a persistent infection in human cells representative of the CNS [64, 65] and that HCoV-OC43 RNA could be detected for at least a year in the CNS of infected mice that survived the virus-induced acute encephalitis [71] . cache = ./cache/cord-294812-nnlzwaf1.txt txt = ./txt/cord-294812-nnlzwaf1.txt === reduce.pl bib === id = cord-297203-f3f31h4r author = Afrough, B. title = Emerging viruses and current strategies for vaccine intervention date = 2019-04-16 pages = extension = .txt mime = text/plain words = 5914 sentences = 263 flesch = 36 summary = While classic approaches to vaccine development are still amenable to emerging viruses, the application of molecular techniques in virology has profoundly influenced our understanding of virus biology, and vaccination methods based on replicating, attenuated and non‐replicating virus vector approaches have become useful vaccine platforms. Modified vaccinia virus Ankara (MVA) is licensed as a third-generation vaccinia type vaccine against smallpox and serves as a potent vector system for the development of new candidate vaccines against a range of infectious diseases, including those caused by emerging pathogens. Additionally, MVA elicits a strong immunological response against a range of other orthopoxviruses (OPXVs) (including Variola), and vaccines based on this platform can be considered as providing added value, as human immunity to OPXVs is low (after the cessation of the smallpox vaccination campaign) opening a gap for OPXV emergence, as evidenced by the recent occurrence of monkeypox virus in West Africa and onward cross boarder transmissions [39, 40] . cache = ./cache/cord-297203-f3f31h4r.txt txt = ./txt/cord-297203-f3f31h4r.txt === reduce.pl bib === id = cord-295041-5vpawtef author = Jakhmola, Shweta title = SARS-CoV-2, an Underestimated Pathogen of the Nervous System date = 2020-09-28 pages = extension = .txt mime = text/plain words = 5012 sentences = 310 flesch = 39 summary = Numerous clinical studies have reported neurological symptoms in COVID-19 patients since the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), apart from the atypical signs of pneumonia. Angiotensin-converting enzyme-2 (ACE-2), a potential receptor for SARS-CoV-2 entry, is expressed on various brain cells and cerebral parts, i.e., subfornical organ, paraventricular nucleus, nucleus of the tractus solitarius, and rostral ventrolateral medulla, as well as in non-cardiovascular areas such as the motor cortex and raphe. The resident CNS cells like astrocytes and microglia also express ACE-2, thus highlighting the vulnerability of the nervous system to SARS-CoV-2 infection. Furthermore, the presence of SARS-CoV-2 in cerebrospinal fluid (CSF) of COVID-19 patients is confirmed through genome sequencing [4] ; however, experimental evidence is needed to validate virusmediated neurological damage. Furthermore, the interaction of SARS-CoV-2 and ACE-2-expressing neuronal/glial cells may facilitate virus entry into the nervous system through different routes. cache = ./cache/cord-295041-5vpawtef.txt txt = ./txt/cord-295041-5vpawtef.txt === reduce.pl bib === id = cord-293732-rxd1lyi7 author = Manoj, M.G. title = Potential link between compromised air quality and transmission of the novel corona virus (SARS-CoV-2) in affected areas date = 2020-08-01 pages = extension = .txt mime = text/plain words = 4180 sentences = 210 flesch = 49 summary = Through a critical review of the current literature and a preliminary analysis of the link between SARS-CoV-2 transmission and air pollution in the affected regions, we offer a perspective that polluted environment could enhance the transmission rate of such deadly viruses under moderate-to-high humidity conditions. The aqueous atmospheric aerosols offer a conducive surface for adsorption/absorption of organic molecules and viruses onto them, facilitating a pathway for higher rate of transmission under favourable environmental conditions. Analysis of the air quality index (AQI, Fig. S1 , acquired on 16 th March 2020) reveals that the effected countries or regions had witnessed enhanced level of pollution ( frequently AQI > 100) which are qualified as "unhealthy" and even "hazardous", in the cold winter period. (2020) reports that air pollutants measured over Italy (PM 10 and PM 2.5 ) have a substantial influence on the COVID-19 transmission and infection rate there. cache = ./cache/cord-293732-rxd1lyi7.txt txt = ./txt/cord-293732-rxd1lyi7.txt === reduce.pl bib === id = cord-294585-dl5v9p50 author = Klein, H. G. title = Pathogen‐reduction methods: advantages and limits date = 2009-02-13 pages = extension = .txt mime = text/plain words = 4519 sentences = 216 flesch = 40 summary = However, because blood contains numerous labile proteins and fragile cells, and because there is a wide array of potentially infectious agents, no single method of pathogen-inactivation will likely preserve all blood components, yet effectively remove all viruses, bacteria, spores, protozoa and prions. Riboflavin/ultraviolet light treatment has been evaluated in preclinical studies and found to result in reduction of infectivity by many pathogens including west Nile virus, intracellular HIV, bacteria and protozoa. Therapeutic efficacy and safety of platelets treated with a photochemical process for pathogen inactivation: the SPRINT Trial Clinical safety of platelets photochemically treated with amotosalen HCl and ultraviolet A light for pathogen inactivation: the SPRINT trial Fresh frozen plasma prepared with amotosalen HCl (S-59) photochemical pathogen inactivation: transfusion of patients with congenital coagulation factor deficiencies Therapeutic efficacy and safety of red blood cells treated with a chemical process (S-303) for pathogen inactivation: a Phase III clinical trial in cardiac surgery patients cache = ./cache/cord-294585-dl5v9p50.txt txt = ./txt/cord-294585-dl5v9p50.txt === reduce.pl bib === id = cord-295191-xu26mvc3 author = Avirutnan, Panisadee title = Complement and its role in protection and pathogenesis of flavivirus infections date = 2008-12-30 pages = extension = .txt mime = text/plain words = 6120 sentences = 333 flesch = 32 summary = Complement evasion mechanisms include: (a) use of complement receptors to enhance viral entry or suppress adaptive immune response (e.g., HIV, West Nile virus (WNV), measles virus, adenoviruses, herpesviruses, enteroviruses, hepatitis B and C viruses ); (b) expression of viral proteins that directly inhibit complement (e.g., herpesviruses, coronaviruses, and astroviruses [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] ); (c) modulation of expression of complement regulators on host cells to prevent complement-dependent lysis (e.g., herpesviruses [137] [138] [139] ); (d) incorporation of human regulators on the surface of virions to protect from complement-mediated virolysis (e.g. HIV, HTLV, cytomegalovirus, and vaccinia virus [140] [141] [142] [143] [144] [145] [146] ); (e) recruitment of soluble complement regulatory proteins to the virion or infected cell surface (e.g., WNV and HIV [147] [148] [149] [150] [151] ); (f) expression of viral decoy proteins that structurally or functionally mimic complement regulatory proteins (e.g., poxviruses and herpesviruses [152] [153] [154] [155] [156] [157] [158] [159] . cache = ./cache/cord-295191-xu26mvc3.txt txt = ./txt/cord-295191-xu26mvc3.txt === reduce.pl bib === id = cord-295531-zojb3cew author = Huggett, Kathryn D. title = Influenza A date = 2008-01-10 pages = extension = .txt mime = text/plain words = 2094 sentences = 141 flesch = 50 summary = Subtypes of influenza A viruses that are prominent in one species may on occasion infect and cause disease in another. Influenza A is a single-stranded RNA virus that causes an acute and highly contagious upper respiratory disease. It was approved in 1966 for chemoprophylaxis and in 1976 for treatment and chemoprophylaxis of influenza type A virus in both adults and children 1 year of age. It was approved in 1993 for the treatment and chemoprophylaxis of influenza A infections in adults and prophylaxis in children. It was approved in 1999 for the treatment of uncomplicated influenza infections in patients aged 1 year. It was approved in 1999 for the treatment of uncomplicated influenza infections in patients aged 1 year. Basic information on the diagnosis, clinical findings, complications, prevention and treatment of influenza, including vaccine safety recommendations, can be found at: http://www3.accessmedicine.com/content.aspx?aID=17572#17572 Information on the common cold and flu can be located at: http://familydoctor.org/517. cache = ./cache/cord-295531-zojb3cew.txt txt = ./txt/cord-295531-zojb3cew.txt === reduce.pl bib === id = cord-298032-3zlu8g8y author = Nan, Yuchen title = Antisense Phosphorodiamidate Morpholino Oligomers as Novel Antiviral Compounds date = 2018-04-20 pages = extension = .txt mime = text/plain words = 10577 sentences = 524 flesch = 46 summary = An earlier study showed that a 22mer PPMO targeting the translation start site region of EBOV VP35 positive-sense RNA exhibited sequence-specific, time-and dose-dependent inhibition of EBOV replication in cultured cells (Enterlein et al., 2006) . However, PPMO targeting conserved internal ribosome entry site (IRES) sequences have been shown to be highly effective in protecting cultured cells against infection by human rhinovirus type 14, coxsackievirus type B2, and poliovirus type 1 (PV1) (Stone et al., 2008) , with reduction of PV1 titers by up to 6 log10. In this study, virus replication in MDCK cells was significantly inhibited by three PPMO targeting either the translation start site region of PB1 or NP mRNA or the 3 -terminal region of NP viral RNA (vRNA). Inhibition of influenza virus infection in human airway cell cultures by an antisense peptide-conjugated morpholino oligomer targeting the hemagglutinin-activating protease TMPRSS2 cache = ./cache/cord-298032-3zlu8g8y.txt txt = ./txt/cord-298032-3zlu8g8y.txt === reduce.pl bib === id = cord-296309-i1mpov7k author = Houldcroft, Charlotte J. title = Clinical and biological insights from viral genome sequencing date = 2017-01-16 pages = extension = .txt mime = text/plain words = 9050 sentences = 389 flesch = 35 summary = We will also explore two areas in which viral WGS has recently proven its clinical utility: metagenomic sequencing to identify viruses that cause encephalitis (BOX 1) ; and the role of WGS in molecular epidemiology and public health management of the Pan-American Zika virus outbreak (BOX 2) . However, the increasing number of resistance genes that are located across viral genomes, together with decreasing costs of sequencing and the use of sequence data for transmission studies, are driving a reappraisal of the need for WGS. The numerous phylogenetically informative variant sites that can be obtained from full-length or near full-length genomes removes the need for high-quality sequences, which enabled the robust linking of cases of Ebola virus infection and public health interventions in real time during the 2015 epidemic 39 . There are several methods that are available to achieve WGS of viruses from clinical samples; amplicon sequencing, target enrichment or metagenomics. cache = ./cache/cord-296309-i1mpov7k.txt txt = ./txt/cord-296309-i1mpov7k.txt === reduce.pl bib === id = cord-296819-gztmidn2 author = Sambri, Vittorio title = Diagnosis of West Nile Virus Human Infections: Overview and Proposal of Diagnostic Protocols Considering the Results of External Quality Assessment Studies date = 2013-09-25 pages = extension = .txt mime = text/plain words = 6732 sentences = 304 flesch = 42 summary = title: Diagnosis of West Nile Virus Human Infections: Overview and Proposal of Diagnostic Protocols Considering the Results of External Quality Assessment Studies This paper reviews the presently available methods to achieve the laboratory diagnosis of West Nile virus infections in humans, discussing the most prominent advantages and disadvantages of each in light of the results obtained during four different External Quality Assessment studies carried out by the European Network for 'Imported' Viral Diseases (ENIVD). For the routine detection of WNV RNA using molecular techniques there are two distinct diagnostic settings: the first involves blood and organ donation screening from subjects living in an area where WNV circulation is known to be occurring, and the second involves the identification of viral genomes in serum, plasma and CSF samples from patients presenting with a clinical picture typical of WNV infection [21] . cache = ./cache/cord-296819-gztmidn2.txt txt = ./txt/cord-296819-gztmidn2.txt === reduce.pl bib === id = cord-297834-me1ajoyb author = Schountz, Tony title = Hantavirus Immunology of Rodent Reservoirs: Current Status and Future Directions date = 2014-03-14 pages = extension = .txt mime = text/plain words = 6425 sentences = 334 flesch = 38 summary = The immune response is energetically expensive for wild animals, thus the findings of experimental studies will be critical for understanding the ecoimmunology of reservoir hosts of hantaviruses [6, 7] , and experiments using wild rodents in natural or semi-natural environments [8, 9] will be required to validate laboratory findings. Currently, three laboratory infection systems have been developed to study hantavirus infections of reservoir hosts: Seoul virus (SEOV) infection of the Norway rat (Rattus norvegicus), Puumala virus (PUUV) infection of the bank vole (Myodes glareolus), and Sin Nombre virus (SNV) infection of the deer mouse (Peromyscus maniculatus) [12, 14, 16] . Experimental data have also shown that patterns of the expression of genes related to the immune response are different in infected males and females [32] , and it is likely these differences have important roles in hantavirus ecology. cache = ./cache/cord-297834-me1ajoyb.txt txt = ./txt/cord-297834-me1ajoyb.txt === reduce.pl bib === id = cord-297494-6yxmaihl author = Katsurada, Naoko title = The impact of virus infections on pneumonia mortality is complex in adults: a prospective multicentre observational study date = 2017-12-06 pages = extension = .txt mime = text/plain words = 4336 sentences = 217 flesch = 38 summary = However, influenza virus A and B were associated with three-fold higher mortality in patients with chronic respiratory disease but not with other comorbidities (ARR 3.38, 95% CI 1.54–7.42). We conducted this prospective multicentre study to determine the distribution of viruses associated with pneumonia in adults and to establish their virus-specific effects on pneumonia mortality stratified by age group and comorbidity status. To the best of our knowledge, this study is the first to systematically investigate virus-specific effects on pneumonia mortality by age group and comorbidity status among adults. In our study, multiple viruses were identified in 5.1% of virus-associated pneumonia and were associated with higher mortality than single viral infection in patients with chronic respiratory disease and other comorbidities. Systematic reviews have shown that multiple viral infections in patients with respiratory disease are not associated with disease severity [27, 28] ; however, the majority of previous studies included young children but not adults. cache = ./cache/cord-297494-6yxmaihl.txt txt = ./txt/cord-297494-6yxmaihl.txt === reduce.pl bib === id = cord-294108-uvnh0s9r author = Dube, Taru title = Repurposed Drugs, Molecular Vaccines, Immune‐Modulators, and Nanotherapeutics to Treat and Prevent COVID‐19 Associated with SARS‐CoV‐2, a Deadly Nanovector date = 2020-10-25 pages = extension = .txt mime = text/plain words = 13885 sentences = 845 flesch = 44 summary = [2, [8] [9] [10] This article discusses SARS-CoV-2 nanostructure, the virus biology in connection to its epidemiology, clinical manifestations, and potential and future therapeutic options including repurposed drugs, vaccine/protein therapies, immune therapies, and nanotherapeutics. Mechanisms such as inhibition of viral enzymes (DNA and RNA polymerases, 3CL pro, TMPRSS2, reverse transcriptase, neuraminidase, endonucleases, and other proteases) or processes such as ACE2 cellular receptor inhibitors and endosomal acidification mediators prohibiting viral fusion; molecules interfering with glycosylation of the viral protein, viral assembly, new viral particle transport, and release, and immunomodulation of cytokine release can be potential targets in developing various antiviral drugs for the SARS-CoV-2. [85] A randomized, placebo-controlled, Phase IV clinical trial assessing the safety and efficacy of umifenovir as an adjuvant therapy to the combined therapeutic regimen of IFN 1a, lopinavir/ritonavir and hydroxychloroquine in moderate to severe COVID-19 patients (NCT04350684) is underway. cache = ./cache/cord-294108-uvnh0s9r.txt txt = ./txt/cord-294108-uvnh0s9r.txt === reduce.pl bib === id = cord-297131-3a9vjpvn author = Charlton Hume, Hayley K. title = Synthetic biology for bioengineering virus‐like particle vaccines date = 2018-12-31 pages = extension = .txt mime = text/plain words = 6833 sentences = 366 flesch = 32 summary = Current and developing technologies for the identification of novel target‐specific antigens and their usefulness for rational engineering of VLP functions (e.g., presentation of structurally diverse antigens, enhanced antigen immunogenicity, and improved vaccine stability) are described. Seconded by a multitude of tools, such as omics technologies, structural biology, system immunology, and bioinformatics and computational biology, one can now screen for pathogen-specific antigens with high immunogenic potential and apply that information to rationally design modern VLP vaccines ( Figure 1 ). Virus-like particles as a highly efficient vaccine platform: Diversity of targets and production systems and advances in clinical development Synthetic biology design to display an 18 kDa rotavirus large antigen on a modular virus-like particle Integrated molecular and bioprocess engineering for bacterially produced immunogenic modular virus-like particle vaccine displaying 18 kDa rotavirus antigen A novel virus-like particle based vaccine platform displaying the placental malaria antigen VAR2CSA cache = ./cache/cord-297131-3a9vjpvn.txt txt = ./txt/cord-297131-3a9vjpvn.txt === reduce.pl bib === id = cord-295062-8rl4kswe author = Marsh, Mark title = Virus Entry: Open Sesame date = 2006-02-24 pages = extension = .txt mime = text/plain words = 8504 sentences = 401 flesch = 42 summary = Virus Particles as Devices for Targeted Gene Transfer A viral particle is composed of nucleic acids (RNA or DNA), protein, and, in the case of enveloped viruses, membrane lipids. Viruses use signaling activities to induce changes in the cell that promote viral entry and early cytoplasmic events, as well as to optimize later processes in the replication cycle. Like cholera toxin, these viruses bind to the sugar moiety of gangliosides and enter cells via caveolar/raft pathways that are dependent on cholesterol ( Figures 2D and 2E ) and the activation of tyrosine-kinase signaling cascades (Anderson et al., 1996; Pelkmans et al., 2001; Smith et al., 2003a; Stang et al., 1997; Tsai et al., 2003) . Nevertheless, in the majority of cases, the transfer of viral genomes from cell to cell appears to occur through the formation of virus particles that are released from infected cells and use the mechanisms described above to enter new uninfected hosts. cache = ./cache/cord-295062-8rl4kswe.txt txt = ./txt/cord-295062-8rl4kswe.txt === reduce.pl bib === id = cord-298905-c2uuvfm5 author = Horzinek, M. C. title = Molecular pathogenesis of virus infections date = 1987 pages = extension = .txt mime = text/plain words = 3888 sentences = 193 flesch = 40 summary = Using coronaviruses as examples the changes in virulence have been traced back to single mutational events; recombination, however, is likely to be an alternative mechanism by which virus-host interactions (e.g. the cell-, organor animal species-spectrum) can dramatically change. Parainfluenzaviruses, for example, attach to neuraminic acid-containing receptors; since glycolipids and glycoproteins containing neuraminic acid abound in vertebrate cell membranes the adsorption/penetration process lacks the specificity required to explain the restrictions in host range and tissue tropism of paramyxoviruses 29. Also in influenza virus infection cap structures are essential: these are cannibalized from host cell nuclear RNA precursor molecules and used as primers for viral RNA replication and synthesis 28. Autoimmune phenomena involving both the humoral and cellular limbs of the immune response have been identified in neurological conditions following infections with e.g. canine distemper virus3; invasion of brain tissue is supposed to cause changes in the molecular constitution of myelin and membrane components, making them recognizable as 'nonself'. cache = ./cache/cord-298905-c2uuvfm5.txt txt = ./txt/cord-298905-c2uuvfm5.txt === reduce.pl bib === id = cord-295873-kykyubdq author = Morikawa, Saeko title = Seasonal variations of respiratory viruses and etiology of human rhinovirus infection in children date = 2015-10-22 pages = extension = .txt mime = text/plain words = 2888 sentences = 171 flesch = 49 summary = authors: Morikawa, Saeko; Kohdera, Urara; Hosaka, Taisuke; Ishii, Kousuke; Akagawa, Shohei; Hiroi, Satoshi; Kase, Tetsuo STUDY DESIGN: Nasal aspirate samples were obtained from outpatients and inpatients of a children's hospital and these samples were subjected to real-time PCR to detect 16 respiratory viruses. Seasonal variations of the 16 viruses and the clinical outcomes such as wheezing, the need for oxygenation and prolonged hospitalization of patients with single viral infections and multiple infections were determined for the 5 most often detected viruses. PCR makes it possible to detect uncultivable viruses such as human bocavirus and rhinovirus C and discover concurrent viral infections. Though there was no significant difference in the number of hospitalization days of patients with single infections by rhinoviruses or other respiratory viruses, our data suggested the importance of rhinoviruses as a potential cause of pediatric pneumonia. cache = ./cache/cord-295873-kykyubdq.txt txt = ./txt/cord-295873-kykyubdq.txt === reduce.pl bib === id = cord-298036-2zurc60t author = Imre, Gergely title = Cell death signalling in virus infection date = 2020-09-12 pages = extension = .txt mime = text/plain words = 8002 sentences = 414 flesch = 37 summary = Subsequently, granzyme-B induces mitochondrial apoptosis by performing cleavage of the BCL-2 homology domain-3 (BH3)-only protein, BH3 interacting domain death agonist (BID), which then leads to BAX/BAK-mediated MOMP and the initiation of the caspase-9-driven apoptotic pathway [16] . Still, the mechanism, by which IRF-3 triggers cell death signalling pathways is only partially understood and the studies indicate a strong cell type specificity in the apoptosis sensitivity in response to viral PAMPs Z-RNA and z-DNA fragments, which are distinct from the B-structure of eukaryotic RNA and DNA are recognized by z-DNA/RNA binding protein-1 (ZBP1; also: DAI). Necroptosis initiation takes place upon TNFR ligation, which, however, primarily leads to NFkB activation via the assembly of so called complex-I, including adaptor proteins TNFRSF1A associated via death domain (TRADD), TRAF2, cellular IAP (cIAP) and ubiquitinated receptor interacting serine/threonine kinase 1 (RIPK1) [10] . cache = ./cache/cord-298036-2zurc60t.txt txt = ./txt/cord-298036-2zurc60t.txt === reduce.pl bib === id = cord-300020-edolh7ww author = Nielsen, Anne Ahlmann title = Persistence of Low-Pathogenic Avian Influenza H5N7 and H7N1 Subtypes in House Flies (Diptera: Muscidae) date = 2011-05-01 pages = extension = .txt mime = text/plain words = 4313 sentences = 259 flesch = 56 summary = The objective of the present work was to investigate the potential transmission of LPAIV by persistence of the virus in the alimentary tract of house flies, Musca domestica L. The persistence of HPAIV H5N1 in house ßies and blow ßies as well as Newcastle disease virus (family Paramyxoviridae, genus avulavirus, NDV), turkey coronavirus (family Coronaviridae, genus Coronavirus, TCV), and reticuloendotheliosis virus (family Retroviridae, genus Gammaretrovirus, REV) has been studied in the laboratory (Calibeo-Hayes et al. The current study investigated the persistence of LPAIV in the alimentary tract of house ßies that were fed various concentrations of subtypes H5N7 and H7N1 viruses and incubated at different temperatures for up to 24 h. Our study demonstrated that infective low-pathogenic avian inßuenza virus of the H7N1 and H5N7 subtypes can be isolated from the alimentary tract of house ßies for at least 24 h postfeeding and that factors such as temperature, incubation period postfeeding, and load of ingested virus play an important role in the persistence of infective virus. cache = ./cache/cord-300020-edolh7ww.txt txt = ./txt/cord-300020-edolh7ww.txt === reduce.pl bib === id = cord-295445-f4p00yaw author = Wang, Hao title = Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments date = 2018-02-01 pages = extension = .txt mime = text/plain words = 6889 sentences = 284 flesch = 48 summary = Previous studies conducted in wastewater treatment plants have shown that ozone disinfection might be highly efficient in inactivating bacteria and bacteriophages after conventional sewage treatments (Kim et al., 1999; Tyrrell et al., 1995) , but knowledge regarding its effect for reducing human enteric viruses is relatively scarce. The four concentrated water samples (incoming sewage, conventionally treated, ozone treated, and outlet water) from each of the three weeks were also analyzed by qPCR for 14 common enteric viruses (adenovirus, astrovirus, hepatitis A virus, hepatitis E virus, norovirus GI, norovirus GII, norovirus GIV, parechovirus, sapovirus, aichivirus, mengovirus, torovirus, enterovirus, and rotavirus). However, in this study some viruses that were undetectable in the ozone-treated samples reoccurred in the outlet water, including parvovirus, norovirus GII, human feces pecovirus, parvovirus-like virus, gokushovirus, and HAdV-F41, although the amounts were significantly lower compared with raw sewage. cache = ./cache/cord-295445-f4p00yaw.txt txt = ./txt/cord-295445-f4p00yaw.txt === reduce.pl bib === id = cord-297960-4x1j0iqg author = Bösl, Korbinian title = Common Nodes of Virus–Host Interaction Revealed Through an Integrated Network Analysis date = 2019-10-04 pages = extension = .txt mime = text/plain words = 5482 sentences = 301 flesch = 44 summary = Furthermore, we performed an interactome-informed drug re-purposing screen and identified novel activities for broad-spectrum antiviral agents against hepatitis C virus and human metapneumovirus. Furthermore, we performed an interactome-informed drug re-purposing screen and identified novel activities for broad-spectrum antiviral agents against hepatitis C virus and human metapneumovirus. Global systems-level approaches including functional RNAi screens, interactome mapping technologies such as affinity-purification mass spectrometry (AP-MS), quantitative proteomics, and CRISPR/Cas9-based screens have provided unparalleled details and insights into the dynamics of host proteome in immune cells (21) (22) (23) (24) , host-virus interactome (15-17, 25, 26) , and also identified important host dependency factors of various viruses (25, 27, 28) . We hypothesized that combining a meta-analysis of host-virus protein-protein interactions of multiple viruses and functional RNAi screens would provide novel insights for developing broadspectrum antiviral strategies. High-Definition analysis of host protein stability during human cytomegalovirus infection reveals antiviral factors and viral evasion mechanisms cache = ./cache/cord-297960-4x1j0iqg.txt txt = ./txt/cord-297960-4x1j0iqg.txt === reduce.pl bib === id = cord-296635-8r3tm966 author = Breed, Andrew C. title = Evidence of Endemic Hendra Virus Infection in Flying-Foxes (Pteropus conspicillatus)—Implications for Disease Risk Management date = 2011-12-14 pages = extension = .txt mime = text/plain words = 4573 sentences = 199 flesch = 47 summary = title: Evidence of Endemic Hendra Virus Infection in Flying-Foxes (Pteropus conspicillatus)—Implications for Disease Risk Management This study investigated the seroepidemiology of Hendra virus in a spectacled flying-fox (Pteropus conspicillatus) population in northern Australia, near the location of an equine and associated human Hendra virus infection in late 2004. Hendra virus (HeV) and Nipah virus (NiV) are paramyxoviruses of the genus Henipavirus with pteropid bats (i.e. flying-foxes; Pteropus sp., Family Pteropodidae) being the primary wildlife reservoir [1] . Henipaviruses have the potential to infect a wide range of mammalian species, and Hendra virus has spread from flying-foxes to horses in Australia on at least 20 reported separate occasions (five involving horse-human transmission), most recently in 2011 [5, 6, 7] . [14] on the infection dynamics of HeV in the little red flying-fox, Pteropus scapulatus, in the Northern Territory of Australia suggested that viral transmission may be predominantly horizontal, with pregnancy and lactation suggested as risk factors for infection. cache = ./cache/cord-296635-8r3tm966.txt txt = ./txt/cord-296635-8r3tm966.txt === reduce.pl bib === id = cord-295433-olmein3q author = Banerjee, Arinjay title = Bats and Coronaviruses date = 2019-01-09 pages = extension = .txt mime = text/plain words = 5655 sentences = 298 flesch = 52 summary = Initial studies investigating animal sources of the virus from "wet markets" in the Guangdong province of China suggested that Himalayan palm civets and raccoon dogs were the most likely hosts responsible for human transmission [22] ; however, the role of bats as the original animal reservoir hosts of SARS-CoV was speculated as similar viruses were detected in them [27, 28] . A recent study found that 16 out of 30 camel workers surveyed in Saudi Arabia show evidence of prior MERS-CoV infection via seroconversion and/or virus-specific CD8+ T cell responses without any history of significant respiratory disease. The primary bat species being used to study the bat immune response to virus infections in vitro and in vivo are Pteropus alecto (black flying fox), Rousettus aegyptiacus (Egyptian rousette), and Artibeus jamaicensis (Jamaican fruit bat). Multiple studies with PEDV, SARS-and MERS-CoVs have identified accessory proteins that can effectively inhibit an IFN response in mammalian cells [12] [13] [14] [91] [92] [93] [94] [95] . cache = ./cache/cord-295433-olmein3q.txt txt = ./txt/cord-295433-olmein3q.txt === reduce.pl bib === id = cord-298214-ivu4erpq author = Castrignano, Silvana Beres title = The metagenomic approach and causality in virology date = 2015-04-01 pages = extension = .txt mime = text/plain words = 2673 sentences = 126 flesch = 41 summary = 9, 13, 16 Among these recent propositions, both the criteria of Mokili et al, 16 based on the comparison of metagenomic characteristics among infected and healthy individuals, and the criteria of Lipkin, 13 who grouped laboratory, clinical and epidemiological data into three certainty levels to establish an association between pathogens and diseases, considered the inoculation of the infectious agent in a healthy individual as INTRODUCTION a criterion for the confirmation of causality (this criterion was inherited from Koch's postulates). This virus was identified in human Merkel cell carcinoma (MCC) samples, 8 and the investigation of the causal association between MCV and the disease began with the investigation of 10 MCC samples from different patients; of these, the viral genome was detected in eight samples. cache = ./cache/cord-298214-ivu4erpq.txt txt = ./txt/cord-298214-ivu4erpq.txt === reduce.pl bib === id = cord-300189-gsp1dozg author = Franci, Gianluigi title = Infectivity inhibition by overlapping synthetic peptides derived from the gH/gL heterodimer of herpes simplex virus type 1 date = 2017-02-14 pages = extension = .txt mime = text/plain words = 6345 sentences = 322 flesch = 50 summary = To date, few peptide molecules outside the well-known inhibitory regions of Class 1 viral fusion proteins, the heptad repeats, should be as fusion; therefore, a brute force approach to the identification of peptide entry inhibitors may help in the dissection of HSV-1 glycoproteins domains. Previous works using a physico-chemical algorithm, the Wimley-White Interfacial Hydrophobicity Scale (WWIHS), in combination with other structural data allowed us to predict regions in gH potentially involved in membrane interactions during the entry and fusion process, and some of them were found to possess HSV antiviral activity in dose-dependent inhibition assays [66] . [76] used a phage display methodology to identify a peptide (named P1) to inhibit West Nile virus (WNV) infectivity, possibly by binding to the envelope glycoprotein (E protein) necessary for membrane fusion. Substitution of herpes simplex virus 1 entry glycoproteins with those of saimiriine herpesvirus 1 reveals a gD-gH/gL functional interaction and a region within the gD profusion domain that is critical for fusion cache = ./cache/cord-300189-gsp1dozg.txt txt = ./txt/cord-300189-gsp1dozg.txt === reduce.pl bib === id = cord-298051-ej8qxkce author = Louten, Jennifer title = Detection and Diagnosis of Viral Infections date = 2016-05-06 pages = extension = .txt mime = text/plain words = 11204 sentences = 602 flesch = 57 summary = Cell lines can be infected with patient samples to allow viral replication within the cells; observable cytopathic effects can help to identify the identity of the virus. Infected cells can also be used for immunofluorescence assays, which use fluorescently labeled virus-specific antibodies to identify viruses in fixed cells or tissues. In the process of PCR, DNA (including any viral DNA present) is isolated from the clinical specimen, generally blood cells or tissue, and added to a tube containing primers, DNA polymerase, and nucleotides ( Fig. 7.14) . The diagnostic techniques described in this chapter identify the presence of a virus in a sample, or even the amount of viral nucleic acid, but these assays cannot determine the amount of virus present that is capable of productively infecting cells. Fluorescently labeled antibodies bind to viral antigens present in infected cells. cache = ./cache/cord-298051-ej8qxkce.txt txt = ./txt/cord-298051-ej8qxkce.txt === reduce.pl bib === id = cord-297662-slmlhqnb author = Yap, Sally S. L. title = Dengue Virus Glycosylation: What Do We Know? date = 2017-07-25 pages = extension = .txt mime = text/plain words = 11116 sentences = 526 flesch = 48 summary = In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis. Since high mannose binding DC-SIGN interacts only with N67 glycans on the viral surface (Pokidysheva et al., 2006) and N153-glycan is dispensable for virus production in mosquito and mammalian cells (Bryant et al., 2007) , this suggests that N153 glycans may serve a distinct function from N67 glycans in DEN pathogenesis possibly via interaction with an unknown fucose binder or act as a viral glycan shield. Finally, N153 deglycosylated (N153 − ) DENV mutant displayed reduced infectivity (10-fold lower) in both mammalian and mosquito cells compared to WT, possibly due to impaired virus entry process (Lee et al., 1997; Hacker et al., 2009) , whereby loss of the N153-glycan affected the conformational stability of E proteins and led to premature exposure of the fusion peptide (Yoshii et al., 2013) . N-linked glycosylation of dengue virus NS1 protein modulates secretion, cell-surface expression, hexamer stability, and interactions with human complement cache = ./cache/cord-297662-slmlhqnb.txt txt = ./txt/cord-297662-slmlhqnb.txt === reduce.pl bib === id = cord-298862-8bijio30 author = Eltom, Kamal H. title = Buffalopox Virus: An Emerging Virus in Livestock and Humans date = 2020-08-20 pages = extension = .txt mime = text/plain words = 4318 sentences = 231 flesch = 47 summary = Buffalopox was first described in India, later in other countries, and has become an emerging contagious viral zoonotic disease infecting milkers with high morbidity among affected domestic buffalo and cattle. Over time, VACV evolved into BPXV by establishing itself in buffaloes to be increasingly pathogenic to this host and to make infections in cattle and humans. The full-length sequences of these four genes of BPXVs-obtained from outbreaks in buffaloes, cattle, and humans in India-were analyzed, to investigate their evolutionary relationship to other OPXVs circulating in the world vis-à The full-length sequences of these four genes of BPXVs-obtained from outbreaks in buffaloes, cattle, and humans in India-were analyzed, to investigate their evolutionary relationship to other OPXVs circulating in the world vis-à-vis the vaccine strains. Sequence and phylogenetic analysis of host-range (E3L, K3L, and C7L) and structural protein (B5R) genes of buffalopox virus isolates from buffalo, cattle, and human in India cache = ./cache/cord-298862-8bijio30.txt txt = ./txt/cord-298862-8bijio30.txt === reduce.pl bib === id = cord-298019-gf2asni1 author = Galdiero, Stefania title = gH625: A milestone in understanding the many roles of membranotropic peptides date = 2014-10-12 pages = extension = .txt mime = text/plain words = 8586 sentences = 354 flesch = 37 summary = While they have been initially discovered in viral fusion proteins and have been involved in the mechanism of viral entry, it is now clear that their features and their mode of interaction with membrane bilayers can be exploited to design viral inhibitors as well as to favor delivery of cargos across the cell membrane and across the blood–brain barrier. Peptides with a propensity for membrane binding can also interfere with enveloped virus entry by direct physical interaction with the hydrophobic surfaces present on cell membranes and/or fusion proteins. Since not all membranotropic peptides are able to cross the membrane bilayer, it is essential to identify structural characteristics of hydrophobic peptides know to enter the cell membrane to highlight any feature that is involved in the penetration which may help in the design of novel delivery tools. Dendrimer functionalization with a membrane-interacting domain of herpes simplex virus type 1: towards intracellular delivery cache = ./cache/cord-298019-gf2asni1.txt txt = ./txt/cord-298019-gf2asni1.txt === reduce.pl bib === id = cord-302277-c66xm2n4 author = Bakaletz, Lauren O. title = Developing animal models for polymicrobial diseases date = 2004 pages = extension = .txt mime = text/plain words = 10910 sentences = 537 flesch = 33 summary = Briefly, viral infection compromises the protective functions of the Eustachian tube, alters respiratory-tract secretions, damages the mucosal epithelial lining, interferes with antibiotic efficacy, modulates the immune response and enhances bacterial adherence 77 and colonization 78 to predispose the host to bacterial OM. In otitis media, which is a middle ear infection, a synergistic interaction that results in disease owing to co-infection with an upper respiratory tract virus and three bacterial species -Streptococcus pneumoniae, nontypeable Haemophilus influenzae (NTHI) and Moraxella catarrhalis -is well documented. It seems likely that the transient suppression of RDC migration and the delayed development of an effective adaptive immune response to a second infection might be another mechanism by which influenza virus predisposes the host to bacterial co-infection. Using this criterion, a mouse model of polymicrobial-induced osteoclastogenesis, bacterial penetration, leukocyte recruitment and softtissue necrosis has been developed to clarify the role of cytokines in periodontal disease. cache = ./cache/cord-302277-c66xm2n4.txt txt = ./txt/cord-302277-c66xm2n4.txt === reduce.pl bib === id = cord-302425-aaxvlktp author = Cortey, Martí title = High levels of unreported intraspecific diversity among RNA viruses in faeces of neonatal piglets with diarrhoea date = 2019-12-05 pages = extension = .txt mime = text/plain words = 4998 sentences = 248 flesch = 52 summary = In contrast, other RNA viruses including Kobuvirus, Astrovirus, Sapovirus, Sapelovirus, Teschovirus, and Torovirus, have been detected in pig faeces but its role as causative agents of neonatal diarrhoea has not so far been fully elucidated [10] [11] [12] [13] [14] . The results reported among the 47 diarrhoeic samples analysed include representatives of 12 virus species corresponding to 8 genera of RNA viruses (Additional file 1): Kobuvirus, Rotavirus (RVA, RVB and RVC), Sapovirus (SAV), Mamastrovirus (Porcine Astrovirus types 3 -AstV3 -, 4 -AstV4 -and 5 -AstV5 -), Alphacoronavirus (PEDV), Enterovirus (Enterovirus G, EntVG), Pasivirus (PasiV) and Posavirus (PosaV). Regarding KobuV, our results also agree with an increased prevalence of this agent observed in cases of diarrhoea in suckling piglets worldwide: Brazil [22] , Korea [29] and Vietnam [30] ; despite several (See figure on previous page.) Fig. 5 Neighbor-joining phylogenetic tree based on the p-distance among the nucleotide sequences of the VP7 segment for Rotavirus B. cache = ./cache/cord-302425-aaxvlktp.txt txt = ./txt/cord-302425-aaxvlktp.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-298033-kzdp9edn author = Domingo, Esteban title = Quasispecies dynamics in disease prevention and control date = 2019-11-08 pages = extension = .txt mime = text/plain words = 16346 sentences = 735 flesch = 37 summary = Quasispecies dynamics in disease prevention and control following statement will be obvious to the reader: "If a single mutation is able to confer resistance to an antiviral agent, and the mutation does not cause a significant selective disadvantage to the virus (fitness decrease) in the considered environment, a drug-resistant virus mutant will be present in most, if not all, virus populations" (Domingo, 1989) . The phenotypic barrier to drug resistance is equivalent to the fitness cost inflicted upon the virus by the mutations and corresponding amino acid substitution(s) required for resistance [Fitness cost is treated in Chapter 4 (Section 4.6) and in Chapter 7 (Section 7.4.2) in connection with the frequency of monoclonal antibody-or cytotoxic T-cell-escape mutants in viral populations]. For viruses that replicate in cell culture, it is possible to estimate the minimal viral population size needed to select a drug-resistant mutant which is generally positively correlated with the genetic barrier ( Fig. 8.5 ). cache = ./cache/cord-298033-kzdp9edn.txt txt = ./txt/cord-298033-kzdp9edn.txt === reduce.pl bib === id = cord-300837-d0a8y5qh author = Khetawat, Dimple title = A Functional Henipavirus Envelope Glycoprotein Pseudotyped Lentivirus Assay System date = 2010-11-12 pages = extension = .txt mime = text/plain words = 8988 sentences = 355 flesch = 44 summary = To circumvent this problem, we have developed a henipavirus envelope glycoprotein pseudotyped lentivirus assay system using either a luciferase gene or green fluorescent protein (GFP) gene encoding human immunodeficiency virus type-1 (HIV-1) genome in conjunction with the HeV and NiV fusion (F) and attachment (G) glycoproteins. Pseudotyped virus particles generated with the NiV F and G glycoproteins were able to infect and produce luciferase reporter gene activity at various levels on all permissive receptor expressing cells ( Figure 1A ) while no signal was observed with the receptor negative HeLa-USU or with control virus particles generated by transfection with empty vector (pCAGGs). To confirm these findings and demonstrate an expanded utility of the henipavirus envelope glycoprotein pseudotyping systems, NiV and HeV F and G glycoprotein bearing lentivirus particles were prepared with the GFP reporter gene encoding construct pNL4-3-GFP-E-R + and used to infect receptor positive 293T cells ( Figure 2 ). cache = ./cache/cord-300837-d0a8y5qh.txt txt = ./txt/cord-300837-d0a8y5qh.txt === reduce.pl bib === id = cord-301064-ex6qb6zj author = Elena, Santiago F. title = Editorial: A home for virology, ecology, epidemiology, and evolutionary biology date = 2015-03-26 pages = extension = .txt mime = text/plain words = 1316 sentences = 66 flesch = 42 summary = Although genetic diversity is an essential part of virus biology, classical approaches to virus control often ignore evolutionary processes and focus on understanding in great detail the molecular bases of pathogenesis, virus-host interaction, and drug-virus interference. Although many studies appear in evolutionary biology journals, particularly those on viral experimental evolution, mathematical modeling, molecular evolution, and phylogenetics, a large proportion are submitted to journals that focus on virology and pathogenesis. We have established the journal Virus Evolution with this aim in mind, and we hope that it will grow into a successful and dynamic inter-disciplinary community of researchers interested in understanding why and how viruses have and continue to evolve. The Board has expertise in animal, plant, and bacterial viruses and in a wide range of techniques, including experimental evolutionary biology, molecular epidemiology, metagenomics, structural biology, population genetics, ecology, and molecular virology. cache = ./cache/cord-301064-ex6qb6zj.txt txt = ./txt/cord-301064-ex6qb6zj.txt === reduce.pl bib === id = cord-298489-uqrzzh0e author = Bale, James F. title = Emerging Viral Infections date = 2012-08-11 pages = extension = .txt mime = text/plain words = 3861 sentences = 219 flesch = 42 summary = The viruses and disorders discussed herein include West Nile virus, an arboviral infection that swept across the United States in the early years of the 21st century; Nipah encephalitis, a paramyxovirus-induced disorder endemic to India, Bangladesh, and South Asia; chikungunya, a mosquito-borne viral disorder that affects persons in Africa, India, and Southeast Asia; dengue virus, an arthropod-borne Flavivirus that infects more than 100 million persons annually; and parechovirus, a picornavirus that can cause severe disease in neonates and permanent neurodevelopmental disability in surviving infants. 6 Infection control measures, including the slaughter and disposal of Ͼ1 million pigs, contained the disease; during this outbreak, human-to-human transmission of Nipah virus was not observed. The virus, first associated with human disease in Tanzania in the early 1950s, reemerged in 2005-2006 when Ͼ200,000 persons living in the Reunion Islands contracted chikungunya disease 29 ; nearly 1000 deaths among children and adults were reported. cache = ./cache/cord-298489-uqrzzh0e.txt txt = ./txt/cord-298489-uqrzzh0e.txt === reduce.pl bib === id = cord-298733-jole21wq author = Tyrrell, D.A.J. title = A view from the common cold unit date = 1992-06-30 pages = extension = .txt mime = text/plain words = 9565 sentences = 394 flesch = 50 summary = Furthermore, the old empirical idea of the existence of 'the common cold virus' was soon replaced by data collected by epidemiologically controlled field studies in which infection was detected with a range of viruses following which their pathogenicity was confirmed and studied by inoculating them into volunteers and observing their effects. Thus, after years of frustration the work of the Unit developed to the point where relevant human infections could be produced at will and precisely documented by clinical and laboratory methods -this was the ideal setting for preliminary trials of the efficacy of antiviral drugs or vaccines without which nowadays it would rarely be justifiable to go on to a field study of naturally acquired colds. When natural and recombinant interferons were tested in this way against experimental influenza and rhinovirus infections in volunteers, they were no longer effective, possibly because by then the subject was already producing substantial amounts. cache = ./cache/cord-298733-jole21wq.txt txt = ./txt/cord-298733-jole21wq.txt === reduce.pl bib === id = cord-300133-yc2wxgid author = Martínez, Miguel J. title = Ebola Virus Infection: Overview and Update on Prevention and Treatment date = 2015-09-12 pages = extension = .txt mime = text/plain words = 4302 sentences = 243 flesch = 50 summary = In 2014 and 2015, the largest Ebola virus disease (EVD) outbreak in history affected large populations across West Africa. Relevant information was identified through a comprehensive literature search using Medline, PubMed and CINAHL Complete and using the search terms Ebola, Ebola virus disease, Ebola hemorrhagic fever, West Africa outbreak, Ebola transmission, Ebola symptoms and signs, Ebola diagnosis, Ebola treatment, vaccines for Ebola and clinical trials on Ebola. Over the past 17 months, the West Africa EVD outbreak has provided an important opportunity to consider use of and evaluate several therapeutic and prophylactic agents (e.g., vaccines) to determine their safety and efficacy [5, 6] . FGI-103, FGI-104, and FGI-106 are a group of broad-spectrum antiviral agents that inhibit viral replication in a dose-dependent manner among multiple and genetically distinct viruses including EBOV, bunyaviruses, dengue virus, Use of convalescent whole blood or plasma collected from patients recovered from Ebola virus disease for transfusion, as an emprical treatment during outbreaks cache = ./cache/cord-300133-yc2wxgid.txt txt = ./txt/cord-300133-yc2wxgid.txt === reduce.pl bib === id = cord-297790-tpjxt0w5 author = Mandl, Judith N. title = Going to Bat(s) for Studies of Disease Tolerance date = 2018-09-20 pages = extension = .txt mime = text/plain words = 9486 sentences = 393 flesch = 40 summary = Among them are filoviruses (e.g., Marburg, Ebola), coronaviruses (e.g., SARS, MERS), henipaviruses (e.g., Hendra, Nipah) which share the common features that they are all RNA viruses, and that a dysregulated immune response is an important contributor to the tissue damage and hence pathogenicity that results from infection in humans. It is likely that differences in evolutionary history of pathogen exposure between bats and humans have led to distinct adaptations in anti-viral immune responses and the ability to tolerate certain infections without disease while being susceptible to others. We summarize this work below, but comparisons of observations made across species suggest that although a number of species appear to be capable of avoiding the pathological effects of RNA virus infection, each bat species may have achieved this through distinct pathways, possibly involving changes to both increase pathogen replication control and to mitigate any immunopathology through decreased inflammatory responses and hence increased disease tolerance. cache = ./cache/cord-297790-tpjxt0w5.txt txt = ./txt/cord-297790-tpjxt0w5.txt === reduce.pl bib === id = cord-299207-lw0cv74b author = Upadhyay, Ranjit Kumar title = Modeling the spread of bird flu and predicting outbreak diversity date = 2007-05-08 pages = extension = .txt mime = text/plain words = 4388 sentences = 252 flesch = 58 summary = We have designed a statistical transmission model of bird flu taking into account the factors that affect the epidemic transmission such as source of infection, social and natural factors and various control measures are suggested. Among these researches, an important approach to study bird flu is to establish a statistical transmission model, from which the general trends of epidemics can be predicted, and the effect of various control measures can be assessed [13] . We know the major factors that play an important role in the transmission of bird flu are the way the infected poultry products are transported, air temperature, the control measures (for example, culling the poultry in the infected form, introducing compulsory vaccination to enhance the resistibility of poultry in the non-infected farms forbidding live birds being sold under crowded and unsanitary conditions, etc.), migratory birds and other infected transportation vehicles (which means the vehicles carry infected poultry or bird dropping or contaminated soil, etc.). cache = ./cache/cord-299207-lw0cv74b.txt txt = ./txt/cord-299207-lw0cv74b.txt === reduce.pl bib === id = cord-300810-a1skdp67 author = Lafay, F. title = Spread of the CVS strain of rabies virus and of the avirulent mutant AvO1 along the olfactory pathways of the mouse after intranasal inoculation date = 1991-07-31 pages = extension = .txt mime = text/plain words = 5731 sentences = 292 flesch = 54 summary = title: Spread of the CVS strain of rabies virus and of the avirulent mutant AvO1 along the olfactory pathways of the mouse after intranasal inoculation Abstract After intranasal instillation in the mouse, rabies virus (CVS strain) selectively infected olfactory receptor cells. On the other hand, other neuronal cells permissive for CVS, such as mitral cells or the anterior olfactory nucleus, are completely free of infection with the mutant, indicating that restriction is related to the ability of AvO1 to penetrate several categories of neurons. The G protein plays a pivotal role in the pathogenicity of the virus because of its interaction with the host cells ' Abbreviations used: AON, anterior olfactory nucleus; CNS, central nervous system; GABA, Gamma aminobutyric acid; HDB, horizontal limb of the diagonal band; HRP, horseradish peroxidase; HSVl, herpes simplex type 1; IPL, internal plexiform layer: LC, locus coeruleus; LD50, lethal dose 50%; LPA. cache = ./cache/cord-300810-a1skdp67.txt txt = ./txt/cord-300810-a1skdp67.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-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-299786-wuve0tjz author = Anderson, Robert title = Manipulation of cell surface macromolecules by flaviviruses date = 2004-02-27 pages = extension = .txt mime = text/plain words = 13584 sentences = 696 flesch = 41 summary = Dengue virus infection of immature myeloid dendritic cells has been shown to induce their maturation accompanied by the expression of major histocompatibility complex (MHC) class I and II antigens; the costimulatory molecules CD40, CD80, and CD86; and the dendritic cell marker CD83 (Libraty et al., 2001) . Flaviviruses, including dengue and West Nile (Shen et al., 1997) viruses, activate endothelial cell adhesion molecule expression by either direct (virus-mediated) or indirect (cytokine-mediated) mechanisms (see Section V,C). A major candidate event in such a route is the activation of endothelial cell adhesion molecules by a factor(s) (particularly TNF-) produced by dengue virus-infected blood monocytes . Thus the roles of prior immunity, antibody-enhanced virus infection, and immune-mediated pathologic effects on the vascular system are key points in understanding the pathogenesis of dengue hemorrhagic disease. Activation of endothelial cells via antibody-enhanced dengue virus infection of peripheral blood monocytes cache = ./cache/cord-299786-wuve0tjz.txt txt = ./txt/cord-299786-wuve0tjz.txt === reduce.pl bib === id = cord-301285-p83ondy8 author = Kautz, Tiffany F title = Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy date = 2018-03-06 pages = extension = .txt mime = text/plain words = 8836 sentences = 472 flesch = 53 summary = To validate the safety of low-fidelity mutations to increase vaccine attenuation, several mutations in the RNA-dependent RNA-polymerase (RdRp) were tested in the live-attenuated Venezuelan equine encephalitis virus vaccine strain, TC-83. Due to the error-prone nature of the RNA-dependent RNApolymerase (RdRp), RNA virus replication is characterized by a high mutation rate that results in increased genetic diversity of progeny viruses (Domingo et al. When compared with unpassaged, wild-type (wt) viruses, fidelity mutants have similar growth kinetics in vitro, but are attenuated in vivo due to the alteration of diversity produced during replication, which hampers the ability of the virus to overcome bottlenecks in the host (Pfeiffer and Kirkegaard 2005; Vignuzzi et al. The 4x mutant, while exhibiting phenotypic similarities with other altered fidelity mutants, had no significant difference in virus diversity compared with the TC-83 parent after one cell culture passage. cache = ./cache/cord-301285-p83ondy8.txt txt = ./txt/cord-301285-p83ondy8.txt === reduce.pl bib === id = cord-301592-n5ns3m34 author = Ivaska, Lauri title = Aetiology of febrile pharyngitis in children: Potential of myxovirus resistance protein A (MxA) as a biomarker of viral infection date = 2017-01-07 pages = extension = .txt mime = text/plain words = 4142 sentences = 249 flesch = 47 summary = We aimed to document the viral and bacterial aetiology of pharyngitis and to assess the pathogenic role of viruses by determining the myxovirus resistance protein A (MxA) in the blood as a marker of interferon response. We aimed to document the viral and bacterial aetiology of pharyngitis and to assess the pathogenic role of viruses by determining the myxovirus resistance protein A (MxA) in the blood as a marker of interferon response. Methods: In this prospective observational study, throat swabs and blood samples were collected from children (age 1e16 years) presenting to the emergency department with febrile pharyngitis. Methods: In this prospective observational study, throat swabs and blood samples were collected from children (age 1e16 years) presenting to the emergency department with febrile pharyngitis. 23e25 The aim of this study was to document the microbial causes of acute pharyngitis in children and adolescents in an outpatient setting and to evaluate the causative role of viruses by determining myxovirus resistance protein A (MxA) and other biomarker levels. cache = ./cache/cord-301592-n5ns3m34.txt txt = ./txt/cord-301592-n5ns3m34.txt === reduce.pl bib === id = cord-298736-9bvyp21d author = Gerold, Gisa title = Decoding protein networks during virus entry by quantitative proteomics date = 2016-06-15 pages = extension = .txt mime = text/plain words = 12159 sentences = 626 flesch = 38 summary = In the past decade mass spectrometry based proteomics methods have reached sensitivities and high throughput compatibilities of genomics methods and now allow the reliable quantitation of proteins in complex samples from limited material. Since then technological developments like antibody based affinity purification (AP), mass spectrometry (MS) of proteins, DNA mediated transformation and molecular cloning led to the discovery of dozens of receptors for human pathogenic viruses (Fig. 1) . While transcriptomics can reveal long-term alterations of the cellular state, virus entry usually occurs within minutes and typically relies on rapid changes of protein conformation, localization, interactions and post-translational modifications (PTM). Of note, high resolution proteomics can not only reveal transient interactions of VAP with enzymes, but also has the potential to identify proteolytic cleavage sites and redox modifications in VAPs. It is conceivable that virus induced protein interactions during entry not only serve to promote the virus uptake pathway, but can also help cloak viruses and lead to immune evasion. cache = ./cache/cord-298736-9bvyp21d.txt txt = ./txt/cord-298736-9bvyp21d.txt === reduce.pl bib === id = cord-298678-hjxph9jm author = Petrović, T. title = Viral Contamination of Food date = 2016-02-05 pages = extension = .txt mime = text/plain words = 10126 sentences = 479 flesch = 52 summary = Results of surveys on the presence of viruses in different kind of foods commodities (fresh produces and shellfish) and in some cases connections to caused outbreaks are presented. Human Norovirus followed by hepatitis A virus are the most common foodborne viruses, which are transmitted by food consumed raw, such as shellfish, fresh vegetables, and berry fruit. These viruses have been identified in a variety of environmental samples, including wastewater, sludge, in marine, surface, and drinking waters, and shellfish, but no foodborne or waterborne outbreaks associated with the enteric HAdV have been reported (Greening, 2006) . The presented data suggest a high prevalence of different human enteric viruses, but mostly NoV, HAV, EV, HAdV, and HRV were found in shellfish samples collected from growing areas, as well as from the market in different countries. cache = ./cache/cord-298678-hjxph9jm.txt txt = ./txt/cord-298678-hjxph9jm.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-302716-wfla3l20 author = Popov, Vsevolod L. title = Electron Microscopy in Discovery of Novel and Emerging Viruses from the Collection of the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA) date = 2019-05-25 pages = extension = .txt mime = text/plain words = 5445 sentences = 318 flesch = 45 summary = Viruses can be differentiated by their specific morphology (ultrastructure): shape, size, intracellular location, or from the ultrastructural cytopathic effects and specific structures forming in the host cell Upolu, Aransas Bay [22] , Sinu [23] , and Trinity [24] orthobunyaviruses [25] [26] [27] , nyamiviruses [28] , a new reovirus from Cameroon (Fako virus) [29] and Colombia [30] , a new paramyxovirus [31] , an insect-specific (capable of replication in insects but not in vertebrates) alphavirus [32] , a new flavivirus genus [33] and other novel flaviviruses [34] [35] [36] [37] and rhabdoviruses [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] . Insect-specific viruses isolated recently from mosquitoes and phlebotomine sandflies have been characterized and proposed to represent a new genus (Negevirus) related to genera of mite-infecting plant viruses (Blunervirus, Cilevirus, and Higrevirus) in the new family Kitaviridae [49, 73] , or novel members of Entomobirnavirus, family Birnaviridae ( Figure 10D ). cache = ./cache/cord-302716-wfla3l20.txt txt = ./txt/cord-302716-wfla3l20.txt === reduce.pl bib === id = cord-302047-vv5gpldi author = Willemsen, Anouk title = On the stability of sequences inserted into viral genomes date = 2019-11-14 pages = extension = .txt mime = text/plain words = 12557 sentences = 598 flesch = 43 summary = Viruses are widely used as vectors for heterologous gene expression in cultured cells or natural hosts, and therefore a large number of viruses with exogenous sequences inserted into their genomes have been engineered. Viruses genera covered in relevant studies Conclusions of this review All viruses • Inserted sequences are often unstable and rapidly lost upon passaging of an engineered virus • The position at which a sequence is integrated in the genome can be important for stability • Sequence stability is not an intrinsic property of genomes because demographic parameters, such as population size and bottleneck size, can have important effects on sequence stability • The multiplicity of cellular infection affects sequence stability, and can in some cases directly affect whether there is selection for deletion variants • Deletions are not the only class of mutations that can reduce the cost of inserted sequences, although they are the most common I: dsDNA cache = ./cache/cord-302047-vv5gpldi.txt txt = ./txt/cord-302047-vv5gpldi.txt === reduce.pl bib === id = cord-302021-42vqmndl author = Stanley, Mathew title = Synthesis and inhibitory activity of sialic acid derivatives targeted at viral sialate-O-acetylesterases date = 2011-04-08 pages = extension = .txt mime = text/plain words = 3461 sentences = 207 flesch = 55 summary = Besides sialidases, the haemagglutinin-esterases (HE) of influenza C virus, isavirus, betacoronaviruses and toroviruses represent another class of RDEs. They are sialate-O-acetylesterases (SOAE) hydrolysing O-acetyl esters of O-acetylated sialic acid derivatives (Fig. 1) . Alkylation of 7 under Williamson-conditions followed by acid-mediated ketal hydrolysis and basic saponification of the methyl ester gave crude inhibitor 1 which was purified by gel permeation chromatography. Inhibition of the SOAE activity of three viruses, influenza C virus (INF-C), bovine coronavirus (BCoV) and mouse hepatitis virus strain S (MHV-S) and of two chimeric recombinant viral haemagglutinin esterases, from influenza C/Cal/78 virus (HE12-GFP) and sialodacryoadenitis virus (SDAV-HE) was investigated. The crude product was purified by flash chromatography (EA / EA:MeOH; 5:1) to yield the 9-O-methyl ether ( The ether (5 mg, 0.0132 mmol) was dissolved in dioxane (0.5 mL) and NaOH (0.05M, 0.5 mL) was added with stirring. cache = ./cache/cord-302021-42vqmndl.txt txt = ./txt/cord-302021-42vqmndl.txt === reduce.pl bib === id = cord-298745-3rrlap70 author = Field, H. E. title = Henipaviruses: Emerging Paramyxoviruses Associated with Fruit Bats date = 2007 pages = extension = .txt mime = text/plain words = 8409 sentences = 419 flesch = 46 summary = The apparent temporally clustered emergence of Hendra virus and Nipah virus in Australia and Malaysia, respectively, and the identification of species of fruit bats ( Pteropus spp., commonly known as flying foxes) as likely reservoir hosts, poses a number of important questions on the ecology of henipaviruses. Hendra virus was first described in 1994 in Australia when it caused an outbreak of severe acute respiratory disease with high mortality in thoroughbred horses in a training stable in the city of Brisbane (Murray et al. The negative surveillance findings (based on a highly sensitive serum neutralisation test) provided a high level of confidence that Hendra virus was not being sustained by in-contact domestic animal transmission, was not established in the Queensland horse population, and that the outbreak was unlikely to have originated from domestic species. giganteus , Nipah virus infection dynamics in the species, potential modes of transmission to humans, and identification of factors precipitating emergence. cache = ./cache/cord-298745-3rrlap70.txt txt = ./txt/cord-298745-3rrlap70.txt === reduce.pl bib === id = cord-302486-z36hcvrx author = Cobo, Fernando title = Diagnostic approaches for viruses and prions in stem cell banks date = 2006-03-30 pages = extension = .txt mime = text/plain words = 7276 sentences = 347 flesch = 41 summary = Viral and prion contamination of cell cultures and "feeder" cells, which is a common risk in all biotechnological products derived from the cell lines, is the most challenging and potentially serious outcome to address, due to the difficulty involved in virus and prion detection and the potential to cause serious disease in recipients of these cell products. The use of bovine fetal serum in stem cell cultures requires an urgent need for a risk assessment for Transmissible Spongiform Encephalopathies (TSEs) by means of a sensitive and specific test in all products derived from ruminants (U.S. Food and Drugs Administration, 1999; Directive 2004/C 24/ 03). This panel of tests should necessarily include reverse transcriptase detection as a general test for retroviruses, electron microscopy that can detect different kinds of viral particles and characterize many unknown isolates present in cell cultures and molecular techniques like PCR (conventional or real-time) and RT-PCR tests to include all the viruses that we know pose a risk to the product. cache = ./cache/cord-302486-z36hcvrx.txt txt = ./txt/cord-302486-z36hcvrx.txt === reduce.pl bib === id = cord-302055-s155i4e9 author = Mitchell, Edith P. title = Corona Virus: Global Pandemic Causing World-Wide Shutdown date = 2020-04-03 pages = extension = .txt mime = text/plain words = 898 sentences = 70 flesch = 59 summary = Human coronaviruses constitute a large family of viruses that usually cause mild to moderate upper respiratory illnesses in people such as the common cold. 1 Initial characterization of the coronavirus occurred in the 1960's when Tyrell and Bynoe described passage of a virus named B814 at the time, as a group of viruses causing a large proportion of respiratory tract infections in humans. Strategies to prevent infection with the new coronavirus from World Health Organization (WHO) and the Center for Disease Control (CDC) recommend following these precautions for avoiding COVID-19: The Publisher of Journal of the National Medical Association, Elsevier, has compiled an extensive list of publications that may also be useful to physicians and other clinicians and can be found at: Elsevier's Novel Coronavirus Information Center. A previously undescribed coronavirus associated with respiratory disease in humans cache = ./cache/cord-302055-s155i4e9.txt txt = ./txt/cord-302055-s155i4e9.txt === reduce.pl bib === id = cord-302614-siyyve9e author = Shigeta, Shiro title = Anti-RNA virus activity of polyoxometalates date = 2006-05-24 pages = extension = .txt mime = text/plain words = 3511 sentences = 165 flesch = 52 summary = Among these, HS-054 exhibited broad spectrum anti-myxovirus activity and its selectivity indices (SI) for FluV-A, RSV-A, MLSV and PfluV-2 were 333, 31, 167, and 111, respectively, which exceeded those of ribavirin for each virus. We examined anti-FluV A activity with several different ratio combination of PM-523 and ribavirin in vitro and compared this with the individual respective compounds in terms of the effective dose by several parameters of inhibition. We examined seven titanium or vanadium substituted polyoxotungstates (all have Keggin or Keggin All of the compounds exhibited broad spectrum anti-RNA virus activity except that PM-43, PM-518 and PM-523 did not have antiviral activities against PfluV 2, CDV and DFV, respectively. Although, as yet there are no reports of POMs in clinical use, most of the in vitro and some of the in vivo experiments have shown these compounds to be potent and broad spectrum in terms of their antiviral activities against acute respiratory disease viruses. cache = ./cache/cord-302614-siyyve9e.txt txt = ./txt/cord-302614-siyyve9e.txt === reduce.pl bib === id = cord-299549-bjqwwzam author = Zhang, Lei title = Against Ebola: type I interferon guard risk and mesenchymal stromal cell combat sepsis date = 2015-01-01 pages = extension = .txt mime = text/plain words = 3644 sentences = 191 flesch = 47 summary = When the viral infection proceeds to the terminal stage, the key factor would be applying a non-specific immune modulation approach to suppress the cytokine storm that causes multiple organ failure, in an attempt to open a time window for the host's immune system to recover. In most patients, Ebola viral burden elevates by time and triggers an extremely strong immune attack-a phenomenon called 'cytokine storm' (Sullivan et al., 2003) , during which monocytes and/or macrophages produce a massive amount of pro-inflammatory cytokines, including tumor necrosis factor-α (TNF-α) and interleukins (ILs), and The virus burden, inflammatory response, and specific antibodies are the main contributors to different outcomes: mortality, survival, or symptomless infection (Fig. 2) , suggesting that the appropriate intervention strategy in each stage would accordingly be able to control the Ebola virus. Nonetheless, this phenomenon does give clues to the treatment against Ebola virus disease (EVD)-early activated innate immune responses may prevent the viral infection. cache = ./cache/cord-299549-bjqwwzam.txt txt = ./txt/cord-299549-bjqwwzam.txt === reduce.pl bib === id = cord-303297-fiievwy7 author = Oberemok, Volodymyr V. title = SARS-CoV-2 will continue to circulate in the human population: an opinion from the point of view of the virus-host relationship date = 2020-04-30 pages = extension = .txt mime = text/plain words = 4082 sentences = 174 flesch = 49 summary = In this article, we will concentrate on the facts currently available about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has caused COVID-19 (coronavirus disease 2019) pandemic and try to predict its development and consequences based on the virus-host relationship. In addition, it seems that the virus is also more likely to affect the heart than any other similar viruses, so although pneumonia is often the main cause of death, cardiologists and infectionists, for example in Russia, are seeing infected patients whose worst symptoms are not respiratory, but cardiac and many people infected with COVID-19 are dying from heart attacks, as a possible complication of SARS-CoV-2 infection. Despite the initial reports stating that most of the laboratory-confirmed infected patients (27 of 41 cases) had links to the Wuhan seafood market where different animals, including bats, snakes, birds, pangolins, and other small mammals are normally traded within the market [6] , it is now obvious that the newly identified coronavirus SARS-CoV-2 is transmitted with enormous efficacy from human to human via respiratory droplets or close contact. cache = ./cache/cord-303297-fiievwy7.txt txt = ./txt/cord-303297-fiievwy7.txt === reduce.pl bib === id = cord-300522-okbupw61 author = Sansone, Clementina title = Marine Algal Antioxidants as Potential Vectors for Controlling Viral Diseases date = 2020-05-07 pages = extension = .txt mime = text/plain words = 4774 sentences = 248 flesch = 31 summary = Given the ability of various algal molecules—mainly sulfated polysaccharides—to inhibit viral infection at Stage I (adsorption and invasion of cells), we envisage a need to further investigate the antiviral ability of algae, and their mechanisms of action. Oxidative stress-a loss in the balance between the production of free radicals including reactive oxygen species (ROS) and antioxidant cell signaling pathways [2] -can be a key factor of the pathogenesis in many acute or chronical human diseases [3] . For that, we explore the relationship between oxidative stress and viral infections, looking for solutions through the deciphering of cell signaling pathways that can inhibit virus replication and infections, and the mechanisms of action of potential antiviral molecules. Three polysaccharides extracted from marine microalgae, naviculan from the diatom Navicula directa, and two others (named A1 and A2) from the dinoflagellate Cochlodinium polykrikoides also displayed antiviral activities against several enveloped viruses, such as HIV-1, HSV-1 or influenza virus type A (IFV-A) [71] . cache = ./cache/cord-300522-okbupw61.txt txt = ./txt/cord-300522-okbupw61.txt === reduce.pl bib === id = cord-304481-yqc8r3ll author = Luis, Angela D. title = Network analysis of host–virus communities in bats and rodents reveals determinants of cross‐species transmission date = 2015-08-24 pages = extension = .txt mime = text/plain words = 5992 sentences = 307 flesch = 52 summary = Here, we use a network approach to identify ecological and biological correlates of cross‐species virus transmission in bats and rodents, another important host group. We identify multiple communities of viral sharing within bats and rodents and highlight potential species traits that can help guide studies of novel pathogen emergence. Rodents are a suitable group for comparison because they also host many important zoonotic viruses and share many of the characteristics hypothesised to make bats suitable as viral reservoirs. Host traits that correlated with the highest degree within the bat network (the most connections or viruses shared), in order of importance, were gregariousness and sympatry; diet was marginally important (Fig. 2b, Table S6 and S7). For rodents, sympatry was the most important host trait; species whose distributions overlapped with a greater number of other rodent species had more viruses and higher degree and betweenness (Fig. 2d-f and Table S11-S19). cache = ./cache/cord-304481-yqc8r3ll.txt txt = ./txt/cord-304481-yqc8r3ll.txt === reduce.pl bib === id = cord-303186-2hxlx1j2 author = Won, Hokeun title = Generation and protective efficacy of a cold-adapted attenuated genotype 2b porcine epidemic diarrhea virus date = 2019-07-09 pages = extension = .txt mime = text/plain words = 8115 sentences = 320 flesch = 45 summary = In this study, we generated a cold-adapted live attenuated vaccine candidate (Aram-P29-CA) by short-term passage of a virulent PEDV isolate at successively lower temperatures in Vero cells. In this study, we sought to create a cold-adapted attenuated G2b PEDV low-passage strain by progressively decreasing growth temperatures to 32°C in Vero cells and then attempted to evaluate its protective efficacy on neonatal piglets against virulent PEDV challenge. Overall, the quantities of viruses in the feces of animals of group 2 significantly declined compared to those in group 1, with wide Ct ranges of 34.46-24.34 ( Efficacy of cold-adapted attenuated PEDV vaccine All animals in the parental Aram-P5-infected group were necropsied upon death at 4 or 5 DPI, while piglets in the remaining groups were euthanized at the end of the study for postmortem examinations (Fig. 7) . cache = ./cache/cord-303186-2hxlx1j2.txt txt = ./txt/cord-303186-2hxlx1j2.txt === reduce.pl bib === id = cord-304807-j2k1oel2 author = Herrera-Rodriguez, José title = Inactivated or damaged? Comparing the effect of inactivation methods on influenza virions to optimize vaccine production date = 2019-03-14 pages = extension = .txt mime = text/plain words = 5758 sentences = 274 flesch = 43 summary = The properties of the viral formulation, such as successful inactivation, preservation of hemagglutinin (HA) binding ability, fusion capacity and the potential to stimulate a Toll-like receptor 7 (TLR7) reporter cell line were then assessed and compared to the properties of the untreated virus. Hemagglutination and fusion ability were highly affected by those treatments that conferred higher inactivation, with BPL-treated virus binding and fusing at a lower degree compared to FA-inactivated samples. Our aim was to compare the effects of these procedures on the key properties, namely residual infectivity, receptor binding, fusion, and Toll-like receptor 7 (TLR7) mediated activation of innate immune mechanisms, and to determine whether these effects are similar for different virus strains. Previous studies show that BPL is capable of complete inactivation of influenza virus; however, the effectivity might vary depending on the incubation time and temperature. cache = ./cache/cord-304807-j2k1oel2.txt txt = ./txt/cord-304807-j2k1oel2.txt === reduce.pl bib === id = cord-304278-0qy1nngs author = Raj, G. Dhinakar title = Infectious bronchitis virus: immunopathogenesis of infection in the chicken date = 2007-11-12 pages = extension = .txt mime = text/plain words = 12530 sentences = 665 flesch = 45 summary = While infectious bronchitis (IB) is considered primarily a disease of the respiratory system, different IBV strains may show variable tissue tropisms and also affect the oviduct and the kidneys, with serious consequences. Nevertheless, the lack of correlation between antibodies and resistance, discrepancies between in vitro strain differentiation by VN tests and in vivo cross-protection results (Darbyshire, 1985) and re-excretion of virus in the presence of high titres of circulating antibodies (Jones & Ambali, 1987) all suggest that while humoral antibodies play a role in recovery from IBV infection, other immunological mechanisms are involved. Comparison of the susceptibility of chicks of different ages to infection with nephrosis-nephritis causing strain of infectious bronchitis virus Challenge experiments to evaluate cross-protection induced at the trachea and kidney level by vaccine strains and Belgian nephropathogenic isolates of avian infectious bronchitis virus Effects of avian infectious bronchitis virus (Arkansas strain) on vaccinated laying chickens cache = ./cache/cord-304278-0qy1nngs.txt txt = ./txt/cord-304278-0qy1nngs.txt === reduce.pl bib === id = cord-304251-dohglrm1 author = Scully, C title = Emerging and changing viral diseases in the new millennium date = 2015-08-06 pages = extension = .txt mime = text/plain words = 6254 sentences = 322 flesch = 47 summary = Thus recent decades have seen a most dramatic change with the emergence globally also of new viral infections – notably human immunodeficiency viruses (HIV) – and the appearance of some other dangerous and sometimes lethal infections formerly seen mainly in, and reported from, resource‐poor areas especially in parts of Asia, Latin America and Africa. Gradually, however, the unexpected consequences of some oral viral infections have emerged and been recognised, not without some surprise (Scully, 1983) especially the oncogenicity of some herpesviruses (Eglin et al, 1983) and human papillomaviruses (HPVs) which we (Eglin et al, 1983; Maitland et al, 1987; Cox et al, 1993 ) and many others (e.g. Lind et al, 1986) have explored, culminating in the appreciation of unanticipated transmission routes for some cancers, such as sexual (Scully, 2002) . The recent several decades have also seen a most dramatic change with the emergence globally of new viral infectionsnotably human immunodeficiency viruses (HIV)and the appearance also in resource-rich countries, of some other dangerous and sometimes lethal infections hitherto latent, unrecognised or unappreciated in resource-poor areas. cache = ./cache/cord-304251-dohglrm1.txt txt = ./txt/cord-304251-dohglrm1.txt === reduce.pl bib === id = cord-300435-vs0ntcsb author = Katz, Al title = Heteroaggregation of an enveloped bacteriophage with colloidal sediments and effect on virus viability date = 2018-10-01 pages = extension = .txt mime = text/plain words = 5297 sentences = 295 flesch = 46 summary = Four sediments in the colloidal size range: goethite, montmorillonite, illite, and kaolinite, were suspended with the bacteriophage φ6, a model enveloped virus, to determine relative rates of heteroaggregation and the effect of aggregation on virus viability. A study of heteroaggregation of the non-enveloped cowpea mosaic virus with colloidal hematite revealed that at pH 6, at which hematite carries a positive surface charge and the virus a negative charge, the aggregates accumulated four times as many viruses as hematite particles Vilker et al. In this work, we employ turbidity measurements to investigate the heteroaggregation of a model envelope virus, the bacteriophage φ6, with colloidal goethite and three clay minerals: illite, kaolinite and montmorillonite. Although imprecise knowledge of doublet shape complicates calculations of heteroaggregation rates, analysis of the turbidity slope coupled with particle concentrations allows one to determine relative aggregation rates between φ6 and the four sediment types, elucidating the nature of the interaction. cache = ./cache/cord-300435-vs0ntcsb.txt txt = ./txt/cord-300435-vs0ntcsb.txt === reduce.pl bib === id = cord-301362-f3lp10lm author = Delgui, Laura R. title = A Novel Mechanism Underlying the Innate Immune Response Induction upon Viral-Dependent Replication of Host Cell mRNA: A Mistake of +sRNA Viruses' Replicases date = 2017-01-20 pages = extension = .txt mime = text/plain words = 7007 sentences = 343 flesch = 42 summary = Recognition of viral double-strand RNA (dsRNA) molecules by intracellular Toll-like receptors (TLRs) or retinoic acid inducible gene I-like receptors (RLRs) is a central event which entails the early steps of the immune response elicited during viral infections. Despite several differences among host range, viral structure, genome organization or membrane-donor organelles from the cell, these analyses revealed that +sRNA viruses are able to induce two types of membranous modifications as replicative niches: invaginated vesicles or spherules or a double membrane vesicle type. Endogenous RNAs forming secondary double-stranded structures that are released after necrosis and tissue damage after viral infection represent another source of dsRNA molecules reaching the endosomes, inducing host-derived dsRNA-mediated inflammatory responses through TLR-3 recognition (Kawai and Akira, 2010) . Other +sRNA viruses such as the enterovirus Coxsackievirus (Kemball et al., 2010) , Hepatitis C virus (Flaviviridae family) (Sir et al., 2012) , or Coronavirus such as MVH (Reggiori et al., 2010) also usurp the autophagy pathway and induce remarkably alterations in intracellular membranous components to harbor the sites for viral RNA replication. cache = ./cache/cord-301362-f3lp10lm.txt txt = ./txt/cord-301362-f3lp10lm.txt === reduce.pl bib === id = cord-305336-wxiazglk author = Li, Ji Lian title = Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera date = 2014-01-21 pages = extension = .txt mime = text/plain words = 6907 sentences = 319 flesch = 50 summary = In the present study, we showed that a plant-pathogenic RNA virus, tobacco ringspot virus (TRSV), could replicate and produce virions in honeybees, Apis mellifera, resulting in infections that were found throughout the entire body. While intracellular life cycle, species-level genetic variation, and pathogenesis of the virus in honeybee hosts remain to be determined, the increasing prevalence of TRSV in conjunction with other bee viruses from spring toward winter in infected colonies was associated with gradual decline of host populations and winter colony collapse, suggesting the negative impact of the virus on colony survival. Conventional RT-PCR was performed on RNA samples extracted from adult bees, Varroa mites, different tissues, and bee bread collected from the same colony for the presence and distribution of TRSV. cache = ./cache/cord-305336-wxiazglk.txt txt = ./txt/cord-305336-wxiazglk.txt === reduce.pl bib === id = cord-304850-9xetsc2c author = Drosten, Christian title = Virus ecology: a gap between detection and prediction date = 2013-05-22 pages = extension = .txt mime = text/plain words = 1500 sentences = 95 flesch = 51 summary = 7, 8 These and other recent findings remind us of an important issue in viral reservoir ecology: non-persisting viruses are maintained on a social level, requiring large, dense and interconnected host groups for their perpetual transmission. 13 There are prominent examples of bat-borne viruses that can be passed between humans, including Ebola virus, Marburg virus, Nipah virus and the severe acute respiratory syndrome agent. However, there remains a large gap between the many studies describing novel reservoir-borne viruses and our capabilities to use this knowledge to predict or prevent future human disease outbreaks. 13 As we dig deeper into viral reservoir ecology, including its man-made modifications, we may find that changes in host populations affect the transmission and maintenance of viruses with possible consequences for their potential to infect humans (Figure 1 ). Habitat fragmentation Resource abundance Change of social structure Risk Virus replication / transmission Duration of excretion / infectivity Figure 1 Modification of viral maintenance optimum. cache = ./cache/cord-304850-9xetsc2c.txt txt = ./txt/cord-304850-9xetsc2c.txt === reduce.pl bib === id = cord-303533-6s01qplg author = Neuman, Benjamin W. title = Does form meet function in the coronavirus replicative organelle? date = 2014-07-15 pages = extension = .txt mime = text/plain words = 3642 sentences = 177 flesch = 39 summary = This review takes a virus-centric look at the coronavirus replication transcription complex organelle in the context of the wider world of positive sense RNA viruses, examining how the mechanisms of protein expression and function act to produce the factories that power the viral replication cycle. This review takes a virus-centric look at the coronavirus replication transcription complex organelle in the context of the wider world of positive sense RNA viruses, examining how the mechanisms of protein expression and function act to produce the factories that power the viral replication cycle. Whatever their purpose, it is clear that the coronavirus organelle is dynamic [9] , closely tied to vesicular transport in the host cell [5, 10] , and consists mainly of paired membranes that form a variety of complex shapes including convoluted membranes and double-membrane vesicles (DMVs) [2, 11] . Formation of plant RNA virus replication complexes on membranes: role of an endoplasmic reticulum-targeted viral protein cache = ./cache/cord-303533-6s01qplg.txt txt = ./txt/cord-303533-6s01qplg.txt === reduce.pl bib === id = cord-304343-m7tbdfri author = Khandia, Rekha title = A Comprehensive Review of Autophagy and Its Various Roles in Infectious, Non-Infectious, and Lifestyle Diseases: Current Knowledge and Prospects for Disease Prevention, Novel Drug Design, and Therapy date = 2019-07-03 pages = extension = .txt mime = text/plain words = 20281 sentences = 1088 flesch = 32 summary = Similarly, inhibiting the mTOR signaling pathway can prevent apoptosis and even enhance necroptosis, whereas starvation, which induces autophagy, protects cells from zVAD-mediated necroptotic death [194] . For instance, autophagy has been demonstrated to be actively involved in the replication of influenza A virus (IAV), which induces autophagosome formation during the early phase of infection and later inhibits autophagosomal maturation by preventing autophagosomal-lysosomal fusion and promoting autophagosomes to accumulate in virus-infected cells [253] . (5) A novel anti-cancer molecule, HA15, which targets HSPA5/BIP was shown to induce endoplasmic reticulum stress and increase the unfolded protein response, resulting in cancer cell death through autophagy and apoptosis. (5) A novel anti-cancer molecule, HA15, which targets HSPA5/BIP was shown to induce endoplasmic reticulum stress and increase the unfolded protein response, resulting in cancer cell death through autophagy and apoptosis. In addition, the novel anti-cancer molecule HA15, which targets HSPA5/BIP, was shown to induce ER stress and increase the unfolded protein response, resulting in cancer cell death via autophagy and apoptosis [304] . cache = ./cache/cord-304343-m7tbdfri.txt txt = ./txt/cord-304343-m7tbdfri.txt === reduce.pl bib === id = cord-303665-l57e54hu author = Lahrich, S. title = Review on the contamination of wastewater by COVID-19 virus: Impact and treatment date = 2020-09-10 pages = extension = .txt mime = text/plain words = 5849 sentences = 329 flesch = 48 summary = Under these circumstances, the passive, but effective, method of sewage or wastewater monitoring can be used to trace and track the presence of SARS-CoV-2, through their genetic material RNA, and screen entire community. Since wastewater contains viruses that are repelled by everyone, regardless of their health, monitoring for viruses in wastewater and environmental waters that receive effluent from wastewater treatment plants (WWTPs) can determine the true prevalence and molecular epidemiology of gastroenteritis viruses and the risks to human health (Guan et al., 2020; Huang et al., 2020; Wang et al., 2020a) in a given geographical area rather than clinical research (Prevost et al., 2015; Kazama et al., 2017) . Therefore, the safety of drinking water and wastewater depends on the appropriate selection of the disinfectant dose and contact time in the treated environment, which are very important analytical techniques and methods that can detect viruses. Understanding how the virus breaks down in the aquatic environment is also critical to assessing risks to human health at present; the stability of the SARS-CoV-2 genome in wastewater is unclear. cache = ./cache/cord-303665-l57e54hu.txt txt = ./txt/cord-303665-l57e54hu.txt === reduce.pl bib === id = cord-306983-6w2fvtfy author = Wang, Siye title = Influenza Virus—Cytokine-Protease Cycle in the Pathogenesis of Vascular Hyperpermeability in Severe Influenza date = 2010-10-01 pages = extension = .txt mime = text/plain words = 3808 sentences = 223 flesch = 39 summary = Influenza A virus infection resulted in significant increases in TNF-α, IL-6, IL-1β, viral hemagglutininprocessing protease trypsin levels, and viral replication with vascular hyperpermeability in lung and brain in the first 6 days of infection. The present study reports several new observations: (1) proinflammatory cytokines, TNF-a, IL-1b, and IL-6, when upregulated by influenza A virus infection, induce trypsin expression in various organs and human endothelial cells; (2) the upregulated trypsin induces [Ca 2+ ] i mobilization via activation of the PAR-2, followed by loss of zonula occludens-1 and vascular hyperpermeability; (3) inhibitors of NF-kB and activator protein 1 effectively suppress the upregulation of proinflammatory cytokines and trypsin and improve the survival rates of infected mice. The present results allow us to propose a new mechanism of junctional permeability regulation: upregulated trypsin by influenza A virus and/or proinflammatory cytokines induces increase in [Ca 2+ ] i and loss of zonula occludens-1 in endothelial cells via PAR-2 signaling. cache = ./cache/cord-306983-6w2fvtfy.txt txt = ./txt/cord-306983-6w2fvtfy.txt === reduce.pl bib === id = cord-305263-fgwf6wy3 author = Wang, Ben X. title = The yin and yang of viruses and interferons date = 2012-02-07 pages = extension = .txt mime = text/plain words = 6285 sentences = 294 flesch = 38 summary = IFN therapy therefore has the advantage over DAA treatments in that, in addition to stimulating genes that block viral replication in infected cells, IFNs activate other innate and adaptive immune responses to combat the virus. For example, polymorphisms in host genes encoding proteins associated with regulation of an IFN response such as interferon receptor a-chain (IFNAR1) [10] , the IFN-inducible myxovirus resistance GTPase protein, Mx [11] , the IFN-inducible 2 0 ,5 0 -oligoadenylate synthetase (OAS) [12] and the suppressor of cytokine signaling (SOCS) 3 associated with regulation of an IFN response [13] , are predictive markers linked with the rate of sustained virological response (SVR) to HCV infection following IFN-a treatment. Remarkably, distinct highly pathogenic respiratory viruses, namely influenza viruses and the SARS-CoV, encode nonstructural proteins in their genomes that function as virulence factors that specifically target the host innate IFN response, further emphasizing the importance of IFNs as broad-spectrum antivirals. cache = ./cache/cord-305263-fgwf6wy3.txt txt = ./txt/cord-305263-fgwf6wy3.txt === reduce.pl bib === id = cord-304498-ty41xob0 author = Denison, Mark R title = Coronaviruses: An RNA proofreading machine regulates replication fidelity and diversity date = 2011-03-01 pages = extension = .txt mime = text/plain words = 7332 sentences = 345 flesch = 38 summary = Genetic inactivation of exoN activity in engineered SArS-Cov and MHv genomes by alanine substitution at conserved De-D-D active site residues results in viable mutants that demonstrate 15-to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other rNA viruses. Genetic inactivation of exoN activity in engineered SArS-Cov and MHv genomes by alanine substitution at conserved De-D-D active site residues results in viable mutants that demonstrate 15-to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other rNA viruses. The high mutation rates of RNA viruses also render them particularly susceptible to repeated genetic bottleneck events during replication, transmission between hosts or spread within a host, resulting in progressive deviation from the consensus sequence associated with decreased viral fitness and sometimes extinction. cache = ./cache/cord-304498-ty41xob0.txt txt = ./txt/cord-304498-ty41xob0.txt === reduce.pl bib === id = cord-307893-mvl0wrsj author = Goulter-Thorsen, R.M. title = Disciplines Associated with Food Safety: Food Virology date = 2014-01-13 pages = extension = .txt mime = text/plain words = 4993 sentences = 249 flesch = 46 summary = Poliovirus was the first enteric virus to be widely recognized, causing foodborne disease outbreaks in the early 1900s associated with the consumption of contaminated raw milk. This method, as well as cultivation methods for the vaccine strain of poliovirus, eventually allowed for the quantification of infective virus plaque forming units and facilitated studies on detection and control of enteric viruses in water and foods, with a particular focus on molluscan shellfish. Although promising, the utility of these molecular amplification methods for virus detection in food and environmental samples was limited by low levels of contamination; high levels of matrix-associated inhibitory substances that interfered with nucleic acid amplification; and the lack of broadly reactive primers and probes for HuNoV. Recent epidemiological data continue to support the fact that viruses, particularly HuNoV, are the most common cause of foodborne disease of known etiology in USA. HEV is a positive-sense single-stranded RNA virus that is transmitted via the fecal-oral route, generally through the consumption of water and sometimes food that has become contaminated with human feces. cache = ./cache/cord-307893-mvl0wrsj.txt txt = ./txt/cord-307893-mvl0wrsj.txt === reduce.pl bib === id = cord-306733-df36w6l7 author = Rosales-Mendoza, Sergio title = What Does Plant-Based Vaccine Technology Offer to the Fight against COVID-19? date = 2020-04-14 pages = extension = .txt mime = text/plain words = 8591 sentences = 420 flesch = 39 summary = Transient nuclear genome transformation Rapid production; high productivity; implemented at the industrial level Seed bank cannot be generated; requires purification of the antigen to eliminate toxic compounds from the host and ag-robacteria residues S protein; multiepitope vaccines A chimeric protein of GFP and amino acids 1-658 of the SARS-CoV-1 S protein (S1:GFP) was transiently expressed in tobacco leaves and stably transformed in tobacco and lettuce. No immunization assays were performed The SARS-CoV-1 N protein was transiently expressed in Nicotiana benthamiana, which induced in mice high levels of IgG1 and IgG2a and up regulation of IFN-γ and IL-10 in splenocytes. The precedents of SARS-CoV-1 and MERS antigens expressed in recombinant systems leading to the formation of VLPs constitute important guides for the topic of COVID-19 vaccine development. Thus, VLPs based on the main SARS-CoV-2 structural proteins is an attractive approach for vaccine development against coronavirus infections. cache = ./cache/cord-306733-df36w6l7.txt txt = ./txt/cord-306733-df36w6l7.txt === reduce.pl bib === id = cord-308385-bcph664h author = Yan, Zishuo title = Modeling COVID-19 infection in a confined space date = 2020-07-15 pages = extension = .txt mime = text/plain words = 3529 sentences = 182 flesch = 57 summary = In our model, states of individuals with diverse physiological conditions are subject to dynamic changes according to their interaction with viruses in a closed environment, where spatial factors play an essential role in that the spreading of the virus and the infection of human are tightly correlated in both space and time. Based on the SEIR model, Joseph T Wu [7] estimated the basic regeneration number as 2.68 and the doubling time as 6.4 days; Qun Li [18] analyzed data on the first 425 confirmed cases in the early stage and found that the epidemic is doubled in size every 7.4 days with a mean serial interval of 7.5 days. Through the newly constructed virus infection model, we provide useful guidance for effective prevention and control of the COVID-19 spreading, such as restricting the movement of people and placing the ventilation opening in the right position, reducing the releasing of the virus and the contact of susceptibles with unfriendly environment. cache = ./cache/cord-308385-bcph664h.txt txt = ./txt/cord-308385-bcph664h.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-305302-go87uu06 author = Gessain, Antoine title = Editorial overview: Emerging viruses: interspecies transmission date = 2015-02-28 pages = extension = .txt mime = text/plain words = 2482 sentences = 112 flesch = 45 summary = Furthermore, some of these diseases, associated with emerging viruses, had recent major public health impact, as exemplified in humans by the AIDS [1] , hepatitis C pandemics [2] , or the current Ebola disease epidemic, or in crops by cassava mosaic disease, which seriously compromises food security in East Africa [3] . The emergence of a new viral associated disease or of a new virus is indeed the result of a sequence of successive steps, sometimes complex, and is often related to the entanglement of several factors: socioeconomic or particular cultural activities, increased mobility of human, animal and plant mobility ('the world is a global village'), human exploitation of the environment as deforestation or increase of agricultural or otherwise human managed land, resulting in loss of biodiversity or ecosystem simplification, disruption of human, animal and plant health systems in armed conflict, urbanization with development of huge slums of great poverty and basic hygiene, decreased interest in the surveillance and control of infectious diseases, use of unsterile medical equipment as part of therapeutic and/or mass vaccination and, finally, the ability of certain viruses to adapt quickly to a changing environment. cache = ./cache/cord-305302-go87uu06.txt txt = ./txt/cord-305302-go87uu06.txt === reduce.pl bib === id = cord-304747-ojyxs3cp author = Gaynor, Anne M title = Identification of a Novel Polyomavirus from Patients with Acute Respiratory Tract Infections date = 2007-05-04 pages = extension = .txt mime = text/plain words = 6665 sentences = 328 flesch = 51 summary = Screening of 2,135 patients with acute respiratory tract infections in Brisbane, Queensland, Australia, and St. Louis, Missouri, United States, using WU virus–specific PCR primers resulted in the detection of 43 additional specimens that contained WU virus. The virus was detected in the respiratory secretions from an additional 43 patients in two continents, and the complete genomes of multiple isolates were sequenced. In the early region, an unspliced open reading frame of 194 amino acids was detected that possibly encodes for the STAg. As the paradigm in other polyomaviruses is that STAg is expressed from a spliced message, analysis of potential splice sites revealed the presence of a putative splice donor sequence just one nucleotide 59 of the initially predicted The initial screen used primers targeting the VP2 region, which possessed less than 20% amino acid homology to JC and BK virus to minimize the possibility of cross reactivity with the known human polyomaviruses. cache = ./cache/cord-304747-ojyxs3cp.txt txt = ./txt/cord-304747-ojyxs3cp.txt === reduce.pl bib === id = cord-305807-n3fs7533 author = Ferreira, T B title = Use of adenoviral vectors as veterinary vaccines date = 2005-10-18 pages = extension = .txt mime = text/plain words = 8466 sentences = 437 flesch = 40 summary = 11 Then recognition that purified replication-defective Ads could be propagated on 293 cells without helper viruses paved the way toward intentional production of genetically modified Ads. 12 The popularity of Ad as a recombinant viral vector is largely due to the successful and safe immunization of millions of US military recruits in 1971 with enterically coated Ad4 and Ad7 as a prevention against acute respiratory disease (ARD) outbreaks. Gonin et al, 37 10 years ago, constructed a replicationdefective HAd5, containing the envelope protein ENV gene of FIV; however, despite the fact that an antibody response to pseudorabies virus in cats showed the potential of rHAd5 vectors to be used in this species, cats injected with 10 10.8 -10 11.8 of 50% tissue culture infectious dose (TCID 50 ) adjuvanted with montanide ISA 708 (water in nonmineral oil) or with montanide ISA 206 (double water/mineral oil/water) of this rAd did not develop detectable antibody response against ENV. cache = ./cache/cord-305807-n3fs7533.txt txt = ./txt/cord-305807-n3fs7533.txt === reduce.pl bib === id = cord-307817-2vy28i4m author = Lou, Zhiyong title = Current progress in antiviral strategies date = 2014-01-14 pages = extension = .txt mime = text/plain words = 7555 sentences = 343 flesch = 36 summary = The prevalence of chronic viral infectious diseases, such as human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus; the emergence and re-emergence of new viral infections, such as picornaviruses and coronaviruses; and, particularly, resistance to currently used antiviral drugs have led to increased demand for new antiviral strategies and reagents. Based on the complex structure of the PA C-terminal domain (PA C ) and the first 25 amino acids of PB1 [99] , a subset of modifications on N-terminal peptide of PB1 was shown to diminish the binding affinity of PA and PB1, inhibit polymerase activity, and attenuate the replication of influenza virus [100] [101] [102] . Because both the polymerase complex and NP show significant conservation between different influenza viruses, these results demonstrated that targeting the formation of viral RNP is a valid approach to the development of small molecule therapies against serious antiviral resistance to currently available drugs, such as adamantanes or neuraminidase inhibitors. cache = ./cache/cord-307817-2vy28i4m.txt txt = ./txt/cord-307817-2vy28i4m.txt === reduce.pl bib === id = cord-302529-43pd2qsp author = El Moussi, Awatef title = Virological Surveillance of Influenza Viruses during the 2008–09, 2009–10 and 2010–11 Seasons in Tunisia date = 2013-09-19 pages = extension = .txt mime = text/plain words = 3251 sentences = 163 flesch = 45 summary = METHOD: We describe in this report the findings of laboratory-based surveillance of human cases of influenza virus and other respiratory viruses' infection during three seasons in Tunisia. A subset of sentinel primary care physicians participating in virological surveillance schemes in the community submits respiratory samples for virological testing from patients presenting in primary health care with an ILI, as well as all regional emergency centres and hospitals that take on surveillance of influenza from community, hospitalized and fatal cases. Phylogenetic analysis of the HA1 nucleotid sequence of 23 influenza A(H1N1)pdm09 viruses from mild, severe (patients hospitalized with severe pneumonia and severe acute respiratory syndrome) and fatal cases, shows that all viruses characterised in Tunisia during season 2009-2010 were outside the seven genetic groups described in the European Centre for Disease Prevention and Control (ECDC) report [19] . cache = ./cache/cord-302529-43pd2qsp.txt txt = ./txt/cord-302529-43pd2qsp.txt === reduce.pl bib === id = cord-305165-3twlnkac author = Bourgueil, E. title = Experimental infection of pigs with the porcine respiratory coronavirus (PRCV): measure of viral excretion date = 1992-04-30 pages = extension = .txt mime = text/plain words = 2331 sentences = 150 flesch = 55 summary = title: Experimental infection of pigs with the porcine respiratory coronavirus (PRCV): measure of viral excretion Common causes of the disease includes pseudorabies virus (PRV), influenza viruses and the porcine respiratory coronavirus (PRCV), the latter being first detected in different European countries in 1983-1984 (Brown et al., 1986; Duret et al., 1988; Pensaert et al., 1986) . Until now, great attention has been given to clinical disorders induced by PRCV in the field (Jestin et al., 1987; Brown and Cartwright, 1986) and under experimental conditions (Vannier, 1990; Pensaert et al., 1986; O'Toole et al., 1989) , but nothing is known about excretion and airborne transmission of the virus. A high correlation rate (r= 0.83 ) was found between viral titres obtained from air samples collected with that medium and the amount of virus in nasal swabs (see tables 1 and cache = ./cache/cord-305165-3twlnkac.txt txt = ./txt/cord-305165-3twlnkac.txt === reduce.pl bib === id = cord-305742-wf6qxplf author = Gomez, Santiago A. title = Binding of SARS–CoV–2 to cell receptors: a tale of molecular evolution date = 2020-09-28 pages = extension = .txt mime = text/plain words = 3457 sentences = 176 flesch = 53 summary = In addition to the formal quantum characterization of bonding interactions, computation of absorption spectra for the specific virus· · · cell interacting residues yields significant shifts of ∆λ max = 47 and 66 nm in the wavelength for maximum absorption in the complex with respect to the isolated host and virus, respectively. In this work, we are interested in two crucial aspects of the initial virus· · · cell interaction problem: to pinpoint the specific residue to residue binding sites between the structurally known spike proteins of the virus [6] and the structurally known ACE2 receptor in cell membranes, [5] and to understand, from a fundamental, quantum perspective, the molecular factors driving the virus· · · cell binding. Therefore, we characterize the virus· · · cell binding as due to a large number of non-covalent contacts between the two proteins, enhanced by the water molecules, acting in conjunction with the specific residue to residue hydrogen bonds. cache = ./cache/cord-305742-wf6qxplf.txt txt = ./txt/cord-305742-wf6qxplf.txt === reduce.pl bib === id = cord-307744-wbr84taq author = Jayadevan, Rajeev title = Does a younger host make the virus weaker? Presenting a new hypothesis date = 2020-09-13 pages = extension = .txt mime = text/plain words = 573 sentences = 46 flesch = 69 summary = RESULTS: Virus become more virulent as it passes through weaker hosts and vice versa. CONCLUSIONS: Viruses become more virulent when it passes through weaker and older hosts. While compiling the data about doctors' deaths in India during the COVID-19 pandemic, the case of a 50-year-old doctor who contracted the infection while taking care of his mother at home was observed. Did the son get a more virulent selection of virus after it passed through his mother, who was an older and weaker host? Coxsackie virus CVB3 is known to become more virulent as it passes through weaker and older mice hosts [4] . In the study of 108 COVID-related deaths among doctors in India, nearly half were general practitioners, who saw older patients [5]. It will be worth analysing the transmission chain of COVID-19 from this perspective, specifically to see if the age and frailty of the donor of the virus made a difference in the outcome in the host. cache = ./cache/cord-307744-wbr84taq.txt txt = ./txt/cord-307744-wbr84taq.txt === reduce.pl bib === id = cord-309048-emmtplv3 author = Lomonossoff, George P. title = TMV Particles: The Journey From Fundamental Studies to Bionanotechnology Applications date = 2018-07-26 pages = extension = .txt mime = text/plain words = 9017 sentences = 407 flesch = 46 summary = (1999) displayed peptides of either 10 or 15 amino acids from the spike protein of the coronavirus murine hepatitis virus on the surface of assembled particles. coli-produced protein with a minimum of 20% of plant-made TMV CP, an approach that enabled efficient RNA-guided assembly of TMV-CP His6 into particles of the expected length (Eiben et al., 2014) . Assembly of the particle of tobacco mosaic virus from RNA and disks of protein β-Structure of the coat protein subunits in spherical particles generated by tobacco mosaic virus thermal denaturation Expression of tobacco mosaic virus coat protein and assembly of pseudovirus particles in Escherichia coli In vitro assembly of tobacco mosaic virus coat protein variants derived from fission yeast expression clones or plants Modified tobacco mosaic virus particles as scaffolds for display of protein antigens for vaccine applications Display of peptides on the surface of tobacco mosaic virus particles Assembly of hybrid RNAs with tobacco mosaic virus coat protein. cache = ./cache/cord-309048-emmtplv3.txt txt = ./txt/cord-309048-emmtplv3.txt === reduce.pl bib === id = cord-304424-048xo7jn author = Greninger, Alexander L. title = A decade of RNA virus metagenomics is (not) enough date = 2018-01-15 pages = extension = .txt mime = text/plain words = 9606 sentences = 495 flesch = 43 summary = That same year 36,789 colony sequences from DNase-treated RNA extracted from viral concentrates of human feces revealed a preponderance of pepper mild mottle virus and other plant viruses, but no new human viruses (Zhang et al., 2005) . While finding a new virus in the environment is not necessarily a problem in either DNA or RNA, the low fidelity of RNA polymerases and the sequence space they are capable of sampling, along with the possibility of recombination, lend themselves to new species and genera that are the trophies of metagenomic viral discovery. While metagenomics delivered on the promise of finding novel human viruses, viral discovery in humans has increasingly become a tragic story of patients interacting with the wrong squirrel or tick on the wrong day and most samples sequenced are frankly negative (Hoffmann et al., 2015; McMullan et al., 2012) . The greatest paradigm shifter in recent viral metagenomics work has been the sheer number and diversity of novel RNA viruses present in arthropods and invertebrates. cache = ./cache/cord-304424-048xo7jn.txt txt = ./txt/cord-304424-048xo7jn.txt === reduce.pl bib === id = cord-305488-vk59ghjm author = Choi, Kang-Seuk title = Newcastle disease virus vectored vaccines as bivalent or antigen delivery vaccines date = 2017-07-26 pages = extension = .txt mime = text/plain words = 4841 sentences = 237 flesch = 45 summary = They also induced a marked and efficient cellular and protective immune response in mice after challenge with vaccinia viruses expressing HIV-1 Env and Gag. These results suggest that vaccination with a single NDV vector coexpressing Env and Gag is a promising strategy that increases vaccine immunogenicity and subsequent protective efficacy against HIV. Immunization of cattle with recombinant Newcastle disease virus expressing bovine herpesvirus-1 (BHV-1) glycoprotein D induces mucosal and serum antibody responses and provides partial protection against BHV-1 Immunization of primates with a Newcastle disease virus-vectored vaccine via the respiratory tract induces a high titer of serum neutralizing antibodies against highly pathogenic avian influenza virus Newcastle disease virus-based live attenuated vaccine completely protects chickens and mice from lethal challenge of homologous and heterologous H5N1 avian influenza viruses Immunization of chickens with Newcastle disease virus expressing H5 hemagglutinin protects against highly pathogenic H5N1 avian influenza viruses cache = ./cache/cord-305488-vk59ghjm.txt txt = ./txt/cord-305488-vk59ghjm.txt === reduce.pl bib === id = cord-304569-o39kl5k4 author = Nguyen-Van-Tam, Jonathan S title = From the Editor's desk date = 2015-04-23 pages = extension = .txt mime = text/plain words = 1210 sentences = 66 flesch = 50 summary = If one shifts the focus away from influenza, the ongoing MERS-CoV outbreak in the Middle East, is also of substantial concern, because despite its likely introduction into humans via close contact with dromedary camels, 9 nosocomial transmission appears to be a central concern, 10,11 case-fatality is high, household transmission is also described, 12 and there are currently no vaccines or specific therapies available. Papers considered for rapid peer-review will need to be of immediate relevance, interest, or importance to scientists, clinicians, public health practitioners or policy makers, usually in relation to a current or evolving event related to respiratory virus activity. Accepted Articles are published online a few days after final acceptance, appear in PDF format only, are given a Digital Object Identifier (DOI), which allows them to be cited and tracked, and are indexed by PubMed. Effectiveness of neuraminidase inhibitors in reducing mortality in patients admitted to hospital with influenza A H1N1pdm09 virus infection: a meta-analysis of individual participant data cache = ./cache/cord-304569-o39kl5k4.txt txt = ./txt/cord-304569-o39kl5k4.txt === reduce.pl bib === id = cord-309489-ubf55eux author = Carvalho, John J. title = OUR COMMON ENEMY: COMBATTING THE WORLD'S DEADLIEST VIRUSES TO ENSURE EQUITY HEALTH CARE IN DEVELOPING NATIONS date = 2009-02-19 pages = extension = .txt mime = text/plain words = 5291 sentences = 231 flesch = 44 summary = Of the emerging viruses, five have particular importance for what scientists and world leaders can learn concerning their impact on geopolitical stability, human rights, and equity health care for the underprivileged in both developed and developing nations. For example, in Latin America, population growth and uncontrolled migration from the countryside to the cities have resulted in poor housing conditions, inappropriate disposal of waste, and lack of adequate food, clean water and health care-all of which are concurrent with an increase in infected mosquitoes carrying different versions of dengue virus (Torres and Castro 2007) . Continuing with these themes, it is clear that the geographical expansion of three viruses (HIV, dengue, and rotavirus), the increase in frequency of the infectious diseases they cause, and the relationship between these viruses and geopolitical stability, human rights, and equity health care for developing nations are problems of great concern promoted not only by biological and technological factors but also by social, religious, and cultural ones. cache = ./cache/cord-309489-ubf55eux.txt txt = ./txt/cord-309489-ubf55eux.txt === reduce.pl bib === id = cord-307046-ko3bdvo0 author = Vasilakis, Nikos title = Exploiting the Legacy of the Arbovirus Hunters date = 2019-05-23 pages = extension = .txt mime = text/plain words = 17749 sentences = 879 flesch = 44 summary = Complete genome sequences are now available for many of the archived isolates, allowing more accurate taxonomic assignments, analysis of their phylogenetic and evolutionary relationships with other viruses, and evaluation of the potential risks they may present to humans and wild or domestic animal populations. Scientists in these field laboratories were involved in the detection and investigation of human diseases in their respective geographic regions, surveying human and animal populations for serologic evidence of past viral infection, and searching for viruses in a wide variety of arthropods, mammals, birds, reptiles, and amphibians [2] . The family contains several serious human pathogens, including dengue, yellow fever, Zika, Japanese encephalitis, West Nile, and tick-borne encephalitis viruses (all arboviruses in the genus Flavivirus) and the hepatitis C virus (a member of the genus Hepacivirus). cache = ./cache/cord-307046-ko3bdvo0.txt txt = ./txt/cord-307046-ko3bdvo0.txt === reduce.pl bib === id = cord-309346-4mdxe6ri author = López-Medrano, Francisco title = Virus respiratorios: los más frecuentes, los más olvidados date = 2008-02-29 pages = extension = .txt mime = text/plain words = 1440 sentences = 149 flesch = 53 summary = Los estudios de descripción epidemiológica, como el de Reina et al 10 son el primer paso para el desarrollo de nuevas posibilidades terapéuticas (antivirales) y profilácticas (vacunas) frente a metapneumovirus y VRS, que a buen seguro tendrían una importante repercusión sobre el control de la patología respiratoria de la población pediátrica. También en este número de ENFERMEDADES INFECCIOSAS Y MICROBIOLOGÍA CLÍNICA se publica un artículo de Perelló et al 12 sobre la implicación de los virus respiratorios en la neumonía adquirida en la comunidad (NAC) en sujetos infectados por el virus de la inmunodeficiencia humana (VIH). Sin embargo, es importante recordar que las infecciones por virus respiratorios pueden complicarse con infección de vías respiratorias bajas y neumonía en sujetos inmunodeprimidos, con una morbimortalidad no despreciable, como se ha demostrado recientemente en cohortes de pacientes con enfermedades hematológicas 5,6 y en portadores de trasplante de órgano sólido 7 . cache = ./cache/cord-309346-4mdxe6ri.txt txt = ./txt/cord-309346-4mdxe6ri.txt === reduce.pl bib === id = cord-307813-elom30nx author = Yip, Tsz-Fung title = Advancements in Host-Based Interventions for Influenza Treatment date = 2018-07-10 pages = extension = .txt mime = text/plain words = 15075 sentences = 735 flesch = 38 summary = Besides controlling virus replication, potential targets for drug development include controlling virus-induced host immune responses such as the recently suggested involvement of innate lymphoid cells and NADPH oxidases in influenza virus pathogenesis and immune cell metabolism. Besides controlling virus replication, potential targets for drug development include controlling virus-induced host immune responses such as the recently suggested involvement of innate lymphoid cells and NADPH oxidases in influenza virus pathogenesis and immune cell metabolism. A recent study using RNAi also demonstrated that cholesterol homeostasis can be regulated via acid phosphatase 2 (ACP2)-mediated Niemann-Pick C2 activity and impaired the membrane fusion of IAV and influenza B virus (IBV) (52) , further suggesting the importance of controlling cholesterol homeostasis in the release of viral genome to cytoplasm. Furthermore, FPR2 antagonists have been described to possess antiviral activity against not only IAV but also IBV infection (111) , promoting the idea that antagonizing FPR2 to suppress Raf/MEK/ERK signaling cascade could potentially be a novel approach for the treatment of a broad spectrum of influenza viruses. cache = ./cache/cord-307813-elom30nx.txt txt = ./txt/cord-307813-elom30nx.txt === reduce.pl bib === id = cord-309179-5hlatbqe author = Bosch, Albert title = New tools for the study and direct surveillance of viral pathogens in water date = 2008-05-26 pages = extension = .txt mime = text/plain words = 3352 sentences = 165 flesch = 36 summary = Main difficulties to overcome for virus detection and characterisation in water samples encompass viral diversity, occurrence of low particle numbers, particularly in drinking water, and the technical challenges of virus assays. Nucleic acid amplification techniques are currently the most widely used methods for detection of viruses in 298 Environmental Biotechnology water, which also enable to gather information of the virus genotypes occurring in the environment, thus providing most relevant epidemiological information, particularly important for the implementation and follow-up of vaccination programmes [2, 3, 4 ] . Nevertheless, as stated above, no alternative to molecular detection analysis exists for highly health significant waterborne viruses such as human norovirus and hepatitis A virus. Development, evaluation, and standardization of a real-time TaqMan reverse transcription-PCR assay for quantification of hepatitis A virus in clinical and shellfish samples cache = ./cache/cord-309179-5hlatbqe.txt txt = ./txt/cord-309179-5hlatbqe.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-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-308857-otsrexqu author = Goel, Saurav title = Resilient and Agile Engineering Solutions to Address Societal Challenges such as Coronavirus Pandemic date = 2020-05-28 pages = extension = .txt mime = text/plain words = 10608 sentences = 526 flesch = 47 summary = This newly identified disease is caused by a new strain of the virus being referred to as Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS CoV-2; formerly called 2019-nCoV). We review the current medical and manufacturing response to COVID-19, including advances in instrumentation, sensing, use of lasers, fumigation chambers and development of novel tools such as lab-on-the-chip using combinatorial additive and subtractive manufacturing techniques and use of molecular modelling and molecular docking in drug and vaccine discovery. However, the coronavirus isolated from pangolins is 99% similar in a specific region of the Spike protein, which corresponds to the 74 amino acids involved in the Angiotensin-Converting Enzyme 2 (ACE 2) receptor binding domain, which allows the virus to enter human cells to infect them as shown in Figure 2 (b). (figures reprinted with permission) Our nasal lining tissue contains a rich number of cell receptors called angiotensinconverting enzyme 2 (ACE2), which are favourable sites for the SARS CoV-2 to attach its spiked protein to, thus paving way for the entrance of the virus inside the body. cache = ./cache/cord-308857-otsrexqu.txt txt = ./txt/cord-308857-otsrexqu.txt === reduce.pl bib === id = cord-309067-aemjbkfj author = Kennedy, Melissa title = Methodology in diagnostic virology date = 2005-03-01 pages = extension = .txt mime = text/plain words = 5885 sentences = 370 flesch = 49 summary = Detection of the virus that causes an infection uses one of several methods: The virus may be propagated in the laboratory and characterized; the virus may be visualized by electron microscopy; the viral proteins may be detected using specific antibody; the viral nucleic acid may be detected; or an activity of the virus, such as red blood cell agglutination, may be assayed. Antigen detection assays involve the use of virus-specific antibody to detect or bind to the viral protein or antigen in the sample. The assays vary in the sample substrate, how the binding of antibody to antigen is visualized, sensitivity, and specificity. Most use pathogen-specific antibody for capture and detection as for IFA assays (Fig. 4B) . Variations on this protocol may be found with different assays, but the underlying technique of pathogen-specific antibody binding the virus in the sample is similar in all (Fig. 4) [1, 3, 4] . cache = ./cache/cord-309067-aemjbkfj.txt txt = ./txt/cord-309067-aemjbkfj.txt === reduce.pl bib === id = cord-310141-2jofy8fo author = Qureshi, Abid title = A review on current status of antiviral siRNA date = 2018-04-15 pages = extension = .txt mime = text/plain words = 3380 sentences = 254 flesch = 42 summary = Short interfering RNA technology affords a potential tractable strategy to combat viral pathogenesis because siRNAs are specific, easy to design, and can be directed against multiple strains of a virus by targeting their conserved gene regions. For example, siRNAs directed against different genes of deadly viruses like human immunodeficiency virus (HIV), 9, 10 influenza virus (INFV), 11, 12 hepatitis B virus (HBV), 13 SARS coronavirus (SARS-CoV), 14, 15 human papillomavirus (HPV), 16 and West Nile virus (WNV) 17 in infected cells displayed encouraging results in inhibiting viral replication. 18, 19 Short interfering RNAs for various human viruses like respiratory syncytial virus (RSV), hepatitis C virus (HCV), HBV, and HIV are also appearing in clinical trials, which further elucidate their importance in inhibiting viral infections. Effective small interfering RNAs targeting matrix and nucleocapsid protein gene inhibit influenza A virus replication in cells and mice cache = ./cache/cord-310141-2jofy8fo.txt txt = ./txt/cord-310141-2jofy8fo.txt === reduce.pl bib === id = cord-307918-8y89p11a author = Onyango, Clayton O. title = Influenza Surveillance Among Children With Pneumonia Admitted to a District Hospital in Coastal Kenya, 2007–2010 date = 2012-12-15 pages = extension = .txt mime = text/plain words = 3678 sentences = 155 flesch = 42 summary = Nasopharyngeal samples from children aged <12 years who were admitted to Kilifi District Hospital during 2007–2010 with severe or very severe pneumonia and resided in the local demographic surveillance system were screened for influenza A, B, and C viruses by molecular methods. The following clinical and laboratory features obtained on admission or that relate to discharge outcome were compared between influenza-positive and influenza-negative children: duration of hospitalization >14 days, very severe pneumonia, wheezing, hypoxia (oxygen saturation level <90%, by fingertip pulse oximetry), circulatory shock (capillary refill time ≥3 seconds), severe anemia (hemoglobin level <5 g/dL), prematurity, congenital heart disease, positivity for HIV antibody (by 2 rapid tests), severe underweight (weight for age Z score ≤3), slide positivity for Plasmodium species, bacteremia, concurrent viral infection diagnosis, and death before discharge [2] . Our study identified all 3 influenza viruses in circulation in this rural coastal Kenya location among patients hospitalized with severe or very severe pneumonia and among outpatients with URTI. cache = ./cache/cord-307918-8y89p11a.txt txt = ./txt/cord-307918-8y89p11a.txt === reduce.pl bib === id = cord-307899-427a7i3h author = BITTLE, JAMES L. title = Vaccines Produced by Conventional Means to Control Major Infectious Diseases of Man and Animals date = 1989-12-31 pages = extension = .txt mime = text/plain words = 17476 sentences = 1073 flesch = 49 summary = Adenoviruses cause significant disease in dogs, foxes, and man, but have also been isolated from cattle, swine, goats, sheep, horses, turkeys, and chickens, where they produce mild infections, mainly associated with the respiratory and intestinal tracts. The latter modified the virus by serial passage in porcine and canine tissue cultures; the resulting vaccine immunized dogs and did not produce clinical signs of infection except for occasional corneal opacity similar to that caused by natural infection. The immunity produced by the attenuated live-virus CAV-1 vaccines is long lasting and has drastically reduced the incidence of the canine disease. The exception is human hepatitis A virus, which causes a serious disease and has one serotype; the development of both inactivated virus and attenuated live-virus vaccines is in progress (Hilleman et al., 1982; Provost et al., 1983) . An attenuated live-virus yellow fever vaccine was developed by passage of the virulent Asibi strain in mouse brain and cell culture until it had lost its pathogenicity for monkeys and man (Theiler, 1951) . cache = ./cache/cord-307899-427a7i3h.txt txt = ./txt/cord-307899-427a7i3h.txt === reduce.pl bib === id = cord-307632-x9bxnrtn author = Wu, Zhiqiang title = Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases date = 2018-10-03 pages = extension = .txt mime = text/plain words = 7230 sentences = 397 flesch = 50 summary = Five virus strains identified from Microtus clarkei, Eothenomys inez, Eothenomys melanogaster, Myodes rufocanus, and Cricetulus longicaudatus in five provinces appeared to be closely related to porcine reproductive and respiratory syndrome virus (PRRSV) with higher sequence similarity than those with other members of the family Arteriviridae (60.1-73.7% versus 25.7-54.2% aa identity for ORF1b, compared with equine arteritis virus, lactate dehydrogenase-elevating virus (LDV) of mice, simian hemorrhagic fever virus, and wobbly possum disease virus; Additional file 1: Table S6 ). Pairwise similarity and phylogenetic analysis ( Fig. 5a and Additional file 3: Figure S6 ) revealed that 29 viruses formed diverse evolutionary clades in lineage A under the genus Betacoronavirus, with sequence identities between 88.1 and 98.9% (RdRp aa identity). cache = ./cache/cord-307632-x9bxnrtn.txt txt = ./txt/cord-307632-x9bxnrtn.txt === reduce.pl bib === id = cord-303265-v6ci69n0 author = Domingo, Esteban title = Introduction to virus origins and their role in biological evolution date = 2019-11-08 pages = extension = .txt mime = text/plain words = 15685 sentences = 764 flesch = 42 summary = Topics covered include molecular mechanisms of genetic variation, with emphasis on high mutation rates, Darwinian principles acting on viruses, quasispecies dynamics and its implications, consequences for virus-host interactions, fitness as a relevant parameter, experimental model systems in cell culture, ex-vivo and in vivo, long-term virus evolution, the current situation of antiviral strategies to confront quasispecies swarms, and conceptual extensions of quasispecies to nonviral systems. With regard to the concepts of genome stability versus variation addressed in this book, it is helpful to divide viruses into four groups, depending on whether it is DNA or RNA the type of genetic material, which acts as a replicative intermediate in the infected cell (bottom gray shaded boxes in Fig. 1.1 ). They were selected for replicability, stability, and evolvability with trade-offs 1.4 Origin of life: a brief historical account and current views (acquisition of benefits for one of the three traits at some cost for another trait) likely play a role at this stage (see Chapter 4 for trade-offs in virus evolution). cache = ./cache/cord-303265-v6ci69n0.txt txt = ./txt/cord-303265-v6ci69n0.txt === reduce.pl bib === id = cord-309381-cb80ntxs author = Nogales, Aitor title = Host Single Nucleotide Polymorphisms Modulating Influenza A Virus Disease in Humans date = 2019-09-30 pages = extension = .txt mime = text/plain words = 10222 sentences = 590 flesch = 45 summary = IAV RNAs are mainly recognized by the endosomal, membrane-associated PRR Toll-like receptors (TLRs) 3 (double-stranded RNAs, dsRNAs) or 7/8 (ssRNAs), respectively [50, 51] , by the cytoplasmic PRR retinoic acid-inducible gene I (RIG-I), which detects dsRNA and 5 -triphosphates of the negative ssRNA viral genome [50, 52] , generated during replication of multiple viruses, by the NOD-like receptor family member NOD-, LRR-and pyrin domain-containing 3 (NLRP3), which recognizes various stimuli (see below) [53] and by the absent in melanoma 2 (AIM2) protein, recognizing not well-characterized influenza stimuli [54] . Another important SNP (rs34481144) associated with risk of severe influenza in humans from the United States (US) infected with seasonal IAVs is located in the 5 -UTR of the IFITM3 gene [123, 124] . cache = ./cache/cord-309381-cb80ntxs.txt txt = ./txt/cord-309381-cb80ntxs.txt === reduce.pl bib === id = cord-305327-hayhbs5u author = Gonzalez, Jean-Paul title = Global Spread of Hemorrhagic Fever Viruses: Predicting Pandemics date = 2017-09-19 pages = extension = .txt mime = text/plain words = 10210 sentences = 424 flesch = 37 summary = Other pathogens that are remarkable for their epidemic expansions include the arenavirus hemorrhagic fevers and hantavirus diseases carried by rodents over great geographic distances and the arthropod-borne viruses (West Nile, chikungunya and Zika) enabled by ecology and vector adaptations. Emergence from a sporadic case to an outbreak, to an epidemic, and ultimately to a pandemic depends upon effective transmission among nonimmune hosts, host availability (density), characteristics of the vector (natural or human made) that would enable it to circumvent distances, and the pathogen infectiousness. Although MARV expansion appears to be limited to a few countries in Africa, the recent emergence (estimated at a few decades ago) of a second human pathogenic marburgvirus known as Ravn virus, and the widely distributed Old World rousette fruit bats (Rousettus spp.) serving as reservoir for both viruses [45] , are two factors that favor pandemic risk. cache = ./cache/cord-305327-hayhbs5u.txt txt = ./txt/cord-305327-hayhbs5u.txt === reduce.pl bib === id = cord-306083-juysx6yo author = Choe, Young June title = Co-seasonality and co-detection of respiratory viruses and bacteraemia in children: a retrospective analysis date = 2020-09-10 pages = extension = .txt mime = text/plain words = 1746 sentences = 108 flesch = 44 summary = OBJECTIVES: The aim of this study was to assess the co-seasonality and co-detection of respiratory viral infections and bacteraemia in children since the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13). Analysis of linked viral-bacterial infections in individual children indicated that the rate ratio (RR) of bacteraemia associated with hMPV (RR=2.73, 95% CI 1.12-6.85, P=0.019) and influenza (RR=2.61, 95% CI 1.21-6.11, P=0.013) were more than double that of RSV. CONCLUSIONS: There is a significant association between hMPV and influenza viruses, and bacteraemia of all causes in hospitalised children at a single paediatric centre in the United States. A study conducted in children before the 9 implementation of PCV13, demonstrated significant associations between invasive 10 pneumococcal disease (IPD) and influenza viruses and respiratory syncytial virus (RSV), as well 11 as human metapneumovirus (hMPV), which was a novel observation [5] . cache = ./cache/cord-306083-juysx6yo.txt txt = ./txt/cord-306083-juysx6yo.txt === reduce.pl bib === id = cord-310255-aixq5mhf author = Charlton, Frank W. title = Ion Channels as Therapeutic Targets for Viral Infections: Further Discoveries and Future Perspectives date = 2020-08-03 pages = extension = .txt mime = text/plain words = 5345 sentences = 321 flesch = 46 summary = More recent evidence highlights how viruses can regulate and/or depend on the ion channels expressed by host cells, highlighting them as new host targets for therapeutic intervention (reviewed by Hover et al., 2017) [14] . We then discuss how intracellular ion channels contribute to the Two-pore channels 1 and 2 (TPC1/2) Gunaratne et al., 2018 [34] Severe fever with thrombocytopenia syndrome virus (SFTSV) Unknown channel Li et al., 2019 [35] Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Two-pore channel 2 (TPC2) Ou et al., 2020 [36] Bunyamwera orthobunyavirus (BUNV) Two-pore domain K + (K 2P ) Hover et al., 2016/18 [28, 37] Hazara orthonairovirus (HAZV) Unknown K + channel Punch et al., 2017 [38] Charlton et al., 2019 [39] Human immunodeficiency virus (HIV) G-Protein coupled inwardly rectifying K + (GIRK) ATP-sensitive K + K ATP Dubey et al., 2019 [40] Merkel cell polyomavirus (MCPyV) cache = ./cache/cord-310255-aixq5mhf.txt txt = ./txt/cord-310255-aixq5mhf.txt === reduce.pl bib === id = cord-310371-pylrg91h author = Bishop, R.F. title = Enteric Viruses date = 2008-07-30 pages = extension = .txt mime = text/plain words = 4467 sentences = 253 flesch = 41 summary = The onset of acute enteritis is associated with infection by viruses that replicate at or near the site of entry into the intestinal mucosa, including caliciviruses, rotaviruses, adenoviruses, astroviruses, and coronaviruses. . viruses causing localized inflammation at any level of the intestinal tract, predominantly in small intestinal mucosa, resulting in acute gastroenteritis, for example, rotaviruses, caliciviruses, adenoviruses, astroviruses; . The family Caliciviridae contain small RNA viruses that cause enteric disease in a wide variety of hosts including cattle, pigs, rabbits, and humans. Caliciviruses causing enteric infections (in humans and other animals) are classified as belonging to the family Caliciviridae, which is divided into four genera. The recent demonstration that human noroviruses can infect and replicate in a three-dimensional cell culture model of human intestinal epithelium, should improve our understanding of the pathogenesis, and antigenic diversity of this important group of enteric viruses. cache = ./cache/cord-310371-pylrg91h.txt txt = ./txt/cord-310371-pylrg91h.txt === reduce.pl bib === id = cord-308686-tbwecf7o author = Mortamet, G. title = Étude prospective de l’écologie virale hivernale dans un service de réanimation pédiatrique date = 2015-04-30 pages = extension = .txt mime = text/plain words = 2233 sentences = 193 flesch = 58 summary = Résumé Le but de cette étude prospective était d'évaluer l'épidémiologie des virus respiratoires chez les enfants hospitalisés dans une unité de réanimation et de soins continus pédiatriques pendant 3 mois d'hiver, en 2012–2013. Ont été inclus tous les enfants admis en réanimation pédiatrique du centre hospitalier universitaire (CHU) de Caen et ayant bénéficié d'une recherche d'infection par un virus respiratoire à partir d'un prélèvement nasal analysé par amplification génique (PCR) multiplex. Cette étude révèle cependant un taux élevé d'infections respiratoires causées par des virus chez les enfants qui ne présentent pas de symptômes respiratoires à leur admission en unité de réanimation et soins continus. Le but de cette étude prospective était d'évaluer l'épidémiologie des virus respiratoires chez les enfants hospitalisés dans une unité de réanimation et de soins continus pédiatrique pendant 3 mois d'hiver. cache = ./cache/cord-308686-tbwecf7o.txt txt = ./txt/cord-308686-tbwecf7o.txt === reduce.pl bib === id = cord-306948-wkisfz1m author = Han, Mingyuan title = Engineering the PRRS virus genome: Updates and perspectives date = 2014-12-05 pages = extension = .txt mime = text/plain words = 9514 sentences = 480 flesch = 45 summary = Serologic marker candidates identified among B-cell linear epitopes of Nsp2 and structural proteins of a North American strain of porcine reproductive and respiratory syndrome virus A full-length cDNA infectious clone of North American type 1 porcine reproductive and respiratory syndrome virus: expression of green fluorescent protein in the Nsp2 region Identification of nonessential regions of the nsp2 replicase protein of porcine reproductive and respiratory syndrome virus strain VR-2332 for replication in cell culture Establishment of a DNA-launched infectious clone for a highly pneumovirulent strain of type 2 porcine reproductive and respiratory syndrome virus: identification and in vitro and in vivo characterization of a large spontaneous deletion in the nsp2 region Recovery of viable porcine reproductive and respiratory syndrome virus from an infectious clone containing a partial deletion within the Nsp2-encoding region Determination of the complete nucleotide sequence of a vaccine strain of porcine reproductive and respiratory syndrome virus and identification of the Nsp2 gene with a unique insertion cache = ./cache/cord-306948-wkisfz1m.txt txt = ./txt/cord-306948-wkisfz1m.txt === reduce.pl bib === id = cord-309635-1tgovkr7 author = Wu, Nicholas C. title = Structural Biology of Influenza Hemagglutinin: An Amaranthine Adventure date = 2020-09-22 pages = extension = .txt mime = text/plain words = 5497 sentences = 289 flesch = 42 summary = Hemagglutinin (HA) glycoprotein is an important focus of influenza research due to its role in antigenic drift and shift, as well as its receptor binding and membrane fusion functions, which are indispensable for viral entry. Similarly, RBS of influenza B HA is composed of the 140-loop, 190-helix, and 240-loop, which are structurally equivalent to the 130-loop, 150-loop, and 190-helix Receptor specificity can also continue to evolve when seasonal viruses circulate in the human population, due to natural mutations that are likely a response to immune selection pressure. A broadly neutralizing human monoclonal antibody that recognizes a conserved, novel epitope on the globular head of the influenza H1N1 virus hemagglutinin Broadly neutralizing human antibody that recognizes the receptor-binding pocket of influenza virus hemagglutinin Design of nanoparticulate group 2 influenza virus hemagglutinin stem antigens that activate unmutated ancestor B cell receptors of broadly neutralizing antibody lineages cache = ./cache/cord-309635-1tgovkr7.txt txt = ./txt/cord-309635-1tgovkr7.txt === reduce.pl bib === id = cord-311748-yr2ep7uf author = Kahyaoglu, L. N. title = 11 New approaches in microbial pathogen detection date = 2013-12-31 pages = extension = .txt mime = text/plain words = 8020 sentences = 381 flesch = 48 summary = In recent years, polymerase chain reaction (PCR)-based methods in particular, have become the gold standard for virus detection in food due to their high sensitivity, specifi city and potential to detect even a single virus particle (Bosch et al. In recent years, qRT-PCR has been widely used in food virology as the most promising nucleic acid detection method, since it offers several advantages over conventional RT-PCR, including high sensitivity, the possibility of simultaneous amplifi cation, detection and quantifi cation of the target nucleic acids in a single step, and with minimum risk of carry-over contamination through the use of a closed system (Mackay et al. The challenges associated with the detection of foodborne viruses, such as PCR inhibitors and low virus concentrations in foods, affect the effi ciency of realtime assay adversely, therefore, for process control (PC) an internal amplifi cation control (IAC), which is extracted and amplifi ed with the target sequence, is crucial in the evaluation of PCR and to prevent false negatives (Di Pasquale et al. cache = ./cache/cord-311748-yr2ep7uf.txt txt = ./txt/cord-311748-yr2ep7uf.txt === reduce.pl bib === id = cord-311823-85wj08gr author = Katze, Michael G. title = Innate immune modulation by RNA viruses: emerging insights from functional genomics date = 2008 pages = extension = .txt mime = text/plain words = 9154 sentences = 392 flesch = 36 summary = In this section, we review recent studies in which genomic approaches have been used to provide new information on how viruses trigger and regulate innate immune pathways, and to evaluate the use of type I IFN-based therapy as a means to enhance the innate immune response to HCV. In RIg-I-deficient cells, influenza virus fails to elicit the expression of IFNβ and of many ISgs, including key antiviral mediators such as IRF3, STAT1 (signal transducer and activator of transcription 1), IFIT1 (IFN-induced protein with tetratricopeptide repeats 1; also known as ISg56) and ISg54 (also known as IFIT2). Although these studies have provided considerable information regarding the genes activated downstream of TlR activation, it will be advantageous to extend genomic analyses in the context of viral infection using cells lacking the expression of specific TlRs. The ability of a virus to establish an infection depends, at least to some extent, on its ability to block the host innate immune response or to modulate the activity of antiviral effector proteins. cache = ./cache/cord-311823-85wj08gr.txt txt = ./txt/cord-311823-85wj08gr.txt === reduce.pl bib === id = cord-312964-vsrqmmv7 author = Doyle, William J. title = Prevention of otitis media caused by viral upper respiratory tract infection: Vaccines, antivirals, and other approaches date = 2003 pages = extension = .txt mime = text/plain words = 6376 sentences = 259 flesch = 29 summary = Past studies show that new episodes of OM are usually a complication of viral upper respiratory infection (vURI), and therefore, a rational approach to achieving that goal is to develop intervention strategies that target vURIassociated OM. Past studies show that new episodes of OM are usually a complication of viral upper respiratory infection (vURI), and therefore, a rational approach to achieving that goal is to develop intervention strategies that target vURIassociated OM. Active synergy between certain upper respiratory viruses and nasopharyngeal pathogens was demonstrated for OM pathogenesis in chinchillas and humans [27] [28] [29] , and pre-existing or concurrent vURI in infants and children with acute, bacterial OM is frequently observed [24, 25] . In one double-blind clinical study, intranasal steroid (fluticasone propionate) was administered for 7 days immediately after onset of vURI symptoms in an attempt to decrease nasopharyngeal inflammation (and possible eustachian-tube obstruction), but was not efficacious in preventing AOM and might have increased OM incidence during rhinovirus infection [69] . cache = ./cache/cord-312964-vsrqmmv7.txt txt = ./txt/cord-312964-vsrqmmv7.txt === reduce.pl bib === id = cord-310140-h7uwl0pb author = Templeton, K.E. title = A multi-centre pilot proficiency programme to assess the quality of molecular detection of respiratory viruses date = 2005-07-12 pages = extension = .txt mime = text/plain words = 4186 sentences = 205 flesch = 50 summary = STUDY DESIGN: Respiratory virus proficiency panels were produced from diluted stocks of respiratory viruses provided and tested by four reference laboratories. Laboratories performing respiratory molecular tests want to report accurate and reliable results regardless of the type of assay in use and one of the best ways to assess performance is to participate in proficiency programmes, enabling laboratories to evaluate their performance (Schirm et al., 2002; Schloss et al., 2003; Noordhoek et al., 2004; Verkooyen et al., 2003) . Laboratories who had expressed an interest to QCMD in participating in a proficiency programme for molecular detection of respiratory viruses were asked to complete a questionnaire detailing technical aspects of the assays they had applied. In this study, samples were grown in cell culture and dilutions were made so sensitivity and limited specificity of assays for these viruses could be assessed. cache = ./cache/cord-310140-h7uwl0pb.txt txt = ./txt/cord-310140-h7uwl0pb.txt === reduce.pl bib === id = cord-308066-lrbi5198 author = Childs, James E. title = Pre-spillover Prevention of Emerging Zoonotic Diseases: What Are the Targets and What Are the Tools? date = 2007 pages = extension = .txt mime = text/plain words = 15698 sentences = 714 flesch = 41 summary = The uneven standards of surveillance, humanor animal-based, for zoonotic diseases or pathogens maintained and transmitted by wildlife H R s, or even domestic species, is a global problem, readily apparent even within the United States, where investment in public health, including surveillance systems, has a long and enviable history. Following an outbreak of human monkeypox in several US states (Centers for Disease Control and Prevention 2003a; see the chapter by Regnery, this volume), local populations of indigenous North American rodents were captured and examined for infection from areas around animal-holding facilities housing African rodents imported for the pet-trade and implicated as the source of monkeypox virus (Cunha 2004; Check 2004) . National institutions charged with strategic planning for emerging diseases or intentional releases of zoonotic agents have emphasized improving diagnostic capabilities for detecting human infections, modifying the immune status of human or domestic animals through vaccines, producing better antiviral or antibacterial drugs, and enhancing human-based surveillance as an early warning system (Fauchi 2002 ; Centers for Disease Control and Prevention 1998). cache = ./cache/cord-308066-lrbi5198.txt txt = ./txt/cord-308066-lrbi5198.txt === reduce.pl bib === id = cord-309488-8guapzke author = Dodd, R. title = Other emerging viral pathogens date = 2006-08-15 pages = extension = .txt mime = text/plain words = 4365 sentences = 215 flesch = 49 summary = Attention was refocused on viral infections as a result of the outbreak of West Nile virus (WNV) disease in the USA along with the recognition that it was transmissible by transfusion [1] . In 1997, Blackbourn and colleagues [17] reported on the detection of HHV-8 DNA in the blood of a seropositive blood donor; based on evidence of in vitro passage of the virus to allogeneic cells, the authors expressed concern about the potential for transmission by transfusion. This concern is based upon the historical fact that there have been periodic pandemics associated with the circulation of new strains of the virus in humans and the current outbreak of the H5N1 strain of avian influenza, which causes high mortality when it does infect humans [27] . Seroprevalence of human herpes virus 8 antibody in populations at high or low risk of transfusion, graft, or sexual transmission of viruses Molecular cloning and disease association of hepatitis G virus: a transfusion-transmissible agent cache = ./cache/cord-309488-8guapzke.txt txt = ./txt/cord-309488-8guapzke.txt === reduce.pl bib === id = cord-310942-191m0e65 author = Boga, Jose Antonio title = Beneficial actions of melatonin in the management of viral infections: a new use for this “molecular handyman”? date = 2012-04-18 pages = extension = .txt mime = text/plain words = 7208 sentences = 362 flesch = 32 summary = The potential protective mechanisms include melatonin acting as a free radical scavenger, an antioxidant enzyme inducer, a positive regulator of immune functions and an inhibitor of inflammation, as well as a regulator of programmed cell death (PCD) [ Table 2 ]. Melatonin treatment also caused a rise in protein expression of the nuclear factor erythroid 2 (Nrf2), a transcription factor that plays a critical role by binding to the antioxidant response element in the promoter region of a number of genes encoding for antioxidant and detoxifying enzymes in several types of cells and tissues [109] . Respiratory syncytial virus infection of human respiratory epithelial cells enhances inducible nitric oxide synthase gene expression Melatonin decreases nitric oxide production and lipid peroxidation and increases interleukin-1 beta in the brain of mice infected by the Venezuelan equine encephalomyelitis virus cache = ./cache/cord-310942-191m0e65.txt txt = ./txt/cord-310942-191m0e65.txt === reduce.pl bib === id = cord-307364-j86t65qu author = Uccellini, Lorenzo title = Identification of a novel nidovirus in an outbreak of fatal respiratory disease in ball pythons (Python regius) date = 2014-08-08 pages = extension = .txt mime = text/plain words = 1917 sentences = 110 flesch = 45 summary = In situ hybridization confirmed the presence of intracellular, intracytoplasmic viral nucleic acids in the lungs of infected snakes. Phylogenetic analysis based on a 1,136 amino acid segment of the polyprotein suggests that this virus may represent a new species in the subfamily Torovirinae. CONCLUSIONS: This report of a novel nidovirus in ball pythons may provide insight into the pathogenesis of respiratory disease in this species and enhances our knowledge of the diversity of nidoviruses. Here we report the discovery of a novel nidovirus in a collection of ball pythons (Python regius) in upstate New York with pneumonia, tracheitis and esophagitis. Based on the phylogenetic position and the genetic distances between In situ hybridization to a 934 nt fragment of the genomic polyprotein 1ab region was used to assess viral infection and distribution in the lung tissue. Identification of a novel nidovirus in an outbreak of fatal respiratory disease in ball pythons (Python regius) cache = ./cache/cord-307364-j86t65qu.txt txt = ./txt/cord-307364-j86t65qu.txt === reduce.pl bib === id = cord-312431-de7zhswl author = Ganesh, Atheesha title = Detecting Virus‐Like Particles from the Umgeni River, South Africa date = 2013-08-30 pages = extension = .txt mime = text/plain words = 7112 sentences = 376 flesch = 48 summary = These results indicate the potential of viruses in the water samples especially from the lower catchment areas of the Umgeni River to infect human hosts throughout the year. It is well recognised that monitoring the presence of enteric viruses could be challenging due to the relatively low level of infectious viral particles towards the respective host species and small viral particle size existing in environmental waters, thus making it essential to start with a large water sample volume and concentrate it to several orders of magnitude [27] [28] [29] [30] [31] . The present study was conducted to optimise procedures to extract and enumerate indigenous virus-like particles (VLPs) and to determine the community structures and infectivity of these viruses from river water. Canonical correspondence analysis (CCA) was used to reveal the association amongst the bacteriophages, VLPs and the physical and chemical water quality variables, which were measured from the same sites and seasons in concurrent studies performed in this laboratory [46] , with a view to defining the significant variables accountable for the observed spatial and temporal distribution of the communities. cache = ./cache/cord-312431-de7zhswl.txt txt = ./txt/cord-312431-de7zhswl.txt === reduce.pl bib === id = cord-314254-9ye8tfvz author = Pfaender, Stephanie title = Natural reservoirs for homologs of hepatitis C virus date = 2014-03-26 pages = extension = .txt mime = text/plain words = 6841 sentences = 322 flesch = 47 summary = To date, there is no evidence for an animal reservoir of viruses closely related to hepatitis C virus which may have crossed the species barrier to cause disease in humans and resulted in the current pandemic. Recently, several studies discovered new viruses related to hepatitis C virus, belonging to the hepaciand pegivirus genera, in small wild mammals (rodents and bats) and domesticated animals which live in close contact with humans (dogs and horses). Non-primate hepaciviruses (NPHV) were initially discovered in domestic dogs and subsequently in horses 12, 13 and other diverse and widespread HCV-like viruses have been reported in wild populations of rodents and bats. Furthermore, liver function analyses revealed no indication for hepatic inflammation as c-glutamyl transferase and glutamate dehydrogenase values were within reference range, with the exception of a mildly elevated c-glutamyl transferase New HCV-like viruses in different mammalian hosts Pfaender et al 4 level in one horse. cache = ./cache/cord-314254-9ye8tfvz.txt txt = ./txt/cord-314254-9ye8tfvz.txt === reduce.pl bib === id = cord-306424-gf0bglm0 author = Scutigliani, Enzo Maxim title = Interaction of the innate immune system with positive-strand RNA virus replication organelles date = 2017-06-27 pages = extension = .txt mime = text/plain words = 8320 sentences = 382 flesch = 36 summary = Thus, these data indicate that MAMs are critical locations for antiviral signaling and have an important role in expression of type I and III IFNs. Moreover, increasing evidence suggests that at least some +RNA viruses in fact occupy or hijack MAM-membranes during infection, as MAMs of HCV-infected cells were found to contain proteins involved in virus assembly and fully assembled virions [111] . At last, based on recent studies that demonstrated how IFN-g inducible GTPases are capable of disrupting PVs, we discussed the possibility of a general function of IFN-inducible GTPases in the targeting of viral ROs. In summary, upon infection, +RNA viruses hamper IFN and ISG induction at multiple levels to decelerate antiviral innate immune signaling. Antiviral innate immune response interferes with the formation of replication-associated membrane structures induced by a +RNA virus cache = ./cache/cord-306424-gf0bglm0.txt txt = ./txt/cord-306424-gf0bglm0.txt === reduce.pl bib === id = cord-310920-itqwhi6a author = Haddad, Christina title = Integrated Approaches to Reveal Mechanisms by which RNA Viruses Reprogram the Cellular Environment date = 2020-07-02 pages = extension = .txt mime = text/plain words = 3698 sentences = 205 flesch = 44 summary = Each of these techniques provide important vantage points to understand the complexities of virus-host interactions, but we attempt to make the case that by integrating these and similar methods, more vivid descriptions of how viruses reprogram the cellular environment emerges. Obtaining structural details of the UTRs and identifying functional binding sites of RBPs will be deeply insightful in elucidating how this virus replicates within host cells. Given the large number of RBPs known to interact with genomic and subgenomic viral RNAs to modulate translation, replication and the shift between these two stages, CLIP-seq can be employed to understand virology at the molecular level. Studying RNA structural interactions and the effects of viral-host RBPs on RNA structure and function are essential for understanding translation, replication, and transcription processes in order to better understand how viruses reprogram the cellular environment. cache = ./cache/cord-310920-itqwhi6a.txt txt = ./txt/cord-310920-itqwhi6a.txt === reduce.pl bib === id = cord-310795-n78s0sg2 author = Brand, H. Kim title = Infection with multiple viruses is not associated with increased disease severity in children with bronchiolitis date = 2011-09-07 pages = extension = .txt mime = text/plain words = 3943 sentences = 220 flesch = 51 summary = This study evaluated the association between the detection of multiple viruses by RT‐PCR and disease severity in children with bronchiolitis. In RSV infected children younger than 3 months, disease severity was not associated with the number of detected viruses. Therefore, we prospectively studied the association between the detection of multiple viral pathogens by RT-PCR and disease severity in young children with bronchiolitis included during three consecutive winter seasons. As the differences in age between the groups may have influenced our results, we also evaluated the association between disease severity and the detection of multiple viruses in children diagnosed with RSV bronchiolitis younger and older than 3 months (Fig. 2) . In the present study, we evaluated the viral etiology in young children with bronchiolitis during three consecutive winter seasons and examined the association between the detection of two or more viruses by RT-PCR and disease severity. cache = ./cache/cord-310795-n78s0sg2.txt txt = ./txt/cord-310795-n78s0sg2.txt === reduce.pl bib === id = cord-311410-lgqup9ug author = Ayers, M. title = A single tube RT-PCR assay for the detection of mosquito-borne flaviviruses date = 2006-05-02 pages = extension = .txt mime = text/plain words = 3106 sentences = 157 flesch = 52 summary = In this study we present the design and validation of a single tube RT-PCR assay using a pair of consensus primers for the detection of mosquito-borne flaviviruses. For specificity studies, several viral samples were used, including clinical samples found to contain CMV and EBV DNA by PCR testing, as described (Johnson et al., 2000) ; a clinical isolate of influenza virus from the 2004-2005 season, typed as H3 by sequencing of the hemagglutinin gene; echovirus 11 from the laboratory collection at the Hospital for Sick Children; hepatitis C virus RNA was obtained by in vitro transcription of the infectious clone pCV-H77C (Yanagi et al., 1997) (the clone was kindly provided by Dr. J. Coupled with sequencing, it could detect with great sensitivity and identify several mosquito-borne flaviviruses including WNV, Kunjin, SLE, YFV and dengue fever viruses. cache = ./cache/cord-311410-lgqup9ug.txt txt = ./txt/cord-311410-lgqup9ug.txt === reduce.pl bib === id = cord-310171-1fmsxx2s author = Goffard, Anne title = Virus and cystic fibrosis: Rhinoviruses are associated with exacerbations in adult patients() date = 2014-02-25 pages = extension = .txt mime = text/plain words = 3325 sentences = 176 flesch = 41 summary = Since the sensitive molecular methods for detection of viruses are more and more common, several recent studies highlight the clinical importance of respiratory viruses especially during exacerbation of asthma, chronic obstructive pulmonary disease (COPD) or CF [3] [4] [5] [6] [7] [8] [9] . In the present study, we reported detection of respiratory viruses from adult patients with CF during either routine visit or acute pulmonary exacerbation. To conclude, we have reported a relatively high frequency of respiratory viruses in a cohort of CF adult patients from France, and demonstrated for the first time that rhinovirus detection including newly identified HRV-Ca variants are the most frequent and significantly associated with respiratory exacerbations. Respiratory viruses in children with cystic fibrosis: viral detection and clinical findings Association of respiratory viral infections with pulmonary deterioration in patients with cystic fibrosis cache = ./cache/cord-310171-1fmsxx2s.txt txt = ./txt/cord-310171-1fmsxx2s.txt === reduce.pl bib === id = cord-312461-5qzpo6l1 author = Adalja, Amesh A. title = Characteristics of Microbes Most Likely to Cause Pandemics and Global Catastrophes date = 2019-08-30 pages = extension = .txt mime = text/plain words = 6830 sentences = 290 flesch = 40 summary = A substantial proportion of pandemic and biological threat preparedness activities have focused on list-based approaches that were in part based on pandemic influenzas of the past, historical biological weapon development programs, or recent outbreaks of emerging infectious diseases (e.g., SARS, MERS, Ebola) (Centers for Disease Control and Prevention 2017; Casadevall and Relman 2010) . Cultivating and maintaining expertise in the epidemiology, surveillance, and pathogenicity of all classes of microbes, with explicit incorporation of a One Health approach-which incorporates and integrates information from infectious diseases of plants, amphibians, and reptiles-will help foster the broad capacities needed for emerging pandemic and global catastrophic biological risks. Pathogen-based lists, both USA and global, based on influenza precedents, historical biological weapon programs, and emerging infectious diseases were responsible for galvanizing early activities in the field of pandemic preparedness and have helped drive many important contributions. cache = ./cache/cord-312461-5qzpo6l1.txt txt = ./txt/cord-312461-5qzpo6l1.txt === reduce.pl bib === id = cord-313356-ninzeazy author = Fiorillo, Luca title = COVID-19 Surface Persistence: A Recent Data Summary and Its Importance for Medical and Dental Settings date = 2020-04-30 pages = extension = .txt mime = text/plain words = 3803 sentences = 248 flesch = 53 summary = title: COVID-19 Surface Persistence: A Recent Data Summary and Its Importance for Medical and Dental Settings Recently, due to the coronavirus pandemic, many guidelines and anti-contagion strategies continue to report unclear information about the persistence of coronavirus disease 2019 (COVID-19) in the environment. The purpose of this article is to highlight all the sources currently present in the literature concerning the persistence of the different coronaviruses in the environment as well as in medical and dental settings. The aim of this article is to evaluate, through the analysis of the current literature, how long this virus can remain active on different surfaces. On average, the different coronaviruses persist in an infectious state on surfaces for several days, even up to nine. Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72314 Cases From the Chinese Center for Disease Control and Prevention cache = ./cache/cord-313356-ninzeazy.txt txt = ./txt/cord-313356-ninzeazy.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-310439-z0bxsjug author = Martin, R. R. title = Pathogen-Tested Planting Material date = 2014-12-31 pages = extension = .txt mime = text/plain words = 7703 sentences = 349 flesch = 50 summary = Buffer zone An area surrounding or adjacent to an area for production of plants in a certification scheme designed to minimize the probability of spread of the target pathogens, pollen, or seed into or out of the block, to meet phytosanitary or other control measures as defined in a certification standard. Many certification programs are based on a published standard that defines site selection and preparation, isolation distances from plants of the same species and other vegetation, number of inspections, record keeping on plant traceability so that tracebacks or traceforwards can be done if a problem should arise, a pest and disease management plan, records of all pest management activities, the conditions and protocols to be followed during plant or seed production, and types and amount of testing that needs to be done at each level in the propagation cycle. cache = ./cache/cord-310439-z0bxsjug.txt txt = ./txt/cord-310439-z0bxsjug.txt === reduce.pl bib === id = cord-311908-sgdq6j6x author = Atkins, G. J. title = Transient virus infection and multiple sclerosis date = 2000-09-28 pages = extension = .txt mime = text/plain words = 6183 sentences = 267 flesch = 40 summary = Multiple sclerosis (MS) is a chronic, demyelinating disease of the CNS in which autoimmunity to myelin plays a role in pathogenesis. These include subacute sclerosing panencephalitis (SSPE), caused by a persistent measles virus infection, and human T cell lymphotropic virus-I (HTLV-I)associated myelopathy, which is a slowly progressive neurological disease characterised by in¯ammatory in®ltrates and demyelination in the CNS, and is caused by an exogenous retrovirus. Another study that does not involve virus infection, but may nonetheless provide information concerning the possible viral aetiology of MS, concerns the exacerbation of brain damage following EAE induction. With regard to the activity of known human viruses in the induction of myelin damage, there is evidence that virus infections associated with CNS demyelination can cause damage to oligodendrocytes. It is possible that virus infection could induce secretion of pro-in¯ammatory cytokines that could penetrate the CNS parenchyma from the blood and lead to the recrudescence of anti-myelin autoimmunity by reactivation of previously primed T-cells. cache = ./cache/cord-311908-sgdq6j6x.txt txt = ./txt/cord-311908-sgdq6j6x.txt === reduce.pl bib === id = cord-310870-w8wu8vno author = Shorten, Robert J. title = The risk of transmission of a viral haemorrhagic fever infection in a United Kingdom laboratory date = 2017-05-18 pages = extension = .txt mime = text/plain words = 1636 sentences = 97 flesch = 45 summary = [9] [10] [11] [12] In addition, over 9,000 cases of Crimean Congo Haemorrhagic Fever (CCHF) were reported in Turkey between 2002 and 2014, with an estimated minimum 180,000 blood samples processed in routine laboratories with no additional precautions. Although it is reassuring that large numbers of samples from patients with CCHF infection have been processed safely in routine laboratories in Turkey, it should be noted that this bunyavirus is rarely transmitted person to person, so the parallels between this and other VHF viruses need to be carefully considered. Manufacturers must validate their decontamination method against appropriate surrogate model enveloped viruses. Viral inactivation validation studies have successfully used surrogate model viruses with properties similar to wildtype viruses to provide evidence for the safety of human blood plasma products for over a decade. Once assessed by appropriately designed viral inactivation validation studies on relevant surrogate model enveloped viruses, the decontamination process has been shown to be effective against all known and future emerging enveloped viruses, which includes Ebola, CCHF, Lassa fever, and Marburg virus. cache = ./cache/cord-310870-w8wu8vno.txt txt = ./txt/cord-310870-w8wu8vno.txt === reduce.pl bib === id = cord-309642-wwaa6ls0 author = Potgieter, Leon N.D. title = Pathogenesis of Viral Infections date = 1986-11-30 pages = extension = .txt mime = text/plain words = 10859 sentences = 770 flesch = 40 summary = 7 · 18 · 84 · 133 Such restrictions function at the cellular level either as the presence or absence of appropriate cell surface receptors (in some instances, they have been shown to be inherited as dominant alleles in a Mendelian manner) 9 · 18 · 26 · 46 · 68 · 97 ·u 9 · 120 or the intracellular hospitality of the cell (several genetic host restrictions on virus replication have been identified).18·32·59·80·82·108·109·120·126 Restricted growth of several DNA viruses in some cells results in transformation without production of progeny viruses. 112 The phenomenon appears to be mediated by virus-induced receptors on the surface membrane of cells and may be one mechanism of the often-encountered secondary bacterial infections associated with viral diseases. 51 · 52 · 104 Viral respiratory tract disease is a consequence of mechanical and biochemical injury to epithelial cells and alveolar macrophages, which can, in the most severe instances, result in secondary bacterial infection, pneumonia, and death. cache = ./cache/cord-309642-wwaa6ls0.txt txt = ./txt/cord-309642-wwaa6ls0.txt === reduce.pl bib === id = cord-314390-q36ye9ff author = Kang, Gagandeep title = Viral Diarrhea date = 2016-10-24 pages = extension = .txt mime = text/plain words = 6020 sentences = 281 flesch = 39 summary = Of the 'non-group A' rotaviruses, group B rotavirus has been identified in epidemic outbreaks of severe diarrhea in adults in China and in symptomatic infections in children. Between 20% and 50% of cases of gastroenteritis caused by rotavirus in hospitals are considered to be of nosocomial origin, and nosocomial viral enteric infections have been documented in up to 6% of children admitted for >72 h in both developed and developing countries. Rotaviruses induce a clinical illness characterized by vomiting, diarrhea, abdominal discomfort, fever, and dehydration (or a combination of some of these symptoms) that occurs primarily in infants and young children and may lead to hospitalization for rehydration therapy. Studies in adult volunteers indicate that people with detectable levels of antibodies do not develop the illness, although epidemiological observations suggest that human astrovirus infections may not induce heterotypic immunity, as an episode of astrovirus diarrhea is not associated with a reduced incidence of a subsequent episode. cache = ./cache/cord-314390-q36ye9ff.txt txt = ./txt/cord-314390-q36ye9ff.txt === reduce.pl bib === id = cord-313312-h607itv2 author = Mok, Darren Z. L. title = The Effects of Pre-Existing Antibodies on Live-Attenuated Viral Vaccines date = 2020-05-08 pages = extension = .txt mime = text/plain words = 7417 sentences = 349 flesch = 34 summary = Pre-existing antibodies, derived from either from maternal–fetal transmission, or by previous infection or vaccination, have been demonstrated to interfere with vaccine immunogenicity of measles, adenovirus, and influenza LAVs. Immune interference of LAVs can be caused by the formation of virus–antibody complexes that neutralize virus infection in antigen-presenting cells, or by the cross-linking of the B-cell receptor with the inhibitory receptor, FcγRIIB. The clinical trial finding that subjects with a limited range of cross-reactive antibodies from a prior Japanese Encephalitis vaccine were able to enhance yellow fever vaccination, by prolonging vaccine viremia duration that leads to higher antibody titers, thus hints at the possibility that whether pre-existing antibodies inhibit or augment flavivirus infection will depend on both antibody titers and the type/specificity of antibodies produced [85] . By contrast, at sub-neutralizing titers, pre-existing antibodies can enable viruses to better infect cells and increase innate immune responses that augment LAV immunogenicity. By contrast, at sub-neutralizing titers, pre-existing antibodies can enable viruses to better infect cells and increase innate immune responses that augment LAV immunogenicity. cache = ./cache/cord-313312-h607itv2.txt txt = ./txt/cord-313312-h607itv2.txt === reduce.pl bib === id = cord-315346-ebfjba4y author = Cummings, Kristin J. title = Exposure to Influenza Virus Aerosols in the Hospital Setting: Is Routine Patient Care an Aerosol Generating Procedure? date = 2014-03-04 pages = extension = .txt mime = text/plain words = 967 sentences = 52 flesch = 39 summary = title: Exposure to Influenza Virus Aerosols in the Hospital Setting: Is Routine Patient Care an Aerosol Generating Procedure? As the authors note, current World Health Organization and Centers for Disease Control and Prevention guidelines for protection of healthcare professionals from influenza virus infection rely on the supposition that, under routine conditions, most transmission occurs via large droplets, rather than via smallparticle aerosols [2, 3] . On each day, influenza virus RNA was detected in particles of respirable size, but a relationship to what we considered to be potential AGPs (mechanical ventilation, suctioning, extubation, and use of an incentive spirometer) was not evident. Indeed, potential respiratory exposures to healthcare professionals in the room appeared highest on hospital day 4, when the patient was breathing on his own and care was routine. This observation corroborates previous work [5] [6] [7] and raises the possibility that aerosol transmission of influenza virus may occur during routine patient care [8] . cache = ./cache/cord-315346-ebfjba4y.txt txt = ./txt/cord-315346-ebfjba4y.txt === reduce.pl bib === id = cord-314325-nquov2i0 author = Murphy, F.A. title = Epidemiology of Human and Animal Viral Diseases date = 2008-07-30 pages = extension = .txt mime = text/plain words = 5495 sentences = 245 flesch = 38 summary = Viral disease epidemiology has come to have a major role in clarifying the etiologic role of particular viruses and viral variants as the cause of specific diseases, in improving our understanding of the overall nature of specific viral diseases, and in determining factors affecting host susceptibility and immunity, in unraveling modes of transmission, in clarifying the interaction of viruses with environmental determinants of disease, in determining the safety, efficacy, and utility of vaccines and antiviral drugs, and especially in alerting and directing disease prevention and control actions. Epidemiology is also effective in (1) clarifying the role of particular viruses and viral variants as the cause of disease, (2) clarifying the interaction of viruses with environmental determinants of disease, (3) determining factors affecting host susceptibility, (4) unraveling modes of transmission, and (5) field testing of vaccines and antiviral drugs. cache = ./cache/cord-314325-nquov2i0.txt txt = ./txt/cord-314325-nquov2i0.txt === reduce.pl bib === id = cord-314166-79323mzd author = Vanderford, Thomas H. title = Adaptation of a Diverse Simian Immunodeficiency Virus Population to a New Host Is Revealed through a Systematic Approach to Identify Amino Acid Sites under Selection date = 2006-12-11 pages = extension = .txt mime = text/plain words = 6453 sentences = 275 flesch = 45 summary = Here, employing previously unused numerical analyses and a more comprehensive phylogenetic analysis of the same viral sequence data, we detect strong RM-specific selection in the V2 loop at days 40 and 70 p.i., which underscores this region's importance in adaptation to the RMs. Most prominently, changes in the position and frequency of an N-glyc motif in the V2 loop likely represent an adaptation either to a divergent CD4 or chemokine coreceptor or to an as-of-yet undetermined target cell population. Taken together, these data suggest that in addition to overall differences in the allelic structure of the SIVsm populations between the 2 host species, the viruses replicating in RMs are significantly more diverged from the SI than viruses replicating in the newly infected SMs. To identify specific amino acid sites that may be responsible for the disparate evolutionary patterns of viruses replicating in the 2 monkey species, we applied 3 site-bysite analyses to detect particular codons under selection. cache = ./cache/cord-314166-79323mzd.txt txt = ./txt/cord-314166-79323mzd.txt === reduce.pl bib === id = cord-311382-ioemd0ij author = Tellier, Raymond title = Recognition of aerosol transmission of infectious agents: a commentary date = 2019-01-31 pages = extension = .txt mime = text/plain words = 5339 sentences = 235 flesch = 39 summary = For example, when the infectious dose (the number of infectious agents required to cause disease) of an organism is low, and where large numbers of pathogen-laden droplets are produced in crowded conditions with poor ventilation (in hospital waiting rooms, in lecture theatres, on public transport, etc.), explosive outbreaks can still occur, even with pathogens whose airborne transmission capacity is controversial, e.g. the spread of influenza in a grounded plane where multiple secondary cases were observed in the absence of any ventilation [11] . For example, tighter control of the environment may reduce or prevent airborne transmission by: 1) isolating infectious patients in a single-bed, negative pressure isolation room [25] ; 2) controlling environmental relative humidity to reduce airborne influenza survival [59] ; 3) reducing exposure from aerosols produced by patients through coughing, sneezing or breathing with the use of personal protective equipment (wearing a mask) on the patient (to reduce source emission) and/or the healthcare worker (to reduce recipient exposure) [60] ; 4) carefully controlling the use and exposure to any respiratory assist devices (high-flow oxygen masks, nebulizers) by only allowing their use in designated, containment areas or rooms [61] . cache = ./cache/cord-311382-ioemd0ij.txt txt = ./txt/cord-311382-ioemd0ij.txt === reduce.pl bib === id = cord-313301-7mkadtp9 author = Duffy, Siobain title = EVOLUTION OF HOST SPECIFICITY DRIVES REPRODUCTIVE ISOLATION AMONG RNA VIRUSES date = 2007-08-23 pages = extension = .txt mime = text/plain words = 6091 sentences = 273 flesch = 45 summary = In particular, the high pernucleotide mutation rates of RNA viruses (Drake 1993) provide extensive genetic variation that fuels evolution by natural selection, making the study of reproductive isolation and speciation especially feasible (Holmes 2004) . We tested the plausibility of the no-gene mechanism of speciation by examining the consequences of adaptation to a novel host in laboratory populations of the RNA phage 6, which infects a number of Pseudomonas species. The same microevolutionary processes of mutation and natural selection, which led to the adaptation of 6 populations to a novel host also resulted in a macroevolutionary event: the evolution of a new virus species that is reproductively isolated from the ancestral phage 6 wt . Beyond uniquely demonstrating the evolution of reproductive isolation in the laboratory, our study extends the literature describing the evolutionary genetics of narrowed host range when viruses adapt to a single host. cache = ./cache/cord-313301-7mkadtp9.txt txt = ./txt/cord-313301-7mkadtp9.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-316245-n6tmn4ph author = Cui, Binglin title = Viral aetiology of acute respiratory infections among children and associated meteorological factors in southern China date = 2015-03-13 pages = extension = .txt mime = text/plain words = 4993 sentences = 247 flesch = 43 summary = METHODS: Paired nasal/throat-flocked swabs collected from 1,074 children with ARIs, who visited outpatient walk-in clinics in a tertiary hospital between December 2010 and November 2011, were examined for fourteen respiratory viruses influenza viruses (FluA, FluB), respiratory syncytial viruses (RSV A and B), human coronaviruses (hCoV: 229E, OC43, HKU1, NL63), human metapneumoviruses (hMPV A and B), parainfluenza viruses (PIV1-4), human rhinoviruses (HRV A, B, C), enteroviruses (EV), adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV) by multiplex real-time PCR. Multiplex real-time PCR was performed using Roche, Lightcycler 480 II (Roche Diagnostics, Penzberg, Germany) to identify the following 14 respiratory viruses: influenza A (FluA), influenza B (FluB), respiratory syncytial viruses A and B (RSV), human coronaviruses 229E, OC43, HKU1 and NL63 (hCoV), human metapneumoviruses A and B (hMPV), human parainfluenza virus types 1, 2 , 3, and 4 (PIV1, PIV2, PIV3, and PIV4), human rhinoviruses A, B, and C (HRV), human enteroviruses (EV), human adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV). cache = ./cache/cord-316245-n6tmn4ph.txt txt = ./txt/cord-316245-n6tmn4ph.txt === reduce.pl bib === id = cord-316295-x636ux34 author = Roth, Bernhard title = Isolation of influenza viruses in MDCK 33016PF cells and clearance of contaminating respiratory viruses date = 2012-01-11 pages = extension = .txt mime = text/plain words = 4140 sentences = 190 flesch = 44 summary = Abstract This paper summarizes results obtained by multiplex PCR screening of human clinical samples for respiratory viruses and corresponding data obtained after passaging of virus-positive samples in MDCK 33016PF cells. Using lower inoculum dilutions than those normally applied for preparations containing influenza virus (total dilution of the original sample of ∼104), the positive results for the different viruses turned negative already after 2 or 3 passages in MDCK 33016PF cells. In a similar way, samples with positive and questionable multiplex PCR results only for viruses other than influenza virus were also cultivated for 2 or 3 passages in MDCK 33016PF cells. Considering the selection of specimens, the high percentage of influenza-positive results is not surprising, but a significant number of samples (66/370 or 17.8%) also tested positive for other viruses, such as adenovirus, bocavirus, coronavirus, enterovirus, metapneumovirus (HMPV), parainfluenza virus (PIV), rhinovirus, and respiratory syncytial virus (RSV). cache = ./cache/cord-316295-x636ux34.txt txt = ./txt/cord-316295-x636ux34.txt === reduce.pl bib === id = cord-311012-wyglrpqh author = Meyers, Craig title = Ethanol and Isopropanol Inactivation of Human Coronavirus on Hard Surfaces date = 2020-09-28 pages = extension = .txt mime = text/plain words = 3271 sentences = 171 flesch = 54 summary = AIM: There are few data showing the efficacy of multiple concentrations of EtOH, IPA, and SH on a human coronavirus (HCoV) dried on surfaces using short contact times. FINDINGS: Concentrations of EtOH and IPA from 62% to 80% were very efficient at inactivating high numbers of HCoV dried on tile surfaces even with a 15 sec contact time. CONCLUSIONS: EtOH, IPA, and SH at multiple concentrations efficiently inactivated infectious virus on hard surfaces, typical of those found in public places. Interestingly, at the highest concentrations tested, 95% EtOH and 95% IPA, we observed significant reductions in inactivating, with some contact times producing less than a 2 log 10 reduction of infectious virus. Our studies demonstrate that EtOH and IPA at concentrations ranging from 62% to 80% are highly effective at inactivating HCoV on tile surfaces even with contact times as low as 15 sec. cache = ./cache/cord-311012-wyglrpqh.txt txt = ./txt/cord-311012-wyglrpqh.txt === reduce.pl bib === id = cord-315781-dejh8q22 author = Konishi, Tomokazu title = Re-evaluation of the evolution of influenza H1 viruses using direct PCA date = 2019-12-17 pages = extension = .txt mime = text/plain words = 4590 sentences = 308 flesch = 65 summary = It should be noted that avian viruses showed lower PC values and appeared around the centre of the PCA, while swine and human viruses exhibited extreme values (Figs. Thus, avian viruses had sequences that were similar to the average among samples at amino acids that were characteristic to the three groups of human and swine viruses: R, M, and U. Avian samples also showed characteristic motifs at other positions, which may appear in lower PCs. The relationships observed among the strains presented here are different from the classic ones 4, [8] [9] [10] [11] [12] in several elements. www.nature.com/scientificreports www.nature.com/scientificreports/ One of the major differences observed was the direct shift from avian to swine or human viruses. Drifts and spreading: the genomes of the R group of human viruses have been changing yearly (Figs. cache = ./cache/cord-315781-dejh8q22.txt txt = ./txt/cord-315781-dejh8q22.txt === reduce.pl bib === id = cord-316951-1swlhdz5 author = Kennedy, Melissa title = General concepts of virology date = 2005-03-01 pages = extension = .txt mime = text/plain words = 1643 sentences = 107 flesch = 50 summary = Virus pathogenesis is defined as the mechanism by which a virus replicates in the cell, and in doing so, injures a cell and produces disease. The virus must first attach to a cell by way of a surface receptor, followed by entry or penetration into the cell The virus uncoats within the cell and releases its nucleic acid For most viruses, the next step is viral transcription to produce mRNA. Genetic characteristics of the host include species, breed, organ, tissue susceptibility, and function at the cellular level (eg, cell receptor types and intracellular hospitality to the virus). It is defined as the specific cells and tissue in the host in which the virus replicates in a natural infection. A basic understanding of viruses and how they replicate and produce disease can aid in the management of virus infections. A basic understanding of viruses and how they replicate and produce disease can aid in the management of virus infections. cache = ./cache/cord-316951-1swlhdz5.txt txt = ./txt/cord-316951-1swlhdz5.txt === reduce.pl bib === id = cord-315167-ph15z424 author = Goka, E. A. title = Pan-human coronavirus and human bocavirus SYBR Green and TaqMan PCR assays; use in studying influenza A viruses co-infection and risk of hospitalization date = 2014-12-05 pages = extension = .txt mime = text/plain words = 3311 sentences = 185 flesch = 52 summary = title: Pan-human coronavirus and human bocavirus SYBR Green and TaqMan PCR assays; use in studying influenza A viruses co-infection and risk of hospitalization This study investigated the association between influenza A viruses co-infection with hBoV and hCoV and severity and the sensitivity of a real-time polymerase chain reaction (RT-PCR) assay for identification of 15 coronaviruses. A series of 217 samples from patients aged 37.7 (SD ± 30.4)] with seasonal influenza A viruses (SeasFluA) identified between 06/2011 and 06/2012 in NW England were tested for hCoV and hBoV using RT-PCR. RESULTS: The limit of detection of hCoV RT-PCR assay was 2 copies/µl of human coronavirus RNA template, a sensitivity comparable to a previously published SYBR green assay for human coronaviruses. This study did not find a significant association between seasonal influenza A viruses co-infection with hCoV and hBoV and severe disease. cache = ./cache/cord-315167-ph15z424.txt txt = ./txt/cord-315167-ph15z424.txt === reduce.pl bib === id = cord-312688-12san3m7 author = Martin, Baptiste title = Filovirus proteins for antiviral drug discovery: A structure/function analysis of surface glycoproteins and virus entry date = 2016-09-14 pages = extension = .txt mime = text/plain words = 10226 sentences = 530 flesch = 50 summary = title: Filovirus proteins for antiviral drug discovery: A structure/function analysis of surface glycoproteins and virus entry After replication of the viral genome and RNA transcription, nascent viral particles are assembled in a process mediated by the matrix protein VP40, and virus budding occurs at the cell surface membrane in a process that involves hijacking the host ESCRT machinery (Hartlieb and Weissenhorn, 2006; Noda et al., 2006) . However, no direct interaction between both molecules has been demonstrated yet, and recent studies suggest that a 5 b 1 -integrin is not required for GP-mediated binding of internalization, but rather is a positive regulator of cathepsins, which play an important role in processing GP 1 into its fusion-competent form within the endosomes of infected cells (Schornberg et al., 2009) . After attachment mediated by interaction between the filovirus surface protein GP 1,2 (PDB: 3CSY) and various attachment factors, the complex is internalized and routed to the endosome, where GP 1,2 is processed to trigger fusion of viral and host membranes. cache = ./cache/cord-312688-12san3m7.txt txt = ./txt/cord-312688-12san3m7.txt === reduce.pl bib === id = cord-314201-6njwigco author = Maher-Sturgess, Sheryl L title = Universal primers that amplify RNA from all three flavivirus subgroups date = 2008-01-24 pages = extension = .txt mime = text/plain words = 4625 sentences = 253 flesch = 54 summary = Tanaka [3] published the first universal primer pair specific for mosquito borne flaviviruses in 1993; the YF1 and YF3 primers targeted the NS5/3'UTR of the genome and were based upon the six flavivirus sequences available at the time. In 2005 Gaunt and Gould designed a universal nested PCR, using six primers targeting the E gene, capable of amplifying cDNA from 60 flavivirus strains. In the present study, we identified conserved sites and developed a universal, non-nested primer pair that amplifies cDNA from each of the major subgroups of flaviviruses, and also TABV, under standard reaction conditions. Since the amplified products represent 8% of the genome, this is sufficient sequence to determine the species of the virus and thus potentially to identify unrecognised flaviviruses. Rapid subgroup identification of the flaviviruses using degenerate primer E-gene RT-PCR and site specific restriction enzyme analysis cache = ./cache/cord-314201-6njwigco.txt txt = ./txt/cord-314201-6njwigco.txt === reduce.pl bib === id = cord-312332-rwmuucsp author = Dicker, Kate title = The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity date = 2020-09-10 pages = extension = .txt mime = text/plain words = 9235 sentences = 480 flesch = 45 summary = title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity Different proteomic studies have identified hundreds of cellular factors within the particles of several RNA viruses [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] , many of which are RBPs. Here, we discuss the 'knowns' and 'unknowns' of the roles that virion-incorporated cellular RBPs could play in the assembly of viral particles and the early steps of infection in the new host cell. Many ivRBPs such as annexins, heat shock family proteins (HSP), peptidylprolyl isomerase A (PPIA -also cyclophilin A), eukaryotic translation elongation factors (EEF), heterogeneous nuclear ribonucleoproteins (HNRNP) or poly(rC) binding protein 1 (PCBP1), have been linked to infection in multiple ways (Fig. S2) , and here we show that they are incorporated in the particles of several viruses (Table S1B) . cache = ./cache/cord-312332-rwmuucsp.txt txt = ./txt/cord-312332-rwmuucsp.txt === reduce.pl bib === id = cord-315131-4yb2b70g author = Hammerschmidt, Sven title = Threat of infection: Microbes of high pathogenic potential – strategies for detection, control and eradication date = 2005-06-28 pages = extension = .txt mime = text/plain words = 7177 sentences = 343 flesch = 40 summary = This report highlights some of the lectures that were presented during the international symposium 'Threat of infection: Microbes of high potential -strategies for detection, control and eradication' in July 2004 in Wu¨rzburg (Germany). E. Kaufmann (Max-Planck-Institute for Infection Biology (MPI), Berlin) suggested that the following vaccination strategies against intracellular bacteria deserve consideration: (i) attenuated viable strains, (ii) naked DNA encoding protective antigens and (iii) protective antigens expressed by recombinant viable vectors (bacteria or viruses). Based on the initial finding that several live-attenuated PrV vaccine strains lack a major surface antigen (glycoprotein E, gE) which is invariably present in all field strains (Mettenleiter et al., 1985) , a simple ELISA system has been developed that is able to specifically detect the presence or absence of anti-gE antibodies in the animal (van Oirschot et al., 1986) . cache = ./cache/cord-315131-4yb2b70g.txt txt = ./txt/cord-315131-4yb2b70g.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-317198-mean7sj9 author = Giamberardin, Heloisa I.G. title = Clinical and epidemiological features of respiratory virus infections in preschool children over two consecutive influenza seasons in southern Brazil date = 2016-02-09 pages = extension = .txt mime = text/plain words = 3534 sentences = 183 flesch = 48 summary = title: Clinical and epidemiological features of respiratory virus infections in preschool children over two consecutive influenza seasons in southern Brazil This study reports the results of a systematic screening for respiratory viruses in pediatric outpatients from an emergency department (ED) in southern Brazil during two consecutive influenza seasons. © 2016 Wiley Periodicals, Inc. Viral acute respiratory infections (ARIs) in pediatric outpatients represent a significant burden on emergency departments (EDs) and the patients' families, mainly during influenza seasons, being associated with around 20% of all deaths in pre-school children worldwide, with 90% of these deaths due to pneumonia. This study reports, the results of a laboratory-based surveillance for respiratory viruses in preschool children who were treated in the ED of a pediatric referral hospital during two consecutive influenza seasons. cache = ./cache/cord-317198-mean7sj9.txt txt = ./txt/cord-317198-mean7sj9.txt === reduce.pl bib === id = cord-317244-4su5on6s author = Maganga, Gael D. title = Identification of an Unclassified Paramyxovirus in Coleura afra: A Potential Case of Host Specificity date = 2014-12-31 pages = extension = .txt mime = text/plain words = 3476 sentences = 191 flesch = 50 summary = In the present study, among 985 bats belonging to 6 species sampled in the Belinga caves of Gabon, RNA of an unclassified paramyxovirus (Belinga bat virus, BelPV) was discovered in 14 African sheath-tailed bats (Coleura afra), one of which exhibited several hemorrhagic lesions at necropsy, and viral sequence was obtained in two animals. To further investigate the presence of the virus in bat populations, a strain-specific real-time RT-PCR assay (primers: GB09-478-F, 59-GGCGGCTCTTAAAAGT-GAATG-39; GB09-478-R, 59-GCGGGGTCAAATTGGTCAT-39; probe: GB09-478-P, 59-TCCAGCACAAACATATCCGAGAAGGCTAG-39) was designed within the initial PCR fragment and was used to test total RNA extracted from mixed liver and spleen samples from each of all the other bat species. In order to determine the organ distribution of this virus in infected bats, total RNA was extracted from heart, liver, spleen, kidney, lung, intestine and brain samples from all 14 real-time RT-PCR-positive bats, as described previously, and screened, using the same strain-specific real-time RT-PCR assay shown above. cache = ./cache/cord-317244-4su5on6s.txt txt = ./txt/cord-317244-4su5on6s.txt === reduce.pl bib === id = cord-317404-jvtozj4v author = Santos, Marfran C.D. title = Spectroscopy with computational analysis in virological studies: A decade (2006–2016) date = 2017-09-21 pages = extension = .txt mime = text/plain words = 8440 sentences = 428 flesch = 43 summary = The potential of spectroscopic techniques in the detection and identification of virus-infected cells has been studied using statistical methods as a sensitive, rapid and reliable methodology. First, we will discuss the most commonly used spectroscopic techniques, then we will discuss the computational processes used to extract useful information from the obtained spectra (spectral preprocessing, multivariate classification algorithms, performance evaluation), and finally we will discuss some works published in the period from 2006 to 2016 using spectroscopy and multivariate analysis in studies involving viruses. For example, the potential of Raman spectroscopy followed by statistical methods in detecting and identifying Herpes Simplex Virus type 1 (HSV-1) infections as a sensitive, rapid and reliable method has been evaluated by Salman et al. (2014) [25] evaluated the potential of Raman spectroscopy as a sensitive, reliable and rapid method for detecting and identifying viral infection by Herpes simplex virus type 1 (HSV-1) in cell culture. cache = ./cache/cord-317404-jvtozj4v.txt txt = ./txt/cord-317404-jvtozj4v.txt === reduce.pl bib === id = cord-313598-2t40ss6h author = Ali, Mohsin title = Throat and nasal swabs for molecular detection of respiratory viruses in acute pharyngitis date = 2015-10-29 pages = extension = .txt mime = text/plain words = 2367 sentences = 115 flesch = 50 summary = Our objective was to determine whether sampling with a throat swab provides incremental benefit—when used in conjunction with a nasal swab—to detect respiratory viruses among patients with acute pharyngitis in the outpatient setting. FINDINGS: Among 83 university students with acute pharyngitis, we detected respiratory viruses with molecular assays on two samples collected per student: with a flocked nasal mid-turbinate swab and a rayon throat swab. Our primary objective was to determine whether sampling with a throat swab provides incremental benefit-when used in conjunction with a nasal swab-to detect respiratory viruses among adults with acute pharyngitis. In addition, previous research among adults has shown that flocked nasal mid-turbinate swabs are as sensitive for respiratory virus testing as flocked nasopharyngeal swabs, and since nasal mid-turbinate swabs are more comfortable and acceptable for patients, these swabs are preferred for sample collection in outpatient studies [5] . cache = ./cache/cord-313598-2t40ss6h.txt txt = ./txt/cord-313598-2t40ss6h.txt === reduce.pl bib === id = cord-316063-9bg2dm8e author = Morgan, Marcus title = Why meaning-making matters: the case of the UK Government’s COVID-19 response date = 2020-10-15 pages = extension = .txt mime = text/plain words = 25744 sentences = 1020 flesch = 52 summary = The paper also offers more specific contributions to cultural sociology by showing why social performance theory needs to consider the effects of casting non-human actors in social dramas, how metaphor forms a powerful tool of political action through simplifying and shaping complex realities, and how casting can shift responsibility and redefine the meaning of emotionally charged events such as human death. On 28th February, the first death of a British national occurred on the quarantined Diamond Princess cruise ship, and the Sunday Times reported that around the same time Dominic Cummings (Johnson's Chief Advisor, and former director of the successful Vote Leave campaign) had 'outlined the government's strategy' for the UK's national response to the virus 'at a private engagement', quoting those present as claiming that it was 'herd immunity, protect the economy, and if that means some pensioners die, too bad' (Shipman and Wheeler 2020) . cache = ./cache/cord-316063-9bg2dm8e.txt txt = ./txt/cord-316063-9bg2dm8e.txt === reduce.pl bib === id = cord-316996-8yimrpaz author = Nicholls, John M. title = The use of sialidase therapy for respiratory viral infections date = 2013-04-17 pages = extension = .txt mime = text/plain words = 7337 sentences = 340 flesch = 43 summary = DAS181 is an inhaled bacterial sialidase which functions by removing sialic acid (Sia) from the surface of epithelial cells, preventing attachment and subsequent infection by respiratory viruses that utilize Sia as a receptor. DAS181 is the first antiviral compound in Phase II development that functions by blocking this pathogen-host interaction, by destroying the influenza host-cell receptor, sialic acid (Sia), on the surface of respiratory epithelial cells. In this paper, we provide background information on Sia and sialidases; discuss the potential role of bacterial sialidases as antiviral agents; review the in vitro and Phase II evaluation of DAS181 for the treatment of influenza; and note evidence that the drug would also be useful against parainfluenza virus infections. Even though influenza virus has been the most well characterized of the pathogens studied, it must be noted that other viruses, including cytomegalovirus (Taylor and Cooper, 1989) , rhinovirus 87 (Blomqvist et al., 2002) , mumps Urabe AM9 (ReyesLeyva et al., 2007) and the paramyxoviruses all utilize Sia (Suzuki et al., 2001) (Paulson et al., 1979) , suggesting that sialidase treatment may potentially be useful for these infections. cache = ./cache/cord-316996-8yimrpaz.txt txt = ./txt/cord-316996-8yimrpaz.txt === reduce.pl bib === id = cord-315918-12rbbe8c author = Mukherjee, Pulok K. title = Antiviral Evaluation of Herbal Drugs date = 2019-06-21 pages = extension = .txt mime = text/plain words = 12776 sentences = 660 flesch = 49 summary = To test the inhibitory activity of a new antiviral agent, it is first necessary to select the host cell system(s) in which the virus replication can be measured. (d) Assay systems based on the measurement of specialized functions and viral products; a number of viruses do not produce plaques nor do they cause CPE readily, but they may be quantified by certain specialized functions based on their unique properties, for example, hemagglutination and hemadsorption tests used to study the antiviral activity against myxoviruses and ELISA, used to determine the extent of virus replication and, thus, obtain a measure of the inhibitory effect of various antiviral agents on virus replication, etc. On the other hand, the antiviral activity is determined by comparing the virus titers of infected cells, which have been cultured with a maintenance medium containing plant extracts or test substances and a maintenance medium without test material (Colegate and Molyneux, 1993) . cache = ./cache/cord-315918-12rbbe8c.txt txt = ./txt/cord-315918-12rbbe8c.txt === reduce.pl bib === id = cord-316273-vo6j8zb0 author = Cosset, François-Loic title = Cell Entry of Enveloped Viruses date = 2011-02-08 pages = extension = .txt mime = text/plain words = 23421 sentences = 1013 flesch = 40 summary = On the one hand, they acquired a domain to bind to a specific cellular protein, named "receptor." On the other hand, they developed in a different manner, according to the genus of the virus, a function of fusion that allows the destabilization of the membrane and the opening of a pore through which the genetic material will enter the cell. Thus, we need to distinguish cell surface molecules such as heparan sulfate proteoglycans, DC-SIGN, or integrins that can enhance infections by concentrating retroviruses onto cells (Bounou et al., 2002; Geijtenbeek et al., 2000; Jinno-Oue et al., 2001; Mondor et al., 1998; Pohlmann et al., 2001; Saphire et al., 2001) from authentic receptors that induce conformational changes in EnvGP that are a prerequisite for fusion of the viral and cellular membranes. cache = ./cache/cord-316273-vo6j8zb0.txt txt = ./txt/cord-316273-vo6j8zb0.txt === reduce.pl bib === id = cord-314825-fzba05wn author = Chauhan, Ravendra P. title = A Systematic Review Analyzing the Prevalence and Circulation of Influenza Viruses in Swine Population Worldwide date = 2020-05-08 pages = extension = .txt mime = text/plain words = 22346 sentences = 1098 flesch = 52 summary = cache = ./cache/cord-314825-fzba05wn.txt txt = ./txt/cord-314825-fzba05wn.txt === reduce.pl bib === id = cord-318172-bdotp9ko author = Blanco, Jorge C. G. title = PROPHYLACTIC ANTIBODY TREATMENT AND INTRAMUSCULAR IMMUNIZATION REDUCE INFECTIOUS HUMAN RHINOVIRUS 16 LOAD IN THE LOWER RESPIRATORY TRACT OF CHALLENGED COTTON RATS date = 2014-01-01 pages = extension = .txt mime = text/plain words = 5190 sentences = 250 flesch = 42 summary = In this work we show that, without requiring any genetic modification of either the host or the virus, intranasal infection of cotton rats with HRV16 resulted in measurable lower respiratory tract pathology, mucus production, and expression of interferon-activated genes. Over the years, the cotton rat (Sigmodon hispidus) has been shown to support replication of a broad spectrum of human viruses including respiratory syncytial virus (RSV) [25] , nonadapted strains of human influenza [26, 27] , and measles [28, 29] , among others [30] , providing modeling capabilities for the corresponding infections. The results of the described experimental work show that HRV16 infection in the cotton rat reproduces aspects of HRVassociated human disease in the respiratory tract, causing detectable inflammation in the lower airways and lung parenchyma and mucus production, and inducing a transient expression of interferon-stimulated genes that merits further investigation. In addition we demonstrated that passive transfer of antibodies generated in vaccinated cotton rats can protect naïve animals from Infectious virus titers in the lung were determined by plaque assay at the indicated times p.i. cache = ./cache/cord-318172-bdotp9ko.txt txt = ./txt/cord-318172-bdotp9ko.txt === reduce.pl bib === id = cord-317501-yblzopc3 author = Kuhn, Philipp title = Recombinant antibodies for diagnostics and therapy against pathogens and toxins generated by phage display date = 2016-06-21 pages = extension = .txt mime = text/plain words = 11086 sentences = 593 flesch = 35 summary = Panning against peptides, recombinant viral proteins, or complete virus particles has led to the identification of antibodies directed against human pathogenic viruses such as Sin nombre virus [100] , Dengue virus [101, 102] , Influenza virus [103, 104] , VEEV [105] , Norovirus [106] , SARS coronavirus [107] , or Hepatitis C [108] from naïve antibody gene libraries. A naïve human Fab-phage library was screened for NS5-specific antibody fragments using various NS5 variants from Dengue Virus serotypes 1-4 as antigens for panning and characterization [128] . [180] reported the isolation of a human monoclonal antibody against the Block 2 region of Plasmodium falciparum merozoite surface protein-1 (PfMSP-1) by phage display from a malaria patient derived scFv library. In this context, the antibody phage display offers a powerful tool for antibody selection and allows the isolation of neutralizing antibodies against complete active toxins or special domains by using different human naïve antibody libraries with high diversity [185] [186] [187] . Single chain variable fragment antibodies against Shiga toxins isolated from a human antibody phage display library cache = ./cache/cord-317501-yblzopc3.txt txt = ./txt/cord-317501-yblzopc3.txt === reduce.pl bib === id = cord-316682-4360s2yu author = Fischer, William A. title = Personal Protective Equipment: Protecting Health Care Providers in an Ebola Outbreak date = 2015-11-01 pages = extension = .txt mime = text/plain words = 5052 sentences = 241 flesch = 47 summary = Given that the Ebola virus is primarily transmitted through direct contact of mucous membranes and cuts in the skin with infected patients and/or their bodily fluids, it is necessary to cover these potential portals of infection with PPE as part of a structured and instructed donning and doffing procedure. Personal protective equipment (PPE) plays a critical role in mitigating the risk of health care personnel (HCP) exposure to contaminated body fluids in the care of patients with communicable infectious diseases, including EVD. 5 In the PAPR PPE set HCP wore a Tyvek (DuPont, Wilmington, Delaware) suit, shoe covers, a surgical gown, and a large hood, whereas the enhanced respiratory and contact precautions system included only a surgical gown, indicating that a second covering significantly reduced exposure to contaminated body fluids and provided evidence for the use of aprons on top of gowns or coveralls in the care of Ebola-infected patients. cache = ./cache/cord-316682-4360s2yu.txt txt = ./txt/cord-316682-4360s2yu.txt === reduce.pl bib === id = cord-317277-rr9zue4l author = Cifuentes-Munoz, Nicolas title = Viral cell-to-cell spread: Conventional and non-conventional ways date = 2020-09-29 pages = extension = .txt mime = text/plain words = 13085 sentences = 638 flesch = 45 summary = Cell-free viral particles can be released into the extracellular space through different mechanisms, such as: (a) cell lysis induced by viral proteins, as is the case for many non-enveloped viruses such as reoviruses, rotaviruses, adenoviruses and picornaviruses (Giorda and Hebert, 2013; Hu et al., 2012; Nieva et al., 2012) ; (b) by budding directly from the plasma membrane, where virions acquire their envelope, as is the case of human immunodeficiency virus (HIV-1), influenza, paramyxoviruses, and pneumoviruses (Lorizate and Krausslich, 2011; Votteler and Sundquist, 2013; Weissenhorn et al., 2013) ; (c) by exocytosis of intracellularly assembled viral particles, as is the case for bunyaviruses, flaviviruses and coronaviruses (Cifuentes-Munoz et al., 2014; Lorizate and Krausslich, 2011) . An interesting observation made for alphaviruses is that the filopodia-like extensions are not able to transfer cytosolic or plasma membrane components, suggesting they are not openended connections like TNTs. Instead, viral particles are hypothesized to bud into a protected space at the filopodial tip and then rapidly enter the target cell, preventing access of neutralizing antibodies. cache = ./cache/cord-317277-rr9zue4l.txt txt = ./txt/cord-317277-rr9zue4l.txt === reduce.pl bib === id = cord-317851-lj07947c author = Elena, S F title = Experimental evolution of plant RNA viruses date = 2008-02-06 pages = extension = .txt mime = text/plain words = 4184 sentences = 191 flesch = 42 summary = In this review, we will focus on recent studies that used plant viruses to address evolutionary questions of general interest, such as the rate and fitness effects of deleterious mutations and the role of neutrality as a source of mutational robustness, the evolution of generalist viruses, or the effect of vertical versus horizontal transmission on virulence. Despite mutation rate is still high compared to that of DNA-based microorganisms, a classic field observation is that natural plant virus populations generally exhibit limited genetic variation (García-Arenal et al., 2001) , which may imply either that purifying selection may be strong or that genome replication occurs mainly by Luria's stamping machine model (Luria, 1951) rather than exponentially (French and Stenger, 2003) , the two hypotheses being nonexclusive. cache = ./cache/cord-317851-lj07947c.txt txt = ./txt/cord-317851-lj07947c.txt === reduce.pl bib === id = cord-317971-kuwargnp author = Opatz, Till title = Thoughts on What Chemists Can Contribute to Fighting SARS‐CoV‐2 – A Short Note on Hand Sanitizers, Drug Candidates and Outreach date = 2020-05-08 pages = extension = .txt mime = text/plain words = 2881 sentences = 176 flesch = 53 summary = [11] Exposure to concentrations of just 30 % of either ethanol or isopropanol for 30 seconds fully suppressed viral infectivity.Likewise,the virucidal activity of the hand rub solutions known as WHO formulation 1, with 85 % ethanol, and WHO formulation 2, with 75 %i sopropanol, against SARS-CoV-2 was found to be excellent, with full inactivation of the coronavirus at 40 %or30%concentration, respectively.W hile the alcohol component is the main virucide,0 .125 % v/v H 2 O 2 is added to kill bacterial spores that may be present in the raw materials or the container.The addition of 1.45 % v/v glycerol as ah umectant improves the dermatological properties and thus the acceptance of the product. cache = ./cache/cord-317971-kuwargnp.txt txt = ./txt/cord-317971-kuwargnp.txt === reduce.pl bib === id = cord-318725-09a32vyg author = Dong, Rui title = Virus Database and Online Inquiry System Based on Natural Vectors date = 2017-12-17 pages = extension = .txt mime = text/plain words = 3379 sentences = 204 flesch = 52 summary = The database stores all viral genomes, their corresponding natural vectors, and the classification information of the single/multiple-segmented viral reference sequences downloaded from National Center for Biotechnology Information. The online inquiry system serves the purpose of computing natural vectors and their distances based on submitted genomes, providing an online interface for accessing and using the database for viral classification and prediction, and back-end processes for automatic and manual updating of database content to synchronize with GenBank. Using the natural vector representation, if a viral genome consists of a single-nucleotide sequence, known as single-segmented, then the virus will be represented by a 12-dimensional numerical vector in the database. As natural vector can reflect core information stored in sequences and genomes, we use it to construct the virus classification system introduced in this article. cache = ./cache/cord-318725-09a32vyg.txt txt = ./txt/cord-318725-09a32vyg.txt === reduce.pl bib === id = cord-319746-6bccxgbd author = Saxena, Latika title = Production and Characterization of Human Monoclonal Antibodies from the Cells of A(H1N1)pdm2009 Influenza Virus Infected Indian Donors date = 2015-12-31 pages = extension = .txt mime = text/plain words = 3526 sentences = 174 flesch = 48 summary = title: Production and Characterization of Human Monoclonal Antibodies from the Cells of A(H1N1)pdm2009 Influenza Virus Infected Indian Donors Abstract Analysis of human monoclonal antibodies (mAbs) developed from influenza infected donors have enormously contributed to the identification of neutralization sensitive epitopes of influenza virus. In this study, we generated strongly neutralizing novel human monoclonal antibodies that were selected from the immune repertoire of influenza infected seropositive patients. Monoclonal antibody 2D8 showed the maximum binding in the in vitro assays and neutralized the human isolate of the pandemic strain as well as the reference strain at lowest concentrations when compared to the 2F12 antibody. The antibodies however, showed comparative neutralization and HAI activity between the laboratory isolates of the pandemic virus and the reference strain A/Cal/07/2009(H1N1). To, the best of our knowledge, these antibodies are the first fully human monoclonal antibodies generated from the immune repertoire of Indian patients infected with A(H1N1)pdm09 virus. cache = ./cache/cord-319746-6bccxgbd.txt txt = ./txt/cord-319746-6bccxgbd.txt === reduce.pl bib === id = cord-317496-6o2upns3 author = Pascual-Iglesias, Alejandro title = Recombinant Chimeric Transmissible Gastroenteritis Virus (TGEV)—Porcine Epidemic Diarrhea Virus (PEDV) Virus Provides Protection against Virulent PEDV date = 2019-07-25 pages = extension = .txt mime = text/plain words = 7100 sentences = 404 flesch = 48 summary = In this line, we engineered an attenuated virus based on the transmissible gastroenteritis virus (TGEV) genome, expressing a chimeric spike protein from a virulent United States (US) PEDV strain. The rTGEV-RS-SPEDV vaccine candidate was also attenuated in three-week-old animals that were used to evaluate the protection conferred by this virus, compared with the protection induced by infection with a virulent PEDV US strain (PEDV-NVSL). Interestingly, Viruses 2019, 11, 682 9 of 18 when viral RNA was isolated from feces of 21-day-old piglets at seven days post-vaccination (see below) and rTGEV-RS-SPEDV virus was sequenced, the same modifications were observed. An attenuated chimeric rTGEV virus expressing the ectodomain of a virulent US PEDV S protein (rTGEV-RS-SPEDV) was engineered as vaccine candidate for PEDV and evaluated in a young piglet model system. An attenuated chimeric rTGEV virus expressing the ectodomain of a virulent US PEDV S protein (rTGEV-RS-SPEDV) was engineered as vaccine candidate for PEDV and evaluated in a young piglet model system. cache = ./cache/cord-317496-6o2upns3.txt txt = ./txt/cord-317496-6o2upns3.txt === reduce.pl bib === id = cord-316894-zhmuzv7z author = Stetzenbach, L.D. title = Airborne Infectious Microorganisms date = 2009-02-17 pages = extension = .txt mime = text/plain words = 4393 sentences = 259 flesch = 40 summary = Viral diseases presented are influenza, severe acute respiratory syndrome (SARS), Norwalk-like viruses (NLVs) and hantavirus disease, measles, and varicella. Exposure to some Gram-negative and Gram-positive bacteria, endotoxin, and actinomycetes when dispersed through the air can result in disease following inhalation. Inhalation of microbial aerosols can elicit adverse human health effects including infection, allergic reaction, inflammation, and respiratory disease. Inhalation of microbial aerosols can elicit adverse human health effects including infection, allergic reaction, inflammation, and respiratory disease. The illnesses resulting from avian influenza infection in humans range from typical mild influenza-like symptoms (e.g., fever, sore throat, cough, and muscle aches) and conjunctivitis to more serious cases of pneumonia, acute respiratory distress, and other severe and life-threatening complications. Disease is spread by aerosol dissemination of the virus during coughing and sneezing by an infected person or it may become airborne directly from the skin lesions. cache = ./cache/cord-316894-zhmuzv7z.txt txt = ./txt/cord-316894-zhmuzv7z.txt === reduce.pl bib === id = cord-319208-jrxz59bb author = Ting, Chun Yi title = Are identity badges and lanyards in pediatrics potentially contaminated with viral pathogens? date = 2015-11-01 pages = extension = .txt mime = text/plain words = 2011 sentences = 113 flesch = 47 summary = Identity (ID) badges and lanyards worn by pediatric health care workers (HCWs) have been shown to be potential vectors of nosocomial bacterial infections. This cross-sectional study determined the contamination of ID badges and lanyards worn by pediatric HCWs with common respiratory and gastrointestinal viruses. The results showed that ID badges and lanyards are not significantly contaminated with common respiratory or gastrointestinal viruses and are unlikely to be a significant vector for nosocomial infection. The principal aim of this study was to determine the contamination rates of ID badges and lanyards worn by pediatric HCWs with common respiratory and gastrointestinal viruses to evaluate their potential as vectors for both nosocomial and patient-topatient transmission of viruses. HCW ID samples were tested for respiratory viruses using viral PCR technique after an automated DNA-RNA extraction procedure, an identical process to routine clinical samples collected from pediatric patients. cache = ./cache/cord-319208-jrxz59bb.txt txt = ./txt/cord-319208-jrxz59bb.txt === reduce.pl bib === id = cord-318786-qd0k8174 author = Mauriz, Elba title = Recent Progress in Plasmonic Biosensing Schemes for Virus Detection date = 2020-08-22 pages = extension = .txt mime = text/plain words = 9868 sentences = 516 flesch = 35 summary = Technological advancements in plasmonic biosensing including colorimetric and fluorescence enhancement as well as the utilization of nanomaterials and optical aperture nanostructures for achieving highly sensitive virus detection are described in this section. Technological advancements in plasmonic biosensing including colorimetric and fluorescence enhancement as well as the utilization of nanomaterials and optical aperture nanostructures for achieving highly sensitive virus detection are described in this section. Typically, most of quantum dots' applications have been exploited in LSPR-based biosensors because the distance and dimensions of the adjacent gold nanoparticles can affect the fluorescence signal and, therefore, be quenched depending on the analyte concentration. Typically, most of quantum dots' applications have been exploited in LSPR-based biosensors because the distance and dimensions of the adjacent gold nanoparticles can affect the fluorescence signal and, therefore, be quenched depending on the analyte concentration. cache = ./cache/cord-318786-qd0k8174.txt txt = ./txt/cord-318786-qd0k8174.txt === reduce.pl bib === id = cord-319754-5isw53wl author = Balgoma, David title = Lipidomics Issues on Human Positive ssRNA Virus Infection: An Update date = 2020-08-31 pages = extension = .txt mime = text/plain words = 12092 sentences = 541 flesch = 41 summary = Some viruses may use different entry mechanisms, this feature being likely dependent upon the membrane lipid composition of the host cell they infect as well as the particular cell surface factor attachment used. The question regarding whether the lipid-raft domains may serve as platforms to concentrate the proteins required for viral entry and, even though some evidence exists, to activate signaling pathways inside the host cell still remains unsolved. More recently, a Ca 2+ -dependent pathway of infection by the Rubella virus (RuV, Rubivirus family, Togaviridae) was demonstrated to proceed through direct binding of the fusion loop in the viral E1 protein to SM/cholesterol-enriched membranes [49] . More recently, a Ca 2+ -dependent pathway of infection by the Rubella virus (RuV, Rubivirus family, Togaviridae) was demonstrated to proceed through direct binding of the fusion loop in the viral E1 protein to SM/cholesterol-enriched membranes [49] . cache = ./cache/cord-319754-5isw53wl.txt txt = ./txt/cord-319754-5isw53wl.txt === reduce.pl bib === id = cord-318495-1w74wf02 author = Vignuzzi, Marco title = Defective viral genomes are key drivers of the virus–host interaction date = 2019-06-03 pages = extension = .txt mime = text/plain words = 8876 sentences = 429 flesch = 33 summary = The demonstration of hotspots for the generation of copyback DVGs from respiratory syncytial virus (RSV) and the identification of specific nucleotides that determine where copy-back DVGs rejoin further demonstrate that the generation of copy-back DVGs is not completely random, but instead that specific sequences encoded in the viral genome direct or facilitate their formation 50 in some infections, DVG generation is not a completely stochastic process and, instead, virus-encoded sequences favour the production and/or amplification of predominant DVGs. It remains to be determined whether conservation is a property of certain DVG types and which specific sequences and/or RNA structures lead to DVG generation in these conditions. Persistent infection with infectious pancreatic necrosis virus mediated by defective-interfering (DI) virus particles in a cell line showing strong interference but little DI replication I Interferon-inducing defective-interfering particles as mediators of cell sparing: possible role in persistent infection by vesicular stomatitis virus cache = ./cache/cord-318495-1w74wf02.txt txt = ./txt/cord-318495-1w74wf02.txt === reduce.pl bib === id = cord-317508-03u2vtzk author = Oldstone, M.B.A. title = History of Virology date = 2019-08-28 pages = extension = .txt mime = text/plain words = 1347 sentences = 73 flesch = 53 summary = were clinically evident in early human history, the initial isolation of individual viruses and their assignment to specific diseases did not occur until about 1898, 120 years ago, a proverbial drop in the bucket of time. Although the majority of life-threatening and debilitating acute virus infections are now controlled through vaccination, it is worthwhile considering the consequences of acute infections like smallpox, measles, and yellow fever in the prevaccine era. This devastating depopulation came primarily from smallpox and measles infections, since these viruses had never before existed in the New World (Oldstone, 2010) . However, measles virus infection was and remains a serious disease today with approximately one per thousand infected persons developing severe destruction of the central nervous system requiring institutionalization. Now these and many other acute virus infections are controlled by vaccination or antivirals and public health policies when and where they are instituted. cache = ./cache/cord-317508-03u2vtzk.txt txt = ./txt/cord-317508-03u2vtzk.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-319210-yqimufdh author = KENNEDY, P.G.E. title = On the possible viral aetiology of multiple sclerosis date = 1994-09-17 pages = extension = .txt mime = text/plain words = 3980 sentences = 181 flesch = 42 summary = 1 The presence of inflammatory histological changes in the MS lesions such as perivenular lymphocytic infiltration, and the raised cerebrospinal fluid (CSF) immunoglobulins in an oligoclonal pattern detected in most MS patients are very suggestive of an immune basis for the disease, 23 one that may possibly be related to some kind of viral infection. Although by their very nature animal models of virus-induced demyelination only produce a form of indirect evidence for the viral aetiology of MS, nevertheless they can reveal important insights into the possible mechanisms by which a virus can initiate a pathogenetic cascade leading to CNS myelin destruction. 36 In the brains, only a small percentage of the oligodendrocytes are infected with the virus, so the main mechanism of demyelination is almost certainly indirect, presumably via the generation of Class II antigen-induced T cell responses and release of cytokines and/or toxic viral proteins. cache = ./cache/cord-319210-yqimufdh.txt txt = ./txt/cord-319210-yqimufdh.txt === reduce.pl bib === id = cord-322748-a5131tv9 author = Yates, Mary K. title = Flex-nucleoside analogues – Novel therapeutics against filoviruses date = 2017-06-15 pages = extension = .txt mime = text/plain words = 1492 sentences = 78 flesch = 53 summary = Most recently GS-5734, a monophosphoramidate prodrug adenosine analogue which targets EBOV RNA-dependent RNA polymerase (RdRp), exhibited very potent activity against both EBOV and MARV, 17, 18 further demonstrating the potential for finding effective nucleoside inhibitors of filoviruses. After the successful synthesis of the three Flex-analogues 1, 2, and 3, the compounds were screened against a panel of filoviruses including EBOV, MARV, and SUDV, as well as other hemorrhagic fever viruses such as Lassa and Rift Valley Fever. The second series of assays utilized Huh7 cells infected with recombinant reporter EBOV, Lassa, and Rift Valley Fever viruses. Within this study we found that both compounds 1 and 3 exhibited antiviral activity against a recombinant reporter EBOV in Huh7 cells, though surprisingly the McGuigan prodrug was 10-fold less potent (EC 50 = 2.2 ± 0.3 lM and 27.2 ± 2.2 lM respectively). cache = ./cache/cord-322748-a5131tv9.txt txt = ./txt/cord-322748-a5131tv9.txt === reduce.pl bib === id = cord-317412-f3ua8ks3 author = Zhang, Xing title = Characterization of the lipidomic profile of BmN cells in response to Bombyx mori cytoplasmic polyhedrosis virus infection date = 2020-08-15 pages = extension = .txt mime = text/plain words = 2584 sentences = 186 flesch = 47 summary = Here, the lipid metabolism in BmCPV-infected BmN cells was studied by lipidomics analysis. Our previous studies have found alterations in a large number of genes related to important signaling pathways, including those associated with innate immunity, development and metabolism following BmCPV infection [3, 5] . An increasing number of studies in recent years have demonstrated changes of lipid metabolism in host cells after virus infection. It has been shown that infection by some single-stranded RNA(ssRNA) viruses can alter the lipid metabolism and other biological processes of the host cells to facilitate the completion of the virus life cycle [11] . Analysis of differential expressed circRNAs has revealed changes in the metabolism of fatty acids upon BmCPV infection [5] . In addition, fatty acid metabolism has been observed to be significantly changed by the differentially expressed circRNAs in the midgut of silkworms infected by BmCPV [5] . cache = ./cache/cord-317412-f3ua8ks3.txt txt = ./txt/cord-317412-f3ua8ks3.txt === reduce.pl bib === id = cord-318551-c1qr27lg author = Boguszewska‐Chachulska, Anna M. title = Rna Viruses Redirect Host Factors to Better Amplify Their Genome date = 2005-12-29 pages = extension = .txt mime = text/plain words = 10673 sentences = 511 flesch = 44 summary = (Adapted with permission from Pasternak et al., 2001.) Transcription of segmented (À) strand RNA viruses such as the Orthomyxoviridae, Arenaviridae, Bunyaviridae, and Tenuiviruses requires a primer to initiate synthesis of the mRNAs. This is achieved by cap-snatching in which the replicase complex, or a protein thereof, binds to the 5 0 region of cell mRNAs, cleaves off the cap together with generally 7-15 nucleotides from the 5 0 end of the cell mRNA, and uses this fragment as a primer to initiate synthesis of the viral mRNAs (Bouloy et al., 1978; Nguyen and Haenni, 2003) . (1996) PV, poliovirus; MHV, mouse hepatitis virus; WNV, West Nile virus; BVDV, bovine viral diarrhea virus; HPIV-3, human parainfluenza virus-3; IG (À), intergenic region in (À) RNA; UTR, untranslated region; Leader RNA (À), 3' end of (À) RNA; Leader RNA (þ), 5' end of (þ) RNA; HF, host factor; PCBP, poly(C)-binding protein; PABP, poly(A)-binding protein; hnRNP A1, heterogeneous nuclear ribonucleoprotein A1; PTB, polypyrimidine tract-binding protein; TIA-1, T-cell-activated intracellular antigen; TIAR, TIA-1-related; RHA, RNA helicase A; GAPDH, glyceraldehyde-3-phosphate dehydrogenase. cache = ./cache/cord-318551-c1qr27lg.txt txt = ./txt/cord-318551-c1qr27lg.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-319761-bu5pzbnv author = Miller, Craig S. title = Pleiotropic mechanisms of virus survival and persistence date = 2005-07-16 pages = extension = .txt mime = text/plain words = 5655 sentences = 308 flesch = 38 summary = Accordingly, this review focuses on specific viral cell interactions that allow the virus to survive the cellular attack and evade the immune system, establish persistent infections, and cause chronic disease. 13, 14 Viruses regulate apoptosis by several mechanisms including the targeting of the tumor suppressor gene product p53, the Fas death receptor, and by producing caspase inhibitors and viral Bcl-2 homologs. 24, 25 The alpha herpesvirus HSV-1 encodes several antiapoptotic gene products (ie, ICP4, ICP27, c34.5, U s 3, gJ) [26] [27] [28] [29] [30] that modulate apoptosis at several levels, including antagonism of double-stranded RNA-activated protein kinase (PKR), a downstream induction molecule of the interferon signaling pathway 31, 32 Of note, all c-herpesviruses express viral homologues of cellular antiapoptotic genes, including 1 or 2 Bcl-2 homologues. In the majority of infections, viruses encode products that antagonize either the IFN signal transduction pathway or cellular proteins induced by IFN that are responsible for inhibiting virus replication (Fig 2) . cache = ./cache/cord-319761-bu5pzbnv.txt txt = ./txt/cord-319761-bu5pzbnv.txt === reduce.pl bib === id = cord-321562-hk4hzl13 author = Liu, Xuan title = Cell membrane-derived biomimetic nanodecoys for viruses date = 2020-05-12 pages = extension = .txt mime = text/plain words = 1412 sentences = 78 flesch = 38 summary = Such pathogenic binding and entry mechanisms offer opportunities for developing broadly applicable anti-viral strategy, which subvert the interaction of specific membrane proteins and viruses. For viral infection inhibition, MVs mimicking cell-surface receptors could compete with native cellular receptors to bind to the specific ligands. To divert Zika virus (ZIKV) away from its intended targets, an anti-ZIKV host-mimicking nanodecoy (ND) constructed by wrapping a polymeric core with mosquito medium host cell membranes was developed (Rao et al., 2019) . What is perhaps most convenient about these cell membrane-based viral decoys is the natural binding ability of host cells that makes the exogenous engineering of receptor moieties unnecessary. Membrane vesicles derived from the modified cells, named hNTCP-MVs, were conferred important surface properties to play a specific biological function. cache = ./cache/cord-321562-hk4hzl13.txt txt = ./txt/cord-321562-hk4hzl13.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-320935-3n157yl4 author = Kumar, Manish title = Making Waves Perspectives of Modelling and Monitoring of SARS-CoV-2 in Aquatic Environment for COVID-19 Pandemic date = 2020-09-12 pages = extension = .txt mime = text/plain words = 6613 sentences = 346 flesch = 44 summary = This paper aims to collate information on recent developments on WBE in monitoring the trend of community-scale SARS-CoV-2 prevalence as well as models to predict virus spread and transmission among populations. While several studies have identified the presence of SARS-CoV-2 in the faecal matter of corona-infected patients [35, 36] , there is a growing concern on the transmission of the virus through water treatment plants (WTPs) and WWTPs. Several studies also detected the genetic material of the virus in raw wastewater across the globe [22, 26, 27] . These studies provided enough excellent reasons for modelling the spread of 2019-nCoV with the external environmental conditions, assuming that the cases of infection will decrease through secondary infection routes due to the inactivation of the virus on different surfaces; however, the possibility of transmission via direct contact remains unchanged. cache = ./cache/cord-320935-3n157yl4.txt txt = ./txt/cord-320935-3n157yl4.txt === reduce.pl bib === id = cord-321053-lgae22f8 author = Gerold, Gisa title = Opportunities and Risks of Host-targeting Antiviral Strategies for Hepatitis C date = 2013-10-04 pages = extension = .txt mime = text/plain words = 9393 sentences = 470 flesch = 42 summary = Numerous in vitro studies in combination with a growing number of HCV sequencing data from patients undergoing DAA treatment underline that the virus can develop drug-resistance and fitness restoring compensatory mutations [11] . An emerging third group of antivirals, so called hosttargeting antivirals (HTA), may be part of such future combination therapies, in particular as HTAs hold the promise of overcoming some of the caveats of DAAs. HTAs are antibodies, RNAs or small molecules, which interfere with host factors needed for HCV propagation. On the one hand, this demonstrates that HCV can in theory evade HTA therapy by mutating the viral binding partner of the targeted host factor and in fact suggests a low genetic barrier to resistance. Targeting HCV RNA Replication: Phosphatidylinositol 4-kinase III alpha (PI4KIIIα) Genome wide RNA interference screens and in depth cell culture replication assays with HCV replicons and full length infectious virus have revealed numerous additional host dependency factors, that could in principle serve as antiviral targets [99] [100] [101] [102] [103] [104] [105] [106] [107] . cache = ./cache/cord-321053-lgae22f8.txt txt = ./txt/cord-321053-lgae22f8.txt === reduce.pl bib === id = cord-320030-ojtp90na author = Montero, Antonio title = Fiebre chikungunya - Una nueva amenaza global date = 2015-08-07 pages = extension = .txt mime = text/plain words = 3949 sentences = 372 flesch = 60 summary = Resumen Las epidemias causadas, entre otros, por los virus Ébola, Marburgo, Nipah, Lassa, coronavirus, virus del Nilo Occidental, virus de Saint Louis, virus de la inmunodeficiencia humana, dengue, fiebre amarilla y fiebre hemorrágica venezolana han puesto sobre el tapete el riesgo que estos agentes representan para la salud pública global. El riesgo de epidemias y endemicidad en las Amé ricas parece muy elevado debido a la existencia de una població n sensible a la enfermedad, la ubicuidad de los mosquitos vectores y la introducció n cada vez má s frecuente de casos importados. Debido a la amplia distribució n de los Aedes en las Amé ricas, toda la regió n es susceptible a la invasió n y la diseminació n de este virus, y la aparició n reciente de epidemias urbanas de dengue en Sudamé rica destaca el peligro potencial de fiebre chikungunya. cache = ./cache/cord-320030-ojtp90na.txt txt = ./txt/cord-320030-ojtp90na.txt === reduce.pl bib === id = cord-318686-we6pveus author = Ehlen, Lukas title = Epithelial cell lines of the cotton rat (Sigmodon hispidus) are highly susceptible in vitro models to zoonotic Bunya-, Rhabdo-, and Flaviviruses date = 2016-05-04 pages = extension = .txt mime = text/plain words = 5608 sentences = 284 flesch = 53 summary = CONCLUSION: In the current study, we showed that newly established cell lines from the cotton rat can serve as host-specific in vitro models for viral infection experiments. The cotton rat (Sigmodon hispidus) is a unique example of a rodent species that is a well-established animal model to study viral pathogenesis and is also associated with a large range of zoonotic viruses in the wild [20] [21] [22] . To evaluate whether the broad viral susceptibility seen in both animalmodel and wild cotton rats was also reflected in in vitro cell culture models, we generated continuous cell lines from the respiratory and renal tracts of a cotton rat, and assessed their use for virus replication studies of known and potentially novel zoonotic viruses. In the work presented herein, we generated epithelial cell lines from the respiratory and renal tracts of a cotton rat due to its susceptibility to a broad range of human viruses, as well as the association of multiple important and emerging zoonotic viruses with this species. cache = ./cache/cord-318686-we6pveus.txt txt = ./txt/cord-318686-we6pveus.txt === reduce.pl bib === id = cord-320693-de1lmzl1 author = Hu, Han title = Antiviral activity of Piscidin 1 against pseudorabies virus both in vitro and in vivo date = 2019-07-31 pages = extension = .txt mime = text/plain words = 5052 sentences = 320 flesch = 52 summary = METHODS: In this study, we evaluated the activities of five broad-spectrum antimicrobial peptides (AMPs) against several important swine-origin pathogenic viruses by TCID(50) assay. The pathogenic viruses isolated from pigs including pseudorabies virus (PRV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and rotavirus (RV) are commonly observed in China. In this study, we investigated the activity of five AMPs including piscidin, caerin, maculatin, lactoferricin B, and indolicidin against several porcine-origin viruses. The antiviral effects of the peptides (maculatin, caerin, piscidin, lactoferricin B, indolicidin) were investigated in vitro against several viral pathogens that severely threaten the porcine industry. Three peptides (caerin, piscidin, maculatin) exhibited inhibitory activity against PRV, PEDV, TGEV, PRRSV, and rotavirus. Our plaque reduction assay result indicated that piscidin, caerin, and maculatin could inhibit PRV by directly interacting with the virus. cache = ./cache/cord-320693-de1lmzl1.txt txt = ./txt/cord-320693-de1lmzl1.txt === reduce.pl bib === id = cord-319933-yp9ofhi8 author = Ruiz, Sara I. title = Chapter 38 Animal Models of Human Viral Diseases date = 2013-12-31 pages = extension = .txt mime = text/plain words = 28834 sentences = 1797 flesch = 46 summary = An experimental study with cell culture-adapted hepatitis Avirus in guinea pigs challenged by oral or intraperitoneal routes did not result in clinical disease, increase in liver enzymes, or seroconversion. 32 NHPs including marmosets, cotton-top tamarins, and rhesus macaques infected with Norwalk virus can be monitored for the extent of viral shedding; however, no clinical disease is observed in these models. 66, 67 Intracerebral and intranasal routes of infection resulted in a fatal disease that was highly dependent on dose, while intradermal and subcutaneous inoculations caused only 50% fatality in mice regardless of the amount of virus. A mouse-adapted (MA) strain of Dengue virus 2 introduced into AG129 mice developed vascular leak syndrome similar to the severe disease seen in humans. [138] [139] [140] [141] [142] [143] [144] Inoculation of WNV into NHPs intracerebrally resulted in the development of either encephalitis, febrile disease, or an asymptomatic infection, depending on the virus strain and dose. cache = ./cache/cord-319933-yp9ofhi8.txt txt = ./txt/cord-319933-yp9ofhi8.txt === reduce.pl bib === id = cord-323333-keshu99t author = Schleis, Thomas G. title = The Process: New Methods of Purification and Viral Safety date = 2013-01-16 pages = extension = .txt mime = text/plain words = 2212 sentences = 132 flesch = 47 summary = From the transmission of hepatitis C virus by gammaglobulins in 1994 to the emergence of new viruses and concern over prions, intravenous immunoglobulin (IGIV) manufacturers have continued to address safety issues and respond to changing needs. Because the different techniques can affect the biologic function of the IgG molecule, the methods of viral inactivation may account for some of the differences among IGIV products in terms of side effects and efficacy (Table 1) . Because intravenous immunoglobulins are derived from human plasma, they are potentially susceptible to contamination by a variety of blood-borne pathogens; consequently, patients receiving and clinicians administering IGIV are concerned about disease transmission. From the transmission of HCV by gammaglobulins in 1994 to the emergence of new viruses or concern over prions, IGIV manufacturers have continued to address safety issues and respond to changing needs. cache = ./cache/cord-323333-keshu99t.txt txt = ./txt/cord-323333-keshu99t.txt === reduce.pl bib === id = cord-320055-6ycp8m89 author = Elliot, Elisa L title = Indicator organisms for estuarine and marine waters date = 1985-07-31 pages = extension = .txt mime = text/plain words = 10567 sentences = 551 flesch = 43 summary = These bacteria and other coliforms were used in the past as indicators of water-borne pathogens, that is, the presence of fecal contamination being correlated with the occurrence of pathogens, for which direct detection methods were not available. Total coliforms are the most universally used indicator group, but include bacteria, in addition to Escherichia coil, that are not specifically associated with fecal pollution, i.e., Klebsiella spp., Citrobacter spp., and Enterobacter spp. Finding an appropriate indicator for the presence of enteric viruses, i.e., poliovirus, coxsackievirus A, coxsackievirus B, and echovirus [50, 147] , in sea water, is a vexing problem, especially for those responsible for regulating the use of sewage-contamined sites, including fresh, estuarine, and marine water and sediment, and shellfish harvested from these waters. Correlations between the number of fecal bacterial pathogens and indicator bacteria and their respective bacteriophages in fresh and marine water have been reported [185] . cache = ./cache/cord-320055-6ycp8m89.txt txt = ./txt/cord-320055-6ycp8m89.txt === reduce.pl bib === id = cord-320713-b37c8aye author = Roberts, Lisa O. title = Chapter 9 Viral Strategies to Subvert the Mammalian Translation Machinery date = 2009-10-27 pages = extension = .txt mime = text/plain words = 20205 sentences = 1067 flesch = 48 summary = 6 The rate of translation initiation in mammalian cells is also controlled by sequence elements within the 5 0 -and 3 0 -UTRs of mRNAs which regulate this process by providing sites for interaction of regulatory proteins and RNAs. These include upstream open reading frames (uORFs), microRNA (miRNA) target sites, and polyadenylation elements. 5 It was suggested that alternative eIF4F complexes lacking PABP could selectively promote the synthesis of viral, but not host, proteins, so that KSHV-encoded mRNAs would compete more effectively for host translation machinery in infected cells. Picornavirus translation is directed by internal ribosome entry sites (IRESs) within the 5 0 -UTRs of the viral RNAs. The central one-third of eIF4G, containing the eIF3 and one eIF4A-binding domain, is sufficient to support translation initiation from these IRESs. 43 This allows picornavirus RNAs to compete effectively for the host translation machinery following infection, although the situation appears to be more complicated than this (see Section III). cache = ./cache/cord-320713-b37c8aye.txt txt = ./txt/cord-320713-b37c8aye.txt === reduce.pl bib === id = cord-318853-mxyxwkhx author = Sallie, Richard title = Replicative homeostasis II: Influence of polymerase fidelity on RNA virus quasispecies biology: Implications for immune recognition, viral autoimmunity and other "virus receptor" diseases date = 2005-08-22 pages = extension = .txt mime = text/plain words = 10541 sentences = 396 flesch = 25 summary = Perhaps more importantly, ineluctable generation of broad phenotypic diversity after viral RNA is translated to protein quasispecies suggests a mechanism of disease that specifically targets, and functionally disrupts, the host cell surface molecules – including hormone, lipid, cell signalling or neurotransmitter receptors – that viruses co-opt for cell entry. Hence, as relative concentrations of wild-type and variant viral proteins vary, alteration of both processivity and fidelity of RNA pol results, permitting viruses to adaptively respond to environmental changes, including immune recognition and reaction to evolving cell receptors. As clear evidence exists for viral disruption of leptin function [106] and virus-associated weight gain in humans [107] and monkeys [108] , is it possible the global epidemics of type II diabetes mellitus, insulin resistance, hyperlipidaemia and obesity now prevalent [109] [110] [111] [112] [113] [114] [115] [116] , are just that; epidemics fundamentally caused by viruses that co-opt insulin or leptin or other associated receptors for cell access and generate protein quasispecies that disrupt receptor function? cache = ./cache/cord-318853-mxyxwkhx.txt txt = ./txt/cord-318853-mxyxwkhx.txt === reduce.pl bib === id = cord-321835-qn33sx8x author = Bailey, Emily S. title = A Mini Review of the Zoonotic Threat Potential of Influenza Viruses, Coronaviruses, Adenoviruses, and Enteroviruses date = 2018-04-09 pages = extension = .txt mime = text/plain words = 3717 sentences = 181 flesch = 44 summary = In particular, respiratory infections are problematic; in early 2003, World Health Organization issued a worldwide alert for a previously unrecognized illness that was subsequently found to be caused by a novel coronavirus [severe acute respiratory syndrome (SARS) virus]. Influenza A virus H3N2 subtypes are frequently reported in swine, avian, and canine hosts that are responsible for highly infectious respiratory diseases in pigs and have been examined as a potential cause of influenza in humans. In a recent review of the risks of potential outbreaks associated with zoonotic Ad (48) , it was noted that intense human-animal interaction is likely to increase the probability of emergent cross-species Ad infection. This suggests that strategies for novel virus detection should incorporate global surveillance at the human-animal interface to detect potentially emerging zoonotic viruses. Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome cache = ./cache/cord-321835-qn33sx8x.txt txt = ./txt/cord-321835-qn33sx8x.txt === reduce.pl bib === id = cord-319379-qe56u93a author = Patil, Vaishali M. title = A systematic review on use of aminoquinolines for the therapeutic management of COVID-19: Efficacy, safety and clinical trials date = 2020-05-11 pages = extension = .txt mime = text/plain words = 2813 sentences = 186 flesch = 34 summary = The well reported and clinically used anti-malarial aminoquinoline drugs (chloroquine and hydroxychloroquine) have shown potential to be repurposed to control the present pandemic by inhibition of COVID-19. The review elaborates the mechanism of action, safety (side effects, adverse effects, toxicity) and worldwide clinical trials for chloroquine and hydroxychloroquine to benefit the clinicians, medicinal chemist, pharmacologist actively involved in the management of COVID-19 infection. In vitro inhibition of human influenza A virus replication by chloroquine Anti-malaria drug chloroquine is highly effective in treating avian influenza A H5N1 virus infection in an animal model Inhibition of human immunodeficiency virus type 1 replication by hydroxychloroquine in T cells and monocytes Inhibition of A/Human/Hubei/3/2005 (H3N2) influenza virus infection by silver nanoparticles in vitro and in vivo Mycophenolic acid inhibits dengue virus infection by preventing replication of viral RNA Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro cache = ./cache/cord-319379-qe56u93a.txt txt = ./txt/cord-319379-qe56u93a.txt === reduce.pl bib === id = cord-321741-aq76s37x author = Andersen, Petter I. title = Discovery and development of safe-in-man broad-spectrum antiviral agents date = 2020-04-30 pages = extension = .txt mime = text/plain words = 5432 sentences = 308 flesch = 41 summary = Although the concept of BSAAs has been around for almost 50 years, the field received a new impetus with recent outbreaks of Ebola, Zika, Dengue, influenza and other viral infections, the discovery of novel host-directed agents, as well as development of drug repositioning methodology. The discovery of novel activities of BSAAs starts with exposing cells to the candidate antiviral agent at different concentrations and infecting the cells with a virus or mock. Given that emetine also inhibits ZIKV, EBOV, RABV, CMV, HCoV-OC43 and HIV-1 infections (Chaves Valadao et al., 2015; MacGibeny et al., 2018; Mukhopadhyay et al., 2016; Shen et al., 2019; Yang et al., 2018) , and that it is an FDA-approved anti-protozoal drug, it may represent a promising safe-in-man BSAA candidate. Thereby, novel antiviral activities of BSAAs should be further validated in primary human cells using different viral strains (including wild-type viruses), different viral loads, different times of compound addition, different endpoint measurements and compound concentration range. cache = ./cache/cord-321741-aq76s37x.txt txt = ./txt/cord-321741-aq76s37x.txt === reduce.pl bib === id = cord-320015-lbr2q4qh author = Chinchar, V. Gregory title = The Molecular Biology of Frog Virus 3 and other Iridoviruses Infecting Cold-Blooded Vertebrates date = 2011-10-20 pages = extension = .txt mime = text/plain words = 9130 sentences = 433 flesch = 43 summary = Additional IE and DE proteins include proteins that may play roles in blocking host immune responses such as a virus-encoded, CARD (caspase activation and recruitment domain) motif-containing protein (vCARD), β-hydroxysteroid dehydrogenase (βHSD), and a RNAse III-like protein, catalytic proteins involved in nucleic acid synthesis (Proliferating Cell Nuclear Antigen [PCNA], DNA methyltransferase [DMTase], the large and small subunits of the viral homolog of cellular RNA polymerase II [vPOL-IIα and -IIβ], transcription factor IIS), catalytic proteins that may act to increase dTTP pool sizes and influence host range (deoxyuridine triphosphatase [dUTPase], deoxynucleotide kinase, the large and small subunits of ribonucleotide reductase), and proteins non-essential for replication in vitro, but needed for growth in vivo (the 18K protein) [22] . Lastly, Sample and co-workers observed that KD of the 18K IE protein had no observable effect on viral gene expression or replication in vitro suggesting that, at least in fathead minnow cells, 18K was not required for the production of infectious virions. cache = ./cache/cord-320015-lbr2q4qh.txt txt = ./txt/cord-320015-lbr2q4qh.txt === reduce.pl bib === id = cord-322082-80ym2rsq author = Monto, Arnold S title = Lessons From Influenza Pandemics of the Last 100 Years date = 2020-03-01 pages = extension = .txt mime = text/plain words = 4089 sentences = 229 flesch = 46 summary = Since this was the first true pandemic since 1918, there was immediate concern about its potential impact and great relief when it was found to resemble seasonal influenza with morbidity highest in children and mortality at the extremes of age [26, 27] (Figure 3 ). However, the new A(H3N2) virus completely replaced the previous subtype, and its variants, more than 50 years later, have been responsible for the greatest proportion of mortality from influenza viruses. In the United States, there was particular attention directed to nonpharmaceutical interventions, a result of the recognition that pandemic-specific vaccines would be available relatively late and that influenza-specific antiviral drugs, while important, would be limited in quantity. " The latter issue has been made worse by the repeated recognition of the pandemic potential of different avian influenza virus variants that have infected humans [63] [64] [65] . cache = ./cache/cord-322082-80ym2rsq.txt txt = ./txt/cord-322082-80ym2rsq.txt === reduce.pl bib === id = cord-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-323195-buzcb8ya author = Valtonen, Maarit title = Common cold in Team Finland during 2018 Winter Olympic Games (PyeongChang): epidemiology, diagnosis including molecular point-of-care testing (POCT) and treatment date = 2019-05-29 pages = extension = .txt mime = text/plain words = 4234 sentences = 285 flesch = 54 summary = title: Common cold in Team Finland during 2018 Winter Olympic Games (PyeongChang): epidemiology, diagnosis including molecular point-of-care testing (POCT) and treatment 13 14 The aim of our prospective observational study was to investigate the occurrence and aetiology of the common cold in Team Finland during the 2018 Winter Olympic Games. Six days later, the neighbouring team member in the aeroplane developed symptomatic respiratory syncytial virus A -infection. One subject developed nasal congestion during the 9-hour flight, later detected to be a respiratory syncytial virus B infection. First, 45% of the elite athletes and 32% of the staff members suffered from the symptoms of the common cold during the median stay of 3 weeks at the Winter Olympic Games. Our study is the first to detect the aetiology of respiratory infections in elite athletes using molecular POCT at a major event. cache = ./cache/cord-323195-buzcb8ya.txt txt = ./txt/cord-323195-buzcb8ya.txt === reduce.pl bib === id = cord-323358-05bk91lm author = Bhaskar, Sathyamoorthy title = Engineering protein nanocages as carriers for biomedical applications date = 2017-04-07 pages = extension = .txt mime = text/plain words = 9541 sentences = 557 flesch = 39 summary = We review natural and synthetic protein nanocages that have been modified using chemical and genetic engineering techniques to impart non-natural functions that are responsive to the complex cellular microenvironment of malignant cells while delivering molecular cargos with improved efficiencies and minimal toxicity. 1, 3 Examples of naturederived nanocarriers include protein nanocages such as viruses, ferritin and many others that are formed by the self-assembly of protein subunits, resulting in a cage-like structure. 8 In this review, we focus on natural and synthetic protein scaffolds engineered with specific functional groups to impart non-native functions, including aiding the delivery of active molecules through targeting of malignant cells and overcoming cellular barriers. 3 In addition to cell targeting ability and gene delivery efficiency, these protein-based multifaceted systems have highly ordered spatial configurations, and the stability and functionality of these materials have already been established through intensive research with advances in understanding virus infection, replication and assembly pathways. cache = ./cache/cord-323358-05bk91lm.txt txt = ./txt/cord-323358-05bk91lm.txt === reduce.pl bib === id = cord-323404-3mw4q7m3 author = Bomsel, Morgane title = Entry of viruses through the epithelial barrier: pathogenic trickery date = 2003 pages = extension = .txt mime = text/plain words = 8104 sentences = 428 flesch = 43 summary = In polarized monostratified epithelium -where the plasma membrane is divided into two domains that have a different lipid and protein composition and different membrane dynamics -viruses usually attach and penetrate the cell cytosol preferentially at the restricted pole of the by epithelial cells and cross the epithelial barrier using TRANSCYTOSIS (BOX 1), as has been described recently for the human immunodeficiency virus (HIV) 3, 4 . Similarly, human JC virus 49 and Sendai 50 virus, as well as sialyloligosaccharide-dependent strains of rotavirus 20 and reovirus, also attach themselves to epithelial cells to block or abuse normal cell processes and, as with bacteria 43 , the surface proteins of enveloped or naked viruses bind to host-cell molecules that have receptor functions. As the cell attachment receptors for numerous enveloped and naked viruses, the glycosyl epitopes of the epithelial-cell-surface proteoglycans mediate virus adhesion, in turn initiating signal transduction as described for the GLYCOSYNAPSE 54 . cache = ./cache/cord-323404-3mw4q7m3.txt txt = ./txt/cord-323404-3mw4q7m3.txt === reduce.pl bib === id = cord-321112-w7x1dkds author = Zhao, Xuesen title = IFITM Genes, Variants, and Their Roles in the Control and Pathogenesis of Viral Infections date = 2019-01-08 pages = extension = .txt mime = text/plain words = 6973 sentences = 350 flesch = 43 summary = Similar to many other host defense genes that evolve under the selective pressure of microorganism infection, IFITM genes evolved in an accelerated speed in vertebrates and many single-nucleotide polymorphisms (SNPs) have been identified in the human population, some of which have been associated with severity and prognosis of viral infection (e.g., influenza A virus). Similar to many other host defense genes that evolve under the selective pressure of microorganism infection, IFITM genes evolved in an accelerated speed in vertebrates and many single-nucleotide polymorphisms (SNPs) have been identified in the human population, some of which have been associated with severity and prognosis of viral infection (e.g., influenza A virus). Among the number of single-nucleotide polymorphisms (SNPs) in IFITM3 gene that have been identified in human populations, several are associated with disease severity and prognosis of influenza A virus (IAV) and other viral infections (Everitt et al., 2012; Zhang et al., 2015; Xu-Yang et al., 2016; Allen et al., 2017) . cache = ./cache/cord-321112-w7x1dkds.txt txt = ./txt/cord-321112-w7x1dkds.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-322234-1zyy536y author = Lorusso, Alessio title = One-step real-time RT-PCR for pandemic influenza A virus (H1N1) 2009 matrix gene detection in swine samples date = 2009-12-17 pages = extension = .txt mime = text/plain words = 4162 sentences = 195 flesch = 51 summary = To evaluate the applicability of the test as a diagnostic tool in the screening of field specimens from swine, 64 field isolates of North American swine, 5 equine and 48 avian influenza viruses collected during diagnostic investigations were analyzed retrospectively as well as samples collected during an experimental in vivo infection with two novel H1N1 isolates, A/California/04/2009 (H1N1)v virus and A/Mexico/4108/2009 (H1N1)v. Swine and equine influenza virus isolates and the clinical samples from pigs infected experimentally with 2009 (H1N1)v were subjected to the USDA-validated qRT-PCR procedure for the general detection of type A influenza virus RNA (matrix screening assay), following procedures described previously (Spackman and Suarez, 2008) . All endemic North American swine influenza virus isolates were negative for (H1N1) 2009 specific matrix gene RNA using the present qRT-PCR assay, whereas the (H1N1) 2009 strains used as positive control were positive. cache = ./cache/cord-322234-1zyy536y.txt txt = ./txt/cord-322234-1zyy536y.txt === reduce.pl bib === id = cord-322904-9mta0aem author = Neu, Ursula title = The Polyomaviridae: Contributions of virus structure to our understanding of virus receptors and infectious entry date = 2009-02-01 pages = extension = .txt mime = text/plain words = 9629 sentences = 493 flesch = 53 summary = The mPyV and the two human polyomaviruses, JCV and BKV are known to require sialic acid for binding to host cells as "receptor destroying enzyme" or neuraminidase inhibits the viruses' ability to agglutinate red blood cells and to infect cells (Table 1) . High-resolution structural information on the interaction of viral attachment proteins with sialylated carbohydrates is available for the following systems: Influenza virus A haemagglutinin (HA) in complex with oligosaccharides containing α2,3-linked and α2,6linked NeuNAc (Eisen et al., 1997; Gamblin et al., 2004; Ha et al., 2001; Ha et al., 2003; Russell et al., 2006; Sauter et al., 1992; Stevens et al., 2006; Stevens et al., 2004; Weis et al., 1988) , mPyV VP1 with a fragment of ganglioside GD1a (Stehle and Harrison, 1997) , rhesus, swine and human rotavirus VP8⁎ with methyl-α2,3-sialoside (Blanchard et al., 2007; Dormitzer et al., 2002a) , adenovirus Ad37 fiber knob (Ad37) with α2,3and α2,6-sialyllactose (Burmeister et al., 2004) and SV40 VP1 with ganglioside GM1 (Neu et al., 2008) . cache = ./cache/cord-322904-9mta0aem.txt txt = ./txt/cord-322904-9mta0aem.txt === reduce.pl bib === id = cord-323311-xl2fv0qx author = Kahn, R. E. title = 6th International Conference on Emerging Zoonoses date = 2012-09-07 pages = extension = .txt mime = text/plain words = 19161 sentences = 802 flesch = 41 summary = The three key characteristics of this integrated approach to so many infectious diseases are as follows: (i) to use cell culture, primary cells, nonhuman primate and human clinical models to study viral infection; (ii) to combine traditional histopathological, virological and biochemical approaches with functional genomics, proteomics and computational biology (Haagmans et al., 2009); and (iii) to obtain signatures of virulence and insights into mechanisms of host defense response, viral evasion and pathogenesis (Casadevaill et al., 2011) . The unity of human, animal and ecosystem health outlined by Professor Aguirre, as well as the interactions among multiple tick-borne pathogens in a natural reservoir host set out by Professor Fish and his research team, both summarized in Topic 1 above, highlight the necessity of cross-disciplinary collaboration in studying zoonotic bacterial diseases (Daszak et al., 2007, pp. cache = ./cache/cord-323311-xl2fv0qx.txt txt = ./txt/cord-323311-xl2fv0qx.txt === reduce.pl bib === id = cord-322206-roxa3ix6 author = I. Sardi, Silvia title = High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics date = 2020-07-21 pages = extension = .txt mime = text/plain words = 4199 sentences = 212 flesch = 46 summary = Herein, we used RNA-based metatranscriptomics associated with Ion Torrent deep sequencing to allow for the high-quality reconstitution of an outbreak-related Zika virus (ZIKV) genome (10,739 nt), with extended 5′-UTR and 3′-UTR regions, using a newly-implemented bioinformatics approach. Besides allowing for the assembly of one of the largest complete ZIKV genomes to date, our strategy also yielded high-quality complete genomes of two arthropod-infecting viruses co-infecting C6/36 cell lines, namely: Alphamesonivirus 1 strain Salvador (20,194 nt) and Aedes albopictus totivirus-like (4618 nt); the latter likely represents a new viral species. Altogether, our results demonstrate that our bioinformatics approach associated with Ion Torrent sequencing allows for the high-quality reconstruction of known and unknown viral genomes, overcoming the main limitation of RNA deep sequencing for virus identification. Here, we applied RNA-based metatranscriptomics associated with Ion Torrent deep sequencing and a newly developed Bioinformatics approach to the high-quality reconstitution of viral genomes. cache = ./cache/cord-322206-roxa3ix6.txt txt = ./txt/cord-322206-roxa3ix6.txt === reduce.pl bib === id = cord-323987-gh1m05gi author = Dziąbowska, Karolina title = Detection Methods of Human and Animal Influenza Virus—Current Trends date = 2018-10-18 pages = extension = .txt mime = text/plain words = 11112 sentences = 760 flesch = 46 summary = RIDTs with digital readout systems showed many similarities to conventional assays like small sample volume (less than 150 µL) and short analysis time (around 15 min) but exhibited much better sensitivities, even one order of magnitude lower limits of detection (LODs). Among methods mentioned, general diagnostic tests for influenza base on virus culture (conventional and shellvial), detection of viral nucleic acid (PCR) or antigens (by neuraminidase enzymatic activity, fluorescent antibody or enzyme/optical immunoassay) and serologic tests. Main trends for influenza virus detection are: (I) modifications of traditional 'gold star' methods like PCR, RIDTs, ELISA what results in analysis time shortening, costs lowering, LOD and limit of quantification (LOQ) improvement, (II) conjugating of traditional methods and creating new platforms, micro-biochips and others, (III) introducing known solutions to new ones, like smartphone-based analysis control with results data insertion into Google Maps, (IV) reuse of the functions of known devices, like glucometer, smartphone cameras, (V) the most common used detection methods: spectral/optical, electrical, (VI) and entirely new approaches. cache = ./cache/cord-323987-gh1m05gi.txt txt = ./txt/cord-323987-gh1m05gi.txt === reduce.pl bib === id = cord-325280-4whzcmqv author = Takizawa, Naoki title = Current landscape and future prospects of antiviral drugs derived from microbial products date = 2017-10-11 pages = extension = .txt mime = text/plain words = 6601 sentences = 365 flesch = 34 summary = In this review, we summarize antiviral microbial products discovered by Institute of Microbial Chemistry (IMC) and discuss antiviral compounds against influenza virus and HBV, because these two viruses threaten global human health now and antiviral drug against these two viruses have been developed. THE CONTRIBUTIONS OF IMC TO ANTIVIRAL RESEARCH Nucleos(t)ide analogs are a major class of approved antiviral drugs that exert therapeutic effects through incorporation into viral DNA and RNA to inhibit virus replication. Viral polymerase complex is a promising target for the development of anti-influenza drugs, because transcription and replication are critical steps for virus propagation. Potential applications of microbial products in anti-HBV drug development Approved nucleos(t)ide analogs competitively inhibit DNA elongation of viral polymerase after the conversion to triphosphate form by cellular enzymes. cache = ./cache/cord-325280-4whzcmqv.txt txt = ./txt/cord-325280-4whzcmqv.txt === reduce.pl bib === id = cord-321481-vrfwczve author = Watashi, Koichi title = NTCP and Beyond: Opening the Door to Unveil Hepatitis B Virus Entry date = 2014-02-19 pages = extension = .txt mime = text/plain words = 4936 sentences = 247 flesch = 39 summary = Recently, sodium taurocholate cotransporting polypeptide (NTCP) was identified as an HBV entry receptor and enabled the establishment of a susceptible cell line that can efficiently support HBV infection. HBV infection into host hepatocytes follows a multiple step process: (1) initially, HBV reversibly attaches to host cell surface proteoglycans with a low affinity; (2) this is followed by the process involving more specific receptor(s) with high affinity to mediate the early entry step; and (3) after endocytosis-mediated internalization, the virus fuses with the cellular membrane compartment, probably in an endosomal compartment, although the mechanisms are not fully understood. A myristoylated peptide encompassing amino acids 2-48 of the preS1 region turned out to be the most efficient in infection inhibition of HBV and also the envelope protein-related hepatitis D virus (HDV) [30, 31] . Cyclosporin A and its analogs inhibit hepatitis B virus entry into cultured hepatocytes through targeting a membrane transporter NTCP cache = ./cache/cord-321481-vrfwczve.txt txt = ./txt/cord-321481-vrfwczve.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-324280-e8mj6ecl author = Shaman, Jeffrey title = Asymptomatic Summertime Shedding of Respiratory Viruses date = 2018-04-01 pages = extension = .txt mime = text/plain words = 2600 sentences = 128 flesch = 41 summary = Here, we explore respiratory virus infection rates in a segment of this population through a convenience survey and sampling study of adult visitors to a New York City tourist attraction during spring and summer 2016. Among all participants there was a statistically significant positive association between reporting a greater tendency to get sick and total self-reported symptom score (P < .0001 by the Tukey test); however, there was no significant association between reporting a greater tendency to get sick and actual detection of respiratory virus shedding (P = .10 by χ 2 analysis). The best-fit logistic regression model supported an association between an increased likelihood of testing positive for respiratory virus infection and a higher total symptom score (P < .0001) and being Hispanic (P < .005). cache = ./cache/cord-324280-e8mj6ecl.txt txt = ./txt/cord-324280-e8mj6ecl.txt === reduce.pl bib === id = cord-323700-5awng7h1 author = Goggin, Rachel K. title = Comparative Viral Sampling in the Sinonasal Passages; Different Viruses at Different Sites date = 2018-09-19 pages = extension = .txt mime = text/plain words = 3528 sentences = 197 flesch = 49 summary = The aim of the study here presented was to establish differences in viral detection and species sampled from different sinonasal sites, in an effort to validate and standardise viral collection techniques, and facilitate further investigation of the sinonasal virome. All DNA extracts first underwent an endogenous retrovirus 3 (ERV3) assay (present as two copies per human diploid cell) in order to confirm respiratory sample collection quality. Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control High rates of detection of respiratory viruses in the nasal washes and mucosae of patients with chronic rhinosinusitis Detection of herpesviruses 1-6 and community-acquired respiratory viruses in patients with chronic rhinosinusitis with nasal polyposis Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions Real-time quantitative PCR assays for detection and monitoring of pathogenic human viruses in immunosuppressed pediatric patients cache = ./cache/cord-323700-5awng7h1.txt txt = ./txt/cord-323700-5awng7h1.txt === reduce.pl bib === id = cord-325825-0lyt8gfq author = Griffiths, Samantha J. title = A Systematic Analysis of Host Factors Reveals a Med23-Interferon-λ Regulatory Axis against Herpes Simplex Virus Type 1 Replication date = 2013-08-08 pages = extension = .txt mime = text/plain words = 12504 sentences = 601 flesch = 45 summary = Host factors (HFs) which positively or negatively regulate HSV-1 replication were identified by screening a druggable genome siRNA library (4 siRNAs per gene) targeting 7,237 human genes against a HSV-1 reporter virus expressing the enhanced green fluorescent protein (eGFP; HSV-1 strain C12) in the epithelial Hela cell line, due to their ease of transfection and susceptibility to HSV-1 infection [34] . Combined bioinformatic analyses of protein interaction and siRNA depletion screens found a significant functional enrichment for proteins involved in transcription, and identified multi-protein complexes enriched for pro-viral HFs which strongly inhibited HSV-1 upon depletion, including the RNA-polymerase II, eIF3 and Mediator complexes ( Figure 3a) . Furthermore, qPCR analysis found depletion of Med23 inhibited the induction of IFN-l expression following HSV-1 infection of A549 cells in comparison to cells transfected with the RSCF siRNA control ( Figure 4e ). cache = ./cache/cord-325825-0lyt8gfq.txt txt = ./txt/cord-325825-0lyt8gfq.txt === reduce.pl bib === id = cord-323793-c69joaqs author = Palmieri, V. title = Can graphene take part in the fight against COVID-19? date = 2020-05-07 pages = extension = .txt mime = text/plain words = 2813 sentences = 155 flesch = 41 summary = In response to this global outbreak, we summarized the current state of knowledge of graphene and virus interaction as well as possible successful applications to fight COVID-19. Antibody-conjugated graphene sheets can rapidly detect targeted virus proteins and can be useful for large population screening, but also for the development of environmental sensors and filters, given the low cost of graphene materials. While government bodies are struggling in preventing further spread of COVID-19, researchers immediately started tests on vaccines and a clinical trial is currently underway with potential treatments for severe acute respiratory syndrome coronavirus -2 (SARS-CoV-2) [1] . Ziem and colleagues synthesized thermal rGO sulfate derivatives and demonstrated their antiviral activity against African swine fever virus, orthopoxvirus and herpesvirus strains [14, 15] . Synergistic antiviral effect of curcumin functionalized graphene oxide against respiratory syncytial virus infection cache = ./cache/cord-323793-c69joaqs.txt txt = ./txt/cord-323793-c69joaqs.txt === reduce.pl bib === id = cord-324984-ojrpsdt9 author = Ji, Xingyue title = Medicinal chemistry strategies toward host targeting antiviral agents date = 2020-02-14 pages = extension = .txt mime = text/plain words = 16814 sentences = 825 flesch = 43 summary = In addition, host proteins are not under the genetic control of viral genome, and hence HTAs possess much higher genetic barrier to drug resistance as compared with DAAs. In recent years, much progress has been made to the development of HTAs with the approval of chemokine receptor type 5 antagonist maraviroc for human immunodeficiency virus treatment and more in the pipeline for other viral infections. 3 Altogether, targeting host factors is a very promising strategy with possibility to address the critical challenges faced with the DAAs. In this review, we summarize the recent advances made in HTAs from a medicinal chemistry standpoint, and the host targets are generally classified into three different categories based on the development stage of their corresponding inhibitors/modulators, namely the ones which reached Food and Drug Administration (FDA) approval, that have entered clinical trials and those in preclinical studies. cache = ./cache/cord-324984-ojrpsdt9.txt txt = ./txt/cord-324984-ojrpsdt9.txt === reduce.pl bib === id = cord-325875-93krp81r author = Henao-Diaz, Alexandra title = Guidelines for oral fluid-based surveillance of viral pathogens in swine date = 2020-10-19 pages = extension = .txt mime = text/plain words = 6151 sentences = 289 flesch = 43 summary = (2020) showed that the probability of detecting porcine reproductive and respiratory syndrome virus (PRRSV) ribonucleic acid (RNA) in serum by reverse transcription polymerase chain reaction (RT-PCR) at 98 days post infection (DPI) was~2% versus~30% in lymphoid tissues (tonsil) by bioassay [16] . Similarly, differences in detection rates have been reported for pen-based oral fluids versus individual Table 1 provides examples of the detection of virus-specific nucleic acids and/or antibody in swine oral fluids, i.e., is not comprehensive b Acronyms defined in the list of abbreviations and terms pig buccal or nasal swabs for animals inoculated with FMDV, IAV, Senecavirus A (SVA), and swine vesicular disease virus (SVDV) [45, 62, 63, 68] . Diagnosis of the Lelystad strain of porcine reproductive and respiratory syndrome virus infection in individually housed pigs: comparison between serum and oral fluid samples for viral nucleic acid and antibody detection cache = ./cache/cord-325875-93krp81r.txt txt = ./txt/cord-325875-93krp81r.txt === reduce.pl bib === id = cord-326719-p1ma4akz author = Enjuanes, Luis title = Virus-based vectors for gene expression in mammalian cells: Coronavirus date = 2003-12-31 pages = extension = .txt mime = text/plain words = 5923 sentences = 282 flesch = 52 summary = Coronaviruses have several advantages as vectors over other viral expression systems: (1) coronaviruses are single-stranded RNA viruses that replicate within the cytoplasm without a DNA intermediary, making integration of the virus genome into the host cell chromosome unlikely, (2) these viruses have the largest RNA virus genome and, in principle, have room for the insertion of large foreign genes, (3) a pleiotropic secretory immune response is best induced by the stimulation of gut-associated lymphoid tissues, (4) the tropism of coronaviruses may be modified by manipulation of the spike (S) protein allowing engineering of the tropism of the vector, (5) non-pathogenic coronavirus strains infecting most species of interest (human, porcine, bovine, canine, feline, and avian) are available to develop expression systems, and (6) infectious coronavirus cDNA clones are available to design expression systems. cache = ./cache/cord-326719-p1ma4akz.txt txt = ./txt/cord-326719-p1ma4akz.txt === reduce.pl bib === id = cord-323710-cmbg0ty8 author = Mühlebach, Michael D. title = Development of Recombinant Measles Virus-Based Vaccines date = 2016-11-26 pages = extension = .txt mime = text/plain words = 4306 sentences = 258 flesch = 48 summary = For this purpose, the foreign antigen-encoding genes are cloned into additional transcription units of plasmid based full-length MV vaccine strain genomes, which in turn are used to rescue recombinant MV by providing both full-length viral RNA genomes respective anti-genomes together with all protein components of the viral ribonucleoprotein complex after transient transfection of the so-called rescue cells. After demonstrating efficacy in appropriate mouse and primate animal models [8] , this recombinant vaccine delivered proof of Triggered antigen-specific immune responses after immunization determined by measuring total antibodies (ELISA), neutralizing antibodies (nAbs), or reactive T cells determined by ELISpot or intracellular cytokine staining (ICS) c Protective capacity of vaccine-induced immune responses after challenge of the appropriate animal model determined by reduction of pathogen load or attenuation of etiopathology principle for safety and immunogenicity in human patients, irrespective of preformed anti-measles immunity [9] . cache = ./cache/cord-323710-cmbg0ty8.txt txt = ./txt/cord-323710-cmbg0ty8.txt === reduce.pl bib === id = cord-324696-htx0ul4o author = Chothe, Shubhada K. title = Avian and human influenza virus compatible sialic acid receptors in little brown bats date = 2017-04-06 pages = extension = .txt mime = text/plain words = 3853 sentences = 212 flesch = 50 summary = This first ever study of IAV receptors in a bat species suggest that LBBs, a widely-distributed bat species in North America, could potentially be co-infected with avian and human IAVs, facilitating the emergence of zoonotic strains. To resolve this enigma, we investigated for the first time the distribution of SA receptors in little brown bats (LBBs) (Myotis lucifugus), a widely-distributed bat species in North America and their compatibility to support avian and human IAV binding. H5N2 virus binding pattern was in accordance with the relative abundance of SA α2,3-Gal receptors in tissues such that greater virus binding to the tracheal ( In addition to the virus binding assay using antibody-based detection, we also visualized virus binding using scanning electron microscopy (SEM) which also confirmed abundant binding of avian H5N2 virus (Fig. 5A ) and human H1N1 virus (Fig. 5B ) to LBB trachea (Fig. 5) . time, this study demonstrated that little brown bats (LBBs), a widely-distributed bat species in North America, co-express both avian and human type influenza receptors in their respiratory and gastrointestinal systems. cache = ./cache/cord-324696-htx0ul4o.txt txt = ./txt/cord-324696-htx0ul4o.txt === reduce.pl bib === id = cord-323930-pl3qlcpo author = Sohail, Ayesha title = Forecasting the timeframe of coronavirus and human cells interaction with reverse engineering date = 2020-04-29 pages = extension = .txt mime = text/plain words = 1497 sentences = 95 flesch = 53 summary = The purpose of this article is to review and investigate further the molecular mechanism by which the SARS-CoV2 virus infection proceeds via the formation of a hetero-trimer between its protein S, the ACE2 receptor and the B0AT1 protein, which is the "entry receptor" for the infection process involving membrane fusion [10]. The purpose 11 of this article is to review and investigate further the molecular mechanism by which the SARS-CoV2 12 virus infection proceeds via the formation of a hetero-trimer between its protein S, the ACE2 receptor 13 and the B0AT1 protein, which is the "entry receptor" for the infection process involving membrane "animal to man" and then "man to man " transmission. Our hypothesis is supported by 128 the need for activation of the infection system by the virus, given by the particular molecular kinetics that 129 leads to the formation of the "infection trimer" given by the viral S1 protein and the ACE-2 receptor While developing the computational framework, the virus-target cell interaction was studied in depth. cache = ./cache/cord-323930-pl3qlcpo.txt txt = ./txt/cord-323930-pl3qlcpo.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-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-325230-3kg4oe4g author = Agol, Vadim I. title = Viral security proteins: counteracting host defences date = 2010-11-09 pages = extension = .txt mime = text/plain words = 8716 sentences = 426 flesch = 41 summary = These proteins include: capsid proteins; an RNA-dependent RNA polymerase (3D pol ); a protein (VPg, or 3B) that serves as a primer for the initiation of RNA synthesis; an ATPase with a conserved superfamily 3 helicase motif (2C ATPase ) and an essential but poorly defined role in viral RNA replication; a chymotrypsin-like protease (3C pro ), which, as the mature protein or as a precursor, is a major factor in polyprotein processing; two hydrophobic membrane-binding proteins (2B and 3A) that participate in the generation of a virus-friendly environment; and, flanking the precursor of the capsid proteins, one or two highly variable proteins (L and 2A), the structure and functions of which are the subject of this Review. cache = ./cache/cord-325230-3kg4oe4g.txt txt = ./txt/cord-325230-3kg4oe4g.txt === reduce.pl bib === id = cord-324295-9c1zxjng author = Bonilla-Aldana, D. Katterine title = Bats in Ecosystems and their Wide Spectrum of Viral Infectious Threats: SARS-CoV-2 and other emerging viruses date = 2020-08-20 pages = extension = .txt mime = text/plain words = 3770 sentences = 212 flesch = 51 summary = Examples of such viruses include Marburg, Ebola, Nipah, Hendra, Influenza A, Dengue, Equine Encephalitis viruses, Lyssaviruses, Madariaga and Coronaviruses, involving the now pandemic Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since there is no effective treatment or vaccine for COVID-19 to date, strong regulations---including isolation, quarantine and social distancing---have been established by many countries in an effort to reduce expansion of the disease given the high person-to-person transmissibility of SARS-CoV-2, either directly by respiratory droplets with infective particles or indirectly by fluid-contaminated objects. Fruit bats (genus Pteropus) are the main natural reservoir for Nipah virus (NiV), while pigs serve as intermediate hosts ( Table 3 ). Influenza A viruses (IAV) are one of the leading causes of disease in humans, with important animal reservoirs including birds, pigs, and horses that can potentially produce new zoonotic variants (Table 2) . cache = ./cache/cord-324295-9c1zxjng.txt txt = ./txt/cord-324295-9c1zxjng.txt === reduce.pl bib === id = cord-325750-x7jpsnxg author = Mokili, John L title = Metagenomics and future perspectives in virus discovery date = 2012-01-20 pages = extension = .txt mime = text/plain words = 8742 sentences = 463 flesch = 40 summary = In this article, we review virus discovery techniques with a focus on metagenomic approaches that employ high-throughput sequencing technologies to characterize novel viruses. This method lacks sufficient sensitivity to detect viruses when the viral burden is low or when the DNA sequence of the suspected etiological agent is not clearly distinguishable from the control sample [31] . The following items should be included in any report on viral metagenomic studies: firstly, the sequencing platform and its version number; secondly, raw sequence data accession numbers in a public database; thirdly, details about the bioinformatic analysis, including the homology search tool and the database being used to assign the taxonomy, and their versions; fourthly, a list of known and previously unknown viruses found, clearly showing if the 'novel' viruses are new strains of a previously described species or completely different viruses; and fifthly, causality evidence if any. cache = ./cache/cord-325750-x7jpsnxg.txt txt = ./txt/cord-325750-x7jpsnxg.txt === reduce.pl bib === id = cord-325326-2bbqz4o7 author = Beitzel, Brett F. title = High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and Massively Parallel Sequencing date = 2010-10-14 pages = extension = .txt mime = text/plain words = 7781 sentences = 388 flesch = 51 summary = We have developed a high-resolution genomic mapping technique that combines transposon-mediated insertional mutagenesis with either capillary electrophoresis or massively parallel sequencing to identify functionally important regions of the Venezuelan equine encephalitis virus (VEEV) genome. Toward this goal, we used transposon mutagenesis, reverse genetics, and fragment analysis by capillary electrophoresis to identify regions of the nsP3 gene that are important for replication and that result in temperature sensitive (ts) mutations. We used transposon mutagenesis to construct a cDNA library with small DNA fragments randomly inserted throughout the VEEV genome and then produced replication-competent virus through reverse genetics. Comparing transposon insertion sites in the resultant viruses to those in the starting library, we were able to produce a functional map of the entire genome of VEEV, and to identify several hundred potential ts mutations, including those we originally identified with the capillary electrophoresis method. cache = ./cache/cord-325326-2bbqz4o7.txt txt = ./txt/cord-325326-2bbqz4o7.txt === reduce.pl bib === id = cord-326225-crtpzad7 author = Neill, John D. title = Simultaneous rapid sequencing of multiple RNA virus genomes date = 2014-06-01 pages = extension = .txt mime = text/plain words = 3804 sentences = 204 flesch = 55 summary = This procedure utilized primers composed of 20 bases of known sequence with 8 random bases at the 3′-end that also served as an identifying barcode that allowed the differentiation each viral library following pooling and sequencing. There is a wealth of information in these isolates, but up till now, it has been time consuming and expensive to sequence these viral genomes, often requiring sets of strain-specific primers for PCR amplification and sequencing. These primers were developed so that the 20 base known sequence was used for PCR amplification of the library as well as served as a barcode for identifying each viral library following pooling and sequencing. This virus, a BVDV 1b strain isolated from alpaca (GenBank accession JX297520.1; Table 2 , library 3, barcode 10), was assembled from Ion Torrent data and was found to have only 1 base difference from the sequence determined earlier (data not shown). One virus, library 1, barcode 9, had only 658 viral sequence reads but 94.4% of the genome was assembled. cache = ./cache/cord-326225-crtpzad7.txt txt = ./txt/cord-326225-crtpzad7.txt === reduce.pl bib === id = cord-325969-9zhmmvdg author = To, Kelvin KW title = Additional molecular testing of saliva specimens improves the detection of respiratory viruses date = 2017-06-07 pages = extension = .txt mime = text/plain words = 4543 sentences = 250 flesch = 48 summary = In the first cohort of 159 patients whose nasopharyngeal aspirates (NPAs) tested positive for respiratory viruses during routine testing, the viral load was measured using quantitative reverse transcription PCR. Although NPAs have high viral loads and remain the specimen of choice for most patients with respiratory virus infections, supplementary molecular testing of saliva can improve the clinical management of these patients. The first part of the study consisted of patients whose NPA samples tested positive for respiratory viruses by DFA or the influenza A virus M gene by real-time RT-PCR during routine respiratory virus testing in our clinical microbiology laboratory ( Figure 1 ). In the first part of this study, saliva had a higher viral load than NPA in 17.0% of the patients who tested positive for respiratory viruses by DFA or influenza A virus by RT-PCR in their NPA samples. cache = ./cache/cord-325969-9zhmmvdg.txt txt = ./txt/cord-325969-9zhmmvdg.txt === reduce.pl bib === id = cord-327013-gc6o8ou3 author = Kim, Heui Man title = Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea date = 2020-07-06 pages = extension = .txt mime = text/plain words = 2361 sentences = 142 flesch = 41 summary = title: Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea The Korea Centers for Disease Control and Prevention operates the Korea Influenza and Respiratory Viruses Surveillance System (KINRESS) to monitor epidemics of influenza and Severe Acute Respiratory Infection (SARI) to identify mutated influenza viruses affecting drug resistance, pathogenesis, and transmission. CONCLUSIONS: Our data indicate the utility of monitoring influenza-infected immunocompromised patients in general hospitals for the early detection of emerging neuraminidase inhibitor-resistant viruses and maintaining continuous laboratory surveillance of patients with influenza-like illness in sentinel clinics to monitor the spread of such new variants. If a drug resistance mutation is found in the NA gene, the KINRESS attempts to isolate the virus and perform phenotypic analysis (NA inhibition assay). Here, drug-resistant A(H1N1)pdm09 viruses were detected via the KINRESS in patients with acute hematologic cancer not exhibiting recovery despite oseltamivir and peramivir administration; these were characterized genetically and antigenically following isolation. cache = ./cache/cord-327013-gc6o8ou3.txt txt = ./txt/cord-327013-gc6o8ou3.txt === reduce.pl bib === id = cord-327199-ggomuomb author = Moerdyk-Schauwecker, Megan title = Cellular Proteins Associated with the Interior and Exterior of Vesicular Stomatitis Virus Virions date = 2014-08-08 pages = extension = .txt mime = text/plain words = 6425 sentences = 288 flesch = 43 summary = In another example, the presence of host complement control proteins such as CD46, CD55 and CD59 in the viral envelope has been shown to protect against antibody dependent complement mediated virus lysis in several viruses including human T cell leukemia/ lymphoma virus type I [16] , human cytomegalovirus [16] , hepatitis C virus [17] , HIV-1 [18, 19] , extracellular enveloped vaccinia virus [20] , simian virus 5 [21] and mumps virus [21] . As discussed in the previous section, proteins not associated with the interior of the virion, including proteins embedded in the host derived viral envelope, can be identified by their absence in ProK treated samples or by a size shift upon ProK treatment. While many of the proteins identified in VSV virions appear to be associated with viral assembly, budding or the host-derived viral envelope, they may also have additional functions that affect virus replication. cache = ./cache/cord-327199-ggomuomb.txt txt = ./txt/cord-327199-ggomuomb.txt === reduce.pl bib === id = cord-325915-dw989txm author = Wolf, Michael W title = Downstream processing of cell culture-derived virus particles date = 2014-01-09 pages = extension = .txt mime = text/plain words = 11861 sentences = 655 flesch = 34 summary = The number of publications [24, [38] [39] [40] [41] [42] [43] [44] [45] [46] and patents [301] [302] [303] describing the purification or concentration of virus particles by centrifugation methods demonstrates that these procedures are extensively used at industrial-and small-scale levels for viral vectors and vaccine production processes. In summary, the main advantages of ultrafiltration compared with other methods are their high-throughput and (for the concentration of active virus particles) the gentle processing at optimal operating conditions [43, 47] that results in improved efficacies for purification of viral vectors for gene therapy. Considering a complete purification train for the production of vaccines or gene therapy vectors (Figure 1) , current improvements of the dynamic binding capacities in chromatography media might facilitate the removal of the initial concentration step within the downstream process. cache = ./cache/cord-325915-dw989txm.txt txt = ./txt/cord-325915-dw989txm.txt === reduce.pl bib === id = cord-325827-492xi3ee author = Evermann, J. F. title = Biological and pathological consequences of feline infectious peritonitis virus infection in the cheetah date = 1988 pages = extension = .txt mime = text/plain words = 4215 sentences = 178 flesch = 38 summary = Subsequent observations based upon seroepidemiological surveys and electron microscopy of fecal material verified that cheetahs were indeed capable of being infected by coronaviruses, which were antigenically related to coronaviruses affecting domestic cats, i.e. feline infectious peritonitis virus/feline enteric coronavirus. The purpose of this review is to present desciptions of the various forms of coronaviral infections in the cheetah relying upon studies of both natural infections, as well as experimental infections in other species with coronaviruses, such as mouse hepatitis virus (MHV), canine coronavirus (CCV), transmissible gastroenteritis virus (TGEV) of swine, and bovine coronavirus (BCV) of neonatal calves [28, 36, 39, 49, 57, 60, 61, 75, 79, 92] . The occurrence of coronaviral infections of the cheetah have now been documented based on serology, electron microscopy of fecal contents, and the occurrence of fatal forms of infectious peritonitis compatible with the clinicopathologic signs observed in domestic cats with FIP [7, 10, 26, 29, 38, 43, 56, 72] . cache = ./cache/cord-325827-492xi3ee.txt txt = ./txt/cord-325827-492xi3ee.txt === reduce.pl bib === id = cord-327000-oyg3oyx1 author = Li, Shasha title = Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response date = 2020-05-11 pages = extension = .txt mime = text/plain words = 11098 sentences = 688 flesch = 48 summary = This review highlights the immune evasion mechanisms employed by PEDV, which provides insights for the better understanding of PEDV-host interactions and developing effective vaccines and antivirals against CoVs. Porcine epidemic diarrhea virus (PEDV) is the etiological agent of porcine epidemic diarrhea (PED) that causes an acute and highly contagious enteric disease of swine characterized by vomiting, diarrhea, dehydration, and anorexia in pigs of all ages, especially resulting in severe diarrhea and high mortality rate in piglets. Nsp3 is the largest nsp protein, containing two papain-like protease (PLP1 and PLP2) domains, of which PEDV PLP2 acts as a viral deubiquitinase (DUB), to negatively regulate type I IFN signaling [80] . The evasive strategies utilized by PEDV are classified into four major types: (1) inhibition of RLRs-mediated IFN production pathways, (2) inhibition of the activation of transcription factors responsible for IFN induction, (3) disruption of the signal cascades induced by IFN, and (4) hiding its viral RNA to avoid the exposure of viral RNA to immune sensors. cache = ./cache/cord-327000-oyg3oyx1.txt txt = ./txt/cord-327000-oyg3oyx1.txt === reduce.pl bib === id = cord-326725-0jgw083h author = Klamroth, Robert title = Pathogen inactivation and removal methods for plasma‐derived clotting factor concentrates date = 2013-09-30 pages = extension = .txt mime = text/plain words = 5972 sentences = 303 flesch = 41 summary = These measures include selection of donors, screening of donations and plasma pools for markers of infection with known viruses, and a manufacturing process with a high capacity to inactivate and/or remove viruses by selected steps validated for their virus reduction capacity. [7] [8] [9] Although screening for viral markers by serology and virus nucleic acid by nucleic acid testing (NAT) ensures that nearly all plasma units entering production are free of HBV, HCV, and HIV, inactivation and removal steps are necessary to reduce any viruses that may enter the plasma pool during a "window period" before markers can be detected. 46 Although B19V was reduced by dry heat in validation studies, the reduction factor may not be sufficient for complete inactivation of the virus load in the final product; asymptomatic B19V infection was detected in a patient who received FVIII concentrate treated at 80°C for 72 hours. cache = ./cache/cord-326725-0jgw083h.txt txt = ./txt/cord-326725-0jgw083h.txt === reduce.pl bib === id = cord-325925-010xj69x author = Mordecai, Gideon J title = Endangered wild salmon infected by newly discovered viruses date = 2019-09-03 pages = extension = .txt mime = text/plain words = 5549 sentences = 259 flesch = 48 summary = Population surveys of >6000 wild juvenile Chinook and sockeye salmon showed divergent distributions of viruses, implying different epidemiological processes. The discovery in dead and dying farmed salmon of previously unrecognised viruses that are also widely distributed in wild salmon, emphasizes the potential role that viral disease may play in the population dynamics of wild fish stocks, and the threat that these viruses may pose to aquaculture. Together, sequencing of dead or moribund aquaculture salmon and live-sampled wild salmon, in-situ hybridization, and epidemiological surveys revealed that previously unknown viruses, some of which are associated with disease, infect wild salmon from different populations. High-throughput RT-PCR screening of >6000 wild juvenile Chinook and sockeye salmon showed dissimilar geographical distributions of infected fish, reflecting differences in epidemiological patterns of transmission and infection dynamics for each of the viruses ( Figure 2) . cache = ./cache/cord-325925-010xj69x.txt txt = ./txt/cord-325925-010xj69x.txt === reduce.pl bib === id = cord-326027-58whwspe author = Hernaez, Bruno title = Visualization of the African swine fever virus infection in living cells by incorporation into the virus particle of green fluorescent protein-p54 membrane protein chimera date = 2006-06-20 pages = extension = .txt mime = text/plain words = 7885 sentences = 372 flesch = 45 summary = title: Visualization of the African swine fever virus infection in living cells by incorporation into the virus particle of green fluorescent protein-p54 membrane protein chimera To track the behavior of African swine fever virus (ASFV) in the infected cells in real time, we produced an infectious recombinant ASFV (B54GFP-2) that expresses and incorporates into the virus particle a chimera of the p54 envelope protein fused to the enhanced green fluorescent protein (EGFP). To determine that protein p54, a major component of the external envelope of ASFV, fused to EGFP protein remains incorporated to the viral particle, BA71V and B54GFP-2 virions were Percoll purified and analyzed by SDS-PAGE and Western blotting using specific antibodies (Fig. 2a) . This new role for p54 in morphogenesis supports the selection of p54 as viral fusion protein and suggests that studies about p54-EGFP trafficking during infection in live cells would be helpful to analyze the acquisition of ASFV envelopes from ER during virus assembly. cache = ./cache/cord-326027-58whwspe.txt txt = ./txt/cord-326027-58whwspe.txt === reduce.pl bib === id = cord-325325-xw7627x9 author = Skeik, Nedaa title = Influenza viruses and the evolution of avian influenza virus H5N1 date = 2007-10-02 pages = extension = .txt mime = text/plain words = 4079 sentences = 254 flesch = 51 summary = While the clock is still ticking towards what seems to be inevitable pandemic influenza, on April 17, 2007 the U.S. Food and Drug Administration (FDA) approved the first vaccine against the avian influenza virus H5N1 for humans at high risk. While the clock is still ticking towards what seems to be inevitable pandemic influenza, on April 17, 2007 the U.S. Food and Drug Administration (FDA) approved the first vaccine against the avian influenza virus H5N1 for humans at high risk. [8] [9] [10] [11] The 1957 pandemic was caused by the H2N2 subtype, a product of genetic reassortment in hosts infected with both an avian and human influenza virus. Although immunization with human influenza vaccine will not protect against avian influenza strains, it should be considered in poultry workers, and also be given to those traveling to affected areas, two weeks ahead of departure, to prevent co-infection and reassortment. cache = ./cache/cord-325325-xw7627x9.txt txt = ./txt/cord-325325-xw7627x9.txt === reduce.pl bib === id = cord-328252-dk54w8z9 author = Kikkert, Marjolein title = Innate Immune Evasion by Human Respiratory RNA Viruses date = 2019-10-14 pages = extension = .txt mime = text/plain words = 11552 sentences = 550 flesch = 43 summary = Whether PA-X also degrades viral dsRNA species to prevent recognition by cytosolic RNA sensors is not entirely clear, but mutant viruses in which this PA-X protein was expressed in significantly lower amounts elicited higher levels of innate immune response; for example, IFN-beta production was much higher in these infections [71] . This indeed suggests that PA-X, besides having a role in the degradation of cellular mRNAs, may also degrade viral RNA to prevent recognition by innate immune sensors and activation of innate immune responses, similar to what was shown for the CoVs. To my knowledge, an endoribonuclease has not been identified in the RSV genome, so this virus may use alternative innate immune evasion strategies, as discussed elsewhere in this review. [91] suggested that RSV specifically targets mRNA encoding surfactant protein A, an innate immune factor with an important role in the epithelial tissue of the lung, which directly binds to virus particles to cause their destruction by host defense mechanisms. cache = ./cache/cord-328252-dk54w8z9.txt txt = ./txt/cord-328252-dk54w8z9.txt === reduce.pl bib === id = cord-327855-txryqil7 author = Kulka, M. title = The cytopathic 18f strain of Hepatitis A virus induces RNA degradation in FrhK4 cells date = 2003 pages = extension = .txt mime = text/plain words = 8706 sentences = 394 flesch = 50 summary = Analysis of total cellular RNA from HM175/18f infected FrhK4 cells by denaturing agarose gel electrophoresis and Northern blot hybridization revealed extensive degradation of both the 28S and 18S ribosomal RNA (rRNA) molecules. In this study, we report that infection of FrhK4 cells with the HAV cp strain HM175/18f results in the degradation of ribosomal RNA (rRNA) and the reduction of several cellular mRNAs including β-actin and GAPDH. Degradation of rRNA is a feature of virus infection in interferon (IFN) treated cells and is believed to be due to the availability of double stranded RNA (dsRNA) during replication or transcription of the viral genome, resulting in the activation of the RNase L pathway [58, 59] . While the role of a viral protein in the activation of 2-5A/RNase L pathway in 18f or CBV1 infected FrhK4 cells cannot be ruled out, previous reports with EMC virus and the studies involving dsRNA clearly suggests a similar mechanism of rRNA degradation reported here. cache = ./cache/cord-327855-txryqil7.txt txt = ./txt/cord-327855-txryqil7.txt === reduce.pl bib === id = cord-326177-zzsaf3bl author = Khatri, Mahesh title = Mesenchymal stem cell-derived extracellular vesicles attenuate influenza virus-induced acute lung injury in a pig model date = 2018-01-29 pages = extension = .txt mime = text/plain words = 6655 sentences = 370 flesch = 49 summary = title: Mesenchymal stem cell-derived extracellular vesicles attenuate influenza virus-induced acute lung injury in a pig model In several animal models of human diseases, MSC-EVs mimic the beneficial effects of MSCs. Influenza viruses cause annual outbreaks of acute respiratory illness resulting in significant mortality and morbidity. Next, we examined the anti-influenza activity of MSC-EVs in vitro in lung epithelial cells and anti-viral and immunomodulatory properties in vivo in a pig model of influenza virus. The antiinfluenza activity of MSC-EVs was due to transfer of RNAs from EVs to epithelial cells since pre-incubation of MSC-EVs with RNase enzyme abrogated the anti-influenza activity of MSC-EVs. In a pig model of influenza virus, intratracheal administration of MSC-EVs 12 h after influenza virus infection significantly reduced virus shedding in the nasal swabs, influenza virus replication in the lungs, and virus-induced production of proinflammatory cytokines in the lungs of influenza-infected pigs. cache = ./cache/cord-326177-zzsaf3bl.txt txt = ./txt/cord-326177-zzsaf3bl.txt === reduce.pl bib === id = cord-325712-9kbnyqt3 author = Nathan, Lakshmi title = Single Virion Tracking Microscopy for the Study of Virus Entry Processes in Live Cells and Biomimetic Platforms date = 2019-07-18 pages = extension = .txt mime = text/plain words = 10235 sentences = 489 flesch = 41 summary = title: Single Virion Tracking Microscopy for the Study of Virus Entry Processes in Live Cells and Biomimetic Platforms In addition, for HIV [9] , influenza [10] , and Ebola virus [11] , most virions that encounter a cell are not involved in productive entry so the ability of single virion techniques to distinguish entry-competent particles from non-competent ones and characterize their individual behavior provides valuable data on heterogeneity in viral populations and its ultimate impact on infection. The remaining part of the chapter will focus on single particle tracking microscopy techniques compatible with dynamic/temporal data acquisition, their salient features, and how the data generated complement ensemble methods for studying viral entry processes and their intermediate steps and mechanisms. Here, binding and fusion is studied by monitoring liposomes decorated with host cell receptors interacting with the planar virus-like bilayer containing embedded viral proteins [59] [60] [61] . cache = ./cache/cord-325712-9kbnyqt3.txt txt = ./txt/cord-325712-9kbnyqt3.txt === reduce.pl bib === id = cord-326960-9phlylce author = Felberbaum, Rachael S. title = The baculovirus expression vector system: A commercial manufacturing platform for viral vaccines and gene therapy vectors date = 2015-03-20 pages = extension = .txt mime = text/plain words = 7289 sentences = 374 flesch = 43 summary = This combination of features and product approvals has previously attracted interest from academic researchers, and more recently from industry leaders, to utilize BEVS to develop next generation vaccines, vectors for gene therapy, and other biopharmaceutical complex proteins. expresSF+ cells are used to manufacture three licensed products: Flublok ® influenza vaccine (Protein Sciences Corporation), Glybera ® gene therapy for the treatment of familial lipoprotein lipase deficiency (uniQure), and Ingelvac CircoFLEX ® veterinary vaccine to protect against porcine circovirus type 2 (Boehringer Ingelheim Vetmedica). Recombinant AAV-based gene therapies have been in development and shown promise for some time; however, a major limitation to their implementation had been the inability to scale up the manufacturing process to produce sufficient quantities of rAAVs. The original rAAV vectors were produced in mammalian tissue culture using adherent cells such as HEK293 cells, which required about 5000 175-cm 2 flasks to produce enough material for a large animal study or human clinical trial (~10 15 rAAV particles) [55] . cache = ./cache/cord-326960-9phlylce.txt txt = ./txt/cord-326960-9phlylce.txt === reduce.pl bib === id = cord-327660-p1b07b4t author = Wolf, Yuri I. title = Origins and Evolution of the Global RNA Virome date = 2018-11-27 pages = extension = .txt mime = text/plain words = 13927 sentences = 658 flesch = 45 summary = The current RdRp tree topology combined with gene gain-loss reconstruction suggests the following evolutionary scenario for branch 1 ( Fig. 2A) : a levivirus-like ancestor that, like the extant members of the Leviviridae, possessed a capsid protein unrelated to SJR-CP (19, 52) gave rise to naked eukaryotic RNA replicons known as "mitoviruses" and "narnaviruses." These replicons consist of a single RdRp gene (Fig. 2B ) and replicate in mitochondria and in the cytosol of the host cells of fungal and invertebrate hosts, respectively (the latter hosts were identified in metaviromic holobiont analyses) (14, 53) . This genome architecture could hint at an ancestral flavivirus genome that was assembled from genes borrowed from preexisting viruses, one of which possessed a divergent "tombus-like virus" RdRp. Although the origins of branch 3 are murky, major trends in its subsequent evolution clearly included lineage-specific gene capture, starting with helicases and CapEs in the ancestors of the major lineages and followed by diverse genes in smaller groups (Fig. 4B) . cache = ./cache/cord-327660-p1b07b4t.txt txt = ./txt/cord-327660-p1b07b4t.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-329145-424vv8a8 author = Kuhn, Jens H. title = Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae date = 2012-09-23 pages = extension = .txt mime = text/plain words = 5519 sentences = 229 flesch = 40 summary = Suffixes are proposed for individual names that clarify whether a given genetic variant has been characterized based on passage zero material (-wt), has been passaged in tissue/cell culture (-tc), is known from consensus sequence fragments only (-frag), or does (most likely) not exist anymore (-hist). Unfortunately, most ICTV Study Groups or other expert groups have not provided clear guidelines in the past, accepting strain and genetic variant names as they were suggested by different researchers in their publications rather than creating consistent nomenclature schemes that apply at least to all viruses of one family. To differentiate uncultured or passage 0 filoviruses for which near-complete genomic data are available from those that exist in culture, we propose to follow the suggestions of the Rotavirus Classification Working Group and to add the suffix ''-wt'' (for ''wild-type'') to their genetic variant names as outlined above. cache = ./cache/cord-329145-424vv8a8.txt txt = ./txt/cord-329145-424vv8a8.txt === reduce.pl bib === id = cord-329050-vzsy6xw1 author = Nabi, Ghulam title = Bats and birds as viral reservoirs: A physiological and ecological perspective date = 2020-09-22 pages = extension = .txt mime = text/plain words = 5059 sentences = 296 flesch = 54 summary = These convergent traits in birds and bats and their ecological interactions with domestic animals and humans increase the potential risk of viral spillover transmission and facilitate the emergence of novel viruses that most likely sources of zoonoses with the potential to cause global pandemics. This paper reviews convergent traits in the physiology, immunology and flight-related ecology of birds and bats with the aim of a better understanding of why these species are such important reservoirs of viral zoonoses, and the potential risk of bat and bird viruses infecting humans. The convergent traits of miniaturized body size, enhanced metabolic rate and antioxidant capacity, prolonged lifespan, a short but efficient digestive tract, and possessing some specific immunological features relative to non-flying mammals are thought to be the result of functional constraints on evolution imposed by the demands of powered flight (Thomas and Suthers, 1972; Norberg, 1990; Caviedes-Vidal et al., 2007; Costantini, 2008; Munshi-South and Wilkinson, 2010; Song et al., 2020; ) . cache = ./cache/cord-329050-vzsy6xw1.txt txt = ./txt/cord-329050-vzsy6xw1.txt === reduce.pl bib === id = cord-329857-pcsuu597 author = Chan, Kuan Rong title = Fc receptors and their influence on efficacy of therapeutic antibodies for treatment of viral diseases date = 2015-11-02 pages = extension = .txt mime = text/plain words = 5862 sentences = 280 flesch = 28 summary = The binding affinity of antibodies to viruses can directly impact the efficacy of mAbs [4] , suggesting that target-specific mechanisms likely account for much of the efficacy of therapeutic mAbs. However, many studies have also highlighted the contribution of Fc-mediated immune effector functions in modulating the efficacy of these mAbs [5] . FcgRs have been shown to be important in modulating the efficacy of therapeutic mAbs [5] due to their involvement in FcgRmediated phagocytosis, cytokine production, ADCC and complement-dependent cytotoxicity (CDC) that aids in virus neutralization (FIGURE 1). Given the importance of FcgRs in mediating virus neutralization and Fc effector functions, a better understanding of how therapeutic antibodies neutralize virus infections in FcgRbearing cells will impact implementation of dosing regiments and allow development of improved therapeutic antibodies against infectious diseases. Given the importance of Fc-FcgR interaction in antibodymediated effector functions, Fc modification could lead to the development of therapeutic antibodies with improved interaction to activating FcgRs. This could enhance FcgR-mediated uptake, cytokine production, antigen presentation, ADCC and CDC. cache = ./cache/cord-329857-pcsuu597.txt txt = ./txt/cord-329857-pcsuu597.txt === reduce.pl bib === id = cord-328621-3jda0k2u author = Laporte, Manon title = Airway proteases: an emerging drug target for influenza and other respiratory virus infections date = 2017-04-14 pages = extension = .txt mime = text/plain words = 4302 sentences = 213 flesch = 38 summary = Since the catalytic sites of the diverse serine proteases linked to influenza, parainfluenzaand coronavirus activation are structurally similar, active site inhibitors of these airway proteases could have broad therapeutic applicability against multiple respiratory viruses. Since the catalytic sites of the diverse serine proteases linked to influenza, parainfluenza-and coronavirus activation are structurally similar, active site inhibitors of these airway proteases could have broad therapeutic applicability against multiple respiratory viruses. The best inhibitor (92 in Table 2 ) had a K i value of 0.9 nM and, interestingly, produced clear inhibition of HA0 cleavage and virus replication in Calu-3 cells, which endogenously express HA0-activating proteases like TMPRSS2. Trypsin-like proteases of the human airways represent unique targets to suppress infections with influenza or other respiratory viruses which rely on these enzymes for their replication. Proteolytic activation of influenza viruses by serine proteases TMPRSS2 and HAT from human airway epithelium cache = ./cache/cord-328621-3jda0k2u.txt txt = ./txt/cord-328621-3jda0k2u.txt === reduce.pl bib === id = cord-329078-gnnis7pl author = Musella, Simona title = Identification of an indol-based derivative as potent and selective varicella zoster virus (VZV) inhibitor date = 2016-11-29 pages = extension = .txt mime = text/plain words = 3935 sentences = 215 flesch = 48 summary = title: Identification of an indol-based derivative as potent and selective varicella zoster virus (VZV) inhibitor Tryptamine derivative 17a was found to have a selective inhibitory activity against human varicella zoster virus (VZV) replication in vitro, being inactive against a variety of other DNA and RNA viruses. Arbidol [34] and delavirdine [35] , are examples of marketed indole-containing antiviral drugs, whereas Panobinostat (LBH589) [36] , being a HDAC (histone deacetylase) inhibitor, is actively undergoing clinical evaluation against human immunodeficiency virus (HIV) type 1 (See Fig. 1 ). The antiviral activity was expressed as EC50, being the compound concentration required to reduce virus-plaque formation (VZV) by 50%. The mixture was stirred for 3 h at room temperature, then was washed with water (3 Â 50 mL), dried over anhydrous Na2SO4, filtered, concentrated and purified by column chromatography using DCM/MeOH (9:1 v/v) as mobile phase. 4-Benzyloxy-gamma-sultone derivatives: discovery of a novel family of non-nucleoside inhibitors of human cytomegalovirus and varicella zoster virus cache = ./cache/cord-329078-gnnis7pl.txt txt = ./txt/cord-329078-gnnis7pl.txt === reduce.pl bib === id = cord-327777-pg98zc6o author = Delogu, Mauro title = Eco-Virological Preliminary Study of Potentially Emerging Pathogens in Hedgehogs (Erinaceus europaeus) Recovered at a Wildlife Treatment and Rehabilitation Center in Northern Italy date = 2020-03-01 pages = extension = .txt mime = text/plain words = 3195 sentences = 156 flesch = 48 summary = However, the high mutation rates characterizing members of the Coronaviridae family and their potential successful interspecies host jumps—as that likely occurred in the Novel coronavirus (2019-nCoV) emergence—should be considered in the management of hedgehogs admitted to multi-species wildlife rehabilitation centers, recommending their return back to the original recovery areas. Western European hedgehogs' ecological and feeding habits, along with their high population densities, notable synanthropic attitudes, frequent contacts with sympatric wild and domestic species, including humans, implicate the possible involvement of E. The wild bird Influenza A virus (IAV) gene pool poses significant risks for both animal and human health because of its ability to colonize a wide variety of animal species (included in the Mammalia, Aves and Reptilia classes) in which IAV can cause variable outcomes of infection, with possible high morbidity and fatality rates [20] . cache = ./cache/cord-327777-pg98zc6o.txt txt = ./txt/cord-327777-pg98zc6o.txt === reduce.pl bib === id = cord-326160-mf0vh6iu author = de Wit, Emmie title = Influenza Virus A/Anhui/1/2013 (H7N9) Replicates Efficiently in the Upper and Lower Respiratory Tracts of Cynomolgus Macaques date = 2014-08-12 pages = extension = .txt mime = text/plain words = 6428 sentences = 318 flesch = 42 summary = Given the public health importance of this virus, we performed a pathogenicity study of the H7N9 virus in the cynomolgus macaque model, focusing on clinical aspects of disease, radiographic, histological, and gene expression profile changes in the upper and lower respiratory tracts, and changes in systemic cytokine and chemokine profiles during infection. To elucidate global host responses specifically associated with sites of virus-induced airway injury in influenza virus A/Anhui/1/2013-infected macaques, we used microarrays to assess transcriptional profiles induced in lung lesions compared to the adjacent lung tissue. We identified ten compounds in IPA (Table 1) , four of which were perturbagens listed in CMap. We identified two compounds that met our criteria in IPA and CMap, rosiglitazone and simvastatin, predicted to have inhibitory effects on pathological host responses associated with lesions in influenza virus A/Anhui/1/2013-infected animals ( Table 1) . cache = ./cache/cord-326160-mf0vh6iu.txt txt = ./txt/cord-326160-mf0vh6iu.txt === reduce.pl bib === id = cord-330827-gu2mt6zp author = Shanmugaraj, Balamurugan title = Emergence of Novel Coronavirus 2019-nCoV: Need for Rapid Vaccine and Biologics Development date = 2020-02-22 pages = extension = .txt mime = text/plain words = 3730 sentences = 175 flesch = 40 summary = The emergence of the 2019 novel coronavirus (2019-nCoV) has recently added to the list of problematic emerging pathogens in the 21st century, which was suspected to originate from the persons exposed to a seafood or wet market in Wuhan, Hubei Province, China, suggesting animal-to-human transmission [2, 3] . Several reports in the last two decades have enough evidence to prove that the plant produced biopharmaceuticals are as effective as the mammalian cell-based proteins and also elicit potent neutralizing antibodies, or shown therapeutic effects against the particular pathogen or infection [17] [18] [19] . Many reports reviewed the importance of plant expression system for the rapid production of candidate vaccines and therapeutic antibodies against infectious diseases [22] [23] [24] [25] [26] [27] . As plant-made biopharmaceuticals provide efficacious and cost-effective strategies to protect against emerging infectious diseases, plant expression systems can be employed for the development of vaccines against nCoV. cache = ./cache/cord-330827-gu2mt6zp.txt txt = ./txt/cord-330827-gu2mt6zp.txt === reduce.pl bib === id = cord-330508-uilejxmi author = van den Hoogen, Bernadette title = Immunometabolism pathways as the basis for innovative anti-viral strategies (INITIATE): A Marie Sklodowska-Curie innovative training network date = 2020-07-28 pages = extension = .txt mime = text/plain words = 1781 sentences = 80 flesch = 30 summary = While molecular details of the innate immune response are well characterized, this research field is now being revolutionized with the recognition that cell metabolism has a major impact on the antiviral and inflammatory responses to virus infections. While molecular details of the innate immune response are well characterized, this research field is now being revolutionized with the recognition that cell metabolism has a major impact on the antiviral and inflammatory responses to virus infections. A detailed understanding of the role of metabolic regulation with respect to antiviral and inflammatory responses, together with knowledge of the strategies used by viruses to exploit immunometabolic pathways, will ultimately change our understanding and treatment of pathogenic viral diseases. A detailed understanding of the role of metabolic regulation with respect to antiviral and inflammatory responses, together with knowledge of the strategies used by viruses to exploit immunometabolic pathways, will ultimately change our understanding and treatment of pathogenic viral diseases. cache = ./cache/cord-330508-uilejxmi.txt txt = ./txt/cord-330508-uilejxmi.txt === reduce.pl bib === id = cord-328753-qwdxgk4z author = Lafaye, Pierre title = Use of camel single-domain antibodies for the diagnosis and treatment of zoonotic diseases date = 2018-09-25 pages = extension = .txt mime = text/plain words = 4624 sentences = 251 flesch = 42 summary = The antigen-binding region of such homodimeric heavy-chain only antibodies consists of one single domain, called VHH. VHHs provide many advantages over conventional full-sized antibodies and currently used antibody-based fragments (Fab, scFv), including high specificity, stability and solubility, and small size, allowing them to recognize unusual antigenic sites and deeply penetrate tissues. The active antigen-binding fragment of heavy chain antibodies can be cloned and expressed in the form of VHH, which consists of only one domain (Fig. 1) . Gene therapy with an adenoviral vector expressing a bispecific VHH, consisting of two linked VHHs targeting different PA-neutralizing epitopes, was tested in mice, and found to protect them from anthrax toxin challenge and anthrax spore infection [55] . [92] have been found in the sera of infected camels, whereas antibodies against rabies virus, vesicular stomatitis virus, and FMD virus have been detected in llamas [93] and could lead to the possible isolation of specific broadly neutralizing VHHs. Many neutralizing VHHs that bind to different sites on the same target, including hidden antigenic sites, can be isolated from immunized or infected camelids. cache = ./cache/cord-328753-qwdxgk4z.txt txt = ./txt/cord-328753-qwdxgk4z.txt === reduce.pl bib === id = cord-327392-9psblokc author = Srivastava, A.K. title = Potential of Graphene-based Materials to Combat COVID-19: Properties, Perspectives and Prospects date = 2020-10-21 pages = extension = .txt mime = text/plain words = 4055 sentences = 218 flesch = 52 summary = Graphene and graphene-related materials (GRMs) exhibit extraordinary physicochemical, electrical, optical, antiviral, antimicrobial, and other fascinating properties that warrant them as potential candidates for designing and development of high-performance components and devices required for COVID-19 pandemic and other futuristic calamities. Thus, the effectiveness of graphene-based electrochemical biosensors for the detection of biomolecules, in particular for the viruses, suggests that these biosensors have the potential to effectively detect the novel coronavirus SARS-CoV-2 as well [51] but a lot of high-end research needs to be performed to develop reliable diagnostic devices. We present a hypothetical mechanism in Figure 4 that shows how electrochemical biosensors based on graphene and GRMs could be used for the detection of SARS-CoV-2 virus. These findings reinforce that graphene-based SPR substrates could be used for designing and development of the sensitivity devices for the detection of SARS-CoV-2 and other viruses. cache = ./cache/cord-327392-9psblokc.txt txt = ./txt/cord-327392-9psblokc.txt === reduce.pl bib === id = cord-330296-706hf4qw author = Romette, J. L. title = The European Virus Archive goes global: A growing resource for research date = 2018-10-31 pages = extension = .txt mime = text/plain words = 6297 sentences = 252 flesch = 37 summary = Abstract The European Virus Archive (EVA) was created in 2008 with funding from the FP7-EU Infrastructure Programme, in response to the need for a coordinated and readily accessible collection of viruses that could be made available to academia, public health organisations and industry. The European Virus Archive (EVA) was created in 2008 with funding from the FP7-EU Infrastructure Programme, in response to the need for a coordinated and readily accessible collection of viruses that could be made available to academia, public health organisations and industry (Gould et al., 2012) . In fact, besides the EVAg, we are unaware of any non-profit organization that is concerned with facilitating reliable access globally to viruses and associated reagents from individual virus collections for research and/or diagnostic laboratories, teaching centres or industries involved in the production of diagnostic reagents, pharmaceuticals and vaccines solely for the benefit of science, in a safe and carefully regulated manner. cache = ./cache/cord-330296-706hf4qw.txt txt = ./txt/cord-330296-706hf4qw.txt === reduce.pl bib === id = cord-329527-0rlotyz3 author = Bohmwald, Karen title = Neurologic Alterations Due to Respiratory Virus Infections date = 2018-10-26 pages = extension = .txt mime = text/plain words = 11036 sentences = 559 flesch = 48 summary = In addition to this, a fatal case attributed to the H1N1 pandemic infection was reported, and the clinical finding showed that the cause of death was an intracerebral thrombosis and hemorrhage with presence of the virus in the brain, but not in lungs or CSF (Simon et al., 2013 ; Figure 2) . In another approximation to understand the etiologic agent causing myelopathy post-influenza-like syndrome, CSF obtained from a patient with this disease was inoculated in several cell lines, previously reported to be permissive for the growth FIGURE 2 | Influenza virus (IV) spreads from the lungs to the CNS through the vagus nerve promoting an inflammatory state. As described so far, CoVs are respiratory viruses that exhibit neurotropic capacities that not only allows them to achieve latency and avoid the immune response of the host, but also have neurological implications that can complicate the disease associated to its infection. Although there are extensive case reports that indicate neurological manifestations associated to hMPV-infection in humans, further studies are required in mice models to characterize this disease. cache = ./cache/cord-329527-0rlotyz3.txt txt = ./txt/cord-329527-0rlotyz3.txt === reduce.pl bib === id = cord-329493-ueqlhgn0 author = Stadler, Konrad title = SARS — beginning to understand a new virus date = 2003 pages = extension = .txt mime = text/plain words = 5146 sentences = 248 flesch = 51 summary = A new infectious disease, known as severe acute respiratory syndrome (SARS), appeared in the Guangdong province of southern China in 2002. When Thiel and colleagues 20 isolated one genomic and eight subgenomic RNAs from the FRA strain and sequenced their 5′ ends, they identified a conserved sequence (5′ACGAAC3′) that was located in coronaviruses: S, spike protein; E, envelope protein; M, membrane glycoprotein; and N, nucleocapsid protein. Alternatively, these antigens could be delivered by DNA immunization by Figure 6 | The S1 domain of SARS-CoV spike is structurally related to group 2 coronaviruses. Schematic representation of cysteine positions in the S1 domains of group 1, 2 and 3 coronaviruses, compared with the SARS-CoV spike protein. The complete genome sequence of a SARS-CoV isolate (FRA) and experimental data on its key RNA elements and protein functions are described. Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection cache = ./cache/cord-329493-ueqlhgn0.txt txt = ./txt/cord-329493-ueqlhgn0.txt === reduce.pl bib === id = cord-327883-s9nbr5y8 author = nan title = Section Virology date = 1990-03-31 pages = extension = .txt mime = text/plain words = 10576 sentences = 571 flesch = 48 summary = By improving the enzyme-linked immunosorbent assay (ELISA) for HSV-2-antibodies and additional testing of sera by Western blot, we were able to specifically identify HSV-l-and HSV-2-antibodies in serum samples. To get some insight into the molecular basis of processes controlling the viral expression we studied the sequence-specific DNA-protein interactions within the genomic regulatory regions. for Med. Microbiology, Univ., D-5300 Bonn Semiquantitative detection of Hepatitis B Virus (HBV) DNA in sera of infected individuals has become an important means of modern serological hepatitis diagnostics. THOMSSEN 1 In the course of acute Epstein-Barr virus (EBV) infection IgM antibodies always occur against two cellular antigens that were characterized as proteins with a molecular weight of 26 kD (p26) and 29 kD (p29), respectively. The frequency and specificity of antibodies to P-gene encoded proteins of human hepatitis B virus was tested in sera of acute and chronically infected patients with and without hepatocellular carcinoma (HCC). cache = ./cache/cord-327883-s9nbr5y8.txt txt = ./txt/cord-327883-s9nbr5y8.txt === reduce.pl bib === id = cord-329429-ur8g68vp author = Miłek, Justyna title = Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds date = 2018-12-10 pages = extension = .txt mime = text/plain words = 3809 sentences = 187 flesch = 50 summary = Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3'UTR or 5'UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution. This taxonomic name includes IBV which causes a highly contagious disease of chickens, and genetically similar viruses isolated from other domestic galliformes: turkey coronavirus (TCoV), responsible for turkey enteritis, and the more recently detected guinea fowl coronavirus (GfCoV), the aetiological factor of fulminating disease in this species (2, 6, 27) . cache = ./cache/cord-329429-ur8g68vp.txt txt = ./txt/cord-329429-ur8g68vp.txt === reduce.pl bib === id = cord-329902-db7hl770 author = Li, Desheng title = Influenza A(H1N1)pdm09 Virus Infection in Giant Pandas, China date = 2014-03-17 pages = extension = .txt mime = text/plain words = 1381 sentences = 74 flesch = 41 summary = We confirmed infection with influenza A(H1N1)pdm09 in giant pandas in China during 2009 by using virus isolation and serologic analysis methods. We confirmed infection with influenza A(H1N1)pdm09 in giant pandas in China during 2009 by using virus isolation and serologic analysis methods. Analyses showed that each of the 8 gene segments of the virus we isolated were closely related to pH1N1 viruses circulating among humans, including a human representative strain (A/California/04/2009) and a contemporary strain (A/Sichuan/1/2009); these viruses showed 98.6%-100% nt identity to the panda strain (online Technical Appendix Table 1 , wwwnc.cdc.gov/EID/ article/20/3/13-1531-Techapp1.pdf). One panda (Zhangka) had detectable pH1N1 and H3 subtype HI antibodies before infection; this serum sample was collected before the display of overt clinical signs in the animal but after the onset of the human pH1N1 outbreak in China. cache = ./cache/cord-329902-db7hl770.txt txt = ./txt/cord-329902-db7hl770.txt === reduce.pl bib === id = cord-331217-uup16bhm author = Murphy, Frederick A. title = Adventitious Agents and Smallpox Vaccine in Strategic National Stockpile date = 2005-07-17 pages = extension = .txt mime = text/plain words = 2282 sentences = 105 flesch = 42 summary = In keeping with current standards, we urge that old smallpox vaccines that were made in animal skin and are still a key part of our strategic national stockpile be tested for adventitious infectious agents. However, if these old vaccines are to be considered valid parts of our national stockpile we should expect not only continuing testing of potency and sterility but also testing for adventitious agents with methods that reflect the standards of today. We were unable to find a comprehensive list of possible adventitious agents when ovine materials are used, as is the case for the Lister strain smallpox vaccine produced in Europe and old vaccine stocks held by some European countries for biologic defense. Concerns about the possible presence of adventitious agents in old smallpox vaccine stocks are amplified further by current concerns about prions and the zoonotic potential of prion diseases. cache = ./cache/cord-331217-uup16bhm.txt txt = ./txt/cord-331217-uup16bhm.txt === reduce.pl bib === id = cord-331673-xv1tcugl author = Reina, Giacomo title = Hard Nanomaterials in Time of Viral Pandemics date = 2020-07-15 pages = extension = .txt mime = text/plain words = 15712 sentences = 976 flesch = 44 summary = For instance, in the case of Herpesviridae and Paramyxoviridae viruses (both enveloped viruses with embedded viral-encoded glycoproteins), AgNPs can effectively reduce their infectivity, by blocking the interaction between the viral particles and the host cells with an antiviral activity strictly dependent on the size and ζ potential of the AgNPs. As a general observation, it was reported that smaller nanoparticles have better antiviral effect. cAgNPs could reduce cytopathic effects induced by RSV and showed efficient antiviral activity against infection by directly inactivating the virus prior to entry into the host cells. have reported that porous AuNPs are able to inhibit influenza A infection more efficiently than nonporous AuNPs. 39 This effect has been associated with the higher surface area of the porous material that favors their interaction with capsids and thus increases their antiviral activity ( Figure 4 ). cache = ./cache/cord-331673-xv1tcugl.txt txt = ./txt/cord-331673-xv1tcugl.txt === reduce.pl bib === id = cord-331020-lyxje82u author = M. Najimudeen, Shahnas title = Infectious Bronchitis Coronavirus Infection in Chickens: Multiple System Disease with Immune Suppression date = 2020-09-24 pages = extension = .txt mime = text/plain words = 6966 sentences = 349 flesch = 37 summary = The evolution of new strains of IBV during the last nine decades against vaccine-induced immune response and changing clinical and pathological manifestations emphasize the necessity of the rational development of intervention strategies based on a thorough understanding of IBV interaction with the host. For example, chickens infected with certain strains of IBV such as Mass, QX-like strain or Aust T at ages of 1-14 days develop cystic oviducts without impaired ovarian functions, which leads to false layer syndrome with no egg production [15, [63] [64] [65] . One of the immune cell types that bridges innate and adaptive host responses is the macrophages, and the available data show that certain IBV serotypes (i.e., Mass and Conn) target respiratory tract macrophages and replicate within them, thus leading to a productive infection [59, 88] . cache = ./cache/cord-331020-lyxje82u.txt txt = ./txt/cord-331020-lyxje82u.txt === reduce.pl bib === id = cord-330131-yfhrmbvx author = Danchin, Antoine title = Cytosine drives evolution of SARS‐CoV‐2 date = 2020-04-27 pages = extension = .txt mime = text/plain words = 5318 sentences = 244 flesch = 42 summary = In this article, we show, in the specific case of SARS-CoV-2, that the role of cytosine-based metabolites used as cell growth coordinators is central to understanding both innate antiviral immunity and the evolution of the virus. Here we (i) highlight the deviation of SARS-CoV-2 RNA chemical composition compared with that of its human host; (ii) formulate a hypothesis grounded on the canonical organization of cytosine metabolism as a way to coordinate non-homothetic growth of cells-i.e., the simultaneous growth of the cytoplasm (three dimensions), the membrane (two dimensions) and the genome (one dimension)-, and point out the emergence of the endogenous antinucleotide viperin as a cognate adaptive antiviral metabolite and (iii) predict evolutionary trends of CoV-2 for maximizing compositional fitness-which seem to show up in ongoing mutation survey of radiative evolution. cache = ./cache/cord-330131-yfhrmbvx.txt txt = ./txt/cord-330131-yfhrmbvx.txt === reduce.pl bib === id = cord-323683-9h9mld6x author = Butler, M. title = Virus Removal by Disinfection of Effluents date = 2013-11-17 pages = extension = .txt mime = text/plain words = 6655 sentences = 288 flesch = 45 summary = The removal of viruses from sludges has only relatively recently attracted serious attention (Cliver, 1975; Berg, 1978; Osborn and Hattingh, 1978) but for effluents, various procedures have been adopted for some time, particularly disinfection with chlorine, a treatment now under critical review. Although many different enteric viruses are likely to be present in wastewater, the risks of transmission of infection via contaminated water in developed countries by various routes (Fig. 1 ) is thought to be slight although probably increasing, but elsewhere the risks may be very great indeed (WHO, 1976) . 4. The methods available for the inactivation of viruses in effluent differ little in principle from those applied to potable water, but are distinct from the disinfection of viruses contaminating, laboratory or medical equipment, where highly toxic chemicals like detergents, phenols, formaldehyde or permanganate may be used (Spalding et al 1977) . cache = ./cache/cord-323683-9h9mld6x.txt txt = ./txt/cord-323683-9h9mld6x.txt === reduce.pl bib === id = cord-331244-zaguyxm5 author = Stephenson, Iain title = Confronting the avian influenza threat: vaccine development for a potential pandemic date = 2004-07-30 pages = extension = .txt mime = text/plain words = 8192 sentences = 452 flesch = 38 summary = In clinical trials, conventional surfaceantigen influenza virus vaccines produced from avian viruses have proved poorly immunogenic in immunologically naive populations. In clinical trials, conventional surfaceantigen influenza virus vaccines produced from avian viruses have proved poorly immunogenic in immunologically naive populations. The main antigenic determinants of influenza A and B viruses are two surface glycoproteins: the neuraminidase and the haemagglutinin, both capable of eliciting immune responses in human beings. Pandemic influenza viruses arise by this process of "antigenic shift", when a virus with a new haemagglutinin subtype emerges and spreads efficiently in a naive human population. 14 These reassortant viruses have haemagglutinin receptor-binding sequences potentially capable of human infection, suggesting that new viruses may emerge directly from the avian pool. Improved understanding of the antigenic and molecular associations between potential pandemic strains of same subtype Improved understanding of immunogenicity against drifted avian influenza strains is required as the ability to generate broad crossprotective immunity is desirable in vaccine candidate. cache = ./cache/cord-331244-zaguyxm5.txt txt = ./txt/cord-331244-zaguyxm5.txt === reduce.pl bib === id = cord-330647-w1bpeqzg author = Wong, Samson Sai-Yin title = Ebola virus disease in nonendemic countries date = 2015-05-31 pages = extension = .txt mime = text/plain words = 8637 sentences = 507 flesch = 41 summary = The largest outbreak of Ebola virus disease (EVD) in history has renewed interest in filoviruses and has provided an unprecedented impetus to the development of new therapeutics and vaccines for this highly lethal infection. Nucleic acid amplification is the diagnostic test of choice because of its high sensitivity (especially in the early phase of illness); its ability to differentiate between different agents of viral hemorrhagic fever; and its relatively lower biohazard, if the viruses are appropriately inactivated; and because antigen and antibody assays are often unavailable in laboratories in nonendemic countries. 119e123 Animal studies also demonstrate the efficacy of favipiravir in the treatment of Junín virus, arenavirus, and EBOV hemorrhagic fevers, and the drug was used to treat human EVD in the 2014 West African epidemic. cache = ./cache/cord-330647-w1bpeqzg.txt txt = ./txt/cord-330647-w1bpeqzg.txt === reduce.pl bib === id = cord-332165-31tbc31x author = Rustmeier, Nils H. title = The Symmetry of Viral Sialic Acid Binding Sites—Implications for Antiviral Strategies date = 2019-10-14 pages = extension = .txt mime = text/plain words = 5820 sentences = 316 flesch = 43 summary = In this review, we will evaluate the structures of non-enveloped virus capsid proteins bound to sialylated glycan receptors and discuss the potential of these structures for the development of potent antiviral attachment inhibitors. This concept of targeting multiple, symmetric receptor binding sites by multivalent inhibitors is also applicable for many viruses, since viral capsids are often icosahedral and, therefore, highly symmetric structures. Many members of the polyomavirus family bind sialic acid-based glycans using their VP1 proteins, so the binding sites on individual pentamers are always linked by local five-fold symmetry (Figure 4a , TSPyV). The glycooligopeptide-VP1 complex structures displayed a similar ligand binding mode that was reported for sialic acid in an earlier study [50] and showed, for the compounds, that the linker between the ligand and the scaffold occupies the space that is usually targeted by the natural glycan receptor moieties (Figure 5a,b, right) . cache = ./cache/cord-332165-31tbc31x.txt txt = ./txt/cord-332165-31tbc31x.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-331739-y1d0leic author = Kempf, Christoph title = Pathogen inactivation and removal procedures used in the production of intravenous immunoglobulins date = 2007-03-31 pages = extension = .txt mime = text/plain words = 5089 sentences = 287 flesch = 42 summary = Since plasma pools from 250 to 2000 blood donations were being used to produce albumin, efforts were initiated to inactivate hepatitis virus in human serum albumin solutions [6] . The emergence of human immunodeficiency virus (HIV) and reports of non-A, non-B hepatitis transmission by some IVIG products [11, 12] but not others caused manufacturers and regulatory agencies to examine existing IVIG manufacturing processes for their capacity to eliminate viruses [13e22]. Studies of IVIG manufacturing procedures suggested that cold ethanol fractionation removes viruses by two mechanisms: 1) inactivation and 2) partitioning. Efficient elimination of TSE infectivity from IgG solutions by Table 3 Log 10 reduction factors of model viruses observed during laboratory experiments of IVIG production (Carimune NF Ò ) Process (step in Fig. 1 [53] . To date IVIG therapeutics have reached a high safety standard due to consequent blood and plasma testing and the introduction of virus elimination steps in the manufacturing process. cache = ./cache/cord-331739-y1d0leic.txt txt = ./txt/cord-331739-y1d0leic.txt === reduce.pl bib === id = cord-331584-z43ifmr3 author = Mahy, B.W.J. title = Emerging and Reemerging Virus Diseases of Vertebrates date = 2008-07-30 pages = extension = .txt mime = text/plain words = 3984 sentences = 160 flesch = 49 summary = The threat of a new pandemic of influenza virus in the human population stresses the need for development of better methods for detection, surveillance, and control of emerging virus diseases. Although it is still important to isolate viruses in cell culture for their complete characterization, it is now possible directly to detect viruses in diseased tissues by PCR, then, by sequencing the amplicon, to determine whether a new virus has emerged to cause the disease. For example, when hantavirus pulmonary syndrome, caused by a bunyavirus of rodents, Sin Nombre virus, was initially detected in 1993 in the Four Corners region of Western USA, it was found that rodents inside a house where people had been infected carried a virus identical in sequence to virus isolated from human cases. Then, in 1993, a new hantavirus emerged in the Four Corners region of Southwestern USA as the cause of a severe acute respiratory disease syndrome, with a fatality rate close to 40%, and named Sin Nombre virus. cache = ./cache/cord-331584-z43ifmr3.txt txt = ./txt/cord-331584-z43ifmr3.txt === reduce.pl bib === id = cord-332457-gan10za0 author = de Ángel Solá, David E. title = Weathering the pandemic: How the Caribbean Basin can use viral and environmental patterns to predict, prepare and respond to COVID‐19 date = 2020-04-10 pages = extension = .txt mime = text/plain words = 2867 sentences = 168 flesch = 39 summary = On March 12, 2020, the World Health Organization (WHO) declared a pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, the pathogen responsible for the clinical disease known as COVID-19. Recently, a pattern favoring cold, dry weather was also observed in Hong Kong in a 6-year-long study, though in this case coronaviruses were found yearround 48 Therefore, data from other coronaviruses and the similar portal of infection discussed above do support the idea that SARS-CoV-2 may follow the same patterns as influenza, and that timing interventions around influenza peaks in the Caribbean would be reasonable. If SARS-CoV-2 interacts with climate and weather as theorized above, it is likely that areas in the Greater Caribbean with Air Surface Temperatures (AST) >25°C and RH>70% might be considered areas of relatively decreased environmental risk (Figure 1 ) 53 . cache = ./cache/cord-332457-gan10za0.txt txt = ./txt/cord-332457-gan10za0.txt === reduce.pl bib === id = cord-331652-oc5s1if2 author = Trudeau, Michaela P. title = Comparison of Thermal and Non-Thermal Processing of Swine Feed and the Use of Selected Feed Additives on Inactivation of Porcine Epidemic Diarrhea Virus (PEDV) date = 2016-06-24 pages = extension = .txt mime = text/plain words = 5988 sentences = 294 flesch = 52 summary = title: Comparison of Thermal and Non-Thermal Processing of Swine Feed and the Use of Selected Feed Additives on Inactivation of Porcine Epidemic Diarrhea Virus (PEDV) Feed samples were spiked with PEDV and then heated to 120–145°C for up to 30 min or irradiated at 0–50 kGy. Another set of feed samples spiked with PEDV and mixed with Ultracid P (Nutriad), Activate DA (Novus International), KEM-GEST (Kemin Agrifood), Acid Booster (Agri-Nutrition), sugar or salt was incubated at room temperature (~25°C) for up to 21 days. Therefore, the objective of this study was to determine if thermal and non-thermal methods of microbial inactivation, as well as the use of selected feed additives, are effective in reducing the survival of PEDV in experimentally contaminated swine feed. The PEDV showed a high thermal resistance in the dry feed samples and it was completely inactivated (3.0 log reduction) at each of the tested temperatures within 30 min. cache = ./cache/cord-331652-oc5s1if2.txt txt = ./txt/cord-331652-oc5s1if2.txt === reduce.pl bib === id = cord-331289-02411gfv author = Di Minno, Giovanni title = Current concepts in the prevention of pathogen transmission via blood/plasma-derived products for bleeding disorders() date = 2015-07-20 pages = extension = .txt mime = text/plain words = 8171 sentences = 395 flesch = 43 summary = In general, clinicians assess the level of risk associated with the use of blood/ plasma-derived products by evaluating factors such as patient characteristics (e.g. age, immune status, geographical location, lifestyle) and the nature of the pathogen (e.g. physical characteristics, level of virulence, chronicity of infection, prevalence). Current donor selection and screening practices have improved our ability to detect or reduce the presence of pathogens in blood/plasma-derived products; for example, the residual risk of transfusion-transmitted infection (TTI) with HIV/HBV/HCV has fallen to near or less than 1 per million transfused units [14, 15] . Since TTV is often detected in healthy individuals and is not associated with any particular disease, routine screening for this virus is not considered to be necessary; even a test with excellent sensitivity/specificity would not contribute to increase the level of safety of blood/plasma-derived products with regard to TTV. cache = ./cache/cord-331289-02411gfv.txt txt = ./txt/cord-331289-02411gfv.txt === reduce.pl bib === id = cord-332181-k90i33gp author = Degeling, Chris title = Hendra in the news: Public policy meets public morality in times of zoonotic uncertainty date = 2012-12-29 pages = extension = .txt mime = text/plain words = 7062 sentences = 279 flesch = 47 summary = Because flying foxes are a highly visible, widespread and relatively novel source of infectious risk for humans, the emergence of Hendra virus presents an opportunity to track and compare media representations of disease 'events', health policy goals, political discourses and public opinions in ways that are difficult for noncommunicable diseases. Articles then were coded for: mention of horses, flying foxes/fruit bats or Hendra virus mention of debates about flying fox control report of distal ecological causes (loss of natural habitat) for the emergence of Hendra virus or the possibility of viral mutation mention of ignorance about Hendra virus amongst scientists, healthcare providers or members of the public reference to government inaction as a factor contributing to the Hendra problem reference to people's health and welfare not being high enough on the political agenda. cache = ./cache/cord-332181-k90i33gp.txt txt = ./txt/cord-332181-k90i33gp.txt === reduce.pl bib === id = cord-332088-5c77h0of author = Beena, V. title = Emerging horizon for bat borne viral zoonoses date = 2019-10-26 pages = extension = .txt mime = text/plain words = 4568 sentences = 237 flesch = 50 summary = In Asia and Pacific regions, bats were demonstrated as natural reservoirs for a large number of this types of emerging as well as re-emerging pathogens such as SARS, Ebola, Marburg, Nipha, Hendra, Tioman, Menangle, Australian bat lyssa virus, Rabies and many encephalitis causing viruses in humans and animals [2] . From bats the pathogen get transmitted to humans via intermediate hosts like horses(hendra) and pigs(nipah) and different species of animals get infected by consumption of partially eaten fruits of bats and the chewed out materials of bats after extracting the juice. The first report of a transmission of a viral disease from bats to humans was a rabies virus (RABV) belonging to the Lyssa virus genus [5] . Identification and complete genome analysis of three novel paramyxoviruses, Tuhoko virus 1, 2 and 3, in fruit bats from China cache = ./cache/cord-332088-5c77h0of.txt txt = ./txt/cord-332088-5c77h0of.txt === reduce.pl bib === id = cord-333043-fe24ezt6 author = Traavik, T. title = “Runde“ virus, a coronavirus-like agent associated with seabirds and ticks date = 1977 pages = extension = .txt mime = text/plain words = 4191 sentences = 318 flesch = 63 summary = uriae collected in the seabird colonies at Runde, Norway, two identical virus strains demonstrating no antigenic relationships to major arbovirus groups were isolated. Until then., no arbovirus isolates had been reported from this country, although ecological and cli-nicaI/epidemiological considerations (3, 24, 26) and a limited serological survey on bovine sera (28) indicated the existence of Central-European tick-borne encephalitis virus fool. uriae ticks collected at Runde in late September 1973, three virus strains have been isolated. Cells were washed with saline, virus was diluted ~enfold from 10 -1 to t0 -6 in the medium, A volume of 0.2 ml of each dilution was inoculated into three tubes and allowed to adsorb for 1 hour at room temperature before washing with saline and addition, of new medium, Culture tubes were incubated for 8 days at 37 ° C and inspected daily for a Cytopathie effect (CPE). Virus from mouse brains and cell culture demonstrated total i d e n t i t y b y these methods. cache = ./cache/cord-333043-fe24ezt6.txt txt = ./txt/cord-333043-fe24ezt6.txt === reduce.pl bib === id = cord-332632-u2ud0vmq author = Lussi, Carmela title = What can pestiviral endonucleases teach us about innate immunotolerance? date = 2016-03-17 pages = extension = .txt mime = text/plain words = 8703 sentences = 394 flesch = 44 summary = In particular, the unique extension of 'self' to include the viral genome by degrading immunostimulatory viral RNA by E(rns) is reminiscent of various host nucleases that are important to prevent inappropriate IFN activation by the host's own nucleic acids in autoimmune diseases such as Aicardi-Goutières syndrome or systemic lupus erythematosus. Thus, the survival strategy of BVDV consists of being non-cytopathogenic and producing less dsRNA than its cp counterpart, and expressing the IFN antagonists N pro as the first protein in order to reduce or even avoid IFN production in infected cells and E rns to degrade immunostimulatory viral RNA before they might activate the host's PRRs. Notably, both pestiviral IFN antagonists are not only required to constantly maintain innate immunotolerance during persistent infections, but they also play an important role in acute infections [25] . cache = ./cache/cord-332632-u2ud0vmq.txt txt = ./txt/cord-332632-u2ud0vmq.txt === reduce.pl bib === id = cord-332205-ydijp66b author = Hufsky, Franziska title = Virologists—Heroes need weapons date = 2018-02-08 pages = extension = .txt mime = text/plain words = 1165 sentences = 69 flesch = 53 summary = Nowadays, nearly everyone in the life sciences has used BLAST [8] at least once, or made an alignment, or asked a bioinformatician to analyze high-throughput sequencing data. Bioinformaticians routinely have to develop tailored, study-specific algorithms and tools used by a wide variety of scientists, including biochemists, biologists, geneticists, and molecular life scientists; but we rarely find virus-specific tools used by virologists. But astonishingly, we now know that the human genome consists of 8%-60% virus-derived sequences (depending on how this is measured: 8% can be directly traced back to viruses, whereas a figure of 60% includes LINEs and SINEs that are thought to be of viral origin [12] ). The EVBC aims to develop bioinformatical tools for nearly all areas: (1) for detection of viruses, e.g., from high-throughput sequencing data; (2) virus assembly; (3) quasispecies reconstruction; (4) intraviral interactions; (5) virus entry, i.e., protein-protein interaction; (6) virus -host interactions; (7) phylogeny/cophylogeny; and (8) therapy. cache = ./cache/cord-332205-ydijp66b.txt txt = ./txt/cord-332205-ydijp66b.txt === reduce.pl bib === id = cord-332992-8rmqg4rf author = de Vries, A. A. F. title = SARS-CoV-2/COVID-19: a primer for cardiologists date = 2020-07-15 pages = extension = .txt mime = text/plain words = 9182 sentences = 433 flesch = 39 summary = Although SARS-CoV-2 particles/components have been detected in, for example, endothelial cells, the digestive tract and the liver, not all extrarespiratory manifestations of COVID-19 are necessarily caused by direct viral injury but may also be the consequence of the hypoxaemia, (hyper)inflammatory response, neuroendocrine imbalance and other pathophysiological changes induced by the airway infection [43] . Factors that may contribute to the thrombophilia observed in severely ill COVID-19 patients include the following: (1) a disturbed balance between pro-and anticoagulant activities due to excessive production of proinflammatory cytokines, activation of complement, formation of neutrophil extracellular traps and activation of platelets; (2) inflammation-related endothelial activation; (3) death of SARS-CoV-2-infected endothelial cells; (4) endothelial dysfunction caused by unbalanced angiotensin IIangiotensin II type-1 receptor signalling; (5) formation of prothrombotic antiphospholipid antibodies; (6) immobility-associated reduction of blood flow; (7) hypoxia due to respiratory impairment resulting from SARS-CoV-2-induced lung injury [79] [80] [81] . cache = ./cache/cord-332992-8rmqg4rf.txt txt = ./txt/cord-332992-8rmqg4rf.txt === reduce.pl bib === id = cord-332046-ihc031ly author = Li, Yan‐Chao title = Neurotropic virus tracing suggests a membranous‐coating‐mediated mechanism for transsynaptic communication date = 2013-01-01 pages = extension = .txt mime = text/plain words = 4865 sentences = 236 flesch = 47 summary = This study has systematically examined the assembly and dissemination of HEV 67N in the primary motor cortex of infected rats and provides additional evidence indicating that mem-branous-coating-mediated endo-/exocytosis can be used by HEV for its transsynaptic transfer. Consistent with the results in the previous experiments, the present study showed that at day 4 p.i. HEV-positive cells were observed in only a certain population of neurons with different sizes in layer V of the primary motor cortex (Fig. 1A,B) . Extracellular virions were not enclosed by any vesicular structures, whereas vesicle-enclosed virus particles were otherwise observed in the axonal terminals touching on the infected neurons, so it seemed that the virions within the synapses had acquired new vesicular membrane after entry. D shows a virion within a coated vesicle (arrow; see also the inset for details) in the axon terminal adjacent to an infected pyramidal cell. cache = ./cache/cord-332046-ihc031ly.txt txt = ./txt/cord-332046-ihc031ly.txt === reduce.pl bib === id = cord-333730-qsx0m68e author = Tsai, Y. C. title = Oral disease-modifying antirheumatic drugs and immunosuppressants with antiviral potential, including SARS-CoV-2 infection: a review date = 2020-09-03 pages = extension = .txt mime = text/plain words = 4920 sentences = 297 flesch = 35 summary = However, some immunosuppressants or disease-modifying antirheumatic drugs (DMARDs) show antiviral activity and may be safely used or even beneficial in patients with selected concomitant viral infections. In vitro anti-CMV properties of leflunomide were not through blocking the replication of viral DNA, so it is effective even in patients with direct antiviral drug-resistance history. The combination of MMF and highly active antiretroviral therapy improved the control of viral replication and delayed viral-load rebound in a randomized pilot study (n = 17 The effectiveness of thalidomide for KS might be related to anti-angiogenesis, and experts hypothesized the modulation of the immune system to trigger an antiviral action. Although in most instances, the antiviral activity of DMARDs is based on in vitro or small-scale controlled studies, this property would be useful in the choice of DMARDs for patients with concomitant viral infections. Effects of hydroxychloroquine on immune activation and disease progression among HIV-infected patients not receiving antiretroviral therapy: a randomized controlled trial cache = ./cache/cord-333730-qsx0m68e.txt txt = ./txt/cord-333730-qsx0m68e.txt === reduce.pl bib === id = cord-331343-qzvwwca9 author = Mason, Andrew L. title = Metagenomics and the case of the deadly hamster date = 2008-06-09 pages = extension = .txt mime = text/plain words = 2836 sentences = 172 flesch = 49 summary = 1 The authors then tried panmicrobial microarray analysis with 29,455 oligonucleotide probes reactive to known vertebrate viruses, bacteria, fungi, and parasites, 5 and after drawing a blank with all these studies, they resorted to brute sequencing of all RNA in the infected tissue to discover the new virus. 8 In humans, metagenomic analysis has been used to study viral communities in blood and respiratory secretions, 6 to differentiate bacterial species in gut flora, 9 and to catalog the collective DNA and RNA viral species in stool samples of healthy subjects 10, 11 and patients with diarrhea. 16 They would have saved a considerable amount of time and effort if they could have sequenced RNA from a few "non-A non-B virus" infected livers (assuming that they could have had access to human genome data that were not available at the time). cache = ./cache/cord-331343-qzvwwca9.txt txt = ./txt/cord-331343-qzvwwca9.txt === reduce.pl bib === id = cord-333853-p2kbjwpy author = Smee, Donald F. title = Therapy and Long-Term Prophylaxis of Vaccinia Virus Respiratory Infections in Mice with an Adenovirus-Vectored Interferon Alpha (mDEF201) date = 2011-10-13 pages = extension = .txt mime = text/plain words = 4585 sentences = 222 flesch = 48 summary = title: Therapy and Long-Term Prophylaxis of Vaccinia Virus Respiratory Infections in Mice with an Adenovirus-Vectored Interferon Alpha (mDEF201) An adenovirus 5 vector encoding for mouse interferon alpha, subtype 5 (mDEF201) was evaluated for efficacy against lethal vaccinia virus (WR strain) respiratory infections in mice. Lung virus titers were significantly (>100-fold) lower than in the placebo group, and the other infection parameters in mDEF201 treated mice were nearly at baseline. Ad5-vectored mouse interferon (mDEF201) resulted in sustained IFN levels [16] , that completely protected mice from a lethal Western equine encephalitis virus infection when given intramuscularly at 10 7 plaque forming units (PFU)/ mouse up to 7 days prior to virus challenge [16] . The extent of inhibition of lung Intranasal treatments with mDEF201 (10 7 PFU/mouse) were given one time only on the indicated day prior to virus exposure. cache = ./cache/cord-333853-p2kbjwpy.txt txt = ./txt/cord-333853-p2kbjwpy.txt === reduce.pl bib === id = cord-333228-ejkgune0 author = Ball, Andrew S title = Chapter 1 Introduction into nanotechnology and microbiology date = 2019-12-31 pages = extension = .txt mime = text/plain words = 5317 sentences = 287 flesch = 32 summary = Abstract The current chapter summaries the world of Microbiology and boom of Nanotechnology and how both the exciting fields come together to help men kind with various new applications in water, food, medical biology and immunology. It is now possible to build materials atom by atom and impose desired characteristics for numerous applications in almost every area, such as composite materials development, electronics, nano-electro-mechanical systems (NEMS), biomedical technologies, renewable energy solutions and environmental remediation (Navya & Daima, 2016 Nanomaterials are classified into nine major groups based on their shape, size, composition, surface charge, aggregation and chemical nature. However, due to instances where the frequent use of drugs has led to antibiotic/multidrug resistance in microorganisms, and the delivery of metal nanoparticles is impacting the food chain, it is now necessary to develop interdisciplinary approaches combining Microbiology and Nanotechnology to combat secondary human health, and environmental and ecological damage. cache = ./cache/cord-333228-ejkgune0.txt txt = ./txt/cord-333228-ejkgune0.txt === reduce.pl bib === id = cord-330852-n7j0c4ne author = Fischer, Wolfgang B. title = Mechanism of Function of Viral Channel Proteins and Implications for Drug Development date = 2012-02-23 pages = extension = .txt mime = text/plain words = 23680 sentences = 1178 flesch = 53 summary = By adding data from functional studies like Cys scanning and electrophysiological measurements as mentioned as well as computational modeling data (Sansom and Kerr, 1993; Sansom et al., 1997; Zhong et al., 1998) , an approximate structural model of the tetrameric assembly of the TMDs of M2 with the histidines and tryptophans as important pore lining residues has been generated. Amiloride derivatives block ion channel activity and enhancement of virus-like particle budding caused by HIV-1 protein Vpu Backbone structure of the amantadine-blocked trans-membrane domain M2 protein channel from influenza A virus Molecular dynamics investigation of membrane-bound bundles of the channel-forming transmembrane domain of viral protein U from the Human Immunodeficiency Virus HIV-1 Influenza B virus BM2 protein has ion channel activity that conducts protons across membranes Three-dimensional structure of the channel-forming trans-membrane domain of virus protein "u" (Vpu) from HIV-1 cache = ./cache/cord-330852-n7j0c4ne.txt txt = ./txt/cord-330852-n7j0c4ne.txt === reduce.pl bib === id = cord-334010-gxu0refq author = Banerjee, Nilotpal title = Viral glycoproteins: biological role and application in diagnosis date = 2016-01-18 pages = extension = .txt mime = text/plain words = 6657 sentences = 406 flesch = 46 summary = The sema-domain is the [18, 43] Fusion with host cell membrane Sialic Acid and attachment [43] 3-5 million cases Worldwide [78, 105] SARS-CoV Spike(S) glycoprotein [25, 115] Membrane fusion [115] 8422 within the duration of 1st November 2002 to 7th August 2003 occurring worldwide [113, 114] Hepatitis C virus E1 and E2 [55, 98] Binding to Host receptor and Conformational change necessary for membrane fusion [98] 130 to 150 million people globally [103, 106] Human immunodeficiency virus 1 gp120, gp160, gp41 [16] Intracellular transport [16] 35 million globally up to 2013 [83, 104, 108, 112] Zaire Ebola virus Spike Protein Gp1-Gp2 [64] Primary Host cell activation [64] up to 28th June 2015 total 27,550 cases [107, 110, 111] Dengue virus E (dimer) [64] Host cell fusion and attachment [64] WHO reported recently that there are 390 million dengue infections per year globally [109] . cache = ./cache/cord-334010-gxu0refq.txt txt = ./txt/cord-334010-gxu0refq.txt === reduce.pl bib === id = cord-333351-homxj9uz author = Rodhain, F. title = Bats and Viruses: complex relationships date = 2015-10-10 pages = extension = .txt mime = text/plain words = 10167 sentences = 794 flesch = 63 summary = Plus d'une soixantaine de virus a été isolée ou détectée chez des chauves-souris qui, selon différentes modalités, se trouvent ainsi impliquées dans la circulation de beaucoup d'entre eux ; c'est le cas, notamment, de Rhabdoviridae du genre Lyssavirus, de Paramyxoviridae comme les virus Nipah et Hendra, de Filoviridae (virus Ebola et Marburg) ou de Coronaviridae comme les agents du syndrome respiratoire aigu sévère (SRAS) et du syndrome respiratoire du Moyen-Orient (MERS). Cependant, même si les contacts entre les Hommes et les chauves-souris sont faibles, la rareté des infections humaines par des Lyssavirus n'appartenant pas au génotype 1 n'est pas clairement expliquée car certains au moins de ces virus sont très largement répandus depuis longtemps ; sans doute leur véritable pathogénicité pour l'Homme est-elle faible (l'observation de cas non mortels et de sujets en bonne santé apparente porteurs d'anticorps semble en témoigner), mais les déterminants de cette pathogénicité demeurent inconnus. cache = ./cache/cord-333351-homxj9uz.txt txt = ./txt/cord-333351-homxj9uz.txt === reduce.pl bib === id = cord-334947-pa0p5dif author = Rozen-Gagnon, Kathryn title = Alphavirus Mutator Variants Present Host-Specific Defects and Attenuation in Mammalian and Insect Models date = 2014-01-16 pages = extension = .txt mime = text/plain words = 8887 sentences = 415 flesch = 44 summary = Since residue 483 is conserved among alphaviruses, we examined the analogous mutations in Sindbis virus (SINV), which also reduced polymerase fidelity and generated replication defects in mosquito cells. To estimate the population diversity of variants by deep sequencing, cDNA libraries were prepared by Superscript III from RNA extracted from virus generated in BHK-21 or C6/36 cells, and the viral genome was amplified using a high fidelity polymerase (Phusion) to generate 5 overlapping amplicons 2-3 kb in length. To address the possibility that the fitness cost of defective replication, observed in mosquito cell culture, would favor the reversion of these mutant polymerases to wildtype, we deep sequenced virus from the body of an individual mosquito that presented the median titer from each group. cache = ./cache/cord-334947-pa0p5dif.txt txt = ./txt/cord-334947-pa0p5dif.txt === reduce.pl bib === id = cord-334027-xhfmio7k author = Fagre, Anna C. title = Can Bats Serve as Reservoirs for Arboviruses? date = 2019-03-03 pages = extension = .txt mime = text/plain words = 8738 sentences = 492 flesch = 43 summary = No demonstrable pathologic effects noted during infection of three bat species [big brown bats (Eptesicus fuscus), little brown bats (Myotis lucifigus) and Mexican free-tailed bats (Tadarida brasiliensie mexicana) with various strains of JBEV or St. Louis encephalitis virus (SLEV) [69] . While experimental data demonstrated that some bat species can sustain JBEV infections and support mosquito-borne transmission of this virus, the epidemiological significance of these observations in the field remains unclear. To truly elucidate the role of bats as reservoirs for arboviruses, field surveillance studies documenting natural infection and transmission dynamics among vector and vertebrate species must be supplemented with experimental infections to characterize viremia profiles and infectiousness to vectors, virus-induced pathology, and immune kinetics following infection. The isolation of Marburg virus from Egyptian rousette bats in Uganda in addition to experimental infections demonstrating viremia and shedding in the absence of overt pathology support the role of this bat species as the reservoir for Marburg virus [6, 7, 208] . cache = ./cache/cord-334027-xhfmio7k.txt txt = ./txt/cord-334027-xhfmio7k.txt === reduce.pl bib === id = cord-334941-6uattdti author = Espmark, Åke title = Other viruses date = 2014-06-27 pages = extension = .txt mime = text/plain words = 3579 sentences = 210 flesch = 54 summary = Of the orbiviruses, the Colorado tick fever virus is the only one known to cause disease in man. Of the orbiviruses, the Colorado tick fever virus is the only one known to cause disease in man. It has recently been demonstrated that its aetiological agent probably is a bunyavirus which is antigenically related to haemorrhagic fever virus, and is endemic in the Soviet Union and large parts of Asia {Korean haemorrhagic fevery see also Chapter 34). In non-endemic areas units for the hospital care of imported cases of Lassa fever are needed as are the high-risk units of the national virological laboratories permitting work with highly contagious viruses like that of the Lassa fever. In 1967 a number of cases of a haemorrhagic disease with a considerable mortality rate was reported from laboratories at Marburg in the Federal Republic of Germany. Rabies virus causes an acute CNS disease which is lethal for man. cache = ./cache/cord-334941-6uattdti.txt txt = ./txt/cord-334941-6uattdti.txt === reduce.pl bib === id = cord-334560-1j9zmuub author = Hunt, Catherine L. title = Filovirus Entry: A Novelty in the Viral Fusion World date = 2012-02-07 pages = extension = .txt mime = text/plain words = 6445 sentences = 301 flesch = 48 summary = Details of the molecular events following cathepsin-dependent trimming of GP(1) are currently incomplete; however, the processed GP(1) specifically interacts with endosomal/lysosomal membranes that contain the Niemann Pick C1 (NPC1) protein and expression of NPC1 is required for productive infection, suggesting that GP/NPC1 interactions may be an important late step in the entry process. However, for reasons that are not entirely clear, this type of study has not been successful in identifying cell surface proteins that directly interact with EBOV GP to mediate virus entry [41, 42] . However, as both of these regions can be deleted from EBOV GP 1 without loss of viral transduction efficiency [16, [50] [51] [52] , it is likely that C-type lectins increase filovirus attachment to cells rather than serving as cellular receptors that mediate internalization of the virus into endosomes [53] . cache = ./cache/cord-334560-1j9zmuub.txt txt = ./txt/cord-334560-1j9zmuub.txt === reduce.pl bib === id = cord-333655-lylt7qld author = Van Breedam, Wander title = Bitter‐sweet symphony: glycan–lectin interactions in virus biology date = 2013-12-06 pages = extension = .txt mime = text/plain words = 18667 sentences = 875 flesch = 42 summary = In sum, it appears that the dimeric lectin galectin-1 can enhance HIV-1 infection efficiency by cross-linking viral and host cell glycans and thereby promoting firmer adhesion of the virus to the target cell surface and facilitating virus-receptor interactions (Ouellet et al., 2005; Mercier et al., 2008; St-Pierre et al., 2011; Sato et al., 2012) . As has been shown for IAV, acquisition or deletion of glycosylation sites may affect crucial steps in the viral infection/replication process (e.g. receptor binding, fusion, release of newly formed virions) (Ohuchi et al., 1997; Wagner et al., 2000; Tsuchiya et al., 2002; Kim & Park, 2012) , alter the capacity of the virus to avoid induction of/recognition by virus-specific antibodies (glycan shielding) Wei et al., 2010; Wanzeck et al., 2011; Kim & Park, 2012; Job et al., 2013; Sun et al., 2013) , and modulate viral interaction with various immune system lectins (Reading et al., 2007; Vigerust et al., 2007; Reading et al., 2009; Tate et al., 2011a, b) . cache = ./cache/cord-333655-lylt7qld.txt txt = ./txt/cord-333655-lylt7qld.txt === reduce.pl bib === id = cord-334082-fyxn0g3v author = O’Carroll, I.P. title = Viral Nucleic Acids date = 2015-08-20 pages = extension = .txt mime = text/plain words = 5495 sentences = 271 flesch = 54 summary = This scheme in turn places two requirements on the nucleic acid: it must be replicated in the virus-producing cell, to provide the genetic material encased in the progeny virus particles; and it must encode the proteins needed for the production of the progeny particles, including at a minimum the structural proteins from which the particles will be assembled. The DNAs of ssDNA viruses are replicated by a mechanism similar to 'rolling circle' replication, involving synthesis of dsDNA intermediates containing multiple tandem copies of the viral genome. These viruses are unique in that their genomic RNA is translated immediately upon infection; that is, the virus particle is simply a package that introduces an mRNA molecule into the cell. When the particle infects a new host cell, the RNA-dependent DNA polymerase or 'reverse transcriptase' in the virus copies this RNA into dsDNA. cache = ./cache/cord-334082-fyxn0g3v.txt txt = ./txt/cord-334082-fyxn0g3v.txt === reduce.pl bib === id = cord-334771-uy3s6443 author = Rao, BL title = A large outbreak of acute encephalitis with high fatality rate in children in Andhra Pradesh, India, in 2003, associated with Chandipura virus date = 2004-09-09 pages = extension = .txt mime = text/plain words = 3672 sentences = 187 flesch = 49 summary = Samples obtained were: 54 blood samples, 22 throat swabs, ten CSF samples, and one brain aspirate from 55 patients with encephalitis; five blood samples and nine throat swabs from 13 fever cases; and ten blood samples and one throat swab from ten family contacts (including specimens from the brother and mother of a patient who Methods Cell lines and peripheral blood lymphocyte co-cultures were used to isolate the causative agent from clinical samples. The confirmed Chandipura virus encephalitis group consisted of individuals from whose samples we isolated the virus, viral RNA, or reactive IgM antibodies. The viruses isolated in different cell lines from clinical samples from patients with encephalitis were confirmed as Chandipura virus with various techniques including complement fixation, neutralisation test, and immunofluorescence assay. Moreover, the presence of Chandipura virus RNA in nine patients with encephalitis, all from samples obtained before day 4 after onset of illness, suggests an early viraemic phase of the infection process. cache = ./cache/cord-334771-uy3s6443.txt txt = ./txt/cord-334771-uy3s6443.txt === reduce.pl bib === id = cord-336212-ueh4q408 author = Koenig, Kristi L. title = Identify-Isolate-Inform: A Tool for Initial Detection and Management of Zika Virus Patients in the Emergency Department date = 2016-04-04 pages = extension = .txt mime = text/plain words = 3597 sentences = 207 flesch = 52 summary = The identify-isolate-inform (3I) tool, originally conceived for initial detection and management of Ebola virus disease patients in the ED, and later adjusted for measles and Middle East Respiratory Syndrome, can be adapted for real-time use for any emerging infectious disease. This paper describes the adaptation of the identify-isolateinform (3I) tool (initially developed for Ebola virus disease 8, 9 and modified for measles 10 and Middle East Respiratory Syndrome (MERS)) 11 for use in the detection and management of potential Zika virus patients presenting to the ED, including women who are pregnant or contemplating pregnancy, and their partners. The identify-isolate-inform (3I) tool, initially developed for Ebola virus disease and subsequently adapted for measles and MERS, can be modified for the ED evaluation and management of patients under investigation for Zika ( Figure 3 ). The identify-isolate-inform (3I) tool is an instrument that can be used real-time on the front lines to rapidly detect and manage patients at risk for Zika virus disease presenting to the ED. cache = ./cache/cord-336212-ueh4q408.txt txt = ./txt/cord-336212-ueh4q408.txt === reduce.pl bib === id = cord-333810-57d4oopv author = Leroy, Éric Maurice title = L’Émergence du virus EBOLA chez l’homme: un long processus pas totalement élucidé date = 2015-05-31 pages = extension = .txt mime = text/plain words = 4845 sentences = 439 flesch = 66 summary = Plusieurs études ont montré que la contamination de l'homme s'est parfois produite lors de la manipulation de carcasses infectées de gorilles, chimpanzés et de céphalophes [21, 41] Les grands singes se contamineraient eux-mêmes probablement directement auprès des chauves-souris, en particulier lorsque les animaux de ces espèces animales consomment en même temps les fruits d'un même arbre. Cette diversité génétique des souches virales observées chez les carcasses d'animaux morts exclut par conséquent une transmission du virus d'un individu à l'autre et suggère au contraire que l'infection des grands singes résulterait de contaminations simultanées mais indépendantes à partir de sources animales distinctes, probablement le réservoir naturel du virus Ébola [21, 45] . Je pense que cette impression est purement factuelle, et est amplifiée par la couverture médiatique des maladies dues à certains virus dont les chauves-souris sont réservoirs (SARS, Ébola, Marburg ...). cache = ./cache/cord-333810-57d4oopv.txt txt = ./txt/cord-333810-57d4oopv.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-333463-u7je0d1o author = Diaz-Salazar, Carlos title = Natural killer cell responses to emerging viruses of zoonotic origin date = 2020-08-09 pages = extension = .txt mime = text/plain words = 6193 sentences = 353 flesch = 43 summary = Nearly all emerging viruses, including Ebola, Dengue, Nipah, West Nile, Zika, and coronaviruses (including SARS-Cov2, the causative agent of the current COVID-19 pandemic), have zoonotic origins, indicating that animal-to-human transmission constitutes a primary mode of acquisition of novel infectious diseases. Natural killer (NK) cells are innate lymphocytes that play a critical role in the early antiviral response, secreting effector cytokines and clearing infected cells. This review describes the role of Natural killer (NK) cells, a critical component of early antiviral immunity, in the establishment of tolerance to viral infections in natural hosts, as well as their role in the development of disease in nonnatural hosts. Altogether, it is believed that quick control of viral infections and reduced induction of pro-inflammatory cytokines have allowed bat viruses to rapidly co-evolve with their host without provoking major immuneThe careful study of the immune system in reservoirs of zoonotic diseases will certainly offer insights into how these animals carry high viral loads while remaining asymptomatic. cache = ./cache/cord-333463-u7je0d1o.txt txt = ./txt/cord-333463-u7je0d1o.txt === reduce.pl bib === id = cord-333262-xvfl7ycj author = Robson, B. title = COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles’ heel conserved region to minimize probability of escape mutations and drug resistance date = 2020-04-11 pages = extension = .txt mime = text/plain words = 21671 sentences = 953 flesch = 50 summary = The Wuhan and related isolates revealed a coronavirus that resides in the subgenus Sarbecovirus of the genus Betacoronavirus [2] , and although genetically distinct from its predecessor SARS-CoV it appeared to have similar external binding proteins, meaning here the spike glycoprotein discussed extensively in the present paper. In brief summary, the justifications for the ensemble pharmacophore in the coronavirus case, i.e. the contributions to "fuzziness", include parsimony, that proteins and parts of proteins sometimes have more than one function [12] encouraged by limited numbers of accessible sites (due to e.g. glycosylation) and exemplified by parallel alternative mechanisms of cell entry, multiple methods of drug action, escape from scientific defense measures by virus mutation, polymorphism of human proteins involved, different expression levels of human proteins involved, and the potential problem of the "specter of vaccine development" (concerns about missing the appropriate region of the virus that allows common cold viruses to escape the appropriate immune response). cache = ./cache/cord-333262-xvfl7ycj.txt txt = ./txt/cord-333262-xvfl7ycj.txt === reduce.pl bib === id = cord-336157-aqc9zrrm author = Liang, Guodong title = Factors responsible for the emergence of arboviruses; strategies, challenges and limitations for their control date = 2015-03-25 pages = extension = .txt mime = text/plain words = 4111 sentences = 221 flesch = 42 summary = Slave trading of Africans to the Americas, during the 16th to the 19th century was responsible for the first recorded emergence in the New World of two arthropod-borne viruses (arboviruses), yellow fever virus and dengue virus. [2] [3] Chikungunya virus (CHIKV), West Nile virus (WNV) and dengue virus (DENV) are three of a large number of neglected human pathogenic arthropod-borne viruses (arboviruses) whose combined figures for morbidity and mortality far exceed those for Ebola, severe acute respiratory syndrome and Middle East respiratory syndrome viruses. However, many other arthropod species, in which viruses have been identified, may be involved in perpetuating the virus life cycle without having been associated with overt disease in humans or animals. 55 However, implementation of temporary localized arthropod control measures during epidemics, for example in high density urbanized areas, can still play an important but transient role in reducing the impact on humans and animals of emerging arboviruses. cache = ./cache/cord-336157-aqc9zrrm.txt txt = ./txt/cord-336157-aqc9zrrm.txt === reduce.pl bib === id = cord-334365-idjvbcy4 author = Gooding, J. Justin title = Virus Detection: What Were We Doing before COVID-19 Changed the World? date = 2020-05-29 pages = extension = .txt mime = text/plain words = 969 sentences = 69 flesch = 55 summary = The papers in this virtual issue are by some of the researchers that have been developing tests to detect viruses. It is clear that a rapid, portable test that could detect the virus directly, with high sensitivity and specificity, would be a brilliant advance. In this virtual issue we concentrate on the development of molecular tests for viruses, a focus not surprising for two chemistry journals dealing with analytical measurement. The issue leads with a review on detection of biothreats (Mother Nature is an accomplished bioterrorist!), and then covers a range of innovative technologies 1 that focus on assays for point of care testing, 2−4 faster diagnostic testing, 5−8 more sensitive diagnostic testing, 9−17 characterizing the response to the virus, 18−21 and highly sensitive methods for biologically tracking and characterizing the virus. Development of an Electrochemical Paper-Based Analytical Device for Trace Detection of Virus Particles cache = ./cache/cord-334365-idjvbcy4.txt txt = ./txt/cord-334365-idjvbcy4.txt === reduce.pl bib === id = cord-335948-qkfxfmxb author = Ampofo, William K. title = Improving influenza vaccine virus selectionReport of a WHO informal consultation held at WHO headquarters, Geneva, Switzerland, 14–16 June 2010 date = 2011-08-08 pages = extension = .txt mime = text/plain words = 10006 sentences = 401 flesch = 24 summary = • The selection process is highly coordinated and involves continual year‐round integration of virological data and epidemiological information by National Influenza Centres (NICs), thorough antigenic and genetic characterization of viruses by WHO Collaborating Centres (WHOCCs) as part of selecting suitable candidate vaccine viruses, and the preparation of suitable reassortants and corresponding reagents for vaccine standardization by WHO Essential Regulatory Laboratories (ERLs). • The selection process is highly coordinated and involves continual year-round integration of virological data and epidemiological information by National Influenza Centres (NICs), thorough antigenic and genetic characterization of viruses by WHO Collaborating Centres (WHOCCs) as part of selecting suitable candidate vaccine viruses, and the preparation of suitable reassortants and corresponding reagents for vaccine standardization by WHO Essential Regulatory Laboratories (ERLs). The continuing threat posed by avian H5N1, the aftermath of the 2009 H1N1 pandemic, the increased knowledge of influenza, and the development and availability of new technologies provide a timely opportunity to review the complex processes and issues involved in influenza vaccine virus selection and to identify potential areas for improvement. cache = ./cache/cord-335948-qkfxfmxb.txt txt = ./txt/cord-335948-qkfxfmxb.txt === reduce.pl bib === id = cord-335774-15fhg8o9 author = Mull, Nathaniel title = Ecology of Neglected Rodent-Borne American Orthohantaviruses date = 2020-04-26 pages = extension = .txt mime = text/plain words = 6842 sentences = 333 flesch = 38 summary = Information regarding the presence and genetic diversity of many orthohantaviruses throughout the distributional range of their hosts is minimal and would significantly benefit from virus isolations to indicate a reservoir role. However, mammals, particularly rodents, are still the most common natural hosts of hantaviruses, encompassing viruses in the largest subfamily (Mammantavirinae) and genus (Orthohantavirus) [9] , and only rodent-borne orthohantaviruses have been linked to human disease [10] . For example, range expansion of a North American grassland rodent species, Baiomys taylori, was recently found in New Mexico, United States, likely due to an increase in grassland areas, particularly along roadsides, due to climate change and habitat disturbance [61] . In the absence of empirical data, we shed light on the diversity, transmission, and risk of spillover for neglected American orthohantaviruses and viral genotypes using the ecology of their hosts and information on ANDV and SNV. Since multiple rodent species are commonly found RT-PCR positive for particular American orthohantavirus strains (Table A1) , virus-host relationships are unclear. cache = ./cache/cord-335774-15fhg8o9.txt txt = ./txt/cord-335774-15fhg8o9.txt === reduce.pl bib === id = cord-336045-8qcj5uiy author = Langlois, Isabelle title = Viral diseases of ferrets date = 2005-03-01 pages = extension = .txt mime = text/plain words = 7196 sentences = 424 flesch = 41 summary = A tentative diagnosis of canine distemper is based on the presence of typical clinical signs, severe leukopenia, a history of potential exposure to the virus, and questionable vaccination. The severity of disease depends on the origin (mink or ferret) of the ADV strain that is involved as well as the immune status and genotype of the infected individual [25] . Ferrets are used extensively as an animal model for influenza virus pathogenesis and immunity studies because their biologic response to influenza infection is similar to that of humans [53, 54] . Neurologic symptoms, including ataxia, hind-limb paresis, and torticollis, were reported in ferrets that were infected experimentally with avian influenza A (H5N1) viruses that were isolated from the 1997 outbreaks of disease in domestic poultry markets in Hong Kong [50, 65] . Detection of Aleutian disease virus DNA in tissues of naturally infected mink cache = ./cache/cord-336045-8qcj5uiy.txt txt = ./txt/cord-336045-8qcj5uiy.txt === reduce.pl bib === id = cord-331714-2qj2rrgd author = Lvov, Dimitry Konstantinovich title = Single-Stranded RNA Viruses date = 2015-05-29 pages = extension = .txt mime = text/plain words = 64283 sentences = 4009 flesch = 55 summary = Among them are viruses associated with sporadic cases or outbreaks of human disease, such as hemorrhagic fever with renal syndrome (viruses of the genus Hantavirus), Crimean–Congo hemorrhagic fever (CCHFV, Nairovirus), California encephalitis (INKV, TAHV, and KHATV; Orthobunyavirus), sandfly fever (SFCV and SFNV, Phlebovirus), Tick-borne encephalitis (TBEV, Flavivirus), Omsk hemorrhagic fever (OHFV, Flavivirus), West Nile fever (WNV, Flavivirus), Sindbis fever (SINV, Alphavirus) Chikungunya fever (CHIKV, Alphavirus) and others. Artashat virus (ARTSV, strain LEIV-2236Ar) was originally isolated from Ornithodoros alactagalis ticks (family Argasidae) collected in the burrows of a small five-toed jerboa (Allactaga elater) near Arevashat village (40 02 absence of antigenic relationships with any known viruses, it was referred to as an "unclassified bunyavirus." 1À3 Taxonomy. cache = ./cache/cord-331714-2qj2rrgd.txt txt = ./txt/cord-331714-2qj2rrgd.txt === reduce.pl bib === id = cord-335279-cfv18qn0 author = Paillot, Romain title = Special Issue “Equine Viruses”: Old “Friends” and New Foes? date = 2020-01-29 pages = extension = .txt mime = text/plain words = 2070 sentences = 112 flesch = 49 summary = With this Special Issue, which assembles a collection of communications, research articles, and reviews, we intend to explore our understanding of a panel of equine viruses, looking at their pathogenicity, their importance in terms of welfare and potential association with diseases, their economic importance and impact on performance, and how their identification can be helped by new technologies and methods. The authors highlight the potential protective role of eqMx1, which primarily targets the virus nucleoprotein (NP), against the transmission of new IAVs in horses (i.e., eqMx1 could only inhibit the polymerase activity of IAVs of avian and human origin but remained inactive against the equine IAVs tested). To date, equine influenza virus remains one of the most important respiratory pathogens of horses worldwide, with a potential damaging impact on the equine industry, as clearly illustrated in 2007 in Australia and in 2019 in Europe [20, 21] . cache = ./cache/cord-335279-cfv18qn0.txt txt = ./txt/cord-335279-cfv18qn0.txt === reduce.pl bib === id = cord-334108-4ey725dv author = Seymour, I.J. title = Foodborne viruses and fresh produce date = 2008-07-07 pages = extension = .txt mime = text/plain words = 10241 sentences = 596 flesch = 52 summary = The most frequently reported foodborne viral infections are viral gastroenteritis and hepatitis A: both have been associated with the consumption of fresh fruit or vegetables. There are many groups of viruses which could contaminate food items, but the major foodborne viral pathogens are those that infect via the gastrointestinal tract, such as the gastroenteritis viruses and hepatitis A virus. There is a need to develop more effective quantitative methods in order to assess the survival of viruses on fresh produce and to determine the decontamination ef®ciencies of current commercial washing systems for fruit and vegetables. Mounting evidence suggests that viruses can survive long enough and in high enough numbers to cause human diseases through direct contact with polluted water or contaminated foods (Nasser 1994; Bosch 1995) . When hepatitis A virus was detected in lettuce from Costa Rica, it was suggested that the possible source of contamination was the discharge of untreated sewage into river water used to irrigate crops, which is common practice in some less well-developed countries (Hernandez et al. cache = ./cache/cord-334108-4ey725dv.txt txt = ./txt/cord-334108-4ey725dv.txt === reduce.pl bib === id = cord-336447-hpnkou41 author = Pitlik, Silvio Daniel title = COVID-19 Compared to Other Pandemic Diseases date = 2020-07-31 pages = extension = .txt mime = text/plain words = 6148 sentences = 396 flesch = 49 summary = Despite multiple publications and increasing knowledge regarding the biological secrets of SARS-CoV-2, as of the writing of this paper, there is neither an approved vaccine nor medication to prevent infection or cure for this highly infectious disease. 7, 8 This paper reviews the microbiological, clinical, and epidemiological characteristics of the coronavirus disease 2019 (COVID-19) pandemic, as well as its socio-economic impact. In the early days of the pandemic great effort was invested into understanding the life cycle of SARS-CoV-2, 9 so as to provide a basis for discovery of an effective vaccine to prevent COVID-19 and/or a safe and efficacious drug to cure it, or at the least, to ameliorate its symptoms, shorten its duration, and/ or block its mechanism of transmission. 59 Unfortunately, to date, no human genetic markers predisposing to SARS-CoV-2 infection, nor the severity of COVID-19, have been found-although recent isolated exceptions to this statement can be found. cache = ./cache/cord-336447-hpnkou41.txt txt = ./txt/cord-336447-hpnkou41.txt === reduce.pl bib === id = cord-336493-ggo9wsrm author = Huang, Stephen S. H. title = Immunity toward H1N1 influenza hemagglutinin of historical and contemporary strains suggests protection and vaccine failure date = 2013-04-23 pages = extension = .txt mime = text/plain words = 6444 sentences = 342 flesch = 46 summary = In our present study, we investigated the clinical characteristics and immune cross-reactivity of significant H1N1 influenza strains in the past 100 years in ferrets to determine the immunogenicity of important H1N1 viruses. Ferrets show respiratory illness similar to humans and clinical features of disease are easily observed where fevers can persist days following infection of viruses such as 2009 H1N1pdm influenza 21, 23, 30 . As well as fever, nasal discharge and sneezing can also be observed in animals infected with influenza viruses 21 These influenza A viruses were chosen due to their emergence and influence in H1N1 genetic history (Fig. 1 , strains used in this study are marked with an asterisks) as covered in the introduction. The immunogenic findings showed antisera produced from ferret infection with Taiwan/86 was not able to inhibit hemagglutination with the other viruses on our virus panel, which compliments the literature describing the 1986 strain. cache = ./cache/cord-336493-ggo9wsrm.txt txt = ./txt/cord-336493-ggo9wsrm.txt === reduce.pl bib === id = cord-337149-cjon7ihb author = Van Vliet, Kim M. title = The Role of the Adeno-Associated Virus Capsid in Gene Transfer date = 2008 pages = extension = .txt mime = text/plain words = 10774 sentences = 681 flesch = 52 summary = Adeno-associated virus (AAV) is one of the most promising viral gene transfer vectors that has been shown to effect long-term gene expression and disease correction with low toxicity in animal models, and is well tolerated in human clinical trials. Prior to developing a gene therapy strategy that utilizes AAV, the serotype should be carefully considered since each capsid exhibits a unique tissue tropism and transduction efficiency. Several approaches have been undertaken in an effort to target AAV vectors to specific cell types, including utilizing natural serotypes that target a desired cellular receptor, producing pseudotyped vectors, and engineering chimeric and mosaic AAV capsids. The atomic structure of adeno-associated virus (AAV-2), a vector for human gene therapy Adeno-associated virus serotypes 1 to 5 mediated tumor cell directed gene transfer and improvement of transduction efficiency Adeno-associated virus vectors serotyped with AAV8 capsid are more efficient than AAV-1 or -2 serotypes for widespread gene delivery to the neonatal mouse brain cache = ./cache/cord-337149-cjon7ihb.txt txt = ./txt/cord-337149-cjon7ihb.txt === reduce.pl bib === id = cord-336929-2rnkotqy author = Vieira, Flávia Sarmento title = Host‐cell lipid rafts: a safe door for micro‐organisms? date = 2012-01-03 pages = extension = .txt mime = text/plain words = 9925 sentences = 494 flesch = 41 summary = In addition to the lipid components, a variety of cell receptors and signalling proteins are known to be associated with membrane rafts. Many animal viruses exploit the endocytic machinery of their host cell for infection, and lipid rafts are often a site for entry, assembly and budding of microbial pathogens, as confirmed by biochemical approaches and microscopy evidence (Kovbasnjuk et al., 2001; Suomalainen, 2002; Lu et al., 2008) . Interestingly, it had already been demonstrated that Brucella abortus infection is related with PrP C (cellular PrP), one of the lipid raft-associated molecules on the plasma membrane of different cell types. In the macrophage-like cell line RAW 264.7, for example, LPS stimulation induces translocation of CD14, ERK-2 (extracellular-signalregulated kinase 2) and p38 to lipid rafts, but other proteins also involved in the LPS signalling response do not migrate within these microdomains (Triantafilou et al., 2007; Olsson and Sundler, 2006) . cache = ./cache/cord-336929-2rnkotqy.txt txt = ./txt/cord-336929-2rnkotqy.txt === reduce.pl bib === id = cord-336554-n8n5ii5k author = Singh, Thakur Uttam title = Drug repurposing approach to fight COVID-19 date = 2020-09-05 pages = extension = .txt mime = text/plain words = 13032 sentences = 690 flesch = 44 summary = Number of drugs such as remdesivir, favipiravir, ribavirin, lopinavir, ritonavir, darunavir, arbidol, chloroquine, hydroxychloroquine, tocilizumab and interferons have shown inhibitory effects against the SARS-CoV2 in-vitro as well as in clinical conditions. Outbreaks of novel emerging infections such as coronavirus disease 2019 (COVID19) have unique challenges in front of the health professionals to select appropriate therapeutics/pharmacological treatments in the clinical setup with very little time available for the new drug discovery [3] . Currently, with the lack of effective agents against SARS-CoV2 as well as public-health emergency, WHO has identified some therapies which doctors and researchers believe are the most promising, such as a combination of two HIV drugs (lopinavir and ritonavir), anti-malarial drugs (chloroquine and hydroxychloroquine), and an experimental antiviral compound remdesivir. Ribavirin at a dose rate of 500 mg 2-3 times/day in combination with other drugs such as lopinavir/ritonavir or interferon (IFN)-α through intravenous route for not more than 10 days made the SARS-CoV2 infected patients more resistant to respiratory distress syndrome as well as death [41] . cache = ./cache/cord-336554-n8n5ii5k.txt txt = ./txt/cord-336554-n8n5ii5k.txt === reduce.pl bib === id = cord-337361-salby0fu author = Bujarski, Jozef J. title = Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives date = 2013-03-26 pages = extension = .txt mime = text/plain words = 6863 sentences = 335 flesch = 39 summary = In some viruses, the frequency of homologous crossing-over is very high and practically every replicated viral RNA molecule can be considered as chimerical in nature, as we have demonstrated for brome mosaic virus (BMV) RNAs (Urbanowicz et al., 2005) . The generally accepted mechanism of RNA recombination is currently explained by a copy-choice model where the viral RNA polymerase (RdRp) complex in mRNA viruses [reverse transcriptase (RT) in retroviruses] changes templates during synthesis of the nascent strand (Galetto et al., 2006) . Among the factors known to promote replicase to switch are sequence homologies between recombination substrates along with secondary structures at the crossover sites, as demonstrated with the BMV and other systems (Figlerowicz and Bujarski, 1998; Nagy et al., 1999b) . Comparison among three plant RNA virus replication systems (TBSV, BMV, and dianthoviruses) reveals general patterns within the stepwise process of viral replicase complex assembly which requires concerted involvement of protein-protein, RNA-protein, and protein-lipid interactions (Mine and Okuno, 2012) . cache = ./cache/cord-337361-salby0fu.txt txt = ./txt/cord-337361-salby0fu.txt === reduce.pl bib === id = cord-337285-t6qr41wc author = Ikeda, Masanori title = Modulation of host metabolism as a target of new antivirals() date = 2007-10-10 pages = extension = .txt mime = text/plain words = 8180 sentences = 466 flesch = 46 summary = Using cell culture systems, several cellular proteins have been identified as effective molecules for HCV RNA replication (Table 1) . [66] reported that lovastatin (LOV), one of the HMG-CoA reductase inhibitors, inhibited HCV RNA replication in HCV replicon-harboring cells. Depletion of the GGPP by statins may inhibit the geranylgeranylation of cellular proteins such as FBL2 and cause the anti-HCV effect in the cells. During the development of IFN therapy for patients with CH-C, the lack of a robust method of HCV RNA replication in cell culture has hampered research into the HCV life cycle and the discovery of potent new anti-HCV reagents. VX-950, a novel hepatitis C virus (HCV) NS3-4A protease inhibitor, exhibits potent antiviral activities in HCV replicon cells Selectable subgenomic and genome-length dicistronic RNAs derived from an infectious molecular clone of the HCV-N strain of hepatitis C virus replicate efficiently in cultured Huh7 cells cache = ./cache/cord-337285-t6qr41wc.txt txt = ./txt/cord-337285-t6qr41wc.txt === reduce.pl bib === id = cord-337673-1nau263l author = Wu, Chang-Jer title = Antiviral applications of RNAi for coronavirus date = 2006-01-24 pages = extension = .txt mime = text/plain words = 4329 sentences = 253 flesch = 52 summary = Recently, small interfering RNA (siRNA) has shown promise in the protection from viral invasion, as it can inhibit the expression of viral antigens and accessory genes as well as control the transcription and replication of the viral genome. Genes encoding vital proteins in reproducing SARS-CoV virions can be chosen for chemotherapeutic intervention (e.g., those coding for S, 3C-like protease [3CLpro], RNA-dependent RNA polymerase and possibly other gene products involved in viral-protein-mediated processes) [81] first demonstrated that siRNA was able to silence the replicase of SARS-CoV (1a region of the genome) and that this approach was effective in vitro against SARS-CoV. [82] subsequently observed that vector-based siRNAs could inhibit the replication of SARS-CoV, and showed that expression in the plasmid, pSUPER, of siRNAs specifically targeting viral RNA polymerases could block the cytopathic effects of SARS-CoV on Vero cells. [86] showed that three chemically synthesised siRNA duplexes targeting viral RNA polymerases, and one targeting the S gene potently inhibited SARS-CoV infection and replication in fetal rhesus kidney cells (FRhK-4) . cache = ./cache/cord-337673-1nau263l.txt txt = ./txt/cord-337673-1nau263l.txt === reduce.pl bib === id = cord-336225-ijodhrwf author = Chang, Mee Soo title = Severe Fever with Thrombocytopenia Syndrome: Tick-Mediated Viral Disease date = 2013-06-03 pages = extension = .txt mime = text/plain words = 1379 sentences = 90 flesch = 62 summary = title: Severe Fever with Thrombocytopenia Syndrome: Tick-Mediated Viral Disease A small tick Haemaphysalis longicornis called 'Sochamjindeugi' in Korean has bitten a week before, and an onset is characterized by fever, lymph node swelling, diarrhea, thrombocytopenia, leucocytopenia, multiorgan dysfunction, altered consciousness, and occasionally to death in extreme cases (1, 2) . This emerging febrile disease, severe fever with thrombocytopenia syndrome (SFTS), was reported in 2007 by the New England Journal of Medicine (3) and Clinical Infectious Diseases (4) (5) (6) . The vaccine development to combat the SFTS virus is not easy due to its characteristics. Also any treatment by killing the virus is able to give human damage. Severe Fever with Thrombocytopenia Syndrome confirmed cases and follow-up measure Document for physicians about Severe Fever with Thrombocytopenia Syndrome (SFTS) Epidemiologic features of severe Fever with thrombocytopenia syndrome in China Person-to-person transmission of severe fever with thrombocytopenia syndrome bunyavirus through blood contact cache = ./cache/cord-336225-ijodhrwf.txt txt = ./txt/cord-336225-ijodhrwf.txt === reduce.pl bib === id = cord-337914-1hwnxkdd author = Ehlkes, L. title = Epidemiologie des Ebolafiebers und anderer, in Deutschland seltener hochkontagiöser, lebensbedrohlicher Erkrankungen date = 2015-05-22 pages = extension = .txt mime = text/plain words = 2987 sentences = 373 flesch = 54 summary = Hochsicherheitsbetten für die Versorgung von Patienten mit Ebolafieber gibt es -anders als in industrialisierten Ländern -in den Ausbruchsgebieten in der Regel nicht. Subsequent human-to-human transmission can lead to epidemics, such as the current outbreak of Ebola virus disease in West Africa. Subsequent human-to-human transmission can lead to epidemics, such as the current outbreak of Ebola virus disease in West Africa. Ebola virus disease · Highly contagious · Outbreak · Epidemic · Viral hemorrhagic fever laufen derzeit z. Die Epidemiologie von Lassa-Fieber ist eng geknüpft an das zeitliche und räumliche Auftreten des wichtigsten Reservoirtiers, der Vielzitzenmaus (Mastomys natalensis), in der Nähe des Menschen. Neben intensivmedizinischen Maßnahmen wird Ribavirin zur antiviralen Therapie gegen das Lassa-Virus eingesetzt [42] , das bei Behandlung in den ersten sechs Tagen nach Beginn der Symptomatik die Letalität bei Lassa-Fieber von 60-80 % auf 10 % senken kann [43] . Die Falldetektion mit anschließender Isolierung ist auch bei SARS das Rückgrat der Ausbruchs-Kontrolle. cache = ./cache/cord-337914-1hwnxkdd.txt txt = ./txt/cord-337914-1hwnxkdd.txt === reduce.pl bib === id = cord-336948-8yqdhcnz author = Löhner, Rainald title = Detailed simulation of viral propagation in the built environment date = 2020-08-05 pages = extension = .txt mime = text/plain words = 5698 sentences = 314 flesch = 55 summary = If, for the sake of argument, we consider Stoke's law for the drag of spherical particles, valid below Reynolds numbers of Re = 1, the terminal sink velocity (also known as the settling velocity) of particles will be given by [26] : where ρ p , ρ g , g, μ, d denote the density of the particles (essentially water in the present case), density of the gas (air), gravity, dynamic viscosity of the gas and diameter of the particle respectively. -Spatial discretization using unstructured grids (in order to allow for arbitrary geometries and adaptive refinement); -Spatial approximation of unknowns with simple linear finite elements (in order to have a simple input/output and code structure); -Edge-based data structures (for reduced access to memory and indirect addressing); -Temporal approximation using implicit integration of viscous terms and pressure (the interesting scales are the ones associated with advection); -Temporal approximation using explicit, high-order integration of advective terms; -Low-storage, iterative solvers for the resulting systems of equations (in order to solve large 3-D problems); and -Steady results that are independent from the timestep chosen (in order to have confidence in convergence studies). cache = ./cache/cord-336948-8yqdhcnz.txt txt = ./txt/cord-336948-8yqdhcnz.txt === reduce.pl bib === id = cord-337577-dqikrmk7 author = Greenberg, Harry B. title = Vaccination against Viruses date = 2016-05-09 pages = extension = .txt mime = text/plain words = 4789 sentences = 225 flesch = 32 summary = In the elderly, measures of cell-mediated immunity, such as granzyme B levels in virus-stimulated peripheral blood mononuclear cells, may correlate better than serum antibody titers with vaccine-elicited protection (McElhaney et al., 2009 ). Whether cell-mediated effector mechanisms, mucosal antibody, or some other factor is primarily responsible for protection by live attenuated influenza vaccines or natural infection remains controversial despite several decades of study. A key finding has been that, among the neutralizing antibodies elicited in response to influenza virus, HIV, or RSV infection or immunization, some have remarkably broad specificity (Burton and Mascola 2015; Corti et al., 2013 Corti et al., , 2011 . The elucidation of Toll-like receptors as key sentry molecules that detect potential pathogens and recruit antigen-presenting cells for a subsequent antigen-specific response has enabled the rational design of a new generation of potential vaccine adjuvants (Wu et al., 2014) . cache = ./cache/cord-337577-dqikrmk7.txt txt = ./txt/cord-337577-dqikrmk7.txt === reduce.pl bib === id = cord-338400-30vl2hks author = Epstein, Jonathan H. title = Identification of GBV-D, a Novel GB-like Flavivirus from Old World Frugivorous Bats (Pteropus giganteus) in Bangladesh date = 2010-07-01 pages = extension = .txt mime = text/plain words = 4653 sentences = 246 flesch = 50 summary = Phylogenetic analysis indicates that this first GBV-like flavivirus reported in bats constitutes a distinct species within the Flaviviridae family and is ancestral to the GBV-A and -C virus clades. GBV-A viruses have been described in New World primates and are not known to infect humans [17] [18] [19] , while GBV-C (also known as Hepatitis G virus (HGV)) have frequently been isolated from humans in many regions of the World, including India and Bangladesh [19] [20] [21] [22] [23] , and from wild chimpanzees (Pan troglodytes) in Africa [24, 25] . Our findings provide new insight into the range of known hosts for GB-like viruses and demonstrate the power of unbiased sequencing to characterize the diversity of potentially zoonotic pathogens carried by bats and other reservoirs. Molecular analyses of sera from Pteropus giganteus bats from Faridpur, Bangladesh led to the identification of a 9,633 nt sequence consistent in genomic organization with known GBV and other species within the family Flaviviridae [16] . cache = ./cache/cord-338400-30vl2hks.txt txt = ./txt/cord-338400-30vl2hks.txt === reduce.pl bib === id = cord-338083-77re4l0w author = Bolin, Steven R. title = Origination and consequences of bovine viral diarrhea virus diversity date = 2005-03-04 pages = extension = .txt mime = text/plain words = 6748 sentences = 329 flesch = 43 summary = The genetic diversity that occurs among isolates of BVDV is characteristic of RNA viruses that exist in nature as quasispecies (a swarm of viral mutants). However, altered base sequence in this region of the viral genome has been identified after passage of the virus in cell culture, and has been detected in viral RNA that was extracted from tissues of an infected animal [20, 21] . The selection of the antigenic variants likely occurred during the acute infection of the dams of those PI cattle and resulted in transplacental transmission of slightly different BVDV to a group of fetuses. Genetic and antigenic variability in bovine viral diarrhea virus (BVDV) isolates from Belgium Pathogenesis of primary respiratory disease induced by isolates from a new genetic cluster of bovine viral diarrhea virus type I Clinical and immunologic responses of vaccinated and unvaccinated calves to infection with a virulent type-II isolate of bovine viral diarrhea virus cache = ./cache/cord-338083-77re4l0w.txt txt = ./txt/cord-338083-77re4l0w.txt === reduce.pl bib === id = cord-335647-dhcxj7cj author = Vanderlinden, Evelien title = Emerging Antiviral Strategies to Interfere with Influenza Virus Entry date = 2013-06-25 pages = extension = .txt mime = text/plain words = 15104 sentences = 870 flesch = 43 summary = We here focus on emerging options to interfere with the influenza virus entry process, which consists of the following steps: attachment of the viral hemagglutinin to the sialylated host cell receptors, endocytosis, M2‐mediated uncoating, low pH‐induced membrane fusion, and, finally, import of the viral ribonucleoprotein into the nucleus. There are three conceivable strategies for inhibiting attachment of influenza virus to its target cell: (i) an antiviral compound binding to the HA RBS; (ii) an inhibitor blocking the sialic acid-containing receptors on the epithelial cell membrane; or (iii) a receptor-destroying agent. 91 Regarding potential antiviral use, design of modified forms of the porcine SP-D lectin (which has higher anti-influenza virus activity than its human counterpart) is aided by the growing insight into how its carbohydrate recognition domain (CRD) precisely interacts with the high-mannose glycans attached near the RBS of HA. cache = ./cache/cord-335647-dhcxj7cj.txt txt = ./txt/cord-335647-dhcxj7cj.txt === reduce.pl bib === id = cord-336510-qzm9wgde author = Ellermann-Eriksen, Svend title = Macrophages and cytokines in the early defence against herpes simplex virus date = 2005-08-03 pages = extension = .txt mime = text/plain words = 20036 sentences = 986 flesch = 46 summary = In a first wave of responses, cytokines, primarily type I interferons (IFN) and tumour necrosis factor are produced and exert a direct antiviral effect and activate the macrophages themselves. Generally the type I IFNs exhibit a huge range of biological effects, such as antiviral and antiproliferative effects, stimulation of immune cells such as T cells, natural killer (NK) cells, monocytes, macrophages, and dendritic cells, increased expression of MHC-I, activation of pro-apoptotic genes and inhibition of anti-apoptotic mechanisms, modulation of cellular differentiation, and inhibition of angiogenesis [171] . Effect of IL-4 and IL-13 on IFN-gamma-induced production of nitric oxide in mouse macrophages infected with herpes simplex virus type 2 Herpes Simplex virus type 1-induced interferon production and activation of natural killer cells in mice NF-kappaB activation is responsible for the synergistic effect of herpes simplex virus type 2 infection on interferon-gamma-induced nitric oxide production in macrophages cache = ./cache/cord-336510-qzm9wgde.txt txt = ./txt/cord-336510-qzm9wgde.txt === reduce.pl bib === id = cord-337659-x4oywbrj author = Wilson, Brenda A. title = Global biosecurity in a complex, dynamic world date = 2008-07-31 pages = extension = .txt mime = text/plain words = 10626 sentences = 469 flesch = 45 summary = Although one might argue that the principal difference in the infectious disease threat today versus say 10, 25, or 50 years ago is bioterrorism, the resources spend on preparing for a bioterror attack is viewed by most scientists as grossly exorbitant [6] , particularly considering the small numbers of individuals who have been or could be affected by this type of attack and considering the relatively low medical relevance or prevalence of the diseases caused by the limited number of highpriority bioterror bioagents, the socalled ''category A select agents.'' And, while admittedly the preparedness and surveillance measures put in place for one has certainly helped to protect against the other (the improved global response to and curtailment of SARS coming after the anthrax bioterrorist attacks is a prime example of this), most scientists feel that the limited resources available from an already overburdened system should instead be used for studying and preparing against the looming and potentially more devastating infectious disease threats from natural or accidental exposure [7] , which could affect millions of people and animals and could have huge health and economic consequences. cache = ./cache/cord-337659-x4oywbrj.txt txt = ./txt/cord-337659-x4oywbrj.txt === reduce.pl bib === id = cord-338081-ggw5l1qm author = Gorbalenya, Alexander E. title = Phylogeny of Viruses date = 2017-06-26 pages = extension = .txt mime = text/plain words = 3638 sentences = 154 flesch = 41 summary = For inferring phylogeny, the differences between aligned sequences of genomes and proteins are quantified and depicted in the form of a tree, in which contemporary species and their intermediate and common ancestors occupy, respectively, the terminal nodes, internal nodes, and the root. Bayesian methods have the highest computational cost due to their sampling approach and thus show the lowest speed, while realization of the similarly advanced ML algorithm may be largely comparable in speed to distance methods, allowing for the phylogenetic analysis of very large data sets like genome-wide tree reconstructions of cellular organisms or thousands of viruses. In the case of SARS-CoV, poor sampling of the coronavirus diversity in the lineage at the time, some uncertainty over the relationship between phylogeny and taxonomy of coronaviruses, and the complexity of phylogenetic analysis of a virus data set including isolated distant lineages led to considerable controversy over the exact evolutionary position of SARS-CoV among coronaviruses. cache = ./cache/cord-338081-ggw5l1qm.txt txt = ./txt/cord-338081-ggw5l1qm.txt === reduce.pl bib === id = cord-338804-nreqluol author = Heise, M.T. title = Viral Pathogenesis date = 2014-11-28 pages = extension = .txt mime = text/plain words = 6413 sentences = 232 flesch = 35 summary = Viral interactions with these receptors can have a significant impact upon several aspects of viral pathogenesis, including determining the cell or tissue tropism of a virus or even whether a virus can efficiently infect and cause disease in a specific host species. Therefore, viruses that are defective in their ability to antagonize the host type I interferon system are often unable to replicate and spread efficiently within the host, illustrating the importance of viral immune evasion strategies in determining whether a virus will be pathogenic ( Figure 2) . (b) If the virus effectively interferes with the type I interferon response, interferon will be prevented from inducing a robust antiviral state within the host, and the virus is able to replicate to higher levels, will spread more efficiently, and may cause more severe disease. Therefore, like other aspects of viral pathogenesis, a complex series of virus-host interactions determines whether infection with cancer associated viruses ultimately results in disease development. cache = ./cache/cord-338804-nreqluol.txt txt = ./txt/cord-338804-nreqluol.txt === reduce.pl bib === id = cord-338727-1kodz527 author = Ilinskaya, O. N. title = Ribonucleases as antiviral agents date = 2014-10-11 pages = extension = .txt mime = text/plain words = 4605 sentences = 227 flesch = 44 summary = Many ribonucleases (RNases) are able to inhibit the reproduction of viruses in infected cell cultures and laboratory animals, but the molecular mechanisms of their antiviral activity remain unclear. Therefore, the formation of RNA fragments enhanced by RNase L, followed by their interaction with RIG I and MDA5, activates transcription factor NF κB and triggers transcription of interferon β gene, which prevents virus replication and stimulates the growth of immune system cells [9] . Previously, onconase, an RNases from oocytes of the leopard frog Rana pipiens, efficiently suppresses the replication of HIV 1 due to the selective degrada tion of viral RNA, which exhibits no pronounced cytotoxic effect on infected human cells [22] . At the first stage, when binase meets the virus outside cell, its catalytic activity is not inhibited by the natural RNase and it may destroy viral RNA (Fig. 3, C) . Ribonucleases in HIV type 1 inhibition: Effect of recombinant RNases on infection of primary T cells and immune activation induced RNase gene and protein expression cache = ./cache/cord-338727-1kodz527.txt txt = ./txt/cord-338727-1kodz527.txt === reduce.pl bib === id = cord-339209-oe8onyr9 author = Vasilakis, Nikos title = Mesoniviruses are mosquito-specific viruses with extensive geographic distribution and host range date = 2014-05-20 pages = extension = .txt mime = text/plain words = 5817 sentences = 272 flesch = 46 summary = The organization of each genome was similar to that described previously for the mesoniviruses (NDiV, CavV, HanaV, NseV and MenoV), featuring a long 5'-untranslated region (5'-UTR) of 359 to 370 nt, six major long open reading frames (ORFs), and a long terminal region of 1780 to 1804 nt preceding the poly[A] tail ( Figure 2 ). To determine the phylogenetic relationships of the newly identified insect viruses, maximum likelihood (ML) phylogenetic trees were constructed based on the amino acid alignments of ORF2a (unprocessed S protein) and a concatenated region of the highly conserved domains within ORF1ab (3CL pro , RdRp and ZnHel1). A Clustal X alignment of the mesonivirus ORF3a proteins and individual structural analyses using SignalP and TMHMM and NetNGlyc (www.expasy.org) indicated that each is a class I transmembrane glycoprotein with a predicted N-termimal signal peptide, an ectodomain containing a conserved set of 6 cysteine residues and a single conserved N-glycosylation site, a transmembrane domain and a C-terminal cytoplasmic domain ( Figure 4A, 4D) . cache = ./cache/cord-339209-oe8onyr9.txt txt = ./txt/cord-339209-oe8onyr9.txt === reduce.pl bib === id = cord-339854-scb7pz87 author = Overend, Christopher title = The synthetic futures of vesicular stomatitis virus date = 2012-07-11 pages = extension = .txt mime = text/plain words = 1089 sentences = 77 flesch = 42 summary = Vesicular stomatitis virus (VSV) is one of the most promising viruses for engineering vaccines and oncolytic therapies [2] . Of particular interest is a study in which VSV expressing the H5 antigen from highly pathogenic avian influenza induced sterilizing immunity against heterologous challenge in mice [4] . This demonstrates the safety and efficacy potential of VSV when live virus vaccination would otherwise be contraindicated. Even more promising, recombinant VSV expressing a secreted form of a virulence factor protein for Yersinia pestis, LcrV, induced high levels of LcrV-specific antibodies, protecting 90% of the mice challenged with 10 LD 50 [6] . Vesicular stomatitis virus-based Ebola vaccine is well-tolerated and protects immunocompromised nonhuman primates Potent vesicular stomatitis virus-based avian influenza vaccines provide long-term sterilizing immunity against heterologous challenge Heterologous boosting of recombinant adenoviral prime immunization with a novel vesicular stomatitis virus-vectored tuberculosis vaccine SARS vaccine based on a replicationdefective recombinant vesicular stomatitis virus is more potent than one based on a replication-competent vector cache = ./cache/cord-339854-scb7pz87.txt txt = ./txt/cord-339854-scb7pz87.txt === reduce.pl bib === id = cord-339172-210dwhgj author = Knoops, Kèvin title = SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum date = 2008-09-16 pages = extension = .txt mime = text/plain words = 9930 sentences = 411 flesch = 43 summary = Specific þRNA virus replicase subunits are targeted to the membranes of particular cell organelles that are subsequently modified into characteristic structures with which viral RNA synthesis is associated. We used electron microscopy and tomography for the three-dimensional imaging of the membrane alterations induced by severe acute respiratory syndrome (SARS)-coronavirus, a member of the virus group with the largest RNA genome known to date. The lumen of this unique membrane network contains numerous large (diameter 250-300 nm) ''inner vesicles,'' which were formerly thought to reside in isolated DMVs. Intriguingly, although the interior of these vesicles does not appear to be connected to the cytosol, it labels abundantly for double-stranded RNA, which presumably is present at the site of viral RNA synthesis. In some of our images, the SARS-CoV-induced CM appeared to be continuous with both DMV outer membranes ( Figure 2D ; inset) and ER cisternae, suggesting a link to the viral RTC also in coronaviruses. cache = ./cache/cord-339172-210dwhgj.txt txt = ./txt/cord-339172-210dwhgj.txt === reduce.pl bib === id = cord-339062-tq0f6d01 author = Weaver, Scott C. title = Transmission cycles, host range, evolution and emergence of arboviral disease date = 2004 pages = extension = .txt mime = text/plain words = 7314 sentences = 379 flesch = 43 summary = RNA viruses, including HIV 1,2 , dengue virus (DENV) 3, 4 and possibly the severe acute respiratory syndrome (SARS) coronavirus [5] [6] [7] , have caused recent pandemics by changing their host range to amplify in humans. In this review, we focus on selected viruses such as Venezuelan equine and Japanese encephalitis viruses (VEEV and JEV, respectively), which cause epidemics by adapting to domestic animals and exploiting them as amplification hosts. After identification of VEEV as a cause of human disease, experimental animal models revealed that equine infection results in a high titre VIRAEMIA; the animals therefore serve as highly efficient amplification hosts in the presence of abundant competent mosquito vectors 12 However, studies of dengue virus ecology in sylvatic habitats of west Africa 72 and Malaysia 73, 74 have identified transmission cycles involving non-human primates as reservoir hosts and arboreal, tree-hole dwelling Aedes (Stegomyia) spp. cache = ./cache/cord-339062-tq0f6d01.txt txt = ./txt/cord-339062-tq0f6d01.txt === reduce.pl bib === id = cord-339744-xrit0w5i author = Feng, Bo title = Investigation of antiviral state mediated by interferon-inducible transmembrane protein 1 induced by H9N2 virus and inactivated viral particle in human endothelial cells date = 2017-11-03 pages = extension = .txt mime = text/plain words = 6309 sentences = 408 flesch = 52 summary = Our previous microarray analysis showed that H9N2 virus infection and inactivated viral particle inoculation increased the expression of interferon-inducible transmembrane protein 1 (IFITM1) in human umbilical vein endothelial cells (HUVECs). In present study, we deeply investigated the expression patterns of IFITM1 and IFITM1-mediated antiviral response induced by H9N2 virus infection and inactivated viral particle inoculation in HUVECs. Epithelial cells that are considered target cells of the influenza virus were selected as a reference control. The results indicated that the cellular interaction between intracellular molecules and viral particles might be involved in the induction of IFITM1 expression in HUVECs. To determine the antiviral activity of IFITM1 protein induced by H9N2 virus infection, HUVECs or BEAS-2Bs were infected with H9N2 virus at MOI of 5 and incubated for 1 h, then cells were transfected with IFITM1 specific siRNA or control siRNA for 36 h. cache = ./cache/cord-339744-xrit0w5i.txt txt = ./txt/cord-339744-xrit0w5i.txt === reduce.pl bib === id = cord-339885-mpzgrogd author = Zhan, Yangqing title = Respiratory virus is a real pathogen in immunocompetent community-acquired pneumonia: comparing to influenza like illness and volunteer controls date = 2014-09-02 pages = extension = .txt mime = text/plain words = 3889 sentences = 244 flesch = 46 summary = title: Respiratory virus is a real pathogen in immunocompetent community-acquired pneumonia: comparing to influenza like illness and volunteer controls In order to better understand the real role of respiratory virus in pneumonia and better manage the patients, we conducted a prospective observational study to reveal the viral etiology of adult CAP in Guangzhou, as compared with etiology of patients diagnosed with influenza like illness (ILI) and with volunteer controls. Obviously, considering the high prevalence of viral CAP in Guangzhou and influenza infection as an independent variable in the severe disease model, routine laboratory detection should be taken in hospitalized CAP patients at admission for an adequate diagnosis of respiratory viruses, especially influenza virus in severe individuals. Another question was that did all patients with viral community-acquired pneumonia, especially those without evidence of bacteria infection, need to be treated with antibiotics? cache = ./cache/cord-339885-mpzgrogd.txt txt = ./txt/cord-339885-mpzgrogd.txt === reduce.pl bib === id = cord-340907-j9i1wlak author = Zarai, Yoram title = Evolutionary selection against short nucleotide sequences in viruses and their related hosts date = 2020-04-27 pages = extension = .txt mime = text/plain words = 8162 sentences = 415 flesch = 45 summary = Here, based on a novel statistical framework and a large-scale genomic analysis of 2,625 viruses from all classes infecting 439 host organisms from all kingdoms of life, we identify short nucleotide sequences that are under-represented in the coding regions of viruses and their hosts. Figure 3A and B depicts the average number of under-represented sequences of size m ¼ 3, 4, and 5 nucleotides, identified in few subsets of viruses in both the original and random variants of the virus. A sampling analysis that we performed (see Supplementary document, Section 2.8) suggests that the number of under-represented sequences identified in dsDNA viruses matches their genomic size, when compared with RNA viruses. To show that the correspondence between selection against short palindromic sequences in viruses and restriction sites cannot be explained by basic coding region features such as amino-acid content and order, codon usage bias and dinucleotide distribution, we also evaluated the overlap between restriction sites and common under-represented sequences of random variants of viruses. cache = ./cache/cord-340907-j9i1wlak.txt txt = ./txt/cord-340907-j9i1wlak.txt === reduce.pl bib === id = cord-339423-5qym9dsf author = Lina, B. title = Virus émergents ou menaces à répétition date = 2005-05-31 pages = extension = .txt mime = text/plain words = 2886 sentences = 263 flesch = 65 summary = L'analyse des mécanismes ayant permis l'apparition de ces virus montre que pour chaque virus émergent décrit, il ne s'agit en aucun cas de phénomènes purement aléatoires, mais bien de l'accumulation de facteurs qui permettent à ces agents infectieux de diffuser de l'animal vers l'homme. À chaque fois, cette émergence est considérée par le grand public comme un nouveau fléau pouvant potentiellement être responsable d'une mortalité très élevée, ce qui entraîne souvent des comportements irrationnels, ceci d'autant plus que l'importante mortalité autrefois liée aux infections virales et bactériennes a été oubliée (vaccinations et antibiotiques obligent) [2, 3] . Les années 2003 et 2004 ont été particulièrement instructives, permettant d'observer l'épidémie du Syndrome Respiratoire Aigu Sévère ou SRAS [4] , l'émergence de deux épidémies de grippe aviaire transmise à l'homme (influenza A H7N7 en Europe et A H5N1 en Asie) [5, 6] , l'apparition de cas de monkey pox [7] , et la diffusion du virus West Nile sur la quasi totalité du continent Nord Américain [8] . cache = ./cache/cord-339423-5qym9dsf.txt txt = ./txt/cord-339423-5qym9dsf.txt === reduce.pl bib === id = cord-337712-ylqgraos author = Heinz, Franz X. title = Profile of SARS-CoV-2 date = 2020-10-30 pages = extension = .txt mime = text/plain words = 6028 sentences = 301 flesch = 44 summary = Despite these similarities, distinguishing features were identified that are likely to contribute to the biological differences observed between the two viruses, including the significantly higher rate of subclinical and mild infections caused by SARS-CoV-2, which makes control of virus spread currently so difficult. If expectations were too optimistic and results obtained with some of the front runners are disappointing, windows of opportunity will open for an arsenal of alternative developments in progress [54, 59] (https:// www.who.int/publications/m/item/draft-landscapeof-covid-19-candidate-vaccines, accessed 2 October 2020) These include subunit vaccines with S proteins stabilized in their prefusion conformation in combination with potent adjuvants, use of the RBD only as an immunogen instead of the whole S protein [67, 68] , other rationally designed immunogens [69] , other (non-Adeno) vector vaccines including replication-competent vectors [55, 70] , self-amplifying RNA vaccines [71] , live-attenuated vaccines [55] , DNA vaccines [72] , and intranasally applied vaccines with the potential to induce local immunity at the site of virus entry [73] . cache = ./cache/cord-337712-ylqgraos.txt txt = ./txt/cord-337712-ylqgraos.txt === reduce.pl bib === id = cord-339382-ii4xurmr author = Bachofen, Claudia title = Selected Viruses Detected on and in our Food date = 2018-03-21 pages = extension = .txt mime = text/plain words = 6537 sentences = 337 flesch = 46 summary = Two groups of viruses were selected: (a) the most important viruses contaminating food, based on numbers of publications in the last 5 years and (b) viruses infecting sources of food that might have an impact on human health. RECENT FINDINGS: Important foodborne viruses such as norovirus, hepatitis A and rotavirus are usually "only" contaminating food and are detected on the surface of foodstuffs. Furthermore, some plant viruses are known to infect and persist in insect-vectors and one of them, Tomato spotted wilt virus, a member of the genus Tospovirus of the Bunyaviridae family, was even shown to replicate in human cell lines [71] . HEV-3 and 4 strains infect humans, but the reservoir is thought to be in several animal species, whereof the pig plays the most important role for foodborne transmission. While foodborne HEV and TBEV clearly represent a threat for human public health, the role of several other viruses of animal origin detected in food still needs to be assessed. cache = ./cache/cord-339382-ii4xurmr.txt txt = ./txt/cord-339382-ii4xurmr.txt === reduce.pl bib === id = cord-341050-hnuogpqn author = Acharya, Dhiraj title = An Overview of Current Approaches Toward the Treatment and Prevention of West Nile Virus Infection date = 2016-05-18 pages = extension = .txt mime = text/plain words = 10713 sentences = 490 flesch = 37 summary = Among these structural proteins, E protein mediates crucial roles in binding to cellular receptors, membrane fusion, and entry of WNV into host cells, making it a key target for the development of vaccines, neutralizing antibodies, and entry inhibitors . In addition, a recent successful clinical trial of a hepatitis C virus NS5A inhibitor suggests that targeting non-structural proteins may be an ideal strategy to develop therapeutics against other fl aviviruses, including WNV [ 71 ] . In addition, better understanding of the pathogenesis of WNV and other fl aviviruses has offered new opportunities for designing many different classes of promising antiviral therapeutics by targeting both viral replication and the host cell metabolism. Several natural and synthetic compounds, antiviral peptides and siRNAs have been identifi ed to target both structural and nonstructural proteins of WNV and evaluated for their potential therapeutic roles. A VLP-based vaccine targeting domain III of the West Nile virus E protein protects from lethal infection in mice cache = ./cache/cord-341050-hnuogpqn.txt txt = ./txt/cord-341050-hnuogpqn.txt === reduce.pl bib === id = cord-340481-i3qrxnpr author = Pozo, Francisco title = Aplicación de los métodos moleculares al diagnóstico y el estudio epidemiológico de las infecciones respiratorias causadas por virus date = 2008-07-31 pages = extension = .txt mime = text/plain words = 9085 sentences = 740 flesch = 48 summary = En comparación con las técnicas de diagnóstico clásicas, como son el cultivo de virus en líneas celulares (CC) o la detección de antígenos mediante ensayos de inmunofluorescencia (IF) u otros métodos, la reacción en cadena de la polimerasa (PCR), en sus múltiples variantes, ha permitido incre-mentar de manera considerable el número de muestras respiratorias en las que se detecta la presencia de alguno de los virus asociados con IRA. La elevada sensibilidad de los ensayos de PCR también comporta algunos inconvenientes para el diagnóstico etiológico de la IRA, como son la detección de virus que se encuentran colonizando la mucosa respiratoria de personas asintomáticas o la detección, a consecuencia de excreción prolongada, del virus en secreciones de pacientes que ya se han recuperado de una infección. cache = ./cache/cord-340481-i3qrxnpr.txt txt = ./txt/cord-340481-i3qrxnpr.txt === reduce.pl bib === id = cord-338331-27ic5zen author = Boulagnon, Camille title = Influenza A/H1N1 (2009) Infection as a Cause of Unexpected Out‐of‐Hospital Death in the Young date = 2012-05-14 pages = extension = .txt mime = text/plain words = 2729 sentences = 191 flesch = 51 summary = In conclusion, this case report shows that influenza A/H1N1 (2009) virus can be a cause of sudden cardiac death in the young and demonstrates the importance of quantitative virological analyses for the diagnosis of myocarditis. We have reported on an unexpected sudden out-of-hospital death caused by influenza A ⁄ H1N1 (2009) infection involving a young immunocompetent and previously healthy male. In our case, virological investigations were performed, including molecular analyses of common pulmonary and cardiotropic viruses in frozen cardiac samples, as well as genetic analysis of the influenza A ⁄ H1N1 (2009) virus for both hemagglutinin and neuraminidase genes. In our case, determination of viral loads in the absence of any inflammatory infiltrate in the myocardium has shown that influenza A ⁄ H1N1 (2009) virus can be a cause of out-of-hospital unexpected death in the young. Influenza A viral loads in respiratory samples collected from patients infected with pandemic H1N1, seasonal H1N1 and H3N2 viruses cache = ./cache/cord-338331-27ic5zen.txt txt = ./txt/cord-338331-27ic5zen.txt === reduce.pl bib === id = cord-339230-cc7gcy5b author = Smith, Amber M. title = Secondary Bacterial Infections in Influenza Virus Infection Pathogenesis date = 2014-07-16 pages = extension = .txt mime = text/plain words = 10381 sentences = 576 flesch = 34 summary = Several different animal models have been used to study the effect that influenza viruses have on bacterial transmission and colonization and on invasive diseases, such as acute otitis media and pneumonia (Wherry and Butterfield 1921; Shope 1931; Francis and de Torregrosa 1945; Berendt et al. Although the precise mechanisms responsible for enhancing the transmission profile that influenza viruses provide pneumococci are currently unknown, it is likely due to an increase in pathogen density and frequency of secretion events (e.g., sneezing and coughing) in the infected individual combined with a decrease in immunity and resistance from natural barriers breaking down in the person who is newly exposed. The PB1-F2 protein of some influenza viruses increases pathologic effects by causing cell death, increasing viral replication, and altering inflammatory responses to primary viral infections and to bacterial coinfections (Conenello et al. cache = ./cache/cord-339230-cc7gcy5b.txt txt = ./txt/cord-339230-cc7gcy5b.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-340537-pdvpmydk author = Bañon-Gonzalez, Rafael title = Autopsies of suspected SARS-CoV-2 cases date = 2020-07-15 pages = extension = .txt mime = text/plain words = 3682 sentences = 244 flesch = 54 summary = Abstract Forensic physicians should consider the possibility that people who have died from violent or unknown causes may be infected by the virus SARS-CoV-2, or that the diagnosis of the disease has legal implications, which requires adequate knowledge of the epidemiology of the disease, protective measures, adequate sampling and the pathological characteristics. This article reviews the aspects of the pathophysiology of the disease that have an impact on the infectivity of the body's tissues and fluids, measures for preventing biological risk, taking samples and pathological findings, both macroscopic and microscopic, associated with death caused by infection with the SARS-CoV-2 virus. 13 Nevertheless, infection by SARS-CoV-2 is associated with a high rate of mortality, and many carriers are known to exist who have no symptoms or only mild ones, so that it is possible that some of the corpses that will be subjected to a medical-legal autopsy are infected by this virus. cache = ./cache/cord-340537-pdvpmydk.txt txt = ./txt/cord-340537-pdvpmydk.txt === reduce.pl bib === id = cord-340503-zwdewiu1 author = Mokhtarzadeh, Ahad title = Nanomaterial-based biosensors for detection of pathogenic virus date = 2017-10-13 pages = extension = .txt mime = text/plain words = 7710 sentences = 401 flesch = 42 summary = Electron microscopy Viral particle Hours Broad spectrum; rapid method Necessity for presence of around 10 6 virus particles/mL for detection; similarity of morphologies [11] Hemagglutination assay Viral protein Hours Easy; inexpensive Poor sensitivity; necessity for fresh reagents [12] ELISA Viral protein Hours Only one incubation step; no hook effect at high analyte concentrations Limited concentration range in which the analyte can be quantified without sample dilution; and that the antigen or antibody produce the same response and not distinguishable in a one step [13] PCR Viral nucleic acid Hours Extremely high sensitivity; Easy to set up Extremely liable to contamination; Not easy to quantitate results; High degree of operator skill required [14] As an example for HIV, a type of virus that gradually attacks the immune system and makes it harder to fight off infections and diseases in infected body, a QDs-based rapid capture and imaging system was developed by Kim et al. cache = ./cache/cord-340503-zwdewiu1.txt txt = ./txt/cord-340503-zwdewiu1.txt === reduce.pl bib === id = cord-340423-f8ab7413 author = Barr, J.N. title = Genetic Instability of RNA Viruses date = 2016-09-09 pages = extension = .txt mime = text/plain words = 9777 sentences = 454 flesch = 45 summary = We then discuss evidence that at least some RNA viruses have a replication fidelity that is poised to maximize genome sequence space without incurring catastrophic lethal mutations and describe how this can be exploited to control viral infections. The error-prone nature of polymerase activity, coupled with the absence of a proofreading mechanism, is the key reason why RNA virus genomes acquire mutations and exist as a swarm of genetic variants. The mutation rate of the viral polymerase, coupled with the replication mode that the virus employs (and extrinsic factors, described in the following text) will determine the extent of genetic variability of viruses released from an infected cell. Thus, it is possible that the high mutation rates of RNA viruses are simply a consequence of polymerases that are under selective pressure to replicate genomes very rapidly to ensure efficient viral infection [79] [80] [81] . cache = ./cache/cord-340423-f8ab7413.txt txt = ./txt/cord-340423-f8ab7413.txt === reduce.pl bib === id = cord-340610-ex2yjyum author = Wang, De-Yun title = Upper Airway Stem Cells: Understanding the Nose and Role for Future Cell Therapy date = 2014-11-28 pages = extension = .txt mime = text/plain words = 5235 sentences = 195 flesch = 32 summary = In addition to the physical barrier, nasal epithelial cells are known to play an active role in both the innate and acquired immune responses, which have been summarized in the European Position paper on rhinosinusitis and nasal polyps 2012 (EPOS 2012) [1••] as (l) expressing membrane-bound and cytoplasmic pattern recognition receptors (PRRs) that recognize pathogen-associated molecular patterns (PAMPs), which are conserved molecular patterns found in parasites, viruses, yeasts, bacteria, and mycobacteria; (2) secreting a vast arsenal of host defense molecules, such as antimicrobial molecules in several classes of enzymes (lysozyme, chitinases, and peroxidases), opsonins (complement and pentraxin-3), permeabilizing proteins (A defensins, B defensins, and cathelicidins such as LL-37), collectins (surfactant protein-A, surfactant protein-D, and mannose-binding lectin), and binding proteins (lactoferrin and mucins); (3) producing a variety of inflammatory cytokines, such as IL-1, TNF-α, IFNα/β, GM-CSF, eotaxins, RANTES, IP-10, IL-6, IL-8, GRO-α, MDC, SCF, TARC, MCP-4, BAFF, osteopontin, IL-25, IL-32, IL-33, and thymic stromal lymphopoietin (TSLP), in response to stimulation of the antigens. cache = ./cache/cord-340610-ex2yjyum.txt txt = ./txt/cord-340610-ex2yjyum.txt === reduce.pl bib === id = cord-341303-1iayp8oa author = McINTOSH, KENNETH title = Immunofluorescence in Diagnostic Virology date = 2006-12-16 pages = extension = .txt mime = text/plain words = 2850 sentences = 126 flesch = 47 summary = In the 1930s Parker and Muckenfuss first developed the complement fixation reaction using lymph mixed with antibody and a fresh source of complement.s I n fact, this became the procedure of choice for the laboratory diagnosis of smallpox before and even after the general use of tissue culture for viral isolation. Immunofluorescence (IF) was also recognized early as a potentially valuable tool for detection of viral antigen^,'.^.^ but its use as a procedure that could supplement and, at times, replace tissue culture in diagnostic laboratories has been only gradually gaining acceptance. IF has, of course, been used at several stages in the diagnosis of viral diseases: the measurement of antibody, particularly when there is some highly specific antigen in question, as with Epstein-Barr virus or cytomegalovirus; the identification of viruses in tissue culture; and the direct detection of viruses in body fluids. cache = ./cache/cord-341303-1iayp8oa.txt txt = ./txt/cord-341303-1iayp8oa.txt === reduce.pl bib === id = cord-339973-kj56zi59 author = Coleman, Kristen K. title = Bioaerosol Sampling for Respiratory Viruses in Singapore’s Mass Rapid Transit Network date = 2018-11-30 pages = extension = .txt mime = text/plain words = 4775 sentences = 228 flesch = 46 summary = Although baseline metagenomic maps created from these studies are said to be useful for mitigating bioterrorism and infectious disease outbreaks, most of them focus largely on mapping surface-borne bacterial DNA 17 and neglect to address the threat of weaponized or global catastrophic biological risk-level (GCBR-level) agents, both of which would likely be aerosolized or respiratory-borne RNA viruses 19 . Bioaerosol sampling in the field provides a noninvasive way to monitor and characterize the community of aerosolized respiratory viruses that regularly infect the public, as well as potentially detect or discover novel pathogens with pandemic potential, such as the influenza A(H7N9) virus. Although the air pump flow rate and sample collection times used in our study have been demonstrated to efficiently capture aerosolized influenza virus and RSV RNA [33] [34] [35] , it is possible that these parameters are not optimal for capturing the other respiratory virus DNA/RNA targeted in our study. cache = ./cache/cord-339973-kj56zi59.txt txt = ./txt/cord-339973-kj56zi59.txt === reduce.pl bib === id = cord-340042-intxyu46 author = Chaudhry, Sundas Nasir title = New insight on possible vaccine development against SARS-CoV-2 date = 2020-09-11 pages = extension = .txt mime = text/plain words = 5457 sentences = 260 flesch = 43 summary = In December 2019, a novel virus, namely COVID-19, caused by SARS-CoV-2, developed from Wuhan, Hubei territory of China, which used its viral spike glycoprotein receptor-binding domain (RBD) for the entrance into a host cell by binding with ACE-2 receptor and cause acute respiratory distress syndrome (ARDS). Different subunits of spike proteins like the S1 and S2 subunits, and the receptor-binding domain (RBD) are the critical elements for the formation of a vaccine against the newly emerged virus that helped in producing T cell responses and protective immunity against SARS-CoV-2 [29] . The recombinant protein is known as one of the emerging fields for the development of a vaccine against viruses due to several properties including tight binding to specific ACE-2 receptor, provoke immune protection against viral infections, increase antibody-dependent viral entry, and promote antigenicity against virus like SARS-CoV [52] . cache = ./cache/cord-340042-intxyu46.txt txt = ./txt/cord-340042-intxyu46.txt === reduce.pl bib === id = cord-339152-wfakzb6w author = Trovato, Maria title = Viral Emerging Diseases: Challenges in Developing Vaccination Strategies date = 2020-09-03 pages = extension = .txt mime = text/plain words = 12000 sentences = 540 flesch = 38 summary = Ebola and Marburg hemorrhagic fevers, Lassa fever, Dengue fever, Yellow fever, West Nile fever, Zika, and Chikungunya vector-borne diseases, Swine flu, Severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and the recent Coronavirus disease 2019 (COVID-19) are examples of zoonoses that have spread throughout the globe with such a significant impact on public health that the scientific community has been called for a rapid intervention in preventing and treating emerging infections. The occurrence of significant disease outbreaks-such as SARS (severe acute respiratory syndrome) originating in China in 2002 (8) , the 2009 H1N1 swine flu pandemic from Mexico (9) , MERS (Middle East respiratory syndrome) that occurred in Saudi Arabia in 2012 (10) , the West African outbreak of Ebola virus (EBOV) in late 2013 (11) , the Zika virus (ZIKV) outbreak originating in Brazil in 2015 (12) , the 2018 health emergence in Nigeria caused by Lassa virus (13) , and the ongoing Coronavirus disease 2019 (COVID19) pandemic (14) -has renewed interests in developing strategies to faster prevent, treat, and/or control emerging and re-emerging viruses with high epidemic potential. cache = ./cache/cord-339152-wfakzb6w.txt txt = ./txt/cord-339152-wfakzb6w.txt === reduce.pl bib === id = cord-341923-jwckbdnb author = To, Kelvin Kai-Wang title = Pathogenesis of pandemic H1N1 2009 influenza virus infection and the implication on management date = 2010-04-28 pages = extension = .txt mime = text/plain words = 5849 sentences = 306 flesch = 44 summary = Although most patients infected with this novel strain present with mild upper respiratory tract symptoms [6] , the higher fatality rate in children and young adults clearly differentiate this virus from seasonal influenza virus [7, 8] . Known virulence factors in H5N1 virus include Lys627 of PB2, which increases the viral replication; an Asn66Ser substitution in PB1-F2, a protein that induces apoptosis, enhances inflammation in mice, and predisposes to secondary bacterial infection; NS1, which antagonizes the antiviral effect of interferon; and a multibasic HA cleavage sequence, which allows cleavage by ubiquitous proteases [36] . A higher viral load in respiratory tract samples was associated with fatal disease from H5N1 [41] and with disease severity in infection due to respiratory syncytial virus and human metapneumovirus [42] . Delayed clearance of viral load and marked cytokine activation in severe cases of pandemic H1N1 2009 influenza virus infection cache = ./cache/cord-341923-jwckbdnb.txt txt = ./txt/cord-341923-jwckbdnb.txt === reduce.pl bib === id = cord-341138-mxjsp3cm author = Denner, Joachim title = Transspecies Transmission of Gammaretroviruses and the Origin of the Gibbon Ape Leukaemia Virus (GaLV) and the Koala Retrovirus (KoRV) date = 2016-12-20 pages = extension = .txt mime = text/plain words = 4762 sentences = 239 flesch = 47 summary = title: Transspecies Transmission of Gammaretroviruses and the Origin of the Gibbon Ape Leukaemia Virus (GaLV) and the Koala Retrovirus (KoRV) The gibbon ape leukaemia virus (GaLV) and koala retrovirus (KoRV), two gammaretroviruses, are also the result of a transspecies transmission, however from a still unknown host. The transspecies transmission of the gibbon ape leukaemia virus (GaLV) and the koala retrovirus (KoRV) is a prime example of a transmission that is still not yet fully understood. Searching for the precursor virus, retroviruses related to KoRV and GaLV have been described in rodents such as South East Asian mice (e.g., Mus caroli [9, 10] and Mus dunni [11] ), as well as in two subspecies of Melomys burtoni in Australia and Indonesia [12, 13] . The nucleotide sequence of koala (Phascolarctos cinereus) retrovirus: A novel type C endogenous virus related to gibbon ape leukemia virus cache = ./cache/cord-341138-mxjsp3cm.txt txt = ./txt/cord-341138-mxjsp3cm.txt === reduce.pl bib === id = cord-341298-mqpovrms author = Morse, S.A. title = Viruses and Bioterrorism date = 2016-10-31 pages = extension = .txt mime = text/plain words = 4787 sentences = 224 flesch = 44 summary = Requirements for an ideal biological warfare agent may include: availability; ease of production; stability after production; a susceptible population (human or animal); absence of specific treatment; ability to incapacitate or kill the host; appropriate particle size in aerosols so that the virus can be carried long distances by prevailing winds and inhaled deeply into the lungs of unsuspecting victims; ability to be disseminated via food or water; and, the availability of a vaccine to protect certain groups. Classification of viral agents that are considered to be of concern for bioterrorism and biowarfare and those that have been weaponized or studied for offensive or defensive purposes as part of former or current national biological weapons programs incapacitating (eg, VEE) or lethal infections (EEE case fatality rates range from 50 to 75%) (Sidwell and Smee, 2003) . An Australian research group (Jackson et al., 2001) was investigating virally vectored immunocontraceptive vaccines based on ectromelia virus, the causative agent of the disease termed mousepox. cache = ./cache/cord-341298-mqpovrms.txt txt = ./txt/cord-341298-mqpovrms.txt === reduce.pl bib === id = cord-339288-y8woqsii author = Tews, Birke Andrea title = Self-Replicating RNA date = 2016-06-11 pages = extension = .txt mime = text/plain words = 7567 sentences = 338 flesch = 44 summary = Self-replicating RNA derived from the genomes of positive strand RNA viruses represents a powerful tool for both molecular studies on virus biology and approaches to novel safe and effective vaccines. Three years later, the performance of poliovirus cDNA clones could be significantly ameliorated through the introduction of SV40 transcription and replication signals and transfection of the resulting construct into cells expressing the SV40 large T antigen [14] , thus ensuring replication of the DNA-plasmid in eukaryotic cells leading to a higher yield of viral RNA and recovered virus (Fig. 2, left part) . The resulting virus CP7_E2alf was only able to infect pigs and thus displayed the Fig. 3 Generation of a chimeric viral genome from two parental RNAs. On the level of a cDNA construct, one protein-coding sequence is replaced by the corresponding gene of the other virus (principle used for the pestivirus vaccine CP7_E2alf [58] ). cache = ./cache/cord-339288-y8woqsii.txt txt = ./txt/cord-339288-y8woqsii.txt === reduce.pl bib === id = cord-340331-51yq1rdo author = Tonelli, Michele title = Host dihydrofolate reductase (DHFR)-directed cycloguanil analogues endowed with activity against influenza virus and respiratory syncytial virus date = 2017-07-28 pages = extension = .txt mime = text/plain words = 6160 sentences = 285 flesch = 42 summary = We have identified a series of 1-aryl-4,6-diamino-1,2-dihydrotriazines, structurally related to the antimalarial drug cycloguanil, as new inhibitors of influenza A and B virus and respiratory syncytial virus (RSV) via targeting of the host dihydrofolate reductase (DHFR) enzyme. The compounds, object of the present study, are characterized by the 1-aryl-4,6-diamino-1,2-dihydrotriazine scaffold, such as the cited cycloguanil, which was identified by us as prototype (1) of a new class of antiviral agents exploiting a host DHFR inhibition mechanism. Since host cell DHFR inhibition seemed the plausible explanation for the observed antiviral effect, we performed a combination experiment in which RSV-infected HeLa cells were exposed to compound 14 in combination with different concentrations of the natural DHFR substrate dihydrofolic acid ( reaction has a much higher impact on virus replication than on cell growth, which concurs with the promising antiviral selectivity of our host-directed DHFR inhibitors. The interesting dual activity of the 1-aryl-4,6-diamino-1,2dihydrotriazines against influenza and respiratory syncytial viruses, via inhibition of the cellular (human) DHFR enzyme, points to this host factor as a new therapeutic target for these two respiratory viruses. cache = ./cache/cord-340331-51yq1rdo.txt txt = ./txt/cord-340331-51yq1rdo.txt === reduce.pl bib === id = cord-342412-azkamnpa author = Ecker, David J title = The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents date = 2005-04-25 pages = extension = .txt mime = text/plain words = 7206 sentences = 409 flesch = 42 summary = This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. For example, the Centers for Disease Control and Prevention (CDC) maintains an ever-changing list of notifiable diseases, the National Institute of Allergy and Infectious Disease (NIAID) lists agents with potential for use in bioterrorist attacks, and the Department of Health and Human Services (HHS) maintains a list of critical human pathogens. This article focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. It provides a compilation of lists, taken from the database, of important and/or regulated biological agents from a number of agencies including HHS, the United States Department of Agriculture (USDA), the CDC, the World Health Organization (WHO), the NIAID, and other sources. cache = ./cache/cord-342412-azkamnpa.txt txt = ./txt/cord-342412-azkamnpa.txt === reduce.pl bib === id = cord-338737-phv12m1q author = Amor, A. title = Infecciones víricas. Clasificación. Infecciones por virus herpes date = 2006-06-30 pages = extension = .txt mime = text/plain words = 4805 sentences = 518 flesch = 54 summary = Los virus son microorganismos de pequeño tamaño (generalmente de 20-400 nm de diámetro) formados por una molécula de ácido nucleico, ADN o ARN, que puede ser de cadena sencilla (ss) o doble (ds) y una cápside proteica de simetría icosaédrica o helicoidal. Así, la transmisión y reactivación de los virus herpes constituye un problema clínico de primer orden en pacientes infectados por el virus de la inmunodeficiencia humana (VIH) o inmunodeprimidos debido a tratamientos quimioterápicos, corticoideos o tras trasplantes de órganos. La frecuencia de las reactivaciones varía con la localización anatómica, el subtipo vírico y el estado inmunológico del paciente, de tal forma que los sujetos inmunocomprometidos pueden tener mayor número de reactivaciones, cuadros más graves y extensos, y un riesgo elevado de diseminación. cache = ./cache/cord-338737-phv12m1q.txt txt = ./txt/cord-338737-phv12m1q.txt === reduce.pl bib === id = cord-341155-3d64mso0 author = Slots, Jørgen title = Bacterial and viral pathogens in saliva: disease relationship and infectious risk date = 2010-12-07 pages = extension = .txt mime = text/plain words = 9332 sentences = 447 flesch = 36 summary = Human viruses are also frequent inhabitants of the human mouth, and their presence in saliva may be caused by the direct transfer of saliva from infected individuals, a bloodborne infection of the salivary glands, infection of the oral mucosa, or serumal exudates from diseased periodontal sites. Caries risk is assessed by the levels of mutans streptococci and lactobacilli in stimulated saliva (94, 96) , and salivary transmission of cariogenic bacteria frequently occurs from the mother to her child (92, 100) . As high quantities of salivary Epstein-Barr virus DNA can be recovered from fully edentulous patients (155) , the occurrence of the virus in saliva may not be a reliable indicator of its subgingival level or of the periodontitis disease status. Taken together, the saliva of HIV-infected persons is a risk factor for the transmission of several virulent herpesvirus species, and patients receiving HAART cannot be assumed to be less infectious for herpesviruses than individuals not receiving HAART. cache = ./cache/cord-341155-3d64mso0.txt txt = ./txt/cord-341155-3d64mso0.txt === reduce.pl bib === id = cord-340489-yo3cp5vs author = nan title = KAPITEL 13 Infektionskrankheiten date = 2008-12-31 pages = extension = .txt mime = text/plain words = 26536 sentences = 3917 flesch = 45 summary = Die Wirksamkeit von BVDU bei VZV-Infektionen (Varizellen und Zoster) immunkompromittierter Patienten ist durchaus sehr gut und vergleichbar der von i.v. verabreichtem Aciclovir, jedoch fällt die Nutzen-Risiko-Betrachtung insgesamt auch bei VZV-Therapie zu Gunsten von Aciclovir aus, da BVDU eher mutagen zu sein scheint und nicht zusammen mit 5-Fluorouracil (Zytostatikum) gegeben werden darf. In klinischen Studien konnte durch Anwendung von ACV bei EBV-Infektionen auch die Virusausscheidung deutlich vermindert werden, ein wesentlicher Einfluss auf den Krankheitsverlauf ließ sich nicht erreichen. Typisch für viele opportunistische Erreger ist, dass sie weit verbreitet sind und nach einer Primärinfektion, die bereits vor der HIV-Infektion stattfindet, zu latenten Infektionen führen. Die Prophylaxe von Infektionen bereits vor deren erstem Auftreten (Primärprophylaxe) oder nach der ersten Episode (Sekundärprophylaxe) ist weiterhin eine wichtige Aufgabe bei der Betreuung HIV-positiver Patienten, auch wenn opportunistische Infektionen durch die antiretrovirale Therapie insgesamt seltener geworden sind. cache = ./cache/cord-340489-yo3cp5vs.txt txt = ./txt/cord-340489-yo3cp5vs.txt === reduce.pl bib === id = cord-342151-1e6x589e author = Talbot, Pierre J. title = Hemagglutination by Murine Hepatitis Viruses date = 2008-07-29 pages = extension = .txt mime = text/plain words = 1218 sentences = 79 flesch = 54 summary = Erythrocytes from twelve mammalian and avian sources in ten different buffers at three incubation temperatures could not be hemagglutinated with murine hepatitis virus (MHV) strains 3, A59, or S grown on DBT cells. Viral antigen preparation in the absence of fetal calf serum, partial virus purification, or various concentrations of red blood cells still failed to yield detectable hemagglutinating activity. For use as antigen for hemag glutination assays, MHV-3 was grown in the absence of fetal calf serum (FCS) and har vested from clarified medium by precipita tion with 10% (w/v) polyethylene glycol in 0.5 M NaCl. After centrifugation at 10,000 g for 30 min, the pellet was resuspended and dialyzed against TMEN buffer: 50 mM Tris-HCi (pH 6.2), 0.1 M NaCl, 1 m M EDTA. Control hemagglutinating antigens were either rabbit enteric coronavirus (titer 1/64 with rabbit red blood cells ) or pneumonia virus of mice (titer 1/320 with CDI mouse erythrocytes). cache = ./cache/cord-342151-1e6x589e.txt txt = ./txt/cord-342151-1e6x589e.txt === reduce.pl bib === id = cord-340629-1fle5fpz author = O’Shea, Helen title = Viruses Associated With Foodborne Infections date = 2019-05-21 pages = extension = .txt mime = text/plain words = 9409 sentences = 500 flesch = 46 summary = In infants, prior to the introduction of rotavirus vaccines, RVAs could be detected in up to 50%-60% of all childhood hospitalisations due to acute gastroenteritis each year, were estimated to cause 138 million cases of gastroenteritis annually, and 527,000 deaths in children o5 years of age living in developing countries. Recent emerging epidemic and pandemic virus infections that cause severe disease in humans and that are associated with food production, preparation and food contamination include the coronavirus, severe acute respiratory syndrome (SARS-CoV), Nipah virus, Ebola virus and some of the highly pathogenic influenza virus strains, such as the H5N1 subtype. Infections by Severe Acute Respiratory Syndrome (SARS) virus, Nipah virus (NiV), H5N1 virus, Hepatitis A virus (HAV), Hepatitis E virus (HEV), Adenovirus, Astrovirus, Norovirus (NoV) and Rotavirus (RVA) in humans and animals are detected by nucleic acid amplification tests and serologic tests. cache = ./cache/cord-340629-1fle5fpz.txt txt = ./txt/cord-340629-1fle5fpz.txt === reduce.pl bib === id = cord-341968-uc8i9h0m author = Izaguirre, Gonzalo title = The Proteolytic Regulation of Virus Cell Entry by Furin and Other Proprotein Convertases date = 2019-09-09 pages = extension = .txt mime = text/plain words = 7870 sentences = 410 flesch = 45 summary = A wide variety of viruses exploit furin and other proprotein convertases (PCs) of the constitutive protein secretion pathway in order to regulate their cell entry mechanism and infectivity. Like other enveloped viruses that rely on surface glycoproteins for binding and fusion, coronaviruses have the Spike (S) protein, which is cleaved by proteases during virion biosynthesis, as well as during entry into target cells [53] . The location of furin and related PCs in the vesicles of the constitutive protein secretion pathway, where viruses are assembled during morphogenesis or disassembled during cell entry, explains why a diversity of virus types have evolutionarily converged to depend on PCs. Viruses also use other types of proteases for the proteolytic regulation of the binding and fusion functions; however, proteases are restricted to specific cell types, which limits the range of the viral infection, so when some viruses mutate and acquire PC reactivity, they may expand their cell tropism and become more pathogenic. cache = ./cache/cord-341968-uc8i9h0m.txt txt = ./txt/cord-341968-uc8i9h0m.txt === reduce.pl bib === id = cord-344009-hm36pepp author = Nathanson, N. title = Virus perpetuation in populations: biological variables that determine persistence or eradication date = 2005 pages = extension = .txt mime = text/plain words = 3463 sentences = 180 flesch = 46 summary = However, small animal populations can turnover significantly each year, permitting the perpetuation of some viruses that cause acute infections. Measles has several attributes that -in the aggregate -are not seen for other common viral diseases: (i) There are longterm records of measles incidence, collected by many health departments in the United States and other countries; (ii) 95% of all measles infections manifest as illness (in contrast to 1% for poliomyelitis for example); (iii) the symptoms of measles are sufficiently pathognomonic so that it can be distinguished from other viral infections by clinical observers; and (iv) population-wide reports can be corrected for under-reporting (about 15% of measles cases were reported in most cities in the United States prior to the introduction of measles vaccine in 1963). Vaccine-induced reduction of susceptible individuals in such a population can be guesstimated to reduce the number of new infections per trough generation period below the threshold for virus perpetuation. cache = ./cache/cord-344009-hm36pepp.txt txt = ./txt/cord-344009-hm36pepp.txt === reduce.pl bib === id = cord-341029-49360l2a author = Nasir, Arshan title = A phylogenomic data-driven exploration of viral origins and evolution date = 2015-09-25 pages = extension = .txt mime = text/plain words = 14410 sentences = 794 flesch = 49 summary = Viruses harboring different replicon types and infecting distantly related hosts shared many metabolic and informational protein structural domains of ancient origin that were also widespread in cellular proteomes. Here, we analyzed a total of 5080 completely sequenced proteomes from cells and viruses and assigned FSF domains to their proteins using structure-based hidden Markov models (HMMs) defined by the SUPER-FAMILY database (version 1.75) (20) . Viral supergroup behaves similarly to cellular superkingdoms in terms of FSF sharing patterns A total of 1995 significant FSF domains (E < 0.0001) were detected iñ 11 million proteins of 5080 proteomes sampled from cells and viruses. It also suggests that viruses are very ancient and most likely infected the last common ancestor of each superkingdom because viral FSFs were present in a diverse array of cellular organisms ranging from small microbes to large eukaryotes. cache = ./cache/cord-341029-49360l2a.txt txt = ./txt/cord-341029-49360l2a.txt === reduce.pl bib === id = cord-340194-ibli36rq author = To, Kelvin K.W. title = Ebola virus disease: a highly fatal infectious disease reemerging in West Africa date = 2014-11-29 pages = extension = .txt mime = text/plain words = 8870 sentences = 485 flesch = 51 summary = Ebolavirus has been known to cause outbreaks of severe hemorrhagic fever with high fatality in Africa since 1976 [1] . Zaire and Sudan ebolavirus are responsible for most outbreaks, and these species are associated with highest case-fatality rates, ranging from 44e100% and 41e69%, respectively. In addition to clinically apparent EVD outbreaks, seroepidemiology studies showed that there is a high prevalence seropositive individuals, suggesting that asymptomatic or mild infection can occur [15] . The only human case of ebolavirus infection in West Africa before the 2014 outbreak occurred 20 years ago. During the 1976 EVD outbreak, the index case had transmitted the virus to healthcare workers and hospitalized patients with at least 15 generations of person-to-person transmission [29] . Human fatal zaire ebola virus infection is associated with an aberrant innate immunity and with massive lymphocyte apoptosis Analysis of human peripheral blood samples from fatal and nonfatal cases of Ebola (Sudan) hemorrhagic fever: cellular responses, virus load, and nitric oxide levels cache = ./cache/cord-340194-ibli36rq.txt txt = ./txt/cord-340194-ibli36rq.txt === reduce.pl bib === id = cord-344006-0iq9s94n author = Atzrodt, Cassandra L. title = A Guide to COVID‐19: a global pandemic caused by the novel coronavirus SARS‐CoV‐2 date = 2020-05-23 pages = extension = .txt mime = text/plain words = 7283 sentences = 428 flesch = 54 summary = All rights reserved Like other coronaviruses, SARS-CoV-2 is a single-stranded, positive-sense RNA virus that uses spike proteins to bind to human lung epithelial cells (Fig. 2) [67] . Upon membrane fusion, the RNA of the coronavirus genome is released into the host cell cytoplasm via an early endosome -unlike SARS-CoV, which employs a late endosome and therefore must cross higher barriers of antiviral host immunity -where it is translated into a replication-translation complex that in turn translates sub-genomic RNA into accessory and structural proteins (Fig. 3) [82-84]. The Vivalytic VRI (viral respiratory tract infections) COVID-19 Test System pioneered by Bosch and Randox Laboratories is similar to the Abbott RealTime SARS-CoV-2 assay in that it reduces hands-on time and can confirm a positive test within 2.5 hours with a reported 95% accuracy [100]. More specific assays have now emerged that are proving very useful in providing a fuller picture of the rates of asymptomatic or mild SARS-Cov2 infection, through detection of anti-viral antibodies that persist for months and even years after the virus has been cleared [107] . cache = ./cache/cord-344006-0iq9s94n.txt txt = ./txt/cord-344006-0iq9s94n.txt === reduce.pl bib === id = cord-343690-rafvxgx1 author = Hartmann, Katrin title = Clinical Aspects of Feline Retroviruses: A Review date = 2012-10-31 pages = extension = .txt mime = text/plain words = 10289 sentences = 498 flesch = 35 summary = Although FIV can cause an acquired immunodeficiency syndrome in cats ("feline AIDS") comparable to human immunodeficiency virus (HIV) infection in humans, with increased risk for opportunistic infections, neurologic diseases, and tumors, in most naturally infected cats, FIV does not cause a severe clinical syndrome. Experimental FIV infection also progresses through several stages, similar to HIV infection in people, including an acute phase, a clinically asymptomatic phase of variable duration, and a terminal phase sometimes called "feline acquired immunodeficiency syndrome" ("AIDS") [18, 19] . Of 8642 FeLV-infected cats presented to North American Veterinary Teaching Hospitals, various co-infections (including FIV infection, feline infectious peritonitis (FIP), upper respiratory infection, hemotropic mycoplasmosis, and stomatitis) were the most frequent findings (15%), followed by anemia (11%), lymphoma (6%), leukopenia or thrombocytopenia (5%), and leukemia or myeloproliferative diseases (4%) [20] . An early defect in primary and secondary t cell responses in asymptomatic cats during acute feline immunodeficiency virus (fiv) infection cache = ./cache/cord-343690-rafvxgx1.txt txt = ./txt/cord-343690-rafvxgx1.txt === reduce.pl bib === id = cord-341101-5yvjbr5q author = Hashem, Anwar M. title = Therapeutic use of chloroquine and hydroxychloroquine in COVID-19 and other viral infections: A narrative review date = 2020-05-06 pages = extension = .txt mime = text/plain words = 4823 sentences = 275 flesch = 43 summary = While approved specific antiviral drugs against SARS-CoV-2 are still lacking, a large number of existing drugs are being explored as a possible treatment for COVID-19 infected patients. In general, studies showed no significant effect of CQ on CoVs including SARS-CoV and feline infectious peritonitis virus (FIPV) replication or clinical scores in mice and cats, respectively [105, 110] . There are very limited published clinical trials that studied the possible antiviral effect of CQ or HCQ in CoV and non-CoV infected patients (Table 5 ). Anti-malaria drug chloroquine is highly effective in treating avian influenza A H5N1 virus infection in an animal model In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro cache = ./cache/cord-341101-5yvjbr5q.txt txt = ./txt/cord-341101-5yvjbr5q.txt === reduce.pl bib === id = cord-342936-43u7afl3 author = Balzarini, Jan title = Targeting the glycans of glycoproteins: a novel paradigm for antiviral therapy date = 2007 pages = extension = .txt mime = text/plain words = 11304 sentences = 534 flesch = 44 summary = Perhaps more importantly, such carbohydrate-binding agents (CBAs) may force the virus to delete at least part of its glycan shield to escape drug pressure 5 ; this might result in the initiation of an immune response against uncovered immunogenic envelope epitopes. Although such a mechanism may be efficient for a first-line inactivation of HIV, CBA-exposed HIV strains may decrease the efficiency of LCs to eliminate HIV, but at the same time may compromise the ability of the virus to be efficiently transmitted by DCs. The interactions of several CBAs have been extensively investigated, including: the prokaryotic CV-N and actinohivin; a variety of plant lectins, including Hippeastrum hybrid agglutinin (HHA) and UDA; the non-peptidic low-molecular-weight antibiotic PRM-A; and the monoclonal antibody 2G12 with the HIV-envelope gp120 and/or several glycan structures. cache = ./cache/cord-342936-43u7afl3.txt txt = ./txt/cord-342936-43u7afl3.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-342277-v6310fjh author = Carducci, A. title = Environmental survey to assess viral contamination of air and surfaces in hospital settings date = 2011-01-31 pages = extension = .txt mime = text/plain words = 3031 sentences = 166 flesch = 46 summary = The aim of this study was to monitor surfaces and air in hospital settings to reveal the presence of hepatitis C virus, human adenovirus, norovirus, human rotavirus and torque teno virus by nucleic acid assays, in parallel with measurements of total bacterial count and haemoglobin presence. Moreover, viral agents transmitted via the faecaleoral route, such as rotavirus, human adenovirus 40 and 41 and norovirus, are frequently associated with healthcare setting infections spread by air, hand and surface contamination. The nucleic acids extracted from samples were analysed according to published protocols of nested (RT)ePCR to detect and distinguish the target viruses: the primers, virus genome regions and reaction conditions are reported in Table I . Although this is particularly true for viruses, where detection on surfaces and in air is very difficult, the low reliability of bacterial counts as indicators of viral contamination, suggests studying alternative parameters for assessing virological safety. cache = ./cache/cord-342277-v6310fjh.txt txt = ./txt/cord-342277-v6310fjh.txt === reduce.pl bib === id = cord-344408-4ko557n1 author = Cunningham, Andrew A. title = One Health, emerging infectious diseases and wildlife: two decades of progress? date = 2017-07-19 pages = extension = .txt mime = text/plain words = 5977 sentences = 278 flesch = 43 summary = Around this time, emerging diseases were identified in a series of well-reported die-offs in wildlife, including canine distemper in African lions (Panthera leo) in the Serengeti, chytridiomycosis in amphibians globally, pilchard herpesvirus disease in Australasia and West Nile virus in corvids and other birds in New York [10 -13] . There are likely to be multiple causes of novel disease emergence, but the human-mediated transport of pathogens (often in infected hosts) or vectors across geographical or ecological boundaries, a process termed 'pathogen pollution', has been identified as a major driver of this in wildlife [64] and also in plants [65] . salamandrivorans as a novel lethal fungus infecting and killing captive and wild salamanders in Europe [67, 85, 86] Challenges remain to understanding the wildlife origins of zoonotic EIDs. It is often difficult, time-consuming, logistically challenging and very expensive to identify the origins of newly emerged pathogens of humans. cache = ./cache/cord-344408-4ko557n1.txt txt = ./txt/cord-344408-4ko557n1.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-345168-3w32v2fm author = To, Kelvin K.W. title = Viral load in patients infected with pandemic H1N1 2009 influenza A virus date = 2009-11-30 pages = extension = .txt mime = text/plain words = 3774 sentences = 202 flesch = 48 summary = Comparison was made between patients with pandemic H1N1 virus and seasonal influenza virus infection regarding their demographics, underlying diseases, presenting symptoms, total white blood cell counts, absolute lymphocyte counts, and initial pre-treatment viral load in respiratory specimens on the day of diagnosis. Among patients with pandemic H1N1 virus infection, the same parameters was compared between those with longer duration (!5 days) and shorter duration ( 4 days) of viral shedding, as defined by the time from onset of symptoms to the last positive sample by RT-PCR. For both pandemic H1N1 cases and seasonal influenza historical controls, respiratory specimens collected on the day of onset of symptoms (day 0) had the highest mean viral load (Fig. 1 ). For patients who presented to hospital between days 0 and 3 after onset of symptoms, the initial pre-treatment viral load in pandemic H1N1 cases was lower than the seasonal influenza historical controls. cache = ./cache/cord-345168-3w32v2fm.txt txt = ./txt/cord-345168-3w32v2fm.txt === reduce.pl bib === id = cord-343350-04e6wvov author = Liu, Haipeng title = Antiviral immunity in crustaceans date = 2009-02-15 pages = extension = .txt mime = text/plain words = 8002 sentences = 441 flesch = 43 summary = White spot syndrome virus (WSSV) infects specific hemocytes of the shrimp Penaeus merguiensis Preliminary study on haemocyte response to white spot syndrome virus infection in black tiger shrimp Penaeus monodon Time-course and levels of apoptosis in various tissues of black tiger shrimp Penaeus monodon infected with white-spot syndrome virus Protein expression profiling of the shrimp cellular response to white spot syndrome virus infection Cloning and characterization of a caspase gene from black tiger shrimp (Penaeus monodon)-infected with white spot syndrome virus (WSSV) Immunological responses of Penaeus monodon to DNA vaccine and its efficacy to protect shrimp against white spot syndrome virus (WSSV) Multiple envelope proteins are involved in white spot syndrome virus (WSSV) infection in crayfish Identification of white spot syndrome virus (WSSV) envelope proteins involved in shrimp infection DNA fragmentation, an indicator of apoptosis, in cultured black tiger shrimp Penaeus monodon infected with white spot syndrome virus (WSSV) cache = ./cache/cord-343350-04e6wvov.txt txt = ./txt/cord-343350-04e6wvov.txt === reduce.pl bib === id = cord-343784-zgvxl4h3 author = Cho, Chi Hyun title = Evaluation of the AdvanSure™ real-time RT-PCR compared with culture and Seeplex RV15 for simultaneous detection of respiratory viruses date = 2014-05-31 pages = extension = .txt mime = text/plain words = 3707 sentences = 204 flesch = 51 summary = Several studies have demonstrated the advantages of multiplex PCR assays such as xTAG RVP, RVP fast (Luminex Molecular Diagnostics, Toronto, ON, Canada), Resplex II (Qiagen, Mississauga, ON, Canada), FilmArray® Respiratory panel (Idaho Technology Inc., Salt Lake City, UT, USA), and Seeplex RV assays (Seegene, Seoul, Korea), which are used routinely for the detection of respiratory viral infection (Bibby et al., 2011; Couturier et al., 2013; Gharabaghi et al., 2011; Kim et al., 2013; Zhang et al., 2012) . In the previous study evaluating Seeplex RV12 detection kit (Seegene, Rockville, MD, USA), viral culture, RV12, and real-time PCR detected 8, 6, and 11 of 11 influenza B-positive specimens, respectively (Bruijnesteijn van Coppenraet et al., 2010) . Simultaneous detection of influenza A, B, and C viruses, respiratory syncytial virus, and adenoviruses in clinical samples by multiplex reverse transcription nested-PCR assay Evaluation of a multiplex real-time PCR assay for the detection of respiratory viruses in clinical specimens cache = ./cache/cord-343784-zgvxl4h3.txt txt = ./txt/cord-343784-zgvxl4h3.txt === reduce.pl bib === id = cord-342906-51296y8d author = Li, Zhiping title = Aerosolized avian influenza virus by laboratory manipulations date = 2012-08-06 pages = extension = .txt mime = text/plain words = 4489 sentences = 230 flesch = 46 summary = Many of the routine procedures used to process influenza virus for laboratory research, such as centrifugation or mixing, have a high potential of producing aerosols [21] , and the particle load of each has been estimated to be up to 1-5 μm. To this end, this study was designed to monitor the presence of aerosolized H5N1 virus produced by normal procedures used to process the virus for experimental research and by the most frequently associated "accidents" for each, such as container breakage and accidental subcutaneous injection. None of the aerosol samples collected from any group at the time directly prior to processing of the experiment had detectable levels of H5N1, as evidenced by negative reverse transcription (Rt)-PCR and HA text results. Our results provide evidence that many of the laboratory techniques used to process influenza virus for experimental analysis produce aerosols and, thereby, represent significant risks of infection to laboratory personnel and potential spread beyond the laboratory. cache = ./cache/cord-342906-51296y8d.txt txt = ./txt/cord-342906-51296y8d.txt === reduce.pl bib === id = cord-345359-okmkgsbr author = Ohno, Marumi title = Influenza virus infection affects insulin signaling, fatty acid-metabolizing enzyme expressions, and the tricarboxylic acid cycle in mice date = 2020-07-02 pages = extension = .txt mime = text/plain words = 6474 sentences = 314 flesch = 45 summary = After infecting mice with intranasal applications of 500 plaque-forming units of A/Puerto Rico/8/34 (H1N1; PR8) virus, the serum levels of most intermediates in the tricarboxylic acid (TCA) cycle and related metabolic pathways were significantly reduced. www.nature.com/scientificreports/ investigated metabolic changes by determining the serum levels of metabolites, insulin sensitivity in the liver, glucose availability, and hepatic gene expressions in the early stages of symptom onset as well as the lethal phase of influenza in a mouse model. The results of this study indicate that influenza virus infection dysregulates glucose and fatty acid metabolism and decreases tricarboxylic acid (TCA) cycle activity, leading to enhanced degradation of adenosine triphosphate (ATP) and guanosine triphosphate (GTP). Metabolites that were present at reduced levels in the sera of PR8 virus-infected mice were mainly related to the TCA cycle, urea cycle, and amino acid metabolism, as indicated by the serum levels of metabolite in these pathways at 1, 3, and 6 dpi (Fig. 2) . cache = ./cache/cord-345359-okmkgsbr.txt txt = ./txt/cord-345359-okmkgsbr.txt === reduce.pl bib === id = cord-345157-fhmhpobi author = Qi, Dan title = Virus infection-induced host mRNA degradation and potential application of live cell imaging date = 2018-12-12 pages = extension = .txt mime = text/plain words = 2619 sentences = 158 flesch = 49 summary = Herein, we focus on several possible mechanisms of infection-induced host RNA turnover, which seems to be a common strategy for both prokaryotic and eukaryotic viruses during the very early stage of infection and a potential application of live cell imaging on its visualization. Many viruses also impair the translation of cellular mRNA [1e3], one of the mechanisms during the shift of gene expression from host to virus, a process termed "host shutoff", in order to prevent the production of anti-viral, host protecting proteins [4] . Moreover, Gaglia et al.'s work showed that viral encoded proteins trigger host mRNA degradation by a primary endonucleolytic cleavage causing shutoff of host gene expression and a host exonuclease such as Xrn1, an important 5 0 to 3 0 exonuclease in human cells, were required in subsequent completion of host mRNA turnover [5] . cache = ./cache/cord-345157-fhmhpobi.txt txt = ./txt/cord-345157-fhmhpobi.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-344749-omzhhr0k author = Kaya, Sariye Irem title = Electrochemical virus detections with nanobiosensors date = 2020-02-14 pages = extension = .txt mime = text/plain words = 8402 sentences = 508 flesch = 37 summary = Cell culture-based virus isolation has been accepted as a "gold standard" in the detection and identification of viruses and is the technique by which all other test methods have been compared [35] . A novel method for dengue virus detection and antibody screening using a graphene-polymer based electrochemical biosensor Chitosan-carbon nanofiber modified single-use graphite electrodes developed for electrochemical detection of DNA hybridization related to hepatitis B virus A sensitive electrochemical biosensor for specific DNA sequence detection based on flower-like VS2, graphene and Au nanoparticles signal amplification Electrochemical DNA biosensor based on a tetrahedral nanostructure probe for the detection of avian influenza A (H7N9) virus Electrochemical DNA biosensor based on gold nanorods for detecting hepatitis B virus Electrochemical-DNA biosensor development based on a modified carbon electrode with gold nanoparticles for influenza a (H1N1) detection: effect of spacer Magnetic nanoparticle-based immunosensor for electrochemical detection of hepatitis B surface antigen cache = ./cache/cord-344749-omzhhr0k.txt txt = ./txt/cord-344749-omzhhr0k.txt === reduce.pl bib === id = cord-341324-f9g9gitn author = Rojas, José M. title = Viral pathogen-induced mechanisms to antagonize mammalian interferon (IFN) signaling pathway date = 2020-10-21 pages = extension = .txt mime = text/plain words = 10837 sentences = 595 flesch = 42 summary = This includes for instance cooperating in PRR recognition of viral PAMPs, stabilizing signaling complexes to improve their resistance to degradation, stopping virus entry, blocking viral capsid formation, impairing trafficking and budding of virions from the infected cells, but also modulating the IFN response to avoid the toxicity of these potent immune mediators. The phosphorylated STAT1/STAT2 heterodimer associates with interferon regulatory factor 9 (IRF9) to form the transcriptional factor complex ISGF3, which translocate to the nucleus and binds the IFN-response elements (ISRE) in ISG promoters leading to the expression of ISG products [36] (Fig. 2 The oligoadenylate synthetase (OAS)-latent RNase (RNase L) pathway is another IFN-inducible pathway that provides the cell with an effector mechanism upon recognition of viral dsRNA (reviewed in [44] ). cache = ./cache/cord-341324-f9g9gitn.txt txt = ./txt/cord-341324-f9g9gitn.txt === reduce.pl bib === id = cord-344782-ond1ziu5 author = Zhang, Jing title = Identification of a novel nidovirus as a potential cause of large scale mortalities in the endangered Bellinger River snapping turtle (Myuchelys georgesi) date = 2018-10-24 pages = extension = .txt mime = text/plain words = 6003 sentences = 280 flesch = 49 summary = Nucleic acid sequencing of the virus isolate has identified the entire genome and indicates that this is a novel nidovirus that has a low level of nucleotide similarity to recognised nidoviruses. Following the detection of the novel virus, in November 2015 (about 6 months after the cessation of the outbreak) an intensive survey of the parts of the river where affected turtles had been detected [2] was undertaken by groups of biologists and ecologists and samples collected from a wide range of aquatic species and some terrestrial animals (n = 360) to establish the size of the remaining population and whether any other animals were carrying this virus. BRV, as a novel nidovirus, was isolated from tissues of diseased animals, very high levels of viral RNA were detected in tissues with marked pathological changes and in situ hybridisation assays demonstrated the presence of specific viral RNA in lesions in kidneys and eye tissue-two of the main affected organs. cache = ./cache/cord-344782-ond1ziu5.txt txt = ./txt/cord-344782-ond1ziu5.txt === reduce.pl bib === id = cord-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-343963-99rd3o79 author = Wong, Mun-Teng title = Emerging roles of interferon-stimulated genes in the innate immune response to hepatitis C virus infection date = 2014-12-29 pages = extension = .txt mime = text/plain words = 17253 sentences = 1074 flesch = 42 summary = 13, 14 Upon infection by viruses such as HCV, viral RNA is first sensed by cellular pattern recognition receptors (PRRs), and the PRR-mediated recruitment of adaptor proteins and the activation of downstream signaling lead to IFN production. First, we briefly discuss the signaling triggered by the retinoic acid-inducible gene 1-like receptor (RLR) and the Toll-like receptor (TLR), which leads to type I IFN synthesis and IFN-mediated signaling pathway activation, resulting in the expression of a variety of effector ISGs. We also summarize the strategies that HCV uses to escape IFN antiviral surveillance. 156 demonstrated that HCVinduced SG formation is IFN-and PKR-dependent and is inversely correlated with the induction of ISG proteins, such as myxovirus resistance gene A (MxA) and Ub-like (UBL)specific protease 18 (USP18), in HCV-infected cells without affecting the mRNA levels of these ISGs. Furthermore, the SG proteins TIA-1, TIAR and G3BP1 have been shown to play a critical role in HCV replication and infectious virus production. cache = ./cache/cord-343963-99rd3o79.txt txt = ./txt/cord-343963-99rd3o79.txt === reduce.pl bib === id = cord-344576-upsc9cf8 author = Taylor-Robinson, Andrew W title = A vaccine effective against Zika virus is theoretically possible but may not be delivered anytime soon date = 2016-07-05 pages = extension = .txt mime = text/plain words = 2604 sentences = 154 flesch = 52 summary = In February this year, the World Health Organization declared that further to the then unconfirmed association between the virus and the clinical manifestations of microcephaly and also Guillain-Barré syndrome, the Zika epidemic was a "public health emergency of international concern". No anti-Zika therapy, vaccine or drug, is currently available and while the production of the former has now been prioritized by multiple funding agencies, the history of infectious disease vaccine development indicates that this may take several years to reach the market place. A more rapid spread of the virus via the intercontinental travel of infected persons is an additional concern, although for Zika to become established in a location distant to an endemic area requires local transmission of the initially imported focus of infection; this is dependent on the availability of the vector. Local transmission of Zika virus infection is possible in Australia but should be contained by current vector control measures cache = ./cache/cord-344576-upsc9cf8.txt txt = ./txt/cord-344576-upsc9cf8.txt === reduce.pl bib === id = cord-344093-3bniy5b5 author = Peteranderl, Christin title = The Impact of the Interferon/TNF-Related Apoptosis-Inducing Ligand Signaling Axis on Disease Progression in Respiratory Viral Infection and Beyond date = 2017-03-22 pages = extension = .txt mime = text/plain words = 12546 sentences = 578 flesch = 34 summary = A prominent regulator of disease outcome, especially in-but not limited to-respiratory viral infection, is the IFN-dependent mediator TRAIL (TNF-related apoptosis-inducing ligand) produced by several cell types including immune cells such as macrophages or T cells. (73) Cell death induction, e.g., Bcl-2-associated X protein, caspase-8, Fas-associated protein with death domain, Fas ligand, and TNF-related apoptosis-inducing ligand (TRAIL) dsRNA, polyI:C (4, 110) IAV (4, 5, 10, 115) Sendai virus (110) TRAIL Virus control by apoptosis induction in infected cells IAV (6, 170, 171) Tissue injury by apoptosis of both infected and non-infected alveolar epithelial cells, lung macrophages IAV (5, 7, 10) RSV (137) Necrosis of fibroblasts, dendritic cells, and epithelial cells IAV (146, 147, 168) Increased cellular infiltration CoV (175) Decreased expression of Na,K-ATPase, impaired epithelial fluid reabsorption IAV (11) iNTRODUCTiON In 1957, Isaacs and Lindenmann (1) first recognized the potential of a soluble and probably cell-derived factor to combat influenza virus infection and named this factor interferon [(IFN) from latin interferre, to interfere]. cache = ./cache/cord-344093-3bniy5b5.txt txt = ./txt/cord-344093-3bniy5b5.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-343347-guciupc8 author = Hajj Hussein, Inaya title = Vaccines Through Centuries: Major Cornerstones of Global Health date = 2015-11-26 pages = extension = .txt mime = text/plain words = 12280 sentences = 573 flesch = 47 summary = Consequently, this work tried to put together the major achievements through history stressing the importance, continuous vital role, and the need for immunization for health prevention and protection as well as its impact on human experience. A few years later, word of his success circulated among the public, and Jenner wrote "An Inquiry into the Causes and Effects of the Variolae Vaccinae, a Disease Discovered in some of the Western Counties of England, particularly Gloucestershire and Known by the Name of CowPox, " after adding several cases to his initial achievement with the boy Phipps. Takahashi was able to make this remarkable advance at a time when very few viruses had been attenuated to produce efficacious live-virus vaccines including yellow fever, polio, measles, mumps, and rubella as previously mentioned. As a result of these successful trials, the live varicella virus vaccine (Varivax) was licensed in 1995 for the active immunization of persons 12 months of age and older (51) . cache = ./cache/cord-343347-guciupc8.txt txt = ./txt/cord-343347-guciupc8.txt === reduce.pl bib === id = cord-345020-ai5tib7h author = Price, O. H. title = Using routine testing data to understand circulation patterns of influenza A, respiratory syncytial virus and other respiratory viruses in Victoria, Australia date = 2019-06-17 pages = extension = .txt mime = text/plain words = 4186 sentences = 211 flesch = 40 summary = Studies investigating viral interference since the pandemic are sparser, though two studies reported that the timing and magnitude of respiratory virus epidemics were affected by the timing of the seasonal influenza A peak [15, 16] . We used routine diagnostic testing data of specimens from both the community and hospitals at the Victorian Infectious Diseases Reference Laboratory (VIDRL) between 2002 and 2017 to describe relationships between respiratory viruses, with a focus on influenza A and RSV. Seasonality of viruses was assessed visually by time series analysis and for further investigation each virus was compared with influenza A and RSV using cross-correlations that estimated the association between peaks in epidemic curves at a lag or lead of up to 15 weeks. Results of further investigation by logistic regression adjusted for covariates that are predictors of codetection (sex, age and season) were compatible with influenza A, RSV and picornavirus conferring temporary immunity against infection by another respiratory virus. cache = ./cache/cord-345020-ai5tib7h.txt txt = ./txt/cord-345020-ai5tib7h.txt === reduce.pl bib === id = cord-346836-6jyv0q5e author = Ikegami, Tetsuro title = The Pathogenesis of Rift Valley Fever date = 2011-05-06 pages = extension = .txt mime = text/plain words = 10419 sentences = 483 flesch = 46 summary = RVFV infection in humans usually causes a self-limiting, acute and febrile illness; however, a small number of cases progress to neurological disorders, partial or complete blindness, hemorrhagic fever, or thrombosis. This review describes the pathology of RVF in human patients and several animal models, and summarizes the role of viral virulence factors and host factors that affect RVFV pathogenesis. RVFV infection in humans primarily causes a self-limiting febrile illness; however, some patients develop hemorrhagic fever, neurological disorders, or blindness after the febrile period [5, 7, 8] . Inbred rat strains mimic the disparate human response to rift valley fever virus infection Clinical, virological and serological response of the west african dwarf sheep to experimental infection with different strains of rift valley fever virus cache = ./cache/cord-346836-6jyv0q5e.txt txt = ./txt/cord-346836-6jyv0q5e.txt === reduce.pl bib === id = cord-343918-5yk1j4ms author = Gorbalenya, A.E. title = Phylogeny of Viruses date = 2008-07-30 pages = extension = .txt mime = text/plain words = 3892 sentences = 182 flesch = 40 summary = For inferring phylogeny, the differences between aligned sequences of genomes and proteins are quantified and depicted in the form of a tree, in which contemporary species and their intermediate and common ancestors occupy, respectively, the terminal nodes, internal nodes, and the root. Phylogenetic analysis is used in a wide range of studies to address both applied and fundamental issues of virus research, including epidemiology, diagnostics, forensic studies, phylogeography, origin, evolution, and taxonomy of viruses. With the latter virus, poor sampling of the coronavirus diversity in the SARS-CoV lineage at the time, some uncertainty over the relationship between phylogeny and taxonomy of coronaviruses, and the complexity of phylogenetic analysis of a virus data set including isolated distant lineages led to considerable controversy over the exact evolutionary position of SARS-CoV among coronaviruses. cache = ./cache/cord-343918-5yk1j4ms.txt txt = ./txt/cord-343918-5yk1j4ms.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-346853-0c1qdjb5 author = Holmes, E. C. title = The Evolutionary Genetics of Viral Emergence date = 2007 pages = extension = .txt mime = text/plain words = 6123 sentences = 261 flesch = 45 summary = Despite the wealth of data describing the ecological factors that underpin viral emergence, little is known about the evolutionary processes that allow viruses to jump species barriers and establish productive infections in new hosts. We also emphasize the current lack of convincing data as to whether viral emergence requires adaptation to the new host species during the early stages of infection, or whether it is largely a chance process involving the transmission of a viral strain with the necessary genetic characteristics. For example, one model of viral emergence posits that adaptation to a new host species during the early period of an epidemic is of fundamental importance, because this raises the basic reproductive rate of the virus, R 0 , to greater than 1, so that sustained transmission networks can be established (Anita et al. cache = ./cache/cord-346853-0c1qdjb5.txt txt = ./txt/cord-346853-0c1qdjb5.txt === reduce.pl bib === id = cord-346906-1wmp43ti author = Lewandowski, Kuiama title = Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples date = 2019-12-23 pages = extension = .txt mime = text/plain words = 6766 sentences = 328 flesch = 43 summary = We determine its sensitivity compared to that of existing diagnostic methods and its accuracy compared to short-read (Illumina) sequencing, using clinical samples from hospital patients during an influenza season and samples from a controlled laboratory infection in ferrets. During the study, respiratory samples submitted to the clinical diagnostic laboratory were routinely tested by a PCR-based test using the GeneXpert assay (Cepheid) to detect influenza A and B viruses and respiratory syncytial virus (RSV). Comparing this final method with our original protocol, using triplicate extractions from the pooled set of influenza A virus-positive samples demonstrated no significant loss in performance in the more rapid protocol (Fig. S3) , and we adopted this approach as our routine protocol, giving a wet-lab processing time of ϳ8 h. Future application of this method will involve real-time laboratory testing of respiratory samples, running the platform head to head with existing clinical diagnostics to further assess sensitivity and specificity, and using influenza virus sequence data to investigate transmission events. cache = ./cache/cord-346906-1wmp43ti.txt txt = ./txt/cord-346906-1wmp43ti.txt === reduce.pl bib === id = cord-347577-p0a2rboi author = Bibby, Kyle title = Persistence of Ebola Virus in Sterilized Wastewater date = 2015-08-17 pages = extension = .txt mime = text/plain words = 3216 sentences = 182 flesch = 46 summary = The subsequent viral titer decrease was less rapid, and infectious Ebola virus particles persisted for all 8 days of the test. 17, 18 In response to the EVD epidemic, both the World Health Organization (WHO) and the U.S. Centers for Disease Control and Prevention advised direct disposal of Ebola-contaminated liquid waste into sewage systems (wastewater collection and treatment systems) and latrines without disinfection. A current Ebola virus outbreak strain from Guinea (Makona-WPGC07) was spiked to two end concentrations (10 2 and 10 6 TCID 50 mL −1 ) into a domestic wastewater (untreated sewage) sample. Microbial activity within wastewater matrices would be expected to contribute to more rapid inactivation of infectious viral particles; 36, 42 however, the true effect of microbial activity on Ebola virus persistence is unknown. 34 Further assessment is necessary to determine Ebola inactivation and dilution within this period and potential human exposure routes, including workers within the sewer system and Ebola virus persistence within wastewater sludges. cache = ./cache/cord-347577-p0a2rboi.txt txt = ./txt/cord-347577-p0a2rboi.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-342124-jdv17u86 author = Nieto‐Rabiela, Fabiola title = Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis date = 2019-06-20 pages = extension = .txt mime = text/plain words = 4447 sentences = 264 flesch = 51 summary = title: Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis To address this gap in knowledge, we compared the associative capacity of the host–virus networks in rodents and bats with the identification of those viruses with zoonotic potential. (2015) analyse viral networks between rodents and bats at global scale identifying several ecology factors to explain virus-host associations. The parameter "betweenness" can be used to Impacts • The analysis of virus and host networks (rodents and bats) allows us to measure the potential risk of zoonotic diseases. • Measuring network connectivity can be a useful tool for identifying hosts and viruses of potential importance in the transmission dynamic of zoonotic diseases. Therefore, in this study we aimed to compare and recognize the differences in the associative capacity of the host-virus networks in rodents and bats worldwide, as well as to identify the viruses that may shift across species, including humans, suggesting zoonotic potential. cache = ./cache/cord-342124-jdv17u86.txt txt = ./txt/cord-342124-jdv17u86.txt === reduce.pl bib === id = cord-346904-aa88gtzr author = Bao, Y. title = Virus Classification by Pairwise Sequence Comparison (PASC) date = 2008-07-30 pages = extension = .txt mime = text/plain words = 3831 sentences = 207 flesch = 50 summary = Pairwise sequence comparison (PASC) is a molecular classification tool for viruses. It calculates the pairwise identities of virus sequences within a virus family and displays their distributions, and can help determine demarcations at different taxonomic levels such as strain, species, genus, and subfamily levels. In the PASC system, pairwise global alignment is performed on complete genomes or particular protein sequences for each viral family, and their percentage of identity is calculated. For those virus families that are suitable for PASC analyses, demarcations can be easily determined and new viruses can be clearly placed into the correct taxonomy. PASC is a molecular classification tool for many virus families. It calculates the pairwise identities of virus sequences within a virus family and displays their distributions, and can help determine the demarcations at strains, species, genera, and subfamilies level. cache = ./cache/cord-346904-aa88gtzr.txt txt = ./txt/cord-346904-aa88gtzr.txt === reduce.pl bib === id = cord-348876-v55piprx author = Zhao, Guangyu title = An M2e-based multiple antigenic peptide vaccine protects mice from lethal challenge with divergent H5N1 influenza viruses date = 2010-01-18 pages = extension = .txt mime = text/plain words = 3571 sentences = 185 flesch = 49 summary = In the present study, we designed a tetra-branched multiple antigenic peptide (MAP)-based vaccine, designated M2e-MAP, which contains the sequence overlapping the highly conserved extracellular domain of matrix protein 2 (M2e) of a HPAI H5N1 virus, and investigated its immune responses and cross-protection against different clades of H5N1 viruses. In the present study, we designed and synthesized a tetra-branched multiple antigenic peptide (MAP) derived from the M2e sequence of H5N1 virus VN/1194 strain, denoted as M2e-MAP, with an aim to develop a M2e-based vaccine for induction of M2e-specific immune responses and cross-protection of the vaccinated animals against lethal challenge of divergent H5N1 virus strains. After receiving the lethal dose (10 LD 50 ) of two H5N1 virus strains, the M2e-MAP vaccinated mice were further evaluated in terms of cross-protective ability by daily observation of the clinical symptoms, including weight loss and survival rate for two weeks, and then histopathological examination following removal of lung tissues. cache = ./cache/cord-348876-v55piprx.txt txt = ./txt/cord-348876-v55piprx.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-348141-eskefcwk author = Herrington, CS title = Viruses and disease: emerging concepts for prevention, diagnosis and treatment date = 2014-12-11 pages = extension = .txt mime = text/plain words = 2120 sentences = 93 flesch = 41 summary = Articles on emerging diseases caused by Ebola virus, Marburg virus, coronaviruses such as SARS and MERS, Nipah virus and noroviruses are followed by reviews of enteroviruses, HIV infection, measles, mumps, human respiratory syncytial virus (RSV), influenza, cytomegalovirus (CMV) and varicella zoster virus (VZV). The issue concludes with a series of articles reviewing the relationship between viruses and cancer, including the role played by Epstein–Barr virus (EBV) in the pathogenesis of lymphoma and carcinoma; how human papillomaviruses (HPVs) are involved in the development of skin cancer; the involvement of hepatitis B virus infection in hepatocellular carcinoma; and the mechanisms by which Kaposi's sarcoma‐associated herpesvirus (KSHV) leads to Kaposi's sarcoma. Nevertheless, in this new era, pathology will continue to be a vital component of identifying the true relationships between viruses and human disease, and we hope that this Annual Review Issue will serve as a blueprint for future studies in the diagnosis, treatment and prevention of virus-related conditions through an improved understanding of the processes involved. cache = ./cache/cord-348141-eskefcwk.txt txt = ./txt/cord-348141-eskefcwk.txt === reduce.pl bib === id = cord-348860-zaimorg0 author = Ratra, Ruchi title = Functional genomics as a tool in virus research date = 2008-06-01 pages = extension = .txt mime = text/plain words = 3379 sentences = 171 flesch = 39 summary = The genomics era has revolutionized the biological sciences and has heralded the emergence of new 'omics' methodologies such as transcriptomics (study of the gene expression and expression levels of mRNAs at a given time and condition), proteomics (study of the entire protein content of a cell/tissue under various conditions, their structure and functions), metabolomics (study of the metabolite profi le of different cellular processes), phosphoproteomics (a branch of proteomics that characterizes proteins that are phosphorylated), interactomics/system biology (a science that unifi es transcriptomics, proteomics and metabolomics to look at the organism as a whole) and so on. DNA microarrays, proteomics and bioinformatic analysis are routinely used to analyze changes in host and viral gene and protein expression that occur in a virus infected cell [25] . cache = ./cache/cord-348860-zaimorg0.txt txt = ./txt/cord-348860-zaimorg0.txt === reduce.pl bib === id = cord-348161-757c51xw author = Petrosova, A. title = Development of a highly sensitive, field operable biosensor for serological studies of Ebola virus in central Africa date = 2007-03-26 pages = extension = .txt mime = text/plain words = 5428 sentences = 264 flesch = 48 summary = We employed a photo immobilization methodology based on a photoactivatable electrogenerated poly(pyrrole-benzophenone) film deposited upon an indium tin oxide (ITO) modified conductive surface fiber-optic. The photochemically modified optical fibers were tested as an immunosensor for detection of antibodies against Ebola virus, in animal and human sera, by use of a coupled chemiluminescent reaction. In this study we present a newly developed optical immunosensor for detection of antibodies to Ebola virus strains Zaire and Sudan, by using a photoimmobilization methodology based on a photoactivable electrogenerated polymer film. The optical fibers coated with poly(pyrrole-benzophenone) were soaked in diluted solution containing inactivated Ebola virus antigen (approximately 7.5 g/ml, the concentration was determined by Micro BCA Protein assay kit, PIERCE) and irradiated with UV light. The calibration curve obtained from the optical fiber immunosensor and ELISA for the detection of anti-Ebola subtype Zaire antibodies. cache = ./cache/cord-348161-757c51xw.txt txt = ./txt/cord-348161-757c51xw.txt === reduce.pl bib === id = cord-348427-worgd0xu author = Hatcher, Eneida L. title = Virus Variation Resource – improved response to emergent viral outbreaks date = 2017-01-04 pages = extension = .txt mime = text/plain words = 5552 sentences = 258 flesch = 48 summary = The resource now includes expanded data processing pipelines and analysis tools, and supports selection and retrieval of nucleotide and protein sequences from four new viral groups: Ebolaviruses, MERS coronavirus, rotavirus, and Zika virus ( Table 2 ). New processes have been added to parse source descriptor terms from Gen-Bank records and map these to controlled vocabulary, and the resource now supports retrieval of sequences based on standardized isolation source and host terms in addition to standardized gene and protein names. The resource includes data processing pipelines that retrieve sequences from GenBank, provide standardized gene and protein an-notation, and map sequence source descriptors (i.e. metadata) to uniform vocabularies. To resolve this issue, the Virus Variation database loading pipeline parses Gen-Bank records, identifies important metadata terms, such as sample isolation host, date, country and source, and maps these to a standardized vocabulary using a hierarchical approach. cache = ./cache/cord-348427-worgd0xu.txt txt = ./txt/cord-348427-worgd0xu.txt === reduce.pl bib === id = cord-348163-9q1rt8i7 author = Hussein, Hosni A. M. title = Beyond RGD: virus interactions with integrins date = 2015-09-01 pages = extension = .txt mime = text/plain words = 5945 sentences = 301 flesch = 36 summary = Integrins are a family of receptor molecules that serve as entry receptors for a variety of different viruses, including foot-and-mouth disease virus (FMDV) [97] , Kaposi's sarcoma-associated herpesvirus (KSHV) [5], herpes simplex virus-2 (HSV-2) [31], adenovirus [168] , human papillomavirus-16 (HPV-16) [3] , reovirus [40] , and others. On the other hand, interactions of viruses with cellular integrins induce conformational changes in the viral surface proteins, helping to expose the essential domains required for virus entry into a host cell [107] . Similarly, several human herpesviruses, including HSV [147] , KSHV [4], and CMV [93] , make their initial contact with cells by binding to cellsurface HSPGs. In general, binding of viruses to carbohydrate moieties on the surface of cells is the key step that induces conformational changes in the viral structure that are critical for interactions with entry-promoting receptors such as integrins. cache = ./cache/cord-348163-9q1rt8i7.txt txt = ./txt/cord-348163-9q1rt8i7.txt === reduce.pl bib === id = cord-346063-7u1a198p author = De Clercq, Erik title = Avian influenza A (H5N1) infection: targets and strategies for chemotherapeutic intervention date = 2007-05-04 pages = extension = .txt mime = text/plain words = 3496 sentences = 184 flesch = 42 summary = We have recently reviewed the antiviral agents that are active against influenza viruses and that could be used, either therapeutically and/or prophylactically, in an influenza virus pandemic, whether it be human, avian, equine, porcine or other [1] . Even if based only on the currently available drugs, there are several double-, tripleand quadruple-drug combinations that could be envisaged for the prevention and treatment of avian H5N1 (Figure 3 ) -including the combination of oseltamivir and zanamivir (because their resistance profiles overlap only partially), the combination of these neuraminidase inhibitors with M2 ion channel blockers, and further extension of these combinations to include pegylated interferon and ribavirin. In addition to viral RNA polymerase and/or endonuclease, mentioned earlier as potential targets for new anti-influenza-virus agents, there are some other clues regarding the virulence of H5N1 viruses in humans [41] that could be considered as points of attack for chemotherapeutic intervention. cache = ./cache/cord-346063-7u1a198p.txt txt = ./txt/cord-346063-7u1a198p.txt === reduce.pl bib === id = cord-349225-504kr50e author = Alcami, Antonio title = Viral mechanisms of immune evasion date = 2000-09-01 pages = extension = .txt mime = text/plain words = 3610 sentences = 188 flesch = 44 summary = Viruses such as HIV, human cytomegalovirus (HCMV) and vaccinia virus (VV) utilize a clever strategy, 'borrowing' host cellular factors, including CD59, which normally protects cells from complement lysis, and incorporating them into the viral envelope. Additionally, several viruses inhibit the activity of IFN-␥, a key activator of cellular immunity, by blocking the synthesis or activity of factors required for its production, such as interleukin (IL)-18 or IL-12 (Table 4 ): CPV cytokine response modifier (Crm A) inhibits caspase-1, which processes the mature forms of IL-1␤ and IL-18 (Refs 2,6); various poxviruses encode soluble IL-18binding proteins (IL-18BPs) [8] [9] [10] ; measles virus (MeV) binds CD46 in macrophages and inhibits IL-12 production 1 ; and herpesviruses and poxviruses express IL-10 homologs that diminish the Th1 response by downregulating the production of IL-12 (Refs 1,11,12). cache = ./cache/cord-349225-504kr50e.txt txt = ./txt/cord-349225-504kr50e.txt === reduce.pl bib === id = cord-346916-jj4l9ydl author = Girardi, Erika title = Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell date = 2020-08-23 pages = extension = .txt mime = text/plain words = 13119 sentences = 728 flesch = 45 summary = Moreover, despite the molecular mimicry set by RNA viruses to resemble cellular mRNAs and escape host recognition, the viral nucleic acid still needs to embark on a long journey through a hostile cell environment and must overcome the obstacles put in place by the host antiviral system in order to be translated and replicated. Another example, is the zinc-finger antiviral protein (ZAP), which binds vRNAs containing a ZAP response element (ZRE) and induces RNA degradation via interaction of its N-terminal domain with host decay machinery mediated [75] (Fig. 1 ). In fact, IRES elements present in the genome of different families of RNA viruses lack overall conserved features [146, 147] .The classification of viral IRESs in four types stems from their structural organization, their respective dependence on sets of translation initiation factors, and whether they use scanning or instead directly recruit ribosomes to the start codon [148] (Fig. 2) . cache = ./cache/cord-346916-jj4l9ydl.txt txt = ./txt/cord-346916-jj4l9ydl.txt === reduce.pl bib === id = cord-348867-c0xpzd4d author = Zhai, Jun-Qiong title = First complete genome sequence of parainfluenza virus 5 isolated from lesser panda date = 2017-01-30 pages = extension = .txt mime = text/plain words = 1980 sentences = 117 flesch = 54 summary = In this study, a PIV5 variant (named ZJQ-221) was isolated from a lesser panda with respiratory disease in Guangzhou zoo in Guangdong province, southern China. Sequence alignment and genetic analysis revealed that ZJQ-221 shared a close relationship with a PIV5 strain of canine-origin (1168-1) from South Korea. In this study, a novel variant of PIV5 (designated as ZJQ-221) was isolated from a lesser panda with respiratory disease in Guangzhou zoo in Guangdong province, southern China. Fourteen samples were tested for the possible presence of three respiratory-related pathogens (including PIV5, canine distemper virus, and coronavirus) by RT-PCR according to previous studies [27, 28] . In summary, we have identified a novel PIV5 isolate in lesser panda and performed whole genome sequencing, indicating that this mammal may act as a possible natural reservoir for this virus. The complete genome sequencing and analysis of canine parainfluenza virus strain CC-14 cache = ./cache/cord-348867-c0xpzd4d.txt txt = ./txt/cord-348867-c0xpzd4d.txt === reduce.pl bib === id = cord-349249-jwvz1ux2 author = Singh, Gagandeep title = A Minimally Replicative Vaccine Protects Vaccinated Piglets Against Challenge With the Porcine Epidemic Diarrhea Virus date = 2019-10-22 pages = extension = .txt mime = text/plain words = 6553 sentences = 314 flesch = 46 summary = To combine the safety and efficacy advantages of inactivated and attenuated PEDV vaccines, respectively, in this study, we tested the hypothesis that subjecting PEDV virions to heat treatment at 44°C for 10 min to reversibly unfold structural proteins, followed by exposure to RNAse to fragment the genome, would result in a vaccine preparation with intact viral structure/antigenicity but highly diminished replicative abilities. to that of the spike protein-specific Abs. Strong virus neutralizing Ab responses, were detected in animals vaccinated with the heat and RNAse treated virions but not in the pigs which received the irradiated viral vaccine. Although the heat and RNAse treated virus culture was amplified after 3 passages in cell culture (Figure 2) , the absence its detection by RT-qPCR (Figure 4) , or immunohistochemistry (Table 1 and Figure 5 ) and the lack of strong Ab responses to the non-structural NP (Figure 3) , in vaccinated pigs prior to challenge indicates that active vaccine viral replication was absent in the host or was undetectable by the techniques used. cache = ./cache/cord-349249-jwvz1ux2.txt txt = ./txt/cord-349249-jwvz1ux2.txt === reduce.pl bib === id = cord-345654-vyz6f3he author = Dennehy, John J. title = Evolutionary ecology of virus emergence date = 2016-12-30 pages = extension = .txt mime = text/plain words = 11475 sentences = 701 flesch = 43 summary = Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between‐host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between‐host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead‐end spillover infections. Virus quasispecies may facilitate host range expansion Viruses are among the smallest nucleic acid-based replicating entities and possess characteristics associated with exceptionally fast evolutionary change: small genomes, short generation times, high mutation rates, large population sizes, high levels of genetic diversity, and strong selection pressures. cache = ./cache/cord-345654-vyz6f3he.txt txt = ./txt/cord-345654-vyz6f3he.txt === reduce.pl bib === id = cord-345848-s84lxe6l author = Everitt, Aaron R. title = IFITM3 restricts the morbidity and mortality associated with influenza date = 2012-03-25 pages = extension = .txt mime = text/plain words = 4570 sentences = 278 flesch = 52 summary = We find that a statistically significant number of hospitalized subjects show enrichment for a minor IFITM3 allele (SNP rs12252-C) that alters a splice acceptor site, and functional assays show the minor CC genotype IFITM3 has reduced influenza virus restriction in vitro. We find that a statistically significant number of hospitalised subjects show enrichment for a minor IFITM3 allele (SNP rs12252-C) that alters a splice acceptor site, and functional assays show the minor CC genotype IFITM3 has reduced influenza virus restriction in vitro. Given the higher viral load in Ifitm3 −/− mice and increased replication of influenza A virus in Ifitm3 deleted cells in vitro (Fig. 1d) , we examined both viral nucleic acid and protein distribution in the lung. Analysis of cell populations resident in the lung tissue on day 6 post-infection showed that Ifitm3 −/− mice displayed significantly reduced proportions of CD4+ (p=0.004) and CD8+ Tcells (p=0.02) and natural killer (NK) cells (p=0.0001) but an elevated proportion of neutrophils (p=0.007) (Fig. 3a) . cache = ./cache/cord-345848-s84lxe6l.txt txt = ./txt/cord-345848-s84lxe6l.txt === reduce.pl bib === id = cord-345689-5ns1onkw author = Kusters, Inca C. title = Manufacturing Vaccines for an Emerging Viral Infection–Specific Issues Associated with the Development of a Prototype SARS Vaccine date = 2009-01-30 pages = extension = .txt mime = text/plain words = 6218 sentences = 287 flesch = 42 summary = Taking into account all the uncertainties and anticipating the worst-case scenario, many laboratories and vaccine manufacturers started working on a vaccine approach against SARS infection, largely based on what was known from animal CoVs. In this chapter, we will discuss the necessity for international cooperation and the importance of discretionary funding for rapidly developing a prototype vaccine candidate. When the laboratory work on the SARS-CoV vaccine development started, no data were available on the inactivation characteristics of the virus. The results from the experiments performed to evaluate the viral loss of the SARS-CoV due to drying on glass surface were also surprising: 35 -42 days were necessary to inactivate the virus to the detection limit of the technique. Based on our experience to date, the inactivated, adjuvanted SARS-CoV prototype vaccine seems to be a good candidate for further evaluation in Phase 1 studies. cache = ./cache/cord-345689-5ns1onkw.txt txt = ./txt/cord-345689-5ns1onkw.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-347727-wka9q98s author = Vong, Sirenda title = Assessment of Ebola virus disease preparedness in the WHO South-East Asia Region date = 2016-12-01 pages = extension = .txt mime = text/plain words = 4899 sentences = 266 flesch = 46 summary = OBJECTIVE: To conduct assessments of Ebola virus disease preparedness in countries of the World Health Organization (WHO) South-East Asia Region. 2 In January 2015, nine of the 11 countries from the WHO South-East Asia Region agreed to a joint assessment by WHO and ministries of health of their preparedness and operational readiness for Ebola virus disease. Each assessment component comprised several Objective To conduct assessments of Ebola virus disease preparedness in countries of the World Health Organization (WHO) South-East Asia Region. However, only seven of the countries had developed a specific, written Ebola virus disease preparedness plan (task A1), including four that had detailed a risk-based approach and some level of linkage with their pandemic influenza preparedness plans. Our review showed that risk assessment (i.e. evaluating the likelihood of Ebola virus disease being imported or introduced into a non-affected country) had been formally or informally conducted in six countries (Bhutan, Indonesia, Maldives, Sri Lanka, Thailand and Timor-Leste). cache = ./cache/cord-347727-wka9q98s.txt txt = ./txt/cord-347727-wka9q98s.txt === reduce.pl bib === id = cord-344970-ud1lhkyi author = Fecchi, Katia title = Coronavirus Interplay With Lipid Rafts and Autophagy Unveils Promising Therapeutic Targets date = 2020-08-11 pages = extension = .txt mime = text/plain words = 5433 sentences = 276 flesch = 43 summary = Lipid rafts are specialized plasma membrane microdomains involved in important processes of the virus infections and of the host target cells (Rosenberger et al., 2000) . This minireview reports on the available knowledge about the interplay between coronaviruses, including the SARS-CoV-2, with lipid rafts and autophagic pathways, in order to focus the attention to novel potential targets to inhibit coronavirus infections. As outlined in this review, lipid rafts and autophagic pathways play a pivotal role in coronavirus infection, being critical for viral entry and replication, as well as for viral release from the host cells. In fact, different drugs described as inhibitors or inducers of the autophagy that control host cell pathways process involved in coronavirus infection, have sparked interest for their potential antiviral activity (Shakya et al., 2018; Liu et al., 2019; Xu et al., 2020; Yang et al., 2020 ; Table 1 ). cache = ./cache/cord-344970-ud1lhkyi.txt txt = ./txt/cord-344970-ud1lhkyi.txt === reduce.pl bib === id = cord-349011-kxhpdvri author = Grandvaux, Nathalie title = CSV2018: The 2nd Symposium of the Canadian Society for Virology date = 2019-01-18 pages = extension = .txt mime = text/plain words = 8844 sentences = 375 flesch = 42 summary = Invited keynote speakers included David Kelvin (Dalhousie University and Shantou University Medical College) who provided a historical perspective on influenza on the 100th anniversary of the 1918 pandemic; Sylvain Moineau (Université Laval) who described CRISPR-Cas systems and anti-CRISPR proteins in warfare between bacteriophages and their host microbes; and Kate O'Brien (then from Johns Hopkins University, now relocated to the World Health Organization where she is Director of Immunization, Vaccines and Biologicals), who discussed the underlying viral etiology for pneumonia in the developing world, and the evidence for respiratory syncytial virus (RSV) as a primary cause. The "Viral Subversion of Host Cell Processes" session also included presentations from the following trainees: Nichole McMullen (Dalhousie University) who reported the unconventional egress mechanisms of non-enveloped reoviruses, Justine Sitz (Université Laval) who described interactions between a human papillomavirus protein and a host DNA repair-specific E3 ubiquitin ligase, and Quentin Osseman (Université de Montréal) who described interactions between respiratory syncytial virus (RSV) and the host autophagy pathway. cache = ./cache/cord-349011-kxhpdvri.txt txt = ./txt/cord-349011-kxhpdvri.txt === reduce.pl bib === id = cord-347039-eap592i7 author = Lee, Seung-Hwan title = Maneuvering for advantage: the genetics of mouse susceptibility to virus infection date = 2003-08-31 pages = extension = .txt mime = text/plain words = 6177 sentences = 299 flesch = 38 summary = Receptors are recognized as important determinants of virus host range and tissue tropism; and some host resistance/susceptibility loci encode molecules that are expressed on the cell surface. Another example of natural host resistance is the restriction of ecotropic Murine LEUKEMIA VIRUS (MuLV) infection by the mouse Fv4 gene. The effort to understand the genetic basis of susceptibility to viral disease is driven by three considerations: (1) the increased public awareness of the toll imposed by viruses on the host; (2) the increase in susceptible human populations because of longer life expectancy, frequently accompanied by chronic illness, and the consequences of advances in medical technology, including immunosuppressive therapies for organ transplantation or treatment of malignancy; and (3) the need to develop new therapies for infections caused by multidrug-resistant Human killer-cell immunoglobulin-type receptor (KIR) is considered to be a functional homolog of mouse Ly49. Mouse genetics has also demonstrated that recognition and destruction of virus-infected cells by NK cells is mediated by specific interactions between activating NKcell receptors and viral target molecules. cache = ./cache/cord-347039-eap592i7.txt txt = ./txt/cord-347039-eap592i7.txt === reduce.pl bib === id = cord-349358-leicos9j author = Ketzinel‐Gilad, Mali title = RNA interference for antiviral therapy date = 2006-06-16 pages = extension = .txt mime = text/plain words = 12734 sentences = 684 flesch = 44 summary = During the past few years, it has been demonstrated that RNAi, induced by specifically designed double‐stranded RNA (dsRNA) molecules, can silence gene expression of human viral pathogens both in acute and chronic viral infections. Likewise, expression vectors of siRNAs specific for two different regions of the WNV genome protected 293T cells from WNV infection, and significantly reduced viral RNA replication and virus production [35] . From the reports on the use of siRNA against human viral pathogens causing acute disease, we could learn that for each specific pathogen infecting a specific cell lineage or tissue, we would probably need to perform an indepth assessment, with proper in vitro and in vivo models, and develop specific delivery systems. The most challenging part of RNAi approaches for chronic viral infections is to design the best delivery method that would facilitate the targeting of the specific organ/cells with the appropriate expression system, for durable intracellular levels of gene-silencing effect. cache = ./cache/cord-349358-leicos9j.txt txt = ./txt/cord-349358-leicos9j.txt === reduce.pl bib === id = cord-348669-mizygp4j author = Beall, Anne title = Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A date = 2016-01-05 pages = extension = .txt mime = text/plain words = 6021 sentences = 293 flesch = 43 summary = title: Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A The infectious-clone-derived PEDV (icPEDV) replicated as efficiently as the parental virus in cell culture and in pigs, resulting in lethal disease in vivo. Importantly, recombinant PEDV was rapidly transmitted to uninoculated pigs via indirect contact, demonstrating virulence and efficient transmission while replicating phenotypes seen in the wild-type virus. While the recombinant icPEDV replicated the clinical phenotypes of parental PC22A in vivo, icPEDV-⌬ORF3-RFP infection resulted in a partial attenuation in pigs based on lower diarrhea scores. Both the parental PEDV PC22A strain and its derivative recombinant cloned virus were genetically stable and fully pathogenic in neonatal gnotobiotic pigs, demonstrating that icPEDV provides not only a strategy that allows for the systematic evaluation of the role of viral genes in pathogenesis, tropism, and virulence but also a translational platform for the development of rationally attenuated live virus vaccines. cache = ./cache/cord-348669-mizygp4j.txt txt = ./txt/cord-348669-mizygp4j.txt === reduce.pl bib === id = cord-350467-18bvwxci author = Clark, K.J title = In vitro studies on the use of clay, clay minerals and charcoal to adsorb bovine rotavirus and bovine coronavirus date = 1998-10-01 pages = extension = .txt mime = text/plain words = 3418 sentences = 175 flesch = 48 summary = Experiments were designed to test the ability of various adsorbent materials to tightly bind bovine rotavirus and coronavirus. The suspended samples of clay bound virus or clay/virus complex retained from the adsorption and desorption experiments were used for infectivity testing. Charcoal, sodium bentonite, attapulgite, kaolinite, and HSCAS III were found to adsorb greater than 99.0% of bovine rotavirus while the other materials assayed ranged in their adsorptive capabilities from less than 99% to greater than 78% (Table 1) . As both bovine rotavirus and coronavirus bound to various adsorbent materials, including HSCAS I and II, with high affinity, both were tested for infectivity when in the bound state. They may have a distinct advantage in prevention of infection and/or disease because most agents that cause gastroenteritis, including rotavirus and coronavirus, are generally contracted orally, usually via contaminated food and water. cache = ./cache/cord-350467-18bvwxci.txt txt = ./txt/cord-350467-18bvwxci.txt === reduce.pl bib === id = cord-350964-0jtfc271 author = Van Nguyen, Dung title = Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam date = 2018-02-28 pages = extension = .txt mime = text/plain words = 4803 sentences = 246 flesch = 51 summary = In this study of pegivirus and human hepatitis-related viruses, liver and serum samples from Vietnamese rodents and bats were examined by PCR and sequencing. Nucleic acids homologous to human hepatitis B, C, E viruses were detected in liver samples of 2 (1.3%) of 157 bats, 38 (8.1%), and 14 (3%) of 470 rodents, respectively. Hepacivirus-like viruses were frequently detected (42.7%) in the bamboo rat, Rhizomys pruinosus, while pegivirus RNA was only evident in 2 (0.3%) of 638 rodent serum samples. Nucleic acid that was extracted from liver samples of 157 bats (29 species; Table S1 ) and 470 rodents (six species) was screened for pegivirus and human hepatitis B, C, E viruses and their homologues ( Table 1 ) by nested and semi-nested PCR assays with degenerate primers. cache = ./cache/cord-350964-0jtfc271.txt txt = ./txt/cord-350964-0jtfc271.txt === reduce.pl bib === id = cord-347710-ff64y6ef author = Wan, Qianya title = Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development date = 2020-07-13 pages = extension = .txt mime = text/plain words = 36567 sentences = 2487 flesch = 46 summary = hnRNPs involve in a large number of cellular processes, including chromatin remodelling, transcription regulation, RNP assembly and stabilization, RNA export, virus replication, histone-like nucleoid structuring, and even intracellular immunity. 6, 13 It is well known that Hsp90 not only interacts and contributes to RNA polymerase assembly and nuclear import of some (−) ssRNA viruses (e.g., PB2 of influenza virus), but plays crucial roles in the folding process of viral capsid proteins and virion assemblies as well. 17, 18 As a critical component of cellular protein surveillance, the ATP-dependent molecular chaperone protects cells from damage caused by stress and takes part in a number of folding processes, including folding of newly synthesized polypeptides, recognition and refolding of misfolded or aggregated proteins, solubilization or degradation of proteins, transporting proteins, assembly or disassembly of oligomeric protein complexes, and the regulation of certain natively folded proteins. cache = ./cache/cord-347710-ff64y6ef.txt txt = ./txt/cord-347710-ff64y6ef.txt === reduce.pl bib === id = cord-351197-xv6ymc4l author = Cibulski, Samuel title = A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil date = 2020-09-28 pages = extension = .txt mime = text/plain words = 1711 sentences = 124 flesch = 54 summary = From chicken, six distinct gyroviruses (GyV) were detected, including GyV3 and GyV6, which for the first time were detected in samples from avian species, plus a novel smacovirus species and two highly divergent circular Rep-encoding ssDNA (CRESS-DNA) viruses. A detailed taxonomic 136 classification, including the numbers of reads for each Eukarya-related viral contig 137 recovered is this study, is provided in Supplementary gives them the ability to persist and spread in the environment. A detailed taxonomic classification, including the numbers of 245 J o u r n a l P r e -p r o o f sequenced reads of each Eukarya-related viral contig recovered in this study, is 246 provided in Supplementary Table 1 . including numbers of sequenced reads of each Eukarya-related viral contig recovered in 334 this study, is provided in Supplementary Table 1 . Cressdnaviricota: a virus phylum unifying 7 families of Rep-encoding 519 viruses with single-stranded, circular DNA genomes cache = ./cache/cord-351197-xv6ymc4l.txt txt = ./txt/cord-351197-xv6ymc4l.txt === reduce.pl bib === id = cord-351170-belbcrcd author = Symonds, Erin M. title = Affordable Enteric Virus Detection Techniques Are Needed to Support Changing Paradigms in Water Quality Management date = 2014-10-16 pages = extension = .txt mime = text/plain words = 3018 sentences = 135 flesch = 29 summary = Although this method is known to be flawed (see below), FIB are still widely used as an indicator of enteric pathogens and human health risks due to their consistent presence in wastewater and the readily available, low cost, culture-based methods for detection that require minimal laboratory training [14] [15] [16] [17] . As a result of the inadequacy of FIB monitoring to determine human health risks associated with enteric pathogens, particularly viruses, alternative approaches to traditional microbial quality monitoring have been recommended (Fig. 1C) . Finally, the utility of incorporating specific enteric viruses and/or a viral indicator to identify wastewater pollution/poor microbial quality and to better predict human health risks related to wastewater exposure has been demonstrated throughout the world [14-16, 22, 24, 25] . In conjunction with water management advances, the development of simple, affordable, lab-free tests for the rapid detection of enteric viruses and/or viral indicators is essential for ensuring worldwide improvements in microbial safety. cache = ./cache/cord-351170-belbcrcd.txt txt = ./txt/cord-351170-belbcrcd.txt === reduce.pl bib === id = cord-350151-s75d1hat author = Wiramus, S. title = Rianimazione e influenza grave: pandemia influenzale A (H1N1) date = 2013-04-30 pages = extension = .txt mime = text/plain words = 6539 sentences = 767 flesch = 61 summary = A causa delle mutazioni costanti dei virus influenzali, la composizione del vaccino è generalmente diversa da un anno all'altro: ogni anno, l'Organizzazione Mondiale della Sanità (OMS) emette una raccomandazione sui ceppi che devono essere inclusi nel vaccino. • personale paramedico e medico: rischio importante di riduzione del personale disponibile negli ospedali e rischio maggiore di infettare dei pazienti fragili; • donne gravide: rischio elevato di complicanze gravi e di morte; • bambini di meno di 6 mesi e persone che se ne occupano; • persone da 6 mesi a 24 anni; • persone da 25 a 64 anni che hanno delle comorbilità: enfisema polmonare, broncopneumopatia cronica ostruttiva (BPCO), asma, obesità patologica, insufficienza cardiaca, diabete instabile, immunodepressione e malattie neurologiche. Solo i soggetti poco o non immuni nei confronti del virus sono suscettibili di essere colpiti in questa maniera ed è per questo che la vaccinazione contro l'influenza stagionale sembra conferire una protezione contro queste forme più gravi [6] . cache = ./cache/cord-350151-s75d1hat.txt txt = ./txt/cord-350151-s75d1hat.txt === reduce.pl bib === id = cord-350235-yoy3hj3j author = Sansonetti, Philippe J title = COVID‐19, chronicle of an expected pandemic date = 2020-05-04 pages = extension = .txt mime = text/plain words = 2988 sentences = 152 flesch = 56 summary = Philippe Sansonetti, Infectious disease specialist and Chief Editor of EMBO Molecular Medicine, explains why the fate of the epidemic is in our hands.[Image: see text] Philippe Sansonetti, Infectious Disease Specialist and Chief Editor of EMBO Molecular Medicine, explains why the fate of the epidemic is in our hands. Beta-coronaviruses like SARS-CoV-2 (the official name of COVID-19 virus) on the other hand are well adapted to their reservoir, the bat, but not to humans, which explains why human infections are so damaging. Molecular diagnosis has revolutionized this field, and despite the initial delays in communicating about this epidemic, Chinese doctors and biologists quickly reported the first evidence for SARS-CoV-2, and provided the first sequences, clearing the way for the global scientific community to further develop diagnostic tools and engage in a race to discover dedicated drugs and vaccines. cache = ./cache/cord-350235-yoy3hj3j.txt txt = ./txt/cord-350235-yoy3hj3j.txt === reduce.pl bib === id = cord-351482-hzh5tyoo author = Peng, Xinxia title = Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection date = 2011-11-15 pages = extension = .txt mime = text/plain words = 7697 sentences = 348 flesch = 49 summary = The small RNAs identified also included many non-miRNA small RNAs, such as small nucleolar RNAs (snoRNAs), in addition to nonannotated small RNAs. An integrative sequencing analysis of both small RNAs and long transcripts from the same samples showed that the results revealing differential expression of miRNAs during infection were largely due to transcriptional regulation and that the predicted miRNA-mRNA network could modulate global host responses to virus infection in a combinatorial fashion. In total, of 4,473,273 start positions in the genome with at least one uniquely mapped read, we found that about 5% (233,236) gave at least 4 reads of the same length in a sample, resulting in 16,054 nonredundant candidate loci for putative small RNAs. About 1.7% (276/16,054) of the candidate loci (median length, 39 nt) were differentially expressed during SARS-CoV and/or influenza virus infection (see Table S2 and Fig. S4a in the supplemental material); 46 of those candidate loci overlapped with annotated miRNA precursors (miRBase version 16). cache = ./cache/cord-351482-hzh5tyoo.txt txt = ./txt/cord-351482-hzh5tyoo.txt === reduce.pl bib === id = cord-350703-vrqltz3s author = nan title = ISAR News date = 2016-01-31 pages = extension = .txt mime = text/plain words = 11202 sentences = 497 flesch = 45 summary = She is studying the response of primary human mononuclear cells to dengue virus infection, aiming to establish a more relevant in vitro model for antiviral drug testing and to identify potential new antiviral targets, using genome-wide transcriptomic analysis. According to ISAR member Robert Jordan, who heads the Gilead team developing antivirals against respiratory viruses, the parent compound was originally discovered as part of the hepatitis C program, targeting the HCV polymerase, but the strong clinical efficacy of sofosbuvir, especially in combination with ledipasvir, resulted in the molecule being evaluated for other indications, including respiratory viruses such as respiratory syncytial virus (RSV). ISAR members know Andrea (standing, above, with Cardiff colleague Salvatore Ferla) as the winner of the 2013 Prusoff Young Investigator Award, but not all of us are familiar with the direction of his career, which has increasingly explored the use of computer-based methods to design new antivirals and anticancer drugs. cache = ./cache/cord-350703-vrqltz3s.txt txt = ./txt/cord-350703-vrqltz3s.txt === reduce.pl bib === id = cord-351377-xorj8tnz author = Kao, Chi-Fei title = The Characterization of Immunoprotection Induced by a cDNA Clone Derived from the Attenuated Taiwan Porcine Epidemic Diarrhea Virus Pintung 52 Strain date = 2018-10-04 pages = extension = .txt mime = text/plain words = 5936 sentences = 234 flesch = 48 summary = Moreover, inoculation with iPEDVPT-P96 elicited comparable levels of anti-PEDV specific plasma IgG and fecal/salivary IgA, neutralizing antibody titers, and similar but less effective immunoprotection against the virulent PEDVPT-P5 challenge compared to the parental PEDVPT-P96. In the present study, an infectious cDNA clone of an attenuated G2b PEDV strain was successfully generated for the first time, and the in vitro and in vivo data indicate that iPEDVPT-P96 is further attenuated but remains immunogenic compared to its parental PEDVPT-P96 viral stock. While one piglet in the PEDVPT-P96 group showed intermittent loose diarrhea (score = 1) and viral shedding at 6 to 11 days post-inoculation (DPI) with the peak viral titer of 1.45 ± 3.24 log 10 RNA copies/mL at 8 DPI (Figure 4) , no evidence of PEDV-associated clinical signs and fecal viral shedding were demonstrated in both iPEDVPT-P96 and mock groups. cache = ./cache/cord-351377-xorj8tnz.txt txt = ./txt/cord-351377-xorj8tnz.txt === reduce.pl bib === id = cord-350948-oog6m4h3 author = Leclercq, Loïc title = How to improve the chemical disinfection of contaminated surfaces by viruses, bacteria and fungus? date = 2020-09-17 pages = extension = .txt mime = text/plain words = 4571 sentences = 256 flesch = 51 summary = The disinfectants, based on equimolar mixtures of didecyldimethylammonium chloride ([DiC(10)][Cl]), dodecyloctaglycol (C(12)E(8)), and cyclodextrin (CD), show synergistic effects against enveloped viruses (RSV, HSV-1, VACV) and fungi (C. In this context, the didecyldimethylammonium chloride ([DiC 10 ] [Cl] ), one of the most widely used quaternary ammonium compounds in healthcare systems to prevent and control viral infections due to its ability to disorganize and to disrupt the envelopes of viruses (Leclercq et al., 2010) , is associated with detergents, such as dodecyloctaglycol (C 12 E 8 ), making the detergent-disinfectant combination ideal for general sanitation purposes (Rauwel et al., 2012) . As, some ethoxylated surfactants (e.g. Triton X-100, Nonoxynol-9 or Brij-97) have been shown to exhibit a virucidal activity due to their ability to solubilize the viral envelope of Epstein-Barr or herpes simplex viruses (Qualtiere and Pearson, 1979; Asculai et al., 1978) , and, as, CDs "are able to participate in the attack of viruses, and specifically SARS-CoV-2, in a large range of different ways" (Garrido et al., 2020) , we have investigated [DiC 10 ][Cl]/C 12 E 8 /CD ternary systems to obtain synergistic effects against enveloped viruses such as RSV instead of hazardous SARS-CoV-2. cache = ./cache/cord-350948-oog6m4h3.txt txt = ./txt/cord-350948-oog6m4h3.txt === reduce.pl bib === id = cord-351571-gwtkrt5u author = Mackay, Ian M. title = Community-Wide, Contemporaneous Circulation of a Broad Spectrum of Human Rhinoviruses in Healthy Australian Preschool-Aged Children During a 12-Month Period date = 2013-05-01 pages = extension = .txt mime = text/plain words = 3374 sentences = 160 flesch = 43 summary = Human rhinovirus (HRV) infections trigger exacerbations of asthma and chronic obstructive pulmonary disease and the majority of acute respiratory illnesses (ARIs), some of which meet criteria for influenza-like illness. Nevertheless, each available majority sequence of an HRV-C type has to date represented a genetically unique, phylogenetically distinct, and globally distributed virus detected in patients with ARIs. There are specific seasonal and annual variations in respiratory virus circulation and interactions [11] [12] [13] . We sought to quantify the genetic diversity, epidemiology, and impact of HRV and enterovirus species, conjointly referred to hereafter as picornaviruses, circulating among a community cohort of preschool-aged children who provided respiratory samples over a 1-year period. 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 cache = ./cache/cord-351571-gwtkrt5u.txt txt = ./txt/cord-351571-gwtkrt5u.txt === reduce.pl bib === id = cord-352054-g7q2z4l5 author = Kolivoška, Viliam title = Electrophoresis on a microfluidic chip for analysis of fluorescence‐labeled human rhinovirus date = 2007-11-15 pages = extension = .txt mime = text/plain words = 3710 sentences = 190 flesch = 55 summary = Resolution of the sample constituents (virions, a contaminant present in all virus preparations, and excess dye) was improved upon adaptation of the separation conditions, mainly by adjusting the SDS concentration of the BGE. As the applied instrumentation (a commercial microdevice) utilized a red laser at l ex 630 nm for high-sensitivity detection, virus particles were fluorescence (FL)-labeled prior to analysis and preseparated from the excess of dye by size-exclusion chromatography (SEC). Separation from a contaminant, which also becomes labeled upon reaction of the virus sample with reactive Cy5, and from the excess free dye was improved by addition of SDS and varying its concentration in the BGE. Chip electrophoresis with the finally selected BGE (100 mM borate buffer, pH 8.3, containing 3.1 mM SDS), enabled an extremely rapid assessment of virus purity, and the investigation of bioaffinity reactions of labeled virus with a number of soluble artificial receptor fragments. cache = ./cache/cord-352054-g7q2z4l5.txt txt = ./txt/cord-352054-g7q2z4l5.txt === reduce.pl bib === id = cord-352379-q5inrxcm author = Lai, Michael M. C. title = SARS virus: The beginning of the unraveling of a new coronavirus date = 2003-10-17 pages = extension = .txt mime = text/plain words = 7004 sentences = 376 flesch = 49 summary = Nevertheless, the lack of a firm association of coronaviruses with any serious human illnesses had dampened the public's interest in this virus family until the sudden emergence of the SARS coronavirus [24, 41, 62] , which caused the first new infectious disease of this millennium. In the SARS virus genome, the organization of gene la-lb, which accounts for more than two-thirds of the viral RNA, is very similar to that of the murine coronavirus MHV, except that it contains only one papain-like protease (PLpro-2) ( fig. Based on the predicted cleavage site specificity, the SARS virus gene la-lb is likely processed into thirteen final protein products. However, the published sequence analysis indicated that the entire SARS virus RNA resembled that of group II viruses; no evidence of recombination was noted [55, 66] . Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection cache = ./cache/cord-352379-q5inrxcm.txt txt = ./txt/cord-352379-q5inrxcm.txt === reduce.pl bib === id = cord-352475-cmmpy5u7 author = Pemmada, Rakesh title = Science-Based Strategies of Antiviral Coatings with Viricidal Properties for the COVID-19 Like Pandemics date = 2020-09-11 pages = extension = .txt mime = text/plain words = 7770 sentences = 402 flesch = 37 summary = The worldwide, extraordinary outbreak of coronavirus pandemic (i.e., COVID-19) and other emerging viral expansions have drawn particular interest to the design and development of novel antiviral, and viricidal, agents, with a broad-spectrum of antiviral activity. Hence, it is highly desirable to search for potential antiviral and viricidal elements (materials and coatings) to design personal protective equipment (PPE), hygienic implements, and other devices to fight against the rise of viral pandemics and virus-associated fatal risks [22] . In addition, a large number of studies have reported coating materials containing metal ions (i.e., silver, copper, zinc), which have demonstrated an excellent antiviral ability with long-term, persistent effects [30] [31] [32] [33] [51] [52] [53] [54] [55] . Various strategies involved in the development of antiviral and viricidal coatings, like modifying the surface of a substrate via antiviral polymers, incorporation of metal ions/oxides, and functional nanoparticles were discussed. cache = ./cache/cord-352475-cmmpy5u7.txt txt = ./txt/cord-352475-cmmpy5u7.txt === reduce.pl bib === id = cord-350747-5t5xthk6 author = Gmyl, A. P. title = Diverse Mechanisms of RNA Recombination date = 2005 pages = extension = .txt mime = text/plain words = 8187 sentences = 463 flesch = 41 summary = It was believed until recently that the only possible mechanism of RNA recombination is replicative template switching, with synthesis of a complementary strand starting on one viral RNA molecule and being completed on another. An illustrative example of deletions is provided by defective interfering (DI) genomes, which accumulate in a virus population upon high-multiplicity infections and lack a fragment of the sequence coding for viral proteins [5] [6] [7] . A special role in the variation of RNA viruses is played by recombination, the generation of new genomes from two or more parental RNAs. Recombination between viral RNA molecules was observed for the first time as early as in the 1960s in the poliovirus [14, 15] . In other words, it is possible to assume that some of the mechanisms of nonreplicative RNA recombination play an important role in the evolution of not only viral, but also cell genomes [51, 90] . cache = ./cache/cord-350747-5t5xthk6.txt txt = ./txt/cord-350747-5t5xthk6.txt === reduce.pl bib === id = cord-351365-dc9t3vh3 author = Todt, Daniel title = Mutagenic Effects of Ribavirin on Hepatitis E Virus—Viral Extinction versus Selection of Fitness-Enhancing Mutations date = 2016-10-13 pages = extension = .txt mime = text/plain words = 6318 sentences = 320 flesch = 40 summary = Consequently, the onset of RBV treatment in chronically HEV-infected individuals can result in two divergent outcomes: viral extinction versus selection of fitness-enhanced viruses. Following an overview of RNA viruses treated with RBV in clinics and a summary of the different antiviral modes of action of this drug, we focus on the mutagenic effect of RBV on HEV intrahost populations, and how HEV is able to overcome lethal mutagenesis. Figure 1 provides an overview of a selection of RNA viruses against which RBV was shown to be active: hepatitis C virus (HCV, Flaviviridae), dengue virus (DENV, Flaviviridae), respiratory syncytial virus (RSV, Paramyxoviridae), influenza A and B virus (Orthomyxoviridae), chikungunya virus (CHIKV, Togaviridae), poliovirus (Picornaviridae), Hantaan virus (Bunyaviridae), and Lassa virus (Arenaviridae) [28, 29] ( Figure 1 ). Furthermore, mechanisms on the virus itself were described by inhibition of the capping efficiency, the viral polymerase, and a mutagenic effect on newly synthesized RNA genomes. A Mutation in the hepatitis E virus RNA polymerase promotes its replication and associates with ribavirin treatment failure in organ transplant recipients cache = ./cache/cord-351365-dc9t3vh3.txt txt = ./txt/cord-351365-dc9t3vh3.txt === reduce.pl bib === id = cord-352178-irjhmxsg author = Saxton-Shaw, Kali D. title = O'nyong nyong Virus Molecular Determinants of Unique Vector Specificity Reside in Non-Structural Protein 3 date = 2013-01-24 pages = extension = .txt mime = text/plain words = 5953 sentences = 299 flesch = 49 summary = Fifteen distinct chimeric viruses were constructed to evaluate both structural and non-structural regions of the genome and infection patterns were determined through artificial infectious feeds in An. gambiae with each of these chimeras. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from CHIKV virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. Our study analyzed both structural and non-structural regions of the ONNV genome using chimeric viruses and artificially infected Anopheles gambiae mosquitoes. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from chikungunya virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. Six additional non-structural chimeric viruses were also constructed using a novel type II restriction enzyme cloning strategy to examine the broader genome with respect to ONNV's unique vector specificity for An. gambiae mosquitoes (Figure 2) . cache = ./cache/cord-352178-irjhmxsg.txt txt = ./txt/cord-352178-irjhmxsg.txt === reduce.pl bib === id = cord-353290-1wi1dhv6 author = Kustin, Talia title = Biased mutation and selection in RNA viruses date = 2020-09-28 pages = extension = .txt mime = text/plain words = 7611 sentences = 402 flesch = 52 summary = We investigated possible reasons for the advantage of A-rich sequences including weakened RNA secondary structures, codon usage bias, and selection for a particular amino-acid composition, and conclude that host immune pressures may have led to similar biases in coding sequence composition across very divergent RNA viruses. Nevertheless, RNA viruses do share several common features that drive their evolution: (a) their ultimate dependence on the cell, (b) their high mutation rates, (c) strong purifying selection derived from constraints operating on a small and densely coding genome, and (d) sporadic but powerful positive selection driven by an evolutionary arms race with the host they infect. Two non-mutually exclusive hypotheses may be put forth to explain the consistent pattern of A-richness that we observe: there is selection for more A in viral sequences, and/or there is a mutational bias that leads to more A in genomes of viruses. cache = ./cache/cord-353290-1wi1dhv6.txt txt = ./txt/cord-353290-1wi1dhv6.txt === reduce.pl bib === id = cord-354536-c9v9kbw8 author = Han, Yan-Jie title = Advances and challenges in the prevention and treatment of COVID-19 date = 2020-07-09 pages = extension = .txt mime = text/plain words = 5268 sentences = 330 flesch = 48 summary = This article introduced the origin, virological characteristics and epidemiological overview of SARS-CoV-2, reviewed the currently known drugs that may prevent and treat coronavirus, explained the characteristics of the new coronavirus and provided novel information for the prevention and treatment of COVID-19. 18 In view of the curative effect of ribavirin in the treatment of diseases caused by SARS-CoV and MERS-CoV, 21 it is expected to become one of the effective drugs to treat coronavirus. 16 The "Pneumonitis Diagnosis and Treatment Scheme for New Coronavirus Infection (Trial Version 7)" states that aerosolized interferon alpha can be used as a trial treatment against SARS-CoV-2 virus to improve the virus clearance effect of respiratory mucosa in patients. 64 It has been revealed that chlorpromazine is a broad-spectrum virus inhibitor that can inhibit HCV, alpha virus, and various coronaviruses including human coronavirus 229E, SARS-CoV and MERS-CoV in vitro. cache = ./cache/cord-354536-c9v9kbw8.txt txt = ./txt/cord-354536-c9v9kbw8.txt === reduce.pl bib === id = cord-350925-1h6pbfwp author = da Silva, Priscilla Gomes title = Airborne spread of infectious SARS-CoV-2: moving forward using lessons from SARS-CoV and MERS-CoV date = 2020-10-08 pages = extension = .txt mime = text/plain words = 5221 sentences = 279 flesch = 49 summary = Transmission of viruses through air can happen via droplets or aerosols generated during coughing, sneezing, talking, singing or breathing (Jones and CoV-2 is that most studies performed only focused on the detection of viral RNA and do not correlate to the infectivity of these viral particles. Therefore, in this systematic review, the viability/stability of aerosols containing SARS-CoV and MERS-CoV viruses will be discussed to provide information on potential mitigation strategies for SARS-CoV-2 airborne transmission. The presence of MERS-CoV was also confirmed by RT-PCR of viral cultures of 4 out of 7 air samples from two hospitals in South Korea (Kim et al., 2016) , and showed to be very stable in aerosol at 20°C and 40% relative humidity (van Doremalen et al., 2013) . cache = ./cache/cord-350925-1h6pbfwp.txt txt = ./txt/cord-350925-1h6pbfwp.txt === reduce.pl bib === id = cord-353297-jizitnfl author = Meyer, R.F. title = Viruses and Bioterrorism date = 2008-07-30 pages = extension = .txt mime = text/plain words = 3817 sentences = 184 flesch = 43 summary = The requirements for an ideal biological warfare agent include availability, ease of production, stability after production, a susceptible population, absence of specific treatment, ability to incapacitate or kill the host, appropriate particle size in aerosol so that the virus can be carried long distances by prevailing winds and inhaled deeply into the lungs of unsuspecting victims, ability to be disseminated via food or water, and the availability of a vaccine to protect certain groups. Instead, the ectromelia virus vector expressing IL-4 altered the host's immune response to this virus resulting in lethal infections in normally genetically Classification of viral agents that are considered to be of concern for bioterrorism and biowarfare and those that have been weaponized or studied for offensive or defensive purposes as part of former or current national biological weapons programs resistant mice (e.g., C57BL/6). cache = ./cache/cord-353297-jizitnfl.txt txt = ./txt/cord-353297-jizitnfl.txt === reduce.pl bib === id = cord-353509-yfkiaq80 author = Nugraha, Rhea Veda title = Traditional Herbal Medicine Candidates as Complementary Treatments for COVID-19: A Review of Their Mechanisms, Pros and Cons date = 2020-10-10 pages = extension = .txt mime = text/plain words = 7433 sentences = 413 flesch = 48 summary = This review discusses some herbal agents extracted from various plants, including Echinacea, Cinchona, Curcuma longa, and Curcuma xanthorrhiza, which are considered for the treatment of COVID-19. e single cause of this highly communicable disease is a novel coronavirus, called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the seventh known virus of the Coronaviridae family capable of infecting humans [2] . Studies that describe the relation of some herbal drugs with the molecular mechanisms of COVID-19 infection, treatment, and prevention remain to be explained. in their systematic review about convalescent plasma transfusion (CPT) for the treatment of COVID-19 suggested that CPT could be an effective therapeutic option with promising evidence on safety, improvement of clinical symptoms, and reduced mortality, in addition to antiviral/antimicrobial drugs. A clinical trial study is needed to confirm the effect of using curcumin as a preventive agent against COVID-19. cache = ./cache/cord-353509-yfkiaq80.txt txt = ./txt/cord-353509-yfkiaq80.txt === reduce.pl bib === id = cord-352619-s2x53grh author = Payne, Natalie title = Novel Circoviruses Detected in Feces of Sonoran Felids date = 2020-09-15 pages = extension = .txt mime = text/plain words = 3263 sentences = 177 flesch = 45 summary = Genomes from several families of circular Rep-encoding single-stranded DNA viruses (CRESS-DNA viruses) are part of the phylum Cressdnaviricota [22] and have been identified in fecal samples of other mammals, including domestic cats [23, 24] , bobcats, African lions [25] , capybaras [26] , and Tasmanian devils [27] . Here we used a metagenomic approach to identify novel circoviruses in the feces of two species of Sonoran felids, the puma and bobcat; although not endangered, knowledge of viral threats facing these species could help prevent future population decline, as well as indicate potential threats to the endangered ocelot and jaguar. Based on the species-demarcation threshold for circoviruses which is 80% genome-wide identity [28] , both of these belong to a new species which we refer to as Sonfela (derived from Sonoran felid associated) circovirus 1. As the viral genomes were derived from scat samples, the circoviruses could have infected the bobcat prey species or the felids themselves or be environmentally derived. cache = ./cache/cord-352619-s2x53grh.txt txt = ./txt/cord-352619-s2x53grh.txt === reduce.pl bib === id = cord-352200-i05h8csb author = Xu, Yi title = Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus date = 2012-04-27 pages = extension = .txt mime = text/plain words = 5286 sentences = 278 flesch = 47 summary = title: Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus METHODOLOGY/PRINCIPAL FINDINGS: By de novo transcriptome assembling and massive parallel pyrosequencing, we constructed two transcriptomes of WBPH and profiled the alternation of gene expression in response to SRBSDV infection in transcriptional level. As a whole, 81388 distinct unigenes have been identified and the results indicated that SRBSDV infection can potentially perturb primary metabolism and the ubiquitin-proteasome pathway of WBPH and activate immune regulatory systems, such as RNA interfering, autophagy and antimicrobial peptide production. However, some unigenes were obtained only from viruliferous or non-viruliferous samples (data not shown) and we believe these differences may be caused by distinctions that arise from long-term ecological adaptation to virus infection. In addition, GO analysis also showed a similar distribution of gene functions for non-viruliferous and viruliferous WBPH (Figure 4 ), indicating that the number of genes expressed in each GO category was not significantly affected by SRBSDV infection. cache = ./cache/cord-352200-i05h8csb.txt txt = ./txt/cord-352200-i05h8csb.txt === reduce.pl bib === id = cord-353609-no3mbg5d author = Vandegrift, Kurt J. title = An Ecological and Conservation Perspective on Advances in the Applied Virology of Zoonoses date = 2011-04-15 pages = extension = .txt mime = text/plain words = 6925 sentences = 350 flesch = 42 summary = Conducting viral surveillance in animal reservoirs and invertebrate vectors can help explain circulation within host species; observed patterns of zoonotic transmission; and even allow for the prediction of periods of increased risk of zoonotic transmission (e.g., Rift valley fever and rainfall [25] ; West Nile virus (WNV) and American robin (Turdus turdus) migration [26] ; as well as hantavirus in mice [27, 28] ). Globalization, host ecology, host-virus dynamics, climate change, and anthropogenic landscape changes all contribute to the complexity of zoonotic viral emergence and disease, and create significant conservation and public health challenges. While the lasting efficacy of wildlife vaccination efforts has yet to be demonstrated with either endangered species or in breaking the transmission cycle of human pathogens, an increasing number of researchers are drawing attention to systems where it seems feasible [99, 103] ; demonstrating that intricate knowledge of host and virus ecology can greatly reduce the amount of vaccine coverage that is necessary to control these viruses. cache = ./cache/cord-353609-no3mbg5d.txt txt = ./txt/cord-353609-no3mbg5d.txt === reduce.pl bib === id = cord-354109-mli0c97c author = Faezi, Nasim Asadi title = Viral infections in patients with acute respiratory infection in Northwest of Iran date = 2017-01-22 pages = extension = .txt mime = text/plain words = 3171 sentences = 166 flesch = 47 summary = The aim of this study was to determine the frequency, mortality and association with clinical entities of influenza virus type A, influenza virus type B, respiratory syncytial virus (RSV), coronavirus, and adenoviruses in patients with ARI. Aim of the present study was to determine the frequency and mortality of the viral respiratory infections including influenza virus type A, influenza virus type B, respiratory syncytial virus (RSV), coronavirus, and adenoviruses in patients with ARI that referred to central Hospital in Northwest of Iran during September 2014 till May 2015. In another study that conducted in a Tehran hospital on children with acute respiratory infection, influenza A virus, RSV, and adenovirus were detected in 4.4, 5.7, and 6.3%, respectively [15] . Diagnosis of the adenovirus, RSV, and influenza virus by rapid detection test (immunochromatography) in children with acute respiratory infection, Iran cache = ./cache/cord-354109-mli0c97c.txt txt = ./txt/cord-354109-mli0c97c.txt === reduce.pl bib === id = cord-354035-i3sl2r0k author = Wylie, Kristine M. title = The Virome of the Human Respiratory Tract date = 2016-12-10 pages = extension = .txt mime = text/plain words = 3901 sentences = 215 flesch = 46 summary = Sensitive, culture-independent molecular assays (polymerase chain reaction and high-throughput sequencing) reveal that in addition to common viruses that cause acute, symptomatic infections the virome also includes viruses that do not cause clinical symptoms, have unknown pathogenic effect, or cause symptoms but are not among the most common viral respiratory tract pathogens. However, as characterization of the respiratory tract virome using molecular methods is a relatively new area of exploration, these studies can be useful in order to determine if viruses beyond the common, known respiratory pathogens are detected. In a study of 71 patients, viruses were assessed in nasal swabs using a panel of targeted PCR assays for common respiratory pathogens. Another study tested 89 nasopharyngeal swabs from adults with upper respiratory tract infections using reverse transcription (RT)-PCR assays for a series of common viruses, including human rhinoviruses, coronaviruses, influenza viruses and others, and by RNA sequencing. cache = ./cache/cord-354035-i3sl2r0k.txt txt = ./txt/cord-354035-i3sl2r0k.txt === reduce.pl bib === id = cord-355181-affuyn8z author = Poggio, Claudio title = Copper-Alloy Surfaces and Cleaning Regimens against the Spread of SARS-CoV-2 in Dentistry and Orthopedics. From Fomites to Anti-Infective Nanocoatings date = 2020-07-22 pages = extension = .txt mime = text/plain words = 5793 sentences = 304 flesch = 43 summary = SARS-CoV-2 (acronym for severe acute respiratory syndrome coronavirus 2), responsible for the current outbreak that causes COVID-19 (acronym for "corona virus disease 2019"), is reported to be able of surviving on inanimate surfaces for days. An interesting 2008 article that dealt with environmental hygiene focused on the importance of the transmission of respiratory tract infections Genetic material of SARS-CoV-2 has recently been demonstrated in the plasma of patients with COVID-19, thus feeding concerns for virus shedding during surgical procedures [16] . Incorporation of copper alloy surfaces in conjunction with effective cleaning regimens and good clinical practice could help to control transmission of respiratory coronaviruses, including MERS and SARS [52, 53] . Incorporation of copper alloy surfaces in conjunction with effective cleaning regimens and good clinical practice could help to control transmission of respiratory coronaviruses, including MERS and SARS [52, 53] . cache = ./cache/cord-355181-affuyn8z.txt txt = ./txt/cord-355181-affuyn8z.txt === reduce.pl bib === id = cord-354151-psog34u3 author = van Asten, Liselotte title = Early occurrence of influenza A epidemics coincided with changes in occurrence of other respiratory virus infections date = 2015-12-11 pages = extension = .txt mime = text/plain words = 4227 sentences = 203 flesch = 40 summary = METHODS: We investigated time trends of and the correlation between positive laboratory diagnoses of eight common viruses in the Netherlands over a 10‐year time period (2003–2012): influenza viruses types A and B, respiratory syncytial virus (RSV), rhinovirus, coronavirus, norovirus, enterovirus, and rotavirus. [1] [2] [3] [4] A few population-level studies in Europe were based on observations in one respiratory season only (the 2009 H1N1 pandemic) in which the annually recurring influenza epidemic occurred relatively early. Almost all of the included respiratory viruses (influenza A and B virus, RSV, coronavirus) except rhinovirus showed very clear seasonality in their reporting over time. Viruses that showed a shifted trend of reporting during years with early influenza A epidemics were of respiratory nature with clear winter seasonality and with epidemics occurring relatively close in time to influenza A virus epidemics. cache = ./cache/cord-354151-psog34u3.txt txt = ./txt/cord-354151-psog34u3.txt === reduce.pl bib === id = cord-354848-7aakik9a author = Sayres, Lauren title = Contemporary Understanding of Ebola and Zika Virus in Pregnancy date = 2020-10-16 pages = extension = .txt mime = text/plain words = 4375 sentences = 253 flesch = 41 summary = In particular, Ebola virus is associated with high case fatality and pregnancy and neonatal loss rates, while Zika virus has been associated with multiple congenital anomalies; these features present critical clinical dilemmas for management of pregnant and reproductive aged women. The Monitored Emergency Use of Unregistered and Investigational Interventions ethical framework recommends that vulnerable Contemporary Understanding of Ebola and Zika Virus populations including pregnant women be offered similar treatments to the nonpregnant population when potential benefits can outweigh risks. 75 Attention must be paid to the successes and failures of the response to the Ebola and Zika outbreaks as physicians strive to provide excellent care for pregnant women who are affected by or at risk for emerging infectious diseases. Prevention of Ebola virus includes containment of infected substances and personal protection equipment use, and prevention of Zika virus entails protection against mosquito bites, avoidance of high-risk regions, and delay of childbearing. cache = ./cache/cord-354848-7aakik9a.txt txt = ./txt/cord-354848-7aakik9a.txt === reduce.pl bib === id = cord-353869-l53ms3q8 author = Friesen, Robert H. E. title = New Class of Monoclonal Antibodies against Severe Influenza: Prophylactic and Therapeutic Efficacy in Ferrets date = 2010-02-08 pages = extension = .txt mime = text/plain words = 4680 sentences = 202 flesch = 44 summary = METHODOLOGY/PRINCIPAL FINDINGS: We evaluated the prophylactic and therapeutic efficacy of the human monoclonal antibody CR6261 against lethal challenge with the highly pathogenic avian H5N1 virus in ferrets, the optimal model of human influenza infection. CONCLUSIONS/SIGNIFICANCE: These data demonstrate the prophylactic and therapeutic efficacy of this new class of human monoclonal antibodies in a highly stringent and clinically relevant animal model of influenza and justify clinical development of this approach as intervention for both seasonal and pandemic influenza. Mean decline in body weight at the end of the experiment was 6.2% in the group of ferrets that received CR6261 4 hours after challenge ( Figure 2B) , which was significantly less (p = 0.025) than the 10.1% observed in control animals. These findings were in accordance with the observation that the mean lung weights of ferrets treated with CR6261 at 4 hours post challenge were lower compared to the control group (5.7 g versus 14.9 g, p,0.001; Figure 2F ). cache = ./cache/cord-353869-l53ms3q8.txt txt = ./txt/cord-353869-l53ms3q8.txt === reduce.pl bib === id = cord-355489-tkvfneje author = Mendez, Jairo A title = Phylogenetic history demonstrates two different lineages of dengue type 1 virus in Colombia date = 2010-09-14 pages = extension = .txt mime = text/plain words = 4615 sentences = 235 flesch = 48 summary = Yet, the phylogenetic relationships between strains isolated along the covered period of time suggests that viral strains detected in some years, although belonging to the same genotype V, have different recent origins corresponding to multiple re-introduction events of viral strains that were circulating in neighbor countries. Due to the importance of DENV in public health, the particular goals of this research were to reconstruct the phylogenetic history of DENV-1 and to date the phylogenetic tree using isolation time as calibration points to establish date of introduction of virus and rate evolution patterns of virus in Colombia. Previously reported genotypes were represented in the tree and placed most of the Colombian isolates nesting in the genotype V clade (America, Africa) and were closely related to Argentina, Brazil and Paraguay virus strains. cache = ./cache/cord-355489-tkvfneje.txt txt = ./txt/cord-355489-tkvfneje.txt === reduce.pl bib === id = cord-355872-z6vsjmxn author = Colón-López, Daisy D. title = Emerging viral infections date = 2019-08-15 pages = extension = .txt mime = text/plain words = 3708 sentences = 194 flesch = 36 summary = Characterization of bacterial and viral relationships in mosquito arthropods demonstrated a symbiotic relationship between the bacterium and host, limiting dengue virus infection and potentially revealing new antiviral strategies [39, 40] . The Ebola virus outbreak in West Africa resulted in 26,648 cases and 11,017 documented deaths, and genomic sequencing was applied in near real-time to provide information to aid in containing the outbreak [44, 45] . During the Ebola virus outbreak, sequence analysis of the viral genome over time demonstrated changes which could make the pathogen resistant to therapeutics such as siRNAs, phosphorodiamidate morpholino oligomers (PMOs), and antibodies [56] . This agnostic method is appropriate for identifying changes in the human transcriptome as a result of an emerging viral infection to show specific mechanisms of immune response evasion and other effects in the host's biology at the transcriptomic level. cache = ./cache/cord-355872-z6vsjmxn.txt txt = ./txt/cord-355872-z6vsjmxn.txt === reduce.pl bib === id = cord-353190-7qcoxl81 author = Nicklas, Werner title = Viral Infections of Laboratory Mice date = 2012-05-17 pages = extension = .txt mime = text/plain words = 27775 sentences = 1482 flesch = 39 summary = This chapter covers infections of mice with the following viruses: herpesviruses, mousepox virus, murine adenoviruses, polyomaviruses, parvoviruses, lactate dehydrogenase-elevating virus, lymphocytic choriomeningitis virus, mammalian orthoreovirus serotype 3, murine hepatitis virus, murine norovirus, murine pneumonia virus, murine rotavirus, Sendai virus, and Theiler's murine encephalomyelitis virus. These results are very difficult to summarize because the outcome of experimental infection in laboratory mice depends on various factors such as mouse strain and age, virus strain and passage history [26] , virus dose and route of inoculation [24] . Experimental infection of laboratory mice with MHV-68 is a frequently used model system for the study of human gammaherpesvirus pathogenesis, e.g. of Kaposi's sarcoma-associated herpesvirus or Epstein-Barr virus (EBV) [62, 63] which are members of the same subfamily. Early descriptions of naturally occurring disease may have been complicated by concurrent infections such as MHV (murine hepatitis virus) or murine rotavirus A (MuRV-A)/epizootic diarrhoea of infant mice (EDIM) virus that contributed to the severity of the lesions especially in liver, pancreas, CNS and intestine. cache = ./cache/cord-353190-7qcoxl81.txt txt = ./txt/cord-353190-7qcoxl81.txt === reduce.pl bib === id = cord-355685-wgad0eoh author = Francesconi, Valeria title = Synthesis and Biological Evaluation of Novel (thio)semicarbazone-Based Benzimidazoles as Antiviral Agents against Human Respiratory Viruses date = 2020-03-25 pages = extension = .txt mime = text/plain words = 6010 sentences = 322 flesch = 45 summary = Compounds 6, 8, 16 and 17, bearing the 5-(thio)semicarbazone and 5-hydrazone functionalities in combination with the 2-benzyl ring on the benzimidazole core structure, acted as dual inhibitors of influenza A virus and human coronavirus. For respiratory syncytial virus (RSV), activity is limited to the 5-thiosemicarbazone (25) and 5-hydrazone (22) compounds carrying the 2-[(benzotriazol-1/2-yl)methyl]benzimidazole scaffold. The herein-investigated benzimidazole-based derivatives may represent valuable hit compounds, deserving subsequent structural improvements towards more efficient antiviral agents for the treatment of pathologies caused by these human respiratory viruses. For RSV, activity is restricted to the 5-(thio)semicarbazone (25) and hydrazone (22) compounds carrying the 2-[(benzotriazol-1/2-yl)methyl]benzimidazole scaffold, in line with the previously synthesized analogues (see above), which show comparable potency in the low micromolar range. In summary, this study reports the synthesis of a series of (thio)semicarbazone-and hydrazone-containing benzimidazoles for the development of novel antiviral agents which have shown the ability to inhibit the replication of three human respiratory viruses. cache = ./cache/cord-355685-wgad0eoh.txt txt = ./txt/cord-355685-wgad0eoh.txt === reduce.pl bib === id = cord-354068-4qlk6y7h author = Friedrich, Brian M. title = Potential Vaccines and Post-Exposure Treatments for Filovirus Infections date = 2012-09-21 pages = extension = .txt mime = text/plain words = 10605 sentences = 540 flesch = 44 summary = Due to the difficulties in evaluating wild-type filovirus infection in small animals and the generally high level of immune protection correlates derived from non-human primate (NHP) models of infection, therapeutics and vaccines are ultimately evaluated in NHP species for efficacy against filovirus. In their study, a heterologous prime/boost strategy with recombinant adenovirus serotypes 26 and 35 carrying GP (Z) and GP (S/G) demonstrated complete protection among NHPs. Each of these vectors was capable of stimulating humoral and cell-mediated immune responses in the context of NHPs pre-vaccinated with rAd5 as evidenced by antibody titers reaching an order of magnitude above those achieved in rAd5 vaccinated subjects (1:32,000 compared to 1:6,800), and CD8 + intracellular cytokine staining was 4.7-fold greater among heterologous prime/boosted subjects (0.41% compared to 0.09%) [59] . This GP-Fc fusion protein induced both cell-mediated and humoral immune responses, and mice vaccinated with ZEBOVGP-Fc demonstrated 90% protection against a lethal EBOV challenge. cache = ./cache/cord-354068-4qlk6y7h.txt txt = ./txt/cord-354068-4qlk6y7h.txt === reduce.pl bib === id = cord-355771-pxkkd3s1 author = Olagnier, David title = Oncolytic Viral Immunotherapy in the Time of COVID-19 date = 2020-11-04 pages = extension = .txt mime = text/plain words = 1793 sentences = 81 flesch = 38 summary = The 2020 global pandemic of Covid-19 has refocused the entire scientific community towards understanding the SARS coronavirus-2 (SARS-CoV-2) and developing urgently needed therapies and vaccines to halt the spread of this newly emerging virus. In this special issue of Cytokines and Growth Factor Reviews -Oncolytic Viral Immunotherapy 2020, international experts discuss the innovative approaches developed for OV-based immunotherapies. Interferons (IFNs) are the most potent anti-viral cytokines induced by virus-infected cells and can reduce the efficacy of OVs. However, many types of cancer cells have been shown to be compromised in terms of generating a potent IFN antiviral state, thus making these tumours a particularly sensitive niche population for oncolytic virus replication. Four reviews in this issue describe our current understanding of the factors that can contribute to a successful super-spreading oncolytic and immune stimulating event within tumours. cache = ./cache/cord-355771-pxkkd3s1.txt txt = ./txt/cord-355771-pxkkd3s1.txt === reduce.pl bib === id = cord-356176-1nwjjgul author = Atherton, J. G. title = The effect of ascorbic acid on infection of chick-embryo ciliated tracheal organ cultures by coronavirus date = 1978 pages = extension = .txt mime = text/plain words = 1753 sentences = 117 flesch = 61 summary = Chick embryo tracheal organ cultures showed increased resistance to infection by a coronavirus after exposure to ascorbate, while chick respiratory epithelium and allantois-on-shell preparations showed no increase in resistance to infection by an influenza virus or a paramyxovirus. Titrations of avian infectious bronchitis virus were performed by inoculating 4 replicate chick-embryo tracheal organ culture tubes previously selected for ciliat activity, with dilutions of virus made in half-log steps, then continuing to incubate the preparations on a roller drum at 15 rev/hour at 37 ° C. However resistance of CETO cultures to IB virus infection rose with increasing ascorbic acid content (Table t and Fig. 1 ). Our results show t h a t aseorbic acid exerted no direct effect on the infectivity of a n y of the three viruses tested, nor did it affect the resistance of cells to infection by the 0 r t h o m y x o v i r u s (influenza) or the P a r a m y x o v i r u s (NDV). cache = ./cache/cord-356176-1nwjjgul.txt txt = ./txt/cord-356176-1nwjjgul.txt === reduce.pl bib === id = cord-355535-01h8yyqj author = Zheng, Xue-yan title = Regional, age and respiratory-secretion-specific prevalence of respiratory viruses associated with asthma exacerbation: a literature review date = 2018-01-11 pages = extension = .txt mime = text/plain words = 3290 sentences = 179 flesch = 39 summary = The primary focus was on the prevalence of respiratory viruses, including AdV (adenovirus), BoV (bocavirus), CoV (coronavirus), CMV (cytomegalovirus), EnV (enterovirus), HSV (herpes simplex virus), IfV (influenza virus), MpV (metapneumovirus), PiV (parainfluenzavirus), RV (rhinovirus) and RSV (respiratory syncytial virus) during asthma exacerbations. A standardized form was used for data extraction, including the main characteristics (author, year of publication, sample size, age, definition of exacerbation, quality, detection method, study design and season), primary outcome (the prevalence of viral infection during asthma exacerbations), and secondary outcomes (the prevalence of viruses in different strata). We also did a subgroup analysis to assess the weight of viral infection on asthma exacerbations with respect to geographic region, population, type of respiratory tract secretion examined, and detection method. Because difference in the geographic regions, age, study population, type of respiratory tract secretion, and detection method significantly confound the determination of the prevalence of individual viruses, heterogeneity was not assessed in this study. cache = ./cache/cord-355535-01h8yyqj.txt txt = ./txt/cord-355535-01h8yyqj.txt === reduce.pl bib === id = cord-355259-779czzzx author = Yang, Xiaoyun title = A Beneficiary Role for Neuraminidase in Influenza Virus Penetration through the Respiratory Mucus date = 2014-10-15 pages = extension = .txt mime = text/plain words = 6143 sentences = 324 flesch = 47 summary = Swine influenza virus (SIV) has a strong tropism for pig respiratory mucosa, which consists of a mucus layer, epithelium, basement membrane and lamina propria. The microscopic diffusion of SIV particles in the mucus was analyzed by single particle tracking (SPT), and the macroscopic penetration of SIV through mucus was studied by a virus in-capsule-mucus penetration system, followed by visualizing the translocation of the virions with time by immunofluorescence staining. These findings clearly show that the neuraminidase helps SIV move through the mucus, which is important for the virus to reach and infect epithelial cells and eventually become shed into the lumen of the respiratory tract. To this purpose, we applied swine influenza virus to a model we previously set up using porcine respiratory mucus, pseudorabies virus (PRV) and single particle tracking (SPT) [20] . This does not only confirm the beneficial effect of neuraminidase on releasing SIV from respiratory mucus, but also highlights bidirectional synergistic interactions between influenza virus and bacterial infections. cache = ./cache/cord-355259-779czzzx.txt txt = ./txt/cord-355259-779czzzx.txt === reduce.pl bib === id = cord-356188-rwf78stz author = Oshansky, Christine M. title = The human side of influenza date = 2012-07-01 pages = extension = .txt mime = text/plain words = 9515 sentences = 486 flesch = 36 summary = Few studies have examined the role of monocytes during influenza infection in humans, particularly regarding the specific subsets mentioned above, but comparison of IFN-␥ production from T cells cocultured with CD64 ϩ CD16 Ϫ and CD64 Ϫ CD16 ϩ monocytes [119, 120] Cellular immunity Class I HLA presents peptides from internal and external viral proteins. As influenza primarily infects epithelial cells lining the respiratory tract, lung-resident DCs and macrophages are particularly important for efficient development of an adaptive immune response. [189] ), and in vitro studies suggest that activated human V␥9V␦2 T cells may have a role in the antiviral response by killing influenza-infected, monocyte-derived macrophages and producing high levels of IFN-␥ [190, 191] . Broadly cross-reactive antibodies dominate the human B cell response against 2009 pandemic H1N1 influenza virus infection Characterization of the human CD8ϩ T cell response following infection with 2009 pandemic influenza H1N1 virus cache = ./cache/cord-356188-rwf78stz.txt txt = ./txt/cord-356188-rwf78stz.txt === reduce.pl bib === id = cord-355913-fhvt1ht1 author = Burrell, Christopher J. title = Virus Replication date = 2016-11-11 pages = extension = .txt mime = text/plain words = 9861 sentences = 405 flesch = 42 summary = Little is known about what determines whether a given picornavirus positive-sense RNA molecule will be directed (1) to a replication complex (a structure bound to smooth endoplasmic reticulum), where it serves as template for transcription by RNA-dependent RNA polymerase into negative-sense RNA, or (2) to a ribosome, where it serves as mRNA for translation into protein, or (3) to a procapsid, with which it associates to form a virion. In the case of positive-sense single-stranded RNA viruses, the incoming RNA genome can bind directly to ribosomes and be translated in full or in part without the need for any prior transcription; all other forms of incoming viral RNA must first be transcribed to produce mRNA, in order to begin the process of expression of the infecting viral genome. cache = ./cache/cord-355913-fhvt1ht1.txt txt = ./txt/cord-355913-fhvt1ht1.txt === reduce.pl bib === id = cord-355906-yeaw9nr8 author = Nedjadi, Taoufik title = Tackling dengue fever: Current status and challenges date = 2015-12-09 pages = extension = .txt mime = text/plain words = 6821 sentences = 355 flesch = 46 summary = Recent advances in molecular biology have revealed that the genetic makeup of the three elements of dengue infection (the virus, the vector, and the host) plays a primordial role in the pathogenesis of the disease and could potentially contribute to the DHF progression [19, 24, 35] . Dengue virus serotype-1 antigen was expressed in a vector based on pediatric live-attenuated Schwarz measles vaccine (MV) by using the envelope domain III (EDIII) fused with the ectodomain of the membrane protein (ectoM). The Centers for Disease Control and Prevention (USA) have also developed a live-attenuated vaccine named DENVax, which was found to be highly immunogenic in both children and adults and has currently entered phase I clinical trial in the United States [96, 97] . cache = ./cache/cord-355906-yeaw9nr8.txt txt = ./txt/cord-355906-yeaw9nr8.txt === reduce.pl bib === id = cord-354582-fniymnmf author = Ma, Zhiqian title = Reverse genetic systems: Rational design of coronavirus live attenuated vaccines with immune sequelae date = 2020-06-30 pages = extension = .txt mime = text/plain words = 8373 sentences = 423 flesch = 44 summary = In this review, we systematically describe the role of reverse genetics technology in studying the effects of coronavirus proteins on viral virulence and innate immunity, cell and tissue tropism and antiviral drug screening. Recently, reverse genetics techniques, including targeted RNA recombination, in vitro ligation and bacterial artificial chromosome systems, vaccinia virus vectors and transformation associated recombination (TAR) cloning, have been successfully used to manipulate the genome of coronaviruses (Fig. 2 ). Using a recombinant SARS-CoV strain with reduced nsp3 de-ADP-ribosylation activity showed that this mutant strain led to virus attenuation in mice but protected them from an otherwise lethal SARS-CoV infection and significantly enhanced the innate immune response, indicating that it is an important virulence factor for SARS-CoV . The N protein plays an important role in viral pathogenesis since BALB/c mice immunized with recombinant virus MVA-MERS-N exhibit stronger T cell responses and anti-N monoclonal antibodies protect mice from lethal infection by MHV (Nakanaga et al., 1986; Veit et al., 2018) . cache = ./cache/cord-354582-fniymnmf.txt txt = ./txt/cord-354582-fniymnmf.txt ===== Reducing email addresses cord-003707-fbe47bgi cord-005258-gps8rzb5 cord-018393-5jlqn7wq cord-020789-slsfhrkx cord-020010-q58x6xb0 cord-023608-w2g7v7g1 cord-022830-tvt58gtn cord-024188-d7tnku8z cord-103688-n7hzpbyf cord-270161-vaejyy4i cord-271568-qgpi2kcs cord-271076-436nxsua cord-275602-cog4nma0 cord-290481-i2ppvsh5 cord-295873-kykyubdq cord-302111-kg0dmgq0 cord-301064-ex6qb6zj cord-302047-vv5gpldi cord-303297-fiievwy7 cord-304569-o39kl5k4 cord-323009-frej2qmb cord-330296-706hf4qw cord-331673-xv1tcugl cord-348163-9q1rt8i7 cord-348427-worgd0xu cord-345848-s84lxe6l cord-348860-zaimorg0 cord-350151-s75d1hat cord-350703-vrqltz3s cord-355535-01h8yyqj Creating transaction Updating adr table ===== Reducing keywords cord-001065-j4hvyyoi cord-000180-howix091 cord-003232-nquw7qga cord-000708-iuo2cw23 cord-002274-6rddtogo cord-001834-6xf4o3oy cord-001542-f089bs8r cord-002423-1u44tdrj cord-002601-d8908t93 cord-003122-a3f4l6iu cord-000265-llilwq1u cord-002937-7xauocti cord-003092-3owcqt3d cord-003004-iif2lnez cord-002932-5e7xrd1y cord-000012-p56v8wi1 cord-002581-r7mskri0 cord-000539-uh3q65we cord-001616-9sc2xmqr cord-002072-qbh728ec cord-000902-ew8orn0z cord-000114-f0vud3gu cord-000937-8vk89i4h cord-001985-iwfidoer cord-001676-68y733y3 cord-000113-d0eur1hq cord-001958-2gt3fwpy cord-003523-byxuruk1 cord-002136-mkl89qkt cord-001120-fxd533b4 cord-001420-b4zcvd04 cord-001528-33f94doo cord-000777-7cty5s6o cord-000804-0hlj6r10 cord-001397-nrq4ncdf cord-001748-7e8px4vx cord-001142-puj74k7y cord-001974-wjf3c7a7 cord-000238-om92cx5q cord-000359-y0m1utug cord-000729-iq30z094 cord-002337-8v907g24 cord-004477-qu2o2iu1 cord-003926-ycdaw2vh cord-003861-qeao4ghg cord-001207-yjaiybwf cord-003993-3bozjfv7 cord-002728-6oyw5sqv cord-002921-i5jxn1vj cord-003130-p2h8p5bm cord-001831-3aonqyub cord-002338-ri7v2ka3 cord-000501-qz68gtd4 cord-003166-k3jxvzfi cord-002327-tocqabgu cord-003492-rodqdtfj cord-002874-9rxv6fy9 cord-004280-c470nlie cord-000760-4yfohp9w cord-000050-tfcerilc cord-002407-25cawzi0 cord-003216-5qioku84 cord-004211-58x3nnsc cord-003880-uuuzfyjm cord-003482-f1uvohf0 cord-003302-vxk7uqlc cord-002410-2zi5iv2t cord-000933-nn9gj0z1 cord-003817-k3m72uxw cord-003503-t6cnjwpd cord-004608-3u00cpsc cord-003044-9uqa39j9 cord-004761-cgby8bhz cord-002076-7t4d4vvo cord-003707-fbe47bgi cord-003466-599x0euj cord-002482-2t09zqqi cord-002933-zmx4k46v cord-003792-v48xeqdz cord-003767-9xbu4hnq cord-003639-bjtxf1y8 cord-003961-gs75ebo4 cord-004501-guiy89x8 cord-002757-upwe0cpj cord-004771-4yinnncj cord-004672-0lf5j8lo cord-003598-m2fsrwvw cord-004034-mjkixqhs cord-004751-4vl0cvyq cord-004724-llex3yed cord-004719-3stcx0dd cord-003403-ypefqm71 cord-004774-fvf671jn cord-003917-bswndfvk cord-004781-ajf9zig0 cord-004775-foaf3vyl cord-004743-ido065mh cord-004827-bnf3mvaf cord-004830-vmka378d cord-001521-l36f1gp7 cord-004841-wf0o3whi cord-005876-d8sid7gd cord-005081-kxrzv16n cord-005246-cskb0njm cord-006819-sxz1s6kz cord-005281-wy0zk9p8 cord-005885-r3qtoqu1 cord-005258-gps8rzb5 cord-006790-lye0qjw8 cord-006997-sghhdjyi cord-006089-08g206kf cord-004848-2cfphi88 cord-006129-5rog0s98 cord-004998-wuixnqy5 cord-007149-m4xsx9ev cord-007176-61e9obb3 cord-006252-cbelsymu cord-007898-nky7bo6u cord-008700-knbf8m4x cord-006106-u5npu6ng cord-006954-ec9x8thb cord-007796-zggk0x2q cord-007362-pjpkz6wv cord-006892-n2ncamqh cord-007733-zh8e76w7 cord-008454-8brxpotx cord-007792-596jxrm5 cord-009615-xcz8m9a7 cord-006640-25ykas09 cord-007575-5ekgabx5 cord-008013-blf57r7u cord-007445-2folsh35 cord-006285-kkxdmzk9 cord-008556-oetrdm8g cord-007094-ur9sz21s cord-008149-kdlcaium cord-007717-7x1mqqmf cord-007417-az8xd66p cord-007764-7750z41g cord-009383-ozx5u0t3 cord-009504-sn00p8iw cord-008686-9ybxuy00 cord-008333-1wepke2o cord-007784-fq2urilg cord-007170-svsfu7fj cord-008716-38sqkh9m cord-009820-fi54s0x7 cord-009589-xfdgk2j6 cord-007710-0u5ot5h4 cord-009577-29u7pdpk cord-009702-02bo7pnl cord-007731-wu7i548j cord-009561-pg4jmvw4 cord-007843-yqdqm4rh cord-009836-7o6htufh cord-010248-ln800g5z cord-007530-eyk015n3 cord-008551-yu71iewp cord-009144-3slh1nbk cord-010159-uo47oab1 cord-009791-k09vcq96 cord-010016-fs8pjy1z cord-010189-makhaypd cord-011917-6u0t4hy8 cord-008764-j9qmw4zy cord-010235-hu6o1ggc cord-009846-o6wj8z6e cord-010168-aiqbqnaa cord-011129-btaxvmsr cord-010188-884d196k cord-010273-0c56x9f5 cord-010001-u0d5jkp1 cord-011438-imbpgsub cord-010343-tqqt0hj7 cord-011457-hqxybv1k cord-013412-gj443yei cord-010222-5oxie0zc cord-012582-k1mjik27 cord-013073-siy7dvlo cord-015871-1tuf4zxi cord-011880-qlutgfu2 cord-014541-2i0jga5v cord-013176-6ckuya1w cord-014462-11ggaqf1 cord-014796-6rw2wk1q cord-016070-e9ix35x3 cord-016171-17ut32bu cord-010374-z9ygudv6 cord-014397-7b88ycv8 cord-012418-6ralcn8p cord-015023-ishxfinx cord-011106-h20vbmbo cord-015619-msicix98 cord-015764-ly68q5z0 cord-013526-6fip93l2 cord-016475-7ldxvbpz cord-016796-g4kqqpy1 cord-016652-x8t3lf1x cord-016309-6mw8okmt cord-014908-jys1y0k9 cord-016798-tv2ntug6 cord-016451-k8m2xz0e cord-016808-gy8d8285 cord-017070-05vlz5dn cord-016928-yigz9qiz cord-016663-qnp99m7o cord-016990-ot1wi3xi cord-016499-5iqpl23p cord-016538-4og05fuo cord-016995-5izyl234 cord-017249-la5sum39 cord-017158-w2tlq6ho cord-016882-c9ts2g7w cord-016754-6fv8mjld cord-016576-1yqwci0y cord-017429-3evwlfac cord-017008-c7skxte0 cord-017489-ftz9190a cord-017364-d9zmdm23 cord-017326-1caeui30 cord-017748-xy26tk0t cord-017287-70lk77zb cord-017537-ztdz4a2s cord-017959-g0nf1iwm cord-017527-ylng1us2 cord-017568-8fnr4zzv cord-018164-h5k1zsyg cord-017764-h1w9gbxk cord-017167-8cdbcrh7 cord-017331-ru7mvfc0 cord-018078-clxzp1ph cord-018058-n3majqes cord-017758-zfudssm9 cord-018364-b06084r1 cord-018040-k0h5ejjt cord-018463-a6qu0cuv cord-018166-savdgy0u cord-018302-lmly43rd cord-018319-tylkbh4h cord-018165-afzjx2ci cord-018555-3lta1tbp cord-018089-m94q75xn cord-018265-twp33bb6 cord-018816-v3ylisbt cord-019982-hyxrgamj cord-018393-5jlqn7wq cord-018724-ss8x2g3b cord-017752-ofzm3x3a cord-018017-c8myq6bi cord-020101-5rib7pe8 cord-018477-hgvqd1ej cord-018811-zhwr3h07 cord-020087-gs0pc6ee cord-018804-wj35q88f cord-021034-hnw7a3a1 cord-017824-0pinevfc cord-018437-yjvwa1ot cord-020235-stcrozdw cord-018441-r6wwpfcy cord-021069-v9f9874x cord-020097-eh5deunk cord-020714-h1fevqcw cord-018706-gykw2nvt cord-020789-slsfhrkx cord-018639-0g1ov96t cord-020969-lh2ergpm cord-020712-l9cn0n99 cord-021588-ec7udsmw cord-021413-1ht1xm88 cord-021894-lq8yr710 cord-019051-gtruu1op cord-021499-up5vftj4 cord-021116-rh0e4n2w cord-020756-d9f5fd7x cord-021770-zn7na974 cord-021375-lca26xum cord-021805-2j07zw6q cord-021552-6jbm869r cord-022254-8y5sq72c cord-021465-2pj26fmv cord-022348-w7z97wir cord-020010-q58x6xb0 cord-022084-hap7flng cord-022324-tcltmhi7 cord-021990-a8ku5rke cord-022163-7klzsrpu cord-022674-90g0461f cord-021555-rrverrsj cord-022349-z8w1wkm8 cord-022262-ck2lhojz cord-022439-8wy7rpqv cord-022305-uvor9rts cord-022196-1tionxun cord-022378-ovxmy1as cord-022947-ruizhgwh cord-022399-66mzbynu cord-023584-yaxawqhj cord-022822-7346069t cord-023034-j8zwcfys cord-021966-5m21bsrw cord-022453-xe5v7947 cord-023608-w2g7v7g1 cord-022354-aqtceqqo cord-023092-unjv71qv cord-022128-r8el8nqm cord-022393-s26d54ew cord-022383-pz0htccp cord-023200-3caevjvh cord-025181-eg108wcd cord-022830-tvt58gtn cord-022980-tkii8se4 cord-022960-u4s23x1r cord-023622-tul7bonh cord-023678-9q68ftr9 cord-023564-kpqvyxxe cord-023740-g84fa45m cord-026641-eemp6b5j cord-023831-93xqrblk cord-022252-9yiuuye3 cord-023293-te0n2vvp cord-026130-ki7bn67o cord-025995-nxeg03xj cord-023488-jf2xl3vl cord-023721-e0zp2gux cord-024188-d7tnku8z cord-023726-2fduzqyb cord-023731-jqgervt7 cord-027654-k0uby99n cord-023724-5at0rhqk cord-023925-qrr7jcwe cord-027752-xcpv9k22 cord-031840-k9l91unc cord-023705-3q9yr6np cord-027550-yyqsatqw cord-025704-icedihm2 cord-023143-fcno330z cord-029419-b0w9nomq cord-026340-2nf97zvc cord-030961-5gzc7193 cord-103135-nly9vojr cord-027473-8zerjwa0 cord-102704-wfuzk2dp cord-030279-pv770doe cord-102862-oq54sfx6 cord-030028-s6sxi8uj cord-035163-tqh5wv12 cord-076082-4kpkhz0o cord-048368-wm4c7rk6 cord-103688-n7hzpbyf cord-102908-sr7j8z9c cord-102383-m5ahicqb cord-035015-slgywe0c cord-214795-8jweuq50 cord-104286-5yw4zwo4 cord-161674-nk0wie0w cord-203232-1nnqx1g9 cord-048466-fj9l8che cord-171099-d0qr84xg cord-104317-t30dg6oj cord-252456-971d0sir cord-102905-rlee32x7 cord-102898-eyyd7ent cord-245161-xbw72k4m cord-252466-usrpodjx cord-212761-4bwatc2r cord-253594-9gbo8viu cord-253143-73dsc6q3 cord-252397-qlu7dilh cord-252012-hdjbxah8 cord-151024-qe7c2uks cord-254200-9bpdfxrt cord-252725-e3pazjdi cord-232446-vvb2ffhv cord-253705-utp8po48 cord-252769-fe50u028 cord-252871-qfrpuy3t cord-253466-7gpije5d cord-254932-b447w202 cord-252147-bvtchcbt cord-254090-x8tnweih cord-255075-6azu6k3h cord-254592-wa5il5go cord-255479-yd5cbwnx cord-254527-zddwajzg cord-255026-fdp6mies cord-254194-962vynwk cord-253825-d9borky8 cord-252974-pwx27kdi cord-255623-qdpdsye9 cord-255137-utg8k7qs cord-254963-cnvxlv6h cord-252048-ftbjsoup cord-254100-u6x5zd4i cord-255096-27dfbhsl cord-255217-l2ak5ygj cord-254890-4ynsgu6c cord-255697-trig04hd cord-256837-100ir651 cord-257064-iafm3pcc cord-256510-orr2roxz cord-256325-q70rky3r cord-257569-36qx1sy9 cord-255181-du6rqc6i cord-255690-xc4bxin4 cord-256917-6h1ip37z cord-257019-lj1yzjn0 cord-255339-oudj079q cord-255734-038xu4hq cord-256036-gd53s4dv cord-256370-cz88t29n cord-257321-l1swyr6g cord-258489-pyfc7jde cord-257163-hodykbcb cord-257299-z9u12yqb cord-257220-fe2sacjj cord-259505-7hiss0j3 cord-257255-n5o368ih cord-258333-jmk8hdk2 cord-257553-479x7av6 cord-259458-o2yts5pq cord-259233-smmhhroe cord-256615-gvq8uyfk cord-259627-8stewshp cord-260420-4s7akmdp cord-259927-xh9cw9ao cord-257665-12gyrmh2 cord-258027-f3rr5el1 cord-260472-xvvfguht cord-258389-1u05w7r4 cord-257008-7q5s1vu1 cord-257652-ndt8f812 cord-260554-nao59qx4 cord-261417-4pf5nsw2 cord-260705-huyyw5z6 cord-260168-rb7j94dh cord-262722-cz3ce29n cord-260147-w19hl2vs cord-261160-g92zhv19 cord-258783-ev0h95b9 cord-260014-q5sug7uu cord-260956-w6wxsg4p cord-258626-p469ysi8 cord-259235-p0yj9qug cord-259260-qcfgigga cord-260496-s2ba7uy3 cord-260708-l9w5jhsw cord-263017-rh86g4jk cord-261961-u4d0vvmq cord-262776-6k7tcgfs cord-263245-2qub96mz cord-262752-bwofzbwa cord-260690-h5pjv2dw cord-262748-v4xue7ha cord-261241-eqf6ame6 cord-263165-bv4dh9eu cord-263315-g7os15m1 cord-264291-0czphube cord-263157-8jin6oru cord-262514-1e2bc0bi cord-264264-7j3xirfg cord-261171-iknoqb4d cord-265445-bazcczdj cord-263484-afcgqjwq cord-263764-2ewz8ok4 cord-263868-ewnf96cz cord-264794-bgygebgx cord-263785-0iift8zy cord-264350-4zxp3uae cord-263619-p17oomzn cord-264308-y6xuxj16 cord-264884-ydkigome cord-264699-l8db5gll cord-264406-s5c0grz0 cord-266138-yibbiiij cord-266136-81sx505i cord-264916-c4n0kyog cord-265461-hj2b1wc4 cord-265751-q1ecpfyg cord-265681-ab8j4o1u cord-266985-9qwttt2y cord-267326-355q6k6k cord-265642-7mu530yp cord-264408-vk4lt83x cord-266822-ecq50ye2 cord-267003-k7eo2c26 cord-267134-5gz2dotn cord-267194-i6vetquk cord-268999-6748c617 cord-266199-smlq11y9 cord-267831-uu883ofc cord-269324-zh1a3gwh cord-267140-vdcf6vok cord-269623-9pxdeva3 cord-268501-z4oztgi0 cord-267567-w39f584z cord-266762-z08rn959 cord-269519-8hr8wyrr cord-267261-8z4aqfff cord-269975-1ebmq7t8 cord-268417-6eyetb5i cord-267733-fuz8r3vj cord-268593-rvxxv1dn cord-268788-jcu3pasy cord-269193-a647hwu9 cord-270243-moxleyjg cord-271105-eyigl0wz cord-270772-zshjrc87 cord-271709-5frm3dnb cord-270911-z637eh2z cord-270091-sqrh8ylt cord-268645-5op2m7pu cord-270161-vaejyy4i cord-269126-d81z6t0a cord-271171-tohbzenc cord-268540-wrjzr3ws cord-270803-jtv5jmkn cord-271692-60nlid3c cord-267671-ys43n672 cord-271927-u8p6c9w4 cord-270940-acwkh6ed cord-272052-8vvpm4tx cord-270647-vn4kirrx cord-272099-26nhza2s cord-270335-8vqi9c68 cord-272405-jmwn8pdn cord-273343-als886fe cord-271568-qgpi2kcs cord-272829-i4jh6bcn cord-269426-82g5eiyg cord-271172-y48dovux cord-271076-436nxsua cord-271313-h9v0nmx5 cord-271884-86yl9ren cord-273372-69rlh9or cord-270670-cubh9jxc cord-274765-3wzht843 cord-272981-8gahvdt0 cord-274112-6t0wpiqy cord-271650-biq0chyn cord-275013-na6319rg cord-274306-cxvnv8dy cord-273019-hbpfz8rt cord-271790-3s8o774l cord-271091-ffn59sgf cord-275602-cog4nma0 cord-274643-vjb2yt93 cord-272066-f6q6q3io cord-271122-3fsl5589 cord-273326-gmw8gl2r cord-273708-2q64at3z cord-276006-mjjnkqv6 cord-273777-qb0vp9gr cord-276193-cngz535o cord-276348-vr5fit8r cord-276585-m1dkkbq7 cord-276212-ys5njiw0 cord-275719-ru33ubss cord-276009-p98wjtjb cord-276052-gk6n8slx cord-276715-d1nh2dvb cord-275821-yu39aw54 cord-275795-ee7qyw5h cord-275570-i9fw0afj cord-274080-884x48on cord-277392-s0bldxg9 cord-277107-gs7j6fxo cord-276583-j8bf0eme cord-278093-0twnkv93 cord-277327-il8uaavn cord-275683-1qj9ri18 cord-277010-2iecsho0 cord-276039-nqqwnmwc cord-278250-dwok857k cord-275538-c44gmu22 cord-277400-w7mvk3x4 cord-277641-nb1p1akx cord-278099-ypov9ha3 cord-276506-dj7dyo0x cord-278456-gsv6dh36 cord-276616-odmnvv7m cord-277309-kelebqr6 cord-278635-vwdxr1bl cord-277970-sb1wjd3b cord-278465-tjjkz16y cord-276364-zyw5aukk cord-279694-25rblhwb cord-279798-b5tduubu cord-278973-82n0d1dh cord-279617-xuzu55cg cord-276908-9jthjf24 cord-280854-cxpgwwjd cord-278482-j5zlismf cord-277417-f71jwdzj cord-280987-uhxk5b1b cord-280048-b4dz1lnn cord-279557-hk77e3pp cord-280391-5kiu2pb6 cord-278913-u6vihq3u cord-280986-i27mge10 cord-278876-il7g78w1 cord-281332-5mddyv0n cord-278479-vl296i1b cord-278511-je1509ar cord-280429-4fota9rl cord-278684-txlvla0j cord-280427-smqc23vr cord-279691-v5kpmk0b cord-280130-ewqe9edq cord-280564-kgoczioe cord-282628-6uoberfu cord-281061-uoszpnst cord-280878-1kt51viz cord-279849-zzkliu76 cord-281593-bq12grqo cord-281158-vjh9z7l4 cord-282344-o1rkx2z4 cord-280781-u3wd27rn cord-283405-aozxvxxs cord-283641-2u16otbf cord-279418-3r1ijafm cord-282204-j1slaefb cord-281429-6lv3di4x cord-284523-lknyehsa cord-281844-c0uhcatg cord-284880-xsh3wkqy cord-282343-cko4curf cord-281281-knelqmzx cord-285462-9i61rsei cord-285148-bch7814v cord-283880-lrrkuist cord-285367-jxlt0gby cord-284941-wfn0pnev cord-285856-0sw3wt1i cord-284266-tbndldhr cord-290034-4b0mshqa cord-285330-td4vr0zv cord-282742-eyukbot7 cord-286137-4cbh3u3z cord-284372-v95fzp8n cord-283756-ycjzitlk cord-286708-igu984oc cord-286298-pn9nwl64 cord-283964-k3hy2ewx cord-286219-qcx5ehnh cord-288703-wdh1jiry cord-285935-5rsk6g7l cord-284156-btb4oodz cord-287286-4l963z2q cord-288111-0ufc54kw cord-288348-b10e023s cord-284479-75zgljet cord-286719-1xjmlwqr cord-287711-gw8mgg4m cord-287348-00yaxpkp cord-287337-2ljbsia2 cord-288372-48wao8a0 cord-288231-vg8bwed9 cord-287554-2lqy2ix9 cord-288238-36hiiw91 cord-286559-y8z0pwgn cord-287151-4hlvrfeh cord-287466-ag5y781z cord-285547-7m3dh8hu cord-288879-rj03dsib cord-286741-h3oix9zc cord-287851-9p0dr7rl cord-287770-oxfnt2n4 cord-288945-c9ow1q5c cord-288930-h13cxuh3 cord-289360-h6wvx7gw cord-288734-xinkqs6u cord-289593-81vu2kbu cord-290481-i2ppvsh5 cord-289406-54vyzxjf cord-290385-0smnl70i cord-290231-4m9lj0uq cord-290133-4ou7ubb4 cord-290556-x7t7zqjd cord-289093-si8btsab cord-291294-w5ecsht4 cord-290282-oxyzndsj cord-290352-0pc5eji4 cord-290432-4dli5emd cord-289017-vwye3pk9 cord-291707-dzmvjh7j cord-290149-eed4v2jl cord-290851-1e5e033r cord-290509-56pfww0l cord-290539-8ak2tths cord-290855-6umgvt28 cord-291860-dw1sfzqx cord-290617-45be6gxe cord-290540-r0d6oaez cord-291534-c6cjxq07 cord-291816-d4j8samu cord-290548-0wezrr1b cord-291561-sxvgue36 cord-291156-zxg3dsm3 cord-290993-bsnja161 cord-292075-t9z7zqz4 cord-293375-qcy56ui7 cord-293472-d3iwlpsr cord-293975-np9xdag5 cord-292830-gcfx1095 cord-292643-n6xp5mlz cord-292286-ygomb3oi cord-291063-de7v4e5s cord-291113-iizj932l cord-291946-kq0rsuxj cord-292353-z86rjwle cord-294568-12eyo13f cord-297339-et2305rz cord-292416-3hhi4wps cord-292657-gq3965se cord-293540-45awgabp cord-295189-bz3gi15h cord-295792-hajvtzj9 cord-295640-mhfu0e9r cord-294323-mryiqmsw cord-294544-iutcduix cord-294478-3ickafd3 cord-293097-poh1y6o7 cord-292828-29jbf9ik cord-292575-vsswxwdi cord-294842-aesiff1f cord-294312-ju6vuywm cord-296935-y77c4ro4 cord-293387-0m1ngob3 cord-293421-0ksn0fc7 cord-294812-nnlzwaf1 cord-294125-v2dr4hm0 cord-295041-5vpawtef cord-297203-f3f31h4r cord-293732-rxd1lyi7 cord-294585-dl5v9p50 cord-295191-xu26mvc3 cord-295531-zojb3cew cord-298032-3zlu8g8y cord-296309-i1mpov7k cord-296819-gztmidn2 cord-297834-me1ajoyb cord-297494-6yxmaihl cord-294108-uvnh0s9r cord-297131-3a9vjpvn cord-298905-c2uuvfm5 cord-295062-8rl4kswe cord-295873-kykyubdq cord-298036-2zurc60t cord-295445-f4p00yaw cord-300020-edolh7ww cord-297960-4x1j0iqg cord-296635-8r3tm966 cord-295433-olmein3q cord-298214-ivu4erpq cord-300189-gsp1dozg cord-297662-slmlhqnb cord-298051-ej8qxkce cord-298019-gf2asni1 cord-298862-8bijio30 cord-302277-c66xm2n4 cord-302111-kg0dmgq0 cord-302425-aaxvlktp cord-298033-kzdp9edn cord-300837-d0a8y5qh cord-301064-ex6qb6zj cord-298489-uqrzzh0e cord-298733-jole21wq cord-300133-yc2wxgid cord-297790-tpjxt0w5 cord-299207-lw0cv74b cord-299379-ch7a39d6 cord-300810-a1skdp67 cord-303040-ha8gufh8 cord-299786-wuve0tjz cord-301285-p83ondy8 cord-301592-n5ns3m34 cord-298736-9bvyp21d cord-300711-yibdumij cord-298678-hjxph9jm cord-302716-wfla3l20 cord-302047-vv5gpldi cord-302021-42vqmndl cord-298745-3rrlap70 cord-302486-z36hcvrx cord-302055-s155i4e9 cord-302614-siyyve9e cord-299549-bjqwwzam cord-303297-fiievwy7 cord-304278-0qy1nngs cord-303186-2hxlx1j2 cord-300522-okbupw61 cord-300435-vs0ntcsb cord-304251-dohglrm1 cord-301362-f3lp10lm cord-304850-9xetsc2c cord-305336-wxiazglk cord-304807-j2k1oel2 cord-304481-yqc8r3ll cord-306983-6w2fvtfy cord-303533-6s01qplg cord-304343-m7tbdfri cord-303665-l57e54hu cord-305263-fgwf6wy3 cord-304498-ty41xob0 cord-307893-mvl0wrsj cord-306733-df36w6l7 cord-308385-bcph664h cord-304876-txaoz7oh cord-305302-go87uu06 cord-304747-ojyxs3cp cord-305807-n3fs7533 cord-307817-2vy28i4m cord-302529-43pd2qsp cord-305165-3twlnkac cord-305742-wf6qxplf cord-309048-emmtplv3 cord-304424-048xo7jn cord-305488-vk59ghjm cord-307744-wbr84taq cord-304569-o39kl5k4 cord-309489-ubf55eux cord-307046-ko3bdvo0 cord-307813-elom30nx cord-309346-4mdxe6ri cord-309120-05bg7rfa cord-309179-5hlatbqe cord-307918-8y89p11a cord-309067-aemjbkfj cord-310141-2jofy8fo cord-308201-lavcsqov cord-308857-otsrexqu cord-307899-427a7i3h cord-307632-x9bxnrtn cord-303265-v6ci69n0 cord-305327-hayhbs5u cord-309381-cb80ntxs cord-306083-juysx6yo cord-310255-aixq5mhf cord-310371-pylrg91h cord-306948-wkisfz1m cord-308686-tbwecf7o cord-309635-1tgovkr7 cord-311823-85wj08gr cord-311748-yr2ep7uf cord-312964-vsrqmmv7 cord-310140-h7uwl0pb cord-308066-lrbi5198 cord-309488-8guapzke cord-310942-191m0e65 cord-307364-j86t65qu cord-312431-de7zhswl cord-314254-9ye8tfvz cord-306424-gf0bglm0 cord-310920-itqwhi6a cord-311410-lgqup9ug cord-310795-n78s0sg2 cord-310171-1fmsxx2s cord-312461-5qzpo6l1 cord-313356-ninzeazy cord-314190-fvdock94 cord-310439-z0bxsjug cord-311908-sgdq6j6x cord-310870-w8wu8vno cord-309642-wwaa6ls0 cord-314390-q36ye9ff cord-313312-h607itv2 cord-315346-ebfjba4y cord-314325-nquov2i0 cord-314166-79323mzd cord-313301-7mkadtp9 cord-311382-ioemd0ij cord-316295-x636ux34 cord-315037-lmur80te cord-316245-n6tmn4ph cord-311012-wyglrpqh cord-315167-ph15z424 cord-315781-dejh8q22 cord-316951-1swlhdz5 cord-314201-6njwigco cord-312688-12san3m7 cord-312332-rwmuucsp cord-315131-4yb2b70g cord-317198-mean7sj9 cord-315339-dcui85lw cord-317244-4su5on6s cord-313598-2t40ss6h cord-317404-jvtozj4v cord-316063-9bg2dm8e cord-316996-8yimrpaz cord-316273-vo6j8zb0 cord-315918-12rbbe8c cord-316682-4360s2yu cord-314825-fzba05wn cord-317501-yblzopc3 cord-318172-bdotp9ko cord-317277-rr9zue4l cord-317851-lj07947c cord-317971-kuwargnp cord-318725-09a32vyg cord-319746-6bccxgbd cord-317496-6o2upns3 cord-316894-zhmuzv7z cord-319208-jrxz59bb cord-318786-qd0k8174 cord-319754-5isw53wl cord-318495-1w74wf02 cord-317508-03u2vtzk cord-319814-tyqb473m cord-319210-yqimufdh cord-322748-a5131tv9 cord-317412-f3ua8ks3 cord-318551-c1qr27lg cord-321756-a7eh4dkb cord-319761-bu5pzbnv cord-317619-o7qfugjw cord-321053-lgae22f8 cord-321562-hk4hzl13 cord-320935-3n157yl4 cord-318686-we6pveus cord-320030-ojtp90na cord-320693-de1lmzl1 cord-319933-yp9ofhi8 cord-323333-keshu99t cord-320055-6ycp8m89 cord-320713-b37c8aye cord-318853-mxyxwkhx cord-321835-qn33sx8x cord-319379-qe56u93a cord-321741-aq76s37x cord-320015-lbr2q4qh cord-322082-80ym2rsq cord-324775-3x5os79m cord-323195-buzcb8ya cord-323358-05bk91lm cord-323404-3mw4q7m3 cord-321112-w7x1dkds cord-322234-1zyy536y cord-323009-frej2qmb cord-322904-9mta0aem cord-323311-xl2fv0qx cord-323987-gh1m05gi cord-322206-roxa3ix6 cord-324950-ux7shvji cord-324280-e8mj6ecl cord-321481-vrfwczve cord-325280-4whzcmqv cord-323700-5awng7h1 cord-325825-0lyt8gfq cord-323793-c69joaqs cord-324984-ojrpsdt9 cord-326719-p1ma4akz cord-323710-cmbg0ty8 cord-325875-93krp81r cord-324696-htx0ul4o cord-323930-pl3qlcpo cord-325635-don9qjpz cord-325830-mrtpihc7 cord-324295-9c1zxjng cord-325230-3kg4oe4g cord-325750-x7jpsnxg cord-326225-crtpzad7 cord-325326-2bbqz4o7 cord-325969-9zhmmvdg cord-327013-gc6o8ou3 cord-327199-ggomuomb cord-325915-dw989txm cord-325827-492xi3ee cord-327000-oyg3oyx1 cord-326725-0jgw083h cord-325925-010xj69x cord-326027-58whwspe cord-325325-xw7627x9 cord-328252-dk54w8z9 cord-326177-zzsaf3bl cord-327855-txryqil7 cord-325712-9kbnyqt3 cord-326960-9phlylce cord-327660-p1b07b4t cord-328621-3jda0k2u cord-329857-pcsuu597 cord-325611-tu1bn4hu cord-329145-424vv8a8 cord-329050-vzsy6xw1 cord-329078-gnnis7pl cord-327777-pg98zc6o cord-330827-gu2mt6zp cord-330508-uilejxmi cord-326160-mf0vh6iu cord-328753-qwdxgk4z cord-327392-9psblokc cord-329527-0rlotyz3 cord-330296-706hf4qw cord-329493-ueqlhgn0 cord-327883-s9nbr5y8 cord-329429-ur8g68vp cord-331217-uup16bhm cord-329902-db7hl770 cord-331020-lyxje82u cord-331673-xv1tcugl cord-330131-yfhrmbvx cord-323683-9h9mld6x cord-330647-w1bpeqzg cord-331244-zaguyxm5 cord-332165-31tbc31x cord-332361-pdoln3nr cord-332457-gan10za0 cord-331739-y1d0leic cord-331584-z43ifmr3 cord-331652-oc5s1if2 cord-331289-02411gfv cord-332088-5c77h0of cord-332181-k90i33gp cord-332632-u2ud0vmq cord-333043-fe24ezt6 cord-332205-ydijp66b cord-332992-8rmqg4rf cord-332046-ihc031ly cord-331343-qzvwwca9 cord-333730-qsx0m68e cord-333228-ejkgune0 cord-334010-gxu0refq cord-333351-homxj9uz cord-333853-p2kbjwpy cord-330852-n7j0c4ne cord-334027-xhfmio7k cord-334941-6uattdti cord-333463-u7je0d1o cord-335116-c83xyev5 cord-336212-ueh4q408 cord-334560-1j9zmuub cord-334947-pa0p5dif cord-333655-lylt7qld cord-334082-fyxn0g3v cord-336157-aqc9zrrm cord-333810-57d4oopv cord-334771-uy3s6443 cord-333262-xvfl7ycj cord-334365-idjvbcy4 cord-335948-qkfxfmxb cord-336045-8qcj5uiy cord-335774-15fhg8o9 cord-331714-2qj2rrgd cord-335279-cfv18qn0 cord-334108-4ey725dv cord-337149-cjon7ihb cord-336493-ggo9wsrm cord-336929-2rnkotqy cord-336447-hpnkou41 cord-337285-t6qr41wc cord-336554-n8n5ii5k cord-337361-salby0fu cord-337673-1nau263l cord-336225-ijodhrwf cord-337914-1hwnxkdd cord-336948-8yqdhcnz cord-337577-dqikrmk7 cord-338400-30vl2hks cord-338083-77re4l0w cord-335647-dhcxj7cj cord-336510-qzm9wgde cord-337659-x4oywbrj cord-338081-ggw5l1qm cord-338727-1kodz527 cord-338804-nreqluol cord-339209-oe8onyr9 cord-339854-scb7pz87 cord-339172-210dwhgj cord-339062-tq0f6d01 cord-339744-xrit0w5i cord-339885-mpzgrogd cord-340907-j9i1wlak cord-339423-5qym9dsf cord-337712-ylqgraos cord-339382-ii4xurmr cord-341050-hnuogpqn cord-338331-27ic5zen cord-340481-i3qrxnpr cord-339230-cc7gcy5b cord-339386-sxyeuiw1 cord-340537-pdvpmydk cord-340503-zwdewiu1 cord-340423-f8ab7413 cord-340610-ex2yjyum cord-341303-1iayp8oa cord-340042-intxyu46 cord-339973-kj56zi59 cord-339152-wfakzb6w cord-341923-jwckbdnb cord-341298-mqpovrms cord-339288-y8woqsii cord-341138-mxjsp3cm cord-340331-51yq1rdo cord-342412-azkamnpa cord-338737-phv12m1q cord-341155-3d64mso0 cord-340489-yo3cp5vs cord-342151-1e6x589e cord-340629-1fle5fpz cord-341968-uc8i9h0m cord-341029-49360l2a cord-344009-hm36pepp cord-340194-ibli36rq cord-344006-0iq9s94n cord-343690-rafvxgx1 cord-342936-43u7afl3 cord-341101-5yvjbr5q cord-342915-r9kv67we cord-341765-ml6eo8r3 cord-345168-3w32v2fm cord-344408-4ko557n1 cord-342277-v6310fjh cord-343350-04e6wvov cord-343784-zgvxl4h3 cord-342906-51296y8d cord-345359-okmkgsbr cord-345157-fhmhpobi cord-347509-2ysw9a0a cord-344782-ond1ziu5 cord-346673-kyc1wks5 cord-344749-omzhhr0k cord-341324-f9g9gitn cord-344576-upsc9cf8 cord-347465-yu6oj30v cord-343963-99rd3o79 cord-344093-3bniy5b5 cord-345020-ai5tib7h cord-343347-guciupc8 cord-346836-6jyv0q5e cord-343918-5yk1j4ms cord-346290-my8ow5ee cord-346853-0c1qdjb5 cord-346906-1wmp43ti cord-347577-p0a2rboi cord-346096-aml84iv1 cord-346904-aa88gtzr cord-342124-jdv17u86 cord-348876-v55piprx cord-344889-1y4ieamp cord-348141-eskefcwk cord-348860-zaimorg0 cord-348161-757c51xw cord-348427-worgd0xu cord-348163-9q1rt8i7 cord-346916-jj4l9ydl cord-348867-c0xpzd4d cord-346063-7u1a198p cord-349225-504kr50e cord-349249-jwvz1ux2 cord-345654-vyz6f3he cord-345848-s84lxe6l cord-345689-5ns1onkw cord-349606-lup6tm2s cord-347727-wka9q98s cord-344970-ud1lhkyi cord-349011-kxhpdvri cord-347039-eap592i7 cord-350964-0jtfc271 cord-349358-leicos9j cord-348669-mizygp4j cord-350467-18bvwxci cord-347710-ff64y6ef cord-351197-xv6ymc4l cord-351170-belbcrcd cord-350151-s75d1hat cord-350235-yoy3hj3j cord-350703-vrqltz3s cord-350948-oog6m4h3 cord-351571-gwtkrt5u cord-351482-hzh5tyoo cord-352054-g7q2z4l5 cord-352379-q5inrxcm cord-351377-xorj8tnz cord-352475-cmmpy5u7 cord-350747-5t5xthk6 cord-351365-dc9t3vh3 cord-352178-irjhmxsg cord-353290-1wi1dhv6 cord-354536-c9v9kbw8 cord-350925-1h6pbfwp cord-353509-yfkiaq80 cord-352200-i05h8csb cord-352619-s2x53grh cord-353297-jizitnfl cord-353609-no3mbg5d cord-354109-mli0c97c cord-354035-i3sl2r0k cord-355181-affuyn8z cord-354151-psog34u3 cord-354848-7aakik9a cord-355489-tkvfneje cord-353869-l53ms3q8 cord-355872-z6vsjmxn cord-353190-7qcoxl81 cord-355685-wgad0eoh cord-354068-4qlk6y7h cord-355771-pxkkd3s1 cord-355535-01h8yyqj cord-356176-1nwjjgul cord-355259-779czzzx cord-356188-rwf78stz cord-355913-fhvt1ht1 cord-355906-yeaw9nr8 cord-354582-fniymnmf Creating transaction Updating wrd table ===== Reducing urls cord-001065-j4hvyyoi cord-002274-6rddtogo cord-002601-d8908t93 cord-003092-3owcqt3d cord-003004-iif2lnez cord-002932-5e7xrd1y cord-000902-ew8orn0z cord-000012-p56v8wi1 cord-000114-f0vud3gu cord-002072-qbh728ec cord-000937-8vk89i4h cord-002136-mkl89qkt cord-001120-fxd533b4 cord-001974-wjf3c7a7 cord-002337-8v907g24 cord-003861-qeao4ghg cord-003926-ycdaw2vh cord-003993-3bozjfv7 cord-003130-p2h8p5bm cord-002338-ri7v2ka3 cord-002874-9rxv6fy9 cord-003166-k3jxvzfi cord-004280-c470nlie cord-003880-uuuzfyjm cord-003503-t6cnjwpd cord-003707-fbe47bgi cord-003792-v48xeqdz cord-003767-9xbu4hnq cord-002933-zmx4k46v cord-003961-gs75ebo4 cord-004034-mjkixqhs cord-003917-bswndfvk cord-001521-l36f1gp7 cord-005885-r3qtoqu1 cord-006129-5rog0s98 cord-006954-ec9x8thb cord-006106-u5npu6ng cord-006892-n2ncamqh cord-007094-ur9sz21s cord-008686-9ybxuy00 cord-011129-btaxvmsr cord-011880-qlutgfu2 cord-013526-6fip93l2 cord-016798-tv2ntug6 cord-016576-1yqwci0y cord-016754-6fv8mjld cord-016499-5iqpl23p cord-017748-xy26tk0t cord-017287-70lk77zb cord-018164-h5k1zsyg cord-018393-5jlqn7wq cord-017331-ru7mvfc0 cord-020789-slsfhrkx cord-018811-zhwr3h07 cord-018441-r6wwpfcy cord-020969-lh2ergpm cord-021116-rh0e4n2w cord-021499-up5vftj4 cord-022084-hap7flng cord-021555-rrverrsj cord-023608-w2g7v7g1 cord-023200-3caevjvh cord-031840-k9l91unc cord-027550-yyqsatqw cord-030961-5gzc7193 cord-030028-s6sxi8uj cord-103688-n7hzpbyf cord-102908-sr7j8z9c cord-214795-8jweuq50 cord-102383-m5ahicqb cord-171099-d0qr84xg cord-035015-slgywe0c cord-252397-qlu7dilh cord-252725-e3pazjdi cord-232446-vvb2ffhv cord-252147-bvtchcbt cord-254592-wa5il5go cord-255026-fdp6mies cord-255479-yd5cbwnx cord-255137-utg8k7qs cord-253825-d9borky8 cord-252048-ftbjsoup cord-255217-l2ak5ygj cord-256837-100ir651 cord-257321-l1swyr6g cord-258489-pyfc7jde cord-258389-1u05w7r4 cord-260014-q5sug7uu cord-261241-eqf6ame6 cord-263315-g7os15m1 cord-265445-bazcczdj cord-263484-afcgqjwq cord-263868-ewnf96cz cord-264308-y6xuxj16 cord-264406-s5c0grz0 cord-267326-355q6k6k cord-265642-7mu530yp cord-267003-k7eo2c26 cord-267134-5gz2dotn cord-269519-8hr8wyrr cord-268593-rvxxv1dn cord-270243-moxleyjg cord-271171-tohbzenc cord-268540-wrjzr3ws cord-271927-u8p6c9w4 cord-267671-ys43n672 cord-270940-acwkh6ed cord-271568-qgpi2kcs cord-273372-69rlh9or cord-274112-6t0wpiqy cord-273326-gmw8gl2r cord-276193-cngz535o cord-275719-ru33ubss cord-278250-dwok857k cord-277400-w7mvk3x4 cord-278099-ypov9ha3 cord-278456-gsv6dh36 cord-278465-tjjkz16y cord-278973-82n0d1dh cord-280854-cxpgwwjd cord-280391-5kiu2pb6 cord-278876-il7g78w1 cord-281332-5mddyv0n cord-280429-4fota9rl cord-283405-aozxvxxs cord-281281-knelqmzx cord-288703-wdh1jiry cord-284156-btb4oodz cord-284479-75zgljet cord-286559-y8z0pwgn cord-288879-rj03dsib cord-285547-7m3dh8hu cord-289360-h6wvx7gw cord-289093-si8btsab cord-291860-dw1sfzqx cord-291816-d4j8samu cord-290617-45be6gxe cord-290548-0wezrr1b cord-291561-sxvgue36 cord-291156-zxg3dsm3 cord-293472-d3iwlpsr cord-292830-gcfx1095 cord-294312-ju6vuywm cord-293732-rxd1lyi7 cord-296309-i1mpov7k cord-295531-zojb3cew cord-295873-kykyubdq cord-295445-f4p00yaw cord-300020-edolh7ww cord-297960-4x1j0iqg cord-300189-gsp1dozg cord-298862-8bijio30 cord-294108-uvnh0s9r cord-302425-aaxvlktp cord-298033-kzdp9edn cord-300837-d0a8y5qh cord-299207-lw0cv74b cord-299379-ch7a39d6 cord-301592-n5ns3m34 cord-298678-hjxph9jm cord-302047-vv5gpldi cord-302614-siyyve9e cord-302055-s155i4e9 cord-304481-yqc8r3ll cord-304251-dohglrm1 cord-301362-f3lp10lm cord-303665-l57e54hu cord-305263-fgwf6wy3 cord-304747-ojyxs3cp cord-302529-43pd2qsp cord-305488-vk59ghjm cord-308201-lavcsqov cord-308857-otsrexqu cord-310141-2jofy8fo cord-307918-8y89p11a cord-307632-x9bxnrtn cord-303265-v6ci69n0 cord-308066-lrbi5198 cord-310920-itqwhi6a cord-314166-79323mzd cord-315037-lmur80te cord-315781-dejh8q22 cord-316245-n6tmn4ph cord-315131-4yb2b70g cord-312332-rwmuucsp cord-317244-4su5on6s cord-317501-yblzopc3 cord-318725-09a32vyg cord-317508-03u2vtzk cord-319814-tyqb473m cord-322748-a5131tv9 cord-321562-hk4hzl13 cord-318853-mxyxwkhx cord-321741-aq76s37x cord-323404-3mw4q7m3 cord-322234-1zyy536y cord-322206-roxa3ix6 cord-324696-htx0ul4o cord-323930-pl3qlcpo cord-325830-mrtpihc7 cord-325750-x7jpsnxg cord-326225-crtpzad7 cord-327013-gc6o8ou3 cord-325925-010xj69x cord-326177-zzsaf3bl cord-329145-424vv8a8 cord-327660-p1b07b4t cord-325611-tu1bn4hu cord-329050-vzsy6xw1 cord-329078-gnnis7pl cord-326160-mf0vh6iu cord-330508-uilejxmi cord-330296-706hf4qw cord-331217-uup16bhm cord-331020-lyxje82u cord-329902-db7hl770 cord-330131-yfhrmbvx cord-331673-xv1tcugl cord-332361-pdoln3nr cord-331289-02411gfv cord-332457-gan10za0 cord-332992-8rmqg4rf cord-334010-gxu0refq cord-334947-pa0p5dif cord-333262-xvfl7ycj cord-336157-aqc9zrrm cord-331714-2qj2rrgd cord-336225-ijodhrwf cord-338400-30vl2hks cord-339209-oe8onyr9 cord-339172-210dwhgj cord-337712-ylqgraos cord-339382-ii4xurmr cord-339973-kj56zi59 cord-342412-azkamnpa cord-341029-49360l2a cord-345359-okmkgsbr cord-344782-ond1ziu5 cord-343963-99rd3o79 cord-346673-kyc1wks5 cord-346290-my8ow5ee cord-346906-1wmp43ti cord-342124-jdv17u86 cord-344889-1y4ieamp cord-348860-zaimorg0 cord-348427-worgd0xu cord-346916-jj4l9ydl cord-348867-c0xpzd4d cord-344970-ud1lhkyi cord-350964-0jtfc271 cord-347710-ff64y6ef cord-351482-hzh5tyoo cord-350703-vrqltz3s cord-353290-1wi1dhv6 cord-352619-s2x53grh cord-352200-i05h8csb cord-353190-7qcoxl81 cord-354582-fniymnmf Creating transaction Updating url table ===== Reducing named entities cord-001065-j4hvyyoi cord-003232-nquw7qga cord-000180-howix091 cord-002274-6rddtogo cord-001834-6xf4o3oy cord-000708-iuo2cw23 cord-002423-1u44tdrj cord-002601-d8908t93 cord-001542-f089bs8r cord-003122-a3f4l6iu cord-003092-3owcqt3d cord-003004-iif2lnez cord-000265-llilwq1u cord-002937-7xauocti cord-000902-ew8orn0z cord-000012-p56v8wi1 cord-002932-5e7xrd1y cord-002581-r7mskri0 cord-001616-9sc2xmqr cord-000114-f0vud3gu cord-000539-uh3q65we cord-000937-8vk89i4h cord-002072-qbh728ec cord-001985-iwfidoer cord-001958-2gt3fwpy cord-001676-68y733y3 cord-000113-d0eur1hq cord-001528-33f94doo cord-001420-b4zcvd04 cord-003523-byxuruk1 cord-002136-mkl89qkt cord-001120-fxd533b4 cord-001748-7e8px4vx cord-000804-0hlj6r10 cord-000777-7cty5s6o cord-001974-wjf3c7a7 cord-001397-nrq4ncdf cord-001142-puj74k7y cord-000729-iq30z094 cord-000238-om92cx5q cord-004477-qu2o2iu1 cord-003926-ycdaw2vh cord-002337-8v907g24 cord-000359-y0m1utug cord-003861-qeao4ghg cord-002728-6oyw5sqv cord-001207-yjaiybwf cord-001831-3aonqyub cord-003993-3bozjfv7 cord-002921-i5jxn1vj cord-003130-p2h8p5bm cord-002338-ri7v2ka3 cord-002327-tocqabgu cord-002874-9rxv6fy9 cord-000501-qz68gtd4 cord-003166-k3jxvzfi cord-003492-rodqdtfj cord-000760-4yfohp9w cord-004280-c470nlie cord-000050-tfcerilc cord-002407-25cawzi0 cord-003216-5qioku84 cord-004211-58x3nnsc cord-003880-uuuzfyjm cord-003482-f1uvohf0 cord-003302-vxk7uqlc cord-002410-2zi5iv2t cord-000933-nn9gj0z1 cord-003503-t6cnjwpd cord-003817-k3m72uxw cord-004608-3u00cpsc cord-003044-9uqa39j9 cord-004761-cgby8bhz cord-003707-fbe47bgi cord-002076-7t4d4vvo cord-003466-599x0euj cord-002933-zmx4k46v cord-003792-v48xeqdz cord-003767-9xbu4hnq cord-002482-2t09zqqi cord-003639-bjtxf1y8 cord-003961-gs75ebo4 cord-004501-guiy89x8 cord-004771-4yinnncj cord-003598-m2fsrwvw cord-004672-0lf5j8lo cord-004034-mjkixqhs cord-002757-upwe0cpj cord-004751-4vl0cvyq cord-004719-3stcx0dd cord-004724-llex3yed cord-003403-ypefqm71 cord-004774-fvf671jn cord-003917-bswndfvk cord-004743-ido065mh cord-004781-ajf9zig0 cord-004775-foaf3vyl cord-004830-vmka378d cord-004827-bnf3mvaf cord-004841-wf0o3whi cord-005876-d8sid7gd cord-005081-kxrzv16n cord-005246-cskb0njm cord-006819-sxz1s6kz cord-005281-wy0zk9p8 cord-005885-r3qtoqu1 cord-005258-gps8rzb5 cord-006790-lye0qjw8 cord-006997-sghhdjyi cord-004848-2cfphi88 cord-006089-08g206kf cord-006129-5rog0s98 cord-004998-wuixnqy5 cord-007149-m4xsx9ev cord-006252-cbelsymu cord-007176-61e9obb3 cord-006954-ec9x8thb cord-007898-nky7bo6u cord-007796-zggk0x2q cord-007362-pjpkz6wv cord-008700-knbf8m4x cord-006106-u5npu6ng cord-006892-n2ncamqh cord-008454-8brxpotx cord-007733-zh8e76w7 cord-007792-596jxrm5 cord-009615-xcz8m9a7 cord-006640-25ykas09 cord-007575-5ekgabx5 cord-008013-blf57r7u cord-007445-2folsh35 cord-006285-kkxdmzk9 cord-007094-ur9sz21s cord-008149-kdlcaium cord-007717-7x1mqqmf cord-007764-7750z41g cord-008556-oetrdm8g cord-009383-ozx5u0t3 cord-009504-sn00p8iw cord-008686-9ybxuy00 cord-007417-az8xd66p cord-008333-1wepke2o cord-007784-fq2urilg cord-007170-svsfu7fj cord-009820-fi54s0x7 cord-001521-l36f1gp7 cord-008716-38sqkh9m cord-009589-xfdgk2j6 cord-007710-0u5ot5h4 cord-009577-29u7pdpk cord-009702-02bo7pnl cord-007731-wu7i548j cord-009561-pg4jmvw4 cord-009836-7o6htufh cord-007843-yqdqm4rh cord-010248-ln800g5z cord-009144-3slh1nbk cord-007530-eyk015n3 cord-008551-yu71iewp cord-010159-uo47oab1 cord-009791-k09vcq96 cord-010189-makhaypd cord-010016-fs8pjy1z cord-011917-6u0t4hy8 cord-008764-j9qmw4zy cord-009846-o6wj8z6e cord-010168-aiqbqnaa cord-010235-hu6o1ggc cord-010188-884d196k cord-011129-btaxvmsr cord-010273-0c56x9f5 cord-010222-5oxie0zc cord-011438-imbpgsub cord-010343-tqqt0hj7 cord-010001-u0d5jkp1 cord-011457-hqxybv1k cord-012582-k1mjik27 cord-013073-siy7dvlo cord-013412-gj443yei cord-014541-2i0jga5v cord-011880-qlutgfu2 cord-015871-1tuf4zxi cord-013176-6ckuya1w cord-016171-17ut32bu cord-014796-6rw2wk1q cord-014397-7b88ycv8 cord-010374-z9ygudv6 cord-016070-e9ix35x3 cord-015023-ishxfinx cord-012418-6ralcn8p cord-014462-11ggaqf1 cord-011106-h20vbmbo cord-015619-msicix98 cord-015764-ly68q5z0 cord-016475-7ldxvbpz cord-016928-yigz9qiz cord-016796-g4kqqpy1 cord-016663-qnp99m7o cord-016309-6mw8okmt cord-013526-6fip93l2 cord-016652-x8t3lf1x cord-016798-tv2ntug6 cord-014908-jys1y0k9 cord-016754-6fv8mjld cord-016576-1yqwci0y cord-016808-gy8d8285 cord-017070-05vlz5dn cord-016451-k8m2xz0e cord-016990-ot1wi3xi cord-016499-5iqpl23p cord-016538-4og05fuo cord-016995-5izyl234 cord-017249-la5sum39 cord-017158-w2tlq6ho cord-016882-c9ts2g7w cord-017429-3evwlfac cord-017008-c7skxte0 cord-017489-ftz9190a cord-017326-1caeui30 cord-017364-d9zmdm23 cord-017748-xy26tk0t cord-017537-ztdz4a2s cord-017287-70lk77zb cord-017959-g0nf1iwm cord-017527-ylng1us2 cord-017568-8fnr4zzv cord-017764-h1w9gbxk cord-018164-h5k1zsyg cord-018078-clxzp1ph cord-017167-8cdbcrh7 cord-018058-n3majqes cord-017824-0pinevfc cord-017752-ofzm3x3a cord-017758-zfudssm9 cord-018364-b06084r1 cord-017331-ru7mvfc0 cord-018040-k0h5ejjt cord-018166-savdgy0u cord-018319-tylkbh4h cord-018463-a6qu0cuv cord-018165-afzjx2ci cord-018555-3lta1tbp cord-018265-twp33bb6 cord-018816-v3ylisbt cord-018089-m94q75xn cord-019982-hyxrgamj cord-018302-lmly43rd cord-018724-ss8x2g3b cord-018017-c8myq6bi cord-018437-yjvwa1ot cord-020101-5rib7pe8 cord-020789-slsfhrkx cord-018477-hgvqd1ej cord-018639-0g1ov96t cord-018811-zhwr3h07 cord-020087-gs0pc6ee cord-018804-wj35q88f cord-021034-hnw7a3a1 cord-020235-stcrozdw cord-018393-5jlqn7wq cord-018441-r6wwpfcy cord-021069-v9f9874x cord-020097-eh5deunk cord-020714-h1fevqcw cord-018706-gykw2nvt cord-020712-l9cn0n99 cord-020969-lh2ergpm cord-021413-1ht1xm88 cord-021588-ec7udsmw cord-021894-lq8yr710 cord-019051-gtruu1op cord-021499-up5vftj4 cord-021116-rh0e4n2w cord-020756-d9f5fd7x cord-021770-zn7na974 cord-021805-2j07zw6q cord-021375-lca26xum cord-021552-6jbm869r cord-021465-2pj26fmv cord-022254-8y5sq72c cord-022348-w7z97wir cord-022324-tcltmhi7 cord-021990-a8ku5rke cord-022084-hap7flng cord-022163-7klzsrpu cord-022674-90g0461f cord-022349-z8w1wkm8 cord-022196-1tionxun cord-022305-uvor9rts cord-022947-ruizhgwh cord-022439-8wy7rpqv cord-020010-q58x6xb0 cord-022262-ck2lhojz cord-022378-ovxmy1as cord-022399-66mzbynu cord-023584-yaxawqhj cord-022822-7346069t cord-021966-5m21bsrw cord-021555-rrverrsj cord-023034-j8zwcfys cord-022453-xe5v7947 cord-023608-w2g7v7g1 cord-022354-aqtceqqo cord-022383-pz0htccp cord-022128-r8el8nqm cord-023092-unjv71qv cord-023200-3caevjvh cord-022393-s26d54ew cord-022830-tvt58gtn cord-025181-eg108wcd cord-022960-u4s23x1r cord-022980-tkii8se4 cord-023622-tul7bonh cord-023564-kpqvyxxe cord-023678-9q68ftr9 cord-023740-g84fa45m cord-026641-eemp6b5j cord-023831-93xqrblk cord-022252-9yiuuye3 cord-023293-te0n2vvp cord-026130-ki7bn67o cord-025995-nxeg03xj cord-023488-jf2xl3vl cord-023721-e0zp2gux cord-024188-d7tnku8z cord-023726-2fduzqyb cord-023731-jqgervt7 cord-027654-k0uby99n cord-023724-5at0rhqk cord-023925-qrr7jcwe cord-023705-3q9yr6np cord-027752-xcpv9k22 cord-031840-k9l91unc cord-027550-yyqsatqw cord-025704-icedihm2 cord-029419-b0w9nomq cord-026340-2nf97zvc cord-030961-5gzc7193 cord-103135-nly9vojr cord-027473-8zerjwa0 cord-102704-wfuzk2dp cord-030279-pv770doe cord-102862-oq54sfx6 cord-030028-s6sxi8uj cord-035163-tqh5wv12 cord-076082-4kpkhz0o cord-048368-wm4c7rk6 cord-102908-sr7j8z9c cord-023143-fcno330z cord-035015-slgywe0c cord-103688-n7hzpbyf cord-104286-5yw4zwo4 cord-102383-m5ahicqb cord-161674-nk0wie0w cord-214795-8jweuq50 cord-203232-1nnqx1g9 cord-048466-fj9l8che cord-171099-d0qr84xg cord-104317-t30dg6oj cord-252456-971d0sir cord-102905-rlee32x7 cord-245161-xbw72k4m cord-102898-eyyd7ent cord-252012-hdjbxah8 cord-252397-qlu7dilh cord-253594-9gbo8viu cord-212761-4bwatc2r cord-252466-usrpodjx cord-253143-73dsc6q3 cord-254200-9bpdfxrt cord-151024-qe7c2uks cord-252725-e3pazjdi cord-232446-vvb2ffhv cord-252871-qfrpuy3t cord-253705-utp8po48 cord-252769-fe50u028 cord-252147-bvtchcbt cord-255075-6azu6k3h cord-254090-x8tnweih cord-254932-b447w202 cord-253466-7gpije5d cord-255026-fdp6mies cord-254592-wa5il5go cord-255479-yd5cbwnx cord-253825-d9borky8 cord-254194-962vynwk cord-254527-zddwajzg cord-252974-pwx27kdi cord-255623-qdpdsye9 cord-255137-utg8k7qs cord-254963-cnvxlv6h cord-252048-ftbjsoup cord-254100-u6x5zd4i cord-255096-27dfbhsl cord-255217-l2ak5ygj cord-254890-4ynsgu6c cord-257064-iafm3pcc cord-255697-trig04hd cord-256325-q70rky3r cord-256837-100ir651 cord-256510-orr2roxz cord-257569-36qx1sy9 cord-255690-xc4bxin4 cord-255181-du6rqc6i cord-257019-lj1yzjn0 cord-256917-6h1ip37z cord-255339-oudj079q cord-255734-038xu4hq cord-256036-gd53s4dv cord-256370-cz88t29n cord-257321-l1swyr6g cord-258489-pyfc7jde cord-257163-hodykbcb cord-257299-z9u12yqb cord-257220-fe2sacjj cord-259505-7hiss0j3 cord-257255-n5o368ih cord-258333-jmk8hdk2 cord-257553-479x7av6 cord-259458-o2yts5pq cord-259627-8stewshp cord-256615-gvq8uyfk cord-260420-4s7akmdp cord-259233-smmhhroe cord-259927-xh9cw9ao cord-257665-12gyrmh2 cord-260472-xvvfguht cord-258027-f3rr5el1 cord-258389-1u05w7r4 cord-260554-nao59qx4 cord-257008-7q5s1vu1 cord-257652-ndt8f812 cord-261417-4pf5nsw2 cord-260168-rb7j94dh cord-261160-g92zhv19 cord-258783-ev0h95b9 cord-260147-w19hl2vs cord-260014-q5sug7uu cord-262722-cz3ce29n cord-258626-p469ysi8 cord-260956-w6wxsg4p cord-259260-qcfgigga cord-260705-huyyw5z6 cord-259235-p0yj9qug cord-260496-s2ba7uy3 cord-260708-l9w5jhsw cord-263017-rh86g4jk cord-261961-u4d0vvmq cord-262776-6k7tcgfs cord-263245-2qub96mz cord-262752-bwofzbwa cord-260690-h5pjv2dw cord-262748-v4xue7ha cord-261241-eqf6ame6 cord-263315-g7os15m1 cord-264291-0czphube cord-263165-bv4dh9eu cord-262514-1e2bc0bi cord-263157-8jin6oru cord-264264-7j3xirfg cord-261171-iknoqb4d cord-265445-bazcczdj cord-263484-afcgqjwq cord-263868-ewnf96cz cord-263764-2ewz8ok4 cord-263785-0iift8zy cord-264794-bgygebgx cord-263619-p17oomzn cord-264350-4zxp3uae cord-264308-y6xuxj16 cord-264884-ydkigome cord-264699-l8db5gll cord-264406-s5c0grz0 cord-266138-yibbiiij cord-266136-81sx505i cord-264916-c4n0kyog cord-265751-q1ecpfyg cord-265461-hj2b1wc4 cord-265681-ab8j4o1u cord-267326-355q6k6k cord-266985-9qwttt2y cord-265642-7mu530yp cord-266822-ecq50ye2 cord-264408-vk4lt83x cord-267003-k7eo2c26 cord-267194-i6vetquk cord-267134-5gz2dotn cord-266199-smlq11y9 cord-268999-6748c617 cord-267140-vdcf6vok cord-267831-uu883ofc cord-269324-zh1a3gwh cord-269623-9pxdeva3 cord-268501-z4oztgi0 cord-266762-z08rn959 cord-269519-8hr8wyrr cord-269975-1ebmq7t8 cord-267261-8z4aqfff cord-267567-w39f584z cord-268417-6eyetb5i cord-267733-fuz8r3vj cord-268788-jcu3pasy cord-268593-rvxxv1dn cord-269193-a647hwu9 cord-270243-moxleyjg cord-270772-zshjrc87 cord-271105-eyigl0wz cord-271709-5frm3dnb cord-270911-z637eh2z cord-270091-sqrh8ylt cord-270161-vaejyy4i cord-268645-5op2m7pu cord-269126-d81z6t0a cord-268540-wrjzr3ws cord-271171-tohbzenc cord-270803-jtv5jmkn cord-271692-60nlid3c cord-270940-acwkh6ed cord-271927-u8p6c9w4 cord-272052-8vvpm4tx cord-270647-vn4kirrx cord-272405-jmwn8pdn cord-270335-8vqi9c68 cord-272099-26nhza2s cord-273343-als886fe cord-267671-ys43n672 cord-271568-qgpi2kcs cord-272829-i4jh6bcn cord-269426-82g5eiyg cord-271172-y48dovux cord-271076-436nxsua cord-271313-h9v0nmx5 cord-273372-69rlh9or cord-271884-86yl9ren cord-274765-3wzht843 cord-270670-cubh9jxc cord-272981-8gahvdt0 cord-271650-biq0chyn cord-274112-6t0wpiqy cord-275013-na6319rg cord-271790-3s8o774l cord-274306-cxvnv8dy cord-273019-hbpfz8rt cord-271091-ffn59sgf cord-275602-cog4nma0 cord-274643-vjb2yt93 cord-272066-f6q6q3io cord-271122-3fsl5589 cord-276006-mjjnkqv6 cord-273708-2q64at3z cord-273326-gmw8gl2r cord-273777-qb0vp9gr cord-276348-vr5fit8r cord-276585-m1dkkbq7 cord-276193-cngz535o cord-276212-ys5njiw0 cord-276009-p98wjtjb cord-275719-ru33ubss cord-276715-d1nh2dvb cord-276052-gk6n8slx cord-275821-yu39aw54 cord-275795-ee7qyw5h cord-275570-i9fw0afj cord-274080-884x48on cord-277392-s0bldxg9 cord-277107-gs7j6fxo cord-278093-0twnkv93 cord-276583-j8bf0eme cord-277327-il8uaavn cord-275683-1qj9ri18 cord-277010-2iecsho0 cord-276039-nqqwnmwc cord-278250-dwok857k cord-277400-w7mvk3x4 cord-275538-c44gmu22 cord-278099-ypov9ha3 cord-277641-nb1p1akx cord-276506-dj7dyo0x cord-278456-gsv6dh36 cord-276616-odmnvv7m cord-277309-kelebqr6 cord-278635-vwdxr1bl cord-277970-sb1wjd3b cord-278465-tjjkz16y cord-276364-zyw5aukk cord-279798-b5tduubu cord-276908-9jthjf24 cord-279694-25rblhwb cord-279617-xuzu55cg cord-278973-82n0d1dh cord-277417-f71jwdzj cord-280854-cxpgwwjd cord-278482-j5zlismf cord-280987-uhxk5b1b cord-280048-b4dz1lnn cord-279557-hk77e3pp cord-280391-5kiu2pb6 cord-278913-u6vihq3u cord-280986-i27mge10 cord-278876-il7g78w1 cord-278479-vl296i1b cord-281332-5mddyv0n cord-278511-je1509ar cord-280429-4fota9rl cord-278684-txlvla0j cord-280427-smqc23vr cord-279691-v5kpmk0b cord-280130-ewqe9edq cord-282628-6uoberfu cord-280564-kgoczioe cord-281061-uoszpnst cord-279849-zzkliu76 cord-280878-1kt51viz cord-281593-bq12grqo cord-281158-vjh9z7l4 cord-282344-o1rkx2z4 cord-280781-u3wd27rn cord-283405-aozxvxxs cord-281429-6lv3di4x cord-282204-j1slaefb cord-284523-lknyehsa cord-283641-2u16otbf cord-279418-3r1ijafm cord-284880-xsh3wkqy cord-281844-c0uhcatg cord-282343-cko4curf cord-281281-knelqmzx cord-285462-9i61rsei cord-285148-bch7814v cord-283880-lrrkuist cord-285367-jxlt0gby cord-284941-wfn0pnev cord-285856-0sw3wt1i cord-285330-td4vr0zv cord-290034-4b0mshqa cord-284266-tbndldhr cord-282742-eyukbot7 cord-286708-igu984oc cord-286137-4cbh3u3z cord-286219-qcx5ehnh cord-284372-v95fzp8n cord-283756-ycjzitlk cord-283964-k3hy2ewx cord-288703-wdh1jiry cord-286298-pn9nwl64 cord-285935-5rsk6g7l cord-284156-btb4oodz cord-287286-4l963z2q cord-288111-0ufc54kw cord-288348-b10e023s cord-284479-75zgljet cord-286719-1xjmlwqr cord-287348-00yaxpkp cord-287711-gw8mgg4m cord-287337-2ljbsia2 cord-288372-48wao8a0 cord-287554-2lqy2ix9 cord-287151-4hlvrfeh cord-286559-y8z0pwgn cord-288231-vg8bwed9 cord-288238-36hiiw91 cord-287466-ag5y781z cord-285547-7m3dh8hu cord-288879-rj03dsib cord-286741-h3oix9zc cord-287770-oxfnt2n4 cord-288945-c9ow1q5c cord-287851-9p0dr7rl cord-288930-h13cxuh3 cord-289360-h6wvx7gw cord-288734-xinkqs6u cord-289593-81vu2kbu cord-290481-i2ppvsh5 cord-289406-54vyzxjf cord-290385-0smnl70i cord-290231-4m9lj0uq cord-290133-4ou7ubb4 cord-289093-si8btsab cord-290556-x7t7zqjd cord-291294-w5ecsht4 cord-290282-oxyzndsj cord-290352-0pc5eji4 cord-289017-vwye3pk9 cord-291707-dzmvjh7j cord-290432-4dli5emd cord-290149-eed4v2jl cord-290851-1e5e033r cord-290509-56pfww0l cord-290855-6umgvt28 cord-290539-8ak2tths cord-291860-dw1sfzqx cord-290617-45be6gxe cord-291816-d4j8samu cord-290540-r0d6oaez cord-291534-c6cjxq07 cord-290548-0wezrr1b cord-291561-sxvgue36 cord-291156-zxg3dsm3 cord-290993-bsnja161 cord-292075-t9z7zqz4 cord-293472-d3iwlpsr cord-293375-qcy56ui7 cord-292830-gcfx1095 cord-293975-np9xdag5 cord-292643-n6xp5mlz cord-292286-ygomb3oi cord-291113-iizj932l cord-292353-z86rjwle cord-291946-kq0rsuxj cord-291063-de7v4e5s cord-294568-12eyo13f cord-292416-3hhi4wps cord-297339-et2305rz cord-292657-gq3965se cord-293540-45awgabp cord-295189-bz3gi15h cord-295792-hajvtzj9 cord-295640-mhfu0e9r cord-294544-iutcduix cord-294323-mryiqmsw cord-294478-3ickafd3 cord-292828-29jbf9ik cord-293097-poh1y6o7 cord-292575-vsswxwdi cord-294842-aesiff1f cord-294312-ju6vuywm cord-293387-0m1ngob3 cord-293421-0ksn0fc7 cord-296935-y77c4ro4 cord-294812-nnlzwaf1 cord-294125-v2dr4hm0 cord-293732-rxd1lyi7 cord-295041-5vpawtef cord-294585-dl5v9p50 cord-297203-f3f31h4r cord-295191-xu26mvc3 cord-295531-zojb3cew cord-298032-3zlu8g8y cord-296309-i1mpov7k cord-296819-gztmidn2 cord-297494-6yxmaihl cord-297834-me1ajoyb cord-294108-uvnh0s9r cord-297131-3a9vjpvn cord-295062-8rl4kswe cord-298905-c2uuvfm5 cord-295873-kykyubdq cord-298036-2zurc60t cord-295445-f4p00yaw cord-300020-edolh7ww cord-297960-4x1j0iqg cord-296635-8r3tm966 cord-295433-olmein3q cord-298214-ivu4erpq cord-300189-gsp1dozg cord-297662-slmlhqnb cord-298051-ej8qxkce cord-298862-8bijio30 cord-298019-gf2asni1 cord-302277-c66xm2n4 cord-302425-aaxvlktp cord-302111-kg0dmgq0 cord-300837-d0a8y5qh cord-301064-ex6qb6zj cord-298033-kzdp9edn cord-298489-uqrzzh0e cord-298733-jole21wq cord-297790-tpjxt0w5 cord-300133-yc2wxgid cord-300810-a1skdp67 cord-299207-lw0cv74b cord-299379-ch7a39d6 cord-299786-wuve0tjz cord-301285-p83ondy8 cord-303040-ha8gufh8 cord-301592-n5ns3m34 cord-298736-9bvyp21d cord-298678-hjxph9jm cord-300711-yibdumij cord-302716-wfla3l20 cord-302047-vv5gpldi cord-302021-42vqmndl cord-298745-3rrlap70 cord-302486-z36hcvrx cord-302055-s155i4e9 cord-302614-siyyve9e cord-299549-bjqwwzam cord-303297-fiievwy7 cord-300522-okbupw61 cord-304481-yqc8r3ll cord-303186-2hxlx1j2 cord-304807-j2k1oel2 cord-304278-0qy1nngs cord-300435-vs0ntcsb cord-304251-dohglrm1 cord-301362-f3lp10lm cord-305336-wxiazglk cord-304850-9xetsc2c cord-303533-6s01qplg cord-303665-l57e54hu cord-304343-m7tbdfri cord-306983-6w2fvtfy cord-305263-fgwf6wy3 cord-304498-ty41xob0 cord-307893-mvl0wrsj cord-306733-df36w6l7 cord-308385-bcph664h cord-304876-txaoz7oh cord-305302-go87uu06 cord-304747-ojyxs3cp cord-305807-n3fs7533 cord-307817-2vy28i4m cord-302529-43pd2qsp cord-305165-3twlnkac cord-304424-048xo7jn cord-305742-wf6qxplf cord-307744-wbr84taq cord-309048-emmtplv3 cord-305488-vk59ghjm cord-304569-o39kl5k4 cord-309489-ubf55eux cord-307046-ko3bdvo0 cord-309346-4mdxe6ri cord-307813-elom30nx cord-309179-5hlatbqe cord-309120-05bg7rfa cord-308201-lavcsqov cord-308857-otsrexqu cord-309067-aemjbkfj cord-310141-2jofy8fo cord-307918-8y89p11a cord-307899-427a7i3h cord-303265-v6ci69n0 cord-309381-cb80ntxs cord-307632-x9bxnrtn cord-305327-hayhbs5u cord-306083-juysx6yo cord-306948-wkisfz1m cord-310255-aixq5mhf cord-309635-1tgovkr7 cord-310371-pylrg91h cord-308686-tbwecf7o cord-311748-yr2ep7uf cord-312964-vsrqmmv7 cord-311823-85wj08gr cord-310140-h7uwl0pb cord-308066-lrbi5198 cord-310942-191m0e65 cord-309488-8guapzke cord-312431-de7zhswl cord-307364-j86t65qu cord-314254-9ye8tfvz cord-306424-gf0bglm0 cord-310920-itqwhi6a cord-310795-n78s0sg2 cord-311410-lgqup9ug cord-310171-1fmsxx2s cord-312461-5qzpo6l1 cord-314190-fvdock94 cord-313356-ninzeazy cord-310439-z0bxsjug cord-311908-sgdq6j6x cord-310870-w8wu8vno cord-309642-wwaa6ls0 cord-314390-q36ye9ff cord-313312-h607itv2 cord-315346-ebfjba4y cord-311382-ioemd0ij cord-314166-79323mzd cord-314325-nquov2i0 cord-316295-x636ux34 cord-313301-7mkadtp9 cord-315037-lmur80te cord-316245-n6tmn4ph cord-311012-wyglrpqh cord-315781-dejh8q22 cord-315167-ph15z424 cord-316951-1swlhdz5 cord-314201-6njwigco cord-312688-12san3m7 cord-315131-4yb2b70g cord-312332-rwmuucsp cord-315339-dcui85lw cord-317198-mean7sj9 cord-317404-jvtozj4v cord-313598-2t40ss6h cord-316063-9bg2dm8e cord-316996-8yimrpaz cord-316273-vo6j8zb0 cord-315918-12rbbe8c cord-316682-4360s2yu cord-314825-fzba05wn cord-318172-bdotp9ko cord-317244-4su5on6s cord-317501-yblzopc3 cord-317277-rr9zue4l cord-317851-lj07947c cord-317971-kuwargnp cord-318725-09a32vyg cord-319746-6bccxgbd cord-317496-6o2upns3 cord-316894-zhmuzv7z cord-319208-jrxz59bb cord-318786-qd0k8174 cord-319754-5isw53wl cord-318495-1w74wf02 cord-317508-03u2vtzk cord-319814-tyqb473m cord-322748-a5131tv9 cord-319210-yqimufdh cord-321756-a7eh4dkb cord-318551-c1qr27lg cord-317412-f3ua8ks3 cord-321562-hk4hzl13 cord-319761-bu5pzbnv cord-317619-o7qfugjw cord-320030-ojtp90na cord-320935-3n157yl4 cord-321053-lgae22f8 cord-318686-we6pveus cord-320693-de1lmzl1 cord-319933-yp9ofhi8 cord-323333-keshu99t cord-320055-6ycp8m89 cord-320713-b37c8aye cord-321835-qn33sx8x cord-318853-mxyxwkhx cord-319379-qe56u93a cord-321741-aq76s37x cord-320015-lbr2q4qh cord-322082-80ym2rsq cord-324775-3x5os79m cord-323358-05bk91lm cord-323195-buzcb8ya cord-323404-3mw4q7m3 cord-321112-w7x1dkds cord-323009-frej2qmb cord-322234-1zyy536y cord-322904-9mta0aem cord-323311-xl2fv0qx cord-323987-gh1m05gi cord-322206-roxa3ix6 cord-324950-ux7shvji cord-324280-e8mj6ecl cord-325280-4whzcmqv cord-321481-vrfwczve cord-323700-5awng7h1 cord-325825-0lyt8gfq cord-324984-ojrpsdt9 cord-323793-c69joaqs cord-325875-93krp81r cord-326719-p1ma4akz cord-324696-htx0ul4o cord-325830-mrtpihc7 cord-325230-3kg4oe4g cord-323710-cmbg0ty8 cord-325635-don9qjpz cord-325750-x7jpsnxg cord-324295-9c1zxjng cord-323930-pl3qlcpo cord-325969-9zhmmvdg cord-326225-crtpzad7 cord-325326-2bbqz4o7 cord-327013-gc6o8ou3 cord-327199-ggomuomb cord-325915-dw989txm cord-327000-oyg3oyx1 cord-325827-492xi3ee cord-326725-0jgw083h cord-325925-010xj69x cord-326027-58whwspe cord-328252-dk54w8z9 cord-325325-xw7627x9 cord-327855-txryqil7 cord-326177-zzsaf3bl cord-325712-9kbnyqt3 cord-327660-p1b07b4t cord-326960-9phlylce cord-329145-424vv8a8 cord-325611-tu1bn4hu cord-329857-pcsuu597 cord-329050-vzsy6xw1 cord-327777-pg98zc6o cord-326160-mf0vh6iu cord-330827-gu2mt6zp cord-328621-3jda0k2u cord-329078-gnnis7pl cord-330508-uilejxmi cord-328753-qwdxgk4z cord-327392-9psblokc cord-330296-706hf4qw cord-329527-0rlotyz3 cord-329493-ueqlhgn0 cord-327883-s9nbr5y8 cord-329429-ur8g68vp cord-331673-xv1tcugl cord-331217-uup16bhm cord-330131-yfhrmbvx cord-329902-db7hl770 cord-331020-lyxje82u cord-323683-9h9mld6x cord-331244-zaguyxm5 cord-332165-31tbc31x cord-330647-w1bpeqzg cord-332361-pdoln3nr cord-331739-y1d0leic cord-332457-gan10za0 cord-331584-z43ifmr3 cord-331289-02411gfv cord-331652-oc5s1if2 cord-333043-fe24ezt6 cord-332088-5c77h0of cord-332181-k90i33gp cord-332632-u2ud0vmq cord-332205-ydijp66b cord-332992-8rmqg4rf cord-332046-ihc031ly cord-333730-qsx0m68e cord-333853-p2kbjwpy cord-331343-qzvwwca9 cord-330852-n7j0c4ne cord-334010-gxu0refq cord-333228-ejkgune0 cord-333351-homxj9uz cord-334947-pa0p5dif cord-334027-xhfmio7k cord-334941-6uattdti cord-334560-1j9zmuub cord-334082-fyxn0g3v cord-333655-lylt7qld cord-336212-ueh4q408 cord-334771-uy3s6443 cord-333810-57d4oopv cord-335116-c83xyev5 cord-333463-u7je0d1o cord-333262-xvfl7ycj cord-336157-aqc9zrrm cord-334365-idjvbcy4 cord-335948-qkfxfmxb cord-335774-15fhg8o9 cord-336045-8qcj5uiy cord-335279-cfv18qn0 cord-334108-4ey725dv cord-336447-hpnkou41 cord-337149-cjon7ihb cord-336493-ggo9wsrm cord-336554-n8n5ii5k cord-336929-2rnkotqy cord-337285-t6qr41wc cord-337361-salby0fu cord-336225-ijodhrwf cord-337673-1nau263l cord-331714-2qj2rrgd cord-337914-1hwnxkdd cord-336948-8yqdhcnz cord-337577-dqikrmk7 cord-338400-30vl2hks cord-338083-77re4l0w cord-335647-dhcxj7cj cord-336510-qzm9wgde cord-337659-x4oywbrj cord-338081-ggw5l1qm cord-338727-1kodz527 cord-338804-nreqluol cord-339209-oe8onyr9 cord-339854-scb7pz87 cord-339172-210dwhgj cord-339062-tq0f6d01 cord-339744-xrit0w5i cord-339885-mpzgrogd cord-339423-5qym9dsf cord-337712-ylqgraos cord-340907-j9i1wlak cord-339382-ii4xurmr cord-341050-hnuogpqn cord-340481-i3qrxnpr cord-338331-27ic5zen cord-339230-cc7gcy5b cord-339386-sxyeuiw1 cord-340537-pdvpmydk cord-340503-zwdewiu1 cord-340423-f8ab7413 cord-340610-ex2yjyum cord-341303-1iayp8oa cord-339973-kj56zi59 cord-341923-jwckbdnb cord-339152-wfakzb6w cord-340042-intxyu46 cord-341298-mqpovrms cord-341138-mxjsp3cm cord-339288-y8woqsii cord-340331-51yq1rdo cord-342412-azkamnpa cord-338737-phv12m1q cord-341155-3d64mso0 cord-342151-1e6x589e cord-340629-1fle5fpz cord-340489-yo3cp5vs cord-341968-uc8i9h0m cord-340194-ibli36rq cord-341029-49360l2a cord-344009-hm36pepp cord-344006-0iq9s94n cord-343690-rafvxgx1 cord-341101-5yvjbr5q cord-342936-43u7afl3 cord-342915-r9kv67we cord-342277-v6310fjh cord-344408-4ko557n1 cord-341765-ml6eo8r3 cord-345168-3w32v2fm cord-343350-04e6wvov cord-343784-zgvxl4h3 cord-342906-51296y8d cord-345157-fhmhpobi cord-345359-okmkgsbr cord-347509-2ysw9a0a cord-344749-omzhhr0k cord-344782-ond1ziu5 cord-341324-f9g9gitn cord-346673-kyc1wks5 cord-343963-99rd3o79 cord-344576-upsc9cf8 cord-347465-yu6oj30v cord-343347-guciupc8 cord-345020-ai5tib7h cord-344093-3bniy5b5 cord-343918-5yk1j4ms cord-346836-6jyv0q5e cord-346906-1wmp43ti cord-347577-p0a2rboi cord-346096-aml84iv1 cord-346853-0c1qdjb5 cord-346290-my8ow5ee cord-346904-aa88gtzr cord-342124-jdv17u86 cord-348876-v55piprx cord-344889-1y4ieamp cord-348141-eskefcwk cord-348860-zaimorg0 cord-348161-757c51xw cord-348427-worgd0xu cord-348163-9q1rt8i7 cord-346063-7u1a198p cord-346916-jj4l9ydl cord-349225-504kr50e cord-349249-jwvz1ux2 cord-348867-c0xpzd4d cord-345654-vyz6f3he cord-345848-s84lxe6l cord-345689-5ns1onkw cord-349606-lup6tm2s cord-347727-wka9q98s cord-344970-ud1lhkyi cord-349011-kxhpdvri cord-347039-eap592i7 cord-349358-leicos9j cord-350964-0jtfc271 cord-348669-mizygp4j cord-350467-18bvwxci cord-351197-xv6ymc4l cord-351170-belbcrcd cord-350151-s75d1hat cord-350235-yoy3hj3j cord-351482-hzh5tyoo cord-350948-oog6m4h3 cord-350703-vrqltz3s cord-351377-xorj8tnz cord-347710-ff64y6ef cord-351571-gwtkrt5u cord-352054-g7q2z4l5 cord-352379-q5inrxcm cord-352475-cmmpy5u7 cord-350747-5t5xthk6 cord-351365-dc9t3vh3 cord-352178-irjhmxsg cord-353290-1wi1dhv6 cord-354536-c9v9kbw8 cord-353509-yfkiaq80 cord-350925-1h6pbfwp cord-352619-s2x53grh cord-353297-jizitnfl cord-353609-no3mbg5d cord-352200-i05h8csb cord-354035-i3sl2r0k cord-354848-7aakik9a cord-354109-mli0c97c cord-354151-psog34u3 cord-355489-tkvfneje cord-355181-affuyn8z cord-353869-l53ms3q8 cord-355872-z6vsjmxn cord-353190-7qcoxl81 cord-354068-4qlk6y7h cord-355685-wgad0eoh cord-355771-pxkkd3s1 cord-355259-779czzzx cord-356176-1nwjjgul cord-355535-01h8yyqj cord-356188-rwf78stz cord-355906-yeaw9nr8 cord-354582-fniymnmf cord-355913-fhvt1ht1 Creating transaction Updating ent table ===== Reducing parts of speech cord-003232-nquw7qga cord-001065-j4hvyyoi cord-000708-iuo2cw23 cord-001834-6xf4o3oy cord-000180-howix091 cord-002274-6rddtogo cord-002601-d8908t93 cord-000265-llilwq1u cord-002423-1u44tdrj cord-002937-7xauocti cord-000902-ew8orn0z cord-003004-iif2lnez cord-002932-5e7xrd1y cord-000114-f0vud3gu cord-000012-p56v8wi1 cord-003122-a3f4l6iu cord-003092-3owcqt3d cord-000539-uh3q65we cord-001542-f089bs8r cord-002581-r7mskri0 cord-001616-9sc2xmqr cord-000937-8vk89i4h cord-002072-qbh728ec cord-001985-iwfidoer cord-000113-d0eur1hq cord-001528-33f94doo cord-002136-mkl89qkt cord-001676-68y733y3 cord-001958-2gt3fwpy cord-001420-b4zcvd04 cord-003523-byxuruk1 cord-001120-fxd533b4 cord-001748-7e8px4vx cord-001142-puj74k7y cord-001974-wjf3c7a7 cord-004477-qu2o2iu1 cord-000359-y0m1utug cord-000238-om92cx5q cord-000729-iq30z094 cord-003926-ycdaw2vh cord-003861-qeao4ghg cord-002728-6oyw5sqv cord-000777-7cty5s6o cord-000804-0hlj6r10 cord-001831-3aonqyub cord-003993-3bozjfv7 cord-001397-nrq4ncdf cord-001207-yjaiybwf cord-002921-i5jxn1vj cord-002338-ri7v2ka3 cord-002874-9rxv6fy9 cord-003130-p2h8p5bm cord-000501-qz68gtd4 cord-003166-k3jxvzfi cord-004280-c470nlie cord-000760-4yfohp9w cord-000050-tfcerilc cord-002327-tocqabgu cord-003492-rodqdtfj cord-002337-8v907g24 cord-004211-58x3nnsc cord-003216-5qioku84 cord-003880-uuuzfyjm cord-003482-f1uvohf0 cord-002407-25cawzi0 cord-003302-vxk7uqlc cord-002410-2zi5iv2t cord-003817-k3m72uxw cord-003503-t6cnjwpd cord-004608-3u00cpsc cord-004761-cgby8bhz cord-002076-7t4d4vvo cord-000933-nn9gj0z1 cord-003466-599x0euj cord-003792-v48xeqdz cord-003044-9uqa39j9 cord-003707-fbe47bgi cord-003767-9xbu4hnq cord-002933-zmx4k46v cord-003961-gs75ebo4 cord-004771-4yinnncj cord-004672-0lf5j8lo cord-003598-m2fsrwvw cord-003639-bjtxf1y8 cord-004034-mjkixqhs cord-002482-2t09zqqi cord-004751-4vl0cvyq cord-004724-llex3yed cord-004719-3stcx0dd cord-003403-ypefqm71 cord-004774-fvf671jn cord-004501-guiy89x8 cord-003917-bswndfvk cord-004743-ido065mh cord-004781-ajf9zig0 cord-004775-foaf3vyl cord-004827-bnf3mvaf cord-004830-vmka378d cord-004841-wf0o3whi cord-005876-d8sid7gd cord-005081-kxrzv16n cord-005246-cskb0njm cord-006819-sxz1s6kz cord-005281-wy0zk9p8 cord-005885-r3qtoqu1 cord-005258-gps8rzb5 cord-006790-lye0qjw8 cord-006997-sghhdjyi cord-006089-08g206kf cord-004848-2cfphi88 cord-002757-upwe0cpj cord-006129-5rog0s98 cord-004998-wuixnqy5 cord-007149-m4xsx9ev cord-007176-61e9obb3 cord-006252-cbelsymu cord-007898-nky7bo6u cord-008700-knbf8m4x cord-006954-ec9x8thb cord-006106-u5npu6ng cord-008149-kdlcaium cord-007796-zggk0x2q cord-007362-pjpkz6wv cord-006892-n2ncamqh cord-009615-xcz8m9a7 cord-006640-25ykas09 cord-007445-2folsh35 cord-008013-blf57r7u cord-006285-kkxdmzk9 cord-007094-ur9sz21s cord-009383-ozx5u0t3 cord-007733-zh8e76w7 cord-007792-596jxrm5 cord-007575-5ekgabx5 cord-007717-7x1mqqmf cord-007764-7750z41g cord-009504-sn00p8iw cord-008686-9ybxuy00 cord-008333-1wepke2o cord-007170-svsfu7fj cord-009820-fi54s0x7 cord-008454-8brxpotx cord-009589-xfdgk2j6 cord-007784-fq2urilg cord-007710-0u5ot5h4 cord-009577-29u7pdpk cord-009702-02bo7pnl cord-009561-pg4jmvw4 cord-007843-yqdqm4rh cord-007530-eyk015n3 cord-009144-3slh1nbk cord-010159-uo47oab1 cord-007731-wu7i548j cord-009836-7o6htufh cord-008556-oetrdm8g cord-009791-k09vcq96 cord-010016-fs8pjy1z cord-010189-makhaypd cord-011917-6u0t4hy8 cord-008764-j9qmw4zy cord-008551-yu71iewp cord-010235-hu6o1ggc cord-010168-aiqbqnaa cord-010188-884d196k cord-009846-o6wj8z6e cord-010248-ln800g5z cord-011129-btaxvmsr cord-008716-38sqkh9m cord-007417-az8xd66p cord-010273-0c56x9f5 cord-010222-5oxie0zc cord-010001-u0d5jkp1 cord-011457-hqxybv1k cord-010343-tqqt0hj7 cord-012582-k1mjik27 cord-013073-siy7dvlo cord-011880-qlutgfu2 cord-014541-2i0jga5v cord-013176-6ckuya1w cord-011438-imbpgsub cord-015871-1tuf4zxi cord-014796-6rw2wk1q cord-016070-e9ix35x3 cord-010374-z9ygudv6 cord-013412-gj443yei cord-016171-17ut32bu cord-015764-ly68q5z0 cord-011106-h20vbmbo cord-014397-7b88ycv8 cord-015619-msicix98 cord-015023-ishxfinx cord-016928-yigz9qiz cord-016796-g4kqqpy1 cord-013526-6fip93l2 cord-016663-qnp99m7o cord-016309-6mw8okmt cord-016652-x8t3lf1x cord-012418-6ralcn8p cord-016798-tv2ntug6 cord-014908-jys1y0k9 cord-016754-6fv8mjld cord-016576-1yqwci0y cord-016808-gy8d8285 cord-017070-05vlz5dn cord-016451-k8m2xz0e cord-016475-7ldxvbpz cord-016538-4og05fuo cord-016995-5izyl234 cord-017158-w2tlq6ho cord-017429-3evwlfac cord-017249-la5sum39 cord-017489-ftz9190a cord-016882-c9ts2g7w cord-017537-ztdz4a2s cord-017959-g0nf1iwm cord-018058-n3majqes cord-017748-xy26tk0t cord-016990-ot1wi3xi cord-017326-1caeui30 cord-014462-11ggaqf1 cord-017287-70lk77zb cord-017527-ylng1us2 cord-017764-h1w9gbxk cord-018078-clxzp1ph cord-017008-c7skxte0 cord-017824-0pinevfc cord-016499-5iqpl23p cord-017364-d9zmdm23 cord-017167-8cdbcrh7 cord-017758-zfudssm9 cord-018040-k0h5ejjt cord-018463-a6qu0cuv cord-017752-ofzm3x3a cord-018319-tylkbh4h cord-018364-b06084r1 cord-018302-lmly43rd cord-018165-afzjx2ci cord-017568-8fnr4zzv cord-018164-h5k1zsyg cord-018816-v3ylisbt cord-018265-twp33bb6 cord-018555-3lta1tbp cord-018724-ss8x2g3b cord-018166-savdgy0u cord-018017-c8myq6bi cord-018437-yjvwa1ot cord-020101-5rib7pe8 cord-018477-hgvqd1ej cord-020789-slsfhrkx cord-018804-wj35q88f cord-020087-gs0pc6ee cord-018089-m94q75xn cord-018811-zhwr3h07 cord-018639-0g1ov96t cord-021034-hnw7a3a1 cord-018441-r6wwpfcy cord-021069-v9f9874x cord-019982-hyxrgamj cord-018706-gykw2nvt cord-021588-ec7udsmw cord-021894-lq8yr710 cord-020969-lh2ergpm cord-021116-rh0e4n2w cord-020714-h1fevqcw cord-018393-5jlqn7wq cord-017331-ru7mvfc0 cord-020712-l9cn0n99 cord-021413-1ht1xm88 cord-020235-stcrozdw cord-019051-gtruu1op cord-020097-eh5deunk cord-021375-lca26xum cord-021805-2j07zw6q cord-021552-6jbm869r cord-022254-8y5sq72c cord-021770-zn7na974 cord-022324-tcltmhi7 cord-022674-90g0461f cord-020756-d9f5fd7x cord-022349-z8w1wkm8 cord-021990-a8ku5rke cord-022348-w7z97wir cord-022378-ovxmy1as cord-023034-j8zwcfys cord-022822-7346069t cord-021465-2pj26fmv cord-022196-1tionxun cord-022453-xe5v7947 cord-021499-up5vftj4 cord-022163-7klzsrpu cord-022399-66mzbynu cord-022439-8wy7rpqv cord-022084-hap7flng cord-022947-ruizhgwh cord-023584-yaxawqhj cord-023608-w2g7v7g1 cord-023092-unjv71qv cord-023200-3caevjvh cord-022305-uvor9rts cord-025181-eg108wcd cord-022980-tkii8se4 cord-022960-u4s23x1r cord-023622-tul7bonh cord-023564-kpqvyxxe cord-023740-g84fa45m cord-023831-93xqrblk cord-026641-eemp6b5j cord-023678-9q68ftr9 cord-023293-te0n2vvp cord-022830-tvt58gtn cord-026130-ki7bn67o cord-023721-e0zp2gux cord-022393-s26d54ew cord-024188-d7tnku8z cord-021966-5m21bsrw cord-022354-aqtceqqo cord-022128-r8el8nqm cord-025995-nxeg03xj cord-023488-jf2xl3vl cord-022383-pz0htccp cord-023726-2fduzqyb cord-022262-ck2lhojz cord-023731-jqgervt7 cord-027654-k0uby99n cord-023925-qrr7jcwe cord-027752-xcpv9k22 cord-023705-3q9yr6np cord-027550-yyqsatqw cord-025704-icedihm2 cord-023724-5at0rhqk cord-029419-b0w9nomq cord-031840-k9l91unc cord-026340-2nf97zvc cord-103135-nly9vojr cord-102704-wfuzk2dp cord-030961-5gzc7193 cord-027473-8zerjwa0 cord-020010-q58x6xb0 cord-102862-oq54sfx6 cord-035163-tqh5wv12 cord-022252-9yiuuye3 cord-030279-pv770doe cord-076082-4kpkhz0o cord-048368-wm4c7rk6 cord-030028-s6sxi8uj cord-103688-n7hzpbyf cord-102908-sr7j8z9c cord-102383-m5ahicqb cord-104286-5yw4zwo4 cord-214795-8jweuq50 cord-203232-1nnqx1g9 cord-161674-nk0wie0w cord-048466-fj9l8che cord-171099-d0qr84xg cord-035015-slgywe0c cord-104317-t30dg6oj cord-252456-971d0sir cord-102905-rlee32x7 cord-102898-eyyd7ent cord-245161-xbw72k4m cord-252397-qlu7dilh cord-001521-l36f1gp7 cord-252012-hdjbxah8 cord-253594-9gbo8viu cord-212761-4bwatc2r cord-252466-usrpodjx cord-253143-73dsc6q3 cord-232446-vvb2ffhv cord-151024-qe7c2uks cord-252725-e3pazjdi cord-252769-fe50u028 cord-252871-qfrpuy3t cord-254200-9bpdfxrt cord-254932-b447w202 cord-254090-x8tnweih cord-021555-rrverrsj cord-255075-6azu6k3h cord-254592-wa5il5go cord-023143-fcno330z cord-255026-fdp6mies cord-253705-utp8po48 cord-253825-d9borky8 cord-252147-bvtchcbt cord-254194-962vynwk cord-255479-yd5cbwnx cord-252974-pwx27kdi cord-255623-qdpdsye9 cord-255137-utg8k7qs cord-254963-cnvxlv6h cord-252048-ftbjsoup cord-254100-u6x5zd4i cord-254527-zddwajzg cord-254890-4ynsgu6c cord-255217-l2ak5ygj cord-257064-iafm3pcc cord-256325-q70rky3r cord-255697-trig04hd cord-253466-7gpije5d cord-256837-100ir651 cord-256510-orr2roxz cord-257569-36qx1sy9 cord-255096-27dfbhsl cord-255181-du6rqc6i cord-255690-xc4bxin4 cord-257019-lj1yzjn0 cord-256917-6h1ip37z cord-255734-038xu4hq cord-256036-gd53s4dv cord-255339-oudj079q cord-257321-l1swyr6g cord-258489-pyfc7jde cord-256370-cz88t29n cord-257163-hodykbcb cord-257299-z9u12yqb cord-258333-jmk8hdk2 cord-259505-7hiss0j3 cord-257553-479x7av6 cord-257255-n5o368ih cord-259458-o2yts5pq cord-259627-8stewshp cord-256615-gvq8uyfk cord-259233-smmhhroe cord-260420-4s7akmdp cord-259927-xh9cw9ao cord-257220-fe2sacjj cord-258027-f3rr5el1 cord-257665-12gyrmh2 cord-260472-xvvfguht cord-260554-nao59qx4 cord-258389-1u05w7r4 cord-257008-7q5s1vu1 cord-257652-ndt8f812 cord-261417-4pf5nsw2 cord-260705-huyyw5z6 cord-260168-rb7j94dh cord-262722-cz3ce29n cord-260147-w19hl2vs cord-261160-g92zhv19 cord-258783-ev0h95b9 cord-260014-q5sug7uu cord-260956-w6wxsg4p cord-258626-p469ysi8 cord-259260-qcfgigga cord-259235-p0yj9qug cord-260496-s2ba7uy3 cord-260708-l9w5jhsw cord-261961-u4d0vvmq cord-263017-rh86g4jk cord-263245-2qub96mz cord-262776-6k7tcgfs cord-262752-bwofzbwa cord-260690-h5pjv2dw cord-262748-v4xue7ha cord-261241-eqf6ame6 cord-263165-bv4dh9eu cord-263315-g7os15m1 cord-264291-0czphube cord-262514-1e2bc0bi cord-263157-8jin6oru cord-261171-iknoqb4d cord-264264-7j3xirfg cord-265445-bazcczdj cord-263484-afcgqjwq cord-263868-ewnf96cz cord-263764-2ewz8ok4 cord-263619-p17oomzn cord-263785-0iift8zy cord-264794-bgygebgx cord-264350-4zxp3uae cord-264308-y6xuxj16 cord-264699-l8db5gll cord-264406-s5c0grz0 cord-266138-yibbiiij cord-266136-81sx505i cord-264916-c4n0kyog cord-265751-q1ecpfyg cord-265461-hj2b1wc4 cord-265681-ab8j4o1u cord-267326-355q6k6k cord-266985-9qwttt2y cord-265642-7mu530yp cord-266822-ecq50ye2 cord-267003-k7eo2c26 cord-267194-i6vetquk cord-264884-ydkigome cord-267134-5gz2dotn cord-268999-6748c617 cord-266199-smlq11y9 cord-267140-vdcf6vok cord-267831-uu883ofc cord-269623-9pxdeva3 cord-269324-zh1a3gwh cord-268501-z4oztgi0 cord-266762-z08rn959 cord-269975-1ebmq7t8 cord-269519-8hr8wyrr cord-267261-8z4aqfff cord-267567-w39f584z cord-267733-fuz8r3vj cord-268788-jcu3pasy cord-268593-rvxxv1dn cord-269193-a647hwu9 cord-270243-moxleyjg cord-270772-zshjrc87 cord-271105-eyigl0wz cord-271709-5frm3dnb cord-270911-z637eh2z cord-270091-sqrh8ylt cord-268645-5op2m7pu cord-270161-vaejyy4i cord-269126-d81z6t0a cord-271171-tohbzenc cord-271692-60nlid3c cord-270803-jtv5jmkn cord-264408-vk4lt83x cord-271927-u8p6c9w4 cord-268417-6eyetb5i cord-272052-8vvpm4tx cord-268540-wrjzr3ws cord-270647-vn4kirrx cord-270940-acwkh6ed cord-270335-8vqi9c68 cord-272405-jmwn8pdn cord-272099-26nhza2s cord-273343-als886fe cord-272829-i4jh6bcn cord-271568-qgpi2kcs cord-269426-82g5eiyg cord-271172-y48dovux cord-271076-436nxsua cord-271313-h9v0nmx5 cord-273372-69rlh9or cord-271884-86yl9ren cord-270670-cubh9jxc cord-274765-3wzht843 cord-272981-8gahvdt0 cord-271650-biq0chyn cord-274112-6t0wpiqy cord-275013-na6319rg cord-271790-3s8o774l cord-274306-cxvnv8dy cord-273019-hbpfz8rt cord-271091-ffn59sgf cord-275602-cog4nma0 cord-274643-vjb2yt93 cord-272066-f6q6q3io cord-271122-3fsl5589 cord-273326-gmw8gl2r cord-273708-2q64at3z cord-273777-qb0vp9gr cord-276348-vr5fit8r cord-276585-m1dkkbq7 cord-276212-ys5njiw0 cord-276006-mjjnkqv6 cord-275719-ru33ubss cord-276009-p98wjtjb cord-276052-gk6n8slx cord-276715-d1nh2dvb cord-275821-yu39aw54 cord-275570-i9fw0afj cord-277392-s0bldxg9 cord-277107-gs7j6fxo cord-276193-cngz535o cord-276583-j8bf0eme cord-278093-0twnkv93 cord-277327-il8uaavn cord-275683-1qj9ri18 cord-277010-2iecsho0 cord-276039-nqqwnmwc cord-278250-dwok857k cord-275538-c44gmu22 cord-277400-w7mvk3x4 cord-278099-ypov9ha3 cord-277641-nb1p1akx cord-276506-dj7dyo0x cord-274080-884x48on cord-277309-kelebqr6 cord-278456-gsv6dh36 cord-276616-odmnvv7m cord-278635-vwdxr1bl cord-278465-tjjkz16y cord-277970-sb1wjd3b cord-276364-zyw5aukk cord-279798-b5tduubu cord-279694-25rblhwb cord-279617-xuzu55cg cord-276908-9jthjf24 cord-278973-82n0d1dh cord-275795-ee7qyw5h cord-277417-f71jwdzj cord-278482-j5zlismf cord-280854-cxpgwwjd cord-280987-uhxk5b1b cord-279557-hk77e3pp cord-280048-b4dz1lnn cord-278913-u6vihq3u cord-280986-i27mge10 cord-280391-5kiu2pb6 cord-281332-5mddyv0n cord-278876-il7g78w1 cord-278479-vl296i1b cord-267671-ys43n672 cord-280429-4fota9rl cord-280427-smqc23vr cord-278684-txlvla0j cord-278511-je1509ar cord-279691-v5kpmk0b cord-280130-ewqe9edq cord-282628-6uoberfu cord-280564-kgoczioe cord-281061-uoszpnst cord-279849-zzkliu76 cord-281593-bq12grqo cord-281158-vjh9z7l4 cord-280781-u3wd27rn cord-282344-o1rkx2z4 cord-280878-1kt51viz cord-283405-aozxvxxs cord-283641-2u16otbf cord-279418-3r1ijafm cord-281429-6lv3di4x cord-284523-lknyehsa cord-282204-j1slaefb cord-281844-c0uhcatg cord-284880-xsh3wkqy cord-282343-cko4curf cord-285462-9i61rsei cord-285148-bch7814v cord-285367-jxlt0gby cord-283880-lrrkuist cord-281281-knelqmzx cord-285856-0sw3wt1i cord-284266-tbndldhr cord-284941-wfn0pnev cord-290034-4b0mshqa cord-285330-td4vr0zv cord-282742-eyukbot7 cord-286137-4cbh3u3z cord-284372-v95fzp8n cord-283756-ycjzitlk cord-286708-igu984oc cord-286219-qcx5ehnh cord-283964-k3hy2ewx cord-288703-wdh1jiry cord-286298-pn9nwl64 cord-285935-5rsk6g7l cord-284156-btb4oodz cord-287286-4l963z2q cord-288111-0ufc54kw cord-284479-75zgljet cord-288348-b10e023s cord-287348-00yaxpkp cord-287711-gw8mgg4m cord-287337-2ljbsia2 cord-288372-48wao8a0 cord-288238-36hiiw91 cord-288231-vg8bwed9 cord-287554-2lqy2ix9 cord-286559-y8z0pwgn cord-287151-4hlvrfeh cord-285547-7m3dh8hu cord-286719-1xjmlwqr cord-288879-rj03dsib cord-286741-h3oix9zc cord-288945-c9ow1q5c cord-287851-9p0dr7rl cord-287466-ag5y781z cord-287770-oxfnt2n4 cord-288930-h13cxuh3 cord-289360-h6wvx7gw cord-288734-xinkqs6u cord-289593-81vu2kbu cord-290481-i2ppvsh5 cord-289406-54vyzxjf cord-290385-0smnl70i cord-290231-4m9lj0uq cord-290556-x7t7zqjd cord-290133-4ou7ubb4 cord-291294-w5ecsht4 cord-290352-0pc5eji4 cord-289093-si8btsab cord-290282-oxyzndsj cord-289017-vwye3pk9 cord-290432-4dli5emd cord-290851-1e5e033r cord-290149-eed4v2jl cord-291707-dzmvjh7j cord-290855-6umgvt28 cord-290539-8ak2tths cord-290509-56pfww0l cord-291860-dw1sfzqx cord-290617-45be6gxe cord-290540-r0d6oaez cord-291816-d4j8samu cord-290548-0wezrr1b cord-291534-c6cjxq07 cord-291561-sxvgue36 cord-290993-bsnja161 cord-292075-t9z7zqz4 cord-293375-qcy56ui7 cord-292830-gcfx1095 cord-293472-d3iwlpsr cord-293975-np9xdag5 cord-292643-n6xp5mlz cord-292286-ygomb3oi cord-291113-iizj932l cord-292353-z86rjwle cord-291946-kq0rsuxj cord-291156-zxg3dsm3 cord-294568-12eyo13f cord-291063-de7v4e5s cord-297339-et2305rz cord-292657-gq3965se cord-292416-3hhi4wps cord-293540-45awgabp cord-295189-bz3gi15h cord-295792-hajvtzj9 cord-295640-mhfu0e9r cord-294544-iutcduix cord-294323-mryiqmsw cord-294478-3ickafd3 cord-293097-poh1y6o7 cord-292828-29jbf9ik cord-292575-vsswxwdi cord-294312-ju6vuywm cord-294842-aesiff1f cord-293387-0m1ngob3 cord-296935-y77c4ro4 cord-293421-0ksn0fc7 cord-294812-nnlzwaf1 cord-294125-v2dr4hm0 cord-295041-5vpawtef cord-297203-f3f31h4r cord-293732-rxd1lyi7 cord-295191-xu26mvc3 cord-295531-zojb3cew cord-294585-dl5v9p50 cord-298032-3zlu8g8y cord-296309-i1mpov7k cord-296819-gztmidn2 cord-297494-6yxmaihl cord-297834-me1ajoyb cord-297131-3a9vjpvn cord-294108-uvnh0s9r cord-295062-8rl4kswe cord-295873-kykyubdq cord-298905-c2uuvfm5 cord-298036-2zurc60t cord-295445-f4p00yaw cord-300020-edolh7ww cord-297960-4x1j0iqg cord-298214-ivu4erpq cord-295433-olmein3q cord-297662-slmlhqnb cord-296635-8r3tm966 cord-300189-gsp1dozg cord-298051-ej8qxkce cord-298862-8bijio30 cord-302277-c66xm2n4 cord-298019-gf2asni1 cord-302425-aaxvlktp cord-302111-kg0dmgq0 cord-300837-d0a8y5qh cord-301064-ex6qb6zj cord-298489-uqrzzh0e cord-298033-kzdp9edn cord-298733-jole21wq cord-300133-yc2wxgid cord-297790-tpjxt0w5 cord-299207-lw0cv74b cord-300810-a1skdp67 cord-299379-ch7a39d6 cord-303040-ha8gufh8 cord-299786-wuve0tjz cord-301285-p83ondy8 cord-301592-n5ns3m34 cord-298736-9bvyp21d cord-298678-hjxph9jm cord-300711-yibdumij cord-302716-wfla3l20 cord-302047-vv5gpldi cord-302021-42vqmndl cord-298745-3rrlap70 cord-302486-z36hcvrx cord-302055-s155i4e9 cord-302614-siyyve9e cord-299549-bjqwwzam cord-303297-fiievwy7 cord-300522-okbupw61 cord-304481-yqc8r3ll cord-303186-2hxlx1j2 cord-304807-j2k1oel2 cord-304278-0qy1nngs cord-300435-vs0ntcsb cord-304251-dohglrm1 cord-301362-f3lp10lm cord-305336-wxiazglk cord-304850-9xetsc2c cord-303533-6s01qplg cord-303665-l57e54hu cord-306983-6w2fvtfy cord-305263-fgwf6wy3 cord-304498-ty41xob0 cord-306733-df36w6l7 cord-307893-mvl0wrsj cord-308385-bcph664h cord-305302-go87uu06 cord-304876-txaoz7oh cord-307817-2vy28i4m cord-304747-ojyxs3cp cord-305807-n3fs7533 cord-304343-m7tbdfri cord-305165-3twlnkac cord-302529-43pd2qsp cord-309048-emmtplv3 cord-305742-wf6qxplf cord-304424-048xo7jn cord-307744-wbr84taq cord-304569-o39kl5k4 cord-305488-vk59ghjm cord-309346-4mdxe6ri cord-309489-ubf55eux cord-309179-5hlatbqe cord-309120-05bg7rfa cord-308857-otsrexqu cord-307813-elom30nx cord-307046-ko3bdvo0 cord-308201-lavcsqov cord-310141-2jofy8fo cord-307918-8y89p11a cord-309067-aemjbkfj cord-307632-x9bxnrtn cord-303265-v6ci69n0 cord-309381-cb80ntxs cord-305327-hayhbs5u cord-307899-427a7i3h cord-306083-juysx6yo cord-310255-aixq5mhf cord-310371-pylrg91h cord-308686-tbwecf7o cord-306948-wkisfz1m cord-309635-1tgovkr7 cord-311748-yr2ep7uf cord-311823-85wj08gr cord-312964-vsrqmmv7 cord-310140-h7uwl0pb cord-308066-lrbi5198 cord-310942-191m0e65 cord-309488-8guapzke cord-307364-j86t65qu cord-306424-gf0bglm0 cord-312431-de7zhswl cord-314254-9ye8tfvz cord-310795-n78s0sg2 cord-310920-itqwhi6a cord-310171-1fmsxx2s cord-311410-lgqup9ug cord-314190-fvdock94 cord-312461-5qzpo6l1 cord-313356-ninzeazy cord-310439-z0bxsjug cord-311908-sgdq6j6x cord-310870-w8wu8vno cord-314390-q36ye9ff cord-309642-wwaa6ls0 cord-315346-ebfjba4y cord-313312-h607itv2 cord-314166-79323mzd cord-314325-nquov2i0 cord-311382-ioemd0ij cord-316295-x636ux34 cord-313301-7mkadtp9 cord-315037-lmur80te cord-316245-n6tmn4ph cord-311012-wyglrpqh cord-315781-dejh8q22 cord-316951-1swlhdz5 cord-315167-ph15z424 cord-314201-6njwigco cord-312688-12san3m7 cord-312332-rwmuucsp cord-315131-4yb2b70g cord-317198-mean7sj9 cord-317244-4su5on6s cord-317404-jvtozj4v cord-313598-2t40ss6h cord-316996-8yimrpaz cord-315918-12rbbe8c cord-316682-4360s2yu cord-318172-bdotp9ko cord-317501-yblzopc3 cord-317851-lj07947c cord-317971-kuwargnp cord-317277-rr9zue4l cord-318725-09a32vyg cord-319746-6bccxgbd cord-317496-6o2upns3 cord-316894-zhmuzv7z cord-319208-jrxz59bb cord-318786-qd0k8174 cord-319754-5isw53wl cord-318495-1w74wf02 cord-317508-03u2vtzk cord-319814-tyqb473m cord-315339-dcui85lw cord-316063-9bg2dm8e cord-316273-vo6j8zb0 cord-314825-fzba05wn cord-319210-yqimufdh cord-322748-a5131tv9 cord-317412-f3ua8ks3 cord-318551-c1qr27lg cord-321756-a7eh4dkb cord-319761-bu5pzbnv cord-321562-hk4hzl13 cord-317619-o7qfugjw cord-320935-3n157yl4 cord-321053-lgae22f8 cord-320030-ojtp90na cord-318686-we6pveus cord-320693-de1lmzl1 cord-323333-keshu99t cord-320055-6ycp8m89 cord-318853-mxyxwkhx cord-321835-qn33sx8x cord-319379-qe56u93a cord-321741-aq76s37x cord-320015-lbr2q4qh cord-322082-80ym2rsq cord-324775-3x5os79m cord-323195-buzcb8ya cord-323358-05bk91lm cord-320713-b37c8aye cord-321112-w7x1dkds cord-323404-3mw4q7m3 cord-322234-1zyy536y cord-323009-frej2qmb cord-322206-roxa3ix6 cord-322904-9mta0aem cord-319933-yp9ofhi8 cord-323987-gh1m05gi cord-324950-ux7shvji cord-324280-e8mj6ecl cord-325280-4whzcmqv cord-321481-vrfwczve cord-323700-5awng7h1 cord-323311-xl2fv0qx cord-325875-93krp81r cord-325825-0lyt8gfq cord-323793-c69joaqs cord-326719-p1ma4akz cord-323710-cmbg0ty8 cord-324696-htx0ul4o cord-323930-pl3qlcpo cord-325830-mrtpihc7 cord-324984-ojrpsdt9 cord-325635-don9qjpz cord-325230-3kg4oe4g cord-324295-9c1zxjng cord-325750-x7jpsnxg cord-326225-crtpzad7 cord-325326-2bbqz4o7 cord-325969-9zhmmvdg cord-327013-gc6o8ou3 cord-327199-ggomuomb cord-325915-dw989txm cord-325827-492xi3ee cord-327000-oyg3oyx1 cord-326725-0jgw083h cord-325925-010xj69x cord-326027-58whwspe cord-325325-xw7627x9 cord-328252-dk54w8z9 cord-326177-zzsaf3bl cord-327855-txryqil7 cord-325712-9kbnyqt3 cord-326960-9phlylce cord-329857-pcsuu597 cord-327660-p1b07b4t cord-325611-tu1bn4hu cord-329050-vzsy6xw1 cord-329145-424vv8a8 cord-328621-3jda0k2u cord-329078-gnnis7pl cord-327777-pg98zc6o cord-326160-mf0vh6iu cord-330827-gu2mt6zp cord-330508-uilejxmi cord-328753-qwdxgk4z cord-327392-9psblokc cord-330296-706hf4qw cord-329527-0rlotyz3 cord-329493-ueqlhgn0 cord-327883-s9nbr5y8 cord-329429-ur8g68vp cord-331217-uup16bhm cord-329902-db7hl770 cord-331020-lyxje82u cord-330131-yfhrmbvx cord-323683-9h9mld6x cord-331673-xv1tcugl cord-331244-zaguyxm5 cord-330647-w1bpeqzg cord-332165-31tbc31x cord-332361-pdoln3nr cord-331584-z43ifmr3 cord-331739-y1d0leic cord-332457-gan10za0 cord-331652-oc5s1if2 cord-331289-02411gfv cord-332181-k90i33gp cord-333043-fe24ezt6 cord-332632-u2ud0vmq cord-332088-5c77h0of cord-332205-ydijp66b cord-332992-8rmqg4rf cord-332046-ihc031ly cord-333730-qsx0m68e cord-331343-qzvwwca9 cord-333228-ejkgune0 cord-333853-p2kbjwpy cord-333351-homxj9uz cord-334010-gxu0refq cord-334947-pa0p5dif cord-334027-xhfmio7k cord-334941-6uattdti cord-334560-1j9zmuub cord-334082-fyxn0g3v cord-334771-uy3s6443 cord-333810-57d4oopv cord-335116-c83xyev5 cord-336157-aqc9zrrm cord-333463-u7je0d1o cord-330852-n7j0c4ne cord-335948-qkfxfmxb cord-334365-idjvbcy4 cord-333655-lylt7qld cord-335774-15fhg8o9 cord-336045-8qcj5uiy cord-335279-cfv18qn0 cord-336447-hpnkou41 cord-336493-ggo9wsrm cord-334108-4ey725dv cord-337149-cjon7ihb cord-336554-n8n5ii5k cord-333262-xvfl7ycj cord-336929-2rnkotqy cord-337285-t6qr41wc cord-337673-1nau263l cord-337361-salby0fu cord-336225-ijodhrwf cord-337914-1hwnxkdd cord-336948-8yqdhcnz cord-337577-dqikrmk7 cord-338400-30vl2hks cord-338083-77re4l0w cord-337659-x4oywbrj cord-338081-ggw5l1qm cord-339209-oe8onyr9 cord-335647-dhcxj7cj cord-338727-1kodz527 cord-339854-scb7pz87 cord-338804-nreqluol cord-336212-ueh4q408 cord-339062-tq0f6d01 cord-339172-210dwhgj cord-339744-xrit0w5i cord-340907-j9i1wlak cord-339885-mpzgrogd cord-339423-5qym9dsf cord-337712-ylqgraos cord-339382-ii4xurmr cord-341050-hnuogpqn cord-336510-qzm9wgde cord-340481-i3qrxnpr cord-338331-27ic5zen cord-339230-cc7gcy5b cord-339386-sxyeuiw1 cord-340537-pdvpmydk cord-340423-f8ab7413 cord-340610-ex2yjyum cord-340503-zwdewiu1 cord-341303-1iayp8oa cord-339973-kj56zi59 cord-340042-intxyu46 cord-341923-jwckbdnb cord-339152-wfakzb6w cord-341138-mxjsp3cm cord-341298-mqpovrms cord-340331-51yq1rdo cord-339288-y8woqsii cord-342412-azkamnpa cord-338737-phv12m1q cord-341155-3d64mso0 cord-342151-1e6x589e cord-340629-1fle5fpz cord-341968-uc8i9h0m cord-344009-hm36pepp cord-341029-49360l2a cord-340194-ibli36rq cord-344006-0iq9s94n cord-341101-5yvjbr5q cord-343690-rafvxgx1 cord-342936-43u7afl3 cord-342915-r9kv67we cord-343350-04e6wvov cord-344408-4ko557n1 cord-341765-ml6eo8r3 cord-345168-3w32v2fm cord-342277-v6310fjh cord-342906-51296y8d cord-343784-zgvxl4h3 cord-345359-okmkgsbr cord-345157-fhmhpobi cord-340489-yo3cp5vs cord-347509-2ysw9a0a cord-344749-omzhhr0k cord-341324-f9g9gitn cord-344782-ond1ziu5 cord-346673-kyc1wks5 cord-344576-upsc9cf8 cord-347465-yu6oj30v cord-331714-2qj2rrgd cord-344093-3bniy5b5 cord-345020-ai5tib7h cord-343347-guciupc8 cord-343963-99rd3o79 cord-346836-6jyv0q5e cord-346290-my8ow5ee cord-343918-5yk1j4ms cord-346853-0c1qdjb5 cord-346906-1wmp43ti cord-347577-p0a2rboi cord-346904-aa88gtzr cord-346096-aml84iv1 cord-342124-jdv17u86 cord-348876-v55piprx cord-344889-1y4ieamp cord-348141-eskefcwk cord-348161-757c51xw cord-348427-worgd0xu cord-348860-zaimorg0 cord-348163-9q1rt8i7 cord-346063-7u1a198p cord-346916-jj4l9ydl cord-349225-504kr50e cord-348867-c0xpzd4d cord-349249-jwvz1ux2 cord-345848-s84lxe6l cord-345654-vyz6f3he cord-345689-5ns1onkw cord-349606-lup6tm2s cord-347727-wka9q98s cord-344970-ud1lhkyi cord-349011-kxhpdvri cord-349358-leicos9j cord-347039-eap592i7 cord-350964-0jtfc271 cord-348669-mizygp4j cord-350467-18bvwxci cord-350151-s75d1hat cord-351197-xv6ymc4l cord-350235-yoy3hj3j cord-351482-hzh5tyoo cord-350703-vrqltz3s cord-351377-xorj8tnz cord-350948-oog6m4h3 cord-351571-gwtkrt5u cord-352054-g7q2z4l5 cord-352379-q5inrxcm cord-352475-cmmpy5u7 cord-350747-5t5xthk6 cord-351365-dc9t3vh3 cord-352178-irjhmxsg cord-353290-1wi1dhv6 cord-354536-c9v9kbw8 cord-350925-1h6pbfwp cord-352619-s2x53grh cord-353509-yfkiaq80 cord-353297-jizitnfl cord-351170-belbcrcd cord-352200-i05h8csb cord-354109-mli0c97c cord-353609-no3mbg5d cord-354035-i3sl2r0k cord-355181-affuyn8z cord-354151-psog34u3 cord-354848-7aakik9a cord-353869-l53ms3q8 cord-355489-tkvfneje cord-355771-pxkkd3s1 cord-356176-1nwjjgul cord-355872-z6vsjmxn cord-355685-wgad0eoh cord-355535-01h8yyqj cord-355259-779czzzx cord-354068-4qlk6y7h cord-355906-yeaw9nr8 cord-356188-rwf78stz cord-355913-fhvt1ht1 cord-354582-fniymnmf cord-347710-ff64y6ef cord-353190-7qcoxl81 Creating transaction Updating pos table Building ./etc/reader.txt cord-001521-l36f1gp7 cord-331714-2qj2rrgd cord-264408-vk4lt83x cord-001521-l36f1gp7 cord-314825-fzba05wn cord-264408-vk4lt83x number of items: 1,203 sum of words: 8,584,216 average size in words: 7,231 average readability score: 45 nouns: virus; viruses; infection; influenza; cells; cell; protein; disease; host; infections; proteins; replication; vaccine; studies; mice; patients; study; type; transmission; gene; response; genome; activity; vaccines; detection; species; antibody; treatment; time; analysis; expression; role; antibodies; data; humans; membrane; cases; children; sequence; system; coronavirus; animals; use; dna; acid; strains; number; receptor; diseases; development verbs: using; shown; infect; including; associated; caused; induced; based; found; bind; detected; developing; increasing; occur; identified; contain; reported; suggested; followed; requires; provide; results; known; described; leading; isolated; produced; involves; observed; mediated; reduced; inhibits; seen; indicate; made; determine; emerging; express; demonstrated; compare; related; targeted; affecting; considered; remains; given; allowed; preventing; tested; revealed adjectives: viral; human; respiratory; immune; clinical; different; specific; antiviral; high; new; infectious; many; severe; acute; several; important; cellular; genetic; infected; molecular; non; avian; first; similar; like; common; positive; novel; low; large; small; single; anti; recent; major; possible; multiple; present; potential; early; available; natural; recombinant; effective; dependent; significant; structural; bacterial; higher; negative adverbs: also; however; well; highly; therefore; often; even; recently; previously; respectively; usually; still; currently; especially; first; directly; significantly; now; less; particularly; furthermore; approximately; generally; moreover; relatively; yet; later; frequently; together; rather; mainly; probably; commonly; rapidly; encephalitis; interestingly; potentially; indeed; much; newly; closely; far; finally; similarly; primarily; subsequently; typically; likely; already; specifically pronouns: it; their; we; its; they; i; our; them; his; he; us; itself; one; themselves; her; you; she; your; my; em; me; him; himself; mrnas; ourselves; rad5; ifitm3; yourself; ns3/4a; ours; p~; pdcs; nsp15; nsp10; herself; s; mg; isgf3; oneself; myself; igg1; e4narrow; sgp; nsp7; irfibv32; gh625; clustalx; 's; ⍬; theirs proper nouns: RNA; SARS; C; PCR; Fig; RSV; A; H1N1; IFN; HIV; Ebola; H5N1; HA; HCV; HIV-1; B; Influenza; T; CoV; Virus; ⁄; CoV-2; RT; China; der; Table; United; West; II; M; DNA; Zika; Health; States; COVID-19; IAV; NA; MERS; Africa; USA; Nile; S; F; N; Human; CD4; H3N2; hepatitis; C.; IBV keywords: virus; rna; infection; cell; sars; influenza; respiratory; viral; dna; protein; pcr; disease; vaccine; human; rsv; hiv; ifn; h5n1; ebola; covid-19; hiv-1; host; hcv; h1n1; bat; antiviral; detection; zika; cns; antibody; mouse; mers; iav; patient; gene; china; sequence; hbv; genome; animal; ibv; drug; pandemic; nipah; membrane; child; zikv; wnv; west; water one topic; one dimension: virus file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3764161/ titles(s): In Vitro Infection of Pupae with Israeli Acute Paralysis Virus Suggests Disturbance of Transcriptional Homeostasis in Honey Bees (Apis mellifera) three topics; one dimension: virus; virus; virus file(s): https://api.elsevier.com/content/article/pii/B9780123820082000192, https://api.elsevier.com/content/article/pii/B9783437428319100130, https://www.ncbi.nlm.nih.gov/pubmed/33078075/ titles(s): Viral Infections of Laboratory Mice | KAPITEL 13 Infektionskrankheiten | Why meaning-making matters: the case of the UK Government’s COVID-19 response five topics; three dimensions: virus influenza infection; virus disease infection; virus protein viral; virus viruses viral; virus viruses viral file(s): https://api.elsevier.com/content/article/pii/B9780123820082000192, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7150219/, https://api.elsevier.com/content/article/pii/B9783437428319100130, https://www.ncbi.nlm.nih.gov/pubmed/26601271/, https://www.ncbi.nlm.nih.gov/pubmed/32214924/ titles(s): Viral Infections of Laboratory Mice | Biology and Diseases of Ruminants: Sheep, Goats, and Cattle | KAPITEL 13 Infektionskrankheiten | A phylogenomic data-driven exploration of viral origins and evolution | Cellulose-based virus-retentive filters: a review Type: cord title: keyword-virus-cord date: 2021-05-25 time: 17:24 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: keywords:virus ==== 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-341050-hnuogpqn author: Acharya, Dhiraj title: An Overview of Current Approaches Toward the Treatment and Prevention of West Nile Virus Infection date: 2016-05-18 words: 10713.0 sentences: 490.0 pages: flesch: 37.0 cache: ./cache/cord-341050-hnuogpqn.txt txt: ./txt/cord-341050-hnuogpqn.txt summary: Among these structural proteins, E protein mediates crucial roles in binding to cellular receptors, membrane fusion, and entry of WNV into host cells, making it a key target for the development of vaccines, neutralizing antibodies, and entry inhibitors . In addition, a recent successful clinical trial of a hepatitis C virus NS5A inhibitor suggests that targeting non-structural proteins may be an ideal strategy to develop therapeutics against other fl aviviruses, including WNV [ 71 ] . In addition, better understanding of the pathogenesis of WNV and other fl aviviruses has offered new opportunities for designing many different classes of promising antiviral therapeutics by targeting both viral replication and the host cell metabolism. Several natural and synthetic compounds, antiviral peptides and siRNAs have been identifi ed to target both structural and nonstructural proteins of WNV and evaluated for their potential therapeutic roles. A VLP-based vaccine targeting domain III of the West Nile virus E protein protects from lethal infection in mice abstract: The persistence of West Nile virus (WNV) infections throughout the USA since its inception in 1999 and its continuous spread throughout the globe calls for an urgent need of effective treatments and prevention measures. Although the licensing of several WNV vaccines for veterinary use provides a proof of concept, similar efforts on the development of an effective vaccine for humans remain still unsuccessful. Increased understanding of biology and pathogenesis of WNV together with recent technological advancements have raised hope that an effective WNV vaccine may be available in the near future. In addition, rapid progress in the structural and functional characterization of WNV and other flaviviral proteins have provided a solid base for the design and development of several classes of inhibitors as potential WNV therapeutics. Moreover, the therapeutic monoclonal antibodies demonstrate an excellent efficacy against WNV in animal models and represent a promising class of WNV therapeutics. However, there are some challenges as to the design and development of a safe and efficient WNV vaccine or therapeutic. In this chapter, we discuss the current approaches, progress, and challenges toward the development of WNV vaccines, therapeutic antibodies, and antiviral drugs. url: https://doi.org/10.1007/978-1-4939-3670-0_19 doi: 10.1007/978-1-4939-3670-0_19 id: cord-312461-5qzpo6l1 author: Adalja, Amesh A. title: Characteristics of Microbes Most Likely to Cause Pandemics and Global Catastrophes date: 2019-08-30 words: 6830.0 sentences: 290.0 pages: flesch: 40.0 cache: ./cache/cord-312461-5qzpo6l1.txt txt: ./txt/cord-312461-5qzpo6l1.txt summary: A substantial proportion of pandemic and biological threat preparedness activities have focused on list-based approaches that were in part based on pandemic influenzas of the past, historical biological weapon development programs, or recent outbreaks of emerging infectious diseases (e.g., SARS, MERS, Ebola) (Centers for Disease Control and Prevention 2017; Casadevall and Relman 2010) . Cultivating and maintaining expertise in the epidemiology, surveillance, and pathogenicity of all classes of microbes, with explicit incorporation of a One Health approach-which incorporates and integrates information from infectious diseases of plants, amphibians, and reptiles-will help foster the broad capacities needed for emerging pandemic and global catastrophic biological risks. Pathogen-based lists, both USA and global, based on influenza precedents, historical biological weapon programs, and emerging infectious diseases were responsible for galvanizing early activities in the field of pandemic preparedness and have helped drive many important contributions. abstract: Predicting which pathogen will confer the highest global catastrophic biological risk (GCBR) of a pandemic is a difficult task. Many approaches are retrospective and premised on prior pandemics; however, such an approach may fail to appreciate novel threats that do not have exact historical precedent. In this paper, based on a study and project we undertook, a new paradigm for pandemic preparedness is presented. This paradigm seeks to root pandemic risk in actual attributes possessed by specific classes of microbial organisms and leads to specific recommendations to augment preparedness activities. url: https://www.ncbi.nlm.nih.gov/pubmed/31463536/ doi: 10.1007/82_2019_176 id: cord-293472-d3iwlpsr author: Afilalo, Marc title: Evaluation and Management of Seasonal Influenza in the Emergency Department date: 2012-04-06 words: 9919.0 sentences: 516.0 pages: flesch: 38.0 cache: ./cache/cord-293472-d3iwlpsr.txt txt: ./txt/cord-293472-d3iwlpsr.txt summary: During influenza season (testing should be done in the following persons if the result will influence clinical management) Outpatient immunocompetent persons of any age at high risk of developing influenza complications (eg, hospitalization or death) presenting with acute febrile respiratory symptoms 5 days or less after illness onset (when virus is usually being shed) Outpatient immunocompromised persons of any age presenting with febrile respiratory symptoms, irrespective of time since illness onset (because immunocompromised persons can shed influenza viruses for weeks to months) Hospitalized persons of any age (immunocompetent or immunocompromised) with fever and respiratory symptoms, including those with a diagnosis of community-acquired pneumonia, irrespective of time since illness onset Elderly persons and infants presenting with suspected sepsis or fever of unknown origin, irrespective of time since illness onset Children with fever and respiratory symptoms presenting for medical evaluation, irrespective of time since illness onset Persons of any age who develop fever and respiratory symptoms after hospital admission, irrespective of time since illness onset Immunocompetent persons with acute febrile respiratory symptoms who are not at high risk of developing complications secondary to influenza infection may be tested for purposes of obtaining local surveillance data abstract: Seasonal influenza causes significant morbidity and mortality, primarily due to increased complication rates among the elderly population and patients with chronic diseases. Timely diagnosis of influenza and early recognition of an influenza outbreak or epidemic are key components in preventing influenza-related complications, hospitalizations, and deaths. Emergency departments are the most frequent points of entry for most influenza cases and are well positioned to identify and manage influenza community outbreaks and epidemics. Emergency departments need specific infection control measures to curb the spread of influenza in the Emergency Department and hospital during the influenza season. url: https://api.elsevier.com/content/article/pii/S0733862711001209 doi: 10.1016/j.emc.2011.10.011 id: cord-297203-f3f31h4r author: Afrough, B. title: Emerging viruses and current strategies for vaccine intervention date: 2019-04-16 words: 5914.0 sentences: 263.0 pages: flesch: 36.0 cache: ./cache/cord-297203-f3f31h4r.txt txt: ./txt/cord-297203-f3f31h4r.txt summary: While classic approaches to vaccine development are still amenable to emerging viruses, the application of molecular techniques in virology has profoundly influenced our understanding of virus biology, and vaccination methods based on replicating, attenuated and non‐replicating virus vector approaches have become useful vaccine platforms. Modified vaccinia virus Ankara (MVA) is licensed as a third-generation vaccinia type vaccine against smallpox and serves as a potent vector system for the development of new candidate vaccines against a range of infectious diseases, including those caused by emerging pathogens. Additionally, MVA elicits a strong immunological response against a range of other orthopoxviruses (OPXVs) (including Variola), and vaccines based on this platform can be considered as providing added value, as human immunity to OPXVs is low (after the cessation of the smallpox vaccination campaign) opening a gap for OPXV emergence, as evidenced by the recent occurrence of monkeypox virus in West Africa and onward cross boarder transmissions [39, 40] . abstract: During the past decade several notable viruses have suddenly emerged from obscurity or anonymity to become serious global health threats, provoking concern regarding their sustained epidemic transmission in immunologically naive human populations. With each new threat comes the call for rapid vaccine development. Indeed, vaccines are considered a critical component of disease prevention for emerging viral infections because, in many cases, other medical options are limited or non‐existent, or that infections result in such a rapid clinical deterioration that the effectiveness of therapeutics is limited. While classic approaches to vaccine development are still amenable to emerging viruses, the application of molecular techniques in virology has profoundly influenced our understanding of virus biology, and vaccination methods based on replicating, attenuated and non‐replicating virus vector approaches have become useful vaccine platforms. Together with a growing understanding of viral disease emergence, a range of vaccine strategies and international commitment to underpin development, vaccine intervention for new and emerging viruses may become a possibility. url: https://www.ncbi.nlm.nih.gov/pubmed/30993690/ doi: 10.1111/cei.13295 id: cord-016808-gy8d8285 author: Agol, Vadim I. title: The Origin and Evolution of Viruses date: 2008 words: 3255.0 sentences: 172.0 pages: flesch: 44.0 cache: ./cache/cord-016808-gy8d8285.txt txt: ./txt/cord-016808-gy8d8285.txt summary: Modern hypotheses of viral origin are based on two major developments of the molecular biology: discovery of ribozymes (RNA-based enzymes) and formulation of the "RNA World" theory (RNA had been "invented" before proteins and DNA), on the one hand, and achievements of genomics (determination of the nucleotide sequences of a great number of cellular and viral genomes), on the other. Three distinct DNA viruses, which had infected RNA genome-containing cells, gave rise to the three distinct domains of life, bacteria, archea, and eukarya (Forterre, 2006) . To infect a human, an avian flu virus should change its receptor specificity, which depends on the interaction of viral hemagglutinin (HA) with a cellular membrane glycoprotein receptor. Such a change in the host range may be achieved by either mutations in the avian HA or acquisition by an avian virus of the HA gene from human influenza virus as a result of genetic exchange (reassortment) between these viruses during mixed infections. Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain abstract: The lecture covers three main topics: (i) Viruses: properties, place in the living world, and possible origin; (ii) Molecular basis of viral variability and evolution; and (iii) Evolution of viral pathogenicity and emerging viral infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121209/ doi: 10.1007/978-1-4020-8761-5_7 id: cord-325230-3kg4oe4g author: Agol, Vadim I. title: Viral security proteins: counteracting host defences date: 2010-11-09 words: 8716.0 sentences: 426.0 pages: flesch: 41.0 cache: ./cache/cord-325230-3kg4oe4g.txt txt: ./txt/cord-325230-3kg4oe4g.txt summary: These proteins include: capsid proteins; an RNA-dependent RNA polymerase (3D pol ); a protein (VPg, or 3B) that serves as a primer for the initiation of RNA synthesis; an ATPase with a conserved superfamily 3 helicase motif (2C ATPase ) and an essential but poorly defined role in viral RNA replication; a chymotrypsin-like protease (3C pro ), which, as the mature protein or as a precursor, is a major factor in polyprotein processing; two hydrophobic membrane-binding proteins (2B and 3A) that participate in the generation of a virus-friendly environment; and, flanking the precursor of the capsid proteins, one or two highly variable proteins (L and 2A), the structure and functions of which are the subject of this Review. abstract: Interactions with host defences are key aspects of viral infection. Various viral proteins perform counter-defensive functions, but a distinct class, called security proteins, is dedicated specifically to counteracting host defences. Here, the properties of the picornavirus security proteins L and 2A are discussed. These proteins have well-defined positions in the viral polyprotein, flanking the capsid precursor, but they are structurally and biochemically unrelated. Here, we consider the impact of these two proteins, as well as that of a third security protein, L(*), on viral reproduction, pathogenicity and evolution. The concept of security proteins could serve as a paradigm for the dedicated counter-defensive proteins of other viruses. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nrmicro2452) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1038/nrmicro2452 doi: 10.1038/nrmicro2452 id: cord-017167-8cdbcrh7 author: Ahola, Tero title: Functions of Chikungunya Virus Nonstructural Proteins date: 2016-12-03 words: 10491.0 sentences: 530.0 pages: flesch: 49.0 cache: ./cache/cord-017167-8cdbcrh7.txt txt: ./txt/cord-017167-8cdbcrh7.txt summary: The nonstructural proteins (nsPs) of chikungunya virus (CHIKV) are expressed as one or two polyprotein precursors, which are translated directly from the viral genomic RNA. Similar to other alphaviruses, CHIKV nsPs not only perform virus RNA replication but are also crucial for other activities essential for virus infection and pathogenesis. However, recent studies of SFV P1234 processing reveal that a second mechanism, the presentation of cleavage sequences via long-range interactions between different domains of the polyprotein, Processing of CHIKV ns polyprotein P1234 and RNA synthesis. The main interaction appears to be mediated by a membrane-binding peptide located in the central part of the protein (approximately residues 244-263 in CHIKV nsP1; Fig. 2 ), which forms an amphipathic alpha helix, as characterized for the corresponding peptide from SFV (Ahola et al. However, the effects of mutations introduced into the NTPase/helicase active site were different for these viruses: in SINV such a mutation strongly reduced the nsP2-dependent degradation of Rpb1 whereas CHIKV nsP2 mostly retained its ability to block host gene expression. abstract: The nonstructural proteins (nsPs) of chikungunya virus (CHIKV) are expressed as one or two polyprotein precursors, which are translated directly from the viral genomic RNA. Mature nsPs are generated by precise processing of these polyproteins. Both the precursors and mature nsPs are essential for CHIKV replication. Similar to other alphaviruses, CHIKV nsPs not only perform virus RNA replication but are also crucial for other activities essential for virus infection and pathogenesis. Thus far the best-studied CHIKV ns-protein is nsP2, for which protease, NTPase, RNA triphosphatase, and RNA helicase activities have been demonstrated. In addition, nsP2 is crucial for shut-off of host cell transcription and translation and it counteracts cellular antiviral responses. Compared to their homologues from the well-studied Sindbis and Semliki Forest viruses, CHIKV nsP1, nsP3, and nsP4 have been subjected to only few studies. Nevertheless, there are strong indirect pieces of evidence indicating that these CHIKV proteins have the same enzymatic activities as their counterparts in the other alphaviruses. Information concerning the specific interaction of CHIKV nsPs with host components is beginning to emerge. All the nsPs are involved in the functioning of membrane-bound replication complexes also called spherules, but the finer details of the structure and assembly of these complexes are currently poorly understood. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121661/ doi: 10.1007/978-3-319-42958-8_6 id: cord-280391-5kiu2pb6 author: Akinloye, Oluwabukola M. title: Specific Viruses Detected in Nigerian Children in Association with Acute Respiratory Disease date: 2011-10-11 words: 2499.0 sentences: 126.0 pages: flesch: 48.0 cache: ./cache/cord-280391-5kiu2pb6.txt txt: ./txt/cord-280391-5kiu2pb6.txt summary: Adenoviruses, coronaviruses, human enteroviruses (HEV), human rhinoviruses (HRV), influenza viruses, parainfluenza viruses (PIV), and respiratory syncytial viruses (RSV) are well-known causes of acute respiratory tract infections (ARTI) in both industrialized and developing countries. Moreover, different viruses, including influenza viruses and RSV, are also frequently detected in samples obtained from patients with lower respiratory tract infection (LRTI), either alone or together with pathogenic bacteria. While the overall proportion of virus-positive specimens was similar in children aged under or over two years, as well as in the group with unrecorded age, all adenovirus, influenza virus A, RSV, and all but one HBoV and "true HEV" detections were in the youngest age group (Table 1) . This study revealed that all major respiratory virus groups tested for can be detected in Nigerian children with respiratory tract infection. Rhinoviruses and parainfluenza viruses were the most prevalent virus groups while influenza A and B viruses, as well RSV were rarely detected, possibly due to low season of these viruses during the time of sample collection. abstract: Occurrence of different viruses in acute respiratory tract infections of Nigerian children was examined. Respiratory swabs were collected from 246 children referred to hospital clinics because of acute respiratory symptoms from February through May 2009. Validated real-time RT-PCR techniques revealed nucleic acids of at least one virus group in 189 specimens (77%). Human rhinoviruses and parainfluenza viruses were present each in one third of the children. Adenoviruses, enteroviruses, human metapneumovirus, human bocavirus, and influenza C virus were also relatively common. Possibly due to their seasonal occurrence, influenza A and B virus, and respiratory syncytial virus were detected rarely. We conclude that all major groups of respiratory tract viruses are causing illness in Nigerian children. url: https://www.ncbi.nlm.nih.gov/pubmed/22007241/ doi: 10.1155/2011/690286 id: cord-278876-il7g78w1 author: Akkina, Ramesh title: 2016 International meeting of the Global Virus Network date: 2017-03-16 words: 7538.0 sentences: 315.0 pages: flesch: 35.0 cache: ./cache/cord-278876-il7g78w1.txt txt: ./txt/cord-278876-il7g78w1.txt summary: This report highlights the accomplishments of GVN researchers in many priority areas of medical virology, including the current Zika epidemic, infections by human papillomavirus, influenza, Ebola, Lassa, dengue, HIV, hepatitis C, and chikungunya viruses, and the development of improved diagnostics and new vaccines. This meeting report highlights accomplishments of GVN researchers in many priority areas of human virology, including the current Zika epidemic, infections by human papillomavirus, influenza, Ebola, Lassa, dengue, HIV, hepatitis C and chikungunya viruses, and the development of improved diagnostics and new vaccines. The main objectives of the meeting were to present and discuss current findings in medical virology, including advances in research on HIV vaccines and other important retroviruses; provide a framework to encourage collaborations among world experts; and address the GVN''s annual strategy for continued development. Hideki Hasegawa, a GVN center director at the National Institute of Infectious Diseases in Tokyo, explained that secretory IgA antibodies on mucosal surfaces play an important role in protection against influenza virus infection. abstract: The Global Virus Network (GVN) was established in 2011 in order to strengthen research and responses to current viral causes of human disease and to prepare against new viral pandemic threats. There are now 38 GVN Centers of Excellence and 6 Affiliate laboratories in 24 countries. GVN scientists meet annually to learn about each other's current research, address collaborative priorities and plan future programs. The 2016 meeting was held from October 23–25 in Hokkaido, Japan, in partnership with the Japanese Society for Virology, the National Institute of Infectious Diseases of Japan and the Research Center for Zoonosis Control of Hokkaido University. This report highlights the accomplishments of GVN researchers in many priority areas of medical virology, including the current Zika epidemic, infections by human papillomavirus, influenza, Ebola, Lassa, dengue, HIV, hepatitis C, and chikungunya viruses, and the development of improved diagnostics and new vaccines. url: https://doi.org/10.1016/j.antiviral.2017.03.005 doi: 10.1016/j.antiviral.2017.03.005 id: cord-267733-fuz8r3vj author: Al Ali, Sally title: Use of Reporter Genes in the Generation of Vaccinia Virus-Derived Vectors date: 2016-05-21 words: 7966.0 sentences: 392.0 pages: flesch: 41.0 cache: ./cache/cord-267733-fuz8r3vj.txt txt: ./txt/cord-267733-fuz8r3vj.txt summary: This broad host range allows infection of cell lines with recombinant viruses for large-scale expression of heterologous proteins, which reduces its cost This broad host range allows infection of cell lines with recombinant viruses for large-scale expression of heterologous proteins, which reduces its cost in comparison to other production systems [21, 24] . This reporter gene system has been widely used in transgenic plants, and it has also been successfully used in mammalian cells for VACV recombinant virus selection [54] . Reporter-gene assays have helped the pox virologists in basic research, for example for the study of the location, structure and function of many VACV proteins during the infection cycle and their interaction with proteins of the host cell [44, 70] . The main limitation of using VACV as a vector is the short-term gene expression, since it is a lytic virus killing the infected cells. Insertion sites for recombinant vaccinia virus construction: Effects on expression of a foreign protein abstract: Vaccinia virus (VACV) is one of the most extensively-studied viruses of the Poxviridae family. It is easy to genetically modify, so it has become a key tool for many applications. In this context, reporter genes facilitate the study of the role of foreign genes introduced into the genome of VACV. In this review, we describe the type of reporter genes that have been used to generate reporter-expressing VACV and the applications of the recombinant viruses obtained. Reporter-expressing VACV are currently employed in basic and immunology research, in the development of vaccines and cancer treatment. url: https://doi.org/10.3390/v8050134 doi: 10.3390/v8050134 id: cord-255339-oudj079q author: Al-Tayib, Omar A. title: An Overview of the Most Significant Zoonotic Viral Pathogens Transmitted from Animal to Human in Saudi Arabia date: 2019-02-22 words: 15843.0 sentences: 712.0 pages: flesch: 46.0 cache: ./cache/cord-255339-oudj079q.txt txt: ./txt/cord-255339-oudj079q.txt summary: The most important zoonotic viral diseases of which eight were diagnosed (in dead or diseased animals or through antibody detection) on the Arabian Peninsula over the last years include rabies, Middle East Respiratory Syndrome (MERS-CoV), influenza virus (IFV), Alkhurma hemorrhagic fever, Crimean-Congo hemorrhagic fever (CCHF), Rift Valley fever (RVF), West Nile fever (WNV), and dengue fever virus. The same WHO epidemiological data suggest that in these 22 countries including Saudi Arabia, in recent years, there has been report of steadily increasing number of sporadic human cases, incidence, and outbreaks of the virus [122] . Surprisingly, the current review showed that during an outbreak, each of these eight most zoonotic viruses (rabies, MERS-CoV, influenza, AHFV, CCHFV, RVFV, DHFV, and WNV) which occurred and/or cases confirmed in Saudi Arabia particularly from (Jeddah and/or Makkah) areas with at least one or all of these eight zoonotic viral pathogenic diseases [33, 44, 46, 78, [96] [97] [98] [99] 121, 130, 156, 171] . abstract: Currently, there has been an increasing socioeconomic impact of zoonotic pathogens transmitted from animals to humans worldwide. Recently, in the Arabian Peninsula, including in Saudi Arabia, epidemiological data indicated an actual increase in the number of emerging and/or reemerging cases of several viral zoonotic diseases. Data presented in this review are very relevant because Saudi Arabia is considered the largest country in the Peninsula. We believe that zoonotic pathogens in Saudi Arabia remain an important public health problem; however, more than 10 million Muslim pilgrims from around 184 Islamic countries arrive yearly at Makkah for the Hajj season and/or for the Umrah. Therefore, for health reasons, several countries recommend vaccinations for various zoonotic diseases among preventive protocols that should be complied with before traveling to Saudi Arabia. However, there is a shortage of epidemiological data focusing on the emerging and reemerging of zoonotic pathogens transmitted from animal to humans in different densely populated cities and/or localities in Saudi Arabia. Therefore, further efforts might be needed to control the increasing impacts of zoonotic viral disease. Also, there is a need for a high collaboration to enhance the detection and determination of the prevalence, diagnosis, control, and prevention as well as intervention and reduction in outbreaks of these diseases in Saudi Arabia, particularly those from other countries. Persons in the health field including physicians and veterinarians, pet owners, pet store owners, exporters, border guards, and people involved in businesses related to animal products have adopted various preventive strategies. Some of these measures might pave the way to highly successful prevention and control results on the different transmission routes of these viral zoonotic diseases from or to Saudi Arabia. Moreover, the prevention of these viral pathogens depends on socioeconomic impacts, available data, improved diagnosis, and highly effective therapeutics or prophylaxis. url: https://doi.org/10.3390/pathogens8010025 doi: 10.3390/pathogens8010025 id: cord-294125-v2dr4hm0 author: Albert, Manuel title: ISG15, a Small Molecule with Huge Implications: Regulation of Mitochondrial Homeostasis date: 2018-11-13 words: 8040.0 sentences: 444.0 pages: flesch: 33.0 cache: ./cache/cord-294125-v2dr4hm0.txt txt: ./txt/cord-294125-v2dr4hm0.txt summary: Finally, based on our recent observations, we discuss the essential functions of mitochondria in the antiviral response and examine the role of ISG15 in the regulation of mitochondrial processes, specifically OXPHOS and mitophagy. Binding to IFNARs leads to the activation of the Janus kinase-signal transducer and activator of transcription proteins (JAK-STAT) signaling pathway and the formation of the interferon-stimulated gene factor 3 (ISGF3) complex, with the subsequent expression of IFN-stimulated genes [3] that establish an antiviral state and play important roles in determining the host innate and adaptive immune responses [4] . In the following sections, we discuss the antiviral mechanisms mediated by ISGylation of both viral and cellular proteins, with a focus on mitochondrial proteins, as we recently showed that ISG15 modulates essential mitochondrial metabolic processes such as respiration and mitophagy in macrophages, with important implications for innate immune responses [29] . abstract: Viruses are responsible for the majority of infectious diseases, from the common cold to HIV/AIDS or hemorrhagic fevers, the latter with devastating effects on the human population. Accordingly, the development of efficient antiviral therapies is a major goal and a challenge for the scientific community, as we are still far from understanding the molecular mechanisms that operate after virus infection. Interferon-stimulated gene 15 (ISG15) plays an important antiviral role during viral infection. ISG15 catalyzes a ubiquitin-like post-translational modification termed ISGylation, involving the conjugation of ISG15 molecules to de novo synthesized viral or cellular proteins, which regulates their stability and function. Numerous biomedically relevant viruses are targets of ISG15, as well as proteins involved in antiviral immunity. Beyond their role as cellular powerhouses, mitochondria are multifunctional organelles that act as signaling hubs in antiviral responses. In this review, we give an overview of the biological consequences of ISGylation for virus infection and host defense. We also compare several published proteomic studies to identify and classify potential mitochondrial ISGylation targets. Finally, based on our recent observations, we discuss the essential functions of mitochondria in the antiviral response and examine the role of ISG15 in the regulation of mitochondrial processes, specifically OXPHOS and mitophagy. url: https://www.ncbi.nlm.nih.gov/pubmed/30428561/ doi: 10.3390/v10110629 id: cord-349225-504kr50e author: Alcami, Antonio title: Viral mechanisms of immune evasion date: 2000-09-01 words: 3610.0 sentences: 188.0 pages: flesch: 44.0 cache: ./cache/cord-349225-504kr50e.txt txt: ./txt/cord-349225-504kr50e.txt summary: Viruses such as HIV, human cytomegalovirus (HCMV) and vaccinia virus (VV) utilize a clever strategy, ''borrowing'' host cellular factors, including CD59, which normally protects cells from complement lysis, and incorporating them into the viral envelope. Additionally, several viruses inhibit the activity of IFN-␥, a key activator of cellular immunity, by blocking the synthesis or activity of factors required for its production, such as interleukin (IL)-18 or IL-12 (Table 4 ): CPV cytokine response modifier (Crm A) inhibits caspase-1, which processes the mature forms of IL-1␤ and IL-18 (Refs 2,6); various poxviruses encode soluble IL-18binding proteins (IL-18BPs) [8] [9] [10] ; measles virus (MeV) binds CD46 in macrophages and inhibits IL-12 production 1 ; and herpesviruses and poxviruses express IL-10 homologs that diminish the Th1 response by downregulating the production of IL-12 (Refs 1,11,12). abstract: During the millions of years they have coexisted with their hosts, viruses have learned how to manipulate host immune control mechanisms. Viral gene functions provide an overview of many relevant principles in cell biology and immunology. Our knowledge of viral gene functions must be integrated into virus–host interaction networks to understand viral pathogenesis, and could lead to new anti-viral strategies and the ability to exploit viral functions as tools in medicine. url: https://api.elsevier.com/content/article/pii/S1357431000017755 doi: 10.1016/s1357-4310(00)01775-5 id: cord-313598-2t40ss6h author: Ali, Mohsin title: Throat and nasal swabs for molecular detection of respiratory viruses in acute pharyngitis date: 2015-10-29 words: 2367.0 sentences: 115.0 pages: flesch: 50.0 cache: ./cache/cord-313598-2t40ss6h.txt txt: ./txt/cord-313598-2t40ss6h.txt summary: Our objective was to determine whether sampling with a throat swab provides incremental benefit—when used in conjunction with a nasal swab—to detect respiratory viruses among patients with acute pharyngitis in the outpatient setting. FINDINGS: Among 83 university students with acute pharyngitis, we detected respiratory viruses with molecular assays on two samples collected per student: with a flocked nasal mid-turbinate swab and a rayon throat swab. Our primary objective was to determine whether sampling with a throat swab provides incremental benefit-when used in conjunction with a nasal swab-to detect respiratory viruses among adults with acute pharyngitis. In addition, previous research among adults has shown that flocked nasal mid-turbinate swabs are as sensitive for respiratory virus testing as flocked nasopharyngeal swabs, and since nasal mid-turbinate swabs are more comfortable and acceptable for patients, these swabs are preferred for sample collection in outpatient studies [5] . abstract: BACKGROUND: Detection of specific respiratory viruses is important for surveillance programs, where nasopharyngeal or nasal swabs have traditionally been used. Our objective was to determine whether sampling with a throat swab provides incremental benefit—when used in conjunction with a nasal swab—to detect respiratory viruses among patients with acute pharyngitis in the outpatient setting. FINDINGS: Among 83 university students with acute pharyngitis, we detected respiratory viruses with molecular assays on two samples collected per student: with a flocked nasal mid-turbinate swab and a rayon throat swab. Forty-eight (58 %) patients had virus-positive samples, with 49 virus positives detected by either swab (one patient had a dual viral co-infection). The most common viruses were rhinovirus, coronavirus, and influenza A virus. Specifically, 29 virus positives were detected by both swabs, 14 exclusively by the nasal swab, and six exclusively by the throat swab. The additional six virus positives detected by the throat swab corresponded to an absolute increase in viral detection of 7.1 % (95 % CI: 1.2–12.9 %); the specific viruses detected were four rhinoviruses and two coronaviruses. CONCLUSIONS: The flocked nasal swab samples respiratory viruses well, even among patients whose primary complaint is a sore throat. The rayon throat swab has modest incremental value over and above using the flocked nasal mid-turbinate swab alone, which suggests that while throat swabs alone would not be adequate for respiratory viral surveillance, they may have value as a supplementary test. url: https://doi.org/10.1186/s12985-015-0408-z doi: 10.1186/s12985-015-0408-z id: cord-010343-tqqt0hj7 author: Alidjinou, Enagnon Kazali title: Resistance of Enteric Viruses on Fomites date: 2017-06-15 words: 5031.0 sentences: 268.0 pages: flesch: 40.0 cache: ./cache/cord-010343-tqqt0hj7.txt txt: ./txt/cord-010343-tqqt0hj7.txt summary: The survival of main enteric viruses on fomites and its implication for virus transmission will be analyzed, and the major disinfection procedures and their impact will be described. Available data suggest that the majority of viruses persist longer on nonporous surfaces [7] ; however, results are sometimes conflicting, and the effect of fomite properties might also depend on the viral type. Therefore, survival and inactivation studies are commonly conducted using cultivable surrogates such as feline calicivirus (FCV) or murine norovirus (MNV) [40] . In another study conducted at room temperature, the authors demonstrated that MNV could survive for up to 28 days on 6 different surfaces and the rank order of infectivity reduction from highest to lowest was stainless steel, plastic, rubber, glass, ceramic, and wood [44] . Disinfectants are commonly used for virus inactivation, especially in the health care settings and the food industry, to prevent outbreaks due to enteric viruses. abstract: Human enteric viruses are associated with several clinical features, especially gastroenteritis. Large amounts of these viruses can be released in the environment and spread to people. Enteric viruses are nonenveloped viruses and have displayed good survival in the environment. They can be significantly resistant in food and water but also on fomites, and this is thought to play a role in transmission, leading to sporadic cases or outbreaks. The survival of enteric viruses on fomites relies on many factors including the virus itself, fomite properties, and extrinsic environmental factors such as temperature or relative humidity. Several reports in the literature have found an association with gastroenteritis cases or outbreaks and fomites naturally contaminated by enteric viruses. However, the study of virus survival following natural contamination is challenging, and most published studies are laboratory based, using experimental contamination. In addition, recent and detailed data on the resistance of each of the main enteric viruses on fomites are scarce. Many approaches, both physical and chemical, can be used to inactivate enteric viruses, the efficacy of which depends on the virus and the disinfection conditions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7179519/ doi: 10.1159/000448807 id: cord-278913-u6vihq3u author: Allam, Zaheer title: The Rise of Machine Intelligence in the COVID-19 Pandemic and Its Impact on Health Policy date: 2020-07-24 words: 5397.0 sentences: 214.0 pages: flesch: 51.0 cache: ./cache/cord-278913-u6vihq3u.txt txt: ./txt/cord-278913-u6vihq3u.txt summary: For instance, despite the challenges raised earlier, some startup companies were able to use the available data from social media, airline ticketing, and medical institutions to identify that the world is experiencing a new virus outbreak days before those in medical fraternity had made similar findings (Gaille, 2019) . According to Niiler (2020) , BlueDot, whose profile is shared in the following, was able to employ the services of AIdriven algorithms, to analyze data gathered from sources such as new reports, air ticketing, and animal disease outbreaks to predict that the world is facing a new type of virus outbreak. In the recent case of COVID-19, Metabiota was in the forefront to analyze the outbreak, and during the analysis of the data, some even sourced from social media, the company was able to predict which neighboring countries were at high risk of being the next target of the virus spread, more so because the panic in Wuhan had stated to trigger some fear, forcing people to flee. abstract: The use of advanced technologies, especially predictive computing in the health sector, is on the rise in this era, and they have successfully transformed the sector with quality insights, better decision-making, and quality policies. Even though notable benefits have been achieved through the uptake of the technologies, adoption is still slow, as most of them are still new, hence facing some hurdles in their applications especially in national and international policy levels. But the recent case of COVID-19 outbreak has given an opportunity to showcase that these technologies, especially artificial intelligence (AI), have the capacity to produce accurate, real-time, and reliable predictions on issues as serious as pandemic outbreak. A case in point is how companies such as BlueDot and Metabiota managed to correctly predict the spread route of the virus days before such events happened and officially announced by the World Health Organization. In this chapter, an increase in the use of AI-based technologies to detect infectious diseases is underlined and how such uses have led to early detections of infectious diseases. Nevertheless, there is evidence that there is need to enhance data sharing activities, especially by rethinking how to improve the efficiency of data protocols. The chapter further proposes the need for enhanced use of technologies and data sharing to ensure that future outbreaks are detected even earlier, thus accelerating early preventive measures. url: https://api.elsevier.com/content/article/pii/B9780128243138000061 doi: 10.1016/b978-0-12-824313-8.00006-1 id: cord-285462-9i61rsei author: Almomani, Hesham title: L''ampleur de la réaction des gens aux rumeurs et aux fausses nouvelles à la lumière de la crise du virus Corona date: 2020-06-25 words: 3633.0 sentences: 160.0 pages: flesch: 50.0 cache: ./cache/cord-285462-9i61rsei.txt txt: ./txt/cord-285462-9i61rsei.txt summary: In addition to the concerns that the World Health Organization fears about the Corona virus epidemic, the combination of false information and rumors also contributes to exaggerating the epidemiological situation and the difficulty of combating it, because most users and pioneers of social media are at their best in tracking fake sources and competing to spread misinformation [24, 25] . As the situation worsens and the number of concerns increases, the state of suspicion will increase among the general public, thus spreading false information and rumors greatly [17] , in addition to the presence of free times due to curfews, spacing, and social closures, which will make the situation more anxious and thus persistent and pervasive misinformation [38] , especially with the ease of finding fake news and information about the Corona virus [14] . abstract: Résumé Contexte: Avec la propagation du virus Corona à l'échelle mondiale, les effets négatifs ont augmenté à tous les niveaux, en particulier dans les secteurs économique et social. La situation a été aggravée par la propagation de rumeurs et de fausses informations sur ce qu'est ce virus et les moyens de le prévenir. Objectif: Tester comment les gens interagissent avec différentes informations circulant sur les réseaux sociaux et les plateformes en ligne. Méthodes: Les données ont été extraites d'une enquête menée en 2020 auprès de 1500 personnes en quarantaine âgées de 18 à 60 ans. Un questionnaire a été créé contenant la plupart des rumeurs et fausses informations diffusées, en plus des informations correctes avec une source fiable. Les résultats ont été analysés sous forme de tableaux montrant les proportions de partisans et d'opposants et exprimés en nombre et en pourcentage. Résultats: Deux mille personnes en quarantaine (âge moyen (30,35 ± 9,9 ans) ont participé à l'étude avec un taux de réponse de 100 %. L'analyse a montré un large pourcentage de soutien aux protections de la santé contre le virus Corona et un large rejet de la plupart des fausses informations et rumeurs circulant sur les plateformes Internet. Conclusion: L'ampleur de la propagation des rumeurs et des fausses informations diminue en raison de l’action des gouvernements et des autorités compétentes à travers leurs plateformes officielles dans le cadre du mécanisme de lutte contre le virus Corona, et en prenant appui sur les erreurs actuelles pour faire face à ces crises à l'avenir. Abstract Background: With the spread of the Corona virus globally, the negative effects increased at all levels, especially the economic and social sectors. The situation was made worse by the spread of rumors and false information about what this virus is and ways to prevent it. Objective: Test how people interact with different information circulating through social media and online platforms. Methods: The DATA was taken from a survey conducted in 2020 on 1500 quarantined people between the ages 18-60 years old. A questionnaire was created containing most of the rumors and false information circulated, in addition to the correct information with a reliable source. The results were analyzed in the form of tables showing the proportions of supporters and opponents and expressed in numbers and percentages. Results: A total of 2000 quarantined people participated in the study with the mean age (30.35 ± 9.9 years). Where the response rate is 100%. The analysis showed a large percentage of support for health protections against the Corona virus, and a large rejection of most of the fake information and rumors circulating across the Internet platforms, in addition to their solidarity within the principles of social responsibility. Conclusion: The extent of the spread of rumors and false information is decreasing based on the presence of governments and the competent authorities through their official platforms within the mechanism of fighting against the Corona virus, and also taking advantage of the current mistakes to be a shield in the future in dealing with such crises. url: https://api.elsevier.com/content/article/pii/S0003448720301943 doi: 10.1016/j.amp.2020.06.011 id: cord-018816-v3ylisbt author: Alroy, Joseph title: Viral Pulmonary Disorders in Animals: Neoplastic and Nonneoplastic date: 2013-08-26 words: 2524.0 sentences: 173.0 pages: flesch: 44.0 cache: ./cache/cord-018816-v3ylisbt.txt txt: ./txt/cord-018816-v3ylisbt.txt summary: Gross fi ndings in the lung of a nonneurological EHV-1 infection may include severe edema ( Fig. 24 .6 ) and hydrothorax. The lungs with the diffuse pattern of disease seen in monkeys (Baskin 1987 ) and sheep (Hoover and Thacker 1979 ) are heavy, wet, and consolidated. The alveolar spaces contain proteinaceous exudate with macrophages, neutrophils, and multinucleated giant cells with intranuclear basophilic inclusion bodies (Figs. In some species, such as marmosets and colobus monkeys, measles infection is more severe resulting in primary giant cell pneumonia followed by secondary bacterial bronchopneumonia (Jones et al. The presence of multinucleated giant cells containing intranuclear and intracytoplasmic eosinophilic inclusion bodies is a characteristic fi nding (Fig. 24.18 Histological findings are varied, including mild to moderate interstitial edema, mild infiltration by mononuclear cells (Fig. 24.28 ) , presence of alveolar macrophages, hemorrhagic foci, and capillary thrombosis as well as the presence of syncytial cells and eosinophilic inclusion bodies. abstract: Respiratory infections in animal species are as ubiquitous as they are in humans. Species that may be affected include mammals, birds, and reptiles. In these animal species some viruses primarily infect the respiratory tract, while other viruses infect non-respiratory organs. Viruses are generally classified according to the type of their nucleic acid, their protein structure, and whether or not they have a lipid-containing envelope surrounding the viral particle. In general, most viruses gain entry into the lungs via the conducting airways. In nonprimate mammalians these infections are most prominent in the cranioventral lung lobes because of their horizontal position. Table 24.1 lists some of the major viruses that cause pneumonia and other lung diseases in animals. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123793/ doi: 10.1007/978-3-642-40605-8_24 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-287554-2lqy2ix9 author: Amarelle, Luciano title: Tratamiento antigripal: fármacos actualmente utilizados y nuevos agentes en desarrollo date: 2017-01-31 words: 5858.0 sentences: 471.0 pages: flesch: 46.0 cache: ./cache/cord-287554-2lqy2ix9.txt txt: ./txt/cord-287554-2lqy2ix9.txt summary: El tratamiento disponible con fármacos antivirales, de ser administrado de forma precoz, puede reducir el riesgo de complicaciones severas; sin embargo, muchos tipos de virus desarrollan resistencia a fármacos, reduciendo su efectividad, por lo que ha habido un gran interés en los últimos años en el desarrollo de nuevas opciones terapéuticas para combatir la enfermedad. La estructura del virus influenza A consta de una envoltura lipídica que proviene de la célula huésped y lleva ancladas las glucoproteínas hemaglutinina (HA) y neuraminidasa (NA), antígenos de superficie usados para clasificar a los virus (por ejemplo, H1N1, H3N2, H5N1). Se ha demostrado que posee actividad antiviral en diferentes tiempos del ciclo del virus: en fases tempranas inhibe la transcripción de ARN viral y la síntesis proteica, y en fases tardías bloquea el tráfico citoplasmático de las nuevas ribonucleoproteínas 71 . Por ejemplo, se ha demostrado que los inhibidores de la Na,K-ATPasa poseen actividad antiviral frente a distintos tipos de virus ADN y ARN. abstract: Resumen La gripe es una enfermedad contagiosa altamente prevalente y con significativa morbimortalidad. El tratamiento disponible con fármacos antivirales, de ser administrado de forma precoz, puede reducir el riesgo de complicaciones severas; sin embargo, muchos tipos de virus desarrollan resistencia a estos fármacos, reduciendo notablemente su efectividad. Ha habido un gran interés en el desarrollo de nuevas opciones terapéuticas para combatir la enfermedad. Una gran variedad de fármacos han demostrado tener actividad antiinfluenza, pero aún no están disponibles para su uso en la clínica. Muchos de ellos tienen como objetivo componentes del virus, mientras que otros son dirigidos a elementos de la célula huésped que participan en el ciclo viral. Modular los componentes del huésped es una estrategia que minimiza el desarrollo de cepas resistentes, dado que estos no están sujetos a la variabilidad genética que tiene el virus. Por otro lado, la principal desventaja es que existe un mayor riesgo de efectos secundarios asociados al tratamiento. El objetivo de la presente revisión es describir los principales agentes farmacológicos disponibles en la actualidad, así como los nuevos fármacos en estudio con potencial beneficio en el tratamiento de la gripe. Abstract Influenza is a very common contagious disease that carries significant morbidity and mortality. Treatment with antiviral drugs is available, which if administered early, can reduce the risk of severe complications. However, many virus types develop resistance to those drugs, leading to a notable loss of efficacy. There has been great interest in the development of new drugs to combat this disease. A wide range of drugs has shown anti-influenza activity, but they are not yet available for use in the clinic. Many of these target viral components, which others are aimed at elements in the host cell which participate in the viral cycle. Modulating host components is a strategy which minimizes the development of resistance, since host components are not subject to the genetic variability of the virus. The main disadvantage is the risk of treatment-related side effects. The aim of this review is to describe the main pharmacological agents currently available and new drugs in the pipeline with potential benefit in the treatment of influenza. url: https://api.elsevier.com/content/article/pii/S0300289616302058 doi: 10.1016/j.arbres.2016.07.004 id: cord-338737-phv12m1q author: Amor, A. title: Infecciones víricas. Clasificación. Infecciones por virus herpes date: 2006-06-30 words: 4805.0 sentences: 518.0 pages: flesch: 54.0 cache: ./cache/cord-338737-phv12m1q.txt txt: ./txt/cord-338737-phv12m1q.txt summary: Los virus son microorganismos de pequeño tamaño (generalmente de 20-400 nm de diámetro) formados por una molécula de ácido nucleico, ADN o ARN, que puede ser de cadena sencilla (ss) o doble (ds) y una cápside proteica de simetría icosaédrica o helicoidal. Así, la transmisión y reactivación de los virus herpes constituye un problema clínico de primer orden en pacientes infectados por el virus de la inmunodeficiencia humana (VIH) o inmunodeprimidos debido a tratamientos quimioterápicos, corticoideos o tras trasplantes de órganos. La frecuencia de las reactivaciones varía con la localización anatómica, el subtipo vírico y el estado inmunológico del paciente, de tal forma que los sujetos inmunocomprometidos pueden tener mayor número de reactivaciones, cuadros más graves y extensos, y un riesgo elevado de diseminación. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32287922/ doi: 10.1016/s0211-3449(06)74333-8 id: cord-335948-qkfxfmxb author: Ampofo, William K. title: Improving influenza vaccine virus selectionReport of a WHO informal consultation held at WHO headquarters, Geneva, Switzerland, 14–16 June 2010 date: 2011-08-08 words: 10006.0 sentences: 401.0 pages: flesch: 24.0 cache: ./cache/cord-335948-qkfxfmxb.txt txt: ./txt/cord-335948-qkfxfmxb.txt summary: • The selection process is highly coordinated and involves continual year‐round integration of virological data and epidemiological information by National Influenza Centres (NICs), thorough antigenic and genetic characterization of viruses by WHO Collaborating Centres (WHOCCs) as part of selecting suitable candidate vaccine viruses, and the preparation of suitable reassortants and corresponding reagents for vaccine standardization by WHO Essential Regulatory Laboratories (ERLs). • The selection process is highly coordinated and involves continual year-round integration of virological data and epidemiological information by National Influenza Centres (NICs), thorough antigenic and genetic characterization of viruses by WHO Collaborating Centres (WHOCCs) as part of selecting suitable candidate vaccine viruses, and the preparation of suitable reassortants and corresponding reagents for vaccine standardization by WHO Essential Regulatory Laboratories (ERLs). The continuing threat posed by avian H5N1, the aftermath of the 2009 H1N1 pandemic, the increased knowledge of influenza, and the development and availability of new technologies provide a timely opportunity to review the complex processes and issues involved in influenza vaccine virus selection and to identify potential areas for improvement. abstract: • For almost 60 years, the WHO Global Influenza Surveillance and Response System (GISRS) has been the key player in monitoring the evolution and spread of influenza viruses and recommending the strains to be used in human influenza vaccines. The GISRS has also worked to continually monitor and assess the risk posed by potential pandemic viruses and to guide appropriate public health responses. • The expanded and enhanced role of the GISRS following the adoption of the International Health Regulations (2005), recognition of the continuing threat posed by avian H5N1 and the aftermath of the 2009 H1N1 pandemic provide an opportune time to critically review the process by which influenza vaccine viruses are selected. In addition to identifying potential areas for improvement, such a review will also help to promote greater appreciation by the wider influenza and policy‐making community of the complexity of influenza vaccine virus selection. • The selection process is highly coordinated and involves continual year‐round integration of virological data and epidemiological information by National Influenza Centres (NICs), thorough antigenic and genetic characterization of viruses by WHO Collaborating Centres (WHOCCs) as part of selecting suitable candidate vaccine viruses, and the preparation of suitable reassortants and corresponding reagents for vaccine standardization by WHO Essential Regulatory Laboratories (ERLs). • Ensuring the optimal effectiveness of vaccines has been assisted in recent years by advances in molecular diagnosis and the availability of more extensive genetic sequence data. However, there remain a number of challenging constraints including variations in the assays used, the possibility of complications resulting from non‐antigenic changes, the limited availability of suitable vaccine viruses and the requirement for recommendations to be made up to a year in advance of the peak of influenza season because of production constraints. • Effective collaboration and coordination between human and animal influenza networks is increasingly recognized as an essential requirement for the improved integration of data on animal and human viruses, the identification of unusual influenza A viruses infecting human, the evaluation of pandemic risk and the selection of candidate viruses for pandemic vaccines. • Training workshops, assessments and donations have led to significant increases in trained laboratory personnel and equipment with resulting expansion in both geographical surveillance coverage and in the capacities of NICs and other laboratories. This has resulted in a significant increase in the volume of information reported to WHO on the spread, intensity and impact of influenza. In addition, initiatives such as the WHO Shipment Fund Project have facilitated the timely sharing of clinical specimens and virus isolates and contributed to a more comprehensive understanding of the global distribution and temporal circulation of different viruses. It will be important to sustain and build upon the gains made in these and other areas. • Although the haemagglutination inhibition (HAI) assay is likely to remain the assay of choice for the antigenic characterization of viruses in the foreseeable future, alternative assays – for example based upon advanced recombinant DNA and protein technologies – may be more adaptable to automation. Other technologies such as microtitre neuraminidase inhibition assays may also have significant implications for both vaccine virus selection and vaccine development. • Microneutralization assays provide an important adjunct to the HAI assay in virus antigenic characterization. Improvements in the use and potential automation of such assays should facilitate large‐scale serological studies, while other advanced techniques such as epitope mapping should allow for a more accurate assessment of the quality of a protective immune response and aid the development of additional criteria for measuring immunity. • Standardized seroepidemiological surveys to assess the impact of influenza in a population could help to establish well‐characterized banks of age‐stratified representative sera as a national, regional and global resource, while providing direct evidence of the specific benefits of vaccination. • Advances in high‐throughput genetic sequencing coupled with advanced bioinformatics tools, together with more X‐ray crystallographic data, should accelerate understanding of the genetic and phenotypic changes that underlie virus evolution and more specifically help to predict the influence of amino acid changes on virus antigenicity. • Complex mathematical modelling techniques are increasingly being used to gain insights into the evolution and epidemiology of influenza viruses. However, their value in predicting the timing and nature of future antigenic and genetic changes is likely to be limited at present. The application of simpler non‐mechanistic statistical algorithms, such as those already used as the basis of antigenic cartography, and phylogenetic modelling are more likely to be useful in facilitating vaccine virus selection and in aiding assessment of the pandemic potential of avian and other animal influenza viruses. • The adoption of alternative vaccine technologies – such as live‐attenuated, quadrivalent or non‐HA‐based vaccines – has significant implications for vaccine virus selection, as well as for vaccine regulatory and manufacturing processes. Recent collaboration between the GISRS and vaccine manufacturers has resulted in the increased availability of egg isolates and high‐growth reassortants for vaccine production, the development of qualified cell cultures and the investigation of alternative methods of vaccine potency testing. WHO will continue to support these and other efforts to increase the reliability and timeliness of the global influenza vaccine supply. • The WHO GISRS and its partners are continually working to identify improvements, harness new technologies and strengthen and sustain collaboration. WHO will continue in its central role of coordinating worldwide expertise to meet the increasing public health need for influenza vaccines and will support efforts to improve the vaccine virus selection process, including through the convening of periodic international consultations. url: https://doi.org/10.1111/j.1750-2659.2011.00277.x doi: 10.1111/j.1750-2659.2011.00277.x id: cord-321741-aq76s37x author: Andersen, Petter I. title: Discovery and development of safe-in-man broad-spectrum antiviral agents date: 2020-04-30 words: 5432.0 sentences: 308.0 pages: flesch: 41.0 cache: ./cache/cord-321741-aq76s37x.txt txt: ./txt/cord-321741-aq76s37x.txt summary: Although the concept of BSAAs has been around for almost 50 years, the field received a new impetus with recent outbreaks of Ebola, Zika, Dengue, influenza and other viral infections, the discovery of novel host-directed agents, as well as development of drug repositioning methodology. The discovery of novel activities of BSAAs starts with exposing cells to the candidate antiviral agent at different concentrations and infecting the cells with a virus or mock. Given that emetine also inhibits ZIKV, EBOV, RABV, CMV, HCoV-OC43 and HIV-1 infections (Chaves Valadao et al., 2015; MacGibeny et al., 2018; Mukhopadhyay et al., 2016; Shen et al., 2019; Yang et al., 2018) , and that it is an FDA-approved anti-protozoal drug, it may represent a promising safe-in-man BSAA candidate. Thereby, novel antiviral activities of BSAAs should be further validated in primary human cells using different viral strains (including wild-type viruses), different viral loads, different times of compound addition, different endpoint measurements and compound concentration range. abstract: Abstract Viral diseases are one of the leading causes of morbidity and mortality in the world. Virus-specific vaccines and antiviral drugs are the most powerful tools to combat viral diseases. However, broad-spectrum antiviral agents (BSAAs, i.e. compounds targeting viruses belonging to two or more viral families) could provide additional protection of the general population from emerging and re-emerging viral diseases, reinforcing the arsenal of available antiviral options. Here, we review discovery and development of BSAAs and summarize the information on 120 safe-in-man agents in a freely accessible database (https://drugvirus.info/). Future and ongoing pre-clinical and clinical studies will increase the number of BSAAs, expand the spectrum of their indications, and identify drug combinations for treatment of emerging and re-emerging viral infections as well as co-infections. url: https://www.sciencedirect.com/science/article/pii/S120197122030076X doi: 10.1016/j.ijid.2020.02.018 id: cord-004672-0lf5j8lo author: Anderson, Kevin title: Structural and physiological properties of mengovirus: Avirulent, hemagglutination-defective mutants express altered alpha (1 D) proteins and are adsorption-defective date: 1987 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Structural and physiological properties of two mutants of mengovirus, 205 and 280, were compared to those of wild-type virus to understand the molecular basis of changes exhibited in their biological function. Two dimensional gel electrophoresis of wild-type and mutant structural proteins revealed alterations in the isoelectric character of the alpha (1 D) protein of both mutant 205 and 280. These data suggest that alterations in the alpha (1 D) protein may be responsible for the phenotypic changes by the mutants. A delay in detectable virus-specified protein synthesis was exhibited in mutant-infected cells in comparison to wild-type. The amount of RNA synthesized in mutant- and revertant-infected cells was less than that synthesized in wild-type infected cells. Changes in virus-specified macro-molecular synthesis in mutant and revertant-infected cells reflected a decrease in the ability of the viruses to attach to cells. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086560/ doi: 10.1007/bf01313891 id: cord-299786-wuve0tjz author: Anderson, Robert title: Manipulation of cell surface macromolecules by flaviviruses date: 2004-02-27 words: 13584.0 sentences: 696.0 pages: flesch: 41.0 cache: ./cache/cord-299786-wuve0tjz.txt txt: ./txt/cord-299786-wuve0tjz.txt summary: Dengue virus infection of immature myeloid dendritic cells has been shown to induce their maturation accompanied by the expression of major histocompatibility complex (MHC) class I and II antigens; the costimulatory molecules CD40, CD80, and CD86; and the dendritic cell marker CD83 (Libraty et al., 2001) . Flaviviruses, including dengue and West Nile (Shen et al., 1997) viruses, activate endothelial cell adhesion molecule expression by either direct (virus-mediated) or indirect (cytokine-mediated) mechanisms (see Section V,C). A major candidate event in such a route is the activation of endothelial cell adhesion molecules by a factor(s) (particularly TNF-) produced by dengue virus-infected blood monocytes . Thus the roles of prior immunity, antibody-enhanced virus infection, and immune-mediated pathologic effects on the vascular system are key points in understanding the pathogenesis of dengue hemorrhagic disease. Activation of endothelial cells via antibody-enhanced dengue virus infection of peripheral blood monocytes abstract: Cell surface macromolecules play a crucial role in the biology and pathobiology of flaviviruses, both as receptors for virus entry and as signaling molecules for cell–cell interactions in the processes of vascular permeability and inflammation. This review examines the cell tropism and pathogenesis of flaviviruses from the standpoint of cell surface molecules, which have been implicated as receptors in both virus–cell as well as cell–cell interactions. The emerging picture is one that encompasses extensive regulation and interplay among the invading virus, viral immune complexes, Fc receptors, major histocompatibility complex antigens, and adhesion molecules. url: https://www.sciencedirect.com/science/article/pii/S0065352703590078 doi: 10.1016/s0065-3527(03)59007-8 id: cord-002338-ri7v2ka3 author: Anderson, Tavis K. title: A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses date: 2016-12-14 words: 5842.0 sentences: 276.0 pages: flesch: 42.0 cache: ./cache/cord-002338-ri7v2ka3.txt txt: ./txt/cord-002338-ri7v2ka3.txt summary: A common global nomenclature facilitates comparisons of IAVs infecting humans and pigs, within and between regions, and can provide insight into the diversity of swine H1 influenza virus and its impact on vaccine strain selection, diagnostic reagents, and test performance, thereby simplifying communication of such data. Similarly, IAV in Asia reflects the regional introduction and subsequent evolution and cocirculation of multiple genetic clades of classical-swine H1N1, avian-like H1N1, and human seasonal-like H1N1 and H1N2 viruses (6, 27, 28) . Three major first-order H1 lineages continued to circulate in pigs ( Fig. 1 ; also see Fig. S1 in the supplemental material): the 1A classical lineage, viruses related to the 1918 human influenza pandemic; the 1B human seasonal lineage, the result of multiple human-to-swine transmission episodes of human seasonal H1 strains over decades; and the 1C Eurasian avian lineage, arising from an introduction from wild birds into pigs in the 1970s. abstract: The H1 subtype of influenza A viruses (IAVs) has been circulating in swine since the 1918 human influenza pandemic. Over time, and aided by further introductions from nonswine hosts, swine H1 viruses have diversified into three genetic lineages. Due to limited global data, these H1 lineages were named based on colloquial context, leading to a proliferation of inconsistent regional naming conventions. In this study, we propose rigorous phylogenetic criteria to establish a globally consistent nomenclature of swine H1 virus hemagglutinin (HA) evolution. These criteria applied to a data set of 7,070 H1 HA sequences led to 28 distinct clades as the basis for the nomenclature. We developed and implemented a web-accessible annotation tool that can assign these biologically informative categories to new sequence data. The annotation tool assigned the combined data set of 7,070 H1 sequences to the correct clade more than 99% of the time. Our analyses indicated that 87% of the swine H1 viruses from 2010 to the present had HAs that belonged to 7 contemporary cocirculating clades. Our nomenclature and web-accessible classification tool provide an accurate method for researchers, diagnosticians, and health officials to assign clade designations to HA sequences. The tool can be updated readily to track evolving nomenclature as new clades emerge, ensuring continued relevance. A common global nomenclature facilitates comparisons of IAVs infecting humans and pigs, within and between regions, and can provide insight into the diversity of swine H1 influenza virus and its impact on vaccine strain selection, diagnostic reagents, and test performance, thereby simplifying communication of such data. IMPORTANCE A fundamental goal in the biological sciences is the definition of groups of organisms based on evolutionary history and the naming of those groups. For influenza A viruses (IAVs) in swine, understanding the hemagglutinin (HA) genetic lineage of a circulating strain aids in vaccine antigen selection and allows for inferences about vaccine efficacy. Previous reporting of H1 virus HA in swine relied on colloquial names, frequently with incriminating and stigmatizing geographic toponyms, making comparisons between studies challenging. To overcome this, we developed an adaptable nomenclature using measurable criteria for historical and contemporary evolutionary patterns of H1 global swine IAVs. We also developed a web-accessible tool that classifies viruses according to this nomenclature. This classification system will aid agricultural production and pandemic preparedness through the identification of important changes in swine IAVs and provides terminology enabling discussion of swine IAVs in a common context among animal and human health initiatives. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5156671/ doi: 10.1128/msphere.00275-16 id: cord-009820-fi54s0x7 author: Andries, K. title: Pathogenicity of Hemagglutinating Encephalomyelitis (Vomiting and Wasting Disease) Virus of Pigs, using Different Routes of Inoculation date: 2010-05-13 words: 3845.0 sentences: 289.0 pages: flesch: 56.0 cache: ./cache/cord-009820-fi54s0x7.txt txt: ./txt/cord-009820-fi54s0x7.txt summary: SUMMARY: Forty‐eight pigs were inoculated by different routes with the VW 572 isolate of the hemagglutinating encephalomyelitis (vomiting and wasting disease) virus. The present studies were primarily designed to determine whether a virus isolate, obtained from pigs with the vomiting and wasting syndrome only, could produce clinical signs after inoculation by different routes. When sick, pigs were killed at time intervals varying from one to five days after the appearance of clinical signs and different tissues were collected for virus isolation. From the pigs killed at different time intervals after inoculation, the following tissues were collected for virus isolation : nasal mucosa, tonsils, lungs (apical and cardiac lobes), pyloric region of the stomach, pons and medulla combined, cerebrum, cerebellum and blood clot. Forty-eight pigs were inoculated by different routes with the VW 572 isolate of the hemagglutinating encephalomyelitis (vomiting and wasting disease) virus. abstract: SUMMARY: Forty‐eight pigs were inoculated by different routes with the VW 572 isolate of the hemagglutinating encephalomyelitis (vomiting and wasting disease) virus. All piglets inoculated by the combined oral — nasal route (16) or into the infraorbital nerve (3) became sick after an incubation period of 5 days. Six of the 7 pigs inoculated into the stomach wall, 6 of the 8 pigs inoculated intramuscularly and 3 of the 5 pigs inoculated intracerebrally became ill after an incubation period of 3–3.5 days. None of the pigs inoculated either intravenously or into the abdominal cavity or into the stomach lumen became sick. All diseased pigs showed the vomiting and wasting syndrome. In oronasally inoculated pigs, killed during the early stages of disease, the virus was reisolated consistently from the tonsils and respiratory tract but irregularly from the pons + medulla and the stomach wall. Pigs inoculated by other routes were positive for virus when sick. All except one of the pigs which remained healthy had seroconverted. The site of virus replication which gives rise to the vomition could not be determined. It was concluded from the present studies that virus spread within the body occurs along nerve pathways. ZUSAMMENFASSUNG: Die Pathogenität von hämagglutinierendem Enzephalomyelitis‐Virus (Kümmern und Erbrechen) bei Shweinen nach Infektion über vershiedene Inokulationswege Achtundvierzig Schweine wurden übegr verschiedene Inokulationswege mit dem VW 572‐Isolat des hämagglutinierendtn Enzephalomyelitis‐Virus (Kümmern und Erbrechen) infiziert. Alle Schweine, die entweder kombiniert oro‐nasal (16) oder über den Infraorbitalnerv (3) infiziert wurden, erkrankten nach einer Inkubationszeit von 5 Tagen. Sechs der sieben über die Magenwand inokulierten, 6 oder 8 intramuskulär und 3 der 5 intrazerebral infizierten Tiere wurden nach einer Inkubationszeit von 3–3,5 Tagen krank. Bei den Schweinen, die intravenös oder in die Bauchhöhle bzw. direkt in den Magen inokuliert wurden, kamen Erkrankungsfälle nicht vor. Alle erkrankten Schweine zeigten das Syndrom des Kümmerns und Erbrechens. Von oro‐nasal infizierten Schweinen, die während des Frühstadiums der Erkrankung getötet wurden, konnte das Virus regelmäßig von den Tonsillen und dem Respirationstrakt und gelegentlich vom Gewebe des Pons‐Medulla‐Bereiches sowie aus der Magenwand reisoliert werden. Von Schweinen, die nach Infektion über andere Routen erkrankten, ließ sich immer Virus isolieren. Alle Tiere, die nicht erkrankten (mit Ausnahme eines Ferkels) bildeten jedoch Antikörper. Der Ort der Virusvermehrung, mit dem das Erbrechen zusammenhängt, ließ sich nicht ermitteln. Die Ergebnisse der vorgelegten Untersuchungen lassen den Schluß zu, daß die Virusausbreitung im Körper über die Nervenbahnen erfolgt. RÉSUMÉ: Pathogénicité du virus hémagglutinant de l'encéphalomyélite du porc (dépérissement et vomissement) après infection par différents modes d'inoculation 48 porcs ont été infectés selon différents procédés d'inoculation avec l'isolement VW 572 du virus hémagglutinant de l'encéphalomyélite (dépérissement et vomissement). Tous les porcs infectés soit par la voie combinée oronasale (16) soit par le nerf infraorbital (3) tombèrent malades après une incubation de 5 jours. 6 des 7 animaux infectés par la paroi stomacale, 6 des 8 par voie intramusculaire et 3 des 5 intracérébralement tombèrent malades après un temps d'incubation de 3–3,5 jours. Il n'y a pas eu de maladie chez les porcs inoculés par voie intraveineuse, dans l'abdomen ou directement dans l'estomac. Tous les porcs malades ont présenté le syndrome de dépérissement et de vomissement. Chez les animaux infectés par voie oro‐nasale et sacrifiés au début de la maladie, on a pu régulièrement réisoler le virus à partir des amygdales et de l'appareil respiratoire, parfois du tissu de la région «Pons‐Medulla» et de la paroi stomacale. Le virus a toujours été isolé chez les porcs tombés malades après un mode d'infection différent. Tous les animaux qui ne furent pas malades (à l'exception d'un porcelet) formèrent des anticorps. L'endroit de multiplication du virus lié au syndrome de vomissement n'a pas été déterminé. Les résultats de ces essais permettent de conclure que la propagation du virus dans le corps se fait par voie nerveuse. RESUMEN: La patogeneidad del virus hemoaglutinante de la encéfalomielitis (hipotrepsia y vómitos) en el cerdo tras infección a través de vías diversas de inoculación Se infectaron cuarenta y ocho cerdos a través de diferentes vías de inoculación con el aislamiento VW 572 del virus hemoaglutinante de la encéfalomielitis (hipotrepsia y vómitos). Todos los cerdos infectados bien con arreglo al procedimiento combinado buco‐nasal (16) o bien a través del nervio infraorbitario (3) enfermaron tras un tiempo de incubación de 5 días. Seis de siete animales inoculados a través de la pared gástrica, 6 de 8 por vía intramuscular y 3 de 5 por vía intracerebral enfermaron tras un tiempo de incubación de 3–3,5 días. No se registraron casos de enfermedad en los cerdos inoculados por vía intravenosa o en la cavidad abdominal resp. directamente en el estómago. Todos los cerdos que enfermaron presentaban el síndrome de hipotrepsia y vómitos. De los cerdos infectados por vía buco‐nasal, que se sacrificaron durante el estadio precoz de la enfermedad, se pudo reaislar el virus con regularidad de las tonsilas y del tracto respiratorio y, en ocasiones, del tejido correspondiente al ámbito puente de Varolio‐medula, así como de la pared gástrica. Se logró siempre aislar virus de cerdos que enfermaron tras infección por otras vías. Sin embargo, todos los animales que no enfermaron (excepción hecha por un lechón) produjeron anticuerpos. No se logró descubrir el lugar en donde se multiplicaba el virus, hecho relacionado con los vómitos. Los resultados de los estudios presentados permiten llegar a la conclusión de que la propagación del virus en el organismo acontece a través de las vías nerviosas. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165786/ doi: 10.1111/j.1439-0450.1978.tb00754.x id: cord-273708-2q64at3z author: Annunziata, Giuseppe title: May Polyphenols Have a Role Against Coronavirus Infection? An Overview of in vitro Evidence date: 2020-05-15 words: 3067.0 sentences: 148.0 pages: flesch: 34.0 cache: ./cache/cord-273708-2q64at3z.txt txt: ./txt/cord-273708-2q64at3z.txt summary: In this context, a great interest has been focused on resveratrol (RSV), whose antiviral mechanisms of actions are mainly attributable to its ability to inhibit the viral replication via (i) inhibition of immediate-early virus protein expression (i.e., ICP-4 and−27), (ii) inhibition of the NFκB signaling pathway, and (iii) activation of the AMPK/Sirt1 axis in the host cell (14) . The present mini-review aimed to report the few promising evidence regarding the potential anti-coronavirus activity of polyphenols, which may serve to drive the research toward the development of novel strategies to counteract the SARS-CoV2 pandemic. Studies available in the literature agree in establishing that the reduction of virus titer and the inhibition of nucleocapsid protein expression are their main general mechanisms of action at the base of this promising effect of polyphenols. abstract: The coronavirus infection is constantly diffusing worldwide and the incidence of death is dramatically increasing, representing one of the greatest disasters in human history. Nowadays, no effective therapeutic approaches have been licensed, despite the rising interest of the scientific research in this specific field, and the daily growing number of publications, while the need to find novel strategies is urgent. Evidence in the literature reported the antiviral activity of polyphenols, the largest class of bioactive compounds in nature. Interestingly, a limited number of studies investigated the efficacy of polyphenols from different raw materials, directly against coronaviruses. The present manuscript aimed to report this evidence and provide a viewpoint on the possibility to use it as a start point for the development of novel natural approaches against this viral infection, eventually designing further appropriate researches. url: https://doi.org/10.3389/fmed.2020.00240 doi: 10.3389/fmed.2020.00240 id: cord-271709-5frm3dnb author: Arden, Katherine E. title: Genotypic diversity, circulation patterns and co-detections among rhinoviruses in Queensland, 2001 date: 2019-11-04 words: 3918.0 sentences: 218.0 pages: flesch: 48.0 cache: ./cache/cord-271709-5frm3dnb.txt txt: ./txt/cord-271709-5frm3dnb.txt summary: We aimed to estimate the spectrum of RV genotypes, species seasonality and RV involvement in co-detections in Queensland using a convenience collection of airway sample extracts from patients with suspected respiratory infections, collected during 2001 and tested using molecular tools expected to account for all RV species. Extracts had been previously tested by PQ using direct or culture-amplified direct fluorescent assay to detect respiratory syncytial virus (RSV), adenoviruses (AdV), parainfluenza viruses (PIVs) and influenza viruses A and B (IFAV, IFBV) [9] . Positive correlations included RV with RSV; EV with RSV; AdV with PIVs; HMPV with IFAV, HCoV-OC43, HCoV-NL63 and PIV RVs were detected in all seasons, but a bimodal distribution was evident with peaks in spring (36.5 % of all picornaviruses) and autumn (35.8%) and a trough in winter (13.2 %; summer extract numbers were low, so prevalence was difficult to determine; Fig. 2 ). abstract: PURPOSE: Rhinoviruses (RVs) occur more frequently than other viruses and more often in people displaying symptoms than in those without. We sought to estimate the spectrum of RV diversity, RV species seasonality and to analyse RV involvement in respiratory virus co-detections. METHODOLOGY: A convenience collection of 1179 airway sample extracts from patients with suspected respiratory infections, collected during 2001, was subjected to comprehensive molecular testing. RESULTS: RVs were the most common virus detected. We were able to genotype ~90 % of RV detections, identifying 70 distinct RVs, spanning all three species. RV-Bs were under-represented. We found RV species co-circulated at times, although one species usually dominated. Each species displayed a bimodal distribution. CONCLUSION: Notably, RVs and influenza A viruses (IFAV) seldom co-occurred, supporting their roles as primary pathogens of the airway among acutely ill infants. Whether RV circulation has a moderating or controlling effect on the IFAV season or is controlled by it cannot be determined from these data. Despite the frequent perception that RVs commonly co-occur with another virus, our findings indicated this was not always the case. Nearly 80 % of RV detections occurred alone. Understanding more about population-level interference between viruses may allow us to harness aspects of it to generate a non-specific antiviral intervention that mimics a putative protective effect. For routine respiratory virus screening to best serve the patient, RV testing should be a principal component of any acute respiratory illness testing algorithm throughout the year. url: https://www.ncbi.nlm.nih.gov/pubmed/33062934/ doi: 10.1099/acmi.0.000075 id: cord-002601-d8908t93 author: Arellano-Llamas, Rocío title: Molecular features of influenza A (H1N1)pdm09 prevalent in Mexico during winter seasons 2012-2014 date: 2017-07-10 words: 3376.0 sentences: 177.0 pages: flesch: 51.0 cache: ./cache/cord-002601-d8908t93.txt txt: ./txt/cord-002601-d8908t93.txt summary: Substitutions that have been previously reported are involved in host specificity shift, viral oligomerization interfaces (VOI), binding small ligands (BSL), Ab''s recognition, binding host proteins (BHP), binding nucleic acids (BNA) and antigenic drift. In this study we sequenced the entire genome of pandemic A/H1N1 strains isolated from patients in a reference Hospital in Mexico City (INER) in different years and we compared these sequences with consensus sequences in order to detect mutations that might be associated with viral evolution or might influence the antigenicity of the virus. This might also be a reflection of differences in selective pressure once the virus is in the infected host; regarding the rest of the viral genome segments, all the Mexican isolates from season 2013-2014 clustered with sequences from New York and Helsinki. In HA we observe changes that could affect immunogenicity of the influenza virus; sequences from 2015 to 2016 had additional mutations (S162N) in antigenic site (Sa) and together with the substitution I276T are defining a new clade 6B.1 [21, 22] . abstract: Since the emergence of the pandemic H1N1pdm09 virus in Mexico and California, biannual increases in the number of cases have been detected in Mexico. As observed in previous seasons, pandemic A/H1N1 09 virus was detected in severe cases during the 2011–2012 winter season and finally, during the 2013–2014 winter season it became the most prevalent influenza virus. Molecular and phylogenetic analyses of the whole viral genome are necessary to determine the antigenic and pathogenic characteristics of influenza viruses that cause severe outcomes of the disease. In this paper, we analyzed the evolution, antigenic and genetic drift of Mexican isolates from 2009, at the beginning of the pandemic, to 2014. We found a clear variation of the virus in Mexico from the 2011–2014 season due to different markers and in accordance with previous reports. In this study, we identified 13 novel substitutions with important biological effects, including virulence, T cell epitope presented by MHC and host specificity shift and some others substitutions might have more than one biological function. The systematic monitoring of mutations on whole genome of influenza A pH1N1 (2009) virus circulating at INER in Mexico City might provide valuable information to predict the emergence of new pathogenic influenza virus url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5503254/ doi: 10.1371/journal.pone.0180419 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-003861-qeao4ghg author: Aris-Brosou, Stéphane title: Viral Long-Term Evolutionary Strategies Favor Stability over Proliferation date: 2019-07-24 words: 4513.0 sentences: 209.0 pages: flesch: 49.0 cache: ./cache/cord-003861-qeao4ghg.txt txt: ./txt/cord-003861-qeao4ghg.txt summary: To understand how these two processes affect the long-term evolution of viruses infecting humans, we comprehensively analyzed ssRNA, ssDNA, dsRNA, and dsDNA viruses, to find which virus types and which functions show evidence for episodic diversifying selection and correlated evolution. To better understand the role of correlated evolution and positive selection in the evolutionary dynamics of viruses infecting humans, we constructed a nearly exhaustive viral data set spanning all dsDNA, dsRNA, ssRNA, and ssDNA viruses deposited in GenBank (as of August 2017), and conducted an extensive survey of correlated evolution and diversifying selection in these viruses, asking more specifically about the prevalence of these two processes in each viral type, independently or jointly, with the specific hypothesis that the genes affected by both processes encode functions that are most critical to each viral life cycle. abstract: Viruses are known to have some of the highest and most diverse mutation rates found in any biological replicator, with single-stranded (ss) RNA viruses evolving the fastest, and double-stranded (ds) DNA viruses having rates approaching those of bacteria. As mutation rates are tightly and negatively correlated with genome size, selection is a clear driver of viral evolution. However, the role of intragenomic interactions as drivers of viral evolution is still unclear. To understand how these two processes affect the long-term evolution of viruses infecting humans, we comprehensively analyzed ssRNA, ssDNA, dsRNA, and dsDNA viruses, to find which virus types and which functions show evidence for episodic diversifying selection and correlated evolution. We show that selection mostly affects single stranded viruses, that correlated evolution is more prevalent in DNA viruses, and that both processes, taken independently, mostly affect viral replication. However, the genes that are jointly affected by both processes are involved in key aspects of their life cycle, favoring viral stability over proliferation. We further show that both evolutionary processes are intimately linked at the amino acid level, which suggests that it is the joint action of selection and correlated evolution, and not just selection, that shapes the evolutionary trajectories of viruses—and possibly of their epidemiological potential. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6722887/ doi: 10.3390/v11080677 id: cord-004998-wuixnqy5 author: Arnold, W. title: Identic viral infections in four cases of malignant lymphoepithelioma date: 1978 words: 421.0 sentences: 31.0 pages: flesch: 57.0 cache: ./cache/cord-004998-wuixnqy5.txt txt: ./txt/cord-004998-wuixnqy5.txt summary: The viral particles found in this study are not yet described in human lymphoepithelioma; they are very similar to those found in tissue culture lines derived from Burkitt''s lymphoma (Epstein, 1962) and from nasopharyngeal carcinoma (De The et al., 1969) . The demonstration of herpes virus like nucleocapsids in malignant lymphoepithelioma might be of great interest because many of those patients show a changing level of EB-virus antibody titer during therapy or recurrence of the disease (Lynn et al., 1977) . This fact points at the possible role of a specific viral infection although it has to be mentioned that elevated EB-virus antibody titer is also present in mononucleosis or recurrent tonsillitis (Veltri et al., 1975) . Lymphoblastoid transformation and presence of herpes-type viral particles in a Chinese nasopharyngeal tumor cultured in vitro Prognosis of nasopharyngeal carcinoma by Epstein-Barr virus antibody titer abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087948/ doi: 10.1007/bf00455364 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-356176-1nwjjgul author: Atherton, J. G. title: The effect of ascorbic acid on infection of chick-embryo ciliated tracheal organ cultures by coronavirus date: 1978 words: 1753.0 sentences: 117.0 pages: flesch: 61.0 cache: ./cache/cord-356176-1nwjjgul.txt txt: ./txt/cord-356176-1nwjjgul.txt summary: Chick embryo tracheal organ cultures showed increased resistance to infection by a coronavirus after exposure to ascorbate, while chick respiratory epithelium and allantois-on-shell preparations showed no increase in resistance to infection by an influenza virus or a paramyxovirus. Titrations of avian infectious bronchitis virus were performed by inoculating 4 replicate chick-embryo tracheal organ culture tubes previously selected for ciliat activity, with dilutions of virus made in half-log steps, then continuing to incubate the preparations on a roller drum at 15 rev/hour at 37 ° C. However resistance of CETO cultures to IB virus infection rose with increasing ascorbic acid content (Table t and Fig. 1 ). Our results show t h a t aseorbic acid exerted no direct effect on the infectivity of a n y of the three viruses tested, nor did it affect the resistance of cells to infection by the 0 r t h o m y x o v i r u s (influenza) or the P a r a m y x o v i r u s (NDV). abstract: Chick embryo tracheal organ cultures showed increased resistance to infection by a coronavirus after exposure to ascorbate, while chick respiratory epithelium and allantois-on-shell preparations showed no increase in resistance to infection by an influenza virus or a paramyxovirus. url: https://www.ncbi.nlm.nih.gov/pubmed/205194/ doi: 10.1007/bf01317848 id: cord-311908-sgdq6j6x author: Atkins, G. J. title: Transient virus infection and multiple sclerosis date: 2000-09-28 words: 6183.0 sentences: 267.0 pages: flesch: 40.0 cache: ./cache/cord-311908-sgdq6j6x.txt txt: ./txt/cord-311908-sgdq6j6x.txt summary: Multiple sclerosis (MS) is a chronic, demyelinating disease of the CNS in which autoimmunity to myelin plays a role in pathogenesis. These include subacute sclerosing panencephalitis (SSPE), caused by a persistent measles virus infection, and human T cell lymphotropic virus-I (HTLV-I)associated myelopathy, which is a slowly progressive neurological disease characterised by in¯ammatory in®ltrates and demyelination in the CNS, and is caused by an exogenous retrovirus. Another study that does not involve virus infection, but may nonetheless provide information concerning the possible viral aetiology of MS, concerns the exacerbation of brain damage following EAE induction. With regard to the activity of known human viruses in the induction of myelin damage, there is evidence that virus infections associated with CNS demyelination can cause damage to oligodendrocytes. It is possible that virus infection could induce secretion of pro-in¯ammatory cytokines that could penetrate the CNS parenchyma from the blood and lead to the recrudescence of anti-myelin autoimmunity by reactivation of previously primed T-cells. abstract: Multiple sclerosis (MS) is a chronic, demyelinating disease of the CNS in which autoimmunity to myelin plays a role in pathogenesis. The epidemiology of MS indicates that it may be triggered by a virus infection before the age of adolescence, but attempts to associate a specific virus with MS have produced equivocal results. Many studies of the aetiology of MS have postulated that a persistent virus infection is involved, but transient virus infection may provide a plausible alternative mechanism that could explain many of the inconsistencies in MS research. The most studied animal model of MS is chronic relapsing experimental autoimmune encephalomyelitis (CREAE), which is induced in susceptible animals following injection of myelin components. While CREAE cannot provide information on the initiating factor for MS, it may mimic disease processes occurring after an initial trigger that may involve transient virus infection. The disease process may comprise separate triggering and relapse phases. The triggering phase may involve sensitisation to myelin antigens as a result of damage to oligodendrocytes or molecular mimicry. The relapse phase could be similar to CREAE, or alternatively relapses may be induced by further transient virus infections which may not involve infection of the CNS, but which may involve the recrudescence of anti‐myelin autoimmunity. Although current vaccines have a high degree of biosafety, it is suggested that the measles‐mumps‐rubella vaccine in particular could be modified to obviate any possibility of triggering anti‐myelin autoimmunity. Copyright © 2000 John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/11015741/ doi: 10.1002/1099-1654(200009/10)10:5<291::aid-rmv278>3.0.co;2-u id: cord-010235-hu6o1ggc author: Atmar, Robert L. title: Nonculturable agents of viral gastroenteritis date: 1997-12-01 words: 3989.0 sentences: 190.0 pages: flesch: 43.0 cache: ./cache/cord-010235-hu6o1ggc.txt txt: ./txt/cord-010235-hu6o1ggc.txt summary: (3) provided the first clear demonstration of the causal relationship between a virus (Norwalk virus [NV] ) and gastroenteritis by using immune electron microscopy (IEM) to detect the presence of viral particles in the stools of individuals from an epidemic outbreak of gastroenteritis. This article describes the structure and genome organization of the human caliciviruses that cause gastroenteritis, the clinical and epidemiologic features of these viruses, and new methods for the laboratory diagnosis of infection with these viruses. The inability to cultivate the HuCVs and establish neutralization assays has prevented the definition of specific serotypes; however, at least five different serotypes are thought to exist based on early human cross-challenge studies and comparisons of the IEM and enzyme-linked immunosorbent assay (ELISA) reactivities of several prototype virus strains. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172954/ doi: 10.1016/s0196-4399(00)89189-8 id: cord-006106-u5npu6ng author: Attoui, H. title: Genus Coltivirus (family Reoviridae): genomic and morphologic characterization of Old World and New World viruses date: 2002 words: 7023.0 sentences: 357.0 pages: flesch: 51.0 cache: ./cache/cord-006106-u5npu6ng.txt txt: ./txt/cord-006106-u5npu6ng.txt summary: We report a genomic and morphologic study of the European Eyach (EYA) virus (genus Coltivirus, family Reoviridae) and a comparative analysis with the American Colorado tick fever (CTF) virus (the type species of the genus). These findings, together with the comparative analysis to genomes of south-east Asian isolates, support the recent classification of arboviruses with 12 segments of dsRNA within two distinct genera (genus Coltivirus and genus Seadornavirus) and raise interesting questions about the evolutionary origins of coltiviruses. Analyses of VP5 showed the presence of a potential phosphamide linkage site (amino acid 342-347 of CTF virus: LNYDKY and for EYA virus: LNYIKH) comparable to that found in the protein encoded by segment 2 of members of the genus Orthoreovirus (position 1166-1171: ANPDKF, 40). Sequence determination and analysis of the full-length genome of Colorado tick fever virus, the type species of genus Coltivirus (family Reoviridae) abstract: We report a genomic and morphologic study of the European Eyach (EYA) virus (genus Coltivirus, family Reoviridae) and a comparative analysis with the American Colorado tick fever (CTF) virus (the type species of the genus). The previously established, but distant, antigenic relationship between these viruses was strengthened by genetic findings (presence of cognate genes, amino acid identity between 55 and 88%, similar conserved terminal motifs, suspected read-through phenomenon in segment 9 of both viruses) and by indistinguishable ultramicroscopic morphologies. Moreover, putative constitutive modifying enzyme activities were suspected to be carried out by homologous viral proteins (RNA-dependent RNA polymerase, methyl/guanylyl transferase, NTPase). These findings, together with the comparative analysis to genomes of south-east Asian isolates, support the recent classification of arboviruses with 12 segments of dsRNA within two distinct genera (genus Coltivirus and genus Seadornavirus) and raise interesting questions about the evolutionary origins of coltiviruses. The previously proposed hypothesis that EYA virus was derived from an ancestral virus introduced in Europe with the migration of lagomorphs from North-America, would imply a divergence date between American and European isolates of over 50 million years ago (MYA). This analysis allows for the first time to propose an evolutionary rate for virus dsRNA genomes which was found to be in the order of 10(−8) to 10(−9) mutations/nt/year, a rate similar to that of dsDNA genomes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7098428/ doi: 10.1007/s007050200005 id: cord-344006-0iq9s94n author: Atzrodt, Cassandra L. title: A Guide to COVID‐19: a global pandemic caused by the novel coronavirus SARS‐CoV‐2 date: 2020-05-23 words: 7283.0 sentences: 428.0 pages: flesch: 54.0 cache: ./cache/cord-344006-0iq9s94n.txt txt: ./txt/cord-344006-0iq9s94n.txt summary: All rights reserved Like other coronaviruses, SARS-CoV-2 is a single-stranded, positive-sense RNA virus that uses spike proteins to bind to human lung epithelial cells (Fig. 2) [67] . Upon membrane fusion, the RNA of the coronavirus genome is released into the host cell cytoplasm via an early endosome -unlike SARS-CoV, which employs a late endosome and therefore must cross higher barriers of antiviral host immunity -where it is translated into a replication-translation complex that in turn translates sub-genomic RNA into accessory and structural proteins (Fig. 3) [82-84]. The Vivalytic VRI (viral respiratory tract infections) COVID-19 Test System pioneered by Bosch and Randox Laboratories is similar to the Abbott RealTime SARS-CoV-2 assay in that it reduces hands-on time and can confirm a positive test within 2.5 hours with a reported 95% accuracy [100]. More specific assays have now emerged that are proving very useful in providing a fuller picture of the rates of asymptomatic or mild SARS-Cov2 infection, through detection of anti-viral antibodies that persist for months and even years after the virus has been cleared [107] . abstract: The emergence of the SARS‐CoV‐2 strain of the human coronavirus has thrown the world into the midst of a new pandemic. In the human body, the virus causes COVID‐19, a disease characterized by shortness of breath, fever, and pneumonia, which can be fatal in vulnerable individuals. SARS‐CoV‐2 has characteristics of past human coronaviruses, with close genomic similarities to SARS‐CoV, the virus that causes the disease SARS. Like these related coronaviruses, SARS‐CoV‐2 is transmitted through the inhalation of droplets and interaction with contaminated surfaces. Across the world, laboratories are developing candidate vaccines for the virus – with vaccine trials underway in the US and the United Kingdom ‐ and considering various drugs for possible treatments and prophylaxis. Here, we provide an overview of SARS‐CoV‐2 by analyzing its virology, epidemiology, and modes of transmission while examining the current progress of testing procedures and possible treatments through drugs and vaccines. url: https://www.ncbi.nlm.nih.gov/pubmed/32446285/ doi: 10.1111/febs.15375 id: cord-016995-5izyl234 author: Auewarakul, Prasert title: The Past and Present Threat of Avian Influenza in Thailand date: 2008 words: 5093.0 sentences: 275.0 pages: flesch: 54.0 cache: ./cache/cord-016995-5izyl234.txt txt: ./txt/cord-016995-5izyl234.txt summary: The plan aims at effective control of avian influenza spread in animals as well as in humans for a three-year period and at efficient pandemic preparedness within one year. When this result was reported to the Ministry of Public Health, the government announced that there was a highly pathogenic avian influenza (AI) outbreak in Thailand. When this result was reported to the Ministry of Public Health, the government announced that there was a highly pathogenic avian influenza (AI) outbreak in Thailand. Although several clusters of H5N1 infections have been observed in Thailand, Vietnam, and Indonesia, it is difficult to prove human-to-human transmission, as most of these patients had exposure to poultry and it is not possible to prove whether they contracted the disease from animals or humans. The genome sequence analysis of H5N1 avian influenza A virus isolated from the outbreak among poultry populations in Thailand abstract: Avian influenza H5N1 infection was first identified in Thailand in January 2004. Since then, there have been three major outbreaks in the cold season of 2003–2004 and in the rainy and cold seasons of 2004–2005 and 2005–2006. More than 62 million birds died or were culled. The burden shifted from large industrial farming in the first outbreak to small farms, backyard chickens, and free-grazing ducks. Up to November 2005, there were 20 confirmed cases of human H5N1 infection. Thirteen of these died. Most of the confirmed cases were solitary ones except for three persons in a single family, and epidemiological evidence indicated that person-to-person transmission may have been involved in this cluster. However, sequence analysis of the virus in the cluster did not suggest any changes that might enhance the viral ability to get transmitted among humans. H5N1 viruses in Thailand and Vietnam belong to a single lineage genetically and are antigenically distinguishable from the viruses of the same genotype Z from southern China and Indonesia. Despite the seemingly subsiding epidemic in Thailand, the problem is far from resolved. H5N1 viruses are still sporadically isolated from domestic poultry as well as from wildlife. More important, isolates were also found in asymptomatic animals. Natural selection may have adapted the virus to a less aggressive form. This would make the virus more elusive and difficult to control. A threat of a pandemic strain emerging from the H5N1 virus is still imminent. A national strategic plan for avian influenza control and influenza pandemic preparedness has been implemented. The plan aims at effective control of avian influenza spread in animals as well as in humans for a three-year period and at efficient pandemic preparedness within one year. Nevertheless, more regional and international collaboration is needed. With proper collective preparedness, there is a hope that the threatening influenza pandemic can be prevented by confining and eliminating a potential pandemic strain at its origin. In December 2003, poultry farms in the eastern, central, and northern regions of Thailand experienced large-scale die-offs. The outbreak started from the eastern region of the country. The disease caused rapid death, with a very high attack rate. At that time, H5N1 outbreaks had been reported in South Korea, Vietnam, and Japan (OIE, 2005). A few humans with pneumonia were suspected to originate from contact with sick or dead poultry. Final diagnosis in these patients was not done as clinical samples were not available at the time when proper diagnostic testing became available. On 23 January 2004, the first case of human H5N1 infection in Thailand was reported. It was a boy from Kanchanaburi, a province about 100 km west of Bangkok. He was admitted to Siriraj Hospital in Bangkok and was diagnosed to have severe progressive pneumonia. The patient was initially treated with broad spectrum antibiotics, and respiratory samples were tested for influenza virus. The laboratory result showed that the patient harbored influenza virus, and sequencing of the viral RNA indicated that the virus belonged to the H5 subtype (Chokephaibulkit et al., 2005; Puthavathana et al., 2005). When this result was reported to the Ministry of Public Health, the government announced that there was a highly pathogenic avian influenza (AI) outbreak in Thailand. The Department of Livestock Development (DLD) confirmed the presence of H5N1 viruses in poultry on the same day. Subsequent analysis of the virus from patients and animals confirmed that it was H5N1 AI virus of genotype Z and was closely related to the virus from Vietnam (Viseshakul et al., 2004; Puthavathana et al., 2005). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121443/ doi: 10.1007/978-0-387-75722-3_2 id: cord-295191-xu26mvc3 author: Avirutnan, Panisadee title: Complement and its role in protection and pathogenesis of flavivirus infections date: 2008-12-30 words: 6120.0 sentences: 333.0 pages: flesch: 32.0 cache: ./cache/cord-295191-xu26mvc3.txt txt: ./txt/cord-295191-xu26mvc3.txt summary: Complement evasion mechanisms include: (a) use of complement receptors to enhance viral entry or suppress adaptive immune response (e.g., HIV, West Nile virus (WNV), measles virus, adenoviruses, herpesviruses, enteroviruses, hepatitis B and C viruses ); (b) expression of viral proteins that directly inhibit complement (e.g., herpesviruses, coronaviruses, and astroviruses [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] ); (c) modulation of expression of complement regulators on host cells to prevent complement-dependent lysis (e.g., herpesviruses [137] [138] [139] ); (d) incorporation of human regulators on the surface of virions to protect from complement-mediated virolysis (e.g. HIV, HTLV, cytomegalovirus, and vaccinia virus [140] [141] [142] [143] [144] [145] [146] ); (e) recruitment of soluble complement regulatory proteins to the virion or infected cell surface (e.g., WNV and HIV [147] [148] [149] [150] [151] ); (f) expression of viral decoy proteins that structurally or functionally mimic complement regulatory proteins (e.g., poxviruses and herpesviruses [152] [153] [154] [155] [156] [157] [158] [159] . abstract: The complement system is a family of serum and cell surface proteins that recognize pathogen-associated molecular patterns, altered-self ligands, and immune complexes. Activation of the complement cascade triggers several antiviral functions including pathogen opsonization and/or lysis, and priming of adaptive immune responses. In this review, we will examine the role of complement activation in protection and/or pathogenesis against infection by Flaviviruses, with an emphasis on experiments with West Nile and Dengue viruses. url: https://www.sciencedirect.com/science/article/pii/S0264410X08016083 doi: 10.1016/j.vaccine.2008.11.061 id: cord-311410-lgqup9ug author: Ayers, M. title: A single tube RT-PCR assay for the detection of mosquito-borne flaviviruses date: 2006-05-02 words: 3106.0 sentences: 157.0 pages: flesch: 52.0 cache: ./cache/cord-311410-lgqup9ug.txt txt: ./txt/cord-311410-lgqup9ug.txt summary: In this study we present the design and validation of a single tube RT-PCR assay using a pair of consensus primers for the detection of mosquito-borne flaviviruses. For specificity studies, several viral samples were used, including clinical samples found to contain CMV and EBV DNA by PCR testing, as described (Johnson et al., 2000) ; a clinical isolate of influenza virus from the 2004-2005 season, typed as H3 by sequencing of the hemagglutinin gene; echovirus 11 from the laboratory collection at the Hospital for Sick Children; hepatitis C virus RNA was obtained by in vitro transcription of the infectious clone pCV-H77C (Yanagi et al., 1997) (the clone was kindly provided by Dr. J. Coupled with sequencing, it could detect with great sensitivity and identify several mosquito-borne flaviviruses including WNV, Kunjin, SLE, YFV and dengue fever viruses. abstract: Mosquito-borne flaviviruses include several important agents of human disease and have provided striking examples of emerging infections. In this study we present the design and validation of a single tube RT-PCR assay using a pair of consensus primers for the detection of mosquito-borne flaviviruses. Sequencing of the amplicons permits the species identification. The assay was validated using RNA from the yellow fever virus vaccine strain and from representative strains of dengue viruses 1, 2, 3 and 4, West Nile virus, Kunjin virus (a clade of West Nile virus), and St. Louis encephalitis virus. url: https://www.ncbi.nlm.nih.gov/pubmed/16650488/ doi: 10.1016/j.jviromet.2006.03.009 id: cord-006954-ec9x8thb author: Aznar, María title: Viral nanomechanics with a virtual atomic force microscope date: 2018-07-04 words: 9014.0 sentences: 433.0 pages: flesch: 50.0 cache: ./cache/cord-006954-ec9x8thb.txt txt: ./txt/cord-006954-ec9x8thb.txt summary: Rather than focusing on a specific virus, the VAFM will be used to analyze how the mechanical response and breaking of viruses depend on different parameters controlling the effective interactions between capsid''s structural units. Instead of placing the focus on the finest structural details of the nanoindentation of a specific virus, the aim is to provide a highly coarse-grained description, allowing to simulate large viruses at realistic timescales and with the advantage of being able to link the mechanical behavior to the essential physical ingredients of the interaction between capsid''s structural units. Next, we will show how the elastic response of viruses depends on different physical parameters of their effective interactions, including the bending rigidity of the shell, the adsorption to the substrate, the radius of the AFM tip or the capsid shape. abstract: One of the most important components of a virus is the protein shell or capsid that encloses its genetic material. The main role of the capsid is to protect the viral genome against external aggressions, facilitating its safe and efficient encapsulation and delivery. As a consequence, viral capsids have developed astonishing mechanical properties that are crucial for viral function. These remarkable properties have started to be unveiled in single-virus nanoindentation experiments, and are opening the door to the use of viral-derived artificial nanocages for promising bio- and nano-technological applications. However, the interpretation of nanoindentation experiments is often difficult, requiring the support of theoretical and simulation analysis. Here we present a ‘Virtual AFM’ (VAFM), a Brownian Dynamics simulation of a coarse-grained model of virus aimed to mimic the standard setup of atomic force microscopy (AFM) nanoindentation experiments. Despite the heavy level of coarse-graining, these simulations provide valuable information which is not accessible in experiments. Rather than focusing on a specific virus, the VAFM will be used to analyze how the mechanical response and breaking of viruses depend on different parameters controlling the effective interactions between capsid’s structural units. In particular, we will discuss the influence of adsorption, the tip radius, and the rigidity and shape of the shell on its mechanical response. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7104910/ doi: 10.1088/1361-648x/aac57a id: cord-022453-xe5v7947 author: BABIUK, L.A. title: Viral Gastroenteritis in Ruminants date: 2013-11-17 words: 4838.0 sentences: 253.0 pages: flesch: 48.0 cache: ./cache/cord-022453-xe5v7947.txt txt: ./txt/cord-022453-xe5v7947.txt summary: Rotavirus infection is generally limited to the small intestine in calves, pigs and humans (Middleton et al., 1974; Mebus and Newman, 1977; McAdaragh et al., 1980) , but antigen can be found in the colon of lambs (Snodgrass et al., 1977) , pigs (Theil et al., 1978) and mice (Little and Shadduck, 1982) . Bovine Coronavirus diarrhea, like rotavirus diarrhea, occurs within 15-24 h p.i. Early in infection the villous epithelial cells appear morphological normal but they contain large amounts of antigen. Since diarrhea occurs before denudation and loss of enterocytes it is postulated that it is a direct result of infection of the cell and the ensuing redirection of cellular functions from absorption to virus replication. Because of the replication in lymphoid tissue this disease can be more severe, especially in small animals, than other viral infections, because of interference with immune responses and damage to the crypts. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155712/ doi: 10.1016/b978-0-444-87312-5.50076-x id: cord-307899-427a7i3h author: BITTLE, JAMES L. title: Vaccines Produced by Conventional Means to Control Major Infectious Diseases of Man and Animals date: 1989-12-31 words: 17476.0 sentences: 1073.0 pages: flesch: 49.0 cache: ./cache/cord-307899-427a7i3h.txt txt: ./txt/cord-307899-427a7i3h.txt summary: Adenoviruses cause significant disease in dogs, foxes, and man, but have also been isolated from cattle, swine, goats, sheep, horses, turkeys, and chickens, where they produce mild infections, mainly associated with the respiratory and intestinal tracts. The latter modified the virus by serial passage in porcine and canine tissue cultures; the resulting vaccine immunized dogs and did not produce clinical signs of infection except for occasional corneal opacity similar to that caused by natural infection. The immunity produced by the attenuated live-virus CAV-1 vaccines is long lasting and has drastically reduced the incidence of the canine disease. The exception is human hepatitis A virus, which causes a serious disease and has one serotype; the development of both inactivated virus and attenuated live-virus vaccines is in progress (Hilleman et al., 1982; Provost et al., 1983) . An attenuated live-virus yellow fever vaccine was developed by passage of the virulent Asibi strain in mouse brain and cell culture until it had lost its pathogenicity for monkeys and man (Theiler, 1951) . abstract: Publisher Summary This chapter reviews the development of some of vaccines and their use in controlling such major diseases as diphtheria, rinderpest, Newcastle disease, smallpox, pertussis, yellow fever, rabies, etc. Park–Williams Number 8 (PW8) strain is used to make diphtherial toxoid for vaccines. As a source of toxin, it is rendered nontoxic by incubation with formalin under alkaline conditions. The product's retention of antigenicity, enabling it to induce antitoxin antibodies, makes it an excellent pediatric vaccine. Vaccine against Rinderpest Virus was developed by Koch in 1897 by administering bile from infected cattle. Animals that survived were permanently immune. Formalin- and chloroform-inactivated vaccines were developed using tissues from the infected animals. For the control of Newcastle disease, a number of attenuated live-virus vaccines have been developed which are widely used to control the disease. The Bl strain, the LaSota strain, and the F strain are used to immunize birds of all ages by different routes, including by addition to drinking water and by spraying. Protection against rabies correlates with SN antibody, which can be assessed by a number of tests. Pasteur's classical vaccine, developed from infected spinal cord tissue dried at room temperature for 3–14 days, was given in a series of 21–28 inoculations beginning with material dried the longest and progressing through material dried for only 3 days. url: https://www.sciencedirect.com/science/article/pii/B9780120392339500056 doi: 10.1016/b978-0-12-039233-9.50005-6 id: cord-000760-4yfohp9w author: Babapoor, Sankhiros title: A Novel Vaccine Using Nanoparticle Platform to Present Immunogenic M2e against Avian Influenza Infection date: 2012-01-12 words: 6081.0 sentences: 327.0 pages: flesch: 51.0 cache: ./cache/cord-000760-4yfohp9w.txt txt: ./txt/cord-000760-4yfohp9w.txt summary: Using peptide nanoparticle technology, we have designed two novel vaccine constructs representing M2e in monomeric (Mono-M2e) and tetrameric (Tetra-M2e) forms. A multiple antigenic peptide construct containing M2e (M2e-MAP) induced strong M2especific antibody titers in the serum of mice and resulted in significant protection against influenza virus challenge [13] . Chickens after each inoculation developed high levels of antibody against the injected construct and anamnestic response clearly was seen when the plates were coated with Mono-M2e and Tetra-M2e nanoparticles and M2e-GCN4 (tetrameric M2e), respectively (Table 1, Figures 7 and 8) . In the present study, protection efficiency of two different nanoparticle constructs harboring M2e was studied as possible vaccine candidates for low-pathogenicity avian influenza infection. Vaccination of chickens with recombinant Salmonella expressing M2e and CD154 epitopes increases protection and decreases viral shedding after low pathogenic avian influenza challenge abstract: Using peptide nanoparticle technology, we have designed two novel vaccine constructs representing M2e in monomeric (Mono-M2e) and tetrameric (Tetra-M2e) forms. Groups of specific pathogen free (SPF) chickens were immunized intramuscularly with Mono-M2e or Tetra-M2e with and without an adjuvant. Two weeks after the second boost, chickens were challenged with 107.2 EID50 of H5N2 low pathogenicity avian influenza (LPAI) virus. M2e-specific antibody responses to each of the vaccine constructs were tested by ELISA. Vaccinated chickens exhibited increased M2e-specific IgG responses for each of the constructs as compared to a non-vaccinated group. However, the vaccine construct Tetra-M2e elicited a significantly higher antibody response when it was used with an adjuvant. On the other hand, virus neutralization assays indicated that immune protection is not by way of neutralizing antibodies. The level of protection was evaluated using quantitative real time PCR at 4, 6, and 8 days post-challenge with H5N2 LPAI by measuring virus shedding from trachea and cloaca. The Tetra-M2e with adjuvant offered statistically significant (P < 0.05) protection against subtype H5N2 LPAI by reduction of the AI virus shedding. The results suggest that the self-assembling polypeptide nanoparticle shows promise as a potential platform for a development of a vaccine against AI. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3447297/ doi: 10.1155/2011/126794 id: cord-339382-ii4xurmr author: Bachofen, Claudia title: Selected Viruses Detected on and in our Food date: 2018-03-21 words: 6537.0 sentences: 337.0 pages: flesch: 46.0 cache: ./cache/cord-339382-ii4xurmr.txt txt: ./txt/cord-339382-ii4xurmr.txt summary: Two groups of viruses were selected: (a) the most important viruses contaminating food, based on numbers of publications in the last 5 years and (b) viruses infecting sources of food that might have an impact on human health. RECENT FINDINGS: Important foodborne viruses such as norovirus, hepatitis A and rotavirus are usually "only" contaminating food and are detected on the surface of foodstuffs. Furthermore, some plant viruses are known to infect and persist in insect-vectors and one of them, Tomato spotted wilt virus, a member of the genus Tospovirus of the Bunyaviridae family, was even shown to replicate in human cell lines [71] . HEV-3 and 4 strains infect humans, but the reservoir is thought to be in several animal species, whereof the pig plays the most important role for foodborne transmission. While foodborne HEV and TBEV clearly represent a threat for human public health, the role of several other viruses of animal origin detected in food still needs to be assessed. abstract: PURPOSE OF REVIEW: The purpose of this review is to provide an update on recent literature and findings concerning selected foodborne viruses. Two groups of viruses were selected: (a) the most important viruses contaminating food, based on numbers of publications in the last 5 years and (b) viruses infecting sources of food that might have an impact on human health. RECENT FINDINGS: Important foodborne viruses such as norovirus, hepatitis A and rotavirus are usually “only” contaminating food and are detected on the surface of foodstuffs. However, they are threats to human public health and make up for the majority of cases. In contrast, the meaning of viruses born from within the food such as natural animal and plant viruses is still in many cases unknown. An exception is Hepatitis E virus that is endemic in pigs, transmitted via pork meat and is recognised as an emerging zoonosis in industrialised countries. SUMMARY: Even though the clinical meaning of “new” foodborne viruses, often detected by next generation sequencing, still needs clarification, the method has great potential to enhance surveillance and detection particularly in view of an increasingly globalised food trade. url: https://doi.org/10.1007/s40588-018-0087-9 doi: 10.1007/s40588-018-0087-9 id: cord-271313-h9v0nmx5 author: Bagust, T. J. title: A REVIEW OF VIRAL INFECTIONS OF HORSES date: 2008-03-10 words: 2275.0 sentences: 128.0 pages: flesch: 53.0 cache: ./cache/cord-271313-h9v0nmx5.txt txt: ./txt/cord-271313-h9v0nmx5.txt summary: In Australia, extensive investigation of respiratory diseases seen in horses in Victoria and Queensland have shown that equine herpesvirus type 1 (rhinopneumonitis) is the most common aetiological agent (Duxbury and Oxer 1968; Bagust and Pascoe 1968, 1970) . These clinical signs may be produced by any of several groups of viruses (Studdert 1967) , including equine herpesvirus type 1 (previously called equine influenza virus, then *This is the third article in a series of reviews on viral diseases of animals. Virus diseases of the skin of horses in Australia have not been investigated in detail, but there is ample clinical evidence for the occurrence of equine cutaneous papillomatosis (warts), caused by a host-specific papovavirus and appearing approximately 2 -3 months after infection. Equine viral arteritis has not been detected in Australian horses, but the disease is important in that clinical signs of acute infection (fever, depression, ocular and nasal discharges, oedema of the eyelids, limbs and abdomen, coughing and difficulty in breathing, colic, enteritis, jaundice, abortion) could be confused with infection by several viruses previously discussed. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/4346742/ doi: 10.1111/j.1751-0813.1972.tb02314.x id: cord-321835-qn33sx8x author: Bailey, Emily S. title: A Mini Review of the Zoonotic Threat Potential of Influenza Viruses, Coronaviruses, Adenoviruses, and Enteroviruses date: 2018-04-09 words: 3717.0 sentences: 181.0 pages: flesch: 44.0 cache: ./cache/cord-321835-qn33sx8x.txt txt: ./txt/cord-321835-qn33sx8x.txt summary: In particular, respiratory infections are problematic; in early 2003, World Health Organization issued a worldwide alert for a previously unrecognized illness that was subsequently found to be caused by a novel coronavirus [severe acute respiratory syndrome (SARS) virus]. Influenza A virus H3N2 subtypes are frequently reported in swine, avian, and canine hosts that are responsible for highly infectious respiratory diseases in pigs and have been examined as a potential cause of influenza in humans. In a recent review of the risks of potential outbreaks associated with zoonotic Ad (48) , it was noted that intense human-animal interaction is likely to increase the probability of emergent cross-species Ad infection. This suggests that strategies for novel virus detection should incorporate global surveillance at the human-animal interface to detect potentially emerging zoonotic viruses. Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome abstract: During the last two decades, scientists have grown increasingly aware that viruses are emerging from the human–animal interface. In particular, respiratory infections are problematic; in early 2003, World Health Organization issued a worldwide alert for a previously unrecognized illness that was subsequently found to be caused by a novel coronavirus [severe acute respiratory syndrome (SARS) virus]. In addition to SARS, other respiratory pathogens have also emerged recently, contributing to the high burden of respiratory tract infection-related morbidity and mortality. Among the recently emerged respiratory pathogens are influenza viruses, coronaviruses, enteroviruses, and adenoviruses. As the genesis of these emerging viruses is not well understood and their detection normally occurs after they have crossed over and adapted to man, ideally, strategies for such novel virus detection should include intensive surveillance at the human–animal interface, particularly if one believes the paradigm that many novel emerging zoonotic viruses first circulate in animal populations and occasionally infect man before they fully adapt to man; early detection at the human–animal interface will provide earlier warning. Here, we review recent emerging virus treats for these four groups of viruses. url: https://doi.org/10.3389/fpubh.2018.00104 doi: 10.3389/fpubh.2018.00104 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-302277-c66xm2n4 author: Bakaletz, Lauren O. title: Developing animal models for polymicrobial diseases date: 2004 words: 10910.0 sentences: 537.0 pages: flesch: 33.0 cache: ./cache/cord-302277-c66xm2n4.txt txt: ./txt/cord-302277-c66xm2n4.txt summary: Briefly, viral infection compromises the protective functions of the Eustachian tube, alters respiratory-tract secretions, damages the mucosal epithelial lining, interferes with antibiotic efficacy, modulates the immune response and enhances bacterial adherence 77 and colonization 78 to predispose the host to bacterial OM. In otitis media, which is a middle ear infection, a synergistic interaction that results in disease owing to co-infection with an upper respiratory tract virus and three bacterial species -Streptococcus pneumoniae, nontypeable Haemophilus influenzae (NTHI) and Moraxella catarrhalis -is well documented. It seems likely that the transient suppression of RDC migration and the delayed development of an effective adaptive immune response to a second infection might be another mechanism by which influenza virus predisposes the host to bacterial co-infection. Using this criterion, a mouse model of polymicrobial-induced osteoclastogenesis, bacterial penetration, leukocyte recruitment and softtissue necrosis has been developed to clarify the role of cytokines in periodontal disease. abstract: Polymicrobial diseases involve two or more microorganisms that act synergistically, or in succession, to mediate complex disease processes. Although polymicrobial diseases in animals and humans can be caused by similar organisms, these diseases are often also caused by organisms from different kingdoms, genera, species, strains, substrains and even by phenotypic variants of a single species. Animal models are often required to understand the mechanisms of pathogenesis, and to develop therapies and prevention regimes. However, reproducing polymicrobial diseases of humans in animal hosts presents significant challenges. url: https://www.ncbi.nlm.nih.gov/pubmed/15197391/ doi: 10.1038/nrmicro928 id: cord-298489-uqrzzh0e author: Bale, James F. title: Emerging Viral Infections date: 2012-08-11 words: 3861.0 sentences: 219.0 pages: flesch: 42.0 cache: ./cache/cord-298489-uqrzzh0e.txt txt: ./txt/cord-298489-uqrzzh0e.txt summary: The viruses and disorders discussed herein include West Nile virus, an arboviral infection that swept across the United States in the early years of the 21st century; Nipah encephalitis, a paramyxovirus-induced disorder endemic to India, Bangladesh, and South Asia; chikungunya, a mosquito-borne viral disorder that affects persons in Africa, India, and Southeast Asia; dengue virus, an arthropod-borne Flavivirus that infects more than 100 million persons annually; and parechovirus, a picornavirus that can cause severe disease in neonates and permanent neurodevelopmental disability in surviving infants. 6 Infection control measures, including the slaughter and disposal of Ͼ1 million pigs, contained the disease; during this outbreak, human-to-human transmission of Nipah virus was not observed. The virus, first associated with human disease in Tanzania in the early 1950s, reemerged in 2005-2006 when Ͼ200,000 persons living in the Reunion Islands contracted chikungunya disease 29 ; nearly 1000 deaths among children and adults were reported. abstract: Unique disorders appear episodically in human populations and cause life-threatening systemic or neurological disease. Historical examples of such disorders include von Economo encephalitis, a disorder of presumed viral etiology; acquired immune deficiency syndrome, caused by the human immunodeficiency virus; and severe acute respiratory syndrome, caused by a member of the coronavirus family. This article describes the factors that contribute to the emergence of infectious diseases and focuses on selected recent examples of emerging viral infections that can affect the nervous system of infants, children, and adolescents. url: https://doi.org/10.1016/j.spen.2012.02.001 doi: 10.1016/j.spen.2012.02.001 id: cord-319754-5isw53wl author: Balgoma, David title: Lipidomics Issues on Human Positive ssRNA Virus Infection: An Update date: 2020-08-31 words: 12092.0 sentences: 541.0 pages: flesch: 41.0 cache: ./cache/cord-319754-5isw53wl.txt txt: ./txt/cord-319754-5isw53wl.txt summary: Some viruses may use different entry mechanisms, this feature being likely dependent upon the membrane lipid composition of the host cell they infect as well as the particular cell surface factor attachment used. The question regarding whether the lipid-raft domains may serve as platforms to concentrate the proteins required for viral entry and, even though some evidence exists, to activate signaling pathways inside the host cell still remains unsolved. More recently, a Ca 2+ -dependent pathway of infection by the Rubella virus (RuV, Rubivirus family, Togaviridae) was demonstrated to proceed through direct binding of the fusion loop in the viral E1 protein to SM/cholesterol-enriched membranes [49] . More recently, a Ca 2+ -dependent pathway of infection by the Rubella virus (RuV, Rubivirus family, Togaviridae) was demonstrated to proceed through direct binding of the fusion loop in the viral E1 protein to SM/cholesterol-enriched membranes [49] . abstract: The pathogenic mechanisms underlying the Biology and Biochemistry of viral infections are known to depend on the lipid metabolism of infected cells. From a lipidomics viewpoint, there are a variety of mechanisms involving virus infection that encompass virus entry, the disturbance of host cell lipid metabolism, and the role played by diverse lipids in regard to the infection effectiveness. All these aspects have currently been tackled separately as independent issues and focused on the function of proteins. Here, we review the role of cholesterol and other lipids in ssRNA+ infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32878290/ doi: 10.3390/metabo10090356 id: cord-333228-ejkgune0 author: Ball, Andrew S title: Chapter 1 Introduction into nanotechnology and microbiology date: 2019-12-31 words: 5317.0 sentences: 287.0 pages: flesch: 32.0 cache: ./cache/cord-333228-ejkgune0.txt txt: ./txt/cord-333228-ejkgune0.txt summary: Abstract The current chapter summaries the world of Microbiology and boom of Nanotechnology and how both the exciting fields come together to help men kind with various new applications in water, food, medical biology and immunology. It is now possible to build materials atom by atom and impose desired characteristics for numerous applications in almost every area, such as composite materials development, electronics, nano-electro-mechanical systems (NEMS), biomedical technologies, renewable energy solutions and environmental remediation (Navya & Daima, 2016 Nanomaterials are classified into nine major groups based on their shape, size, composition, surface charge, aggregation and chemical nature. However, due to instances where the frequent use of drugs has led to antibiotic/multidrug resistance in microorganisms, and the delivery of metal nanoparticles is impacting the food chain, it is now necessary to develop interdisciplinary approaches combining Microbiology and Nanotechnology to combat secondary human health, and environmental and ecological damage. abstract: Abstract The current chapter summaries the world of Microbiology and boom of Nanotechnology and how both the exciting fields come together to help men kind with various new applications in water, food, medical biology and immunology. Furthermore synthesis of nano materials utilising the potential of microorganisms also opens a newer avenue for ‘green’ synthesis. url: https://api.elsevier.com/content/article/pii/S0580951719300091 doi: 10.1016/bs.mim.2019.04.003 id: cord-342936-43u7afl3 author: Balzarini, Jan title: Targeting the glycans of glycoproteins: a novel paradigm for antiviral therapy date: 2007 words: 11304.0 sentences: 534.0 pages: flesch: 44.0 cache: ./cache/cord-342936-43u7afl3.txt txt: ./txt/cord-342936-43u7afl3.txt summary: Perhaps more importantly, such carbohydrate-binding agents (CBAs) may force the virus to delete at least part of its glycan shield to escape drug pressure 5 ; this might result in the initiation of an immune response against uncovered immunogenic envelope epitopes. Although such a mechanism may be efficient for a first-line inactivation of HIV, CBA-exposed HIV strains may decrease the efficiency of LCs to eliminate HIV, but at the same time may compromise the ability of the virus to be efficiently transmitted by DCs. The interactions of several CBAs have been extensively investigated, including: the prokaryotic CV-N and actinohivin; a variety of plant lectins, including Hippeastrum hybrid agglutinin (HHA) and UDA; the non-peptidic low-molecular-weight antibiotic PRM-A; and the monoclonal antibody 2G12 with the HIV-envelope gp120 and/or several glycan structures. abstract: Several chronic viral infections (such as HIV and hepatitis C virus) are highly prevalent and are a serious health risk. The adaptation of animal viruses to the human host, as recently exemplified by influenza viruses and the severe acute respiratory syndrome coronavirus, is also a continuous threat. There is a high demand, therefore, for new antiviral lead compounds and novel therapeutic concepts. In this Review, an original therapeutic concept for suppressing enveloped viruses is presented that is based on a specific interaction of carbohydrate-binding agents (CBAs) with the glycans present on viral-envelope glycoproteins. This approach may also be extended to other pathogens, including parasites, bacteria and fungi. url: https://www.ncbi.nlm.nih.gov/pubmed/17632570/ doi: 10.1038/nrmicro1707 id: cord-284880-xsh3wkqy author: Bandaly, Victor title: The Fate of Mengovirus on Fiberglass Filter of Air Handling Units date: 2017-06-28 words: 4703.0 sentences: 257.0 pages: flesch: 58.0 cache: ./cache/cord-284880-xsh3wkqy.txt txt: ./txt/cord-284880-xsh3wkqy.txt summary: The aim of this work is to study the characterization of viral bioaerosols in indoor environments and to understand the fate of mengovirus eukaryote RNA virus on glass fiber filter F7 used in AHU. Regarding the virus infectivity on the filter under a constant air flow, mengovirus was remained infectious during 10 h after aerosolization. From an average of 4.43 9 10 8 PFU L -1 of initial solution of virus aerosolized, 3.43 9 10 2 PFU cm -2 of infectious mengovirus was detected after 25 min of air flow. With a continuous air flow in the system, the persistence of mengovirus was assessed at different times and showed infectivity on the filter up to 10 h after aerosolization (Fig. 7) . Thus, time has an effect on the infectivity of the virus; this study showed that, with a continuous air flow in the abstract: One of the most important topics that occupy public health problems is the air quality. That is the reason why mechanical ventilation and air handling units (AHU) were imposed by the different governments in the collective or individual buildings. Many buildings create an artificial climate using heating, ventilation, and air-conditioning systems. Among the existing aerosols in the indoor air, we can distinguish the bioaerosol with biological nature such as bacteria, viruses, and fungi. Respiratory viral infections are a major public health issue because they are usually highly infective. We spend about 90% of our time in closed environments such as homes, workplaces, or transport. Some studies have shown that AHU contribute to the spread and transport of viral particles within buildings. The aim of this work is to study the characterization of viral bioaerosols in indoor environments and to understand the fate of mengovirus eukaryote RNA virus on glass fiber filter F7 used in AHU. In this study, a set-up close to reality of AHU system was used. The mengovirus aerosolized was characterized and measured with the electrical low pressure impact and the scanner mobility particle size and detected with RT-qPCR. The results about quantification and the level of infectivity of mengovirus on the filter and in the biosampler showed that mengovirus can pass through the filter and remain infectious upstream and downstream the system. Regarding the virus infectivity on the filter under a constant air flow, mengovirus was remained infectious during 10 h after aerosolization. url: https://doi.org/10.1007/s12560-017-9310-8 doi: 10.1007/s12560-017-9310-8 id: cord-295433-olmein3q author: Banerjee, Arinjay title: Bats and Coronaviruses date: 2019-01-09 words: 5655.0 sentences: 298.0 pages: flesch: 52.0 cache: ./cache/cord-295433-olmein3q.txt txt: ./txt/cord-295433-olmein3q.txt summary: Initial studies investigating animal sources of the virus from "wet markets" in the Guangdong province of China suggested that Himalayan palm civets and raccoon dogs were the most likely hosts responsible for human transmission [22] ; however, the role of bats as the original animal reservoir hosts of SARS-CoV was speculated as similar viruses were detected in them [27, 28] . A recent study found that 16 out of 30 camel workers surveyed in Saudi Arabia show evidence of prior MERS-CoV infection via seroconversion and/or virus-specific CD8+ T cell responses without any history of significant respiratory disease. The primary bat species being used to study the bat immune response to virus infections in vitro and in vivo are Pteropus alecto (black flying fox), Rousettus aegyptiacus (Egyptian rousette), and Artibeus jamaicensis (Jamaican fruit bat). Multiple studies with PEDV, SARS-and MERS-CoVs have identified accessory proteins that can effectively inhibit an IFN response in mammalian cells [12] [13] [14] [91] [92] [93] [94] [95] . abstract: Bats are speculated to be reservoirs of several emerging viruses including coronaviruses (CoVs) that cause serious disease in humans and agricultural animals. These include CoVs that cause severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), porcine epidemic diarrhea (PED) and severe acute diarrhea syndrome (SADS). Bats that are naturally infected or experimentally infected do not demonstrate clinical signs of disease. These observations have allowed researchers to speculate that bats are the likely reservoirs or ancestral hosts for several CoVs. In this review, we follow the CoV outbreaks that are speculated to have originated in bats. We review studies that have allowed researchers to identify unique adaptation in bats that may allow them to harbor CoVs without severe disease. We speculate about future studies that are critical to identify how bats can harbor multiple strains of CoVs and factors that enable these viruses to “jump” from bats to other mammals. We hope that this review will enable readers to identify gaps in knowledge that currently exist and initiate a dialogue amongst bat researchers to share resources to overcome present limitations. url: https://www.ncbi.nlm.nih.gov/pubmed/30634396/ doi: 10.3390/v11010041 id: cord-334010-gxu0refq author: Banerjee, Nilotpal title: Viral glycoproteins: biological role and application in diagnosis date: 2016-01-18 words: 6657.0 sentences: 406.0 pages: flesch: 46.0 cache: ./cache/cord-334010-gxu0refq.txt txt: ./txt/cord-334010-gxu0refq.txt summary: The sema-domain is the [18, 43] Fusion with host cell membrane Sialic Acid and attachment [43] 3-5 million cases Worldwide [78, 105] SARS-CoV Spike(S) glycoprotein [25, 115] Membrane fusion [115] 8422 within the duration of 1st November 2002 to 7th August 2003 occurring worldwide [113, 114] Hepatitis C virus E1 and E2 [55, 98] Binding to Host receptor and Conformational change necessary for membrane fusion [98] 130 to 150 million people globally [103, 106] Human immunodeficiency virus 1 gp120, gp160, gp41 [16] Intracellular transport [16] 35 million globally up to 2013 [83, 104, 108, 112] Zaire Ebola virus Spike Protein Gp1-Gp2 [64] Primary Host cell activation [64] up to 28th June 2015 total 27,550 cases [107, 110, 111] Dengue virus E (dimer) [64] Host cell fusion and attachment [64] WHO reported recently that there are 390 million dengue infections per year globally [109] . abstract: The viruses that infect humans cause a huge global disease burden and produce immense challenge towards healthcare system. Glycoproteins are one of the major components of human pathogenic viruses. They have been demonstrated to have important role(s) in infection and immunity. Concomitantly high titres of antibodies against these antigenic viral glycoproteins have paved the way for development of novel diagnostics. Availability of appropriate biomarkers is necessary for advance diagnosis of infectious diseases especially in case of outbreaks. As human mobilization has increased manifold nowadays, dissemination of infectious agents became quicker that paves the need of rapid diagnostic system. In case of viral infection it is an emergency as virus spreads and mutates very fast. This review encircles the vast arena of viral glycoproteins, their importance in health and disease and their diagnostic applications. url: https://www.ncbi.nlm.nih.gov/pubmed/26925438/ doi: 10.1007/s13337-015-0293-5 id: cord-346904-aa88gtzr author: Bao, Y. title: Virus Classification by Pairwise Sequence Comparison (PASC) date: 2008-07-30 words: 3831.0 sentences: 207.0 pages: flesch: 50.0 cache: ./cache/cord-346904-aa88gtzr.txt txt: ./txt/cord-346904-aa88gtzr.txt summary: Pairwise sequence comparison (PASC) is a molecular classification tool for viruses. It calculates the pairwise identities of virus sequences within a virus family and displays their distributions, and can help determine demarcations at different taxonomic levels such as strain, species, genus, and subfamily levels. In the PASC system, pairwise global alignment is performed on complete genomes or particular protein sequences for each viral family, and their percentage of identity is calculated. For those virus families that are suitable for PASC analyses, demarcations can be easily determined and new viruses can be clearly placed into the correct taxonomy. PASC is a molecular classification tool for many virus families. It calculates the pairwise identities of virus sequences within a virus family and displays their distributions, and can help determine the demarcations at strains, species, genera, and subfamilies level. abstract: Pairwise sequence comparison (PASC) is a molecular classification tool for viruses. It calculates the pairwise identities of virus sequences within a virus family and displays their distributions, and can help determine demarcations at different taxonomic levels such as strain, species, genus, and subfamily levels. PASC has many advantages over conventional virus classification methods. The tool has been successfully applied to several virus families, although it may not work well for virus families with highly diverse genome organization. The PASC tool at NCBI established distributions of identity for a number of virus families. A new virus sequence can be tested with this system within a few minutes to suggest the taxonomic position of the virus in a specific family. This system eliminates potential discrepancies in the results caused by different algorithms and/or different data used by the virology community. Data in the system can be updated automatically to reflect changes in virus taxonomy and additions of new virus sequences to the public database. The web interface of the tool makes it easy to navigate and perform analyses. url: https://www.sciencedirect.com/science/article/pii/B978012374410400710X doi: 10.1016/b978-012374410-4.00710-x id: cord-011880-qlutgfu2 author: Barberis, Abdelheq title: Full-length genome sequences of the first H9N2 avian influenza viruses isolated in the Northeast of Algeria date: 2020-07-17 words: 7502.0 sentences: 380.0 pages: flesch: 49.0 cache: ./cache/cord-011880-qlutgfu2.txt txt: ./txt/cord-011880-qlutgfu2.txt summary: In addition, different studies, showed that circulating H9N2 strains have acquired affinity to mammalian like-receptors and gained high virulence and pathogenicity through substitutions in their viral proteins [13, 14] ; the most known substitutions are in the HA protein that promotes virus binding to cellular receptors. While the substitution 627 K that confers high pathogenicity, virulence and increased replication in mice [63] , was not detected in our Algerian viruses, three substitutions 318R, 590S and 661 T, associated with mammalian adaptation, were observed [71, 72] . The PB1 substitutions N105S, K577E/M and 578Q, known to be associated with increased polymerase activity, H9N2 pathogenicity in mice as well as adaptation to mammalians [61, 64, 78] , were not observed in the currently circulating Algerian strains, which however shared 105 N, 577 K and 578 K. Amino acids analysis showed that the Algerians H9N2 strains carried out different molecular markers associated with affinity to human-like receptors and increased virulence. abstract: BACKGROUND: H9N2 avian influenza viruses (AIV) has a worldwide geographic distribution and affects poultry of different types of production. H9N2 AIV was first reported in the Northeast of Algeria in April 2017, following an outbreak associated with high mortality, in broiler flocks. In the present study, we report full-length genome sequences of AIV H9N2, and the detailed phylogeny and molecular genetic analyses. METHODS: Ten AIV H9N2 strains, collected in broiler flocks, were amplified in 9-day-old embryonated specific pathogen free (SPF) chicken eggs. Their full-length genomes were successfully sequenced and phylogenetic and molecular characterizations were conducted. RESULTS: Phylogenetic analysis showed that the isolates were monophyletic, grouped within the G-1 lineage and were very close to Moroccan and Algerian strains identified in 2016 and 2017, respectively. The low pathogenicity of the strains was confirmed by the sequence motif (335RSSR/GLF341) at the hemagglutinin (HA) cleavage site. An exclusive substitution (T197A) that had not been previously reported for H9N2 viruses; but, conserved in some pandemic H1N1 viruses, was observed. When compared to the G1-like H9N2 prototype, the studied strains showed one less glycosylation site in HA, but 2–3 additional ones in the stalk of the neuraminidase (NA). The HA protein harbored the substitution 234 L, suggesting binding preference to human-like receptors. The NA protein harbored S372A and R403W substitutions, previously detected in H9N2 from Asia and the Middle East, and especially in H2N2 and H3N2 strains that caused human pandemics. Different molecular markers associated with virulence and mammalian infections have been detected in the viral internal proteins. The matrix M2 protein possessed the S31N substitution associated with drug resistance. The non-structural 1 (NS1) protein showed the “GSEV” PDZ ligand (PL) C-terminal motif and no 80–84 deletion. CONCLUSION: Characterized Algerian AIV isolates showed mutations that suggest increased zoonotic potential. Additional studies in animal models are required to investigate the pathogenicity of these H9N2 AIV strains. Monitoring their evolution in both migratory and domestic birds is crucial to prevent transmission to humans. Implementation of adequate biosecurity measures that limit the introduction and the propagation of AIV H9N2 in Algerian poultry farm is crucial. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7366561/ doi: 10.1186/s12985-020-01377-z id: cord-254200-9bpdfxrt author: Barin, F. title: La sécurité virale des médicaments d’origine biologique date: 2008-06-30 words: 6497.0 sentences: 560.0 pages: flesch: 61.0 cache: ./cache/cord-254200-9bpdfxrt.txt txt: ./txt/cord-254200-9bpdfxrt.txt summary: Résumé Les crises sanitaires survenues dans les années 1980 ont dramatiquement contribué à la prise de conscience des risques iatrogènes liés aux médicaments d''origine biologique et, ainsi, au développement du concept de sécurité virale de ces médicaments, qu''ils soient d''origine humaine, avec notamment les médicaments dérivés du sang (MDS), animale ou issus des biotechnologies (produits par des cellules eucaryotes). La sécurité virale des médicaments repose sur trois éléments : la qualité de la matière première, le procédé de fabrication qui inclue des étapes aptes à éliminer ou à inactiver les virus et, éventuellement, les contrôles des produits intermédiaires ou finis. L''objectif des études de validation virale est de fournir des éléments tangibles, concrets, démontrant que telle ou telle étape permet effectivement d''éliminer ou d''inactiver tel ou tel type de virus, susceptible de contaminer spécifiquement la matière première (par exemple, VIH, VHC ou parvovirus B19 pour le plasma) ou représentatif de familles non encore impliquées dans des contaminations liées aux produits sanguins. abstract: Résumé Les crises sanitaires survenues dans les années 1980 ont dramatiquement contribué à la prise de conscience des risques iatrogènes liés aux médicaments d’origine biologique et, ainsi, au développement du concept de sécurité virale de ces médicaments, qu’ils soient d’origine humaine, avec notamment les médicaments dérivés du sang (MDS), animale ou issus des biotechnologies (produits par des cellules eucaryotes). La sécurité virale des médicaments repose sur trois éléments : la qualité de la matière première, le procédé de fabrication qui inclue des étapes aptes à éliminer ou à inactiver les virus et, éventuellement, les contrôles des produits intermédiaires ou finis. La qualité de la matière première est désormais aisément garantie, pour les MDS, par le screening des dons de sang ou de plasma (screening individuel ou en pool) pour les marqueurs directs (antigènes, génomes) et indirects (anticorps) de virus majeurs. La succession d’étapes de purification des principes actifs (étapes de partition), d’étapes d’inactivation des virus (traitement solvant–détergent, chauffage) et d’étapes dédiées spécifiquement à l’élimination des virus (nanofiltration) au cours du procédé de fabrication permet de réduire considérablement le risque viral. Cette réduction peut être estimée quantitativement lors des études de validation par épreuves de surcharge à échelle réduite. Les contrôles virologiques sur produits intermédiaires ou sur produits finis permettent de conforter la sécurité virale d’un médicament lorsque les contributions des deux premiers éléments, qualité de la matière première et procédé de fabrication, paraissent insuffisants. Le développement des principes et des techniques de sécurisation des médicaments d’origine biologique permet désormais de garantir au mieux l’absence d’infectiosité liée à des virus connus mais également, par anticipation, de garantir l’absence d’infectiosité liée à des virus inconnus. Summary The viral safety of biologicals, either human blood derivatives or animal products or recombinant proteins issued from biotechnology, relies on the quality of the starting material, the manufacturing process and, if necessary, the control of the final product. The quality of the starting material is highly guaranteed for blood derivatives due to the individual screening for specific markers (antigens, genome, antibodies) for major blood borne viruses such as hepatitis B and C viruses (HBV, HCV) and human immunodeficiency virus (HIV). It can be reinforced by the detection through amplification procedures (polymerase chain reaction) in the plasma pool of genomes from viruses that have been implicated in contaminations of blood derivatives in the past (parvovirus B19, hepatitis A virus). The association in the manufacturing process of different steps dedicated to purification of plasma proteins (partitioning), virus inactivation (solvent/detergent treatment, heat inactivation) or specific procedures allowing virus removal (nanofiltration) allows to reduce the viral risk very efficiently. The validation studies using scaled down systems and model viruses allow to evaluate the virus safety of any product quantitatively. The aim of these procedures is to guarantee the lack of infectivity due to any virus, either known or unknown. url: https://www.sciencedirect.com/science/article/pii/S000345090800062X doi: 10.1016/j.pharma.2008.05.004 id: cord-257255-n5o368ih author: Barker, J. title: Spread and prevention of some common viral infections in community facilities and domestic homes date: 2001-12-21 words: 9238.0 sentences: 459.0 pages: flesch: 48.0 cache: ./cache/cord-257255-n5o368ih.txt txt: ./txt/cord-257255-n5o368ih.txt summary: Amongst health care professionals there is growing awareness that improved standards of hand, surface and air hygiene in community settings could do much to prevent the spread of viral infections within these environments. In a preschool daycare centre, respiratory and gastrointestinal infections decreased following implementation of measures which included reinforcing existing handwashing procedures and education of staff and families on issues of infection control including environmental surface cleaning and disinfection and disinfection of toys (Krilov et al. Nevertheless, overall, there is convincing circumstantial evidence to suggest that improved standards of hygiene can have a signi®cant impact in reducing the rates of respiratory, intestinal and other viral infections in childcare facilities, domestic homes, hospitals and adult care centres and the circulation of infections between these communities. Potential role of hands in the spread of respiratory viral infections Ð studies with human parain¯uenza virus 3 and rhinovirus 14 abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/11442709/ doi: 10.1046/j.1365-2672.2001.01364.x id: cord-293975-np9xdag5 author: Barnett, E. M. title: Two neurotropic viruses, herpes simplex virus type 1 and mouse hepatitis virus, spread along different neural pathways from the main olfactory bulb date: 1993-12-31 words: 8286.0 sentences: 435.0 pages: flesch: 46.0 cache: ./cache/cord-293975-np9xdag5.txt txt: ./txt/cord-293975-np9xdag5.txt summary: The data also demonstrate that two viruses can enter the brain via the olfactory system and localize to different structures, suggesting that neurological diseases involving disparate regions of the brain could be caused by different viruses, even if entry occurred at a common A number of viruses have been shown to spread transneuronally into and throughout the rodent CNS following intranasal inoculation, including herpes simplex virus type 1 (HSV-I)," vesicular stomatitis virus,43 Borna disease virus," mouse hepatitis virus (MHV),-pseudorabies viru? Abbreviafions: HSV-1, hernes simplex virus, type 1; LC, locus coeruleus; MHV''-JHM, -mouse hepatitis virus, strain JHM; MOB, main olfactorv bulb; PFU, plaque forming unit; p.i. post-inoculation; TH, tyrosine hydroxylase; TH + , tyrosine hydroxylase immunoreactive; TH -, tyrosine hydroxylase immunonegative; VTA, ventral tegmental area; WGA-HRP, wheatgerm agglutinin-horseradish peroxidase. abstract: Abstract Several neurotropic viruses enter the brain after peripheral inoculation and spread transneuronally along pathways known to be connected to the initial site of entry. In this study, the pathways utilized by two such viruses, herpes simplex virus type 1 and mouse hepatitis virus strain JHM, were compared using in situ hybridization following inoculation into either the nasal cavity or the main olfactory bulb of the mouse. The results indicate that both viruses spread to infect a unique and only partially overlapping set of connections of the main olfactory bulb. Both quantitative and qualitative differences were observed in the patterns of infection of known primary and secondary main olfactory bulb connections. Using immunohistochemistry for tyrosine hydroxylase combined with in situ hybridization, it was shown that only herpes simplex virus infected noradrenergic neurons in the locus coeruleus. In contrast, both viruses infected dopaminergic neurons in the ventral tegmental area, although mouse hepatitis virus produced a more widespread infection in the A10 group, as well as infecting A8 and A9. The results suggest that differential virus uptake in specific neurotransmitter systems contributes to the pattern of viral spread, although other factors, such as differences in access to particular synapses on infected cells and differences in the distribution of the cellular receptor for the two viruses, are also likely to be important. The data show that neural tracing with different viruses may define unique neural pathways from a site of inoculation. The data also demonstrate that two viruses can enter the brain via the olfactory system and localize to different structures, suggesting that neurological diseases involving disparate regions of the brain could be caused by different viruses, even if entry occurred at a common site. url: https://www.sciencedirect.com/science/article/pii/030645229390045H doi: 10.1016/0306-4522(93)90045-h id: cord-340423-f8ab7413 author: Barr, J.N. title: Genetic Instability of RNA Viruses date: 2016-09-09 words: 9777.0 sentences: 454.0 pages: flesch: 45.0 cache: ./cache/cord-340423-f8ab7413.txt txt: ./txt/cord-340423-f8ab7413.txt summary: We then discuss evidence that at least some RNA viruses have a replication fidelity that is poised to maximize genome sequence space without incurring catastrophic lethal mutations and describe how this can be exploited to control viral infections. The error-prone nature of polymerase activity, coupled with the absence of a proofreading mechanism, is the key reason why RNA virus genomes acquire mutations and exist as a swarm of genetic variants. The mutation rate of the viral polymerase, coupled with the replication mode that the virus employs (and extrinsic factors, described in the following text) will determine the extent of genetic variability of viruses released from an infected cell. Thus, it is possible that the high mutation rates of RNA viruses are simply a consequence of polymerases that are under selective pressure to replicate genomes very rapidly to ensure efficient viral infection [79] [80] [81] . abstract: Despite having very limited coding capacity, RNA viruses are able to withstand challenge of antiviral drugs, cause epidemics in previously exposed human populations, and, in some cases, infect multiple host species. They are able to achieve this by virtue of their ability to multiply very rapidly, coupled with their extraordinary degree of genetic heterogeneity. RNA viruses exist not as single genotypes, but as a swarm of related variants, and this genomic diversity is an essential feature of their biology. RNA viruses have a variety of mechanisms that act in combination to determine their genetic heterogeneity. These include polymerase fidelity, error-mitigation mechanisms, genomic recombination, and different modes of genome replication. RNA viruses can vary in their ability to tolerate mutations, or “genetic robustness,” and several factors contribute to this. Finally, there is evidence that some RNA viruses exist close to a threshold where polymerase error rate has evolved to maximize the possible sequence space available, while avoiding the accumulation of a lethal load of deleterious mutations. We speculate that different viruses have evolved different error rates to complement the different “life-styles” they possess. url: https://www.sciencedirect.com/science/article/pii/B9780128033098000021 doi: 10.1016/b978-0-12-803309-8.00002-1 id: cord-022324-tcltmhi7 author: Barthold, Stephen W. title: MOUSE HEPATITIS VIRUS BIOLOGY AND EPIZOOTIOLOGY date: 2012-12-02 words: 5622.0 sentences: 320.0 pages: flesch: 42.0 cache: ./cache/cord-022324-tcltmhi7.txt txt: ./txt/cord-022324-tcltmhi7.txt summary: Interest in MHV has evolved from a number of different perspectives, including emphasis on MHV as a model of viral hepatitis, viral encephalitis and demyelinating disease, genetic mechanisms of host resistance to viral infection, and the molecular biology of coronaviruses, using MHV as a prototype. Virus strain, passage history, dose, route of inoculation, host genotype, age, immune function and co-infection with other agents all interact to determine the ultimate expression of MHV disease. Mice of the semisusceptible C3H genotype that survive intraperitoneal inoculation of virulent MHV-3 can have persistent infections, in which virus can be recovered in low titer from liver, brain and lymphoid organs for up to 42 days (68). Therefore, when MHV initially infects a naive mouse population, neonatal mice suffer high mortality, particularly with enterotropic MHV strains (13,14). Persistent infection with mouse hepatitis virus of low virulence in nude mice Enterotropic mouse hepatitis virus infection in nude mice abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155572/ doi: 10.1016/b978-0-12-095785-9.50032-9 id: cord-340537-pdvpmydk author: Bañon-Gonzalez, Rafael title: Autopsies of suspected SARS-CoV-2 cases date: 2020-07-15 words: 3682.0 sentences: 244.0 pages: flesch: 54.0 cache: ./cache/cord-340537-pdvpmydk.txt txt: ./txt/cord-340537-pdvpmydk.txt summary: Abstract Forensic physicians should consider the possibility that people who have died from violent or unknown causes may be infected by the virus SARS-CoV-2, or that the diagnosis of the disease has legal implications, which requires adequate knowledge of the epidemiology of the disease, protective measures, adequate sampling and the pathological characteristics. This article reviews the aspects of the pathophysiology of the disease that have an impact on the infectivity of the body''s tissues and fluids, measures for preventing biological risk, taking samples and pathological findings, both macroscopic and microscopic, associated with death caused by infection with the SARS-CoV-2 virus. 13 Nevertheless, infection by SARS-CoV-2 is associated with a high rate of mortality, and many carriers are known to exist who have no symptoms or only mild ones, so that it is possible that some of the corpses that will be subjected to a medical-legal autopsy are infected by this virus. abstract: Abstract Forensic physicians should consider the possibility that people who have died from violent or unknown causes may be infected by the virus SARS-CoV-2, or that the diagnosis of the disease has legal implications, which requires adequate knowledge of the epidemiology of the disease, protective measures, adequate sampling and the pathological characteristics. The practice of autopsies on people who have died from COVID-19 has been limited by the mandatory preventive measures against contagion and by the need for facilities with a level of protection against level-3 biological risk, and therefore series published to date are scarce and partial,with limited approaches (minimally invasive autopsy or needle biopsy). This article reviews the aspects of the pathophysiology of the disease that have an impact on the infectivity of the body's tissues and fluids, measures for preventing biological risk, taking samples and pathological findings, both macroscopic and microscopic, associated with death caused by infection with the SARS-CoV-2 virus. url: https://api.elsevier.com/content/article/pii/S2445424920300200 doi: 10.1016/j.remle.2020.05.002 id: cord-348669-mizygp4j author: Beall, Anne title: Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A date: 2016-01-05 words: 6021.0 sentences: 293.0 pages: flesch: 43.0 cache: ./cache/cord-348669-mizygp4j.txt txt: ./txt/cord-348669-mizygp4j.txt summary: title: Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A The infectious-clone-derived PEDV (icPEDV) replicated as efficiently as the parental virus in cell culture and in pigs, resulting in lethal disease in vivo. Importantly, recombinant PEDV was rapidly transmitted to uninoculated pigs via indirect contact, demonstrating virulence and efficient transmission while replicating phenotypes seen in the wild-type virus. While the recombinant icPEDV replicated the clinical phenotypes of parental PC22A in vivo, icPEDV-⌬ORF3-RFP infection resulted in a partial attenuation in pigs based on lower diarrhea scores. Both the parental PEDV PC22A strain and its derivative recombinant cloned virus were genetically stable and fully pathogenic in neonatal gnotobiotic pigs, demonstrating that icPEDV provides not only a strategy that allows for the systematic evaluation of the role of viral genes in pathogenesis, tropism, and virulence but also a translational platform for the development of rationally attenuated live virus vaccines. abstract: Porcine epidemic diarrhea virus (PEDV) is a highly pathogenic alphacoronavirus. In the United States, highly virulent PEDV strains cause between 80 and 100% mortality in suckling piglets and are rapidly transmitted between animals and farms. To study the genetic factors that regulate pathogenesis and transmission, we developed a molecular clone of PEDV strain PC22A. The infectious-clone-derived PEDV (icPEDV) replicated as efficiently as the parental virus in cell culture and in pigs, resulting in lethal disease in vivo. Importantly, recombinant PEDV was rapidly transmitted to uninoculated pigs via indirect contact, demonstrating virulence and efficient transmission while replicating phenotypes seen in the wild-type virus. Using reverse genetics, we removed open reading frame 3 (ORF3) and replaced this region with a red fluorescent protein (RFP) gene to generate icPEDV-ΔORF3-RFP. icPEDV-ΔORF3-RFP replicated efficiently in vitro and in vivo, was efficiently transmitted among pigs, and produced lethal disease outcomes. However, the diarrheic scores in icPEDV-ΔORF3-RFP-infected pigs were lower than those in wild-type-virus- or icPEDV-infected pigs, and the virus formed smaller plaques than those of PC22A. Together, these data describe the development of a robust reverse-genetics platform for identifying genetic factors that regulate pathogenic outcomes and transmission efficiency in vivo, providing key infrastructural developments for developing and evaluating the efficacy of live attenuated vaccines and therapeutics in a clinical setting. url: https://doi.org/10.1128/mbio.01451-15 doi: 10.1128/mbio.01451-15 id: cord-289093-si8btsab author: Beard, Philippa M. title: A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference date: 2014-06-05 words: 6578.0 sentences: 310.0 pages: flesch: 49.0 cache: ./cache/cord-289093-si8btsab.txt txt: ./txt/cord-289093-si8btsab.txt summary: To explore these interactions a functional high throughput small interfering RNA (siRNA) screen targeting 6719 druggable cellular genes was undertaken to identify host factors (HF) influencing the replication and spread of an eGFP-tagged VACV. Multiple components of the AMPK complex were found to act as pro-viral HFs, while several septins, a group of highly conserved GTP binding proteins with a role in sequestering intracellular bacteria, were identified as strong anti-viral VACV HFs. This screen has identified novel and previously unexplored roles for cellular factors in poxvirus replication. The methodology in the previously published VACV screens varied considerably; Mercer et al [32] measured the growth of a thymidine-kinase-deficient VACV (strain Western Reserve) after only 8 h of infection, thereby identifying cellular proteins involved in the initial stages of virus replication but excluding analysis of viral spread. abstract: Vaccinia virus (VACV) is a large, cytoplasmic, double-stranded DNA virus that requires complex interactions with host proteins in order to replicate. To explore these interactions a functional high throughput small interfering RNA (siRNA) screen targeting 6719 druggable cellular genes was undertaken to identify host factors (HF) influencing the replication and spread of an eGFP-tagged VACV. The experimental design incorporated a low multiplicity of infection, thereby enhancing detection of cellular proteins involved in cell-to-cell spread of VACV. The screen revealed 153 pro- and 149 anti-viral HFs that strongly influenced VACV replication. These HFs were investigated further by comparisons with transcriptional profiling data sets and HFs identified in RNAi screens of other viruses. In addition, functional and pathway analysis of the entire screen was carried out to highlight cellular mechanisms involved in VACV replication. This revealed, as anticipated, that many pro-viral HFs are involved in translation of mRNA and, unexpectedly, suggested that a range of proteins involved in cellular transcriptional processes and several DNA repair pathways possess anti-viral activity. Multiple components of the AMPK complex were found to act as pro-viral HFs, while several septins, a group of highly conserved GTP binding proteins with a role in sequestering intracellular bacteria, were identified as strong anti-viral VACV HFs. This screen has identified novel and previously unexplored roles for cellular factors in poxvirus replication. This advancement in our understanding of the VACV life cycle provides a reliable knowledge base for the improvement of poxvirus-based vaccine vectors and development of anti-viral theraputics. url: https://doi.org/10.1371/journal.pone.0098431 doi: 10.1371/journal.pone.0098431 id: cord-018265-twp33bb6 author: Becker, Pablo D. title: Community-acquired pneumonia: paving the way towards new vaccination concepts date: 2007 words: 14121.0 sentences: 697.0 pages: flesch: 36.0 cache: ./cache/cord-018265-twp33bb6.txt txt: ./txt/cord-018265-twp33bb6.txt summary: A live vaccine based on a master virus strain developed at the Institute of Applied Microbiology (Austria) by growing wild influenza virus in Vero cells at 25°C was also demonstrated to be safe, well-tolerated and immunogenic after intranasal immunization in young adults [18]. Candidate vaccines should be able to replicate and induce a protective immune response in young infants, even in the presence of maternally acquired antibodies. This demonstrates that antibodies play a major role in protection against this disease, whereas T-cell immunity targeted to internal viral proteins appears to contribute to clearance. The second generation of PS-based conjugate vaccines stimulates stronger antibody responses, even in infants, young children and immune deficient individuals, as well as immunological memory. The resulting proteins are then used to perform immunological and/or functional studies to select the most promising candidates (e.g., able to induce the production of microbicidal or neutralizing antibodies, capacity to confer protective immunity). abstract: Despite the availability of antimicrobial agents and vaccines, community-acquired pneumonia remains a serious problem. Severe forms tend to occur in very young children and among the elderly, since their immune competence is eroded by immaturity and immune senescence, respectively. The main etiologic agents differ according to patient age and geographic area. Streptococcus pneumoniae, Haemophilus influenzae, respiratory syncytial virus (RSV) and parainfluenza virus type 3 (PIV-3) are the most important pathogens in children, whereas influenza viruses are the leading cause of fatal pneumonia in the elderly. Effective vaccines are available against some of these organisms. However, there are still many agents against which vaccines are not available or the existent ones are suboptimal. To tackle this problem, empiric approaches are now being systematically replaced by rational vaccine design. This is facilitated by the growing knowledge in the fields of immunology, microbial pathogenesis and host response to infection, as well as by the availability of sophisticated strategies for antigen selection, potent immune modulators and efficient antigen delivery systems. Thus, a new generation of vaccines with improved safety and efficacy profiles compared to old and new agents is emerging. In this chapter, an overview is provided about currently available and new vaccination concepts. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123104/ doi: 10.1007/978-3-7643-7563-8_10 id: cord-022349-z8w1wkm8 author: Beeler, Judy A. title: Human and Animal Viruses date: 2007-09-02 words: 4584.0 sentences: 230.0 pages: flesch: 47.0 cache: ./cache/cord-022349-z8w1wkm8.txt txt: ./txt/cord-022349-z8w1wkm8.txt summary: However, freeze-drying provided a way to maintain virally infected material over long periods of time with relative ease when compared to serial passage in a susceptible animal host. The first experiment to demonstrate that this method could provide long-term stability was reported for a bovine virus that had been freeze-dried in 1916 and was shown to be viable after being maintained at room temperature for 30 years (Fasquelle and Barbier, 1950) . In general, most viruses may be "snap frozen" in a dry ice/ethanol bath prior to storage at temperatures _<-70~ It may be preferable to freeze some viruses, such as cytomegalovirus or varicella-zoster virus, as viable infected cells. Calcium lactobionate and human serum albumin were cryoprotective for measles virus during freeze-drying (Greiff and Rightsel, 1967) , whereas cell culture medium alone was less protective. abstract: This chapter provides an overview of the human and animal viruses. Viruses held to a low number of passages in animals or cell cultures represent a viral population that is similar to that found in nature, and freezing these pools guards against genetic mutations that occur during subsequent passage. Aliquots of viral stocks frozen at a designated passage level can then be used for multiple and repeatable experiments with the same viral population. Furthermore, it is important that consistency should be maintained during the production of viral vaccines; new lots of final product are prepared with frozen viral seed stocks that consistently reproduce the desired immunogenic and attenuation characteristics. To better appreciate the requirements for freezing and freeze drying of human and animal viruses, some consideration is given to understanding the structural and functional organization of this diverse group of microorganisms. The classification of viruses is based on morphological and physiochemical properties. Thus, viruses are divided into those with DNA or RNA genomes and subdivided into families based on size and structural properties. Several methods for preservation of viruses are included in the chapter. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155599/ doi: 10.1016/b978-012361946-4/50010-7 id: cord-332088-5c77h0of author: Beena, V. title: Emerging horizon for bat borne viral zoonoses date: 2019-10-26 words: 4568.0 sentences: 237.0 pages: flesch: 50.0 cache: ./cache/cord-332088-5c77h0of.txt txt: ./txt/cord-332088-5c77h0of.txt summary: In Asia and Pacific regions, bats were demonstrated as natural reservoirs for a large number of this types of emerging as well as re-emerging pathogens such as SARS, Ebola, Marburg, Nipha, Hendra, Tioman, Menangle, Australian bat lyssa virus, Rabies and many encephalitis causing viruses in humans and animals [2] . From bats the pathogen get transmitted to humans via intermediate hosts like horses(hendra) and pigs(nipah) and different species of animals get infected by consumption of partially eaten fruits of bats and the chewed out materials of bats after extracting the juice. The first report of a transmission of a viral disease from bats to humans was a rabies virus (RABV) belonging to the Lyssa virus genus [5] . Identification and complete genome analysis of three novel paramyxoviruses, Tuhoko virus 1, 2 and 3, in fruit bats from China abstract: Bats are the only flying placental mammals that constitute the second largest order of mammals and present all around the world except in Arctic, Antarctica and a few oceanic islands. Sixty percent of emerging infectious diseases originating from animals are zoonotic and more than two-thirds of them originate in wildlife. Bats were evolved as a super-mammal for harboring many of the newly identified deadly diseases without any signs and lesions. Their unique ability to fly, particular diet, roosting behavior, long life span, ability to echolocate and critical susceptibility to pathogens make them suitable host to harbor numerous zoonotic pathogens like virus, bacteria and parasite. Many factors are responsible for the emergence of bat borne zoonoses but the most precipitating factor is human intrusions. Deforestation declined the natural habitat and forced the bats and other wild life to move out of their niche. These stressed bats, having lost foraging and behavioral pattern invade in proximity of human habitation. Either directly or indirectly they transmit the viruses to humans and animals. Development of fast detection modern techniques for viruses from the diseased and environmental samples and the lessons learned in the past helped in preventing the severity during the latest outbreaks. url: https://www.ncbi.nlm.nih.gov/pubmed/31803797/ doi: 10.1007/s13337-019-00548-z id: cord-325326-2bbqz4o7 author: Beitzel, Brett F. title: High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and Massively Parallel Sequencing date: 2010-10-14 words: 7781.0 sentences: 388.0 pages: flesch: 51.0 cache: ./cache/cord-325326-2bbqz4o7.txt txt: ./txt/cord-325326-2bbqz4o7.txt summary: We have developed a high-resolution genomic mapping technique that combines transposon-mediated insertional mutagenesis with either capillary electrophoresis or massively parallel sequencing to identify functionally important regions of the Venezuelan equine encephalitis virus (VEEV) genome. Toward this goal, we used transposon mutagenesis, reverse genetics, and fragment analysis by capillary electrophoresis to identify regions of the nsP3 gene that are important for replication and that result in temperature sensitive (ts) mutations. We used transposon mutagenesis to construct a cDNA library with small DNA fragments randomly inserted throughout the VEEV genome and then produced replication-competent virus through reverse genetics. Comparing transposon insertion sites in the resultant viruses to those in the starting library, we were able to produce a functional map of the entire genome of VEEV, and to identify several hundred potential ts mutations, including those we originally identified with the capillary electrophoresis method. abstract: We have developed a high-resolution genomic mapping technique that combines transposon-mediated insertional mutagenesis with either capillary electrophoresis or massively parallel sequencing to identify functionally important regions of the Venezuelan equine encephalitis virus (VEEV) genome. We initially used a capillary electrophoresis method to gain insight into the role of the VEEV nonstructural protein 3 (nsP3) in viral replication. We identified several regions in nsP3 that are intolerant to small (15 bp) insertions, and thus are presumably functionally important. We also identified nine separate regions in nsP3 that will tolerate small insertions at low temperatures (30°C), but not at higher temperatures (37°C, and 40°C). Because we found this method to be extremely effective at identifying temperature sensitive (ts) mutations, but limited by capillary electrophoresis capacity, we replaced the capillary electrophoresis with massively parallel sequencing and used the improved method to generate a functional map of the entire VEEV genome. We identified several hundred potential ts mutations throughout the genome and we validated several of the mutations in nsP2, nsP3, E3, E2, E1 and capsid using single-cycle growth curve experiments with virus generated through reverse genetics. We further demonstrated that two of the nsP3 ts mutants were attenuated for virulence in mice but could elicit protective immunity against challenge with wild-type VEEV. The recombinant ts mutants will be valuable tools for further studies of VEEV replication and virulence. Moreover, the method that we developed is applicable for generating such tools for any virus with a robust reverse genetics system. url: https://doi.org/10.1371/journal.ppat.1001146 doi: 10.1371/journal.ppat.1001146 id: cord-255026-fdp6mies author: Belák, Sándor title: Molecular diagnosis of viral diseases, present trends and future aspects: A view from the OIE Collaborating Centre for the Application of Polymerase Chain Reaction Methods for Diagnosis of Viral Diseases in Veterinary Medicine date: 2007-07-26 words: 5342.0 sentences: 225.0 pages: flesch: 40.0 cache: ./cache/cord-255026-fdp6mies.txt txt: ./txt/cord-255026-fdp6mies.txt summary: The experiences of an OIE-Collaborating Centre and of two EU project consortia are summarised on the diagnostic application of gel-based PCR, general PCR systems, phylogeny, molecular epidemiology, real-time PCR (TaqMan, Molecular Beacons, Primer-Probe Energy Transfer), amplification without thermocycling (Invader), multiplex PCR, nucleic acid extraction and pipetting robotics, automation and quality control, including internal controls. abstract: The emergence and re-emergence of transboundary animal diseases (TADs), e.g., foot-and-mouth disease, classical swine fever and the highly pathogenic avian influenza strongly indicate the need for the development of powerful and robust new diagnostic methods. The experiences of an OIE-Collaborating Centre and of two EU project consortia are summarised on the diagnostic application of gel-based PCR, general PCR systems, phylogeny, molecular epidemiology, real-time PCR (TaqMan, Molecular Beacons, Primer-Probe Energy Transfer), amplification without thermocycling (Invader), multiplex PCR, nucleic acid extraction and pipetting robotics, automation and quality control, including internal controls. By following the steps of OIE validation, the diagnostic assays are nationally and internationally standardised. The development of padlock probes and microarrays, as well as ultra rapid PCR and sequencing methods is further improving the arsenal of nucleic acid based molecular diagnosis. Further trends of diagnostic development are also mentioned, in order to combat TADs and other viral infections more effectively in the future. url: https://www.sciencedirect.com/science/article/pii/S0264410X06012989 doi: 10.1016/j.vaccine.2006.11.068 id: cord-291156-zxg3dsm3 author: Bernasconi, Anna title: Empowering Virus Sequences Research through Conceptual Modeling date: 2020-05-01 words: 4600.0 sentences: 206.0 pages: flesch: 38.0 cache: ./cache/cord-291156-zxg3dsm3.txt txt: ./txt/cord-291156-zxg3dsm3.txt summary: We hereby present the Viral Conceptual Model (VCM), centered on the virus sequence and described from four perspectives: biological (virus type and hosts/sample), analytical (annotations and variants), organizational (sequencing project) and technical (experimental technology). -We propose a new Viral Conceptual Model (VCM), a general conceptual model for describing viral sequences, organized along specific dimensions that highlight a conceptual schema similar to GCM [6] ; -Focusing on SARS-CoV2, we show how VCM can be profitably linked to a phenotype database with information on COVID-19 infected patients; -We provide a list of interesting queries replicating newly released literature on infectious diseases; these can be easily performed on VCM. Some interesting portals have become interfaces to GISAID data with particular focuses: NextStrain [18] overviews emergent viral outbreaks based on the visualization of sequence data integrated with geographic information, serology, and host species; CoV-GLUE, 9 part of the GLUE suite [38] , contains a database of replacements, insertions and deletions observed in sequences sampled from the pandemic. abstract: The pandemic outbreak of the coronavirus disease has attracted attention towards the genetic mechanisms of viruses. We hereby present the Viral Conceptual Model (VCM), centered on the virus sequence and described from four perspectives: biological (virus type and hosts/sample), analytical (annotations and variants), organizational (sequencing project) and technical (experimental technology). VCM is inspired by GCM, our previously developed Genomic Conceptual Model, but it introduces many novel concepts, as viral sequences significantly differ from human genomes. When applied to SARS-CoV2 virus, complex conceptual queries upon VCM are able to replicate the search results of recent articles, hence demonstrating huge potential in supporting virology research. In addition to VCM, we also illustrate the data dictionary for patient’s phenotype used by the COVID-19 Host Genetic Initiative. Our effort is part of a broad vision: availability of conceptual models for both human genomics and viruses will provide important opportunities for research, especially if interconnected by the same human being, playing the role of virus host as well as provider of genomic and phenotype information. url: https://doi.org/10.1101/2020.04.29.067637 doi: 10.1101/2020.04.29.067637 id: cord-323358-05bk91lm author: Bhaskar, Sathyamoorthy title: Engineering protein nanocages as carriers for biomedical applications date: 2017-04-07 words: 9541.0 sentences: 557.0 pages: flesch: 39.0 cache: ./cache/cord-323358-05bk91lm.txt txt: ./txt/cord-323358-05bk91lm.txt summary: We review natural and synthetic protein nanocages that have been modified using chemical and genetic engineering techniques to impart non-natural functions that are responsive to the complex cellular microenvironment of malignant cells while delivering molecular cargos with improved efficiencies and minimal toxicity. 1, 3 Examples of naturederived nanocarriers include protein nanocages such as viruses, ferritin and many others that are formed by the self-assembly of protein subunits, resulting in a cage-like structure. 8 In this review, we focus on natural and synthetic protein scaffolds engineered with specific functional groups to impart non-native functions, including aiding the delivery of active molecules through targeting of malignant cells and overcoming cellular barriers. 3 In addition to cell targeting ability and gene delivery efficiency, these protein-based multifaceted systems have highly ordered spatial configurations, and the stability and functionality of these materials have already been established through intensive research with advances in understanding virus infection, replication and assembly pathways. abstract: Protein nanocages have been explored as potential carriers in biomedicine. Formed by the self-assembly of protein subunits, the caged structure has three surfaces that can be engineered: the interior, the exterior and the intersubunit. Therapeutic and diagnostic molecules have been loaded in the interior of nanocages, while their external surfaces have been engineered to enhance their biocompatibility and targeting abilities. Modifications of the intersubunit interactions have been shown to modulate the self-assembly profile with implications for tuning the molecular release. We review natural and synthetic protein nanocages that have been modified using chemical and genetic engineering techniques to impart non-natural functions that are responsive to the complex cellular microenvironment of malignant cells while delivering molecular cargos with improved efficiencies and minimal toxicity. url: https://doi.org/10.1038/am.2016.128 doi: 10.1038/am.2016.128 id: cord-016928-yigz9qiz author: Bhattacharyya, Sankar title: Inflammation During Virus Infection: Swings and Roundabouts date: 2019-11-05 words: 4847.0 sentences: 255.0 pages: flesch: 42.0 cache: ./cache/cord-016928-yigz9qiz.txt txt: ./txt/cord-016928-yigz9qiz.txt summary: The tissue damage is caused from a combination of either direct neuronal infection which activates intrinsic apoptosis or a hyperactive inflammatory response mediated by PICs or CD8+ cytotoxic T cells (CTLs) (Wang et al. Spread through aerosols, SARS-CoV primarily infect lung cells triggering an often fatal inflammatory response clinically called acute respiratory distress syndrome (ARDS) that starts with severe hypoxia, pulmonary edema progressing to systemic inflammation, and failure of multiple organs, culminating in high rate of mortality (Peiris et al. Although evidence suggests that SARS-CoV can infect multiple cell types, lung type-II pneumocytes and ciliated epithelial cells constitute primary sites of virus replication, consequent to which these cells undergo apoptotic and/or necrotic death attracting innate immune cells and activating them to secrete PICs (Sims et al. Pro-inflammatory cytokines derived from West Nile virus (WNV)-infected SK-N-SH cells mediate neuroinflammatory markers and neuronal death abstract: Inflammation constitutes a concerted series of cellular and molecular responses that follow disturbance of systemic homeostasis, by either toxins or infectious organisms. Leukocytes modulate inflammation through production of secretory mediators, like cytokines and chemokines, which work in an autocrine and/or paracrine manner. These mediators can either promote or attenuate the inflammatory response and depending on differential temporal and spatial expression play a crucial role in the outcome of infection. Even though the objective is clearance of the pathogen with minimum damage to host, the pathogenesis of multiple human pathogenic viruses has been suggested to emanate from a dysregulation of the inflammatory response, sometimes with fatal consequences. This review discusses the nature and the outcome of inflammatory response, which is triggered in the human host subsequent to infection by single-sense plus-strand RNA viruses. In view of such harmful effects of a dysregulated inflammatory response, an exogenous regulation of these reactions by either interference or supplementation of critical regulators has been suggested. Currently multiple such factors are being tested for their beneficial and adverse effects. A successful use of such an approach in diseases of viral etiology can potentially protect the affected individual without directly affecting the virus life cycle. Further, such approaches whenever applicable would be useful in mitigating death and/or debility that is caused by the infection of those viruses which have proven particularly difficult to control by either prophylactic vaccines and/or therapeutic strategies using specific antiviral drugs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121364/ doi: 10.1007/978-981-15-1045-8_3 id: cord-271171-tohbzenc author: Bhola, J. title: Corona Epidemic in Indian context: Predictive Mathematical Modelling date: 2020-04-07 words: 3810.0 sentences: 217.0 pages: flesch: 56.0 cache: ./cache/cord-271171-tohbzenc.txt txt: ./txt/cord-271171-tohbzenc.txt summary: Scientists also believe that peri-domestic mammals may also serve as For long, human viruses have not been considered severe pathogens as infected people develop flu like symptoms and then get cured on their own as innate immune system triggers antibody formation that provides resistance against the diseases (Chiu, 2013; Kistler et al., 2007; Wrammert et al., 2008) . https://doi.org/10.1101/2020.04.03.20047175 doi: medRxiv preprint Figure 2 From what is known about corona viruses, it is evident that the per capita rate of increase in the number of infectives is directly proportional to the number of susceptible in the vicinity of an infective and hence, the total intake in the first compartment looks like (kS)I ; where k signifies the rate of transmission indicated by the average number of people who will catch the virus from one infected person. abstract: The novel Coronavirus pathogen Covid-19 is a cause of concern across the world as the human-to-human infection caused by it is spreading at a fast pace. The virus that first manifested in Wuhan, China has travelled across continents. The increase in number of deaths in Italy, Iran, USA, and other countries has alarmed both the developed and developing countries. Scientists are working hard to develop a vaccine against the virus, but until now no breakthrough has been achieved. India, the second most populated country in the world, is working hard in all dimensions to stop the spread of community infection. Health care facilities are being updated; medical and paramedical staffs are getting trained, and many agencies are raising awareness on the issues related to this virus and its transmission. The administration is leaving no stone unturned to prepare the country to mitigate the adverse effects. However, as the number of infected patients, and those getting cured is changing differently in different states everyday it is difficult to predict the spread of the virus and its fate in Indian context. Different states have adopted measures to stop the community spread. Considering the vast size of the country, the population size and other socio-economic conditions of the states, a single uniform policy may not work to contain the disease. In this paper, we discuss a predictive mathematical model that can give us some idea of the fate of the virus, an indicative data and future projections to understand the further course this pandemic can take. The data can be used by the health care agencies, the Government Organizations and the Planning Commission to make suitable arrangements to fight the pandemic. Though the model is preliminary, it can be used at regional level to manage the health care system in the present scenario. The recommendations can be made, and advisories prepared based on the predictive results that can be implemented at regional levels. url: https://doi.org/10.1101/2020.04.03.20047175 doi: 10.1101/2020.04.03.20047175 id: cord-002072-qbh728ec author: Bi, Yuhai title: A new reassortment of influenza A (H7N9) virus causing human infection in Beijing, 2014 date: 2016-05-27 words: 3096.0 sentences: 170.0 pages: flesch: 48.0 cache: ./cache/cord-002072-qbh728ec.txt txt: ./txt/cord-002072-qbh728ec.txt summary: Genetic and phylogenetic analyses revealed that the virus belonged to a novel genotype, which probably emerged and further reassorted with other H9 or H7 viruses in poultry before transmitting to humans. The IFN-induced transmembrane protein-3 (IFITM3) C/C genotype was reported to be associated with severe clinical outcomes, as reflected by a higher viral load, more rapid progression to ARDS, higher cytokine/chemokine levels, and an increased mortality rate after H7N9 infection 22 . Although this was a severe H7N9-infected case with cytokine storm-like appearances and multiple organ failure, the patient was eventually cured after combination therapy with antivirals, mechanical ventilation, supportive nutrition and symptomatic treatment. Clinical, virological and immunological features from patients infected with re-emergent avian-origin human H7N9 influenza disease of varying severity in Guangdong province Cytokine and chemokine levels in patients infected with the novel avian influenza A (H7N9) virus in China abstract: A 73-year-old man was confirmed to have an influenza A (H7N9) virus infection, and the causative agent A/Beijing/02/2014(H7N9) virus was isolated. Genetic and phylogenetic analyses revealed that the virus belonged to a novel genotype, which probably emerged and further reassorted with other H9 or H7 viruses in poultry before transmitting to humans. This virus caused a severe infection with high levels of cytokines and neutralizing antibodies. Eventually, the patient was cured after serially combined treatments. Taken together, our findings indicated that this novel genotype of the human H7N9 virus did not evolve directly from the first Beijing isolate A/Beijing/01/2013(H7N9), suggesting that the H7N9 virus has not obtained the ability for human-to-human transmissibility and the virus only evolves in poultry and then infects human by direct contact. Hence, the major measures to prevent human H7N9 virus infection are still to control and standardize the live poultry trade. Early antiviral treatment with combination therapies, including mechanical ventilation, nutrition support and symptomatic treatment, are effective for H7N9 infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4882526/ doi: 10.1038/srep26624 id: cord-347577-p0a2rboi author: Bibby, Kyle title: Persistence of Ebola Virus in Sterilized Wastewater date: 2015-08-17 words: 3216.0 sentences: 182.0 pages: flesch: 46.0 cache: ./cache/cord-347577-p0a2rboi.txt txt: ./txt/cord-347577-p0a2rboi.txt summary: The subsequent viral titer decrease was less rapid, and infectious Ebola virus particles persisted for all 8 days of the test. 17, 18 In response to the EVD epidemic, both the World Health Organization (WHO) and the U.S. Centers for Disease Control and Prevention advised direct disposal of Ebola-contaminated liquid waste into sewage systems (wastewater collection and treatment systems) and latrines without disinfection. A current Ebola virus outbreak strain from Guinea (Makona-WPGC07) was spiked to two end concentrations (10 2 and 10 6 TCID 50 mL −1 ) into a domestic wastewater (untreated sewage) sample. Microbial activity within wastewater matrices would be expected to contribute to more rapid inactivation of infectious viral particles; 36, 42 however, the true effect of microbial activity on Ebola virus persistence is unknown. 34 Further assessment is necessary to determine Ebola inactivation and dilution within this period and potential human exposure routes, including workers within the sewer system and Ebola virus persistence within wastewater sludges. abstract: [Image: see text] In the wake of the ongoing 2014/2015 Ebola virus outbreak, significant questions regarding the appropriate handling of Ebola virus-contaminated liquid waste remain, including the persistence of Ebola virus in wastewater. To address these uncertainties, we evaluated the persistence of Ebola virus spiked in sterilized domestic sewage. The viral titer decreased approximately 99% within the first test day from an initial viral titer of 10(6) TCID(50) mL(–1); however, it could not be determined if this initial rapid decrease was due to aggregation or inactivation of the viral particles. The subsequent viral titer decrease was less rapid, and infectious Ebola virus particles persisted for all 8 days of the test. The inactivation constant (k) was determined to be −1.08 (2.1 days for a 90% viral titer decrease). Due to experimental conditions, we believe these results to be an upper bound for Ebola virus persistence in wastewater. Wastewater composition is inherently heterogeneous; subsequently, we caution that interpretation of these results should be made within a holistic assessment, including the effects of wastewater composition, dilution, and potential exposure routes within wastewater infrastructure. While it remains unknown if Ebola virus may be transmitted via wastewater, these data demonstrate a potential exposure route to infectious Ebola virus via wastewater and emphasize the value of a precautionary approach to wastewater handling in an epidemic response. url: https://www.ncbi.nlm.nih.gov/pubmed/26523283/ doi: 10.1021/acs.estlett.5b00193 id: cord-007362-pjpkz6wv author: Bielefeldt-Ohmann, Helle title: The Pathologies of Bovine Viral Diarrhea Virus Infection: A Window on the Pathogenesis date: 2016-01-06 words: 9006.0 sentences: 442.0 pages: flesch: 40.0 cache: ./cache/cord-007362-pjpkz6wv.txt txt: ./txt/cord-007362-pjpkz6wv.txt summary: Pathologic lesions caused by bovine viral diarrhea virus (BVDV) infections comprise a wide spectrum of type, degree, and, by implication, pathogenesis, including congenital defects, necrotic-erosive lesions in mucosal epithelia and skin, and reactive as well as degenerative changes in lymphoid tissues. 3, 22, 29 In PI calves, BVDV can be isolated from lung tissue, and virus antigen is widespread in bronchiolar and alveolar epithelial cells, however, without accompanying histopathologic changes (see section on persistent infection without overt clinical disease and Fig. 5 ).17 Conversely, a proportion (the size varying with study) of cattle succumbing to BRD are positive for BVDV, by virus isolation from or antigen detection in lung tissue, but the ensuing pathologic changes cannot be distinguished from those of other viral pathogens in the BRD complex (perhaps with the exception of BHV-P5), and usually are dominated by the pathology caused by the secondary bacterial agent. abstract: Pathologic lesions caused by bovine viral diarrhea virus (BVDV) infections comprise a wide spectrum of type, degree, and, by implication, pathogenesis, including congenital defects, necrotic-erosive lesions in mucosal epithelia and skin, and reactive as well as degenerative changes in lymphoid tissues. At least some of the pathology may not be solely due to BVDV replication per se, but rather caused by a host response to the virus, particularly the production of pro-inflammatory cytokines. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7111321/ doi: 10.1016/s0749-0720(15)30461-8 id: cord-000012-p56v8wi1 author: Bigot, Yves title: Molecular evidence for the evolution of ichnoviruses from ascoviruses by symbiogenesis date: 2008-09-18 words: 6419.0 sentences: 293.0 pages: flesch: 44.0 cache: ./cache/cord-000012-p56v8wi1.txt txt: ./txt/cord-000012-p56v8wi1.txt summary: CONCLUSION: Our results provide molecular evidence supporting the origin of ichnoviruses from ascoviruses by lateral transfer of ascoviral genes into ichneumonid wasp genomes, perhaps the first example of symbiogenesis between large DNA viruses and eukaryotic organisms. With respect to both species number and mechanisms that lead to successful parasitism, endoparasitic wasps are known to inject secretions at oviposition, but only a few lineages use viruses or virus-like particles (VLPs) to evade or to suppress host defences. Extending our investigations to proteins encoded by open reading frames of certain ascoviruses and bracoviruses, hosts and bacteria, in the light of recent analyses about the involvement of the replication machinery of virus groups related to ascoviruses in lateral gene transfer [29] , we discuss the robustness and the limits of the molecular evidence supporting an ascovirus origin for ichnovirus lineages. abstract: BACKGROUND: Female endoparasitic ichneumonid wasps inject virus-like particles into their caterpillar hosts to suppress immunity. These particles are classified as ichnovirus virions and resemble ascovirus virions, which are also transmitted by parasitic wasps and attack caterpillars. Ascoviruses replicate DNA and produce virions. Polydnavirus DNA consists of wasp DNA replicated by the wasp from its genome, which also directs particle synthesis. Structural similarities between ascovirus and ichnovirus particles and the biology of their transmission suggest that ichnoviruses evolved from ascoviruses, although molecular evidence for this hypothesis is lacking. RESULTS: Here we show that a family of unique pox-D5 NTPase proteins in the Glypta fumiferanae ichnovirus are related to three Diadromus pulchellus ascovirus proteins encoded by ORFs 90, 91 and 93. A new alignment technique also shows that two proteins from a related ichnovirus are orthologs of other ascovirus virion proteins. CONCLUSION: Our results provide molecular evidence supporting the origin of ichnoviruses from ascoviruses by lateral transfer of ascoviral genes into ichneumonid wasp genomes, perhaps the first example of symbiogenesis between large DNA viruses and eukaryotic organisms. We also discuss the limits of this evidence through complementary studies, which revealed that passive lateral transfer of viral genes among polydnaviral, bacterial, and wasp genomes may have occurred repeatedly through an intimate coupling of both recombination and replication of viral genomes during evolution. The impact of passive lateral transfers on evolutionary relationships between polydnaviruses and viruses with large double-stranded genomes is considered in the context of the theory of symbiogenesis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567993/ doi: 10.1186/1471-2148-8-253 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-310371-pylrg91h author: Bishop, R.F. title: Enteric Viruses date: 2008-07-30 words: 4467.0 sentences: 253.0 pages: flesch: 41.0 cache: ./cache/cord-310371-pylrg91h.txt txt: ./txt/cord-310371-pylrg91h.txt summary: The onset of acute enteritis is associated with infection by viruses that replicate at or near the site of entry into the intestinal mucosa, including caliciviruses, rotaviruses, adenoviruses, astroviruses, and coronaviruses. . viruses causing localized inflammation at any level of the intestinal tract, predominantly in small intestinal mucosa, resulting in acute gastroenteritis, for example, rotaviruses, caliciviruses, adenoviruses, astroviruses; . The family Caliciviridae contain small RNA viruses that cause enteric disease in a wide variety of hosts including cattle, pigs, rabbits, and humans. Caliciviruses causing enteric infections (in humans and other animals) are classified as belonging to the family Caliciviridae, which is divided into four genera. The recent demonstration that human noroviruses can infect and replicate in a three-dimensional cell culture model of human intestinal epithelium, should improve our understanding of the pathogenesis, and antigenic diversity of this important group of enteric viruses. abstract: Many viruses use the enteric tract as a route of entry to the human, animal, or avian host. The onset of acute enteritis is associated with infection by viruses that replicate at or near the site of entry into the intestinal mucosa, including caliciviruses, rotaviruses, adenoviruses, astroviruses, and coronaviruses. These ‘enteric’ viruses occur globally and share similar features. Most are RNA viruses that replicate in the cytoplasm of mature absorptive epithelial cells lining the villi of the small intestine, leading to inflammation and villus atrophy. Vomiting and diarrhea can result in dehydration and death if untreated. Despite abundant growth in vivo, they initially proved difficult or impossible to grow in vitro. Most are genetically diverse, species specific, highly infectious within species and transmitted by the fecal–oral route. Severe symptoms are most commonly associated with primary infections of young animals, and are followed by short-lived immunity. Reinfections are common throughout life, but are often only mildly symptomatic. Safe and effective vaccines have been developed to prevent severe rotavirus disease in young children. In addition to these enterotropic viruses, enteric disease can also result from spread to the intestine of HIV or cytomegaloviruses during the later stages of systemic disease in immunocompromised hosts. url: https://www.sciencedirect.com/science/article/pii/B9780123744104003861 doi: 10.1016/b978-012374410-4.00386-1 id: cord-008149-kdlcaium author: Blacklaws, B.A. title: Emerging viruses of zoonotic and veterinary importance date: 2017-12-30 words: 690.0 sentences: 44.0 pages: flesch: 51.0 cache: ./cache/cord-008149-kdlcaium.txt txt: ./txt/cord-008149-kdlcaium.txt summary: Emerging viruses of zoonotic and veterinary importance To enable discussion of all aspects of emerging virus infections, an Emerging Viruses meeting was held at the University of Nottingham, UK, on 27-29 July 2015. Given the success of this meeting, a second meeting was organised, now called ''Emerging Viruses of Zoonotic and Veterinary Importance'', at Churchill College, Cambridge, UK, on 24-26 July 2017 to encourage discussion of emerging virus infections from a One Health perspective. This is formulated in the One Health approach to infectious disease, where the possibility of infectious agent movement between species, including human beings, is key. Whilst a major driver of emerging virus disease research is public health concern over zoonotic infections, there are also veterinary drivers for emerging viral diseases. With the accelerating changes in our world, emerging viral infections will continue to be an important issue for human and veterinary health. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7129228/ doi: 10.1016/j.tvjl.2017.12.022 id: cord-253825-d9borky8 author: Blaising, Julie title: Arbidol as a broad-spectrum antiviral: An update date: 2014-04-24 words: 8757.0 sentences: 431.0 pages: flesch: 44.0 cache: ./cache/cord-253825-d9borky8.txt txt: ./txt/cord-253825-d9borky8.txt summary: ARB has been shown to display antiviral in vitro and/or in vivo activity against a number of enveloped or non-enveloped RNA or DNA viruses, including influenza viruses A, B and C , respiratory syncytial virus, SARS-CoV, adenovirus, parainfluenza type 5, poliovirus 1, rhinovirus 14, coxsackievirus B5, hantaan virus, Chikungunya virus, HBV and HCV [reviewed in Boriskin et al. Shi and coworkers showed a greater inhibitory effect on influenza A H1N1 when ARB was added before infection or when it was pre-incubated with the virus (Shi et al., 2007) , suggesting that membrane impregnation and/or metabolites could underlie ARB antiviral activity (see Section 6.). Recently, Tannock and coworkers reported a potent antiviral activity of ARB on several virus families responsible of respiratory infections in animals and humans, in particular on influenza A H3N2 (IC50 12 lM), and the non-enveloped Picornaviridae poliovirus 1 and rhinovirus 14 (Brooks et al., 2012 ; see also Brooks et al., 2004) . abstract: Arbidol (ARB) is a Russian-made small indole-derivative molecule, licensed in Russia and China for prophylaxis and treatment of influenza and other respiratory viral infections. It also demonstrates inhibitory activity against other viruses, enveloped or not, responsible for emerging or globally prevalent infectious diseases such as hepatitis B and C, gastroenteritis, hemorrhagic fevers or encephalitis. In this review, we will explore the possibility and pertinence of ARB as a broad-spectrum antiviral, after a careful examination of its physico-chemical properties, pharmacokinetics, toxicity, and molecular mechanisms of action. Recent studies suggest that ARB’s dual interactions with membranes and aromatic amino acids in proteins may be central to its broad-spectrum antiviral activity. This could impact on the virus itself, and/or on cellular functions or critical steps in virus-cell interactions, thereby positioning ARB as both a direct-acting antiviral (DAA) and a host-targeting agent (HTA). In the context of recent studies in animals and humans, we will discuss the prospective clinical use of ARB in various viral infections. url: https://www.ncbi.nlm.nih.gov/pubmed/24769245/ doi: 10.1016/j.antiviral.2014.04.006 id: cord-318172-bdotp9ko author: Blanco, Jorge C. G. title: PROPHYLACTIC ANTIBODY TREATMENT AND INTRAMUSCULAR IMMUNIZATION REDUCE INFECTIOUS HUMAN RHINOVIRUS 16 LOAD IN THE LOWER RESPIRATORY TRACT OF CHALLENGED COTTON RATS date: 2014-01-01 words: 5190.0 sentences: 250.0 pages: flesch: 42.0 cache: ./cache/cord-318172-bdotp9ko.txt txt: ./txt/cord-318172-bdotp9ko.txt summary: In this work we show that, without requiring any genetic modification of either the host or the virus, intranasal infection of cotton rats with HRV16 resulted in measurable lower respiratory tract pathology, mucus production, and expression of interferon-activated genes. Over the years, the cotton rat (Sigmodon hispidus) has been shown to support replication of a broad spectrum of human viruses including respiratory syncytial virus (RSV) [25] , nonadapted strains of human influenza [26, 27] , and measles [28, 29] , among others [30] , providing modeling capabilities for the corresponding infections. The results of the described experimental work show that HRV16 infection in the cotton rat reproduces aspects of HRVassociated human disease in the respiratory tract, causing detectable inflammation in the lower airways and lung parenchyma and mucus production, and inducing a transient expression of interferon-stimulated genes that merits further investigation. In addition we demonstrated that passive transfer of antibodies generated in vaccinated cotton rats can protect naïve animals from Infectious virus titers in the lung were determined by plaque assay at the indicated times p.i. abstract: Human rhinoviruses (HRV) represent the single most important etiological agents of the common cold and are the most frequent cause of acute respiratory infections in humans. Currently the performance of available animal models for immunization studies using HRV challenge is very limited. The cotton rat (Sigmodon hispidus) is a well-recognized model for the study of human respiratory viral infections. In this work we show that, without requiring any genetic modification of either the host or the virus, intranasal infection of cotton rats with HRV16 resulted in measurable lower respiratory tract pathology, mucus production, and expression of interferon-activated genes. Intramuscular immunization with live HRV16 generated robust protective immunity that correlated with high serum levels of neutralizing antibodies. In addition, cotton rats treated prophylactically with hyperimmune anti-HRV16 serum were protected against HRV16 intranasal challenge. Finally, protection by immunization was efficiently transferred from mothers to newborn animals resulting in a substantial reduction of infectious virus loads in the lung following intranasal challenge. Overall, our results demonstrate that the cotton rat provides valuable additional model development options for testing vaccines and prophylactic therapies against rhinovirus infection. url: https://api.elsevier.com/content/article/pii/S1879437814000059 doi: 10.1016/j.trivac.2014.02.003 id: cord-005281-wy0zk9p8 author: Blinov, V. M. title: Viral component of the human genome date: 2017-05-09 words: 6583.0 sentences: 306.0 pages: flesch: 44.0 cache: ./cache/cord-005281-wy0zk9p8.txt txt: ./txt/cord-005281-wy0zk9p8.txt summary: In the human genome, this capacity is determined by the portion of chromosomal DNA, which does not contain species-specific protein-encoding sequences and, thus, can basically make a place for novel information that will be modified to reach a new balance. In fact, the scope of the described phenomena is not limited to retroviruses as such, since the ubiquity of retroviral elements in animal genomes, their activity in germline cells [31] , along with the fact that viral replication depends significantly on RNA expression, allow retroviruses to contribute in different ways to the insertion of nonretroviral genes into animal germline cells. Finally, the ability to incorporate parts of the viral genome into the chromosomal DNA of host germline cells can vary strongly among different taxonomic groups of viruses, i.e., orders, families, genera, and even species If insertions of viral sequences remain functionally active in the host cell genome, they can give rise to either proteins that function in a new environment or untranslated RNAs of different sizes. abstract: Relationships between viruses and their human host are traditionally described from the point of view taking into consideration hosts as victims of viral aggression, which results in infectious diseases. However, these relations are in fact two-sided and involve modifications of both the virus and host genomes. Mutations that accumulate in the populations of viruses and hosts may provide them advantages such as the ability to overcome defense barriers of host cells or to create more efficient barriers to deal with the attack of the viral agent. One of the most common ways of reinforcing anti-viral barriers is the horizontal transfer of viral genes into the host genome. Within the host genome, these genes may be modified and extensively expressed to compete with viral copies and inhibit the synthesis of their products or modulate their functions in other ways. This review summarizes the available data on the horizontal gene transfer between viral and human genomes and discusses related problems. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7089383/ doi: 10.1134/s0026893317020066 id: cord-310942-191m0e65 author: Boga, Jose Antonio title: Beneficial actions of melatonin in the management of viral infections: a new use for this “molecular handyman”? date: 2012-04-18 words: 7208.0 sentences: 362.0 pages: flesch: 32.0 cache: ./cache/cord-310942-191m0e65.txt txt: ./txt/cord-310942-191m0e65.txt summary: The potential protective mechanisms include melatonin acting as a free radical scavenger, an antioxidant enzyme inducer, a positive regulator of immune functions and an inhibitor of inflammation, as well as a regulator of programmed cell death (PCD) [ Table 2 ]. Melatonin treatment also caused a rise in protein expression of the nuclear factor erythroid 2 (Nrf2), a transcription factor that plays a critical role by binding to the antioxidant response element in the promoter region of a number of genes encoding for antioxidant and detoxifying enzymes in several types of cells and tissues [109] . Respiratory syncytial virus infection of human respiratory epithelial cells enhances inducible nitric oxide synthase gene expression Melatonin decreases nitric oxide production and lipid peroxidation and increases interleukin-1 beta in the brain of mice infected by the Venezuelan equine encephalomyelitis virus abstract: Melatonin (N‐acetyl‐5‐methoxytryptamine) is a multifunctional signaling molecule that has a variety of important functions. Numerous clinical trials have examined the therapeutic usefulness of melatonin in different fields of medicine. Clinical trials have shown that melatonin is efficient in preventing cell damage under acute (sepsis, asphyxia in newborns) and chronic states (metabolic and neurodegenerative diseases, cancer, inflammation, aging). The beneficial effects of melatonin can be explained by its properties as a potent antioxidant and antioxidant enzyme inducer, a regulator of apoptosis and a stimulator of immune functions. These effects support the use of melatonin in viral infections, which are often associated with inflammatory injury and increases in oxidative stress. In fact, melatonin has been used recently to treat several viral infections, which are summarized in this review. The role of melatonin in infections is also discussed herein. Copyright © 2012 John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/22511571/ doi: 10.1002/rmv.1714 id: cord-318551-c1qr27lg author: Boguszewska‐Chachulska, Anna M. title: Rna Viruses Redirect Host Factors to Better Amplify Their Genome date: 2005-12-29 words: 10673.0 sentences: 511.0 pages: flesch: 44.0 cache: ./cache/cord-318551-c1qr27lg.txt txt: ./txt/cord-318551-c1qr27lg.txt summary: (Adapted with permission from Pasternak et al., 2001.) Transcription of segmented (À) strand RNA viruses such as the Orthomyxoviridae, Arenaviridae, Bunyaviridae, and Tenuiviruses requires a primer to initiate synthesis of the mRNAs. This is achieved by cap-snatching in which the replicase complex, or a protein thereof, binds to the 5 0 region of cell mRNAs, cleaves off the cap together with generally 7-15 nucleotides from the 5 0 end of the cell mRNA, and uses this fragment as a primer to initiate synthesis of the viral mRNAs (Bouloy et al., 1978; Nguyen and Haenni, 2003) . (1996) PV, poliovirus; MHV, mouse hepatitis virus; WNV, West Nile virus; BVDV, bovine viral diarrhea virus; HPIV-3, human parainfluenza virus-3; IG (À), intergenic region in (À) RNA; UTR, untranslated region; Leader RNA (À), 3'' end of (À) RNA; Leader RNA (þ), 5'' end of (þ) RNA; HF, host factor; PCBP, poly(C)-binding protein; PABP, poly(A)-binding protein; hnRNP A1, heterogeneous nuclear ribonucleoprotein A1; PTB, polypyrimidine tract-binding protein; TIA-1, T-cell-activated intracellular antigen; TIAR, TIA-1-related; RHA, RNA helicase A; GAPDH, glyceraldehyde-3-phosphate dehydrogenase. abstract: This chapter provides an updated view of the host factors that are, at present, believed to participate in replication/transcription of RNA viruses. One of the major hurdles faced when attempting to identify host factors specifically involved in viral RNA replication/transcription is how to discriminate these factors from those involved in translation. Several of the host factors shown to affect viral RNA synthesis are factors known to be involved in protein synthesis, for example, translation factors. In addition, some of the factors identified to date appear to influence viral RNA amplification as well as viral protein synthesis, and translation and replication are frequently tightly associated. Several specific host factors actively participating in viral RNA transcription/replication have been identified and the regions of host protein/replicase or host protein/viral RNA interaction have been determined. The chapter centers exclusively on those factors that appear functionally important for viral amplification. It presents a list of the viruses for which a specific host factor associates with the polymerase, affecting viral genome amplification. It also indicates the usually accepted cell function of the factor and the viral polymerase or polymerase subunit to which the host factor binds. url: https://www.sciencedirect.com/science/article/pii/S0065352705650026 doi: 10.1016/s0065-3527(05)65002-6 id: cord-329527-0rlotyz3 author: Bohmwald, Karen title: Neurologic Alterations Due to Respiratory Virus Infections date: 2018-10-26 words: 11036.0 sentences: 559.0 pages: flesch: 48.0 cache: ./cache/cord-329527-0rlotyz3.txt txt: ./txt/cord-329527-0rlotyz3.txt summary: In addition to this, a fatal case attributed to the H1N1 pandemic infection was reported, and the clinical finding showed that the cause of death was an intracerebral thrombosis and hemorrhage with presence of the virus in the brain, but not in lungs or CSF (Simon et al., 2013 ; Figure 2) . In another approximation to understand the etiologic agent causing myelopathy post-influenza-like syndrome, CSF obtained from a patient with this disease was inoculated in several cell lines, previously reported to be permissive for the growth FIGURE 2 | Influenza virus (IV) spreads from the lungs to the CNS through the vagus nerve promoting an inflammatory state. As described so far, CoVs are respiratory viruses that exhibit neurotropic capacities that not only allows them to achieve latency and avoid the immune response of the host, but also have neurological implications that can complicate the disease associated to its infection. Although there are extensive case reports that indicate neurological manifestations associated to hMPV-infection in humans, further studies are required in mice models to characterize this disease. abstract: Central Nervous System (CNS) infections are one of the most critical problems in public health, as frequently patients exhibit neurologic sequelae. Usually, CNS pathologies are caused by known neurotropic viruses such as measles virus (MV), herpes virus and human immunodeficiency virus (HIV), among others. However, nowadays respiratory viruses have placed themselves as relevant agents responsible for CNS pathologies. Among these neuropathological viruses are the human respiratory syncytial virus (hRSV), the influenza virus (IV), the coronavirus (CoV) and the human metapneumovirus (hMPV). These viral agents are leading causes of acute respiratory infections every year affecting mainly children under 5 years old and also the elderly. Up to date, several reports have described the association between respiratory viral infections with neurological symptoms. The most frequent clinical manifestations described in these patients are febrile or afebrile seizures, status epilepticus, encephalopathies and encephalitis. All these viruses have been found in cerebrospinal fluid (CSF), which suggests that all these pathogens, once in the lungs, can spread throughout the body and eventually reach the CNS. The current knowledge about the mechanisms and routes used by these neuro-invasive viruses remains scarce. In this review article, we describe the most recent findings associated to neurologic complications, along with data about the possible invasion routes of these viruses in humans and their various effects on the CNS, as studied in animal models. url: https://www.ncbi.nlm.nih.gov/pubmed/30416428/ doi: 10.3389/fncel.2018.00386 id: cord-338083-77re4l0w author: Bolin, Steven R. title: Origination and consequences of bovine viral diarrhea virus diversity date: 2005-03-04 words: 6748.0 sentences: 329.0 pages: flesch: 43.0 cache: ./cache/cord-338083-77re4l0w.txt txt: ./txt/cord-338083-77re4l0w.txt summary: The genetic diversity that occurs among isolates of BVDV is characteristic of RNA viruses that exist in nature as quasispecies (a swarm of viral mutants). However, altered base sequence in this region of the viral genome has been identified after passage of the virus in cell culture, and has been detected in viral RNA that was extracted from tissues of an infected animal [20, 21] . The selection of the antigenic variants likely occurred during the acute infection of the dams of those PI cattle and resulted in transplacental transmission of slightly different BVDV to a group of fetuses. Genetic and antigenic variability in bovine viral diarrhea virus (BVDV) isolates from Belgium Pathogenesis of primary respiratory disease induced by isolates from a new genetic cluster of bovine viral diarrhea virus type I Clinical and immunologic responses of vaccinated and unvaccinated calves to infection with a virulent type-II isolate of bovine viral diarrhea virus abstract: The potential consequences of BVDV genetic and antigenic diversity are far ranging. The complexity of clinical presentations associated with BVDV likely arises from factors encoded by the virus genome. More importantly,prevention and control of BVDV may be complicated by diagnostic and immunization failure resulting from virus diversity. Evolutionary pressures will continue to drive further diversity, making control of BVDV challenging. Current and the potential for future BVDV strain diversity should be considered when designing BVDV control programs both at the individual farm and national herd level. url: https://www.sciencedirect.com/science/article/pii/S0749072003000811 doi: 10.1016/j.cvfa.2003.11.009 id: cord-017537-ztdz4a2s author: Bologna, Mauro title: Biological Agents and Bioterrorism date: 2014-09-18 words: 3324.0 sentences: 198.0 pages: flesch: 51.0 cache: ./cache/cord-017537-ztdz4a2s.txt txt: ./txt/cord-017537-ztdz4a2s.txt summary: For this very stimulating course, I want to share with you some of my studies and even some of my scientific and phylosophical considerations on biological agents living in the environment and their relations with humans, in the very wide concepts of ecological relationships, parasitism, immunolgical defenses and infectious disease mechanisms. All these concepts must be studied and considered in the event of criminal use of biological agents (bioterrorism) aimed at harming human populations in time and in geographical space. In the light of recent concern and interest about the potential for biological terrorism (biofarware) there are several diseases and bacterial toxins that must be considered in particular, like anthrax [ 1 , 2 ] , smallpox [ 3 , 4 ] , plague [ 5 ] , botulinum toxin [ 6 ] , and tularemia [ 7 ] . abstract: For this very stimulating course, I want to share with you some of my studies and even some of my scientific and phylosophical considerations on biological agents living in the environment and their relations with humans, in the very wide concepts of ecological relationships, parasitism, immunolgical defenses and infectious disease mechanisms. All these concepts must be studied and considered in the event of criminal use of biological agents (bioterrorism) aimed at harming human populations in time and in geographical space. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122122/ doi: 10.1007/978-94-017-9238-7_1 id: cord-323404-3mw4q7m3 author: Bomsel, Morgane title: Entry of viruses through the epithelial barrier: pathogenic trickery date: 2003 words: 8104.0 sentences: 428.0 pages: flesch: 43.0 cache: ./cache/cord-323404-3mw4q7m3.txt txt: ./txt/cord-323404-3mw4q7m3.txt summary: In polarized monostratified epithelium -where the plasma membrane is divided into two domains that have a different lipid and protein composition and different membrane dynamics -viruses usually attach and penetrate the cell cytosol preferentially at the restricted pole of the by epithelial cells and cross the epithelial barrier using TRANSCYTOSIS (BOX 1), as has been described recently for the human immunodeficiency virus (HIV) 3, 4 . Similarly, human JC virus 49 and Sendai 50 virus, as well as sialyloligosaccharide-dependent strains of rotavirus 20 and reovirus, also attach themselves to epithelial cells to block or abuse normal cell processes and, as with bacteria 43 , the surface proteins of enveloped or naked viruses bind to host-cell molecules that have receptor functions. As the cell attachment receptors for numerous enveloped and naked viruses, the glycosyl epitopes of the epithelial-cell-surface proteoglycans mediate virus adhesion, in turn initiating signal transduction as described for the GLYCOSYNAPSE 54 . abstract: Mucosal surfaces — such as the lining of the gut or the reproductive tract — are the main point of entry for viruses into the body. As such, almost all viruses interact with epithelial cells, and make use of the normal epithelial signalling and trafficking pathways of the host cell. In addition to protein receptors, carbohydrate chains of proteoglycans and epithelial-membrane glycosphingolipids have emerged as a new class of receptors for viral attachment to the host cell. url: https://www.ncbi.nlm.nih.gov/pubmed/12511869/ doi: 10.1038/nrm1005 id: cord-001065-j4hvyyoi author: Boncristiani, Humberto F. title: In Vitro Infection of Pupae with Israeli Acute Paralysis Virus Suggests Disturbance of Transcriptional Homeostasis in Honey Bees (Apis mellifera) date: 2013-09-05 words: 6367.0 sentences: 326.0 pages: flesch: 47.0 cache: ./cache/cord-001065-j4hvyyoi.txt txt: ./txt/cord-001065-j4hvyyoi.txt summary: title: In Vitro Infection of Pupae with Israeli Acute Paralysis Virus Suggests Disturbance of Transcriptional Homeostasis in Honey Bees (Apis mellifera) An experimental protocol to test these systems was developed, using injections of Israeli Acute Paralysis Virus (IAPV) into honey bee pupae reared ex-situ under laboratory conditions. Gene expression analyses of three separate experiments suggest IAPV disruption of transcriptional homeostasis of several fundamental cellular functions, including an up-regulation of the ribosomal biogenesis pathway. Little is known about the specific biology of the viruses in these families that infect honey bees, although they contain important bee pathogens, such as Deformed Wing Virus (DWV) and Israeli Acute Paralysis Virus (IAPV). Post-hoc tests of main treatment effects showed significantly higher gene expression in the IAPV-inoculated bees compared to the two control groups for Actin, 28S rRNA, and mGST1. The observed gene expression patterns could be due to viral manipulation of the cells to increase virus replication or present cell compensatory responses to IAPV infection. abstract: The ongoing decline of honey bee health worldwide is a serious economic and ecological concern. One major contributor to the decline are pathogens, including several honey bee viruses. However, information is limited on the biology of bee viruses and molecular interactions with their hosts. An experimental protocol to test these systems was developed, using injections of Israeli Acute Paralysis Virus (IAPV) into honey bee pupae reared ex-situ under laboratory conditions. The infected pupae developed pronounced but variable patterns of disease. Symptoms varied from complete cessation of development with no visual evidence of disease to rapid darkening of a part or the entire body. Considerable differences in IAPV titer dynamics were observed, suggesting significant variation in resistance to IAPV among and possibly within honey bee colonies. Thus, selective breeding for virus resistance should be possible. Gene expression analyses of three separate experiments suggest IAPV disruption of transcriptional homeostasis of several fundamental cellular functions, including an up-regulation of the ribosomal biogenesis pathway. These results provide first insights into the mechanisms of IAPV pathogenicity. They mirror a transcriptional survey of honey bees afflicted with Colony Collapse Disorder and thus support the hypothesis that viruses play a critical role in declining honey bee health. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3764161/ doi: 10.1371/journal.pone.0073429 id: cord-324295-9c1zxjng author: Bonilla-Aldana, D. Katterine title: Bats in Ecosystems and their Wide Spectrum of Viral Infectious Threats: SARS-CoV-2 and other emerging viruses date: 2020-08-20 words: 3770.0 sentences: 212.0 pages: flesch: 51.0 cache: ./cache/cord-324295-9c1zxjng.txt txt: ./txt/cord-324295-9c1zxjng.txt summary: Examples of such viruses include Marburg, Ebola, Nipah, Hendra, Influenza A, Dengue, Equine Encephalitis viruses, Lyssaviruses, Madariaga and Coronaviruses, involving the now pandemic Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since there is no effective treatment or vaccine for COVID-19 to date, strong regulations---including isolation, quarantine and social distancing---have been established by many countries in an effort to reduce expansion of the disease given the high person-to-person transmissibility of SARS-CoV-2, either directly by respiratory droplets with infective particles or indirectly by fluid-contaminated objects. Fruit bats (genus Pteropus) are the main natural reservoir for Nipah virus (NiV), while pigs serve as intermediate hosts ( Table 3 ). Influenza A viruses (IAV) are one of the leading causes of disease in humans, with important animal reservoirs including birds, pigs, and horses that can potentially produce new zoonotic variants (Table 2) . abstract: Bats have populated earth for approximately 52 million years, serving as natural reservoirs for a variety of viruses through the course of evolution. Transmission of highly pathogenic viruses from bats has been suspected and linked to a spectrum of emerging infectious diseases in humans and animals worldwide. Examples of such viruses include Marburg, Ebola, Nipah, Hendra, Influenza A, Dengue, Equine Encephalitis viruses, Lyssaviruses, Madariaga and Coronaviruses, involving the now pandemic Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein, we provide a comprehensive review on the diversity, reservoirs, and geographical distribution of the main bat viruses and their potential for cross-species transmission. url: https://www.sciencedirect.com/science/article/pii/S1201971220306809?v=s5 doi: 10.1016/j.ijid.2020.08.050 id: cord-265681-ab8j4o1u author: Boroomand, Zahra title: Pathogenesis and Tissue Distribution of Avian Infectious Bronchitis Virus Isolate IRFIBV32 (793/B Serotype) in Experimentally Infected Broiler Chickens date: 2012-04-01 words: 3553.0 sentences: 219.0 pages: flesch: 53.0 cache: ./cache/cord-265681-ab8j4o1u.txt txt: ./txt/cord-265681-ab8j4o1u.txt summary: title: Pathogenesis and Tissue Distribution of Avian Infectious Bronchitis Virus Isolate IRFIBV32 (793/B Serotype) in Experimentally Infected Broiler Chickens The aim of this study was to investigate the distribution of avian infectious bronchitis virus isolate IRFIBV32 (793/B serotype) in experimentally infected chicken. Data indicated that the number of infected chickens and viral RNA detection from tissues was reduced with increasing antibody titer on day 20 PI. Gross lesions were recorded, and their trachea, lungs, kidneys, caecal tonsil, testes, and oviduct were aseptically collected for virus detection using RT-PCR assay ( Table 1) . In this study, the pathogenesis of the infectious bronchitis virus isolate IRFIBV32 which was recently isolated in Iran [12] , tissue tropism, and dissemination of the virus throughout the body were evaluated following intranasal (IN) inoculation of commercial broiler chickens by RT-PCR. Immunohistochemistry for detection of avian infectious bronchitis virus strain M41 in the proventriculus and nervous system of experimentally infected chicken embryos abstract: Infectious bronchitis (IB) is one of the most important viral diseases of poultry. The aim of this study was to investigate the distribution of avian infectious bronchitis virus isolate IRFIBV32 (793/B serotype) in experimentally infected chicken. Ninety-one-day-old commercial broilers were divided randomly into two groups (seventy in the experimental and twenty in the control group). Chicks in the experimental group were inoculated intranasally with 10(5) ELD50/0.1 mL of the virus at three weeks of age. The samples from various tissues were collected at1, 2, 3, 5, 7, 11, 13, 15, and 20 days postinoculation. Chickens exhibited mild respiratory signs and depression. Viral RNA was detected in the kidney, lung and tracheas on days 1 to 13 PI, in the oviduct between, days 3 and 13, in testes between days 1 and 11 PI, and in the caecal tonsil consistently up to day 20 PI. The most remarkable clinical signs and virus detection appeared on day 1 PI. Data indicated that the number of infected chickens and viral RNA detection from tissues was reduced with increasing antibody titer on day 20 PI. The results demonstrated that the IRFIBV32 virus has wide tissue distribution for respiratory, urogenital, and digestive systems. url: https://doi.org/10.1100/2012/402537 doi: 10.1100/2012/402537 id: cord-009836-7o6htufh author: Borrow, Persephone title: Cytotoxic T‐lymphocyte escape viral variants: how important are they in viral evasion of immune clearance in vivo? date: 2006-04-28 words: 10041.0 sentences: 299.0 pages: flesch: 34.0 cache: ./cache/cord-009836-7o6htufh.txt txt: ./txt/cord-009836-7o6htufh.txt summary: Epitope mapping performed using the Gpl 60 sequence of the patient''s autologous early HIV-1 population indicated that this response was in fact extremely focused on a single epitope encompassing Gpl60 amino acids 30-38(9), recognized in association with HLA-B44, The frequency of epitope-specific CTL was extremely high: at the earhest timepoint available for study, which may have been shghtly after the peak of the primary immune response, 1 in 1 7 peripheral blood mononuclear cells (EBMCs) were found to score as virus-specific CTL precursors by limiting dilution analysis, a technique which has recently been shown to greatly underestimate the total numher of epitope-specific T cells (55, 56) , As shown in Fig, 1 , viral variants bearing mutations in the epitopic sequence which conferred escape from recognition by epitope-specific CTL rapidly appeared in this patienc, and then increased in frequency until 164/1998 they had cotnpieteiy repiaced the transmitted virai strain. abstract: Summary: Although viral variants which are not recognized by epitope‐specific cytotoxic T lymphocytes (CTL) have been shown lo arise during a number of persistent virus infections, in many cases their significance remains controversial: it has been argued that the immune response is sufficiently plastic to contain their replication. In this review, we describe the mechanisms by which amino acid changes in viral proteins may affect epitope recognition by virus‐specific CTL, and discuss the viral and immunological basis for the emergence of viral variants bearing such amino acid changes during infection. We then consider the impact that viral variation may have on the host CTL response and its ability to contain virus replication. We argue that the emergence of a viral variant demonstrates that it must have an in vivo replicative advantage, and that as such, the variant must tip the balance between virus replication and immune control somewhat in favor of the virus. Further, we suggest that although the immune response can evolve to recognize new viral epitopes, the CTL generated following such evolution frequently have a reduced ability to contain virus replication. We conclude that this escape mechanism likely does make a significant contribution to persistence/pathogenesis during a number of different virus infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165923/ doi: 10.1111/j.1600-065x.1998.tb01206.x id: cord-018166-savdgy0u author: Bosch, Albert title: Survival and Transport of Enteric Viruses in the Environment date: 2006 words: 11473.0 sentences: 548.0 pages: flesch: 38.0 cache: ./cache/cord-018166-savdgy0u.txt txt: ./txt/cord-018166-savdgy0u.txt summary: Environmental virology may be defined as the study of viruses that can be transmitted through various environments (water, sewage, soil, air, or surfaces) or food and persist enough in these vehicles to represent a health threat. Since that time, other enteric viruses responsible for gastroenteritis and hepatitis have replaced enteroviruses as the main target for detection in the environment, although the near eradication of poliomyelitis from the globe calls for exhaustive studies on the occurrence of wild-type and vaccinal-type polioviruses in environmental samples. The possibility nowadays to detect the presence of human enteric viruses in different types of water samples and foodstuff, in particular shellfish samples, should be a valuable tool in the prevention of waterborne and food-borne diseases. These data suggest that temperature, and probably relative humidity, may be meaningful in the seasonal distribution of outbreaks of certain human enteric viruses (Enright, 1954) , due to the influence of these factors on virus persistence. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122973/ doi: 10.1007/0-387-29251-9_6 id: cord-309179-5hlatbqe author: Bosch, Albert title: New tools for the study and direct surveillance of viral pathogens in water date: 2008-05-26 words: 3352.0 sentences: 165.0 pages: flesch: 36.0 cache: ./cache/cord-309179-5hlatbqe.txt txt: ./txt/cord-309179-5hlatbqe.txt summary: Main difficulties to overcome for virus detection and characterisation in water samples encompass viral diversity, occurrence of low particle numbers, particularly in drinking water, and the technical challenges of virus assays. Nucleic acid amplification techniques are currently the most widely used methods for detection of viruses in 298 Environmental Biotechnology water, which also enable to gather information of the virus genotypes occurring in the environment, thus providing most relevant epidemiological information, particularly important for the implementation and follow-up of vaccination programmes [2, 3, 4 ] . Nevertheless, as stated above, no alternative to molecular detection analysis exists for highly health significant waterborne viruses such as human norovirus and hepatitis A virus. Development, evaluation, and standardization of a real-time TaqMan reverse transcription-PCR assay for quantification of hepatitis A virus in clinical and shellfish samples abstract: Half a century ago scientists attempted the detection of poliovirus in water. Since then other enteric viruses responsible for gastroenteritis and hepatitis have replaced enteroviruses as the main target for detection. However, most viral outbreaks are restricted to norovirus and hepatitis A virus, making them the main targets in water. The inclusion of virus analysis in regulatory standards for viruses in water samples must overcome several shortcomings such as the technical difficulties and high costs of virus monitoring, the lack of harmonised and standardised assays and the challenge posed by the ever-changing nature of viruses. However, new tools are nowadays available for the study and direct surveillance of viral pathogens in water that may contribute to fulfil these requirements. url: https://api.elsevier.com/content/article/pii/S0958166908000517 doi: 10.1016/j.copbio.2008.04.006 id: cord-338331-27ic5zen author: Boulagnon, Camille title: Influenza A/H1N1 (2009) Infection as a Cause of Unexpected Out‐of‐Hospital Death in the Young date: 2012-05-14 words: 2729.0 sentences: 191.0 pages: flesch: 51.0 cache: ./cache/cord-338331-27ic5zen.txt txt: ./txt/cord-338331-27ic5zen.txt summary: In conclusion, this case report shows that influenza A/H1N1 (2009) virus can be a cause of sudden cardiac death in the young and demonstrates the importance of quantitative virological analyses for the diagnosis of myocarditis. We have reported on an unexpected sudden out-of-hospital death caused by influenza A ⁄ H1N1 (2009) infection involving a young immunocompetent and previously healthy male. In our case, virological investigations were performed, including molecular analyses of common pulmonary and cardiotropic viruses in frozen cardiac samples, as well as genetic analysis of the influenza A ⁄ H1N1 (2009) virus for both hemagglutinin and neuraminidase genes. In our case, determination of viral loads in the absence of any inflammatory infiltrate in the myocardium has shown that influenza A ⁄ H1N1 (2009) virus can be a cause of out-of-hospital unexpected death in the young. Influenza A viral loads in respiratory samples collected from patients infected with pandemic H1N1, seasonal H1N1 and H3N2 viruses abstract: Abstract: In March 2009, a new strain of influenza A/H1N1 virus was identified in Mexico, responsible for a pandemic. Worldwide, more than 13,500 patients died, most often from acute respiratory distress syndrome. Because sudden death cases were rare, involving mostly young apparently healthy persons, influenza A/H1N1 (2009)‐related deaths may be misdiagnosed, which can raise medico‐legal issues. Case history: we report on an unexpected out‐of‐hospital death involving a young male with no past medical history and no vaccination. Fever was his only symptom. Laboratory tests: histology showed patchy necrotic foci with mononuclear inflammation in the lungs. The heart was histologically normal, but virological analyses using molecular biology on frozen myocardial samples showed high virus load. In conclusion, this case report shows that influenza A/H1N1 (2009) virus can be a cause of sudden cardiac death in the young and demonstrates the importance of quantitative virological analyses for the diagnosis of myocarditis. url: https://www.ncbi.nlm.nih.gov/pubmed/22583168/ doi: 10.1111/j.1556-4029.2012.02180.x id: cord-305165-3twlnkac author: Bourgueil, E. title: Experimental infection of pigs with the porcine respiratory coronavirus (PRCV): measure of viral excretion date: 1992-04-30 words: 2331.0 sentences: 150.0 pages: flesch: 55.0 cache: ./cache/cord-305165-3twlnkac.txt txt: ./txt/cord-305165-3twlnkac.txt summary: title: Experimental infection of pigs with the porcine respiratory coronavirus (PRCV): measure of viral excretion Common causes of the disease includes pseudorabies virus (PRV), influenza viruses and the porcine respiratory coronavirus (PRCV), the latter being first detected in different European countries in 1983-1984 (Brown et al., 1986; Duret et al., 1988; Pensaert et al., 1986) . Until now, great attention has been given to clinical disorders induced by PRCV in the field (Jestin et al., 1987; Brown and Cartwright, 1986) and under experimental conditions (Vannier, 1990; Pensaert et al., 1986; O''Toole et al., 1989) , but nothing is known about excretion and airborne transmission of the virus. A high correlation rate (r= 0.83 ) was found between viral titres obtained from air samples collected with that medium and the amount of virus in nasal swabs (see tables 1 and abstract: Abstract Twelve pigs were experimentally infected with a porcine respiratory coronavirus (PRCV) by the oronasal route. Viral excretion was measured daily by two means-deep nasal swabs and air samples obtained in a cyclone sampler. Clinical signs were very slight on infected pigs. Airborne virus could be recovered from day 1 to day 6 post-infection in the cyclone sampler as well as in petri dishes placed in the same loose-box. Viral titres obtained from nasal swabs were significantly correlated with those obtained from air samples. Different collection media were compared. The most efficient media for the collection of infectious viral particles contained a protective agent such as foetal calf serum. url: https://api.elsevier.com/content/article/pii/037811359290136H doi: 10.1016/0378-1135(92)90136-h id: cord-048466-fj9l8che author: Bragstad, Karoline title: The evolution of human influenza A viruses from 1999 to 2006: A complete genome study date: 2008-03-07 words: 5357.0 sentences: 322.0 pages: flesch: 53.0 cache: ./cache/cord-048466-fj9l8che.txt txt: ./txt/cord-048466-fj9l8che.txt summary: BACKGROUND: Knowledge about the complete genome constellation of seasonal influenza A viruses from different countries is valuable for monitoring and understanding of the evolution and migration of strains. The influenza virus evades host immunity by accumulation of point mutations (drift) in the major surface glycoproteins, haemagglutinin (HA) and neuraminidase (NA) or by reassortment of segments from different viruses co-infecting the same cell leading to a new stain with a HA (and NA) not seen in the population before (shift). The A/Fujian/411/02(H3N2)-like clinical Danish viruses had several substitutions in HA at sites that might influence the virus'' capability for egg growth [10, 37] . Substitutions at antigenic site B and the predicted N-glycosylation at position 144 in HA antigenic site A together with a stronger NA might have contributed to the increased infectivity of the reassorted Fujian-like viruses of the 2003-2004 season, causing an epidemic in Denmark. Positive selection on the H3 hemagglutinin gene of human influenza virus A abstract: BACKGROUND: Knowledge about the complete genome constellation of seasonal influenza A viruses from different countries is valuable for monitoring and understanding of the evolution and migration of strains. Few complete genome sequences of influenza A viruses from Europe are publicly available at the present time and there have been few longitudinal genome studies of human influenza A viruses. We have studied the evolution of circulating human H3N2, H1N1 and H1N2 influenza A viruses from 1999 to 2006, we analysed 234 Danish human influenza A viruses and characterised 24 complete genomes. RESULTS: H3N2 was the prevalent strain in Denmark during the study period, but H1N1 dominated the 2000–2001 season. H1N2 viruses were first observed in Denmark in 2002–2003. After years of little genetic change in the H1N1 viruses the 2005–2006 season presented H1N1 of greater variability than before. This indicates that H1N1 viruses are evolving and that H1N1 soon is likely to be the prevalent strain again. Generally, the influenza A haemagglutinin (HA) of H3N2 viruses formed seasonal phylogenetic clusters. Different lineages co-circulating within the same season were also observed. The evolution has been stochastic, influenced by small "jumps" in genetic distance rather than constant drift, especially with the introduction of the Fujian-like viruses in 2002–2003. Also evolutionary stasis-periods were observed which might indicate well fit viruses. The evolution of H3N2 viruses have also been influenced by gene reassortments between lineages from different seasons. None of the influenza genes were influenced by strong positive selection pressure. The antigenic site B in H3N2 HA was the preferred site for genetic change during the study period probably because the site A has been masked by glycosylations. Substitutions at CTL-epitopes in the genes coding for the neuraminidase (NA), polymerase acidic protein (PA), matrix protein 1 (M1), non-structural protein 1 (NS1) and especially the nucleoprotein (NP) were observed. The N-linked glycosylation pattern varied during the study period and the H3N2 isolates from 2004 to 2006 were highly glycosylated with ten predicted sequons in HA, the highest amount of glycosylations observed in this study period. CONCLUSION: The present study is the first to our knowledge to characterise the evolution of complete genomes of influenza A H3N2, H1N1 and H1N2 isolates from Europe over a time period of seven years from 1999 to 2006. More precise knowledge about the circulating strains may have implications for predicting the following season strains and thereby better matching the vaccine composition. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2311284/ doi: 10.1186/1743-422x-5-40 id: cord-016796-g4kqqpy1 author: Bramhachari, Pallaval Veera title: Advanced Immunotechnological Methods for Detection and Diagnosis of Viral Infections: Current Applications and Future Challenges date: 2019-11-05 words: 5646.0 sentences: 305.0 pages: flesch: 34.0 cache: ./cache/cord-016796-g4kqqpy1.txt txt: ./txt/cord-016796-g4kqqpy1.txt summary: As a part of modern research on immunotechniques, a diagnostic approach for chronic hepatitis C infection (CHC), detects specific antibody to HCV (anti-HCV) (indirect tests) and assays that can detect, quantify, or characterize components of HCV viral particles, viz. Nonetheless, recent studies on respiratory syncytial virus (RSV) developed Luciferase Immunoprecipitation Systems (LIPS) assay to detect IgG Antibodies against Human RSV G-Glycoprotein. Sensitive and specific detection of Crimean-Congo hemorrhagic fever virus (CCHFV) was developed employing specific IgM and IgG antibodies in human sera using recombinant CCHFV nucleoprotein as antigen in μ-capture and IgG immune complex (IC) ELISA tests (Emmerich et al. A rapid diagnostic platform for colorimetric differential detection of DENV and CHIKV viral infections was recently developed with a possibility to alter clinical diagnosis of acute febrile illnesses in resource-limited settings. This novel antibody demonstrates noteworthy specificity to identify H7N9 virus compared to homemade target-captured ELISA, qRT-PCR, and rapid influenza diagnostic test (RIDT) with high sensitivity (Chang et al. abstract: Diagnosis and identification of viruses is an important component of diagnostic virology laboratory. Although various modes of diagnostic methods are now available at disposal, a vast majority of the diseases across the globe remain undiagnosed. This is largely due to the overlapping undifferentiated set of symptoms across myriad set of RNA and DNA viral diseases. As such, it becomes critical to take into consideration several factors for viral diagnosis ranging from the type and quality of specimen collected, time of specimen collection, mode of transport, accuracy, specificity, sensitivity, and the type of diagnostic method used. This chapter broadly emphasizes various methods on diagnostic virology ranging from the classical methods of diagnosis to the most recently developed molecular methods of detection of virus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121190/ doi: 10.1007/978-981-15-1045-8_17 id: cord-310795-n78s0sg2 author: Brand, H. Kim title: Infection with multiple viruses is not associated with increased disease severity in children with bronchiolitis date: 2011-09-07 words: 3943.0 sentences: 220.0 pages: flesch: 51.0 cache: ./cache/cord-310795-n78s0sg2.txt txt: ./txt/cord-310795-n78s0sg2.txt summary: This study evaluated the association between the detection of multiple viruses by RT‐PCR and disease severity in children with bronchiolitis. In RSV infected children younger than 3 months, disease severity was not associated with the number of detected viruses. Therefore, we prospectively studied the association between the detection of multiple viral pathogens by RT-PCR and disease severity in young children with bronchiolitis included during three consecutive winter seasons. As the differences in age between the groups may have influenced our results, we also evaluated the association between disease severity and the detection of multiple viruses in children diagnosed with RSV bronchiolitis younger and older than 3 months (Fig. 2) . In the present study, we evaluated the viral etiology in young children with bronchiolitis during three consecutive winter seasons and examined the association between the detection of two or more viruses by RT-PCR and disease severity. abstract: BACKGROUND: The clinical relevance of parallel detection of multiple viruses by real‐time polymerase chain reaction (RT‐PCR) remains unclear. This study evaluated the association between the detection of multiple viruses by RT‐PCR and disease severity in children with bronchiolitis. METHODS: Children less than 2 years of age with clinical symptoms of bronchiolitis were prospectively included during three winter seasons. Patients were categorized in three groups based on disease severity; mild (no supportive treatment), moderate (supplemental oxygen and/or nasogastric feeding), and severe (mechanical ventilation). Multiplex RT‐PCR of 15 respiratory viruses was performed on nasopharyngeal aspirates. RESULTS: In total, 142 samples were obtained. Respiratory Syncytial virus (RSV) was the most commonly detected virus (73%) followed by rhinovirus (RV) (30%). In 58 samples (41%) more than one virus was detected, of which 41% was a dual infection with RSV and RV. In RSV infected children younger than 3 months, disease severity was not associated with the number of detected viruses. Remarkably, in children older than 3 months we found an association between more severe disease and RSV mono‐infections. CONCLUSION: Disease severity in children with bronchiolitis is not associated with infection by multiple viruses. We conclude that other factors, such as age, contribute to disease severity to a larger extent. Pediatr Pulmonol. 2012; 47:393–400. © 2011 Wiley Periodicals, Inc. url: https://doi.org/10.1002/ppul.21552 doi: 10.1002/ppul.21552 id: cord-000804-0hlj6r10 author: Brauburger, Kristina title: Forty-Five Years of Marburg Virus Research date: 2012-10-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In 1967, the first reported filovirus hemorrhagic fever outbreak took place in Germany and the former Yugoslavia. The causative agent that was identified during this outbreak, Marburg virus, is one of the most deadly human pathogens. This article provides a comprehensive overview of our current knowledge about Marburg virus disease ranging from ecology to pathogenesis and molecular biology. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3497034/ doi: 10.3390/v4101878 id: cord-003817-k3m72uxw author: Braun, Elisabeth title: Furin‐mediated protein processing in infectious diseases and cancer date: 2019-08-05 words: 9070.0 sentences: 557.0 pages: flesch: 41.0 cache: ./cache/cord-003817-k3m72uxw.txt txt: ./txt/cord-003817-k3m72uxw.txt summary: For example, avirulent Newcastle disease virus (NDV) strains harbour a monobasic cleavage site in their Fusion (F) protein and result only in local infections (mainly in the respiratory tract) since expression of the respective host proteases is limited to a few cell types. Notably, proteolytic processing of Env depends on correct N-linked glycosylation as aberrant carbohydrate side chains may result in subcellular mistrafficking or sequestration of Env. 49 Most likely, HIV-1 takes advantage of the redundancy of several proprotein convertases recognising the polybasic cleavage motif in Env. Furin, PCSK5, PCSK6 and PCSK7 have all been shown to cleave gp160 in cells, albeit with different efficiencies. 59, 60 Notably, a subset of H9N2 lowly pathogenic avian influenza A virus strains also harbour R-S-K-R↓ or R-S-R-R↓ sites that are not only cleaved by trypsin-like proteases, such as TMPRSS2 or HAT, but also by PCSKs. 61 However, their cleavage is only efficient in the presence of very high amounts of furin or upon mutation of a glycosylation site in HA. abstract: Proteolytic cleavage regulates numerous processes in health and disease. One key player is the ubiquitously expressed serine protease furin, which cleaves a plethora of proteins at polybasic recognition motifs. Mammalian substrates of furin include cytokines, hormones, growth factors and receptors. Thus, it is not surprising that aberrant furin activity is associated with a variety of disorders including cancer. Furthermore, the enzymatic activity of furin is exploited by numerous viral and bacterial pathogens, thereby enhancing their virulence and spread. In this review, we describe the physiological and pathophysiological substrates of furin and discuss how dysregulation of a simple proteolytic cleavage event may promote infectious diseases and cancer. One major focus is the role of furin in viral glycoprotein maturation and pathogenicity. We also outline cellular mechanisms regulating the expression and activation of furin and summarise current approaches that target this protease for therapeutic intervention. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6682551/ doi: 10.1002/cti2.1073 id: cord-021499-up5vftj4 author: Brayton, Cory title: Viral Infections date: 2007-09-02 words: 20925.0 sentences: 1063.0 pages: flesch: 43.0 cache: ./cache/cord-021499-up5vftj4.txt txt: ./txt/cord-021499-up5vftj4.txt summary: Depending on inoculation route, dose, strain, and age of mice, experimental infections may result in inflammation or cytomegaly with inclusion bodies in a variety of tissues, pneumonitis, myocarditis, meningoencephalitis, or splenic necrosis in susceptible strains (National Research Council, 1991; Osborn, 1982; Percy and Barthold, 2001) . Both strains are apathogenic for adult mice, but the immunosuppressive variant is more pathogenic for neonatal mice than is MMVp. Serological surveys show that the mouse is the primary natural host (Parker et al., 1970; Smith et al., 1993b; Singleton et al., 2000) , but the virus is also infective for rats, hamsters (Garant et al., 1980; Ward and Tattersall, 1982) , and Mastomys (Haag et al., 2000) during foetal development or after parenteral inoculation. Early descriptions of naturally occurring disease may have been complicated by concurrent infections such as MHV or murine rotavirus A (MuRV-A)/epizootic diarrhoea of infant mice (EDIM) virus that contributed to the severity of the lesions especially in liver, pancreas, CNS, and intestine. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7150033/ doi: 10.1016/b978-012336425-8/50076-5 id: cord-296635-8r3tm966 author: Breed, Andrew C. title: Evidence of Endemic Hendra Virus Infection in Flying-Foxes (Pteropus conspicillatus)—Implications for Disease Risk Management date: 2011-12-14 words: 4573.0 sentences: 199.0 pages: flesch: 47.0 cache: ./cache/cord-296635-8r3tm966.txt txt: ./txt/cord-296635-8r3tm966.txt summary: title: Evidence of Endemic Hendra Virus Infection in Flying-Foxes (Pteropus conspicillatus)—Implications for Disease Risk Management This study investigated the seroepidemiology of Hendra virus in a spectacled flying-fox (Pteropus conspicillatus) population in northern Australia, near the location of an equine and associated human Hendra virus infection in late 2004. Hendra virus (HeV) and Nipah virus (NiV) are paramyxoviruses of the genus Henipavirus with pteropid bats (i.e. flying-foxes; Pteropus sp., Family Pteropodidae) being the primary wildlife reservoir [1] . Henipaviruses have the potential to infect a wide range of mammalian species, and Hendra virus has spread from flying-foxes to horses in Australia on at least 20 reported separate occasions (five involving horse-human transmission), most recently in 2011 [5, 6, 7] . [14] on the infection dynamics of HeV in the little red flying-fox, Pteropus scapulatus, in the Northern Territory of Australia suggested that viral transmission may be predominantly horizontal, with pregnancy and lactation suggested as risk factors for infection. abstract: This study investigated the seroepidemiology of Hendra virus in a spectacled flying-fox (Pteropus conspicillatus) population in northern Australia, near the location of an equine and associated human Hendra virus infection in late 2004. The pattern of infection in the population was investigated using a serial cross-sectional serological study over a 25-month period, with blood sampled from 521 individuals over six sampling sessions. Antibody titres to the virus were determined by virus neutralisation test. In contrast to the expected episodic infection pattern, we observed that seroprevalence gradually increased over the two years suggesting infection was endemic in the population over the study period. Our results suggested age, pregnancy and lactation were significant risk factors for a detectable neutralizing antibody response. Antibody titres were significantly higher in females than males, with the highest titres occurring in pregnant animals. Temporal variation in antibody titres suggests that herd immunity to the virus may wax and wane on a seasonal basis. These findings support an endemic infection pattern of henipaviruses in bat populations suggesting their infection dynamics may differ significantly from the acute, self limiting episodic pattern observed with related viruses (e.g. measles virus, phocine distemper virus, rinderpest virus) hence requiring a much smaller critical host population size to sustain the virus. These findings help inform predictive modelling of henipavirus infection in bat populations, and indicate that the life cycle of the reservoir species should be taken into account when developing risk management strategies for henipaviruses. url: https://doi.org/10.1371/journal.pone.0028816 doi: 10.1371/journal.pone.0028816 id: cord-014541-2i0jga5v author: Breedlove, Byron title: The Exploding Aliveness of the World date: 2017-04-17 words: 767.0 sentences: 41.0 pages: flesch: 54.0 cache: ./cache/cord-014541-2i0jga5v.txt txt: ./txt/cord-014541-2i0jga5v.txt summary: "The exploding aliveness of the world" that fuels artistic creativity also finds full expression in dynamic microscopic realms teeming with unfathomable numbers of viruses, bacteria, fungi, prions, and protozoa that lead to an incredible variety of pathologic consequences when infecting their hosts. Those influential reports-which represent the insights of Joshua Lederberg, Robert Shope, and their colleagues-from the Institute of Medicine (now National Academy of Medicine) Committee on Emerging Microbial Threats offered far-reaching recommendations and galvanized support for research and public health action to address the challenges posed by new, emerging, and reemerging infectious diseases. The time and attention given to tending to our backyard gardens, our larger communities, our public health infrastructure, and our approach to addressing emerging infections will be apparent and on display when that inevitable exploding aliveness occurs. Emerging infections: microbial threats to health in the United States abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5367435/ doi: 10.3201/eid2304.ac2304 id: cord-027752-xcpv9k22 author: Bresalier, Michael title: Uses of a Pandemic: Forging the Identities of Influenza and Virus Research in Interwar Britain date: 2011-12-15 words: 10132.0 sentences: 753.0 pages: flesch: 56.0 cache: ./cache/cord-027752-xcpv9k22.txt txt: ./txt/cord-027752-xcpv9k22.txt summary: In May 1922, Walter Morley Fletcher, Secretary of the Medical Research Council (MRC), organized a secret meeting of pathologists at the War Office to outline a new scheme of research on ''diseases probably caused by filter-passing organisms.'' 1 Created in 1913, the MRC had used the war to apply laboratory science to military medicine. The pandemic had ignited interest in the nature of filterable viruses, however, the way forward was unclear, as Fletcher observed: ''The chief problem which the investigator of [filterable viruses] meets is the difficulty of proceeding by sound experimental methods.'' 3 The purported influenza agent was one of a group of pathogens that could not be seen with light microscopes or studied by the culture methods that had been so successful with bacteria. 11 Especially important were military pathology investigations, supported by the War Office and MRC, into the bacteriology of the pandemic and, in due course, into the role of a ''filterable virus''. abstract: This paper counters the tendency to retrospectively viralise the 1918–19 pandemic and to gloss the important historiographical point that, in Britain, such knowledge was in-the-making between 1918 and 1933. It traces the genesis of influenza's virus identity to British efforts in 1918–19 to specify the cause of the pandemic and it examines how, in the 1920s, the British Medical Research Council used the connection between a virus and the pandemic to justify the development of virus research and to make influenza a core problem around which it was organised. It shows that the organisation of medical virus research was inextricably linked to the pandemic before the actual discovery of flu virus in 1933. Recognising that the relationship between the virus and the disease itself has a history demands we rethink the pandemic's medical scientific legacy and the crucial role of virus research in shaping its history. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7313770/ doi: 10.1093/shm/hkr162 id: cord-254592-wa5il5go author: Brierley, Liam title: Tissue tropism and transmission ecology predict virulence of human RNA viruses date: 2019-11-26 words: 5887.0 sentences: 269.0 pages: flesch: 37.0 cache: ./cache/cord-254592-wa5il5go.txt txt: ./txt/cord-254592-wa5il5go.txt summary: To quantify the effects of the most informative risk factors, averaged partial dependence was extracted from the random forests, describing the marginal predicted probabilities of severe virulence associated with each virus trait (Fig 4, S2 Table) . Predicted probability of classifying virulence as ''severe'' for each of the most informative risk factors in random forest models applied to all known human RNA viruses and zoonotic viruses only (primary tissue tropism, any known neural tropism, any known renal tropism, level of human-to-human transmissibility, primary transmission route, and any known vector-borne transmission). In both classification tree and random forest models, viruses were more likely to be predicted to cause severe disease if they caused systemic infections, had neural or renal tropism, transmitted via direct contact or respiratory routes, or had limited capability to transmit between humans (0 < R 0 � 1). abstract: Novel infectious diseases continue to emerge within human populations. Predictive studies have begun to identify pathogen traits associated with emergence. However, emerging pathogens vary widely in virulence, a key determinant of their ultimate risk to public health. Here, we use structured literature searches to review the virulence of each of the 214 known human-infective RNA virus species. We then use a machine learning framework to determine whether viral virulence can be predicted by ecological traits, including human-to-human transmissibility, transmission routes, tissue tropisms, and host range. Using severity of clinical disease as a measurement of virulence, we identified potential risk factors using predictive classification tree and random forest ensemble models. The random forest approach predicted literature-assigned disease severity of test data with mean accuracy of 89.4% compared to a null accuracy of 74.2%. In addition to viral taxonomy, the ability to cause systemic infection was the strongest predictor of severe disease. Further notable predictors of severe disease included having neural and/or renal tropism, direct contact or respiratory transmission, and limited (0 < R(0) ≤ 1) human-to-human transmissibility. We present a novel, to our knowledge, comparative perspective on the virulence of all currently known human RNA virus species. The risk factors identified may provide novel perspectives in understanding the evolution of virulence and elucidating molecular virulence mechanisms. These risk factors could also improve planning and preparedness in public health strategies as part of a predictive framework for novel human infections. url: https://doi.org/10.1371/journal.pbio.3000206 doi: 10.1371/journal.pbio.3000206 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-022163-7klzsrpu author: Broder, Christopher C. title: Henipaviruses date: 2016-09-09 words: 14465.0 sentences: 688.0 pages: flesch: 46.0 cache: ./cache/cord-022163-7klzsrpu.txt txt: ./txt/cord-022163-7klzsrpu.txt summary: Central pathological features of both HeV and NiV infection in humans and several susceptible animal species is a severe systemic and often fatal neurologic and/or respiratory disease (Abdullah and Tan 2014 ; Wong and Ong 2011 ; Playford et al. A new paramyxovirus was isolated and identifi ed in 1994 in an outbreak of fatal cases of respiratory disease in horses and humans in the Brisbane suburb of Hendra, Australia, and was shown to be distantly related to measles virus and other morbilliviruses (Murray et al. HeV in nature appears less transmissible and naturally acquired infections have been observed only in bats, horses, dogs and humans; however, experimentally, HeV can infect and cause disease in guinea pigs, cats, hamsters, ferrets, mice and African green monkeys (reviewed in Geisbert et al. More recently, several viral vector-based henipavirus vaccines have also been examined in animal challenge studies; these have included immunizations using the vesicular stomatitis virus based platform (VSV) expressing either the NiV G or F glycoprotein in the hamster model (DeBuysscher et al. abstract: The first henipaviruses, Hendra virus (HeV), and Nipah virus (NiV) were pathogenic zoonoses that emerged in the mid to late 1990s causing serious disease outbreaks in livestock and humans. HeV was recognized in Australia 1994 in horses exhibiting respiratory disease along with a human case fatality, and then NiV was identified during a large outbreak of human cases of encephalitis with high mortality in Malaysia and Singapore in 1998–1999 along with respiratory disease in pigs which served as amplifying hosts. The recently identified third henipavirus isolate, Cedar virus (CedPV), is not pathogenic in animals susceptible to HeV and NiV disease. Molecular detection of additional henipavirus species has been reported but no additional isolates of virus have been reported. Central pathological features of both HeV and NiV infection in humans and several susceptible animal species is a severe systemic and often fatal neurologic and/or respiratory disease. In people, both viruses can also manifest relapsed encephalitis following recovery from an acute infection, particularly NiV. The recognized natural reservoir hosts of HeV, NiV, and CedPV are pteropid bats, which do not show clinical illness when infected. With spillovers of HeV continuing to occur in Australia and NiV in Bangladesh and India, these henipaviruses continue to be important transboundary biological threats. NiV in particular possesses several features that highlight a pandemic potential, such as its ability to infect humans directly from natural reservoirs or indirectly from other susceptible animals along with a capacity of limited human-to-human transmission. Several henipavirus animal challenge models have been developed which has aided in understanding HeV and NiV pathogenesis as well as how they invade the central nervous system, and successful active and passive immunization strategies against HeV and NiV have been reported which target the viral envelope glycoproteins. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153454/ doi: 10.1007/978-3-319-33133-1_3 id: cord-019982-hyxrgamj author: Brookfield, D.S.K. title: Viruses demonstrated in children in Tanzania: Studies in diarrhoea and measles date: 2005-04-14 words: 1906.0 sentences: 104.0 pages: flesch: 60.0 cache: ./cache/cord-019982-hyxrgamj.txt txt: ./txt/cord-019982-hyxrgamj.txt summary: authors: Brookfield, D.S.K.; Cosgrove, B.P.; Bell, E.J.; Madeley, C.R. title: Viruses demonstrated in children in Tanzania: Studies in diarrhoea and measles Causes of diarrhoea with particular reference to viral agents were investigated in 123 infants and young children in Dar es Salaam, Tanzania. The pattern of virus infection causing infantile diarrhoea was similar in Dar es Salaam to other parts of the world. The present study attempted to investigate the viruses associated with diarrhoea in Dares Salaam and, since electron microscopy was considered essential, the study was limited to the number of stools that could be sent in one consignment by air to Scotland. Examination of stools from 26 cases of measles failed to implicate any particular virus as a likely cause of the associated diarrhoea. However the diarrhoea associated with measles in Tanzanian children does not appear to be caused by any of the electron microscopically detectable viruses. abstract: Causes of diarrhoea with particular reference to viral agents were investigated in 123 infants and young children in Dar es Salaam, Tanzania. Twenty-six of the patients also had measles. Viruses were found in 52 of the 123 patients (43 per cent) and rotavirus occurred in 38 children (31 per cent). Enteroviruses were found in 10 patients, adenoviruses in nine and ‘small round virus’ in one (six patients had dual infection). Four patients died and only one of these children had viral particles in the stools. Breast milk formed part or all of the diet in 77 children (63 per cent) and virus isolation showed a similar pattern in breast fed infants and those not receiving breast milk. In 26 patients with measles only five were excreting viruses in their stools. Therefore no strong evidence was found to link the diarrhoea associated with measles in Tanzanian children to any particular virus. The pattern of virus infection causing infantile diarrhoea was similar in Dar es Salaam to other parts of the world. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133693/ doi: 10.1016/s0163-4453(79)91285-4 id: cord-002410-2zi5iv2t author: Bruening, Janina title: The Role of Type III Interferons in Hepatitis C Virus Infection and Therapy date: 2017-02-01 words: 6696.0 sentences: 374.0 pages: flesch: 44.0 cache: ./cache/cord-002410-2zi5iv2t.txt txt: ./txt/cord-002410-2zi5iv2t.txt summary: Among the three classes of IFNs, type III IFNs, also called IFN lambdas (IFNLs), are an essential component of the innate immune response to hepatitis C virus (HCV). Here, we will review our current knowledge on IFNL gene expression, protein properties, signaling, ISG induction, and its implications on HCV infection and treatment. Type III IFNs and ISGs are similarly inducted upon HCV infection of primary human fetal liver cells [98, 99] . In summary, expression of specific IFNL subtypes is induced in PHH and some hepatoma cell lines upon infection with HCV, resulting in limiting virus production. Viral infection and toll-like receptor agonists induce a differential expression of type I and interferons in humans plasmacytoid and monocyte-derived dendritic cells HepG2 cells mount an effective antiviral interferon-lambda based innate immune response to hepatitis C virus infection HCV infection induces a unique hepatic innate immune response associated with robust production of type III interferons abstract: The human interferon (IFN) response is a key innate immune mechanism to fight virus infection. IFNs are host-encoded secreted proteins, which induce IFN-stimulated genes (ISGs) with antiviral properties. Among the three classes of IFNs, type III IFNs, also called IFN lambdas (IFNLs), are an essential component of the innate immune response to hepatitis C virus (HCV). In particular, human polymorphisms in IFNL gene loci correlate with hepatitis C disease progression and with treatment response. To date, the underlying mechanisms remain mostly elusive; however it seems clear that viral infection of the liver induces IFNL responses. As IFNL receptors show a more restricted tissue expression than receptors for other classes of IFNs, IFNL treatment has reduced side effects compared to the classical type I IFN treatment. In HCV therapy, however, IFNL will likely not play an important role as highly effective direct acting antivirals (DAA) exist. Here, we will review our current knowledge on IFNL gene expression, protein properties, signaling, ISG induction, and its implications on HCV infection and treatment. Finally, we will discuss the lessons learnt from the HCV and IFNL field for virus infections beyond hepatitis C. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5309426/ doi: 10.1155/2017/7232361 id: cord-023584-yaxawqhj author: Bucknall, R.A. title: The Continuing Search for Antiviral Drugs date: 2008-04-10 words: 8497.0 sentences: 339.0 pages: flesch: 48.0 cache: ./cache/cord-023584-yaxawqhj.txt txt: ./txt/cord-023584-yaxawqhj.txt summary: Of course, if wide-spectrum leads appear, the choice of test virus may be irrelevant, but the antiviral compounds (as distinct from interferon inducers) known at present are characterized by their relatively limited spectrum of activity, e.g., methisazone is active only against poxviruses (Bauer and Sadler, 1960) and possibly adenoviruses (Bauer and Apostolov, 1966) ; l-aminoadamantane is active only against influenza A1 and As and not against other myxo-or paramyxoviruses (Davies et al., 1964) ; guanidine and a-hydroxybenzyl benzimidazole are active only against picornaviruses and not against other small ribonucleic acid (RNA) viruses (Eggers and Tamm, 1961) . In summary, a tissue culture screen should be able to proccss large numbers of tcst compounds, using viruses as relevant as possible to the diseases for which a drug is required, and should employ normal rather than neoplastic cells. abstract: This chapter discusses the continuing search for antiviral drugs. Many virus diseases, both of humans and animals, have been successfully controlled by vaccines. These successes have naturally led to improvements in the spectrum and duration of protection offered by vaccines until, at present it is difficult to see how antiviral drugs could compete with vaccines in the control of many virus diseases. One may cite smallpox, yellow fever, polio, and recently measles among human diseases, Newcastle disease, Marek's disease, and infectious bronchitis among poultry diseases—an area of veterinary disease control where vaccines have been particularly important. Research into the treatment of virus diseases by drugs is at present directed toward three general areas: (1) attempts to stimulate the defense mechanism of the host animal, (2) large screening programs to find drugs which directly block some virus-specific process, and (3) alleviation of the symptoms of the disease. The treatment of the symptoms, rather than the cause of a disease, has been the mainstay of medical practice from time immemorial, and this is still the case with most virus disease. The short incubation period of many virus diseases will inevitably restrict the therapeutic use of antiviral drugs and in cases where symptoms have already appeared. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172480/ doi: 10.1016/s1054-3589(08)60460-3 id: cord-171099-d0qr84xg author: Buehler, Markus J. title: Nanomechanical sonification of the 2019-nCoV coronavirus spike protein through a materiomusical approach date: 2020-03-30 words: 4509.0 sentences: 205.0 pages: flesch: 46.0 cache: ./cache/cord-171099-d0qr84xg.txt txt: ./txt/cord-171099-d0qr84xg.txt summary: Presenting musical encoding in two versions one in the amino-acid scale and one based on equal temperament tuning the method allows for expressing protein structures in audible space, offering novel avenues to represent, analyze and design architectural features across lengthand time-scales. We further report a hierarchical frequency spectrum analysis of five distinct protein structures, which offer insights into how genetic mutations, and the binding of the virus spike protein to the human ACE2 cell receptor directly influence the audio. What you hear is a multi-layered algorithmic composition featuring both the vibrational spectrum of the entire protein (expressed in sound and rhythmic elements), the sequence and folding of amino acids that compose the virus spike structure, as well as interwoven melodiesforming counterpoint music -reflecting the complex hierarchical intersecting geometry of the protein. abstract: Proteins are key building blocks of virtually all life, providing the material foundation of spider silk, cells, and hair, but also offering other functions from enzymes to drugs, and pathogens like viruses. Based on a nanomechanical analysis of the structure and motions of atoms and molecules at multiple scales, we report sonified versions of the coronavirus spike protein of the pathogen of COVID-19, 2019-nCoV. The audio signal, created using a novel nanomechanical sonification method, features an overlay of the vibrational signatures of the protein's primary, secondary and higher-order structures. Presenting musical encoding in two versions - one in the amino-acid scale and one based on equal temperament tuning - the method allows for expressing protein structures in audible space, offering novel avenues to represent, analyze and design architectural features across length- and time-scales. We further report a hierarchical frequency spectrum analysis of five distinct protein structures, which offer insights into how genetic mutations, and the binding of the virus spike protein to the human ACE2 cell receptor directly influence the audio. Applications of the approach may include the development of de novo antibodies by designing protein sequences that match, through melodic counterpoints, the binding sites in the spike protein. Other applications of audible coding of matter include material design by manipulating sound, detecting mutations, and offering a way to reach out to broader communities to explain the physics of proteins. It also forms a physics-based compositional technique to create new art, referred to as materiomusic, which is akin to finding a new palette of colors for a painter. Here, the nanomechanical structure of matter, reflected in an oscillatory framework, presents a new palette for sound generation, and can complement or support human creativity. url: https://arxiv.org/pdf/2003.14258v1.pdf doi: nan id: cord-337361-salby0fu author: Bujarski, Jozef J. title: Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives date: 2013-03-26 words: 6863.0 sentences: 335.0 pages: flesch: 39.0 cache: ./cache/cord-337361-salby0fu.txt txt: ./txt/cord-337361-salby0fu.txt summary: In some viruses, the frequency of homologous crossing-over is very high and practically every replicated viral RNA molecule can be considered as chimerical in nature, as we have demonstrated for brome mosaic virus (BMV) RNAs (Urbanowicz et al., 2005) . The generally accepted mechanism of RNA recombination is currently explained by a copy-choice model where the viral RNA polymerase (RdRp) complex in mRNA viruses [reverse transcriptase (RT) in retroviruses] changes templates during synthesis of the nascent strand (Galetto et al., 2006) . Among the factors known to promote replicase to switch are sequence homologies between recombination substrates along with secondary structures at the crossover sites, as demonstrated with the BMV and other systems (Figlerowicz and Bujarski, 1998; Nagy et al., 1999b) . Comparison among three plant RNA virus replication systems (TBSV, BMV, and dianthoviruses) reveals general patterns within the stepwise process of viral replicase complex assembly which requires concerted involvement of protein-protein, RNA-protein, and protein-lipid interactions (Mine and Okuno, 2012) . abstract: RNA recombination is one of the driving forces of genetic variability in (+)-strand RNA viruses. Various types of RNA–RNA crossovers were described including crosses between the same or different viral RNAs or between viral and cellular RNAs. Likewise, a variety of molecular mechanisms are known to support RNA recombination, such as replicative events (based on internal or end-to-end replicase switchings) along with non-replicative joining among RNA fragments of viral and/or cellular origin. Such mechanisms as RNA decay or RNA interference are responsible for RNA fragmentation and trans-esterification reactions which are likely accountable for ligation of RNA fragments. Numerous host factors were found to affect the profiles of viral RNA recombinants and significant differences in recombination frequency were observed among various RNA viruses. Comparative analyses of viral sequences allowed for the development of evolutionary models in order to explain adaptive phenotypic changes and co-evolving sites. Many questions remain to be answered by forthcoming RNA recombination research. (1) How various factors modulate the ability of viral replicase to switch templates, (2) What is the intracellular location of RNA–RNA template switchings, (3) Mechanisms and factors responsible for non-replicative RNA recombination, (4) Mechanisms of integration of RNA viral sequences with cellular genomic DNA, and (5) What is the role of RNA splicing and ribozyme activity. From an evolutionary stand point, it is not known how RNA viruses parasitize new host species via recombination, nor is it obvious what the contribution of RNA recombination is among other RNA modification pathways. We do not understand why the frequency of RNA recombination varies so much among RNA viruses and the status of RNA recombination as a form of sex is not well documented. url: https://www.ncbi.nlm.nih.gov/pubmed/23533000/ doi: 10.3389/fpls.2013.00068 id: cord-016309-6mw8okmt author: Bule, Mohammed title: Antivirals: Past, Present and Future date: 2019-06-06 words: 8200.0 sentences: 405.0 pages: flesch: 36.0 cache: ./cache/cord-016309-6mw8okmt.txt txt: ./txt/cord-016309-6mw8okmt.txt summary: Those included usage restricted to a single virus and specific animal species, problems with high spectrum activity and low cytotoxicity, high costs of development of new chemical compounds and absence of rapid diagnostic techniques allowing prompt use of a specific antiviral agent in the course of an acute infection (Rollinson 1992a, b) . Nevertheless, several licensed human antiviral agents are being used with cascade principle for treatment of animal diseases (e.g. acyclovir, idoxuridine and trifluridine against feline herpesvirus-1 ocular infection in cats) (Thiry et al. The discovery of PAA (Fig. 22.4) as an antiviral drug gave rise to intense research on its biological activities, which demonstrated PAA and its derivatives'' ability to inhibit the replication of a number of viruses such as immunodeficiency, hepatitis and herpes viruses. To conclude with, equine herpesvirus type 1 (EHV-1) infection causes outbreak of respiratory and various neurological diseases in horses, against which acyclovir and valacyclovir are the most common drugs, but also IFN targeting IFNGR complex as a key mediator of virus-specific cellular immunity (Poelaert et al. abstract: The uses of antiviral agents are increasing in the new era along with the development of vaccines for the effective control of viral diseases. The main aims of antiviral agents are to minimize harm to the host system and eradicate deadly viral diseases. However, the replications of viruses in host system represent a massive therapeutic challenge than bacteria and fungi. Antiviral drugs not just penetrate to disrupt the virus’ cellular divisions but also have a negative impact on normal physiological pathways in the host. Due to these issues, antiviral agents have a narrow therapeutic index than antibacterial drugs. Nephrotoxicity is the main adverse reaction of antiviral drugs in human and animals. In this chapter, we summarize the antiviral agents’ past, present and future perspectives with the main focus on the brief history of antiviral in animals, miscellaneous drugs, natural products, herbal and repurposing drugs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120554/ doi: 10.1007/978-981-13-9073-9_22 id: cord-262776-6k7tcgfs author: Burnouf, Thierry title: Assessment of the viral safety of antivenoms fractionated from equine plasma date: 2004-09-30 words: 8211.0 sentences: 417.0 pages: flesch: 43.0 cache: ./cache/cord-262776-6k7tcgfs.txt txt: ./txt/cord-262776-6k7tcgfs.txt summary: Analysis of production parameters indicate that acid pH treatments and caprylic acid precipitations, which have been validated for the manufacture of some human IgG products, appear to provide the best potential for viral inactivation of antivenoms. Among those, caprylic acid and low pH treatments, both of which are commonly used also for the purification of antivenom IgG, have been shown to contribute to the viral safety of human plasma IgG products as described below. It should be kept in mind that treatment of whole plasma or crude fractions, as is the case for equine antivenoms production, may lead to lower rate and kinetics of viral inactivation, due to the high endogenous lipid content, as found in a study that evaluated the virucidal effect of sodium oleate [85] . However, a comparison with validated manufacturing processes used for human IgG clearly indicates that at least two widely used antivenom production steps, caprylic acid treatment and low-pH incubation, are likely to contribute in a robust manner to viral safety, at least against enveloped viruses. abstract: Abstract Antivenoms are preparations of intact or fragmented (F(ab′)2 or Fab) immunoglobulin G (IgG) used in human medicine to treat the severe envenomings resulting from the bites and stings of various animals, such as snakes, spiders, scorpions, or marine animals, or from the contact with poisonous plants. They are obtained by fractionating plasma collected from immunized horses or, less frequently, sheep. Manufacturing processes usually include pepsin digestion at acid pH, papain digestion, ammonium sulphate precipitation, caprylic acid precipitation, heat coagulation and/or chromatography. Most production processes do not have deliberately introduced viral inactivation or removal treatments, but antivenoms have never been found to transmit viruses to humans. Nevertheless, the recent examples of zoonotic diseases highlight the need to perform a careful assessment of the viral safety of antivenoms. This paper reviews the characteristics of equine viruses of antivenoms and discusses the potential of some manufacturing steps to avoid risks of viral contamination. Analysis of production parameters indicate that acid pH treatments and caprylic acid precipitations, which have been validated for the manufacture of some human IgG products, appear to provide the best potential for viral inactivation of antivenoms. As many manufacturers of antivenoms located in developing countries lack the resources to conduct formal viral validation studies, it is hoped that this review will help in the scientific understanding of the viral safety factors of antivenoms, in the controlled implementation of the manufacturing steps with expected impact on viral safety, and in the overall reinforcement of good manufacturing practices of these essential therapeutic products. url: https://www.sciencedirect.com/science/article/pii/S1045105604000223 doi: 10.1016/j.biologicals.2004.07.001 id: cord-355913-fhvt1ht1 author: Burrell, Christopher J. title: Virus Replication date: 2016-11-11 words: 9861.0 sentences: 405.0 pages: flesch: 42.0 cache: ./cache/cord-355913-fhvt1ht1.txt txt: ./txt/cord-355913-fhvt1ht1.txt summary: Little is known about what determines whether a given picornavirus positive-sense RNA molecule will be directed (1) to a replication complex (a structure bound to smooth endoplasmic reticulum), where it serves as template for transcription by RNA-dependent RNA polymerase into negative-sense RNA, or (2) to a ribosome, where it serves as mRNA for translation into protein, or (3) to a procapsid, with which it associates to form a virion. In the case of positive-sense single-stranded RNA viruses, the incoming RNA genome can bind directly to ribosomes and be translated in full or in part without the need for any prior transcription; all other forms of incoming viral RNA must first be transcribed to produce mRNA, in order to begin the process of expression of the infecting viral genome. abstract: Understanding the molecular events accompanying virus replication is essential for the proper understanding and control of all virus diseases. The virus replication cycle generates new viral genomes and proteins in sufficient quantities to ensure propagation of the viral genome; this requires that the extracellular viral genome is protected from enzymatic degradation and can be introduced into further target cells for further rounds of replication. The initial recognition between virus and host is more complex than originally supposed and may involve more than one cellular receptor. A critical first intracellular step is the generation of viral mRNA by one of a limited number of strategies first described by David Baltimore. Lacking ribosomes, viruses have no means of producing protein and are reliant on the host cell for protein synthesis. Viral proteins are often modified by host cell glycosylation during or after virus assembly. Temporal regulation of intracellular events is critical in all but the very simplest of viruses, and some form of suppression of the host innate immune response is common to nearly all human viruses. Infected cells often produce non-infectious particles with incomplete genomes, and these defective interfering particles may play a role in pathogenesis. Understanding these processes will open up a range of targets for the development of novel therapies. url: https://api.elsevier.com/content/article/pii/B9780123751560000047 doi: 10.1016/b978-0-12-375156-0.00004-7 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-323683-9h9mld6x author: Butler, M. title: Virus Removal by Disinfection of Effluents date: 2013-11-17 words: 6655.0 sentences: 288.0 pages: flesch: 45.0 cache: ./cache/cord-323683-9h9mld6x.txt txt: ./txt/cord-323683-9h9mld6x.txt summary: The removal of viruses from sludges has only relatively recently attracted serious attention (Cliver, 1975; Berg, 1978; Osborn and Hattingh, 1978) but for effluents, various procedures have been adopted for some time, particularly disinfection with chlorine, a treatment now under critical review. Although many different enteric viruses are likely to be present in wastewater, the risks of transmission of infection via contaminated water in developed countries by various routes (Fig. 1 ) is thought to be slight although probably increasing, but elsewhere the risks may be very great indeed (WHO, 1976) . 4. The methods available for the inactivation of viruses in effluent differ little in principle from those applied to potable water, but are distinct from the disinfection of viruses contaminating, laboratory or medical equipment, where highly toxic chemicals like detergents, phenols, formaldehyde or permanganate may be used (Spalding et al 1977) . abstract: The safe disposal of effluents can present a major problem to large urban communities because of their inevitable content of potentially pathogenic enteric viruses. At least one hundred types of virus may be present although many of these are difficult or even impossible to characterise under these conditions. Wastewater treatment does not greatly effect the survival of many enteric viruses and some survive well even after effluent disposal. The use of disinfectants for the inactivation of virus in effluent is practicable but requires careful manipulation in order to avoid the disemination of byproducts toxic to man or capable of interferring with the ecology of the receiving waters or soils. No one system is likely to be either universally acceptable because of the variable quality of effluents and much research remains to be done before guidelines can be recommended or established. url: https://www.sciencedirect.com/science/article/pii/B9780080264011500257 doi: 10.1016/b978-0-08-026401-1.50025-7 id: cord-297960-4x1j0iqg author: Bösl, Korbinian title: Common Nodes of Virus–Host Interaction Revealed Through an Integrated Network Analysis date: 2019-10-04 words: 5482.0 sentences: 301.0 pages: flesch: 44.0 cache: ./cache/cord-297960-4x1j0iqg.txt txt: ./txt/cord-297960-4x1j0iqg.txt summary: Furthermore, we performed an interactome-informed drug re-purposing screen and identified novel activities for broad-spectrum antiviral agents against hepatitis C virus and human metapneumovirus. Furthermore, we performed an interactome-informed drug re-purposing screen and identified novel activities for broad-spectrum antiviral agents against hepatitis C virus and human metapneumovirus. Global systems-level approaches including functional RNAi screens, interactome mapping technologies such as affinity-purification mass spectrometry (AP-MS), quantitative proteomics, and CRISPR/Cas9-based screens have provided unparalleled details and insights into the dynamics of host proteome in immune cells (21) (22) (23) (24) , host-virus interactome (15-17, 25, 26) , and also identified important host dependency factors of various viruses (25, 27, 28) . We hypothesized that combining a meta-analysis of host-virus protein-protein interactions of multiple viruses and functional RNAi screens would provide novel insights for developing broadspectrum antiviral strategies. High-Definition analysis of host protein stability during human cytomegalovirus infection reveals antiviral factors and viral evasion mechanisms abstract: Viruses are one of the major causes of acute and chronic infectious diseases and thus a major contributor to the global burden of disease. Several studies have shown how viruses have evolved to hijack basic cellular pathways and evade innate immune response by modulating key host factors and signaling pathways. A collective view of these multiple studies could advance our understanding of virus-host interactions and provide new therapeutic perspectives for the treatment of viral diseases. Here, we performed an integrative meta-analysis to elucidate the 17 different host-virus interactomes. Network and bioinformatics analyses showed how viruses with small genomes efficiently achieve the maximal effect by targeting multifunctional and highly connected host proteins with a high occurrence of disordered regions. We also identified the core cellular process subnetworks that are targeted by all the viruses. Integration with functional RNA interference (RNAi) datasets showed that a large proportion of the targets are required for viral replication. Furthermore, we performed an interactome-informed drug re-purposing screen and identified novel activities for broad-spectrum antiviral agents against hepatitis C virus and human metapneumovirus. Altogether, these orthogonal datasets could serve as a platform for hypothesis generation and follow-up studies to broaden our understanding of the viral evasion landscape. url: https://doi.org/10.3389/fimmu.2019.02186 doi: 10.3389/fimmu.2019.02186 id: cord-003993-3bozjfv7 author: Cagliani, Rachele title: Mode and tempo of human hepatitis virus evolution date: 2019-10-25 words: 7845.0 sentences: 400.0 pages: flesch: 40.0 cache: ./cache/cord-003993-3bozjfv7.txt txt: ./txt/cord-003993-3bozjfv7.txt summary: Technological advances that allow throughput sequencing of viral genomes, as well as the development of computational tools to analyze such genome data, have largely expanded our knowledge on the host range and evolutionary history of human hepatitis viruses. This finding, as well as the increasing availability of the genome sequences of human-infecting viruses sampled across different geographic areas, has largely expanded our knowledge about the genetic diversity and evolutionary origin of these human pathogens. Studies that did not account for the TDRP provided estimates of the time to the most recent common ancestor (TMRCA) of HCV genotypes in a range between $200 and 1000 years ago [63, 64, 76, 87, 88] ; the origin of the horse virus was dated around 1800 CE [85] . Although several human hepatitis E cases have a zoonotic origin and orthohepeviruses A are found in diverse mammals, recent data indicated that one or more reverse zoonoses led to the emergence and radiation of HEV genotypes [121] . abstract: Human viral hepatitis, a major cause of morbidity and mortality worldwide, is caused by highly diverse viruses with different genetic, ecological, and pathogenetic features. Technological advances that allow throughput sequencing of viral genomes, as well as the development of computational tools to analyze such genome data, have largely expanded our knowledge on the host range and evolutionary history of human hepatitis viruses. Thus, with the exclusion of hepatitis D virus, close or distant relatives of these human pathogens were identified in a number of domestic and wild mammals. Also, sequences of human viral strains isolated from different geographic locations and over different time-spans have allowed the application of phylogeographic and molecular dating approaches to large viral phylogenies. In this review, we summarize the most recent insights into our understanding of the evolutionary events and ecological contexts that determined the origin and spread of human hepatitis viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6872792/ doi: 10.1016/j.csbj.2019.09.007 id: cord-290539-8ak2tths author: Cagno, Valeria title: Novel broad spectrum virucidal molecules against enveloped viruses date: 2018-12-07 words: 5524.0 sentences: 276.0 pages: flesch: 51.0 cache: ./cache/cord-290539-8ak2tths.txt txt: ./txt/cord-290539-8ak2tths.txt summary: To further elucidate the mechanism of action we performed a virucidal assay in which 9d was incubated with the virus at 10 μM 5μM or 1μM concentration for different times (Fig 6A) or for 1h with serial dilutions of compound ( Fig 6B) ; subsequently, the mixture was titrated on cells and the viral titer was evaluated at dilutions at which the compound concentration was known not to be active in plaquing efficiency assays. The irreversibility of the mechanism was also tested with an assay in which the compound was incubated with the virus for 1h and subsequently the mixture has been diluted in drug free medium for additional 1, 2, 3 or 4 hours before the addition on cells (S2 Fig) . abstract: Viral infections are an important cause of death worldwide. Unfortunately, there is still a lack of antiviral drugs or vaccines for a large number of viruses, and this represents a remarkable challenge particularly for emerging and re-emerging viruses. For this reason, the identification of broad spectrum antiviral compounds provides a valuable opportunity for developing efficient antiviral therapies. Here we report on a class of rhodanine and thiobarbituric derivatives displaying a broad spectrum antiviral activity against seven different enveloped viruses including an HSV-2 acyclovir resistant strain with favorable selectivity indexes. Due to their selective action on enveloped viruses and to their lipid oxidation ability, we hypothesize a mechanism on the viral envelope that affects the fluidity of the lipid bilayer, thus compromising the efficiency of virus-cell fusion and preventing viral entry. url: https://doi.org/10.1371/journal.pone.0208333 doi: 10.1371/journal.pone.0208333 id: cord-286219-qcx5ehnh author: Calistri, Arianna title: The Ubiquitin-Conjugating System: Multiple Roles in Viral Replication and Infection date: 2014-05-06 words: 10182.0 sentences: 498.0 pages: flesch: 41.0 cache: ./cache/cord-286219-qcx5ehnh.txt txt: ./txt/cord-286219-qcx5ehnh.txt summary: In this review we will present several examples of the complex interplay that links viruses and the ubiquitin conjugation machinery, with a special focus on the mechanisms evolved by the human immunodeficiency virus to escape from cellular restriction factors and to exit from infected cells. Furthermore, small DNA viruses with known oncogenic activity, such as the human papillomavirus (HPV), adenoviruses and polyomaviruses, take control of the cell cycle by usurping specific cellular Ub ligase complexes to target crucial cell cycle regulators such as p53 and the protein of the retinoblastoma (pRB) for degradation [58] . In addition to this important function, which is likely required for proper trafficking and maturation of the viral envelope glycoproteins, Vpu has been more recently characterized for yet another crucial role, connected with the ability of the virus to evade a specific IFN-1 induced antiviral factor: the B cell stromal factor 2 (BST-2) or tetherin. abstract: Through the combined action of ubiquitinating and deubiquitinating enzymes, conjugation of ubiquitin to a target protein acts as a reversible post-translational modification functionally similar to phosphorylation. Indeed, ubiquitination is more and more recognized as a central process for the fine regulation of many cellular pathways. Due to their nature as obligate intracellular parasites, viruses rely on the most conserved host cell machineries for their own replication. Thus, it is not surprising that members from almost every viral family are challenged by ubiquitin mediated mechanisms in different steps of their life cycle and have evolved in order to by-pass or exploit the cellular ubiquitin conjugating system to maximize their chance to establish a successful infection. In this review we will present several examples of the complex interplay that links viruses and the ubiquitin conjugation machinery, with a special focus on the mechanisms evolved by the human immunodeficiency virus to escape from cellular restriction factors and to exit from infected cells. url: https://doi.org/10.3390/cells3020386 doi: 10.3390/cells3020386 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-023724-5at0rhqk author: Cann, Alan J. title: Infection date: 2015-07-24 words: 14979.0 sentences: 755.0 pages: flesch: 48.0 cache: ./cache/cord-023724-5at0rhqk.txt txt: ./txt/cord-023724-5at0rhqk.txt summary: The problems plant viruses face in initiating infections of host cells have already been described (Chapter 4), as has the fact that no known plant virus employs a specific cellular receptor of the types that animal and bacterial viruses use to attach to cells. There are probably many different mechanisms involved in systemic resistance, but in general terms there is a tendency of these processes to increase local necrosis when substances such as proteases and peroxidases are produced by the plant to destroy the virus and to prevent its spread and subsequent systemic infection. Virus-resistant plants have been created by the production of transgenic plants expressing recombinant virus proteins or nucleic acids which interfere with virus replication without producing the pathogenic consequences of infection, for example: I Virus coat proteins, which have a variety of complex effects, including inhibition of virus uncoating and interference of expression of the virus at the level of RNA ("gene silencing" by "untranslatable" RNAs), I Intact or partial virus replicases which interfere with genome replication, I Antisense RNAs, I Defective virus genomes, I Satellite sequences (see Chapter 8), I Catalytic RNA sequences (ribozymes), I Modified movement proteins. abstract: Virus infection of higher organisms is the cumulative result of all the processes of replication and gene expression described in the previous chapters. Together, these determine the overall course of each infection. Infections range in complexity and duration from a very brief, superficial interaction between the virus and its host to infections that may span the entire life of the host organism, from before birth to its eventual death. A common misconception is that virus infection inevitably results in disease. In reality, the reverse is true—only a small minority of virus infections gives rise to any disease symptoms. This chapter provides an overview of the numerous patterns of virus infection and forms an introduction to the discussion of virus pathogenesis in Chapter 7. Unlike previous and subsequent chapters, this chapter deals primarily with the interaction of viruses with intact organisms rather than with the molecular biologist’s usual concern about the interaction between a virus and the cell. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173531/ doi: 10.1016/b978-0-12-801946-7.00006-7 id: cord-277392-s0bldxg9 author: Cann, Alan J. title: Replication date: 2012-02-29 words: 7934.0 sentences: 376.0 pages: flesch: 49.0 cache: ./cache/cord-277392-s0bldxg9.txt txt: ./txt/cord-277392-s0bldxg9.txt summary: This simple step is the key to the entire experiment, because it effectively synchronizes the infection of the cells and allows the subsequent phases of replication in a population of individual cells and virus particles to be viewed as if they were a single interaction (in much the same way that molecular cloning of nucleic acids allows analysis of populations of nucleic acid molecules as single species). (At the time, it was generally believed that proteins, which consist of a much more complex mixture of more than 20 different amino acids, were the carriers of the genes and that DNA was probably a structural component of cells and viruses.) Together, these two experiments illustrate the essential processes of virus replication. n Fusion of the virus envelope (so this is only applicable to enveloped viruses) with the cell membrane, either directly at the cell surface or following endocytosis in a cytoplasmic vesicle (Figure 4.12) , which requires the presence of a specific fusion protein in the virus envelopedfor example, influenza hemagglutinin or retrovirus transmembrane (TM) glycoproteins. abstract: This chapter begins with an overview of virus replication, and explains how studying bacteriophages has helped understand more complex viruses that are harder to work with, and then explains the processes involved in virus replication step by step. The virus replication involves three broad essential stages carried out by all types of viruses: the initiation of infection, replication and expression of the genome, and the release of mature virions from the infected cell. At a detailed level, there are many differences in the replication processes of different viruses that are imposed by the biology of the host cell and the nature of the virus genome. The other stages that have been discussed are: attachment, penetration, uncoating, genome replication, gene expression, assembly, maturation, and release. The chapter illustrates similarities in the pattern of replication of different viruses. Regardless of their hosts, all viruses must undergo each of these stages in some form to successfully complete their replication cycles. url: https://www.sciencedirect.com/science/article/pii/B9780123849397100043 doi: 10.1016/b978-0-12-384939-7.10004-3 id: cord-203232-1nnqx1g9 author: Canturk, Semih title: Machine-Learning Driven Drug Repurposing for COVID-19 date: 2020-06-25 words: 5023.0 sentences: 257.0 pages: flesch: 52.0 cache: ./cache/cord-203232-1nnqx1g9.txt txt: ./txt/cord-203232-1nnqx1g9.txt summary: Using the National Center for Biotechnology Information virus protein database and the DrugVirus database, which provides a comprehensive report of broad-spectrum antiviral agents (BSAAs) and viruses they inhibit, we trained ANN models with virus protein sequences as inputs and antiviral agents deemed safe-in-humans as outputs. Using sequences for SARS-CoV-2 (the coronavirus that causes COVID-19) as inputs to the trained models produces outputs of tentative safe-in-human antiviral candidates for treating COVID-19. For Experiment II, we split the data on virus species, meaning the models were forced to predict drugs for a species that it was not trained on, and have to detect peptide substructures in the amino-acid sequences to suggest drugs. In post-processing, we applied a threshold to the sigmoid function outputs of the neural network, where we assigned each drug a probability of being a potential antiviral for a given amino acid sequence. abstract: The integration of machine learning methods into bioinformatics provides particular benefits in identifying how therapeutics effective in one context might have utility in an unknown clinical context or against a novel pathology. We aim to discover the underlying associations between viral proteins and antiviral therapeutics that are effective against them by employing neural network models. Using the National Center for Biotechnology Information virus protein database and the DrugVirus database, which provides a comprehensive report of broad-spectrum antiviral agents (BSAAs) and viruses they inhibit, we trained ANN models with virus protein sequences as inputs and antiviral agents deemed safe-in-humans as outputs. Model training excluded SARS-CoV-2 proteins and included only Phases II, III, IV and Approved level drugs. Using sequences for SARS-CoV-2 (the coronavirus that causes COVID-19) as inputs to the trained models produces outputs of tentative safe-in-human antiviral candidates for treating COVID-19. Our results suggest multiple drug candidates, some of which complement recent findings from noteworthy clinical studies. Our in-silico approach to drug repurposing has promise in identifying new drug candidates and treatments for other viruses. url: https://arxiv.org/pdf/2006.14707v1.pdf doi: nan id: cord-002728-6oyw5sqv author: Carding, S. R. title: Review article: the human intestinal virome in health and disease date: 2017-09-04 words: 4362.0 sentences: 250.0 pages: flesch: 40.0 cache: ./cache/cord-002728-6oyw5sqv.txt txt: ./txt/cord-002728-6oyw5sqv.txt summary: 2 With the advent of new, sequence-based technologies that do not rely on the ability to isolate viruses for their identification, it is now possible to define and characterise viruses in different environmental samples in greater detail than ever before, which has resulted in an increased interest in the role the viral assemblage of the human gut microbiota plays in health and disease. The genetic content of VLPs comprising bacteriophages (phages) that infect bacteria and archaea and, to a much lesser extent, human-, plant-, amoebae-and animal-infecting viruses found along the GI tract constitute the human intestinal virome (Figure 1 ). Analyses of metagenomic sequence data provide detailed information on phage-host and phage-phage competition within the human faecal microbiome, implying CRISPR spacers are actively and continuously acquired by prokaryotes in response to the presence of phages in the GI tract. abstract: BACKGROUND: The human virome consists of animal‐cell viruses causing transient infections, bacteriophage (phage) predators of bacteria and archaea, endogenous retroviruses and viruses causing persistent and latent infections. High‐throughput, inexpensive, sensitive sequencing methods and metagenomics now make it possible to study the contribution dsDNA, ssDNA and RNA virus‐like particles make to the human virome, and in particular the intestinal virome. AIM: To review and evaluate the pioneering studies that have attempted to characterise the human virome and generated an increased interest in understanding how the intestinal virome might contribute to maintaining health, and the pathogenesis of chronic diseases. METHODS: Relevant virome‐related articles were selected for review following extensive language‐ and date‐unrestricted, electronic searches of the literature. RESULTS: The human intestinal virome is personalised and stable, and dominated by phages. It develops soon after birth in parallel with prokaryotic communities of the microbiota, becoming established during the first few years of life. By infecting specific populations of bacteria, phages can alter microbiota structure by killing host cells or altering their phenotype, enabling phages to contribute to maintaining intestinal homeostasis or microbial imbalance (dysbiosis), and the development of chronic infectious and autoimmune diseases including HIV infection and Crohn's disease, respectively. CONCLUSIONS: Our understanding of the intestinal virome is fragmented and requires standardised methods for virus isolation and sequencing to provide a more complete picture of the virome, which is key to explaining the basis of virome‐disease associations, and how enteric viruses can contribute to disease aetiologies and be rationalised as targets for interventions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5656937/ doi: 10.1111/apt.14280 id: cord-342277-v6310fjh author: Carducci, A. title: Environmental survey to assess viral contamination of air and surfaces in hospital settings date: 2011-01-31 words: 3031.0 sentences: 166.0 pages: flesch: 46.0 cache: ./cache/cord-342277-v6310fjh.txt txt: ./txt/cord-342277-v6310fjh.txt summary: The aim of this study was to monitor surfaces and air in hospital settings to reveal the presence of hepatitis C virus, human adenovirus, norovirus, human rotavirus and torque teno virus by nucleic acid assays, in parallel with measurements of total bacterial count and haemoglobin presence. Moreover, viral agents transmitted via the faecaleoral route, such as rotavirus, human adenovirus 40 and 41 and norovirus, are frequently associated with healthcare setting infections spread by air, hand and surface contamination. The nucleic acids extracted from samples were analysed according to published protocols of nested (RT)ePCR to detect and distinguish the target viruses: the primers, virus genome regions and reaction conditions are reported in Table I . Although this is particularly true for viruses, where detection on surfaces and in air is very difficult, the low reliability of bacterial counts as indicators of viral contamination, suggests studying alternative parameters for assessing virological safety. abstract: The presence of pathogenic viruses in healthcare settings represents a serious risk for both staff and patients. Direct viral detection in the environment poses significant technical problems and the indirect indicators currently in use suffer from serious limitations. The aim of this study was to monitor surfaces and air in hospital settings to reveal the presence of hepatitis C virus, human adenovirus, norovirus, human rotavirus and torque teno virus by nucleic acid assays, in parallel with measurements of total bacterial count and haemoglobin presence. In total, 114 surface and 62 air samples were collected. Bacterial contamination was very low (<1 cfu/cm(2)) on surfaces, whereas the ‘medium’ detected value in air was 282 cfu/m(3). Overall, 19 (16.7%) surface samples tested positive for viral nucleic acids: one for norovirus, one for human adenovirus and 17 (14.9%) for torque teno virus (TTV). Only this latter virus was directly detected in 10 air samples (16.1%). Haemoglobin was found on two surfaces. No relationship was found between viral, biochemical or bacterial indicators. The data obtained confirm the difficulty of assessing viral contamination using bacterial indicators. The frequent detection of TTV suggests its possible use as an indicator for general viral contamination of the environment. url: https://doi.org/10.1016/j.jhin.2010.10.010 doi: 10.1016/j.jhin.2010.10.010 id: cord-287770-oxfnt2n4 author: Caricati, C. P. title: Safety of snake antivenom immunoglobulins: Efficacy of viral inactivation in a complete downstream process date: 2013-06-27 words: 4776.0 sentences: 304.0 pages: flesch: 48.0 cache: ./cache/cord-287770-oxfnt2n4.txt txt: ./txt/cord-287770-oxfnt2n4.txt summary: title: Safety of snake antivenom immunoglobulins: Efficacy of viral inactivation in a complete downstream process In this article, we used a wide panel of viruses to assess viral removal/inactivation of our downstream process for Snake Antivenom Immunoglobulin (SAI). Among the steps analyzed in the process, phenol addition was the most effective one, followed by heat, caprylic acid, and pepsin. The main steps are cited in sequential order (a) ammonium sulfate precipitation of immunoglobulins, (b) pepsin digestion to obtain F(ab'')2 fragments, (c) caprylic acid precipitation of nonimmunoglobulin proteins, (d) heat treatment, (e) ammonium sulfate precipitation of F(ab'')2 fragments, (f) tangential filtration, (g) ion-exchange chromatography, (h) tangential filtration, and (i) phenol addition. 34 We found no reports using both viruses as models for viral inactivation concerning the described purification steps. 52, 55 Phenol inactivated both viruses, which indicates that it might also be an effective preservative for human-derived immunoglobulins, when it comes to viral safety. abstract: Viral safety remains a challenge when processing a plasma‐derived product. A variety of pathogens might be present in the starting material, which requires a downstream process capable of broad viral reduction. In this article, we used a wide panel of viruses to assess viral removal/inactivation of our downstream process for Snake Antivenom Immunoglobulin (SAI). First, we screened and excluded equine plasma that cross‐reacted with any model virus, a procedure not published before for antivenoms. In addition, we evaluated for the first time the virucidal capacity of phenol applied to SAI products. Among the steps analyzed in the process, phenol addition was the most effective one, followed by heat, caprylic acid, and pepsin. All viruses were fully inactivated only by phenol treatment; heat, the second most effective step, did not inactivate the rotavirus and the adenovirus used. We therefore present a SAI downstream method that is cost‐effective and eliminates viruses to the extent required by WHO for a safe product. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:972–979, 2013 url: https://www.ncbi.nlm.nih.gov/pubmed/23804299/ doi: 10.1002/btpr.1758 id: cord-267194-i6vetquk author: Carman, William F. title: The pathogens date: 2007-10-31 words: 4498.0 sentences: 247.0 pages: flesch: 57.0 cache: ./cache/cord-267194-i6vetquk.txt txt: ./txt/cord-267194-i6vetquk.txt summary: In a number of occasions, patients can have a severe lower respiratory tract infection, with no bacteriological cause and the only pathogen found is rhinovirus. hMPV causes both upper and lower tract infections and the signs and symptoms are very similar to those caused by RSV ranging from mild rhinorrhea associated with common colds to severe cough, wheezing, bronchiolitis and pneumonia (Konig et al., 2004; Van den Hoogen et al., 2001) . Although the main clinical symptoms are those of severe respiratory tract disease, the virus also infected other organs. NL63 is predominantly a common cold virus like OC43 and 229E that can cause lower respiratory tract disease in young children, the elderly and immunocompromised patients. HBoV has been associated with both upper and lower tract infections with prevalences ranging from 1% to 19%, with most reports indicating prevalences in the range of 3−6% in hospitalized children <5 years with ARI. abstract: nan url: https://api.elsevier.com/content/article/pii/S1386653207700033 doi: 10.1016/s1386-6532(07)70003-3 id: cord-004848-2cfphi88 author: Carter, M. J. title: Transcription of feline calicivirus RNA date: 1990 words: 3361.0 sentences: 190.0 pages: flesch: 60.0 cache: ./cache/cord-004848-2cfphi88.txt txt: ./txt/cord-004848-2cfphi88.txt summary: In this way these workers have identified three intracellular RNAs (4.8, 4.2, and 2.4 kb) as well as the genome (8.2 kb) and shown that these form a nested set of 3'' co-terminal molecules similar to that observed in coronavirus infected cells. We have used this to probe FCV-infected cells for the synthesis of virus specific RNA and confirm and extend the observations of Neill and Mengeling. Subcloning of the virus 3'' end into a single stranded vector has allowed us to examine the occurrence of positive and negative sense RNA separately. Finally this inference was confirmed by subcloning the terminal EcoRI/PstI fragment into M13 and determining its sequence (Fig. 3a) , This showed a poly A stretch preceded by a short run ofpoly C which is exactly that structure expected for cDNA clones derived by this method from an mRNA 3'' end. However, the negative strand-specific probe also showed hybridization to subgenomic messages 2-4, but this was not observed until later in infection than the detection of the positive forms of these molecules. abstract: We report here the cloning and 3′ sequence determination of feline calicivirus strain F9. Subcloning the 3′ terminus enabled the production of strand specific probes for RNA synthesis. We extend the number of virus specific RNAs detected intracellularly to 8, and show that numbers 1–5 are represented as negative strands which may serve as templates in the synthesis of these RNAs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087285/ doi: 10.1007/bf01310744 id: cord-023293-te0n2vvp author: Carter, M. J. title: Caliciviruses date: 2005-10-18 words: 5075.0 sentences: 307.0 pages: flesch: 55.0 cache: ./cache/cord-023293-te0n2vvp.txt txt: ./txt/cord-023293-te0n2vvp.txt summary: Antibodies to SMSV were also found in some land animals including potential scavengers such as foxes, and the virus was also obtained from a fish preyed on by sealions thus raising the possibility that SMSV could be transmitted through food.'' SMSV is serologically distinct from vesicular exanthema of swine virus (VESV), but the viruses are clearly related by RNA homology, and are also similar in terms of the cells in which the virus can replicate in culture. These include the small round structured viruses (SRSV) which are also associated with diarrhoea, and the virus causing enterically transmitted non-A, non-B hepatitis now termed hepatitis E virus (HEV). Most of the increases in serum titre took place between the ages of 14-36 months.23 Broadly similar results were obtained in studies performed in Ecuador and the phi lip pine^.^^^^^ Volunteers infected with Norwalk virus commonly develop vomiting and diarrhoea, often associated with headache and abdominal discomfort.26 Illness generally lasts 24-48 hours. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169061/ doi: 10.1002/rmv.1980010307 id: cord-309489-ubf55eux author: Carvalho, John J. title: OUR COMMON ENEMY: COMBATTING THE WORLD''S DEADLIEST VIRUSES TO ENSURE EQUITY HEALTH CARE IN DEVELOPING NATIONS date: 2009-02-19 words: 5291.0 sentences: 231.0 pages: flesch: 44.0 cache: ./cache/cord-309489-ubf55eux.txt txt: ./txt/cord-309489-ubf55eux.txt summary: Of the emerging viruses, five have particular importance for what scientists and world leaders can learn concerning their impact on geopolitical stability, human rights, and equity health care for the underprivileged in both developed and developing nations. For example, in Latin America, population growth and uncontrolled migration from the countryside to the cities have resulted in poor housing conditions, inappropriate disposal of waste, and lack of adequate food, clean water and health care-all of which are concurrent with an increase in infected mosquitoes carrying different versions of dengue virus (Torres and Castro 2007) . Continuing with these themes, it is clear that the geographical expansion of three viruses (HIV, dengue, and rotavirus), the increase in frequency of the infectious diseases they cause, and the relationship between these viruses and geopolitical stability, human rights, and equity health care for developing nations are problems of great concern promoted not only by biological and technological factors but also by social, religious, and cultural ones. abstract: In a previous issue of Zygon (Carvalho 2007), I explored the role of scientists—especially those engaging the science‐religion dialogue—within the arena of global equity health, world poverty, and human rights. I contended that experimental biologists, who might have reduced agency because of their professional workload or lack of individual resources, can still unite into collective forces with other scientists as well as human rights organizations, medical doctors, and political and civic leaders to foster progressive change in our world. In this article, I present some recent findings from research on three emerging viruses—HIV, dengue, and rotavirus—to explore the factors that lead to the geographical expansion of these viruses and the increase in frequency of the infectious diseases they cause. I show how these viruses are generating problems for geopolitical stability, human rights, and equity health care for developing nations that are already experiencing a growing poverty crisis. I suggest some avenues of future research for the scientific community for the movement toward resolution of these problems and indicate where the science‐religion field can be of additional aid. url: https://www.ncbi.nlm.nih.gov/pubmed/32336872/ doi: 10.1111/j.1467-9744.2009.00985.x id: cord-245161-xbw72k4m author: Castano, Nicolas title: Fomite transmission and disinfection strategies for SARS-CoV-2 and related viruses date: 2020-05-23 words: 11558.0 sentences: 720.0 pages: flesch: 44.0 cache: ./cache/cord-245161-xbw72k4m.txt txt: ./txt/cord-245161-xbw72k4m.txt summary: Contaminated objects or surfaces, referred to as fomites, play a critical role in the spread of viruses, including SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Elucidating the physicochemical processes and surface science underlying the adsorption and transfer of virus between surfaces, as well as their inactivation, are important in understanding how the disease is transmitted, and in developing effective interception strategies. Three primary transmission routes have been found to contribute to the spread of respiratory viruses (e.g., SARS-CoV-1 and -2, measles, HCoV, rhinovirus, and influenza virus) ( Figure 1A ): 1) direct contact between individuals, 2) indirect contact via contaminated objects (fomites), 3) airborne transmission via droplets and aerosols. A study on SARS-CoV-2 infected patients in isolation rooms showed contamination of high-contact surfaces such as doorknobs and bedrails, as well as air outlet fans which indicated virus transfer from aerosols to a surface. abstract: Contaminated objects or surfaces, referred to as fomites, play a critical role in the spread of viruses, including SARS-CoV-2, the virus responsible for the COVID-19 pandemic. The long persistence of viruses (hours to days) on surfaces calls for an urgent need for surface disinfection strategies to intercept virus transmission and the spread of the disease. Elucidating the physicochemical processes and surface science underlying the adsorption and transfer of virus between surfaces, as well as their inactivation, are important in understanding how the disease is transmitted, and in developing effective interception strategies. This review aims to summarize the current knowledge and underlying physicochemical processes of virus transmission, in particular via fomites, and common disinfection approaches. Gaps in knowledge and needs for further research are also identified. The review focuses on SARS-CoV-2, but will supplement the discussions with related viruses. url: https://arxiv.org/pdf/2005.11443v1.pdf doi: nan id: cord-298214-ivu4erpq author: Castrignano, Silvana Beres title: The metagenomic approach and causality in virology date: 2015-04-01 words: 2673.0 sentences: 126.0 pages: flesch: 41.0 cache: ./cache/cord-298214-ivu4erpq.txt txt: ./txt/cord-298214-ivu4erpq.txt summary: 9, 13, 16 Among these recent propositions, both the criteria of Mokili et al, 16 based on the comparison of metagenomic characteristics among infected and healthy individuals, and the criteria of Lipkin, 13 who grouped laboratory, clinical and epidemiological data into three certainty levels to establish an association between pathogens and diseases, considered the inoculation of the infectious agent in a healthy individual as INTRODUCTION a criterion for the confirmation of causality (this criterion was inherited from Koch''s postulates). This virus was identified in human Merkel cell carcinoma (MCC) samples, 8 and the investigation of the causal association between MCV and the disease began with the investigation of 10 MCC samples from different patients; of these, the viral genome was detected in eight samples. abstract: Nowadays, the metagenomic approach has been a very important tool in the discovery of new viruses in environmental and biological samples. Here we discuss how these discoveries may help to elucidate the etiology of diseases and the criteria necessary to establish a causal association between a virus and a disease. url: https://www.ncbi.nlm.nih.gov/pubmed/25902566/ doi: 10.1590/s0034-8910.2015049005475 id: cord-003044-9uqa39j9 author: Cervera, Héctor title: Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host’s Transcriptome: The Tobacco Etch Potyvirus—Tobacco Case Study date: 2018-03-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Determining the fitness of viral genotypes has become a standard practice in virology as it is essential to evaluate their evolutionary potential. Darwinian fitness, defined as the advantage of a given genotype with respect to a reference one, is a complex property that captures, in a single figure, differences in performance at every stage of viral infection. To what extent does viral fitness result from specific molecular interactions with host factors and regulatory networks during infection? Can we identify host genes in functional classes whose expression depends on viral fitness? Here, we compared the transcriptomes of tobacco plants infected with seven genotypes of tobacco etch potyvirus that differ in fitness. We found that the larger the fitness differences among genotypes, the more dissimilar the transcriptomic profiles are. Consistently, two different mutations, one in the viral RNA polymerase and another in the viral suppressor of RNA silencing, resulted in significantly similar gene expression profiles. Moreover, we identified host genes whose expression showed a significant correlation, positive or negative, with the virus' fitness. Differentially expressed genes which were positively correlated with viral fitness activate hormone- and RNA silencing-mediated pathways of plant defense. In contrast, those that were negatively correlated with fitness affect metabolism, reducing growth, and development. Overall, these results reveal the high information content of viral fitness and suggest its potential use to predict differences in genomic profiles of infected hosts. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5995217/ doi: 10.1093/molbev/msy038 id: cord-290385-0smnl70i author: Chan, Jasper F.W. title: Zika fever and congenital Zika syndrome: An unexpected emerging arboviral disease date: 2016-03-03 words: 8256.0 sentences: 479.0 pages: flesch: 45.0 cache: ./cache/cord-290385-0smnl70i.txt txt: ./txt/cord-290385-0smnl70i.txt summary: Unlike its mosquito-borne relatives, such as dengue, West Nile, and Japanese encephalitis viruses, which can cause severe human diseases, Zika virus (ZIKV) has emerged from obscurity by its association with a suspected "congenital Zika syndrome", while causing asymptomatic or mild exanthematous febrile infections which are dengueor rubella-like in infected individuals. ZIKV RNA could be detected in breast milk and saliva of infected women, although replicative virus particles have not been demonstrated 78, 79 Perinatal transmission of other arboviruses, including DENV, CHIKV, WNV, and YFV, has also been reported. 115,120 74/ 8750 (0.8%) patients with suspected ZIKV infection in the French Polynesia outbreak developed neurological syndromes after presenting with a Zika fever-like illness. Zika fever-related death appears to be extremely rare but a number of probable cases have been reported, especially among immunocompromised patients and neonates with suspected congenital ZIKV infection. abstract: Unlike its mosquito-borne relatives, such as dengue, West Nile, and Japanese encephalitis viruses, which can cause severe human diseases, Zika virus (ZIKV) has emerged from obscurity by its association with a suspected “congenital Zika syndrome”, while causing asymptomatic or mild exanthematous febrile infections which are dengue- or rubella-like in infected individuals. Despite having been discovered in Uganda for almost 60 years, <20 human cases were reported before 2007. The massive epidemics in the Pacific islands associated with the ZIKV Asian lineage in 2007 and 2013 were followed by explosive outbreaks in Latin America in 2015. Although increased mosquito breeding associated with the El Niño effect superimposed on global warming is suspected, genetic changes in its RNA virus genome may have led to better adaptation to mosquitoes, other animal reservoirs, and human. We reviewed the epidemiology, clinical manifestation, virology, pathogenesis, laboratory diagnosis, management, and prevention of this emerging infection. Laboratory diagnosis can be confounded by cross-reactivity with other circulating flaviviruses. Besides mosquito bite and transplacental transmission, the risk of other potential routes of transmission by transfusion, transplantation, sexual activity, breastfeeding, respiratory droplet, and animal bite is discussed. Epidemic control requires adequate clearance of mosquito breeding grounds, personal protection against mosquito bite, and hopefully a safe and effective vaccine. url: https://www.sciencedirect.com/science/article/pii/S016344531600061X doi: 10.1016/j.jinf.2016.02.011 id: cord-283964-k3hy2ewx author: Chan, Jasper Fuk-Woo title: Cross-species transmission and emergence of novel viruses from birds date: 2015-01-31 words: 2810.0 sentences: 147.0 pages: flesch: 38.0 cache: ./cache/cord-283964-k3hy2ewx.txt txt: ./txt/cord-283964-k3hy2ewx.txt summary: Birds may act as a vehicle for vector dissemination, an amplifying host in bird-vector-bird cycles, or the gene source of emerging viruses in cross-species virus transmission ( Figure 1) Sixteen of 18 hemagglutinin (HA) subtypes and nine of 11 neuraminidase (NA) subtypes of influenza viruses can be found in birds, especially waterfowl and shorebirds [2 ] . A study using influenza viruses generated with gene segments originating from circulating avian influenza viruses and the 1918 pandemic A(H1N1) virus showed that substitutions in the HA, PB2 and PA are important for virulence and efficient transmission in ferrets [35] . Human infections with the emerging avian influenza A H7N9 virus from wet market poultry: clinical analysis and characterisation of viral genome A novel psittacine adenovirus identified during an outbreak of avian chlamydiosis and human psittacosis: zoonosis associated with virus-bacterium coinfection in birds abstract: Birds, the only living member of the Dinosauria clade, are flying warm-blooded vertebrates displaying high species biodiversity, roosting and migratory behavior, and a unique adaptive immune system. Birds provide the natural reservoir for numerous viral species and therefore gene source for evolution, emergence and dissemination of novel viruses. The intrusions of human into natural habitats of wild birds, the domestication of wild birds as pets or racing birds, and the increasing poultry consumption by human have facilitated avian viruses to cross species barriers to cause zoonosis. Recently, a novel adenovirus was exclusively found in birds causing an outbreak of Chlamydophila psittaci infection among birds and humans. Instead of being the primary cause of an outbreak by jumping directly from bird to human, a novel avian virus can be an augmenter of another zoonotic agent causing the outbreak. A comprehensive avian virome will improve our understanding of birds’ evolutionary dynamics. url: https://doi.org/10.1016/j.coviro.2015.01.006 doi: 10.1016/j.coviro.2015.01.006 id: cord-329857-pcsuu597 author: Chan, Kuan Rong title: Fc receptors and their influence on efficacy of therapeutic antibodies for treatment of viral diseases date: 2015-11-02 words: 5862.0 sentences: 280.0 pages: flesch: 28.0 cache: ./cache/cord-329857-pcsuu597.txt txt: ./txt/cord-329857-pcsuu597.txt summary: The binding affinity of antibodies to viruses can directly impact the efficacy of mAbs [4] , suggesting that target-specific mechanisms likely account for much of the efficacy of therapeutic mAbs. However, many studies have also highlighted the contribution of Fc-mediated immune effector functions in modulating the efficacy of these mAbs [5] . FcgRs have been shown to be important in modulating the efficacy of therapeutic mAbs [5] due to their involvement in FcgRmediated phagocytosis, cytokine production, ADCC and complement-dependent cytotoxicity (CDC) that aids in virus neutralization (FIGURE 1). Given the importance of FcgRs in mediating virus neutralization and Fc effector functions, a better understanding of how therapeutic antibodies neutralize virus infections in FcgRbearing cells will impact implementation of dosing regiments and allow development of improved therapeutic antibodies against infectious diseases. Given the importance of Fc-FcgR interaction in antibodymediated effector functions, Fc modification could lead to the development of therapeutic antibodies with improved interaction to activating FcgRs. This could enhance FcgR-mediated uptake, cytokine production, antigen presentation, ADCC and CDC. abstract: The lack of vaccines against several important viral diseases necessitates the development of therapeutics to save lives and control epidemics. In recent years, therapeutic antibodies have received considerable attention due to their good safety profiles and clinical success when used against viruses such as respiratory syncytial virus, Ebola virus and Hendra virus. The binding affinity of these antibodies can directly impact their therapeutic efficacy. However, we and others have also demonstrated that the subtype of Fc-gamma receptors (FcγRs) engaged influences the stoichiometric requirement for virus neutralization. Hence, the development of therapeutic antibodies against infectious diseases should consider the FcγRs engaged and Fc-effector functions involved. This review highlights the current state of knowledge about FcγRs and FcγR effector functions involved in virus neutralization, with emphasis on factors that can affect FcγR engagement. A better understanding of Fc-FcγR interactions during virus neutralization will allow development of therapeutic antibodies that are efficacious and can be administered with minimal side effects. url: https://www.ncbi.nlm.nih.gov/pubmed/26466016/ doi: 10.1586/14787210.2015.1079127 id: cord-336225-ijodhrwf author: Chang, Mee Soo title: Severe Fever with Thrombocytopenia Syndrome: Tick-Mediated Viral Disease date: 2013-06-03 words: 1379.0 sentences: 90.0 pages: flesch: 62.0 cache: ./cache/cord-336225-ijodhrwf.txt txt: ./txt/cord-336225-ijodhrwf.txt summary: title: Severe Fever with Thrombocytopenia Syndrome: Tick-Mediated Viral Disease A small tick Haemaphysalis longicornis called ''Sochamjindeugi'' in Korean has bitten a week before, and an onset is characterized by fever, lymph node swelling, diarrhea, thrombocytopenia, leucocytopenia, multiorgan dysfunction, altered consciousness, and occasionally to death in extreme cases (1, 2) . This emerging febrile disease, severe fever with thrombocytopenia syndrome (SFTS), was reported in 2007 by the New England Journal of Medicine (3) and Clinical Infectious Diseases (4) (5) (6) . The vaccine development to combat the SFTS virus is not easy due to its characteristics. Also any treatment by killing the virus is able to give human damage. Severe Fever with Thrombocytopenia Syndrome confirmed cases and follow-up measure Document for physicians about Severe Fever with Thrombocytopenia Syndrome (SFTS) Epidemiologic features of severe Fever with thrombocytopenia syndrome in China Person-to-person transmission of severe fever with thrombocytopenia syndrome bunyavirus through blood contact abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/23772137/ doi: 10.3346/jkms.2013.28.6.795 id: cord-297131-3a9vjpvn author: Charlton Hume, Hayley K. title: Synthetic biology for bioengineering virus‐like particle vaccines date: 2018-12-31 words: 6833.0 sentences: 366.0 pages: flesch: 32.0 cache: ./cache/cord-297131-3a9vjpvn.txt txt: ./txt/cord-297131-3a9vjpvn.txt summary: Current and developing technologies for the identification of novel target‐specific antigens and their usefulness for rational engineering of VLP functions (e.g., presentation of structurally diverse antigens, enhanced antigen immunogenicity, and improved vaccine stability) are described. Seconded by a multitude of tools, such as omics technologies, structural biology, system immunology, and bioinformatics and computational biology, one can now screen for pathogen-specific antigens with high immunogenic potential and apply that information to rationally design modern VLP vaccines ( Figure 1 ). Virus-like particles as a highly efficient vaccine platform: Diversity of targets and production systems and advances in clinical development Synthetic biology design to display an 18 kDa rotavirus large antigen on a modular virus-like particle Integrated molecular and bioprocess engineering for bacterially produced immunogenic modular virus-like particle vaccine displaying 18 kDa rotavirus antigen A novel virus-like particle based vaccine platform displaying the placental malaria antigen VAR2CSA abstract: Vaccination is the most effective method of disease prevention and control. Many viruses and bacteria that once caused catastrophic pandemics (e.g., smallpox, poliomyelitis, measles, and diphtheria) are either eradicated or effectively controlled through routine vaccination programs. Nonetheless, vaccine manufacturing remains incredibly challenging. Viruses exhibiting high antigenic diversity and high mutation rates cannot be fairly contested using traditional vaccine production methods and complexities surrounding the manufacturing processes, which impose significant limitations. Virus‐like particles (VLPs) are recombinantly produced viral structures that exhibit immunoprotective traits of native viruses but are noninfectious. Several VLPs that compositionally match a given natural virus have been developed and licensed as vaccines. Expansively, a plethora of studies now confirms that VLPs can be designed to safely present heterologous antigens from a variety of pathogens unrelated to the chosen carrier VLPs. Owing to this design versatility, VLPs offer technological opportunities to modernize vaccine supply and disease response through rational bioengineering. These opportunities are greatly enhanced with the application of synthetic biology, the redesign and construction of novel biological entities. This review outlines how synthetic biology is currently applied to engineer VLP functions and manufacturing process. Current and developing technologies for the identification of novel target‐specific antigens and their usefulness for rational engineering of VLP functions (e.g., presentation of structurally diverse antigens, enhanced antigen immunogenicity, and improved vaccine stability) are described. When applied to manufacturing processes, synthetic biology approaches can also overcome specific challenges in VLP vaccine production. Finally, we address several challenges and benefits associated with the translation of VLP vaccine development into the industry. url: https://doi.org/10.1002/bit.26890 doi: 10.1002/bit.26890 id: cord-310255-aixq5mhf author: Charlton, Frank W. title: Ion Channels as Therapeutic Targets for Viral Infections: Further Discoveries and Future Perspectives date: 2020-08-03 words: 5345.0 sentences: 321.0 pages: flesch: 46.0 cache: ./cache/cord-310255-aixq5mhf.txt txt: ./txt/cord-310255-aixq5mhf.txt summary: More recent evidence highlights how viruses can regulate and/or depend on the ion channels expressed by host cells, highlighting them as new host targets for therapeutic intervention (reviewed by Hover et al., 2017) [14] . We then discuss how intracellular ion channels contribute to the Two-pore channels 1 and 2 (TPC1/2) Gunaratne et al., 2018 [34] Severe fever with thrombocytopenia syndrome virus (SFTSV) Unknown channel Li et al., 2019 [35] Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Two-pore channel 2 (TPC2) Ou et al., 2020 [36] Bunyamwera orthobunyavirus (BUNV) Two-pore domain K + (K 2P ) Hover et al., 2016/18 [28, 37] Hazara orthonairovirus (HAZV) Unknown K + channel Punch et al., 2017 [38] Charlton et al., 2019 [39] Human immunodeficiency virus (HIV) G-Protein coupled inwardly rectifying K + (GIRK) ATP-sensitive K + K ATP Dubey et al., 2019 [40] Merkel cell polyomavirus (MCPyV) abstract: Ion channels play key roles in almost all facets of cellular physiology and have emerged as key host cell factors for a multitude of viral infections. A catalogue of ion channel-blocking drugs have been shown to possess antiviral activity, some of which are in widespread human usage for ion channel-related diseases, highlighting new potential for drug repurposing. The emergence of ion channel–virus interactions has also revealed the intriguing possibility that channelopathies may explain some commonly observed virus induced pathologies. This field is rapidly evolving and an up-to-date summary of new discoveries can inform future perspectives. We herein discuss the role of ion channels during viral lifecycles, describe the recently identified ion channel drugs that can inhibit viral infections, and highlight the potential contribution of ion channels to virus-mediated disease. url: https://doi.org/10.3390/v12080844 doi: 10.3390/v12080844 id: cord-274306-cxvnv8dy author: Chastel, C. title: Émergence de virus nouveaux en Asie : les changements climatiques sont-ils en cause ? date: 2004-11-30 words: 4564.0 sentences: 448.0 pages: flesch: 70.0 cache: ./cache/cord-274306-cxvnv8dy.txt txt: ./txt/cord-274306-cxvnv8dy.txt summary: L''Asie, en particulier la Chine et le Sud-est asiatique, a également connu l''émergence de viroses humaines graves, telles que la dengue hémorragique (les Philippines, 1954) ou plusieurs pandémies grippales, la grippe asiatique (N2H2) en 1957, la grippe de Hong-Kong (H3N2) en 1968, et la grippe russe (H1N1) en 1977. Mais, c''est surtout au cours des dix dernières années que les émergences virales s''y sont multipliées avec l''apparition de la fièvre hémorragique à virus Alkhurma en Arabie Saoudite (1995), de la grippe aviaire H5N1 à Hong-Kong, en 1997, de l''encéphalite à virus Nipah en Malaisie, en 1998, et surtout du SRAS, en Chine du sud en 2002. Depuis l''extermination des porcs infectés, on a plus signalé de cas d''encéphalite à virus Nipah, mais il convient de rester vigilant car les roussettes et les porcs sont très nombreux dans tout le Sud-est asiatique. abstract: Résumé L’Afrique tropicale n’est pas la seule région du monde où des virus dangereux pour l’homme aient récemment émergé. L’Asie, en particulier la Chine et le Sud-est asiatique, a également connu l’émergence de viroses humaines graves, telles que la dengue hémorragique (les Philippines, 1954) ou plusieurs pandémies grippales, la grippe asiatique (N2H2) en 1957, la grippe de Hong-Kong (H3N2) en 1968, et la grippe russe (H1N1) en 1977. Mais, c’est surtout au cours des dix dernières années que les émergences virales s’y sont multipliées avec l’apparition de la fièvre hémorragique à virus Alkhurma en Arabie Saoudite (1995), de la grippe aviaire H5N1 à Hong-Kong, en 1997, de l’encéphalite à virus Nipah en Malaisie, en 1998, et surtout du SRAS, en Chine du sud en 2002. Les facteurs climatiques n’ont probablement joué qu’un rôle réduit dans le succès émergentiel de ces viroses, favorisé plutôt par des facteurs humains : le développement d’élevages industriels d’animaux de basse cour augmentant les risques d’épizooties, les habitudes alimentaires, les pressions économiques et démographiques, les négligences dans la surveillance épidémiologique et la déclaration des premiers cas. Abstract Tropical Africa is not the only area where deadly viruses have recently emerged. In South-East Asia severe epidemics of dengue hemorrhagic fever started in 1954 and flu pandemics have originated from China such as the Asian flu (H2N2) in 1957, the Hong-Kong flu (H3N2) in 1968, and the Russian flu (H1N1) in 1977. However, it is especially during the last ten years that very dangerous viruses for mankind have repeatedly developed in Asia, with the occurrence of Alkhurma hemorrhagic fever in Saudi Arabia (1995), avian flu (H5N1) in Hong-Kong (1997), Nipah virus encephalitis in Malaysia (1998,) and, above all, the SARS pandemic fever from Southern China (2002). The evolution of these viral diseases was probably not directly affected by climate change. In fact, their emergential success may be better explained by the development of large industry poultry flocks increasing the risks of epizootics, dietary habits, economic and demographic constraints, and negligence in the surveillance and reporting of the first cases. url: https://api.elsevier.com/content/article/pii/S0399077X04001805 doi: 10.1016/j.medmal.2004.07.027 id: cord-340042-intxyu46 author: Chaudhry, Sundas Nasir title: New insight on possible vaccine development against SARS-CoV-2 date: 2020-09-11 words: 5457.0 sentences: 260.0 pages: flesch: 43.0 cache: ./cache/cord-340042-intxyu46.txt txt: ./txt/cord-340042-intxyu46.txt summary: In December 2019, a novel virus, namely COVID-19, caused by SARS-CoV-2, developed from Wuhan, Hubei territory of China, which used its viral spike glycoprotein receptor-binding domain (RBD) for the entrance into a host cell by binding with ACE-2 receptor and cause acute respiratory distress syndrome (ARDS). Different subunits of spike proteins like the S1 and S2 subunits, and the receptor-binding domain (RBD) are the critical elements for the formation of a vaccine against the newly emerged virus that helped in producing T cell responses and protective immunity against SARS-CoV-2 [29] . The recombinant protein is known as one of the emerging fields for the development of a vaccine against viruses due to several properties including tight binding to specific ACE-2 receptor, provoke immune protection against viral infections, increase antibody-dependent viral entry, and promote antigenicity against virus like SARS-CoV [52] . abstract: In December 2019, a novel virus, namely COVID-19, caused by SARS-CoV-2, developed from Wuhan, Hubei territory of China, which used its viral spike glycoprotein receptor-binding domain (RBD) for the entrance into a host cell by binding with ACE-2 receptor and cause acute respiratory distress syndrome (ARDS). Data revealed that the newly emerged SARS-CoV-2 affected more than 24,854,140 people with 838,924 deaths worldwide. Until now, no licensed immunization or drugs are present for the medication of SARS-CoV-2. The present review aims to investigate the latest developments and discuss the candidate antibodies in different vaccine categories to develop a reliable and efficient vaccine against SARS-CoV-2 in a short time duration. Besides, the review focus on the present challenges and future directions, structure, and mechanism of SARS-CoV-2 for better understanding. Based on data, we revealed that most of the vaccines are focus on targeting the spike protein (S) of COVID-19 to neutralized viral infection and develop long-lasting immunity. Up to phase-1 clinical trials, some vaccines showed the specific antigen-receptor T cell response, elicit the humoral and immune response, displayed tight binding with human-leukocytes-antigen (HLA), and recognized specific antibodies to provoke long-lasting immunity against SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32926920/ doi: 10.1016/j.lfs.2020.118421 id: cord-314825-fzba05wn author: Chauhan, Ravendra P. title: A Systematic Review Analyzing the Prevalence and Circulation of Influenza Viruses in Swine Population Worldwide date: 2020-05-08 words: 22346.0 sentences: 1098.0 pages: flesch: 52.0 cache: ./cache/cord-314825-fzba05wn.txt txt: ./txt/cord-314825-fzba05wn.txt summary: abstract: The global anxiety and a significant threat to public health due to the current COVID-19 pandemic reiterate the need for active surveillance for the zoonotic virus diseases of pandemic potential. Influenza virus due to its wide host range and zoonotic potential poses such a significant threat to public health. Swine serve as a “mixing vessel” for influenza virus reassortment and evolution which as a result may facilitate the emergence of new strains or subtypes of zoonotic potential. In this context, the currently available scientific data hold a high significance to unravel influenza virus epidemiology and evolution. With this objective, the current systematic review summarizes the original research articles and case reports of all the four types of influenza viruses reported in swine populations worldwide. A total of 281 articles were found eligible through screening of PubMed and Google Scholar databases and hence were included in this systematic review. The highest number of research articles (n = 107) were reported from Asia, followed by Americas (n = 97), Europe (n = 55), Africa (n = 18), and Australia (n = 4). The H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses were the most common influenza A virus subtypes reported in swine in most countries across the globe, however, few strains of influenza B, C, and D viruses were also reported in certain countries. Multiple reports of the avian influenza virus strains documented in the last two decades in swine in China, the United States, Canada, South Korea, Nigeria, and Egypt provided the evidence of interspecies transmission of influenza viruses from birds to swine. Inter-species transmission of equine influenza virus H3N8 from horse to swine in China expanded the genetic diversity of swine influenza viruses. Additionally, numerous reports of the double and triple-reassortant strains which emerged due to reassortments among avian, human, and swine strains within swine further increased the genetic diversity of swine influenza viruses. These findings are alarming hence active surveillance should be in place to prevent future influenza pandemics. url: https://www.ncbi.nlm.nih.gov/pubmed/32397138/ doi: 10.3390/pathogens9050355 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-257321-l1swyr6g author: Chen, Lihong title: DRodVir: A resource for exploring the virome diversity in rodents date: 2017-05-20 words: 3249.0 sentences: 161.0 pages: flesch: 45.0 cache: ./cache/cord-257321-l1swyr6g.txt txt: ./txt/cord-257321-l1swyr6g.txt summary: The database currently covers 7690 sequences from 5491 rodent-associated mammal viruses of 26 viral families detected from 194 rodent species in 93 countries worldwide. As a data application example, we further compared the current status of rodent-associated viruses with bat-associated viruses to highlight the necessity for including additional host species and geographic regions in future investigations, which will help us achieve a better understanding of the virome diversities in the two major reservoirs of emerging zoonotic infectious diseases. To facilitate online data analysis, two visualization tools are integrated into the result table: i) a statistical pie chart is available with a single click on the column title of virus family, rodent species/family, sample type and sampling country (Fig. 2B) ; ii) a global map with indicative markers is provided for the column of sampling country to better illustrate the geographic distribution of the rodent-associated viruses (http://www.mgc.ac. abstract: Emerging zoonotic diseases have received tremendous interests in recent years, as they pose a significant threat to human health, animal welfare, and economic stability. A high proportion of zoonoses originate from wildlife reservoirs. Rodents are the most numerous, widespread, and diverse group of mammals on the earth and are reservoirs for many zoonotic viruses responsible for significant morbidity and mortality. A better understanding of virome diversity in rodents would be of importance for researchers and professionals in the field. Therefore, we developed the DRodVir database (http://www.mgc.ac.cn/DRodVir/), a comprehensive, up-to-date, and well-curated repository of rodent-associated animal viruses. The database currently covers 7690 sequences from 5491 rodent-associated mammal viruses of 26 viral families detected from 194 rodent species in 93 countries worldwide. In addition to virus sequences, the database provides detailed information on related samples and host rodents, as well as a set of online analytical tools for text query, BLAST search and phylogenetic reconstruction. The DRodVir database will help virologists better understand the virome diversity of rodents. Moreover, it will be a valuable tool for epidemiologists and zoologists for easy monitoring and tracking of the current and future zoonotic diseases. As a data application example, we further compared the current status of rodent-associated viruses with bat-associated viruses to highlight the necessity for including additional host species and geographic regions in future investigations, which will help us achieve a better understanding of the virome diversities in the two major reservoirs of emerging zoonotic infectious diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/28533016/ doi: 10.1016/j.jgg.2017.04.004 id: cord-282343-cko4curf author: Cheng, Han title: A parallel genome-wide RNAi screening strategy to identify host proteins important for entry of Marburg virus and H5N1 influenza virus date: 2015-11-24 words: 5071.0 sentences: 278.0 pages: flesch: 56.0 cache: ./cache/cord-282343-cko4curf.txt txt: ./txt/cord-282343-cko4curf.txt summary: RESULTS: The parallel nature of the strategy allows us to easily identify the host factors for a specific virus with a greatly reduced number of false positives in the initial screen, which is one of the major problems with high throughput screening. This strategy was used for an RNAi screen to identify host proteins specific for the entry process of Marburg virus (MARV) or avian influenza virus H5N1 (AIV), demonstrating the utility of this approach. The key feature of the protocol is that AIV and siRNA showing low signals in assay plates of both viruses is regarded as a "shared" hit by the two viruses MARV pseudovirions were used in parallel in the RNAi screen which allowed us to reduce the number of false positives and to quickly identify Marburg-specific and flu-specific host factors (which will be further discussed below). abstract: BACKGROUND: Genome-wide RNAi screening has been widely used to identify host proteins involved in replication and infection of different viruses, and numerous host factors are implicated in the replication cycles of these viruses, demonstrating the power of this approach. However, discrepancies on target identification of the same viruses by different groups suggest that high throughput RNAi screening strategies need to be carefully designed, developed and optimized prior to the large scale screening. METHODS: Two genome-wide RNAi screens were performed in parallel against the entry of pseudotyped Marburg viruses and avian influenza virus H5N1 utilizing an HIV-1 based surrogate system, to identify host factors which are important for virus entry. A comparative analysis approach was employed in data analysis, which alleviated systematic positional effects and reduced the false positive number of virus-specific hits. RESULTS: The parallel nature of the strategy allows us to easily identify the host factors for a specific virus with a greatly reduced number of false positives in the initial screen, which is one of the major problems with high throughput screening. The power of this strategy is illustrated by a genome-wide RNAi screen for identifying the host factors important for Marburg virus and/or avian influenza virus H5N1 as described in this study. CONCLUSIONS: This strategy is particularly useful for highly pathogenic viruses since pseudotyping allows us to perform high throughput screens in the biosafety level 2 (BSL-2) containment instead of the BSL-3 or BSL-4 for the infectious viruses, with alleviated safety concerns. The screening strategy together with the unique comparative analysis approach makes the data more suitable for hit selection and enables us to identify virus-specific hits with a much lower false positive rate. url: https://www.ncbi.nlm.nih.gov/pubmed/26596270/ doi: 10.1186/s12985-015-0420-3 id: cord-255697-trig04hd author: Cheng, Vincent Chi-Chung title: Viral Infections, an Overview with a Focus on Prevention of Transmission date: 2016-10-24 words: 6422.0 sentences: 301.0 pages: flesch: 42.0 cache: ./cache/cord-255697-trig04hd.txt txt: ./txt/cord-255697-trig04hd.txt summary: Hand hygiene is always the core component of infection control measures in both community and hospitals to prevent the transmission of influenza A virus. Wearing face masks by either the index case as source control or the health-care workers as contacts has shown to be equally effective in the control of nosocomial transmission of pandemic influenza A H1N1 (Cheng et al., 2010) . Timely implementation of infection control measures by single room isolation of index case with strict contact precautions significantly reduced the incidence of hospital-acquired norovirus infection from 131 (baseline) to 16 cases per 1000 potentially infectious patient-days (P < 0.001) (Cheng et al., 2011) . When there is no highly effective antiviral for the treatment of a severe viral illness, especially in patients at the extremes of age or with medical comorbidities, and infection control measures are difficult to implement or comply with, vaccination is the final option to prevent massive outbreaks. abstract: Viruses are obligatory intracellular pathogens with a simple structure consisting of assembled proteins enclosing the nucleic acid genome with or without a lipid envelope. Despite increasing availability of rapid nucleic acid amplification assays for laboratory diagnosis, effective antivirals, and safe vaccines, the control of most viral infections depends on time-honored surveillance and infection control measures. Moreover most viruses can be readily destroyed by common disinfectants. This article is focused on the epidemiology, diagnosis, and control of common and emerging viral diseases. url: https://www.sciencedirect.com/science/article/pii/B9780128036785005142 doi: 10.1016/b978-0-12-803678-5.00514-2 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-308066-lrbi5198 author: Childs, James E. title: Pre-spillover Prevention of Emerging Zoonotic Diseases: What Are the Targets and What Are the Tools? date: 2007 words: 15698.0 sentences: 714.0 pages: flesch: 41.0 cache: ./cache/cord-308066-lrbi5198.txt txt: ./txt/cord-308066-lrbi5198.txt summary: The uneven standards of surveillance, humanor animal-based, for zoonotic diseases or pathogens maintained and transmitted by wildlife H R s, or even domestic species, is a global problem, readily apparent even within the United States, where investment in public health, including surveillance systems, has a long and enviable history. Following an outbreak of human monkeypox in several US states (Centers for Disease Control and Prevention 2003a; see the chapter by Regnery, this volume), local populations of indigenous North American rodents were captured and examined for infection from areas around animal-holding facilities housing African rodents imported for the pet-trade and implicated as the source of monkeypox virus (Cunha 2004; Check 2004) . National institutions charged with strategic planning for emerging diseases or intentional releases of zoonotic agents have emphasized improving diagnostic capabilities for detecting human infections, modifying the immune status of human or domestic animals through vaccines, producing better antiviral or antibacterial drugs, and enhancing human-based surveillance as an early warning system (Fauchi 2002 ; Centers for Disease Control and Prevention 1998). abstract: The uneven standards of surveillance, human- or animal-based, for zoonotic diseases or pathogens maintained and transmitted by wildlife H R s, or even domestic species, is a global problem, readily apparent even within the United States, where investment in public health, including surveillance systems, has a long and enviable history. As of 2006, there appears to be little scientific, social, or political consensus that animalbased surveillance for zoonoses merits investment in international infrastructure, other than the fledgling efforts with avian influenza, or targeted nontraditional avenues of surveillance and research. url: https://www.ncbi.nlm.nih.gov/pubmed/17848073/ doi: 10.1007/978-3-540-70962-6_16 id: cord-320015-lbr2q4qh author: Chinchar, V. Gregory title: The Molecular Biology of Frog Virus 3 and other Iridoviruses Infecting Cold-Blooded Vertebrates date: 2011-10-20 words: 9130.0 sentences: 433.0 pages: flesch: 43.0 cache: ./cache/cord-320015-lbr2q4qh.txt txt: ./txt/cord-320015-lbr2q4qh.txt summary: Additional IE and DE proteins include proteins that may play roles in blocking host immune responses such as a virus-encoded, CARD (caspase activation and recruitment domain) motif-containing protein (vCARD), β-hydroxysteroid dehydrogenase (βHSD), and a RNAse III-like protein, catalytic proteins involved in nucleic acid synthesis (Proliferating Cell Nuclear Antigen [PCNA], DNA methyltransferase [DMTase], the large and small subunits of the viral homolog of cellular RNA polymerase II [vPOL-IIα and -IIβ], transcription factor IIS), catalytic proteins that may act to increase dTTP pool sizes and influence host range (deoxyuridine triphosphatase [dUTPase], deoxynucleotide kinase, the large and small subunits of ribonucleotide reductase), and proteins non-essential for replication in vitro, but needed for growth in vivo (the 18K protein) [22] . Lastly, Sample and co-workers observed that KD of the 18K IE protein had no observable effect on viral gene expression or replication in vitro suggesting that, at least in fathead minnow cells, 18K was not required for the production of infectious virions. abstract: Frog virus 3 (FV3) is the best characterized member of the family Iridoviridae. FV3 study has provided insights into the replication of other family members, and has served as a model of viral transcription, genome replication, and virus-mediated host-shutoff. Although the broad outlines of FV3 replication have been elucidated, the precise roles of most viral proteins remain unknown. Current studies using knock down (KD) mediated by antisense morpholino oligonucleotides (asMO) and small, interfering RNAs (siRNA), knock out (KO) following replacement of the targeted gene with a selectable marker by homologous recombination, ectopic viral gene expression, and recombinant viral proteins have enabled researchers to systematically ascertain replicative- and virulence-related gene functions. In addition, the application of molecular tools to ecological studies is providing novel ways for field biologists to identify potential pathogens, quantify infections, and trace the evolution of ecologically important viral species. In this review, we summarize current studies using not only FV3, but also other iridoviruses infecting ectotherms. As described below, general principles ascertained using FV3 served as a model for the family, and studies utilizing other ranaviruses and megalocytiviruses have confirmed and extended our understanding of iridovirus replication. Collectively, these and future efforts will elucidate molecular events in viral replication, intrinsic and extrinsic factors that contribute to disease outbreaks, and the role of the host immune system in protection from disease. url: https://doi.org/10.3390/v3101959 doi: 10.3390/v3101959 id: cord-343784-zgvxl4h3 author: Cho, Chi Hyun title: Evaluation of the AdvanSure™ real-time RT-PCR compared with culture and Seeplex RV15 for simultaneous detection of respiratory viruses date: 2014-05-31 words: 3707.0 sentences: 204.0 pages: flesch: 51.0 cache: ./cache/cord-343784-zgvxl4h3.txt txt: ./txt/cord-343784-zgvxl4h3.txt summary: Several studies have demonstrated the advantages of multiplex PCR assays such as xTAG RVP, RVP fast (Luminex Molecular Diagnostics, Toronto, ON, Canada), Resplex II (Qiagen, Mississauga, ON, Canada), FilmArray® Respiratory panel (Idaho Technology Inc., Salt Lake City, UT, USA), and Seeplex RV assays (Seegene, Seoul, Korea), which are used routinely for the detection of respiratory viral infection (Bibby et al., 2011; Couturier et al., 2013; Gharabaghi et al., 2011; Kim et al., 2013; Zhang et al., 2012) . In the previous study evaluating Seeplex RV12 detection kit (Seegene, Rockville, MD, USA), viral culture, RV12, and real-time PCR detected 8, 6, and 11 of 11 influenza B-positive specimens, respectively (Bruijnesteijn van Coppenraet et al., 2010) . Simultaneous detection of influenza A, B, and C viruses, respiratory syncytial virus, and adenoviruses in clinical samples by multiplex reverse transcription nested-PCR assay Evaluation of a multiplex real-time PCR assay for the detection of respiratory viruses in clinical specimens abstract: Abstract Recently, AdvanSure™ kit based on multiplex real-time PCR was developed for simultaneous detection of 14 respiratory viruses (RVs). We compared the performance of AdvanSure with those of Seeplex® RV 15 ACE and culture by determining their sensitivities and specificities against a composite reference standard. Four hundred thirty-seven respiratory samples were tested by modified shell vial culture method, RV 15 ACE, and AdvanSure. One hundred fourteen samples (26.2%) out of 437 samples were positive by culture, while additional 91 (20.8%) were positive by AdvanSure or RV15. One hundred twelve of 114 culture-positive samples were positive by AdvanSure except 2 samples (1 adenovirus, 1 respiratory syncytial virus [RSV]). Overall, the sensitivities of culture, RV15, and AdvanSure were 74.5%, 89.8%, and 95.1%, respectively. Sensitivities of culture, RV15, and AdvanSure for each virus tested were as follows: 91/100/96% for influenza A, 60/0/100% for influenza B, 63/95/97% for RSV, 69/81/89% for adenovirus, and 87/93/93% for parainfluenza virus. For viruses not covered by culture, sensitivities of RV15 and AdvanSure were as follows: 77/88% for rhinovirus, 100/100% for coronavirus OC43, 40/100% for coronavirus 229E/NL63, 13/100% for metapneumovirus, and 44/100% for bocavirus. The overall specificities of culture, RV15, and AdvanSure were 100/98.9/99.5%, respectively. Of 45 coinfected specimens, AdvanSure detected 41 specimens (91.1%) as coinfected, while RV15 detected 27 specimens (60.0%) as coinfected. AdvanSure assay demonstrated exquisite performance for the detection of RVs and will be a valuable tool for the management of RV infection. url: https://api.elsevier.com/content/article/pii/S0732889314000492 doi: 10.1016/j.diagmicrobio.2014.01.016 id: cord-306083-juysx6yo author: Choe, Young June title: Co-seasonality and co-detection of respiratory viruses and bacteraemia in children: a retrospective analysis date: 2020-09-10 words: 1746.0 sentences: 108.0 pages: flesch: 44.0 cache: ./cache/cord-306083-juysx6yo.txt txt: ./txt/cord-306083-juysx6yo.txt summary: OBJECTIVES: The aim of this study was to assess the co-seasonality and co-detection of respiratory viral infections and bacteraemia in children since the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13). Analysis of linked viral-bacterial infections in individual children indicated that the rate ratio (RR) of bacteraemia associated with hMPV (RR=2.73, 95% CI 1.12-6.85, P=0.019) and influenza (RR=2.61, 95% CI 1.21-6.11, P=0.013) were more than double that of RSV. CONCLUSIONS: There is a significant association between hMPV and influenza viruses, and bacteraemia of all causes in hospitalised children at a single paediatric centre in the United States. A study conducted in children before the 9 implementation of PCV13, demonstrated significant associations between invasive 10 pneumococcal disease (IPD) and influenza viruses and respiratory syncytial virus (RSV), as well 11 as human metapneumovirus (hMPV), which was a novel observation [5] . abstract: OBJECTIVES: The aim of this study was to assess the co-seasonality and co-detection of respiratory viral infections and bacteraemia in children since the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13). METHODS: Children <18 years were eligible for inclusion if they had a respiratory infection and a positive PCR-based assay for respiratory viruses as well as a positive blood culture from 2010 to 2018 at a single referral centre in the United States regardless of their underlying medical condition or antibiotic treatment history. Monthly incidence rates of respiratory viruses and bacteraemia were analysed with a seasonal-trend decomposition procedure based on loess (STL) and cross-correlation functions using time series regression modelling. RESULTS: We identified 7,415 unique positive respiratory virus tests, including 2,278 RSV (31%), 1,825 influenza viruses (24%), 1,036 parainfluenza viruses (14%), 1,017 hMPV (14%), 677 seasonal coronaviruses (9%), and 582 adenoviruses (8%), and a total of 11,827 episodes of bacteraemia. Significant co-seasonality was found between all-cause bacteraemia and RSV (OR=1.76, 95% CI 1.50-2.06, P<0.001), influenza viruses (OR=1.38, 95% CI 1.13-1.68, P=0.002), and seasonal coronaviruses (OR=1.18, 95% CI 1.09-1.28, P<0.001), respectively. Analysis of linked viral-bacterial infections in individual children indicated that the rate ratio (RR) of bacteraemia associated with hMPV (RR=2.73, 95% CI 1.12-6.85, P=0.019) and influenza (RR=2.61, 95% CI 1.21-6.11, P=0.013) were more than double that of RSV. Staphylococcus aureus and Streptococcus pneumoniae were the most commonly identified pathogens causing bacteraemia. CONCLUSIONS: There is a significant association between hMPV and influenza viruses, and bacteraemia of all causes in hospitalised children at a single paediatric centre in the United States. Large multicentre studies are needed to confirm these findings and to elucidate the mechanisms by which hMPV potentiates the virulence and invasive capacity of diverse bacteria. url: https://www.sciencedirect.com/science/article/pii/S1198743X20305358?v=s5 doi: 10.1016/j.cmi.2020.09.006 id: cord-305488-vk59ghjm author: Choi, Kang-Seuk title: Newcastle disease virus vectored vaccines as bivalent or antigen delivery vaccines date: 2017-07-26 words: 4841.0 sentences: 237.0 pages: flesch: 45.0 cache: ./cache/cord-305488-vk59ghjm.txt txt: ./txt/cord-305488-vk59ghjm.txt summary: They also induced a marked and efficient cellular and protective immune response in mice after challenge with vaccinia viruses expressing HIV-1 Env and Gag. These results suggest that vaccination with a single NDV vector coexpressing Env and Gag is a promising strategy that increases vaccine immunogenicity and subsequent protective efficacy against HIV. Immunization of cattle with recombinant Newcastle disease virus expressing bovine herpesvirus-1 (BHV-1) glycoprotein D induces mucosal and serum antibody responses and provides partial protection against BHV-1 Immunization of primates with a Newcastle disease virus-vectored vaccine via the respiratory tract induces a high titer of serum neutralizing antibodies against highly pathogenic avian influenza virus Newcastle disease virus-based live attenuated vaccine completely protects chickens and mice from lethal challenge of homologous and heterologous H5N1 avian influenza viruses Immunization of chickens with Newcastle disease virus expressing H5 hemagglutinin protects against highly pathogenic H5N1 avian influenza viruses abstract: Recent advances in reverse genetics techniques make it possible to manipulate the genome of RNA viruses such as Newcastle disease virus (NDV). Several NDV vaccine strains have been used as vaccine vectors in poultry, mammals, and humans to express antigens of different pathogens. The safety, immunogenicity, and protective efficacy of these NDV-vectored vaccines have been evaluated in pre-clinical and clinical studies. The vaccines are safe in mammals, humans, and poultry. Bivalent NDV-vectored vaccines against pathogens of economic importance to the poultry industry have been developed. These bivalent vaccines confer solid protective immunity against NDV and other foreign antigens. In most cases, NDV-vectored vaccines induce strong local and systemic immune responses against the target foreign antigen. This review summarizes the development of NDV-vectored vaccines and their potential use as a base for designing other effective vaccines for veterinary and human use. url: https://www.ncbi.nlm.nih.gov/pubmed/28775971/ doi: 10.7774/cevr.2017.6.2.72 id: cord-270243-moxleyjg author: Cholleti, Harindranath title: Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique date: 2018-05-28 words: 3245.0 sentences: 190.0 pages: flesch: 50.0 cache: ./cache/cord-270243-moxleyjg.txt txt: ./txt/cord-270243-moxleyjg.txt summary: Conclusions: In summary, this study has identified a highly divergent virus with in the Orthomyxoviridae family associated with Rhipicephalus ticks from Mozambique. Different studies have shown that viral pathogens, such as Thogoto viruses, Wad Medani virus, Nairobi sheep disease virus, Crimean-Congo hemorrhagic fever virus, African swine fever virus and Tick-borne encephalitis virus [1, [6] [7] [8] , can be found in Rhipicephalus ticks. Numerous studies have used metagenomics to explore viral communities in different arthropod species and have in these identified viruses associated with a broad range of animals, plants and insects. However, the identified ORFs exhibit high genetic diversity to known quaranjavirus genomes, with an amino acid identity of only 32-55%, indicating that these represent novel viral sequences belonging to the Quaranjavirus genus. The parvovirus sequences identified in the current study had closest similarity to non-structural protein 1 of different densoviruses, which were shown previously to integrate into tick genomes such as in Ixodes, Amblyomma and Rhipicephalus genera [28, 29] . abstract: Background: Ticks are primary vectors for many well-known disease-causing agents that affect human and animal populations globally such as tick-borne encephalitis, Crimean-Congo hemorrhagic fever and African swine fever. In this study, viral metagenomics was used to identify what viruses are present in Rhipicephalus spp. ticks collected in the Zambezi Valley of Mozambique. Methods: The RNA was amplified with sequence-independent single primer amplification (SISPA) and high-throughput sequencing was performed on the Ion Torrent platform. The generated sequences were subjected to quality check and classfied by BLAST. CodonCode aligner and SeqMan were used to assemble the sequences. Results: The majority of viral sequences showed closest sequence identity to the Orthomyxoviridae family, although viruses similar to the Parvoviridae and Coronaviridae were also identified. Nearly complete sequences of five orthomyxoviral segments (HA, NP, PB1, PB2, and PA) were obtained and these showed an amino acid identity of 32–52% to known quaranjaviruses. The sequences were most closely related to the Wellfleet Bay virus, detected and isolated from common eider during a mortality event in the USA. Conclusions: In summary, this study has identified a highly divergent virus with in the Orthomyxoviridae family associated with Rhipicephalus ticks from Mozambique. Further genetic and biological studies are needed in order to investigate potential pathogenesis of the identified orthomyxovirus. url: https://www.ncbi.nlm.nih.gov/pubmed/29868166/ doi: 10.1080/20008686.2018.1478585 id: cord-324696-htx0ul4o author: Chothe, Shubhada K. title: Avian and human influenza virus compatible sialic acid receptors in little brown bats date: 2017-04-06 words: 3853.0 sentences: 212.0 pages: flesch: 50.0 cache: ./cache/cord-324696-htx0ul4o.txt txt: ./txt/cord-324696-htx0ul4o.txt summary: This first ever study of IAV receptors in a bat species suggest that LBBs, a widely-distributed bat species in North America, could potentially be co-infected with avian and human IAVs, facilitating the emergence of zoonotic strains. To resolve this enigma, we investigated for the first time the distribution of SA receptors in little brown bats (LBBs) (Myotis lucifugus), a widely-distributed bat species in North America and their compatibility to support avian and human IAV binding. H5N2 virus binding pattern was in accordance with the relative abundance of SA α2,3-Gal receptors in tissues such that greater virus binding to the tracheal ( In addition to the virus binding assay using antibody-based detection, we also visualized virus binding using scanning electron microscopy (SEM) which also confirmed abundant binding of avian H5N2 virus (Fig. 5A ) and human H1N1 virus (Fig. 5B ) to LBB trachea (Fig. 5) . time, this study demonstrated that little brown bats (LBBs), a widely-distributed bat species in North America, co-express both avian and human type influenza receptors in their respiratory and gastrointestinal systems. abstract: Influenza A viruses (IAVs) continue to threaten animal and human health globally. Bats are asymptomatic reservoirs for many zoonotic viruses. Recent reports of two novel IAVs in fruit bats and serological evidence of avian influenza virus (AIV) H9 infection in frugivorous bats raise questions about the role of bats in IAV epidemiology. IAVs bind to sialic acid (SA) receptors on host cells, and it is widely believed that hosts expressing both SA α2,3-Gal and SA α2,6-Gal receptors could facilitate genetic reassortment of avian and human IAVs. We found abundant co-expression of both avian (SA α2,3-Gal) and human (SA α2,6-Gal) type SA receptors in little brown bats (LBBs) that were compatible with avian and human IAV binding. This first ever study of IAV receptors in a bat species suggest that LBBs, a widely-distributed bat species in North America, could potentially be co-infected with avian and human IAVs, facilitating the emergence of zoonotic strains. url: https://doi.org/10.1038/s41598-017-00793-6 doi: 10.1038/s41598-017-00793-6 id: cord-286708-igu984oc author: Chua, Kaw Bing title: Identification and Characterization of a New Orthoreovirus from Patients with Acute Respiratory Infections date: 2008-11-25 words: 4359.0 sentences: 219.0 pages: flesch: 53.0 cache: ./cache/cord-286708-igu984oc.txt txt: ./txt/cord-286708-igu984oc.txt summary: Recently, our group reported the isolation of the Melaka virus from a patient with acute respiratory disease and provided data suggesting that this new orthoreovirus is capable of human-to-human transmission and is probably of bat origin. Here we report yet another Melaka-like reovirus (named Kampar virus) isolated from the throat swab of a 54 year old male patient in Kampar, Perak, Malaysia who was suffering from high fever, acute respiratory disease and vomiting at the time of virus isolation. Here, we report the discovery and characterization of Kampar virus (KamV), the fourth member in the NBV species group and its isolation from a human patient with fever and acute respiratory illness. Due to the similar CPE morphology ( Figure 1 ) and cell line susceptibility patterns between KamV and the recently discovered Melaka virus (MelV), which also causes acute respiratory diseases in humans [5] , immunofluorescent antibody testing was conducted to examine cross reactivity. abstract: First discovered in the early 1950s, reoviruses (respiratory enteric orphan viruses) were not associated with any known disease, and hence named orphan viruses. Recently, our group reported the isolation of the Melaka virus from a patient with acute respiratory disease and provided data suggesting that this new orthoreovirus is capable of human-to-human transmission and is probably of bat origin. Here we report yet another Melaka-like reovirus (named Kampar virus) isolated from the throat swab of a 54 year old male patient in Kampar, Perak, Malaysia who was suffering from high fever, acute respiratory disease and vomiting at the time of virus isolation. Serological studies indicated that Kampar virus was transmitted from the index case to at least one other individual and caused respiratory disease in the contact case. Sequence analysis of the four small class genome segments indicated that Kampar and Melaka viruses are closely related. This was confirmed by virus neutralization assay, showing an effective two-way cross neutralization, i.e., the serum against one virus was able to neutralize the other. Although the exact origin of Kampar virus is unknown, epidemiological tracing revealed that the house of the index case is surrounded by fruit trees frequently visited by fruit bats. There is a high probability that Kampar virus originated from bats and was transmitted to humans via bat droppings or contaminated fruits. The discovery of Kampar virus highlights the increasing trend of emergence of bat zoonotic viruses and the need to expand our understanding of bats as a source of many unknown viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/19030226/ doi: 10.1371/journal.pone.0003803 id: cord-351197-xv6ymc4l author: Cibulski, Samuel title: A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil date: 2020-09-28 words: 1711.0 sentences: 124.0 pages: flesch: 54.0 cache: ./cache/cord-351197-xv6ymc4l.txt txt: ./txt/cord-351197-xv6ymc4l.txt summary: From chicken, six distinct gyroviruses (GyV) were detected, including GyV3 and GyV6, which for the first time were detected in samples from avian species, plus a novel smacovirus species and two highly divergent circular Rep-encoding ssDNA (CRESS-DNA) viruses. A detailed taxonomic 136 classification, including the numbers of reads for each Eukarya-related viral contig 137 recovered is this study, is provided in Supplementary gives them the ability to persist and spread in the environment. A detailed taxonomic classification, including the numbers of 245 J o u r n a l P r e -p r o o f sequenced reads of each Eukarya-related viral contig recovered in this study, is 246 provided in Supplementary Table 1 . including numbers of sequenced reads of each Eukarya-related viral contig recovered in 334 this study, is provided in Supplementary Table 1 . Cressdnaviricota: a virus phylum unifying 7 families of Rep-encoding 519 viruses with single-stranded, circular DNA genomes abstract: A viral metagenomics study was conducted in beef, pork, and chicken sold in supermarkets from Southern Brazil. From chicken, six distinct gyroviruses (GyV) were detected, including GyV3 and GyV6, which for the first time were detected in samples from avian species, plus a novel smacovirus species and two highly divergent circular Rep-encoding ssDNA (CRESS-DNA) viruses. From pork, genomes of numerous anelloviruses, porcine parvovirus 5 (PPV5) and 6 (PPV6), two new genomoviruses and two new CRESS-DNA viruses were found. Finally, two new CRESS-DNA genomes were recovered from beef. Although none of these viruses have history of transmission to humans, the findings reported here reveal that such agents are inevitably consumed in diets that include these types of meat. url: https://www.ncbi.nlm.nih.gov/pubmed/33032031/ doi: 10.1016/j.virol.2020.09.005 id: cord-317277-rr9zue4l author: Cifuentes-Munoz, Nicolas title: Viral cell-to-cell spread: Conventional and non-conventional ways date: 2020-09-29 words: 13085.0 sentences: 638.0 pages: flesch: 45.0 cache: ./cache/cord-317277-rr9zue4l.txt txt: ./txt/cord-317277-rr9zue4l.txt summary: Cell-free viral particles can be released into the extracellular space through different mechanisms, such as: (a) cell lysis induced by viral proteins, as is the case for many non-enveloped viruses such as reoviruses, rotaviruses, adenoviruses and picornaviruses (Giorda and Hebert, 2013; Hu et al., 2012; Nieva et al., 2012) ; (b) by budding directly from the plasma membrane, where virions acquire their envelope, as is the case of human immunodeficiency virus (HIV-1), influenza, paramyxoviruses, and pneumoviruses (Lorizate and Krausslich, 2011; Votteler and Sundquist, 2013; Weissenhorn et al., 2013) ; (c) by exocytosis of intracellularly assembled viral particles, as is the case for bunyaviruses, flaviviruses and coronaviruses (Cifuentes-Munoz et al., 2014; Lorizate and Krausslich, 2011) . An interesting observation made for alphaviruses is that the filopodia-like extensions are not able to transfer cytosolic or plasma membrane components, suggesting they are not openended connections like TNTs. Instead, viral particles are hypothesized to bud into a protected space at the filopodial tip and then rapidly enter the target cell, preventing access of neutralizing antibodies. abstract: A critical step in the life cycle of a virus is spread to a new target cell, which generally involves the release of new viral particles from the infected cell which can then initiate infection in the next target cell. While cell-free viral particles released into the extracellular environment are necessary for long distance spread, there are disadvantages to this mechanism. These include the presence of immune system components, the low success rate of infection by single particles, and the relative fragility of viral particles in the environment. Several mechanisms of direct cell-to-cell spread have been reported for animal viruses which would avoid the issues associated with cell-free particles. A number of viruses can utilize several different mechanisms of direct cell-to-cell spread, but our understanding of the differential usage by these pathogens is modest. Although the mechanisms of cell-to-cell spread differ among viruses, there is a common exploitation of key pathways and components of the cellular cytoskeleton. Remarkably, some of the viral mechanisms of cell-to-cell spread are surprisingly similar to those used by bacteria. Here we summarize the current knowledge of the conventional and non-conventional mechanisms of viral spread, the common methods used to detect viral spread, and the impact that these mechanisms can have on viral pathogenesis. url: https://www.sciencedirect.com/science/article/pii/S0065352720300427 doi: 10.1016/bs.aivir.2020.09.002 id: cord-275821-yu39aw54 author: Ciminski, Kevin title: Novel insights into bat influenza A viruses date: 2017-09-14 words: 5218.0 sentences: 259.0 pages: flesch: 44.0 cache: ./cache/cord-275821-yu39aw54.txt txt: ./txt/cord-275821-yu39aw54.txt summary: Although there is a certain degree of functional compatibility between bat and conventional influenza A virus proteins, there are striking differences, including receptor usage, polarity of infection and reassortment potential. In addition, as the bat IAV non-structural protein 1 (NS1) was previously shown to share the dsRNA-binding property and IFN-suppression characteristics of conventional IAV NS1s [38] , an infectious recombinant PR8 virus encoding the NS1 but not NEP gene of HL17NL10 could be generated [39] . The vRNA packaging signals and the NP proteins of The exchange of genomic segments is known to take place in cells co-infected with different conventional IAV subtypes. Likewise, based on experiments with chimeric bat influenza viruses, genomic reassortment is believed to occur in cells co-infected with the known bat IAV subtypes. abstract: In 2012 and 2013, influenza virus genome sequences of two new influenza A virus (IAV) subtypes were discovered in bat specimens, but further characterization was largely impeded by the lack of infectious virus. With the identification of highly susceptible cell lines, reconstitution of infectious bat IAV by reverse genetics recently succeeded and allowed a first insight into the life cycle of these viruses. Although there is a certain degree of functional compatibility between bat and conventional influenza A virus proteins, there are striking differences, including receptor usage, polarity of infection and reassortment potential. url: https://doi.org/10.1099/jgv.0.000927 doi: 10.1099/jgv.0.000927 id: cord-350467-18bvwxci author: Clark, K.J title: In vitro studies on the use of clay, clay minerals and charcoal to adsorb bovine rotavirus and bovine coronavirus date: 1998-10-01 words: 3418.0 sentences: 175.0 pages: flesch: 48.0 cache: ./cache/cord-350467-18bvwxci.txt txt: ./txt/cord-350467-18bvwxci.txt summary: Experiments were designed to test the ability of various adsorbent materials to tightly bind bovine rotavirus and coronavirus. The suspended samples of clay bound virus or clay/virus complex retained from the adsorption and desorption experiments were used for infectivity testing. Charcoal, sodium bentonite, attapulgite, kaolinite, and HSCAS III were found to adsorb greater than 99.0% of bovine rotavirus while the other materials assayed ranged in their adsorptive capabilities from less than 99% to greater than 78% (Table 1) . As both bovine rotavirus and coronavirus bound to various adsorbent materials, including HSCAS I and II, with high affinity, both were tested for infectivity when in the bound state. They may have a distinct advantage in prevention of infection and/or disease because most agents that cause gastroenteritis, including rotavirus and coronavirus, are generally contracted orally, usually via contaminated food and water. abstract: Rotaviruses are the leading cause and coronaviruses are the major contributors of acute gastroenteritis in the young of various mammalian and avian species. Despite numerous trials and decades of research, vaccines have limited efficacy particularly for calves. As an alternative method of controlling infection, we have investigated broad spectrum antiviral agents that are not discriminatory among various viruses. This report involves testing a variety of adsorbent agents including charcoal, clay, and clay minerals to adsorb rotavirus and coronavirus in vitro. Results revealed that all the adsorbent agents had good to excellent capability of adsorbing rotavirus and excellent capability of adsorbing coronavirus. Percent adsorptions ranged from 78.74% to 99.89% for rotavirus and 99.99% for coronavirus; while sand (negative control) was <0.01%. A high affinity binding was present as determined by a low percent desorption (0.06–3.09%). However, the adsorbent bound virus complex retained, and may have actually enhanced, infectivity. url: https://www.sciencedirect.com/science/article/pii/S0378113598002417 doi: 10.1016/s0378-1135(98)00241-7 id: cord-302486-z36hcvrx author: Cobo, Fernando title: Diagnostic approaches for viruses and prions in stem cell banks date: 2006-03-30 words: 7276.0 sentences: 347.0 pages: flesch: 41.0 cache: ./cache/cord-302486-z36hcvrx.txt txt: ./txt/cord-302486-z36hcvrx.txt summary: Viral and prion contamination of cell cultures and "feeder" cells, which is a common risk in all biotechnological products derived from the cell lines, is the most challenging and potentially serious outcome to address, due to the difficulty involved in virus and prion detection and the potential to cause serious disease in recipients of these cell products. The use of bovine fetal serum in stem cell cultures requires an urgent need for a risk assessment for Transmissible Spongiform Encephalopathies (TSEs) by means of a sensitive and specific test in all products derived from ruminants (U.S. Food and Drugs Administration, 1999; Directive 2004/C 24/ 03). This panel of tests should necessarily include reverse transcriptase detection as a general test for retroviruses, electron microscopy that can detect different kinds of viral particles and characterize many unknown isolates present in cell cultures and molecular techniques like PCR (conventional or real-time) and RT-PCR tests to include all the viruses that we know pose a risk to the product. abstract: Some stem cell lines may contain an endogenous virus or can be contaminated with exogenous viruses (even of animal origin) and may secrete viral particles or express viral antigens on their surface. Moreover, certain biotechnological products (e.g. bovine fetal serum, murine feeder cells) may contain prion particles. Viral and prion contamination of cell cultures and “feeder” cells, which is a common risk in all biotechnological products derived from the cell lines, is the most challenging and potentially serious outcome to address, due to the difficulty involved in virus and prion detection and the potential to cause serious disease in recipients of these cell products. Stem cell banks should introduce adequate quality assurance programs like the microbiological control program and can provide researchers with valuable support in the standardization and safety of procedures and protocols used for the viral and prion testing and in validation programs to assure the quality and safety of the cells. url: https://api.elsevier.com/content/article/pii/S0042682205007725 doi: 10.1016/j.virol.2005.11.026 id: cord-270091-sqrh8ylt author: Cohen, Pascal title: Vascularites associées aux infections virales date: 2004-11-30 words: 6087.0 sentences: 531.0 pages: flesch: 43.0 cache: ./cache/cord-270091-sqrh8ylt.txt txt: ./txt/cord-270091-sqrh8ylt.txt summary: Résumé Des virus, causes de vascularites Si la plupart des vascularites systémiques sont de cause inconnue, la responsabilité d''une infection virale a été démontrée de façon formelle pour certaines d''entre elles, un traitement spécifique pouvant les guérir définitivement. Cryoglobulinemia related to the hepatitis C virus (HCV) The clinical manifestations are those of systemic vasculitis with particular tropism for the skin (involvement generally inaugural and almost constant), peripheral nerves and the glomerula. Des virus, causes de vascularites Si la plupart des vascularites systémiques sont de cause inconnue, la responsabilité d''une infection virale a été démontrée de façon formelle pour certaines d''entre elles, un traitement spécifique pouvant les guérir définitivement. L''infection à HTLV1 est rarement compliquée de vascularite ;cette dernière a un tropisme neurologique central 181 192, 193 qui fut le premier à décrire la responsabilité liée à l''hépatite B au cours de la périartérite noueuse 194 , nous décidâmes d''inclure dans un protocole prospectif tous les patients atteints de PAN HBV+ et de traiter les patients par une combinaison d''antiviraux et d''échanges plasmatiques 195 . abstract: Résumé Des virus, causes de vascularites Si la plupart des vascularites systémiques sont de cause inconnue, la responsabilité d’une infection virale a été démontrée de façon formelle pour certaines d’entre elles, un traitement spécifique pouvant les guérir définitivement. Chaque virus incriminé rend compte d’un type particulier de vascularite. Infection par le virus de l’hépatite B (VHB) Elle est la cause de la périartérite noueuse dans 36 à 50 % des cas. La symptomatologie apparaît de façon aiguë, en général dans les mois suivant l’infection; elle est comparable à celle observée en l’absence d’infection par VHB. Cryoglobulinémies liées au virus de l’hépatite C (VHC) Les manifestations cliniques sont celles d’une vascularite systémique avec un tropisme plus particulier pour la peau (atteinte le plus souvent inaugurale et presque constante), les nerfs périphériques, les glomérules. Elles surviennent assez tardivement au décours de l’infection. Vascularites associées à l’infection par le VIH (virus de l’immunodéficience humaine) Il existe un fort tropisme pour le système nerveux périphérique (multinévrites) et central. Au cours de l’infection aiguë par le Parvovirus B19 Des lésions de vascularite ont été parfois signalées après la phase virémique, se limitant généralement à une ou plusieurs poussées de pupura vasculaire prédominant aux membres inférieurs. Après infection par le virus varicelle-zona Une vascularite se développe parfois, sous la forme d’un déficit neurologique central (déficit moteur avec ou sans aphasie environ un mois après un zona ophtalmologique), d’une atteinte de la rétine, plus rarement de la peau ou des reins. Vascularites associées à l’infection par le cytomégalovirus (CMV) Survenant essentiellement chez le sujet immunodéprimé, les vascularites après infection par le CMV sont diffuses intéressant surtout le tube digestif, en particulier le côlon, le système nerveux central et la peau. Une complication rare de l’infection à HTLV1 (Human T-cell Lymphoma Virus) Une vascularite rétinienne prenant volontiers la forme d’une rétinite nécrosante est souvent associée à une paraparésie spasmodique. Stratégie thérapeutique Pour de nombreuses vascularites d’origine virale, les traitements corticoïdes et immunosuppresseurs ne sont indiqués qu’en seconde intention en cas d’échec des antiviraux et de l’association d’antiviraux et d’échanges plasmatiques. Summary Viruses, the cause of vasculitis Although the majority of systemic vasculitis are of unknown causes, the responsibility of a viral infection has been formally demonstrated in some of them and specific treatment can permanently cure them. Each virus incriminated accounts for a particular type of vasculitis. Hepatitis B viral infection (HBV) is the cause of polyarteritis nodosa in 36 to 50% of cases. The onset of the symptomatology is acute, usually within a few months following the infection; it is comparable to that observed in the absence of HBV infection. Cryoglobulinemia related to the hepatitis C virus (HCV) The clinical manifestations are those of systemic vasculitis with particular tropism for the skin (involvement generally inaugural and almost constant), peripheral nerves and the glomerula. They occur fairly late during the infection. Vasculitis associated with HIV infection There is strong tropism for the peripheral (multi-neuritis) and central nervous system. During acute parvovirus B19 infection Vasculitis lesions have occasionally been reported following the viremic phase, generally limited to one or several flares of vascular purpura predominating on the lower limbs. Following varicella-herpes zoster infection Vasculitis occasionally develops in the form of a central neurological deficiency (locomotor deficiency with or without aphasia around one month after an ophthalmologic herpes zoster) or involving the retina or, more rarely, the skin or the kidneys. Vasculitis associated with cytomegaloviral infection Predominantly observed in immunodepressed patients, vasculitis after CMV infection is diffuse and basically involving the digestive tube, notably the colon, the central nervous system and the skin. A rare complication of an HTLV1 infection Vasculitis of the retina often in the form of necrotic retinitis is often associated with spasmodic paraparessia. Therapeutic strategy For many vasculitis of viral origin, corticosteroid and immunosuppressive treatments are only indicated in second intention following failure with antiviral agents and the combination of antivirals and plasma exchanges. url: https://www.sciencedirect.com/science/article/pii/S0755498204989361 doi: 10.1016/s0755-4982(04)98936-1 id: cord-004501-guiy89x8 author: Cojocaru, Florina-Daniela title: Nanomaterials Designed for Antiviral Drug Delivery Transport across Biological Barriers date: 2020-02-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viral infections are a major global health problem, representing a significant cause of mortality with an unfavorable continuously amplified socio-economic impact. The increased drug resistance and constant viral replication have been the trigger for important studies regarding the use of nanotechnology in antiviral therapies. Nanomaterials offer unique physico-chemical properties that have linked benefits for drug delivery as ideal tools for viral treatment. Currently, different types of nanomaterials namely nanoparticles, liposomes, nanospheres, nanogels, nanosuspensions and nanoemulsions were studied either in vitro or in vivo for drug delivery of antiviral agents with prospects to be translated in clinical practice. This review highlights the drug delivery nanosystems incorporating the major antiviral classes and their transport across specific barriers at cellular and intracellular level. Important reflections on nanomedicines currently approved or undergoing investigations for the treatment of viral infections are also discussed. Finally, the authors present an overview on the requirements for the design of antiviral nanotherapeutics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7076512/ doi: 10.3390/pharmaceutics12020171 id: cord-004280-c470nlie author: Coleman, Kristen K. title: Airborne Influenza A Virus Exposure in an Elementary School date: 2020-02-05 words: 4118.0 sentences: 212.0 pages: flesch: 46.0 cache: ./cache/cord-004280-c470nlie.txt txt: ./txt/cord-004280-c470nlie.txt summary: In this study, we evaluated the use of a bioaerosol sampling method to noninvasively detect and quantify airborne influenza A virus (IAV) densities in a public elementary school. Significantly different (p = 0.049) airborne IAV densities were detected between all three indoor locations (i.e., gymnasium, classroom, and corridor) and all positive samples were collected during the last two weeks of 66 , and a 20-30% relative humidity level; Descriptive of an average elementary school student in the USA weighing ~23-32 kg with an assumed tidal volume (V T ) of 7 mL per kg of body mass. Given the high airborne IAV densities detected in the school corridor, along with elevated student contact rates, it is plausible to conclude that the school corridor is a "hotspot" for influenza virus transmission. abstract: Influenza contributes significantly to childhood morbidity and mortality. Given the magnitude of the school-aged child population, a sizeable proportion of influenza virus transmission events are expected to occur within school settings. However, influenza virus activity in schools is not well-understood, likely due to our limited ability to accurately monitor for respiratory viruses without disrupting the school environment. In this study, we evaluated the use of a bioaerosol sampling method to noninvasively detect and quantify airborne influenza A virus (IAV) densities in a public elementary school. Air samples were collected from multiple locations in the school, two days per week, throughout an eight-week sampling period during influenza season. Real-time RT-PCR targeting the IAV M gene revealed detectable IAV on five occasions in densities ranging from 2.0 × 10(−1) to 1.9 × 10(4). No significant differences in IAV densities were related to student presence/absence. The majority of IAV-associated particles were ≤4 μm in diameter, and theoretical calculations indicate infectious thresholds after minutes of exposure. Our study represents the first identification and quantification of airborne influenza virus in an elementary school, and the results suggest that airborne IAV has the potential to circulate in schools during influenza season, in large enough doses known to cause infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7002614/ doi: 10.1038/s41598-020-58588-1 id: cord-339973-kj56zi59 author: Coleman, Kristen K. title: Bioaerosol Sampling for Respiratory Viruses in Singapore’s Mass Rapid Transit Network date: 2018-11-30 words: 4775.0 sentences: 228.0 pages: flesch: 46.0 cache: ./cache/cord-339973-kj56zi59.txt txt: ./txt/cord-339973-kj56zi59.txt summary: Although baseline metagenomic maps created from these studies are said to be useful for mitigating bioterrorism and infectious disease outbreaks, most of them focus largely on mapping surface-borne bacterial DNA 17 and neglect to address the threat of weaponized or global catastrophic biological risk-level (GCBR-level) agents, both of which would likely be aerosolized or respiratory-borne RNA viruses 19 . Bioaerosol sampling in the field provides a noninvasive way to monitor and characterize the community of aerosolized respiratory viruses that regularly infect the public, as well as potentially detect or discover novel pathogens with pandemic potential, such as the influenza A(H7N9) virus. Although the air pump flow rate and sample collection times used in our study have been demonstrated to efficiently capture aerosolized influenza virus and RSV RNA [33] [34] [35] , it is possible that these parameters are not optimal for capturing the other respiratory virus DNA/RNA targeted in our study. abstract: As a leading global city with a high population density, Singapore is at risk for the introduction of novel biological threats. This risk has been recently reinforced by human epidemics in Singapore of SARS coronavirus, 2009 pandemic H1N1 influenza A virus, and enterovirus 71. Other major threats to Singapore include MERS-coronavirus and various avian and swine influenza viruses. The ability to quickly identify and robustly track such threats to initiate an early emergency response remains a significant challenge. In an effort to enhance respiratory virus surveillance in Singapore, our team conducted a pilot study employing a noninvasive bioaerosol sampling method to detect respiratory viruses in Singapore’s Mass Rapid Transit (MRT) network. Over a period of 52 weeks, 89 aerosol samples were collected during peak MRT ridership hours. Nine (10%) tested positive for adenovirus, four (4.5%) tested positive for respiratory syncytial virus type A, and one (1%) tested positive for influenza A virus using real-time RT-PCR/PCR. To our knowledge, this is the first time molecular evidence for any infectious respiratory agent has been collected from Singapore’s MRT. Our pilot study data support the possibility of employing bioaerosol samplers in crowded public spaces to noninvasively monitor for respiratory viruses circulating in communities. url: https://doi.org/10.1038/s41598-018-35896-1 doi: 10.1038/s41598-018-35896-1 id: cord-355872-z6vsjmxn author: Colón-López, Daisy D. title: Emerging viral infections date: 2019-08-15 words: 3708.0 sentences: 194.0 pages: flesch: 36.0 cache: ./cache/cord-355872-z6vsjmxn.txt txt: ./txt/cord-355872-z6vsjmxn.txt summary: Characterization of bacterial and viral relationships in mosquito arthropods demonstrated a symbiotic relationship between the bacterium and host, limiting dengue virus infection and potentially revealing new antiviral strategies [39, 40] . The Ebola virus outbreak in West Africa resulted in 26,648 cases and 11,017 documented deaths, and genomic sequencing was applied in near real-time to provide information to aid in containing the outbreak [44, 45] . During the Ebola virus outbreak, sequence analysis of the viral genome over time demonstrated changes which could make the pathogen resistant to therapeutics such as siRNAs, phosphorodiamidate morpholino oligomers (PMOs), and antibodies [56] . This agnostic method is appropriate for identifying changes in the human transcriptome as a result of an emerging viral infection to show specific mechanisms of immune response evasion and other effects in the host''s biology at the transcriptomic level. abstract: The emergence of viral infections is driven by multiple factors including changes in human behavior, population growth, reservoir host distribution, viral diversity and environmental changes. Effective surveillance methods, diagnostic assays and containment measures are pivotal to preventing widespread outbreak of a new viral infection. However, the limited understanding of some emerging viruses poses numerous challenges for effective intervention. In this chapter we discuss various genomics-based methods and strategies to overcome these inherent challenges of emerging and re-emerging viral infections with a focus on current viral threats. We also provide an outlook on the use of genomic tools in personalized medicine and potential solutions to current and foreseeable challenges. url: https://api.elsevier.com/content/article/pii/B9780128014967000101 doi: 10.1016/b978-0-12-801496-7.00010-1 id: cord-289017-vwye3pk9 author: Comach, Guillermo title: Sentinel Surveillance of Influenza-Like Illness in Two Hospitals in Maracay, Venezuela: 2006–2010 date: 2012-09-11 words: 6262.0 sentences: 301.0 pages: flesch: 47.0 cache: ./cache/cord-289017-vwye3pk9.txt txt: ./txt/cord-289017-vwye3pk9.txt summary: CONCLUSIONS/SIGNIFICANCE: Influenza viruses were the most commonly detected viral organisms among patients with acute febrile respiratory illnesses presenting at two hospitals in Maracay, Venezuela. Recent prospective studies, which utilized more sensitive methods for detecting respiratory viruses such as multiplex polymerase chain reaction (PCR), have similarly demonstrated that the highest rates of viral respiratory infection occur among children and the frequency of infection tends to decrease with age due to increasing acquired immunity [8] . On the other hand, the percentage of influenza viruses (not including pH1N1) detected in our study during a similar period of time, but in different years accounted for the significant differences found in both studies: a) the collection, preservation and further processing of respiratory samples, and b) the type of cells and IFA reagents used for virus isolation and identification. In contrast, a prospective study of ILI among Brazilian adults, which utilized viral isolation and RT-PCR testing on respiratory samples, detected rhinoviruses in 19.6% of patients [14] . abstract: BACKGROUND: Limited information exists on the epidemiology of acute febrile respiratory illnesses in tropical South American countries such as Venezuela. The objective of the present study was to examine the epidemiology of influenza-like illness (ILI) in two hospitals in Maracay, Venezuela. METHODOLOGY/PRINCIPAL FINDINGS: We performed a prospective surveillance study of persons with ILI who presented for care at two hospitals in Maracay, Venezuela, from October 2006 to December 2010. A respiratory specimen and clinical information were obtained from each participant. Viral isolation and identification with immunofluorescent antibodies and molecular methods were employed to detect respiratory viruses such as adenovirus, influenza A and B, parainfluenza, and respiratory sincytial virus, among others. There were 916 participants in the study (median age: 17 years; range: 1 month – 86 years). Viruses were identified in 143 (15.6%) subjects, and one participant was found to have a co-infection with more than one virus. Influenza viruses, including pandemic H1N1 2009, were the most frequently detected pathogens, accounting for 67.4% (97/144) of the viruses detected. Adenovirus (15/144), parainfluenza virus (13/144), and respiratory syncytial virus (11/144) were also important causes of ILI in this study. Pandemic H1N1 2009 virus became the most commonly isolated influenza virus during its initial appearance in 2009. Two waves of the pandemic were observed: the first which peaked in August 2009 and the second - higher than the preceding - that peaked in October 2009. In 2010, influenza A/H3N2 re-emerged as the most predominant respiratory virus detected. CONCLUSIONS/SIGNIFICANCE: Influenza viruses were the most commonly detected viral organisms among patients with acute febrile respiratory illnesses presenting at two hospitals in Maracay, Venezuela. Pandemic H1N1 2009 influenza virus did not completely replace other circulating influenza viruses during its initial appearance in 2009. Seasonal influenza A/H3N2 was the most common influenza virus in the post-pandemic phase. url: https://www.ncbi.nlm.nih.gov/pubmed/22984519/ doi: 10.1371/journal.pone.0044511 id: cord-020714-h1fevqcw author: Compans, Richard W. title: Membrane Glycoproteins of Enveloped Viruses date: 2008-05-30 words: 14149.0 sentences: 684.0 pages: flesch: 43.0 cache: ./cache/cord-020714-h1fevqcw.txt txt: ./txt/cord-020714-h1fevqcw.txt summary: Other advantages of enveloped viruses in studies of membrane structure and biogenesis include the ease of biosynthetic labeling of viruses grown in cell culture with specific radioactive precursors and the availability of mutants in defined gene products, some of which are proving to be useful in the analysis of viral membrane assembly. Apart from minor differences in carbohydrates of glycoproteins, virion proteins are indistinguishable when the virus is propagated in a variety of cells; therefore there appears to be little or no determining influence of viral proteins on the composition of the lipid bilayer. Based upon the estimated carbohydrate content (12,000 daltons) of the HA glycoprotein obtained by Laver (1971) and Schwarz and Klenk (1974) and the size estimates of the type I and I1 glycopeptides of influenza virus grown in MDBK cells, it was estimated that HA, contains a single type I glycopeptide whereas HA, possesses two type I and one or two type I1 oligosaccharide side-chains for the WSN strain (Nakamura and Com pans, 1978b) . abstract: This chapter focuses on the recent information of the glycoprotein components of enveloped viruses and points out specific findings on viral envelopes. Although enveloped viruses of different major groups vary in size and shape, as well as in the molecular weight of their structural polypeptides, there are general similarities in the types of polypeptide components present in virions. The types of structural components found in viral membranes are summarized briefly in the chapter. All the enveloped viruses studied to date possess one or more glycoprotein species and lipid as a major structural component. The presence of carbohydrate covalently linked to proteins is demonstrated by the incorporation of a radioactive precursor, such as glucosamine or fucose, into viral polypeptides, which is resolved by sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis. Enveloped viruses share many common features in the organization of their structural components, as indicated by several approaches, including electron microscopy, surface-labeling, and proteolytic digestion experiments, and the isolation of subviral components. The chapter summarizes the detailed structure of the glycoproteins of four virus groups: (1) influenza virus glycoproteins, (2) rhabdovirus G protein, (3) togavirus glycoprotein, and (4) paramyxovirus glycoproteins The information obtained includes the size and shape of viral glycoproteins, the number of polypeptide chains in the complete glycoprotein structure, and compositional data on the polypeptide and oligosaccharide portions of the molecules. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7146817/ doi: 10.1016/s0070-2161(08)60750-9 id: cord-280564-kgoczioe author: Conceição-Neto, Nádia title: Identification of an enterovirus recombinant with a torovirus-like gene insertion during a diarrhea outbreak in fattening pigs date: 2017-09-08 words: 6204.0 sentences: 339.0 pages: flesch: 54.0 cache: ./cache/cord-280564-kgoczioe.txt txt: ./txt/cord-280564-kgoczioe.txt summary: title: Identification of an enterovirus recombinant with a torovirus-like gene insertion during a diarrhea outbreak in fattening pigs In the sample, we observed the presence of a small Torovirus contig of 256 bp, which was included in the phylogenetic tree (Fig. 1A , Torovirus/BEL/2015), showing very low similarity with the gene insertion found in the recombinant virus. The enterovirus genome region before the torovirus insertion (VP1-VP4, 2 A, 2B, and 2 C) showed its highest similarity on the amino-acid level (94.5%) with EVG/Porcine/USA/Texas1/ 2014 (Fig. 1C) . In addition to confirming the presence of the enterovirus-torovirus recombinant using Sanger sequencing, we used proteomics to infer whether the protein of the insertion could be found in the sample. Taking the metagenomics data, the Sanger sequence confirmation and the proteomics results all together we can conclude that this recombinant virus is present in the sample and that the inserted protein is being expressed. abstract: Diarrhea outbreaks in pig farms have raised major concerns in Europe and USA, as they can lead to dramatic pig losses. During a suspected outbreak in Belgium of porcine epidemic diarrhea virus (PEDV), we performed viral metagenomics to assess other potential viral pathogens. Although PEDV was detected, its low abundance indicated that other viruses were involved in the outbreak. Interestingly, a porcine bocavirus and several enteroviruses were most abundant in the sample. We also observed the presence of a porcine enterovirus genome with a gene insertion, resembling a C28 peptidase gene found in toroviruses, which was confirmed using re-sequencing, bioinformatics, and proteomics approaches. Moreover, the predicted cleavage sites for the insertion suggest that this gene was being expressed as a single protein, rather than a fused protein. Recombination in enteroviruses has been reported as a major mechanism to generate genetic diversity, but gene insertions across viral families are rather uncommon. Although such inter-family recombinations are rare, our finding suggests that these events may significantly contribute to viral evolution. url: https://doi.org/10.1093/ve/vex024 doi: 10.1093/ve/vex024 id: cord-212761-4bwatc2r author: Contoyiannis, Y. title: On the effectiveness of imposing restrictive measures in a graded Self-Organized Criticality epidemic spread model The case of COVID-19 date: 2020-04-01 words: 4323.0 sentences: 194.0 pages: flesch: 50.0 cache: ./cache/cord-212761-4bwatc2r.txt txt: ./txt/cord-212761-4bwatc2r.txt summary: title: On the effectiveness of imposing restrictive measures in a graded Self-Organized Criticality epidemic spread model The case of COVID-19 However, it is revealed that very close to the critical point, the critical slowing-down (CSD) phenomenon, introduced by the theory of critical phenomena, emerges, leading to a tremendous increase of both the percentage of active carriers and the duration of the epidemic. As expected from the theory of critical phenomena, in the case of initial virus densities ρ below the critical value, time durations of the epidemic spread become significantly small. As already discussed, the proposed self-organized model seems to demonstrate a noteworthy behavior for a virus density equal to its critical value ρc, due to the CSD phenomenon, further leading to spectacularly increased relaxation times (high durations of the epidemic). abstract: The scope of this work is to serve as a guiding tool against subjective estimations on real pandemic situations (mainly due to the inability to acquire objective real data over whole populations). The previously introduced model of closed self-organized criticality (SOC), is adapted in the case of a virus-induced epidemic. In this version this physical model can distinguish the virus spread according to the virus aggressiveness. The study presented, highlights the critical value of virus density over a population. For low values of the initial virus density (lower than the critical value) it is proved that the virus-diffusion behavior is safe and quantitatively similar to usual real epidemical data. However, it is revealed that very close to the critical point, the critical slowing-down (CSD) phenomenon, introduced by the theory of critical phenomena, emerges, leading to a tremendous increase of both the percentage of active carriers and the duration of the epidemic. A behavior of the epidemic obeying to a second order phase transition, also occurs. For virus density values higher than the critical value, the epidemic duration becomes extremely prolonged. Additionally, the effect of the closed system population size revealed interesting properties. All these results, together with an investigation of the effectiveness of applying physical contact restriction measures, document scientifically their worthiness, while they also demonstrate the limits for which herd immunity holds safely. Finally, the model has been compared against real epidemic data in the case of Greece, which imposed restrictive measures consistently and in time. url: https://arxiv.org/pdf/2004.00682v3.pdf doi: nan id: cord-022378-ovxmy1as author: Cook, Jane K.A. title: Coronaviridae date: 2009-05-15 words: 4034.0 sentences: 192.0 pages: flesch: 50.0 cache: ./cache/cord-022378-ovxmy1as.txt txt: ./txt/cord-022378-ovxmy1as.txt summary: IBV also aff ects egg-laying performance, and renal damage associated with infectious bronchitis has become increasingly important, particularly in broilers. Economically, the most important aspects are the eff ects on egg production and quality in laying hens and production performance in broilers, where the initial respiratory infection is frequently exacerbated by secondary infections. In turkeys, coronaviruses (TCoV, also called Bluecomb disease virus and Turkey enteric coronavirus) are known to be associated with enteric disease, mortality and underperformance and to aff ect egg-laying performance in older birds. Th is is a new area of investigation and, while the coronaviruses detected in some gallinaceous and nongallinaceous birds have not so far been associated with disease, these species are potential carriers of IBV and other coronaviruses and could therefore play a role in global transmission of infection. In IBV infection of commercial layers or broiler breeders, respiratory signs may or may not be observed and the most common manifestation is the eff ect on egg production and egg quality. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155630/ doi: 10.1016/b978-0-7020-2862-5.50033-7 id: cord-276506-dj7dyo0x author: Coria, M. F. title: Protective effect of an inactivated avian coronavirus vaccine administered by aerosol date: 1973 words: 1796.0 sentences: 116.0 pages: flesch: 51.0 cache: ./cache/cord-276506-dj7dyo0x.txt txt: ./txt/cord-276506-dj7dyo0x.txt summary: Chickens administered 2 doses of the inactivated Connecticut strain (IBV-46) vaccine by aerosol at 3-week intervals had significant levels of virus-neutralizing antibodies and were resistant to infection by the Massachusetts strain (IBV-41) as determined by virus isolation attempts. Immunity to avian infectious bronchitis (AIB), a highly contagious viral infection of the respiratory tract of chickens has been studied using live and inactivated virus vaccirres (6) . However, more recent evidence shows that a BPL-inactivated AIB virus vaccine administered by an aerosol and concurrent subcutaneous inoculation induced significant levels of VN antibodies and afforded a good degree of protection against infection (4) . Immunization of the human respiratory tract with inactivated influenza A2 I-IongKong virus (13) and rhinovirus type 13 (ii), administered by an aerosol, indicates that a significant protective effect was observed when compared to individuals vaccinated by subcutaneous or intra-muscular routes. The immune response to BPL-inactivated AIB virus vaccines administered by an aerosol, as determined by PI~-NI''s, virus isolation (VI) and respiratory signs are shm~a~ in Table 1 . abstract: The antigenicity and protective effect of 3 strains of avian infectious bronchitis virus inactivated by beta-propiolactone were studied. Chickens administered 2 doses of the inactivated Connecticut strain (IBV-46) vaccine by aerosol at 3-week intervals had significant levels of virus-neutralizing antibodies and were resistant to infection by the Massachusetts strain (IBV-41) as determined by virus isolation attempts. Antibody levels in chickens given inactivated Iowa 33 and Iowa 609 were not significant and they were not resistant to infection by IBV-41. url: https://www.ncbi.nlm.nih.gov/pubmed/4716970/ doi: 10.1007/bf01249930 id: cord-302425-aaxvlktp author: Cortey, Martí title: High levels of unreported intraspecific diversity among RNA viruses in faeces of neonatal piglets with diarrhoea date: 2019-12-05 words: 4998.0 sentences: 248.0 pages: flesch: 52.0 cache: ./cache/cord-302425-aaxvlktp.txt txt: ./txt/cord-302425-aaxvlktp.txt summary: In contrast, other RNA viruses including Kobuvirus, Astrovirus, Sapovirus, Sapelovirus, Teschovirus, and Torovirus, have been detected in pig faeces but its role as causative agents of neonatal diarrhoea has not so far been fully elucidated [10] [11] [12] [13] [14] . The results reported among the 47 diarrhoeic samples analysed include representatives of 12 virus species corresponding to 8 genera of RNA viruses (Additional file 1): Kobuvirus, Rotavirus (RVA, RVB and RVC), Sapovirus (SAV), Mamastrovirus (Porcine Astrovirus types 3 -AstV3 -, 4 -AstV4 -and 5 -AstV5 -), Alphacoronavirus (PEDV), Enterovirus (Enterovirus G, EntVG), Pasivirus (PasiV) and Posavirus (PosaV). Regarding KobuV, our results also agree with an increased prevalence of this agent observed in cases of diarrhoea in suckling piglets worldwide: Brazil [22] , Korea [29] and Vietnam [30] ; despite several (See figure on previous page.) Fig. 5 Neighbor-joining phylogenetic tree based on the p-distance among the nucleotide sequences of the VP7 segment for Rotavirus B. abstract: BACKGROUND: Diarrhoea is a major cause of death in neonate pigs and most of the viruses that cause it are RNA viruses. Next Generation Sequencing (NGS) deeply characterize the genetic diversity among rapidly mutating virus populations at the interspecific as well as the intraspecific level. The diversity of RNA viruses present in faeces of neonatal piglets suffering from diarrhoea in 47 farms, plus 4 samples from non-diarrhoeic piglets has been evaluated by NGS. Samples were selected among the cases submitted to the Veterinary Diagnostic Laboratories of Infectious Diseases of the Universitat Autònoma de Barcelona (Barcelona, Spain) and Universidad de León (León, Spain). RESULTS: The analyses identified the presence of 12 virus species corresponding to 8 genera of RNA viruses. Most samples were co-infected by several viruses. Kobuvirus and Rotavirus were more commonly reported, with Sapovirus, Astrovirus 3, 4 and 5, Enterovirus G, Porcine epidemic diarrhoea virus, Pasivirus and Posavirus being less frequently detected. Most sequences showed a low identity with the sequences deposited in GenBank, allowing us to propose several new VP4 and VP7 genotypes for Rotavirus B and Rotavirus C. CONCLUSIONS: Among the cases analysed, Rotaviruses were the main aetiological agents of diarrhoea in neonate pigs. Besides, in a small number of cases Kobuvirus and Sapovirus may also have an aetiological role. Even most animals were co-infected in early life, the association with enteric disease among the other examined viruses was unclear. The NGS method applied successfully characterized the RNA virome present in faeces and detected a high level of unreported intraspecific diversity. url: https://www.ncbi.nlm.nih.gov/pubmed/31805938/ doi: 10.1186/s12917-019-2204-2 id: cord-316273-vo6j8zb0 author: Cosset, François-Loic title: Cell Entry of Enveloped Viruses date: 2011-02-08 words: 23421.0 sentences: 1013.0 pages: flesch: 40.0 cache: ./cache/cord-316273-vo6j8zb0.txt txt: ./txt/cord-316273-vo6j8zb0.txt summary: On the one hand, they acquired a domain to bind to a specific cellular protein, named "receptor." On the other hand, they developed in a different manner, according to the genus of the virus, a function of fusion that allows the destabilization of the membrane and the opening of a pore through which the genetic material will enter the cell. Thus, we need to distinguish cell surface molecules such as heparan sulfate proteoglycans, DC-SIGN, or integrins that can enhance infections by concentrating retroviruses onto cells (Bounou et al., 2002; Geijtenbeek et al., 2000; Jinno-Oue et al., 2001; Mondor et al., 1998; Pohlmann et al., 2001; Saphire et al., 2001) from authentic receptors that induce conformational changes in EnvGP that are a prerequisite for fusion of the viral and cellular membranes. abstract: Enveloped viruses penetrate their cell targets following the merging of their membrane with that of the cell. This fusion process is catalyzed by one or several viral glycoproteins incorporated on the membrane of the virus. These envelope glycoproteins (EnvGP) evolved in order to combine two features. First, they acquired a domain to bind to a specific cellular protein, named “receptor.” Second, they developed, with the help of cellular proteins, a function of finely controlled fusion to optimize the replication and preserve the integrity of the cell, specific to the genus of the virus. Following the activation of the EnvGP either by binding to their receptors and/or sometimes the acid pH of the endosomes, many changes of conformation permit ultimately the action of a specific hydrophobic domain, the fusion peptide, which destabilizes the cell membrane and leads to the opening of the lipidic membrane. The comprehension of these mechanisms is essential to develop medicines of the therapeutic class of entry inhibitor like enfuvirtide (Fuzeon) against human immunodeficiency virus (HIV). In this chapter, we will summarize the different envelope glycoprotein structures that viruses develop to achieve membrane fusion and the entry of the virus. We will describe the different entry pathways and cellular proteins that viruses have subverted to allow infection of the cell and the receptors that are used. Finally, we will illustrate more precisely the recent discoveries that have been made within the field of the entry process, with a focus on the use of pseudoparticles. These pseudoparticles are suitable for high-throughput screenings that help in the development of natural or artificial inhibitors as new therapeutics of the class of entry inhibitors. url: https://doi.org/10.1016/b978-0-12-380860-8.00004-5 doi: 10.1016/b978-0-12-380860-8.00004-5 id: cord-281844-c0uhcatg author: Costa, Lusmaia D.C. title: Exacerbation of asthma and airway infection: is the virus the villain? date: 2014-12-31 words: 6547.0 sentences: 351.0 pages: flesch: 45.0 cache: ./cache/cord-281844-c0uhcatg.txt txt: ./txt/cord-281844-c0uhcatg.txt summary: Abstract Objective To review the available literature on the association between acute viral respiratory tract infection and the onset of asthma exacerbations, identifying the most prevalent viruses, detection methods, as well as preventive and therapeutic aspects. Studies using reverse transcriptase polymerase chain reaction (RT-PCR) as the detection technique, isolated or combined with traditional methods, observed positivity for respiratory viruses in up to 92.2% of episodes of acute asthma exacerbation in children. Several authors have performed studies aiming to detect viruses in respiratory secretions of exacerbated asthma patients, showing a prevalence of viral identification that varies with several factors, such as patient age, time of the year, method of sample collection, and method of viral detection. The use of viral detection techniques with high sensitivity and specificity has increased the identification of some respiratory viruses in children with asthma exacerbation. abstract: Abstract Objective To review the available literature on the association between acute viral respiratory tract infection and the onset of asthma exacerbations, identifying the most prevalent viruses, detection methods, as well as preventive and therapeutic aspects. Sources A search was conducted in PubMed, Lilacs, and SciELO databases, between the years 2002 and 2013, using the following descriptors: asthma exacerbation, virus, child, and acute respiratory infection. Summary of the findings A total of 42 original articles addressing the identification of respiratory viruses during episodes of asthma exacerbation were selected, mostly cross-sectional studies. There was a wide variation in the methodology of the assessed studies, particularly in relation to the children's age and methods of collection and viral detection. The results indicate that, in up to 92.2% of exacerbations, a viral agent was potentially the main triggering factor, and human rhinovirus was the most frequently identified factor. The pattern of viral circulation may have been responsible for the seasonality of exacerbations. The association between viral infections and allergic inflammation appears to be crucial for the clinical and functional uncontrolled asthma, but few studies have evaluated other triggering factors in association with viral infection. Conclusions Respiratory viruses are present in the majority of asthmatic children during episodes of exacerbation. The involved physiopathological mechanisms are yet to be fully established, and the synergism between allergic inflammation and viral infection appears to determine uncontrolled disease. The role of other triggering and protective agents is yet to be clearly determined. url: https://doi.org/10.1016/j.jped.2014.07.001 doi: 10.1016/j.jped.2014.07.001 id: cord-277327-il8uaavn author: Couch, MD, Robert B. title: Respiratory Viral Infections in Immunocompetent and Immunocompromised Persons date: 1997-03-17 words: 3712.0 sentences: 207.0 pages: flesch: 33.0 cache: ./cache/cord-277327-il8uaavn.txt txt: ./txt/cord-277327-il8uaavn.txt summary: 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. The frequencies of pneumonia and death associated with a documented infection among immunocompromised adult leukemia and bone marrow transplant patients hospitalized at MDACC are shown in Table VII . Although overall frequencies of pneumonia and death appear similar for each virus, analysis of patterns of occurrences suggested a greater severity for RSV infection after bone marrow transplantation or chemotherapy than for the other viruses. Thus, the immune deficiencies described for immunocompromised persons can account for a high frequency of viral respiratory infections as well as an increased severity of illness and a significant risk of death. Combination therapy with aerosolized ribavirin and intravenous immunoglobulin for respiratory syncytial virus disease in adult bone marrow transplant recipients 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-296935-y77c4ro4 author: Couch, Robert B. title: Prior Infections With Seasonal Influenza A/H1N1 Virus Reduced the Illness Severity and Epidemic Intensity of Pandemic H1N1 Influenza in Healthy Adults date: 2011-11-10 words: 3992.0 sentences: 205.0 pages: flesch: 48.0 cache: ./cache/cord-296935-y77c4ro4.txt txt: ./txt/cord-296935-y77c4ro4.txt summary: Serum antibody to the pH1N1 and seasonal A/H1N1 viruses was measured in 579 healthy adults at enrollment (fall 2009) and after surveillance for illness (spring 2010). Preexisting antibody to pH1N1 virus, responses to a single vaccine dose, a low infection-to-illness ratio, and a short duration of illness and virus shedding among those with influenza indicated presence of considerable preexisting immunity to pH1N1 in the population. To assess the clinical and epidemiological impact of pH1N1 infections and to identify immunologic factors correlating with infections and illnesses, we conducted a prospective study of influenza in a young adult population. Occurrences of pH1N1 influenza infections and illnesses in relation to serum HAI antibody titer at enrollment are shown in Table 2 . When the retrospectively identified moderate to severe ARIs with a significant antibody response were included, the inverse correlation between baseline titer and frequency of pH1N1 infection and illness was significant (v 2 for trend, P 5 .01). abstract: Background. A new influenza A/H1N1 (pH1N1) virus emerged in April 2009, proceeded to spread worldwide, and was designated as an influenza pandemic. A/H1N1 viruses had circulated in 1918–1957 and 1977–2009 and were in the annual vaccine during 1977–2009. Methods. Serum antibody to the pH1N1 and seasonal A/H1N1 viruses was measured in 579 healthy adults at enrollment (fall 2009) and after surveillance for illness (spring 2010). Subjects reporting with moderate to severe acute respiratory illness had illness and virus quantitation for 1 week; evaluations for missed illnesses were conducted over holiday periods and at the spring 2010 visit. Results. After excluding 66 subjects who received pH1N1 vaccine, 513 remained. Seventy-seven had reported with moderate to severe illnesses; 31 were infected with pH1N1 virus, and 30 with a rhinovirus. Determining etiology from clinical findings was not possible, but fever and prominent myalgias favored influenza and prominent rhinorrhea favored rhinovirus. Tests of fall and spring antibody indicated pH1N1 infection of 23% had occurred, with the rate decreasing with increasing anti-pH1N1 antibody; a similar pattern was seen for influenza-associated illness. A reducing frequency of pH1N1 infections was also seen with increasing antibody to the recent seasonal A/H1N1 virus (A/Brisbane/59/07). Preexisting antibody to pH1N1 virus, responses to a single vaccine dose, a low infection-to-illness ratio, and a short duration of illness and virus shedding among those with influenza indicated presence of considerable preexisting immunity to pH1N1 in the population. Conclusions. The 2009 A/H1N1 epidemic among healthy adults was relatively mild, most likely because of immunity from prior infections with A/H1N1 viruses. url: https://doi.org/10.1093/cid/cir809 doi: 10.1093/cid/cir809 id: cord-287466-ag5y781z author: Cowley, J.A. title: Nidoviruses of Fish and Crustaceans date: 2016-09-09 words: 17715.0 sentences: 760.0 pages: flesch: 47.0 cache: ./cache/cord-287466-ag5y781z.txt txt: ./txt/cord-287466-ag5y781z.txt summary: As evidenced by the presence of genomic-length and sgmRNA-length replicativeintermediate double-stranded (ds)RNAs in shrimp cells infected with gill-associated virus (GAV) (Cowley et al., 2002a) , the type species okavirus (Cowley et al., 2012) , it is speculated that transcription termination of the antisense RNAs might occur at precise positions, resulting in common 3′-termini, and that these then act directly as promoters for transcription initiation of the genomic and sgmRNAs. In all other nidoviruses, however, and for the longest of the sgmRNAs transcribed by toroviruses, the (−) and (+) strand sgmRNAs are transcribed using a far more complex discontinuous process involving the splicing of a common "anti-leader" sequence derived from the genome 5′-terminus to each (−) strand sgmRNA that then acts as a universal promoter for transcribing each (+) strand sgmRNA (Pasternak et al., 2006; Sawicki et al., 2007; Smits et al., 2005; van Vliet et al., 2002) . Nidoviruses of aquatic species include the rod-shaped okaviruses GAV and yellow head virus (YHV) that primarily infect Penaeid shrimp (Longyant et al., 2005; Flegel, 2012; Flegel et al., 1997a; Cowley et al., 2000a Cowley et al., , 2002a Cowley and Walker, 2002; Sittidilokratna et al., 2008) and a morphologically similar virus with a ~22 kb ssRNA genome detected in diseased Chinese mitten crabs (Zhang and Bonami, 2007) . abstract: Viruses with diverse virion architectures demarcated into four families in the order Nidovirales have been discovered in vertebrate mammalian and fish species, as well as in invertebrate crustacean and mosquito species. The order is unified by nidoviruses sharing intermediate (12.7 kb) to very long (31.7 kb) (+) ssRNA genomes, each possessing a long 5′-terminal gene encoding overlapping ORF1a and ORF1b reading frames that contain a diversity of functionally related enzymes and that are translated in toto using a −1 ribosomal frameshift mechanism, as well as by semiconserved strategies for transcribing a nested set of 3′-coterminal subgenomic mRNAs that translate the viral proteins. The nidovirus that is most important to an aquaculture species is yellow head virus (YHV), which causes disease in shrimp farmed throughout the Eastern Hemisphere and is classified in the genus Okavirus, family Roniviridae. Fathead minnow nidovirus, genus Bafinivirus, subfamily Torovirinae, family Coronaviridae, also causes disease in minnows grown for the baitfish industry in the United States. Virions similar in morphology to okaviruses and bafiniviruses have also been detected in several crab species. Of these, however, only Eriocheir sinensis ronivirus, which causes disease in the Chinese mitten crab, an important freshwater aquaculture species in China, has been shown to possess a ~22 kb ssRNA genome that supports its being a nidovirus, but its taxonomic classification awaits genome sequence analysis. This chapter provides an overview of the structure, replication and biology of these viruses with a particular focus on YHV disease characteristics, diagnostic methods and disease prevention strategies. url: https://www.sciencedirect.com/science/article/pii/B9780128015735000322 doi: 10.1016/b978-0-12-801573-5.00032-2 id: cord-284372-v95fzp8n author: Coyle, Peter V title: A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections date: 2004-10-25 words: 4717.0 sentences: 224.0 pages: flesch: 43.0 cache: ./cache/cord-284372-v95fzp8n.txt txt: ./txt/cord-284372-v95fzp8n.txt summary: title: A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections To overcome this problem we developed a diagnostic molecular strip which combined a generic nested touchdown protocol with in-house primer master-mixes that could recognise 12 common respiratory viruses. CONCLUSIONS: The touchdown protocol with pre-dispensed primer master-mixes was suitable for replacing virus culture for the diagnosis of respiratory viruses which were negative by immunofluorescence. To test the feasibility of its routine use we needed to clinically validate its performance in a routine setting on specimens tested in parallel with our standard immunofluorescence protocol for the diagnosis of acute virus respiratory infections. In conclusion the use of the touchdown protocol with pre-dispensed and quality checked primer master-mixes was suitable for replacing virus culture for the diagnosis of respiratory viruses for immunofluorescence negative specimens. abstract: BACKGROUND: Immunofluorescence and virus culture are the main methods used to diagnose acute respiratory virus infections. Diagnosing these infections using nucleic acid amplification presents technical challenges, one of which is facilitating the different optimal annealing temperatures needed for each virus. To overcome this problem we developed a diagnostic molecular strip which combined a generic nested touchdown protocol with in-house primer master-mixes that could recognise 12 common respiratory viruses. RESULTS: Over an 18 month period a total of 222 specimens were tested by both immunofluorescence and the molecular strip. The specimens came from 103 males (median age 3.5 y), 80 females (median age 9 y) and 5 quality assurance scheme specimens. Viruses were recovered from a number of specimen types including broncho-alveolar lavage, nasopharyngeal secretions, sputa, post-mortem lung tissue and combined throat and nasal swabs. Viral detection by IF was poor in sputa and respiratory swabs. A total of 99 viruses were detected in the study from 79 patients and 4 quality control specimens: 31 by immunofluorescence and 99 using the molecular strip. The strip consistently out-performed immunofluorescence with no loss of diagnostic specificity. CONCLUSIONS: The touchdown protocol with pre-dispensed primer master-mixes was suitable for replacing virus culture for the diagnosis of respiratory viruses which were negative by immunofluorescence. Results by immunofluorescence were available after an average of 4–12 hours while molecular strip results were available within 24 hours, considerably faster than viral culture. The combined strip and touchdown protocol proved to be a convenient and reliable method of testing for multiple viruses in a routine setting. url: https://www.ncbi.nlm.nih.gov/pubmed/15504232/ doi: 10.1186/1471-2180-4-41 id: cord-021588-ec7udsmw author: Craighead, John E. title: Enteric Viral Disease date: 2007-05-09 words: 3474.0 sentences: 188.0 pages: flesch: 45.0 cache: ./cache/cord-021588-ec7udsmw.txt txt: ./txt/cord-021588-ec7udsmw.txt summary: This virus and its soon-to-be-discovered close relatives (the so-called Norwalk-like viruses [NLVs]) proved to be important causes of explosive outbreaks of diarrhea in both children and adults. But, this painstaking approach has now yielded evidence to indicate that viruses of at least six families may contribute to enteric illness in children and in adult citizens whose immunity has waned (Figure 32.1, Table 32 .1). The etiological role of these viruses as a cause of intestinal disease was established by demonstrating a temporal association of naturally occurring infections (as demonstrated by stool examination using electron microscopy) with illness and by experimental induction of disease in both human volunteers and experimental animals (Hall et al, 1984) . Volunteer studies have yielded important histological and ultrastructural documentation of the profound but relatively transient changes that occur in the mucosa of the small intestine during the course of infections with NLVs (Agus ei al, 1973; Schreiber ei al, 1973 Schreiber ei al, , 1974 Dolin ei al, 1975) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7150330/ doi: 10.1016/b978-012195160-3/50033-9 id: cord-001142-puj74k7y author: Crescenzo-Chaigne, Bernadette title: The Panhandle Formed by Influenza A and C Virus NS Non-Coding Regions Determines NS Segment Expression date: 2013-11-21 words: 3355.0 sentences: 183.0 pages: flesch: 55.0 cache: ./cache/cord-001142-puj74k7y.txt txt: ./txt/cord-001142-puj74k7y.txt summary: To investigate whether, or not, and how the complete NC regions of a given segment are involved in type specificity, we attempted to rescue, by reverse genetics, type A and C influenza viruses with chimeric non-coding sequences. The sole difference between 5''A/3''C(C5U) and wild-type 5''A/3''A viruses being the 3'' distal extremity of the NS segment suggested that the level of NS encoded proteins (i.e. NS1 or/and NS2/NEP) was affected at early stages of infection for this virus (5''A/3''C(C5U)). The major role of the proximal panhandle in type specificity that we identified and the hypothesized involvement of the distal panhandle in transcription need to be tested on the other (2 PFU/cell), viral vRNA and mRNA levels for each segment were evaluated by specific two-step RT-qPCRs previously described [23] . abstract: Exchange of the extremities of the NS segment of type A and C influenza viruses in reverse genetics systems was used to assess their putative role in type specificity. Restoration of each specific proximal panhandle was mandatory to allow the rescue of viruses with heterotypic extremities. Moreover, the transcription level of the modified segment seemed to be directly affected by the distal panhandle strength. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3858493/ doi: 10.1371/journal.pone.0081550 id: cord-001420-b4zcvd04 author: Crescenzo-Chaigne, Bernadette title: Chimeric NP Non Coding Regions between Type A and C Influenza Viruses Reveal Their Role in Translation Regulation date: 2014-09-30 words: 6267.0 sentences: 296.0 pages: flesch: 56.0 cache: ./cache/cord-001420-b4zcvd04.txt txt: ./txt/cord-001420-b4zcvd04.txt summary: Interestingly, in type A influenza virus infectious context, the length of the NP segment 5′ NC region once transcribed into mRNA was found to impact its translation, and the level of produced NP protein consequently affected the level of viral genome replication. The sequence of both ends of each segment of each rescued virus was verified as described [9] , and no Influenza NP Non Coding Region Role in Translation PLOS ONE | www.plosone.org genetics, type A and type C viruses with one or both heterotypic ends. These data based on type A influenza virus NP segment showed that it is possible to obtain virus by reverse genetics when a homotypic proximal panhandle and a homotypic strength of the initial distal panhandle are maintained, and that the length of the 59 end plays an important role in the efficiency of rescue. abstract: Exchange of the non coding regions of the NP segment between type A and C influenza viruses was used to demonstrate the importance not only of the proximal panhandle, but also of the initial distal panhandle strength in type specificity. Both elements were found to be compulsory to rescue infectious virus by reverse genetics systems. Interestingly, in type A influenza virus infectious context, the length of the NP segment 5′ NC region once transcribed into mRNA was found to impact its translation, and the level of produced NP protein consequently affected the level of viral genome replication. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4182659/ doi: 10.1371/journal.pone.0109046 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-316245-n6tmn4ph author: Cui, Binglin title: Viral aetiology of acute respiratory infections among children and associated meteorological factors in southern China date: 2015-03-13 words: 4993.0 sentences: 247.0 pages: flesch: 43.0 cache: ./cache/cord-316245-n6tmn4ph.txt txt: ./txt/cord-316245-n6tmn4ph.txt summary: METHODS: Paired nasal/throat-flocked swabs collected from 1,074 children with ARIs, who visited outpatient walk-in clinics in a tertiary hospital between December 2010 and November 2011, were examined for fourteen respiratory viruses influenza viruses (FluA, FluB), respiratory syncytial viruses (RSV A and B), human coronaviruses (hCoV: 229E, OC43, HKU1, NL63), human metapneumoviruses (hMPV A and B), parainfluenza viruses (PIV1-4), human rhinoviruses (HRV A, B, C), enteroviruses (EV), adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV) by multiplex real-time PCR. Multiplex real-time PCR was performed using Roche, Lightcycler 480 II (Roche Diagnostics, Penzberg, Germany) to identify the following 14 respiratory viruses: influenza A (FluA), influenza B (FluB), respiratory syncytial viruses A and B (RSV), human coronaviruses 229E, OC43, HKU1 and NL63 (hCoV), human metapneumoviruses A and B (hMPV), human parainfluenza virus types 1, 2 , 3, and 4 (PIV1, PIV2, PIV3, and PIV4), human rhinoviruses A, B, and C (HRV), human enteroviruses (EV), human adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV). abstract: BACKGROUND: Acute respiratory infections (ARIs) are common in children and mostly caused by viruses, but the significance of the detection of multiple viruses in ARIs is unclear. This study investigated 14 respiratory viruses in ARIs among children and associated meteorological factors in Shantou, southern China. METHODS: Paired nasal/throat-flocked swabs collected from 1,074 children with ARIs, who visited outpatient walk-in clinics in a tertiary hospital between December 2010 and November 2011, were examined for fourteen respiratory viruses - influenza viruses (FluA, FluB), respiratory syncytial viruses (RSV A and B), human coronaviruses (hCoV: 229E, OC43, HKU1, NL63), human metapneumoviruses (hMPV A and B), parainfluenza viruses (PIV1-4), human rhinoviruses (HRV A, B, C), enteroviruses (EV), adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV) - by multiplex real-time PCR. RESULTS: We identified at least one virus in 82.3% (884/1,074) and multiple viruses in 38.6% (415/1,074) of patients. EV and HRV were the most frequently detected single viruses (42.3%, 374/884 and 39.9%, 353/884 respectively) and co-detected pair (23.1%, 96/415). Overlapping seasonal trends of viruses were recorded over the year, with dual peaks for EV and single peaks for the others. By logistic regression analysis, EV was positively associated with the average temperature and humidity, hCoV, and PIV4, but negatively with HRV, PIV3, and hBoV. HRV was inversely associated with EV and PIV3. CONCLUSIONS: This study reports high viral detection and co-detection rates in pediatric ARI cases mainly due to EV and HRV. Many viruses circulated throughout the year with similar seasonal trends in association with temperature, humidity, and wind velocity. Statistically significant associations were present among the viruses. Understanding the polyviral etiology and viral interactions in the cases with multiple viruses warrants further studies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-015-0863-6) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/25884513/ doi: 10.1186/s12879-015-0863-6 id: cord-291113-iizj932l author: Cumbo, Enzo title: Alternative Methods of Sterilization in Dental Practices Against COVID-19 date: 2020-08-08 words: 7441.0 sentences: 273.0 pages: flesch: 40.0 cache: ./cache/cord-291113-iizj932l.txt txt: ./txt/cord-291113-iizj932l.txt summary: It is time to consider a dental practice quite similar to a hospital surgery room, where particular attention should be paid to problems related to the spread of infections caused by air and surface contaminations, especially a time when viruses such as SARS-CoV-2 have emerged as an important public health problem due to their ability to spread through close person-to-person contact. Ultraviolet light has proven effective against corona viruses and, therefore, could be used against COVID-19 both in the case of bioaerosols and in the sterilization of contaminated environmental surfaces in which this microorganism is present-in particular, on products of unstable composition that cannot be treated by conventional means [62, 63] . Now that the risk of spreading COVID-19 is very high, it is necessary to pay particular attention to all the sterilization procedures that should be reviewed, improved, and perhaps used in combinations to obtain a final result that aims to complete the sterilization of all structures present in the operating room, including air, which for some dangerous diseases, such as SARS-CoV-2, is the transmission route. abstract: SARS-CoV-2, and several other microorganisms, may be present in nasopharyngeal and salivary secretions in patients treated in dental practices, so an appropriate clinical behavior is required in order to avoid the dangerous spread of infections. COVID-19 could also be spread when patients touches a contaminated surface with infected droplets and then touch their nose, mouth, or eyes. It is time to consider a dental practice quite similar to a hospital surgery room, where particular attention should be addressed to problems related to the spreading of infections due to air and surface contamination. The effectiveness of conventional cleaning and disinfection procedures may be limited by several factors; first of all, human operator dependence seems to be the weak aspect of all procedures. The improvement of these conventional methods requires the modification of human behavior, which is difficult to achieve and sustain. As alternative sterilization methods, there are some that do not depend on the operator, because they are based on devices that perform the entire procedure on their own, with minimal human intervention. In conclusion, continued efforts to improve the traditional manual disinfection of surfaces are needed, so dentists should consider combining the use of proper disinfectants and no-touch decontamination technologies to improve sterilization procedures. url: https://doi.org/10.3390/ijerph17165736 doi: 10.3390/ijerph17165736 id: cord-315346-ebfjba4y author: Cummings, Kristin J. title: Exposure to Influenza Virus Aerosols in the Hospital Setting: Is Routine Patient Care an Aerosol Generating Procedure? date: 2014-03-04 words: 967.0 sentences: 52.0 pages: flesch: 39.0 cache: ./cache/cord-315346-ebfjba4y.txt txt: ./txt/cord-315346-ebfjba4y.txt summary: title: Exposure to Influenza Virus Aerosols in the Hospital Setting: Is Routine Patient Care an Aerosol Generating Procedure? As the authors note, current World Health Organization and Centers for Disease Control and Prevention guidelines for protection of healthcare professionals from influenza virus infection rely on the supposition that, under routine conditions, most transmission occurs via large droplets, rather than via smallparticle aerosols [2, 3] . On each day, influenza virus RNA was detected in particles of respirable size, but a relationship to what we considered to be potential AGPs (mechanical ventilation, suctioning, extubation, and use of an incentive spirometer) was not evident. Indeed, potential respiratory exposures to healthcare professionals in the room appeared highest on hospital day 4, when the patient was breathing on his own and care was routine. This observation corroborates previous work [5] [6] [7] and raises the possibility that aerosol transmission of influenza virus may occur during routine patient care [8] . abstract: nan url: https://doi.org/10.1093/infdis/jiu127 doi: 10.1093/infdis/jiu127 id: cord-344408-4ko557n1 author: Cunningham, Andrew A. title: One Health, emerging infectious diseases and wildlife: two decades of progress? date: 2017-07-19 words: 5977.0 sentences: 278.0 pages: flesch: 43.0 cache: ./cache/cord-344408-4ko557n1.txt txt: ./txt/cord-344408-4ko557n1.txt summary: Around this time, emerging diseases were identified in a series of well-reported die-offs in wildlife, including canine distemper in African lions (Panthera leo) in the Serengeti, chytridiomycosis in amphibians globally, pilchard herpesvirus disease in Australasia and West Nile virus in corvids and other birds in New York [10 -13] . There are likely to be multiple causes of novel disease emergence, but the human-mediated transport of pathogens (often in infected hosts) or vectors across geographical or ecological boundaries, a process termed ''pathogen pollution'', has been identified as a major driver of this in wildlife [64] and also in plants [65] . salamandrivorans as a novel lethal fungus infecting and killing captive and wild salamanders in Europe [67, 85, 86] Challenges remain to understanding the wildlife origins of zoonotic EIDs. It is often difficult, time-consuming, logistically challenging and very expensive to identify the origins of newly emerged pathogens of humans. abstract: Infectious diseases affect people, domestic animals and wildlife alike, with many pathogens being able to infect multiple species. Fifty years ago, following the wide-scale manufacture and use of antibiotics and vaccines, it seemed that the battle against infections was being won for the human population. Since then, however, and in addition to increasing antimicrobial resistance among bacterial pathogens, there has been an increase in the emergence of, mostly viral, zoonotic diseases from wildlife, sometimes causing fatal outbreaks of epidemic proportions. Concurrently, infectious disease has been identified as an increasing threat to wildlife conservation. A synthesis published in 2000 showed common anthropogenic drivers of disease threats to biodiversity and human health, including encroachment and destruction of wildlife habitat and the human-assisted spread of pathogens. Almost two decades later, the situation has not changed and, despite improved knowledge of the underlying causes, little has been done at the policy level to address these threats. For the sake of public health and wellbeing, human-kind needs to work better to conserve nature and preserve the ecosystem services, including disease regulation, that biodiversity provides while also understanding and mitigating activities which lead to disease emergence. We consider that holistic, One Health approaches to the management and mitigation of the risks of emerging infectious diseases have the greatest chance of success. This article is part of the themed issue ‘One Health for a changing world: zoonoses, ecosystems and human well-being’. url: https://doi.org/10.1098/rstb.2016.0167 doi: 10.1098/rstb.2016.0167 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-004830-vmka378d author: Cursiefen, Dagmar title: In vitro cultivation of cells from the chorioallantoic membrane of chick embryos date: 1975 words: 2554.0 sentences: 177.0 pages: flesch: 57.0 cache: ./cache/cord-004830-vmka378d.txt txt: ./txt/cord-004830-vmka378d.txt summary: By treatment of chorioallantoic membranes from embryonated eggs with collagenase and hyaluronidase before the conventional application of trypsin cells could be grown in culture which supported growth of a large variety of myxoviruses, herpesviruses, avian reoviruses and the infectious bronchitis virus of chickens. In an attempt to plaque-purify and to quantitatc some strains of influenza viruses and of avian reoviruses we succeeded to cultivate cells from the chorioallantoic membrane of chick embryos. The following strains were tested for their ability to grow, induce a cytopathie effect and form plaques in chorioallantoic cells of the chick embryo (CAM-cells). After an incubation period of 8 to 16hrs the media were assayed for hemagglutinating activity and for infectivity by plaque tests on the same cell type used for growing the viruses, i.e. CAM cells or chick embryo fibroblasts. abstract: By treatment of chorioallantoic membranes from embryonated eggs with collagenase and hyaluronidase before the conventional application of trypsin cells could be grown in culture which supported growth of a large variety of myxoviruses, herpesviruses, avian reoviruses and the infectious bronchitis virus of chickens. The cultures could be used for sensitive plaque assays and neutralization tests. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087208/ doi: 10.1007/bf02120764 id: cord-022439-8wy7rpqv author: DENMAN, A.M. title: Viral Etiology of Polymyositis/Dermatomyositis date: 2013-11-17 words: 10782.0 sentences: 523.0 pages: flesch: 43.0 cache: ./cache/cord-022439-8wy7rpqv.txt txt: ./txt/cord-022439-8wy7rpqv.txt summary: Thus, theories based on a viral etiology must invoke a highly un usual host response to ubiquitous agents, the existence of uncommon viruses with the abil ity to provoke the disorder, or the possibility that virus infections operate synergistically with other factors. Attempted isolation Electron-microscopic studies Viral probes Antiviral antibody titers Establishing clones from infiltrating T lymphocytes and screening their antigen specificities Exploring the antigen specificities of associated autoantibodies In vitro models of virus-infected muscle cells In vivo models of experimental polymyositis ceptually. In clinical studies, EBV transformed blood lymphocytes from both normal individuals and patients with autoimmune diseases pro duced monoclonal autoantibodies reactive with antigens in multiple organs [93] . Myocarditis and PM induced by coxsackievirus infection is mediated by immunopathologic mechanisms that may continue to dam age muscle fibers long after infectious virus and even viral antigens have been eliminated. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155693/ doi: 10.1016/b978-0-409-95191-2.50010-0 id: cord-279849-zzkliu76 author: DaPalma, T. title: A systematic approach to virus–virus interactions date: 2010-01-20 words: 8230.0 sentences: 366.0 pages: flesch: 36.0 cache: ./cache/cord-279849-zzkliu76.txt txt: ./txt/cord-279849-zzkliu76.txt summary: Therefore, in this review we identify known and potential types of virus-virus interactions (VVIs) and organize them into three categories: (1) direct interactions of viral genes or gene products, (2) indirect interactions that result from alterations in the host environment, and (3) a subset of indirect interactions called immunological interactions, unique to organisms equipped with an adaptive immune system. One of the first helper-dependent viruses described was bacteriophage P4, a bacteria-infecting virus that is able to replicate its own genome, but requires the presence of a coinfecting bacteriophage, such as P2, to provide capsid components and cell lysis (Shore et al., 1978; Six and Klug, 1973) . While direct binding and activation of viral transactivating proteins to heterologous viral promoters has been documented, more common are reports of viral infections inducing increased expression or activation of cellular transcription factors, which then act on promoters of coinfecting viruses. Human cytomegalovirus TRS1 and IRS1 gene products block the double-stranded-RNA-activated host protein shutoff response induced by herpes simplex virus type 1 infection abstract: A virus–virus interaction is a measurable difference in the course of infection of one virus as a result of a concurrent or prior infection by a different species or strain of virus. Many such interactions have been discovered by chance, yet they have rarely been studied systematically. Increasing evidence suggests that virus–virus interactions are common and may be critical to understanding viral pathogenesis in natural hosts. In this review we propose a system for classifying virus–virus interactions by organizing them into three main categories: (1) direct interactions of viral genes or gene products, (2) indirect interactions that result from alterations in the host environment, and (3) immunological interactions. We have so far identified 15 subtypes of interaction and assigned each to one of these categories. It is anticipated that this framework will provide for a more systematic approach to investigating virus–virus interactions, both at the cellular and organismal levels. url: https://doi.org/10.1016/j.virusres.2010.01.002 doi: 10.1016/j.virusres.2010.01.002 id: cord-330131-yfhrmbvx author: Danchin, Antoine title: Cytosine drives evolution of SARS‐CoV‐2 date: 2020-04-27 words: 5318.0 sentences: 244.0 pages: flesch: 42.0 cache: ./cache/cord-330131-yfhrmbvx.txt txt: ./txt/cord-330131-yfhrmbvx.txt summary: In this article, we show, in the specific case of SARS-CoV-2, that the role of cytosine-based metabolites used as cell growth coordinators is central to understanding both innate antiviral immunity and the evolution of the virus. Here we (i) highlight the deviation of SARS-CoV-2 RNA chemical composition compared with that of its human host; (ii) formulate a hypothesis grounded on the canonical organization of cytosine metabolism as a way to coordinate non-homothetic growth of cells-i.e., the simultaneous growth of the cytoplasm (three dimensions), the membrane (two dimensions) and the genome (one dimension)-, and point out the emergence of the endogenous antinucleotide viperin as a cognate adaptive antiviral metabolite and (iii) predict evolutionary trends of CoV-2 for maximizing compositional fitness-which seem to show up in ongoing mutation survey of radiative evolution. abstract: nan url: https://doi.org/10.1111/1462-2920.15025 doi: 10.1111/1462-2920.15025 id: cord-006819-sxz1s6kz author: Daniel Givens, M. title: Infectious causes of embryonic and fetal mortality date: 2008-05-27 words: 7666.0 sentences: 538.0 pages: flesch: 46.0 cache: ./cache/cord-006819-sxz1s6kz.txt txt: ./txt/cord-006819-sxz1s6kz.txt summary: The clinical presentations of disease due to reproductive pathogens are emphasized, with a focus on assisting development of complete lists of causes that result in abortion and infertility in these species. Fetal maceration results when abortion or parturition fails to occur following fetal death and CL regression (occasionally in bovine www.theriojournal.com Available online at www.sciencedirect.com Theriogenology 70 (2008) 270-285 Table 1 Infectious causes of infertility and abortion in domestic animals Infected animals can experience signs of infertility due to early embryonic death and abortion between 4 and 7 months of gestation. Transmission occurs via contact with materials contaminated by infected respiratory or vaginal discharges; the bacteria then spread hematogenously to the fetus. Affected animals might have no clinical signs of disease, but serve as a source of infection, or they can abort late in gestation and have stillbirths. abstract: The purpose of this review is to summarize bacterial, fungal, protozoan, and viral causes of reproductive dysgenesis in cattle, sheep, goats, pigs, horses, dogs, and cats. The clinical presentations of disease due to reproductive pathogens are emphasized, with a focus on assisting development of complete lists of causes that result in abortion and infertility in these species. Clinicians are encouraged to assess clinical presentation, create complete lists of differential diagnoses, obtain appropriate diagnostic samples, maximize diagnostic laboratory support, and avoid zoonotic infections resulting from reproductive pathogens of animals. The foundation of an accurate diagnosis of reproductive loss due to infectious pathogens facilitates the prudent use of immunization and biosecurity to minimize reproductive losses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103133/ doi: 10.1016/j.theriogenology.2008.04.018 id: cord-276616-odmnvv7m author: Darcel, C. title: Reflections on scrapie and related disorders, with consideration of the possibility of a viral aetiology date: 1995 words: 10478.0 sentences: 494.0 pages: flesch: 48.0 cache: ./cache/cord-276616-odmnvv7m.txt txt: ./txt/cord-276616-odmnvv7m.txt summary: Conclusions drawn from the vaccination trials and transmission experiments were that ~crapie, given by subcutaneous inoculation, had a latent period of 2 years and longer; that the infective agent was resistant to 0.35% formalin; that the disease appeared more quickly and in a higher percentage of recipients following intracerebral than following~subcutaneous injection; and that the causative agent was probably a filtrable virus. There are many difficulties in studying either the natural or experimentally induced diseases: the animals involved, the incubation period required for the emergence of the disease, the innate resistance of a proportion of the population seen as an expression of genetic influences, the differing behaviour of strains of agents isolated from a given species, the symptomatology, the pathology, the uncertain nature of the agent and its means of transmission, the perceived ''lack'' of an immunological response or changes in the immune system, and the biological hazards involved in conducting experiments. abstract: The transmissible spongiform encephalopathies of domesticated animals, scrapie in-sheep and bovine spongiform encephalopathy (BSE), and transmissible mink encephalopathy are more than a scientific curiosity; under certain circumstances their impact on commercial activities can be calamitous. Knowledge of their causation and pathogenesis is still rudimentary, but many consider than an unconventional agent, the prion (a brain protein, PrP), that is not associated with nucleic acid is involved in both. Others believe that conventional viruses, which replicate by virtue of their nucleic acid-defined genes, are involved in the causation and progression of the encephalopathies but that technical problems have prevented their identification. Others postulate even more exotic causative agents. While this paper will particularly address the possibility of a viral aetiology for these diseases, it is also emphasized that our knowledge of the state of the immune system in animals with encephalopathy needs broadening. There are remarkable gaps in our knowledge of the histopathology of these diseases, particularly the nature of the characteristic vacuoles. Much further work is needed on the biochemical changes in the brain and the serum, particularly of the latter as it could lead to an additional means of recognizing clinical cases without waiting for the animal to die with subsequent examination of the brain for characteristic lesions and the presence of protease-K-resistant PrP. url: https://www.ncbi.nlm.nih.gov/pubmed/7571397/ doi: 10.1007/bf01839302 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-292657-gq3965se author: Das, Piyanki title: Decoding the global outbreak of COVID-19: the nature is behind the scene date: 2020-06-22 words: 5030.0 sentences: 221.0 pages: flesch: 43.0 cache: ./cache/cord-292657-gq3965se.txt txt: ./txt/cord-292657-gq3965se.txt summary: The rapid evolving nature by changing host body environment and extreme environmental stability, collectively makes SARS-CoV-2 into an extremely virulent genetic variant. Thus both the host body or internal environment and the external environment performs equally as a source, responsible for shaping the genetic evolution of the SARS-CoV-2 towards theCOVID-19 disease fitness in nature in a pandemic form. The probable line of development for such pandemic outcomes happened by continuous evolutionary procedure within different species or host environment exposure, by mutation during replication or genetic recombination between two different viral species and ultimate adaptation to a susceptible host by natural selection of the new version of the viable pathogen resulting infection [7, 8] . Then genetically close different subtypes of SARS-CoV-2 develops unique spike protein receptor binding domain with high degree of receptor binding property to human cells and adapt itself to fit the character inside the host body. abstract: The sudden emergence of SARS-CoV-2 causing the global pandemic is a major public health concern. Though the virus is considered as a novel entity, it is not a completely new member. It is just a new version of previously emerged human SARS corona virus. The rapid evolving nature by changing host body environment and extreme environmental stability, collectively makes SARS-CoV-2 into an extremely virulent genetic variant. The evolution of the virus has been occurred by the continuous process of molecular genetic manipulation, through mutation, deletion and genetic recombinationevents. Different host body environment acts as the supportive system for the pathogen which creates extreme selective pressure. By the process of genetic evolution the pathogen developes new characters. Then the new version of the virus has been naturally selected by susceptible human host and adapt itself inside the host body causing deadly effect. Moreover, extreme environmental stability helps in the process of viral survival outside the host and its transmission. Thus both the host body or internal environment and the external environment performs equally as a source, responsible for shaping the genetic evolution of the SARS-CoV-2 towards theCOVID-19 disease fitness in nature in a pandemic form. url: https://www.ncbi.nlm.nih.gov/pubmed/32656307/ doi: 10.1007/s13337-020-00605-y id: cord-102862-oq54sfx6 author: Dastjerdi, Akbar M. title: Characterisation of the bovine enteric calici-like virus, Newbury agent 1 date: 2000-11-01 words: 3180.0 sentences: 172.0 pages: flesch: 55.0 cache: ./cache/cord-102862-oq54sfx6.txt txt: ./txt/cord-102862-oq54sfx6.txt summary: A single capsid protein of 49.4 kDa was detected by Western blotting in purified NA1 preparations prepared from post-infection but not pre-infection faecal samples and with postbut not pre-infection sera. Calici-like virus particles were identi¢ed in faecal samples by electron microscopy but no other viruses were seen. Western blotting analysis of NA1 virions puri¢ed from faeces by CsCl density gradient centrifugation demonstrated the presence of a single protein band in each of ¢ve separate preparations from the day 2 p.i. faecal sample from calf 1424 (Fig. 4a, track 2) . The speci¢city of the protein band was con¢rmed by examination of day 0 versus day 2 p.i. faecal samples, staining with pre-and postinoculation antisera and association with the presence of virus particles in CsCl gradients. Capsid diversity in small round-structured viruses : molecular characterization of an antigenically distinct human enteric calicivirus abstract: Abstract The bovine enteric calici-like virus, Newbury agent 1 (NA1) was characterised to determine if it is a member of the Caliciviridae and to establish its antigenic relationship to the established bovine enteric calicivirus Newbury agent 2 (NA2). Solid phase immune electron microscopy (SPIEM) allowed quantification of NA1 virions and identification of faecal samples with optimal virus levels. NA1 particles were 36.6 nm in diameter, had an indefinite surface structure resembling that of human small round structured viruses (SRSVs), and a buoyant density of 1.34 g ml−1. A single capsid protein of 49.4 kDa was detected by Western blotting in purified NA1 preparations prepared from post-infection but not pre-infection faecal samples and with post- but not pre-infection sera. NA1 was antigenically unrelated to the bovine enteric calicivirus NA2 by SPIEM. These properties were consistent with classification of NA1 within the Caliciviridae but demonstrated heterogeneity in the capsid composition of bovine enteric caliciviruses. url: https://api.elsevier.com/content/article/pii/S0378109700004225 doi: 10.1016/s0378-1097(00)00422-5 id: cord-258626-p469ysi8 author: Davis-Wurzler, Gina M. title: 2013 Update on Current Vaccination Strategies in Puppies and Kittens date: 2014-02-26 words: 10938.0 sentences: 543.0 pages: flesch: 43.0 cache: ./cache/cord-258626-p469ysi8.txt txt: ./txt/cord-258626-p469ysi8.txt summary: Criteria for assigning vaccines into these categories, and a third category, "generally not recommended," are based on: (1) morbidity and mortality associated with the specific disease (does the organism cause serious illness or does it cause a mild, transient disease that may pose only minimal risk to the individual or population?); (2) the prevalence and/or incidence rate of the disease (although a specific disease may not commonly be seen, the organism is ubiquitous in the environment and therefore poses risk to the individual or population); (3) the risk of the individual for exposure to the disease (indoor-only animal vs free-roaming individual, regional variations of occurrence); (4) the efficacy of the vaccine (does the vaccine prevent infection or simply ameliorate some signs or length of disease?); (5) the risks associated with administering the vaccine (are the risks associated with that vaccine greater than the risk of the disease?); (6) the potential for zoonotic disease; (7) the route of infection or transmissibility. 9, 13 The current recommendation is to use the CAV-II modified live virus product, as it stimulates the immune system to protect against both CAV-I and CAV-II, without the associated adverse reaction caused by the type I vaccine. abstract: Vaccines remain one of the practitioner’s greatest tools in preventing disease and maintaining individual and population health. This article is an update to “Current Vaccination Strategies in Puppies and Kittens” published in Veterinary Clinics of North America, Small Animal Practitioner, in May 2006. There are now comprehensive guidelines readily available for small animal practitioners regarding canine and feline pediatric (and adult) vaccination recommendations. Perhaps more importantly, there is an increased dialogue regarding all aspects of preventive medicine, of which vaccination is only a small, yet significant portion; and an increased drive to provide scientific evidence for developing vaccination recommendations. url: https://www.ncbi.nlm.nih.gov/pubmed/24580989/ doi: 10.1016/j.cvsm.2013.11.006 id: cord-275538-c44gmu22 author: Davis-Wurzler, Gina M. title: Current Vaccination Strategies in Puppies and Kittens date: 2006-03-24 words: 10385.0 sentences: 472.0 pages: flesch: 41.0 cache: ./cache/cord-275538-c44gmu22.txt txt: ./txt/cord-275538-c44gmu22.txt summary: The current recommendation is to use the CAV-II MLV because it stimulates the immune system to protect against CAV-I and CAV-II without the associated adverse reaction caused by the type I vaccine [4, 14, 20] . There is a killed vaccine available; however, vaccination against this agent is typically not recommended, because most animals are not at risk to contract the parasite, the vaccine does not prevent infection (it may ameliorate clinical signs and decrease cyst shedding), and the disease is readily amenable to therapy (fenbendazole, albendazole, and metronidazole are off-label uses but commonly accepted as standard of care). Because the vaccine does not fully prevent infection and carries an association with adverse events that may be greater than the actual disease, routine vaccination of household pets with this product is generally not recommended. abstract: Motivation in writing this article stems from many things: a lack of time spent in the veterinary curriculum discussing vaccines, a growing concern(by the general public and the veterinary community) regarding adverse reactions associated with vaccines, and a desire to prevent a recurrence of preventable infectious diseases resulting from a fear-driven cessation of vaccine administration. The objectives of this article are to present a basic review of immunology as related to vaccines, to discuss general guidelines for pediatric vaccines in canine and feline patients,and to offer suggestions as to how we can most positively influence our patients' health from the first visit. url: https://www.ncbi.nlm.nih.gov/pubmed/16564416/ doi: 10.1016/j.cvsm.2005.12.003 id: cord-346063-7u1a198p author: De Clercq, Erik title: Avian influenza A (H5N1) infection: targets and strategies for chemotherapeutic intervention date: 2007-05-04 words: 3496.0 sentences: 184.0 pages: flesch: 42.0 cache: ./cache/cord-346063-7u1a198p.txt txt: ./txt/cord-346063-7u1a198p.txt summary: We have recently reviewed the antiviral agents that are active against influenza viruses and that could be used, either therapeutically and/or prophylactically, in an influenza virus pandemic, whether it be human, avian, equine, porcine or other [1] . Even if based only on the currently available drugs, there are several double-, tripleand quadruple-drug combinations that could be envisaged for the prevention and treatment of avian H5N1 (Figure 3 ) -including the combination of oseltamivir and zanamivir (because their resistance profiles overlap only partially), the combination of these neuraminidase inhibitors with M2 ion channel blockers, and further extension of these combinations to include pegylated interferon and ribavirin. In addition to viral RNA polymerase and/or endonuclease, mentioned earlier as potential targets for new anti-influenza-virus agents, there are some other clues regarding the virulence of H5N1 viruses in humans [41] that could be considered as points of attack for chemotherapeutic intervention. abstract: In an avian flu pandemic, which drugs could be used to treat or prevent infection with influenza A (H5N1) virus? Foremost are the viral neuraminidase inhibitors oseltamivir and zanamivir, which have already been used to treat human influenza A (H1N1 and H3N2) and B virus infections. The use of the M2 ion channel blockers amantadine and rimantadine is compounded by the rapid development of drug resistance. Although formally approved for other indications (i.e. treatment of hepatitis C), ribavirin and pegylated interferon might also be useful for controlling avian flu. Combined use of the currently available drugs should be taken into account and attempts should be made to develop new strategies directed at unexplored targets such as the viral proteins hemagglutinin, the viral polymerase (and endonuclease) and the non-structural protein NS1. As has been shown for other viral infections, RNA interference could be a powerful means with which to suppress the replication of avian H5N1. url: https://www.sciencedirect.com/science/article/pii/S0165614707000843 doi: 10.1016/j.tips.2007.04.005 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-004724-llex3yed author: Dea, S. A. title: Isolation of encephalomyocarditis virus among stillborn and post-weaning pigs in Quebec date: 1991 words: 2539.0 sentences: 150.0 pages: flesch: 45.0 cache: ./cache/cord-004724-llex3yed.txt txt: ./txt/cord-004724-llex3yed.txt summary: Encephalomyocarditis (EMC) virus was isolated from aborted fetuses and lungs of suckling pigs from three Quebec pig farms that experienced outbreaks of reproductive failure in sows and respiratory problems in suckling and post-weaning piglets. Encephalomyocarditis (EMC) virus was isolated from aborted fetuses and lungs of suckling pigs from three Quebec pig farms that experienced outbreaks of reproductive failure in sows and respiratory problems in suckling and post-weaning piglets. Serological evidence of EMC virus infection was reported in Canadian swine herds and associated with sudden death in young piglets and reproductive problems [20, 21] . This report describes the isolation of EMC virus from the tissues of aborted fetuses and post-weaning piglets obtained from three different farms. Necropsied fetuses did not show typical gross and microscopic heart lesions previously reported from experimental and natural infection of newborn piglets with EMC virus [12] [13] [14] . An association between encephalomyocarditis virus infection and reproductive failure in pigs abstract: Encephalomyocarditis (EMC) virus was isolated from aborted fetuses and lungs of suckling pigs from three Quebec pig farms that experienced outbreaks of reproductive failure in sows and respiratory problems in suckling and post-weaning piglets. Multifocal interstitial pneumonia and mild non-suppurative myocarditis and meningoencephalitis were the more significant histopathological lesions observed in piglets. Vero cells were found to be more sensitive than BHK-21 cells and pig cell lines for primary isolation of EMC virus. The Quebec EMC virus isolates were highly virulent for mice and were antigenically related to reference strain of EMC virus as demonstrated by indirect immunofluorescence, seroneutralization and Western immunoblotting. Specific virus neutralization antibody titers up to 1:12,800 were detected in samples of thoracic or abdominal fluids of the aborted fetuses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086762/ doi: 10.1007/bf01310497 id: cord-265461-hj2b1wc4 author: Decroly, Etienne title: Biochemical principles and inhibitors to interfere with viral capping pathways date: 2017-05-18 words: 5089.0 sentences: 262.0 pages: flesch: 46.0 cache: ./cache/cord-265461-hj2b1wc4.txt txt: ./txt/cord-265461-hj2b1wc4.txt summary: Some virus families code for two different MTase domains carrying a cap-binding site (e.g., poxviruses [11] , coronaviruses [ Structure of inhibitors targeting enzymes involved in viral RNA capping pathways. Cap analogues exemplified here with m7 GTP, and several inhibitors of cap-binding protein have been identified through X-ray structure analysis of the influenza virus PB2-CBD in complex with the corresponding ligands. The X-ray structure of influenza A or B virus PB2 in complex with m7 GTP [49, 50] reveals a conserved cap-recognition mechanism in which the methylated guanosine is stacked between two aromatic residues similar to its binding mode with the eukaryotic initiation factor (eIF4E). However, the past research decade has a contrario unveiled that RNA capping is essential for virus replication, and is in fact a most interesting target for the design of potent antivirals due to two main reasons: (i) incomplete/inhibited RNA capping triggers a potent host immune response adding up to direct inhibition of viral gene expression, and (ii) structural and functional studies of viral capping enzymes have revealed a profound uniqueness of the viral enzymes involved, which shows promises to achieve high drug selectivity. abstract: Messenger RNAs are decorated by a cap structure, which is essential for their translation into proteins. Many viruses have developed strategies in order to cap their mRNAs. The cap is either synthetized by a subset of viral or cellular enzymes, or stolen from capped cellular mRNAs by viral endonucleases (‘cap-snatching’). Reverse genetic studies provide evidence that inhibition of viral enzymes belonging to the capping pathway leads to inhibition of virus replication. The replication defect results from reduced protein synthesis as well as from detection of incompletely capped RNAs by cellular innate immunity sensors. Thus, it is now admitted that capping enzymes are validated antiviral targets, as their inhibition will support an antiviral response in addition to the attenuation of viral mRNA translation. In this review, we describe the different viral enzymes involved in mRNA capping together with relevant inhibitors, and their biochemical features useful in inhibitor discovery. url: https://doi.org/10.1016/j.coviro.2017.04.003 doi: 10.1016/j.coviro.2017.04.003 id: cord-332181-k90i33gp author: Degeling, Chris title: Hendra in the news: Public policy meets public morality in times of zoonotic uncertainty date: 2012-12-29 words: 7062.0 sentences: 279.0 pages: flesch: 47.0 cache: ./cache/cord-332181-k90i33gp.txt txt: ./txt/cord-332181-k90i33gp.txt summary: Because flying foxes are a highly visible, widespread and relatively novel source of infectious risk for humans, the emergence of Hendra virus presents an opportunity to track and compare media representations of disease ''events'', health policy goals, political discourses and public opinions in ways that are difficult for noncommunicable diseases. Articles then were coded for: mention of horses, flying foxes/fruit bats or Hendra virus mention of debates about flying fox control report of distal ecological causes (loss of natural habitat) for the emergence of Hendra virus or the possibility of viral mutation mention of ignorance about Hendra virus amongst scientists, healthcare providers or members of the public reference to government inaction as a factor contributing to the Hendra problem reference to people''s health and welfare not being high enough on the political agenda. abstract: Public discourses have influence on policymaking for emerging health issues. Media representations of unfolding events, scientific uncertainty, and real and perceived risks shape public acceptance of health policy and therefore policy outcomes. To characterize and track views in popular circulation on the causes, consequences and appropriate policy responses to the emergence of Hendra virus as a zoonotic risk, this study examines coverage of this issue in Australian mass media for the period 2007–2011. Results demonstrate the predominant explanation for the emergence of Hendra became the encroachment of flying fox populations on human settlement. Depictions of scientific uncertainty as to whom and what was at risk from Hendra virus promoted the view that flying foxes were a direct risk to human health. Descriptions of the best strategy to address Hendra have become polarized between recognized health authorities advocating individualized behaviour changes to limit risk exposure; versus populist calls for flying fox control and eradication. Less than a quarter of news reports describe the ecological determinants of emerging infectious disease or upstream policy solutions. Because flying foxes rather than horses were increasingly represented as the proximal source of human infection, existing policies of flying fox protection became equated with government inaction; the plight of those affected by flying foxes representative of a moral failure. These findings illustrate the potential for health communications for emerging infectious disease risks to become entangled in other political agendas, with implications for the public's likelihood of supporting public policy and risk management strategies that require behavioural change or seek to address the ecological drivers of incidence. url: https://api.elsevier.com/content/article/pii/S0277953612008477 doi: 10.1016/j.socscimed.2012.12.024 id: cord-021555-rrverrsj author: Delano, Margaret L. title: Biology and Diseases of Ruminants: Sheep, Goats, and Cattle date: 2007-09-02 words: 71765.0 sentences: 5075.0 pages: flesch: 49.0 cache: ./cache/cord-021555-rrverrsj.txt txt: ./txt/cord-021555-rrverrsj.txt summary: These references also provide information regarding vaccination products licensed for use in ruminants and typical herd and flock vaccination parasite control schedules ("Current Veterinary Therapy," 1986 , 1999 "Council report," 1994; "Large Animal Internal Medicine," 1996; Smith and Sherman, 1994) When designing a vaccination program during qualification of a source or at the research facility, it is important to evaluate the local disease incidence and the potential for exposure. Clinical signs in chronic cases in older animals, such as adult goats, include soft stools, weight loss, anorexia, depression, and severe diarrhea, sometimes with mucus and blood. This pathogen does present a complication due to the carrier status of some animals, the likelihood of herd outbreaks, the severity of disease in younger animals, and the morbidity, possible progression to uveitis, and time and treatment costs associated with infections. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7150219/ doi: 10.1016/b978-012263951-7/50017-x id: cord-301362-f3lp10lm author: Delgui, Laura R. title: A Novel Mechanism Underlying the Innate Immune Response Induction upon Viral-Dependent Replication of Host Cell mRNA: A Mistake of +sRNA Viruses'' Replicases date: 2017-01-20 words: 7007.0 sentences: 343.0 pages: flesch: 42.0 cache: ./cache/cord-301362-f3lp10lm.txt txt: ./txt/cord-301362-f3lp10lm.txt summary: Recognition of viral double-strand RNA (dsRNA) molecules by intracellular Toll-like receptors (TLRs) or retinoic acid inducible gene I-like receptors (RLRs) is a central event which entails the early steps of the immune response elicited during viral infections. Despite several differences among host range, viral structure, genome organization or membrane-donor organelles from the cell, these analyses revealed that +sRNA viruses are able to induce two types of membranous modifications as replicative niches: invaginated vesicles or spherules or a double membrane vesicle type. Endogenous RNAs forming secondary double-stranded structures that are released after necrosis and tissue damage after viral infection represent another source of dsRNA molecules reaching the endosomes, inducing host-derived dsRNA-mediated inflammatory responses through TLR-3 recognition (Kawai and Akira, 2010) . Other +sRNA viruses such as the enterovirus Coxsackievirus (Kemball et al., 2010) , Hepatitis C virus (Flaviviridae family) (Sir et al., 2012) , or Coronavirus such as MVH (Reggiori et al., 2010) also usurp the autophagy pathway and induce remarkably alterations in intracellular membranous components to harbor the sites for viral RNA replication. abstract: Viruses are lifeless particles designed for setting virus-host interactome assuring a new generation of virions for dissemination. This interactome generates a pressure on host organisms evolving mechanisms to neutralize viral infection, which places the pressure back onto virus, a process known as virus-host cell co-evolution. Positive-single stranded RNA (+sRNA) viruses are an important group of viral agents illustrating this interesting phenomenon. During replication, their genomic +sRNA is employed as template for translation of viral proteins; among them the RNA-dependent RNA polymerase (RdRp) is responsible of viral genome replication originating double-strand RNA molecules (dsRNA) as intermediates, which accumulate representing a potent threat for cellular dsRNA receptors to initiate an antiviral response. A common feature shared by these viruses is their ability to rearrange cellular membranes to serve as platforms for genome replication and assembly of new virions, supporting replication efficiency increase by concentrating critical factors and protecting the viral genome from host anti-viral systems. This review summarizes current knowledge regarding cellular dsRNA receptors and describes prototype viruses developing replication niches inside rearranged membranes. However, for several viral agents it's been observed both, a complex rearrangement of cellular membranes and a strong innate immune antiviral response induction. So, we have included recent data explaining the mechanism by, even though viruses have evolved elegant hideouts, host cells are still able to develop dsRNA receptors-dependent antiviral response. url: https://www.ncbi.nlm.nih.gov/pubmed/28164038/ doi: 10.3389/fcimb.2017.00005 id: cord-327777-pg98zc6o author: Delogu, Mauro title: Eco-Virological Preliminary Study of Potentially Emerging Pathogens in Hedgehogs (Erinaceus europaeus) Recovered at a Wildlife Treatment and Rehabilitation Center in Northern Italy date: 2020-03-01 words: 3195.0 sentences: 156.0 pages: flesch: 48.0 cache: ./cache/cord-327777-pg98zc6o.txt txt: ./txt/cord-327777-pg98zc6o.txt summary: However, the high mutation rates characterizing members of the Coronaviridae family and their potential successful interspecies host jumps—as that likely occurred in the Novel coronavirus (2019-nCoV) emergence—should be considered in the management of hedgehogs admitted to multi-species wildlife rehabilitation centers, recommending their return back to the original recovery areas. Western European hedgehogs'' ecological and feeding habits, along with their high population densities, notable synanthropic attitudes, frequent contacts with sympatric wild and domestic species, including humans, implicate the possible involvement of E. The wild bird Influenza A virus (IAV) gene pool poses significant risks for both animal and human health because of its ability to colonize a wide variety of animal species (included in the Mammalia, Aves and Reptilia classes) in which IAV can cause variable outcomes of infection, with possible high morbidity and fatality rates [20] . abstract: SIMPLE SUMMARY: Most of the newly emerging infections arise from animal reservoirs, frequently represented by wildlife species. Western European hedgehogs (Erinaceus europaeus) are mammalian hibernators, mainly nocturnal and insectivorous, living in natural open and green spaces as well as artificial, rural and urban, areas. They are generalist predators of macro-invertebrates, but they may also eat meat, bird eggs and on occasion pet food. These ecological and feeding habits, along with their high population densities, notable synanthropic attitudes, frequent contacts with sympatric wild and domestic species, including humans, implicate the possibility of intra- and interspecies interactions accounting for the possible involvement of E. europaeus in the ecology of several potentially emerging pathogens, including coronaviruses. Using PCR-based and virus isolation methods, we found that 58.3% of 24 hedgehogs’ fecal samples were PCR-positive for Erinaceus coronaviruses (EriCoVs). We did not observe any clinical disease related to the EriCoV infection in hedgehogs. However, the high mutation rates characterizing members of the Coronaviridae family and their potential successful interspecies host jumps—as that likely occurred in the Novel coronavirus (2019-nCoV) emergence—should be considered in the management of hedgehogs admitted to multi-species wildlife rehabilitation centers, recommending their return back to the original recovery areas. ABSTRACT: The Western European Hedgehog (Erinaceus europaeus) is one of the four hedgehog species belonging to the genus Erinaceus. Among them, E. amurensis is extant in East Asia’s areas only, whereas E. europaeus, E. roumanicus and E. concolor are mainly found in Europe. E. europaeus is endemically distributed from western to central and southern Europe, including Italy. Western European hedgehogs’ ecological and feeding habits, along with their high population densities, notable synanthropic attitudes, frequent contacts with sympatric wild and domestic species, including humans, implicate the possible involvement of E. europaeus in the ecology of potentially emerging viruses, such as coronaviruses, influenza A and influenza D viruses, canine distemper virus, pestiviruses and Aujeszky’s disease virus. We examined 24 E. europaeus individuals found injured in urban and rural areas of Northern Italy. Of the 24 fecal samples collected and tested for the above-mentioned pathogens by both PCR-based and virus isolation methods, 14 were found PCR-positive for betacoronaviruses belonging to lineage C and related to the known Erinaceus coronaviruses (EriCoVs), as determined by partial sequencing of the virus genome. Our findings suggest that hedgehogs could be considered natural reservoirs of CoVs, and also act as chronic shedding carriers of these potentially emerging RNA viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32121543/ doi: 10.3390/ani10030407 id: cord-304498-ty41xob0 author: Denison, Mark R title: Coronaviruses: An RNA proofreading machine regulates replication fidelity and diversity date: 2011-03-01 words: 7332.0 sentences: 345.0 pages: flesch: 38.0 cache: ./cache/cord-304498-ty41xob0.txt txt: ./txt/cord-304498-ty41xob0.txt summary: Genetic inactivation of exoN activity in engineered SArS-Cov and MHv genomes by alanine substitution at conserved De-D-D active site residues results in viable mutants that demonstrate 15-to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other rNA viruses. Genetic inactivation of exoN activity in engineered SArS-Cov and MHv genomes by alanine substitution at conserved De-D-D active site residues results in viable mutants that demonstrate 15-to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other rNA viruses. The high mutation rates of RNA viruses also render them particularly susceptible to repeated genetic bottleneck events during replication, transmission between hosts or spread within a host, resulting in progressive deviation from the consensus sequence associated with decreased viral fitness and sometimes extinction. abstract: In order to survive and propagate, RNA viruses must achieve a balance between the capacity for adaptation to new environmental conditions or host cells with the need to maintain an intact and replication competent genome. Several virus families in the order Nidovirales, such as the coronaviruses (CoVs) must achieve these objectives with the largest and most complex replicating RNA genomes known, up to 32 kb of positive-sense RNA. The CoVs encode sixteen nonstructural proteins (nsp 1–16) with known or predicted RNA synthesis and modification activities, and it has been proposed that they are also responsible for the evolution of large genomes. The CoVs, including murine hepatitis virus (MHV) and SARS-CoV, encode a 3′-to-5′ exoribonuclease activity (ExoN) in nsp14. Genetic inactivation of ExoN activity in engineered SARS-CoV and MHV genomes by alanine substitution at conserved DE-D-D active site residues results in viable mutants that demonstrate 15- to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other RNA viruses. Thus nsp14-ExoN is essential for replication fidelity, and likely serves either as a direct mediator or regulator of a more complex RNA proofreading machine, a process previously unprecedented in RNA virus biology. Elucidation of the mechanisms of nsp14-mediated proofreading will have major implications for our understanding of the evolution of RNA viruses, and also will provide a robust model to investigate the balance between fidelity, diversity and pathogenesis. The discovery of a protein distinct from a viral RdRp that regulates replication fidelity also raises the possibility that RNA genome replication fidelity may be adaptable to differing replication environments and selective pressures, rather than being a fixed determinant. url: https://www.ncbi.nlm.nih.gov/pubmed/21593585/ doi: 10.4161/rna.8.2.15013 id: cord-345654-vyz6f3he author: Dennehy, John J. title: Evolutionary ecology of virus emergence date: 2016-12-30 words: 11475.0 sentences: 701.0 pages: flesch: 43.0 cache: ./cache/cord-345654-vyz6f3he.txt txt: ./txt/cord-345654-vyz6f3he.txt summary: Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between‐host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between‐host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead‐end spillover infections. Virus quasispecies may facilitate host range expansion Viruses are among the smallest nucleic acid-based replicating entities and possess characteristics associated with exceptionally fast evolutionary change: small genomes, short generation times, high mutation rates, large population sizes, high levels of genetic diversity, and strong selection pressures. abstract: The cross‐species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between‐host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge. In this paper, I address the evolutionary mechanisms of virus emergence and how they relate to virus ecology. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between‐host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead‐end spillover infections. Despite the relative rarity of pandemic emerging viruses, the potential of viruses to search evolutionary space and find means to spread epidemically and the consequences of pandemic viruses that do emerge necessitate sustained attention to virus research, surveillance, prophylaxis, and treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/28036113/ doi: 10.1111/nyas.13304 id: cord-341138-mxjsp3cm author: Denner, Joachim title: Transspecies Transmission of Gammaretroviruses and the Origin of the Gibbon Ape Leukaemia Virus (GaLV) and the Koala Retrovirus (KoRV) date: 2016-12-20 words: 4762.0 sentences: 239.0 pages: flesch: 47.0 cache: ./cache/cord-341138-mxjsp3cm.txt txt: ./txt/cord-341138-mxjsp3cm.txt summary: title: Transspecies Transmission of Gammaretroviruses and the Origin of the Gibbon Ape Leukaemia Virus (GaLV) and the Koala Retrovirus (KoRV) The gibbon ape leukaemia virus (GaLV) and koala retrovirus (KoRV), two gammaretroviruses, are also the result of a transspecies transmission, however from a still unknown host. The transspecies transmission of the gibbon ape leukaemia virus (GaLV) and the koala retrovirus (KoRV) is a prime example of a transmission that is still not yet fully understood. Searching for the precursor virus, retroviruses related to KoRV and GaLV have been described in rodents such as South East Asian mice (e.g., Mus caroli [9, 10] and Mus dunni [11] ), as well as in two subspecies of Melomys burtoni in Australia and Indonesia [12, 13] . The nucleotide sequence of koala (Phascolarctos cinereus) retrovirus: A novel type C endogenous virus related to gibbon ape leukemia virus abstract: Transspecies transmission of retroviruses is a frequent event, and the human immunodeficiency virus-1 (HIV-1) is a well-known example. The gibbon ape leukaemia virus (GaLV) and koala retrovirus (KoRV), two gammaretroviruses, are also the result of a transspecies transmission, however from a still unknown host. Related retroviruses have been found in Southeast Asian mice although the sequence similarity was limited. Viruses with a higher sequence homology were isolated from Melomys burtoni, the Australian and Indonesian grassland melomys. However, only the habitats of the koalas and the grassland melomys in Australia are overlapping, indicating that the melomys virus may not be the precursor of the GaLV. Viruses closely related to GaLV/KoRV were also detected in bats. Therefore, given the fact that the habitats of the gibbons in Thailand and the koalas in Australia are far away, and that bats are able to fly over long distances, the hypothesis that retroviruses of bats are the origin of GaLV and KoRV deserves consideration. Analysis of previous transspecies transmissions of retroviruses may help to evaluate the potential of transmission of related retroviruses in the future, e.g., that of porcine endogenous retroviruses (PERVs) during xenotransplantation using pig cells, tissues or organs. url: https://www.ncbi.nlm.nih.gov/pubmed/27999419/ doi: 10.3390/v8120336 id: cord-294812-nnlzwaf1 author: Desforges, Marc title: Neuroinvasive and Neurotropic Human Respiratory Coronaviruses: Potential Neurovirulent Agents in Humans date: 2014-03-12 words: 7096.0 sentences: 318.0 pages: flesch: 36.0 cache: ./cache/cord-294812-nnlzwaf1.txt txt: ./txt/cord-294812-nnlzwaf1.txt summary: However, in some circumstances, viruses can avoid the immune response and cause more severe respiratory diseases [1] or even spread to other tissues, including the central nervous system (CNS), where they could induce other types of pathologies [7] . Coronaviruses, a family of enveloped positive-stranded RNA viruses with a characteristic crown-shaped appearance, are widespread in nature and can infect several different species [44] , in which they cause mainly respiratory and enteric pathologies, with neurotropic and neuroinvasive properties in various hosts including humans, cats, pigs, rodents, and fowl [45] [46] [47] [48] . Furthermore, we have shown that these viruses are able to establish a persistent infection in human cells representative of the CNS [64, 65] and that HCoV-OC43 RNA could be detected for at least a year in the CNS of infected mice that survived the virus-induced acute encephalitis [71] . abstract: In humans, viral infections of the respiratory tract are a leading cause of morbidity and mortality worldwide. Several recognized respiratory viral agents have a neuroinvasive capacity since they can spread from the respiratory tract to the central nervous system (CNS). Once there, infection of CNS cells (neurotropism) could lead to human health problems, such as encephalitis and long-term neurological diseases. Among the various respiratory viruses, coronaviruses are important pathogens of humans and animals. Human Coronaviruses (HCoV) usually infect the upper respiratory tract, where they are mainly associated with common colds. However, in more vulnerable populations, such as newborns, infants, the elderly, and immune-compromised individuals, they can also affect the lower respiratory tract, leading to pneumonia, exacerbations of asthma, respiratory distress syndrome, or even severe acute respiratory syndrome (SARS). The respiratory involvement of HCoV has been clearly established since the 1960s. In addition, for almost three decades now, the scientific literature has also demonstrated that HCoV are neuroinvasive and neurotropic and could induce an overactivation of the immune system, in part by participating in the activation of autoreactive immune cells that could be associated with autoimmunity in susceptible individuals. Furthermore, it was shown that in the murine CNS, neurons are the main target of infection, which causes these essential cells to undergo degeneration and eventually die by some form of programmed cell death after virus infection. Moreover, it appears that the viral surface glycoprotein (S) represents an important factor in the neurodegenerative process. Given all these properties, it has been suggested that these recognized human respiratory pathogens could be associated with the triggering or the exacerbation of neurological diseases for which the etiology remains unknown or poorly understood. url: https://doi.org/10.1007/978-81-322-1777-0_6 doi: 10.1007/978-81-322-1777-0_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-004827-bnf3mvaf author: Desselberger, U. title: Report on an ICTV-sponsored symposium on Virus Evolution date: 2005-01-13 words: 2766.0 sentences: 164.0 pages: flesch: 48.0 cache: ./cache/cord-004827-bnf3mvaf.txt txt: ./txt/cord-004827-bnf3mvaf.txt summary: Phylogenetic relationships have been found useful for virus identification, work on origin, speed and mechanisms of evolution, taxonomy, and the elucidation of transmission pathways (e.g. the transmission of HIV from a source to a victim [16] ). In vitro, a single round of replication of HIV-1 in T lymphocytes generated on average 9 recombination events per virus [14] . Approximately 50% of sequence changes are consistent with evolution by point mutations; other changes are due to multiple recombination events. After an introduction in which basic genetic terms were defined (mutation and mutation rate, hypermutation, recombination, reassortment, segmentation etc), the quasispecies concept was presented according to which any sample of an RNA virus represents a ''swarm'' of closely related mutants. ''To maintain RNA structure, evolution selects against better alternatives elsewhere in the genome''. The aim of the talk was to show the significance of RNA structural considerations for the evolution of viruses. Plant RNA virus evolution abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087184/ doi: 10.1007/s00705-004-0466-9 id: cord-010168-aiqbqnaa author: Desselberger, Ulrich title: Classical and molecular techniques for the diagnosis of viral gastroenteritis() date: 1999-03-11 words: 3870.0 sentences: 223.0 pages: flesch: 46.0 cache: ./cache/cord-010168-aiqbqnaa.txt txt: ./txt/cord-010168-aiqbqnaa.txt summary: The vaccine response is widened by applying a cocktail of viruses, e.g. containing a native rhesus rotavirus (RRV) of G3 type and reassortants carrying the VP7 genes of human serotypes G1, G2 and G4 in the RRV genetic background (Rennels et al., 1996) . These have been used as antigens in ELISA, and it was shown that NV or related viruses infect children worldwide in large numbers, and 60 80% of young adults have NV-reactive antibody (Gray et al., 1993) . Norwalk-like viruses are transmitted by the faeco-oral route and were found to be causative agents of various outbreaks of viral gastroenteritis occurring in recreational camps, schools and nursing homes, on cruise ships, around contaminated swimming pools, or in the community (Greenberg et al., 1981) . Sequence and genome organization of a human small, round-structured (Norwalk-like) virus abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172258/ doi: 10.1016/0928-0197(96)00211-5 id: cord-266199-smlq11y9 author: Dhakal, Santosh title: Nanoparticle-based vaccine development and evaluation against viral infections in pigs date: 2019-11-06 words: 7647.0 sentences: 414.0 pages: flesch: 38.0 cache: ./cache/cord-266199-smlq11y9.txt txt: ./txt/cord-266199-smlq11y9.txt summary: The economic burden caused by virus infections such as Porcine Reproductive and Respiratory Syndrome Virus, Swine influenza virus, Porcine Epidemic Diarrhea Virus, Porcine Circovirus 2, Foot and Mouth Disease Virus and many others are associated with severe morbidity, mortality, loss of production, trade restrictions and investments in control and prevention practices. Likewise, DCs targeted chitosan NPs loading plasmid DNA encoding nucleocapsid protein of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) induced better nucleocapsid protein-specific mucosal IgA antibody response compared to soluble unentrapped antigens after nasal immunization in mice [57] . In this review, only studies conducted in pigs related to the development and evaluation of NPs-based vaccine candidates by using virus-like particles (VLPs), biodegradable polymers, polysaccharides and liposomes against porcine viral infections are included (Table 3) . Chitosan-based NPs are used in pigs to deliver adjuvants such as bee venom and plasmid encoding porcine IL-2 and IL-4/IL-6 genes, which improved induction of better virus-specific immune responses of respective vaccines against PRRSV and PCV2 [103, 104] . abstract: Virus infections possess persistent health challenges in swine industry leading to severe economic losses worldwide. The economic burden caused by virus infections such as Porcine Reproductive and Respiratory Syndrome Virus, Swine influenza virus, Porcine Epidemic Diarrhea Virus, Porcine Circovirus 2, Foot and Mouth Disease Virus and many others are associated with severe morbidity, mortality, loss of production, trade restrictions and investments in control and prevention practices. Pigs can also have a role in zoonotic transmission of some viral infections to humans. Inactivated and modified-live virus vaccines are available against porcine viral infections with variable efficacy under field conditions. Thus, improvements over existing vaccines are necessary to: (1) Increase the breadth of protection against evolving viral strains and subtypes; (2) Control of emerging and re-emerging viruses; (3) Eradicate viruses localized in different geographic areas; and (4) Differentiate infected from vaccinated animals to improve disease control programs. Nanoparticles (NPs) generated from virus-like particles, biodegradable and biocompatible polymers and liposomes offer many advantages as vaccine delivery platform due to their unique physicochemical properties. NPs help in efficient antigen internalization and processing by antigen presenting cells and activate them to elicit innate and adaptive immunity. Some of the NPs-based vaccines could be delivered through both parenteral and mucosal routes to trigger efficient mucosal and systemic immune responses and could be used to target specific immune cells such as mucosal microfold (M) cells and dendritic cells (DCs). In conclusion, NPs-based vaccines can serve as novel candidate vaccines against several porcine viral infections with the potential to enhance the broader protective efficacy under field conditions. This review highlights the recent developments in NPs-based vaccines against porcine viral pathogens and how the NPs-based vaccine delivery system induces innate and adaptive immune responses resulting in varied level of protective efficacy. url: https://www.ncbi.nlm.nih.gov/pubmed/31694705/ doi: 10.1186/s13567-019-0712-5 id: cord-331289-02411gfv author: Di Minno, Giovanni title: Current concepts in the prevention of pathogen transmission via blood/plasma-derived products for bleeding disorders() date: 2015-07-20 words: 8171.0 sentences: 395.0 pages: flesch: 43.0 cache: ./cache/cord-331289-02411gfv.txt txt: ./txt/cord-331289-02411gfv.txt summary: In general, clinicians assess the level of risk associated with the use of blood/ plasma-derived products by evaluating factors such as patient characteristics (e.g. age, immune status, geographical location, lifestyle) and the nature of the pathogen (e.g. physical characteristics, level of virulence, chronicity of infection, prevalence). Current donor selection and screening practices have improved our ability to detect or reduce the presence of pathogens in blood/plasma-derived products; for example, the residual risk of transfusion-transmitted infection (TTI) with HIV/HBV/HCV has fallen to near or less than 1 per million transfused units [14, 15] . Since TTV is often detected in healthy individuals and is not associated with any particular disease, routine screening for this virus is not considered to be necessary; even a test with excellent sensitivity/specificity would not contribute to increase the level of safety of blood/plasma-derived products with regard to TTV. abstract: The pathogen safety of blood/plasma-derived products has historically been a subject of significant concern to the medical community. Measures such as donor selection and blood screening have contributed to increase the safety of these products, but pathogen transmission does still occur. Reasons for this include lack of sensitivity/specificity of current screening methods, lack of reliable screening tests for some pathogens (e.g. prions) and the fact that many potentially harmful infectious agents are not routinely screened for. Methods for the purification/inactivation of blood/plasma-derived products have been developed in order to further reduce the residual risk, but low concentrations of pathogens do not necessarily imply a low level of risk for the patient and so the overall challenge of minimising risk remains. This review aims to discuss the variable level of pathogenic risk and describes the current screening methods used to prevent/detect the presence of pathogens in blood/plasma-derived products. url: https://www.sciencedirect.com/science/article/pii/S0268960X15000594 doi: 10.1016/j.blre.2015.07.004 id: cord-011129-btaxvmsr author: Di Paola, Nicholas title: Viral genomics in Ebola virus research date: 2020-05-04 words: 9440.0 sentences: 433.0 pages: flesch: 37.0 cache: ./cache/cord-011129-btaxvmsr.txt txt: ./txt/cord-011129-btaxvmsr.txt summary: Here, we review how recent advances in genomic technologies have shaped past and current responses to outbreaks of Ebola virus disease (EVD), including insights into filovirus diversity and evolution. After this identification, considerations other than sequencing speed (for example, sequencing accuracy and processivity) become paramount in determining virus transmission networks and in detecting changes in the viral genome (between cases in the current outbreak and between the current and previous outbreaks) that could subvert MCMs. However, whereas unbiased sequencing approaches using high fidelity platforms can lead to the discovery of co-infections and reveal important clinical considerations during the treatment of patients near the point of need, targeted methods of pathogen characterization using the portable sequencing platforms iSeq 100 and MiSeq (which use bait-enrichment techniques) and MinION (which uses amplicon sequencing) can still provide useful genomic data albeit with a lower sequencing output (that is, a lower number of reads) than unbiased sequencing. abstract: Filoviruses such as Ebola virus continue to pose a substantial health risk to humans. Advances in the sequencing and functional characterization of both pathogen and host genomes have provided a wealth of knowledge to clinicians, epidemiologists and public health responders during outbreaks of high-consequence viral disease. Here, we describe how genomics has been historically used to investigate Ebola virus disease outbreaks and how new technologies allow for rapid, large-scale data generation at the point of care. We highlight how genomics extends beyond consensus-level sequencing of the virus to include intra-host viral transcriptomics and the characterization of host responses in acute and persistently infected patients. Similar genomics techniques can also be applied to the characterization of non-human primate animal models and to known natural reservoirs of filoviruses, and metagenomic sequencing can be the key to the discovery of novel filoviruses. Finally, we outline the importance of reverse genetics systems that can swiftly characterize filoviruses as soon as their genome sequences are available. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223634/ doi: 10.1038/s41579-020-0354-7 id: cord-007733-zh8e76w7 author: DiMenna, Lauren J. title: Pandemic Influenza Vaccines date: 2009-06-15 words: 12728.0 sentences: 594.0 pages: flesch: 43.0 cache: ./cache/cord-007733-zh8e76w7.txt txt: ./txt/cord-007733-zh8e76w7.txt summary: The efficacy of seasonal vaccines is linked to their ability to induce virus-neutralizing antibodies, which provide subtype-specific protection against influenza A viruses. Alternatively, the scientific community could step up efforts to generate a universal vaccine against influenza A viruses that provides broadly cross-reactive protection through the induction of antibodies or T cells to conserved regions of the virus. Alternatively, the scientific community could step up efforts to generate a universal vaccine against influenza A viruses that provides broadly cross-reactive protection through the induction of antibodies or T cells to conserved regions of the virus. WHO recommends three measures to lessen the impact of the next influenza virus pandemic: (1) increased surveillance to allow for the earliest possible warning that a human pandemic has started; (2) early intervention to stall global spread and prevent further adaptations; and (3) development of an effective pandemic vaccine. abstract: Since their compositions remain uncertain, universal pandemic vaccines are yet to be created. They would aim to protect globally against pandemic influenza viruses that have not yet evolved. Thus they differ from seasonal vaccines to influenza virus, which are updated annually in spring to incorporate the latest circulating viruses, and are then produced and delivered before the peak influenza season starts in late fall and winter. The efficacy of seasonal vaccines is linked to their ability to induce virus-neutralizing antibodies, which provide subtype-specific protection against influenza A viruses. If pandemic vaccines were designed to resemble current vaccines in terms of composition and mode of action, they would have to be developed, tested, and mass-produced after the onset of a pandemic, once the causative virus had been identified. The logistic problems of generating a pandemic vaccine from scratch, conducting preclinical testing, and producing billions of doses within a few months for global distribution are enormous and may well be insurmountable. Alternatively, the scientific community could step up efforts to generate a universal vaccine against influenza A viruses that provides broadly cross-reactive protection through the induction of antibodies or T cells to conserved regions of the virus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121491/ doi: 10.1007/978-3-540-92165-3_15 id: cord-288372-48wao8a0 author: Dia, Ndongo title: Respiratory viruses associated with patients older than 50 years presenting with ILI in Senegal, 2009 to 2011 date: 2014-04-08 words: 3873.0 sentences: 215.0 pages: flesch: 55.0 cache: ./cache/cord-288372-48wao8a0.txt txt: ./txt/cord-288372-48wao8a0.txt summary: The main aim of this study was to determine the prevalence and the diversity of respiratory viruses associated with ILI cases in adults over 50 years old in Senegal. Viral aetiology, prevalence and diversity data in people with influenza like illness (ILI) and/or acute respiratory illness (ARI) in Africa, (especially in West Africa), are scarce and often limited to the influenza viruses'' infection. For example in the United States alone, up to 40% of non-pneumonic lower respiratory illnesses in the elderly have been associated with respiratory viral infection [10] , and an estimated 54,000 deaths annually have been attributed to the influenza and respiratory syncytial viruses (RSV) [11] . The present study is the first description of the etiology of respiratory viruses associated with patients with ILI in a cohort of elderly people in the West African context. abstract: BACKGROUND: In Africa, especially in West Africa, studies about the prevalence and diversity of respiratory viruses (influenza and others) in elderly people are largely lacking. In studies done elsewhere, it is well established that older people, when compared with younger adults, are at greater risk of significant morbidity and mortality from complications arising from influenza. The main aim of this study was to determine the prevalence and the diversity of respiratory viruses associated with ILI cases in adults over 50 years old in Senegal. METHODS: The recruitment period of this study was from January 2009 to December 2011. 232 patients aged 50 years and above presenting ILI cases were enrolled. Nasal-pharyngeal and/or oral pharyngeal swabs were collected from patients. RNA was extracted from 200 μl of each sample followed by a two-step real-time RT-PCR. The Anyplex™ II RV16 Detection kit was used for viral detection. The kit enabled the simultaneous detection of the presence of 16 respiratory viruses. RESULTS: 150 viruses were detected: influenza viruses (44.7%) and rhinoviruses (26.7%) were the most prevalent. We detected 13 human parainfluenza viruses (8.7%), 7 human respiratory syncytial viruses (4.7%), 6 coronaviruses (4%), 5 human metapneumoviruses (3.3%), 5 human adenoviruses (3.3%) and 1 human bocavirus (0.7%). 14 cases (6%) of dual virus infections and one triple viral detection case were encountered. 56 (56.6%) viruses detected were found in the 50-64 year old age group, 59 (76.6%; P < 0.001) from 65–74 year old age group and 35 (62.5%) were detected in the ≥75 year old age group. The viral co-infections were more frequent in the 65-74 age group (9/15). CONCLUSIONS: This pilot study demonstrates a variety of respiratory viruses in the elderly. It also highlights a high prevalence of these viruses in this age group. We speculate from these results that the impact of respiratory viruses other than influenza on the elderly has been considerably underestimated. A more exhaustive study seems necessary in order to provide a more complete picture of the burden of respiratory viruses on morbidity among adults over 50 years old in the sub-Saharan context. url: https://doi.org/10.1186/1471-2334-14-189 doi: 10.1186/1471-2334-14-189 id: cord-333463-u7je0d1o author: Diaz-Salazar, Carlos title: Natural killer cell responses to emerging viruses of zoonotic origin date: 2020-08-09 words: 6193.0 sentences: 353.0 pages: flesch: 43.0 cache: ./cache/cord-333463-u7je0d1o.txt txt: ./txt/cord-333463-u7je0d1o.txt summary: Nearly all emerging viruses, including Ebola, Dengue, Nipah, West Nile, Zika, and coronaviruses (including SARS-Cov2, the causative agent of the current COVID-19 pandemic), have zoonotic origins, indicating that animal-to-human transmission constitutes a primary mode of acquisition of novel infectious diseases. Natural killer (NK) cells are innate lymphocytes that play a critical role in the early antiviral response, secreting effector cytokines and clearing infected cells. This review describes the role of Natural killer (NK) cells, a critical component of early antiviral immunity, in the establishment of tolerance to viral infections in natural hosts, as well as their role in the development of disease in nonnatural hosts. Altogether, it is believed that quick control of viral infections and reduced induction of pro-inflammatory cytokines have allowed bat viruses to rapidly co-evolve with their host without provoking major immuneThe careful study of the immune system in reservoirs of zoonotic diseases will certainly offer insights into how these animals carry high viral loads while remaining asymptomatic. abstract: Emerging viral diseases pose a major threat to public health worldwide. Nearly all emerging viruses, including Ebola, Dengue, Nipah, West Nile, Zika, and coronaviruses (including SARS-Cov2, the causative agent of the current COVID-19 pandemic), have zoonotic origins, indicating that animal-to-human transmission constitutes a primary mode of acquisition of novel infectious diseases. Why these viruses can cause profound pathologies in humans, while natural reservoir hosts often show little evidence of disease is not completely understood. Differences in the host immune response, especially within the innate compartment, have been suggested to be involved in this divergence. Natural killer (NK) cells are innate lymphocytes that play a critical role in the early antiviral response, secreting effector cytokines and clearing infected cells. In this review, we will discuss the mechanisms through which NK cells interact with viruses, their contribution towards maintaining equilibrium between the virus and its natural host, and their role in disease progression in humans and other non-natural hosts. url: https://www.ncbi.nlm.nih.gov/pubmed/32784125/ doi: 10.1016/j.coviro.2020.07.003 id: cord-312332-rwmuucsp author: Dicker, Kate title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity date: 2020-09-10 words: 9235.0 sentences: 480.0 pages: flesch: 45.0 cache: ./cache/cord-312332-rwmuucsp.txt txt: ./txt/cord-312332-rwmuucsp.txt summary: title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity Different proteomic studies have identified hundreds of cellular factors within the particles of several RNA viruses [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] , many of which are RBPs. Here, we discuss the ''knowns'' and ''unknowns'' of the roles that virion-incorporated cellular RBPs could play in the assembly of viral particles and the early steps of infection in the new host cell. Many ivRBPs such as annexins, heat shock family proteins (HSP), peptidylprolyl isomerase A (PPIA -also cyclophilin A), eukaryotic translation elongation factors (EEF), heterogeneous nuclear ribonucleoproteins (HNRNP) or poly(rC) binding protein 1 (PCBP1), have been linked to infection in multiple ways (Fig. S2) , and here we show that they are incorporated in the particles of several viruses (Table S1B) . abstract: RNA is a central molecule in RNA virus biology due to its dual function as messenger and genome. However, the small number of proteins encoded by viral genomes is insufficient to enable virus infection. Hence, viruses hijack cellular RNA-binding proteins (RBPs) to aid replication and spread. In this review we discuss the ‘knowns’ and ‘unknowns’ regarding the contribution of host RBPs to the formation of viral particles and the initial steps of infection in the newly infected cell. Through comparison of the virion proteomes of ten different human RNA viruses, we confirm that a pool of cellular RBPs are typically incorporated into viral particles. We describe here illustrative examples supporting the important functions of these RBPs in viral particle formation and infectivity and we propose that the role of host RBPs in these steps can be broader than previously anticipated. Understanding how cellular RBPs regulate virus infection can lead to the discovery of novel therapeutic targets against viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32921578/ doi: 10.1016/j.semcdb.2020.08.002 id: cord-017070-05vlz5dn author: Dimitrov, Dimiter S. title: Human Monoclonal Antibodies Against HIV and Emerging Viruses date: 2008 words: 6662.0 sentences: 299.0 pages: flesch: 38.0 cache: ./cache/cord-017070-05vlz5dn.txt txt: ./txt/cord-017070-05vlz5dn.txt summary: These antibodies also protected uninfected animals from SARS-CoV infection, e.g., passive transfer of immune serum to naive mice prevented virus replication in the lower respiratory tract following intranasal challenge (61) . Recently, an improved method for Epstein-Barr virus transformation of human B cells has been developed based on CpG oligonucleotide (CpG 2006) that increases the B cell immortalization efficiency from 1-2% to 30-100%, and used for selection of hmAbs specific for SARS-CoV proteins (68) . We have recently identified a novel cross-reactive potent SARS-CoV-neutralizing hmAb, m396, by using a fragment containing residues 317 through 518 as a selecting antigen for panning of a large human antibody library constructed from the B lymphocytes of healthy volunteers (75) . These antibodies specific for SARS-CoV, HeV, and NiV have potential for further development into a clinically useful product for prophylaxis and perhaps treatment of the diseases caused by these infections. Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121542/ doi: 10.1007/978-1-59745-569-5_34 id: cord-260956-w6wxsg4p author: Dimitrov, Kiril M. title: Newcastle disease vaccines—A solved problem or a continuous challenge? date: 2017-07-31 words: 10563.0 sentences: 423.0 pages: flesch: 39.0 cache: ./cache/cord-260956-w6wxsg4p.txt txt: ./txt/cord-260956-w6wxsg4p.txt summary: When administered correctly to healthy birds, ND vaccines formulated with NDV of low virulence or viral-vectored vaccines that express the NDV fusion protein are able to prevent clinical disease and mortality in chickens upon infection with virulent NDV. Characterization of live LaSota vaccine strain-induced protection in chickens upon early challenge with a virulent Newcastle disease virus of heterologous genotype Protection from clinical disease against three highly virulent strains of Newcastle disease virus after in ovo application of an antibody-antigen complex vaccine in maternal antibodypositive chickens Antigenic differences among Newcastle disease virus strains of different genotypes used in vaccine formulation affect viral shedding after a virulent challenge Level of protection of chickens against highly pathogenic H5 avian influenza virus with Newcastle disease virus based live attenuated vector vaccine depends on homology of H5 sequence between vaccine and challenge virus abstract: Abstract Newcastle disease (ND) has been defined by the World Organisation for Animal Health as infection of poultry with virulent strains of Newcastle disease virus (NDV). Lesions affecting the neurological, gastrointestinal, respiratory, and reproductive systems are most often observed. The control of ND must include strict biosecurity that prevents virulent NDV from contacting poultry, and also proper administration of efficacious vaccines. When administered correctly to healthy birds, ND vaccines formulated with NDV of low virulence or viral-vectored vaccines that express the NDV fusion protein are able to prevent clinical disease and mortality in chickens upon infection with virulent NDV. Live and inactivated vaccines have been widely used since the 1950’s. Recombinant and antigenically matched vaccines have been adopted recently in some countries, and many other vaccine approaches have been only evaluated experimentally. Despite decades of research and development towards formulation of an optimal ND vaccine, improvements are still needed. Impediments to prevent outbreaks include uneven vaccine application when using mass administration techniques in larger commercial settings, the difficulties associated with vaccinating free-roaming, multi-age birds of village flocks, and difficulties maintaining the cold chain to preserve the thermo-labile antigens in the vaccines. Incomplete or improper immunization often results in the disease and death of poultry after infection with virulent NDV. Another cause of decreased vaccine efficacy is the existence of antibodies (including maternal) in birds, which can neutralize the vaccine and thereby reduce the effectiveness of ND vaccines. In this review, a historical perspective, summary of the current situation for ND and NDV strains, and a review of traditional and experimental ND vaccines are presented. url: https://doi.org/10.1016/j.vetmic.2016.12.019 doi: 10.1016/j.vetmic.2016.12.019 id: cord-286559-y8z0pwgn author: Ding, Nai-Zheng title: A permanent host shift of rabies virus from Chiroptera to Carnivora associated with recombination date: 2017-03-21 words: 4244.0 sentences: 211.0 pages: flesch: 45.0 cache: ./cache/cord-286559-y8z0pwgn.txt txt: ./txt/cord-286559-y8z0pwgn.txt summary: Bat virus host shifts have resulted in the emergence of several serious diseases in humans and animals, such as SARS 1 , Ebola 2 , and rabies 3 viruses. Interestingly, although evolutionary analyses have demonstrated that bat-to-carnivore host-shifting viruses accumulate few adaptive mutations 4, 6, 11 , in none of these examples did bat RABV establish permanent transmission cycles in the new host species 7 . The second permanent host shift appears to have occurred in North America, producing a lineage including two variants, raccoon rabies virus (RRV) and south-central skunk variant (SCSKV). Since bat RABVs are potentially able to infect carnivore species 6, 11, 14, 45 , we also propose that recombination may function as the third and fourth stages of establishment of a permanent host shift by significantly enhancing the adaptability of a bat virus in terrestrial mammals. abstract: Bat virus host shifts can result in the spread of diseases with significant effects. The rabies virus (RABV) is able to infect almost all mammals and is therefore a useful model for the study of host shift mechanisms. Carnivore RABVs originated from two historical host shifts from bat viruses. To reveal the genetic pathways by which bat RABVs changed their host tropism from bats to carnivores, we investigated the second permanent bat-to-carnivore shift resulting in two carnivore variants, known as raccoon RABV (RRV) and south-central skunk RABV (SCSKV). We found that their glycoprotein (G) genes are the result of recombination between an American bat virus and a carnivore virus. This recombination allowed the bat RABV to acquire the head of the G-protein ectodomain of the carnivore virus. This region is involved in receptor recognition and binding, response to changes in the pH microenvironment, trimerization of G proteins, and cell-to-cell transmission during the viral infection. Therefore, this recombination event may have significantly improved the variant’s adaptability to carnivores, altering its host tropism and thus leading to large-scale epidemics in striped skunk and raccoon. url: https://doi.org/10.1038/s41598-017-00395-2 doi: 10.1038/s41598-017-00395-2 id: cord-291816-d4j8samu author: Diniz Beduschi Travassos Alves, Christian title: Mamastrovirus 5 detected in a crab-eating fox (Cerdocyon thous): Expanding wildlife host range of astroviruses date: 2018-08-15 words: 4285.0 sentences: 270.0 pages: flesch: 47.0 cache: ./cache/cord-291816-d4j8samu.txt txt: ./txt/cord-291816-d4j8samu.txt summary: Herein, we describe the genomic characterization of a MAstV5 (strain crab-eating fox/2016/BRA) identified in a wild canid (Cerdocyon thous) diagnosed with canine distemper virus (CDV) as causa mortis. The present report is the first evidence of MAstV5 infection in an animal species other than the dog and highlights a possible natural astrovirus spillover between domestic and wild canids. The data presented herein shows two important findings: (i) it is the crab-eating fox/BRA/2016 strain was likely derived from the canine host, and (ii) the extra intestinal MAstV5 presence. The sequence for the ribosomal frameshift site between ORF1a and ORF1b, which is conserved in the Astrovirudae family members [38] , is present in the crab-eating fox/2016/BRA nearly full genome (Fig. 2) . The crab-eating fox/2016/BRA nearly full genome, as expected, grouped in the MAstV5 cluster with all other characterized canine astroviruses. abstract: Astroviruses are a common cause of gastroenteritis in children worldwide and can also cause infection in a range of domestic and wild animal species. Canine astrovirus (formally named as Mamastrovirus 5, MAstV5) has been reported worldwide, and its role as an enteric pathogen is still controversial. Herein, we describe the genomic characterization of a MAstV5 (strain crab-eating fox/2016/BRA) identified in a wild canid (Cerdocyon thous) diagnosed with canine distemper virus (CDV) as causa mortis. The nearly complete genome comprised 6579 nt in length and displayed the archetypal organization of astroviruses. The present report is the first evidence of MAstV5 infection in an animal species other than the dog and highlights a possible natural astrovirus spillover between domestic and wild canids. Moreover, these results show the first evidence of extra-intestinal MAstV5, suggesting a virus systemic spread. This work is expected to contribute to a better understanding of the astroviruses biology and their interactions with the wildlife health. url: https://www.sciencedirect.com/science/article/pii/S0147957118300523 doi: 10.1016/j.cimid.2018.08.002 id: cord-282742-eyukbot7 author: Diosa-Toro, Mayra title: Arthropod-Borne Flaviviruses and RNA Interference: Seeking New Approaches for Antiviral Therapy date: 2013-02-20 words: 6493.0 sentences: 364.0 pages: flesch: 48.0 cache: ./cache/cord-282742-eyukbot7.txt txt: ./txt/cord-282742-eyukbot7.txt summary: Geiss, Pierson, and Diamond (2005) observed that siRNAs targeting the C gene had no effect on virus replication when transfected into cells 10 h after WNV infection using lipid-based reagents. In addition, no significant reduction in viral protein or RNA levels was seen in WNV replicon-expressing cells transfected with siRNAs targeting the NS3 gene using lipid-based reagents. Also, a recent report showed that siRNA toward the TNF-a gene reduced cytokine response in DENV-infected DCs, highlighting the potential of targeted RNAi-based approaches to simultaneously decrease viral replication and the detrimental host immune response (Subramanya et al., 2010) . In addition, it has been shown that WNV (Chotkowski et al., 2008) and DENV (Mukherjee & Hanley, 2010) infection (Mukherjee & Hanley, 2010) of Drosophila cell lines induce functional virus-specific siRNAs that promote a protective RNAi response. So far we have described the antiviral effect of the RNAi mechanism induced by exogenous delivery of siRNA or precursors, and how cellular miRNA can target sequences artificially introduced within the genome of flaviviruses. abstract: Flaviviruses are the most prevalent arthropod-borne viruses worldwide, and nearly half of the 70 Flavivirus members identified are human pathogens. Despite the huge clinical impact of flaviviruses, there is no specific human antiviral therapy available to treat infection with any of the flaviviruses. Therefore, there is a continued search for novel therapies, and this review describes the current knowledge on the usage of RNA interference (RNAi) in combating flavivirus infections. RNAi is a process of sequence-specific gene silencing triggered by double-stranded RNA. Antiviral RNAi strategies against arthropod-borne flaviviruses have been reported and although several hurdles must be overcome to employ this technology in clinical applications, they potentially represent a new therapeutic tool. url: https://www.sciencedirect.com/science/article/pii/B9780124081161000045 doi: 10.1016/b978-0-12-408116-1.00004-5 id: cord-104286-5yw4zwo4 author: Doane, F. W. title: Virus morphology as an aid for rapid diagnosis. date: 1980 words: 2206.0 sentences: 138.0 pages: flesch: 39.0 cache: ./cache/cord-104286-5yw4zwo4.txt txt: ./txt/cord-104286-5yw4zwo4.txt summary: A specimen is inoculated into a host system (tissue culture, eggs, animals), and subsequent detection and identification of an isolated virus depends on indicators such as cytopathic effect, hemagglutinin, complement fixation, etc. The following brief review will examine some of the ways in which virus morphology can serve as an important aid for rapid virus diagnosis, some of the limitations of this approach, and current and future developments in electron microscopy relating to diagnostic virology. The same results can be obtained within one hour if one uses immunoelectron microscopy (IEM), by which the virusantiserum mixtures are negatively stained and examined on an EM specimen grid. A major advantage of using electron microscopy for rapid virus diagnosis is that one can actually see the virus and identify it by its morphology. Hepatitis A: detection by immune electron microscopy of a virus-like antigen associated with acute illness abstract: Standard methods of virus diagnosis may take many days to complete. As antiviral drugs are being used with more effectiveness, it becomes more important to develop rapid diagnostic methods. It takes only a few minutes to prepare and examine a specimen for electron microscopy (EM), using the negative staining technique. Viruses in the specimen can readily be identified by their morphology. In order to be detected by EM there must be at least 10(7) virus particles per milliliter of sample. This concentration is frequently found in certain types of specimens. The sensitivity of EM is increased 100-fold if homologous antibody is used to aggregate the virus. Visualization of virus-antibody aggregates forms the basis for serotyping by immunoelectron microscopy (IEM). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2595834/ doi: nan id: cord-309488-8guapzke author: Dodd, R. title: Other emerging viral pathogens date: 2006-08-15 words: 4365.0 sentences: 215.0 pages: flesch: 49.0 cache: ./cache/cord-309488-8guapzke.txt txt: ./txt/cord-309488-8guapzke.txt summary: Attention was refocused on viral infections as a result of the outbreak of West Nile virus (WNV) disease in the USA along with the recognition that it was transmissible by transfusion [1] . In 1997, Blackbourn and colleagues [17] reported on the detection of HHV-8 DNA in the blood of a seropositive blood donor; based on evidence of in vitro passage of the virus to allogeneic cells, the authors expressed concern about the potential for transmission by transfusion. This concern is based upon the historical fact that there have been periodic pandemics associated with the circulation of new strains of the virus in humans and the current outbreak of the H5N1 strain of avian influenza, which causes high mortality when it does infect humans [27] . Seroprevalence of human herpes virus 8 antibody in populations at high or low risk of transfusion, graft, or sexual transmission of viruses Molecular cloning and disease association of hepatitis G virus: a transfusion-transmissible agent abstract: nan url: https://doi.org/10.1111/j.1751-2824.2006.00043.x doi: 10.1111/j.1751-2824.2006.00043.x id: cord-016538-4og05fuo author: Dolja, V. V. title: Biotechnology Applications of Grapevine Viruses date: 2017-03-30 words: 6266.0 sentences: 292.0 pages: flesch: 44.0 cache: ./cache/cord-016538-4og05fuo.txt txt: ./txt/cord-016538-4og05fuo.txt summary: Although in theory any of the grapevine-infecting viruses can be engineered into transient gene expression or VIGS vector, in practice, only one of them, the filamentous Grapevine leafroll-associated virus-2 (GLRaV-2) from the genus Closterovirus (family Closteroviridae), was demonstrated to fulfill these roles (Dolja and Koonin 2013; Kurth et al. Among these viruses, only GLRaV-2, a closterovirus, has been so far engineered into a vector capable of systemic infection of grapevine that either produces recombinant protein or elicits VIGS response (Kurth et al. The more recently developed CTV-based gene expression vectors were shown to be not only capable of systemic infection in the natural citrus hosts but also exhibited remark-able genetic stability in regard to retention of the inserted recombinant gene, as well as VIGS capability (Dawson et al. Another candidate to be developed as a vector for protein expression and VIGS is GRSPaV, which is the only grapevine-infecting member of the genus Foveavirus that was recently characterized (Meng et al. abstract: Plant virus genomes are engineered as vectors for functional genomics and production of foreign proteins. The application of plant virus vectors is of potential interest to the worldwide, multibillion dollar, grape and wine industries. These applications include grapevine functional genomics, pathogen control, and production of beneficial proteins such as vaccines and enzymes. However, grapevine virus biology exerts certain limitations on the utility of the virus-derived gene expression and RNA interference vectors. As is typical for viruses infecting woody plants, several grapevine viruses exhibit prolonged infection cycles and relatively low overall accumulation levels, mainly because of their phloem-specific pattern of systemic infection. Here we consider the biotechnology potential of grapevine virus vectors with a special emphasis on members of the families Closteroviridae and Betaflexiviridae. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120854/ doi: 10.1007/978-3-319-57706-7_31 id: cord-290481-i2ppvsh5 author: Dolja, Valerian V. title: Comparative and functional genomics of closteroviruses date: 2006-03-09 words: 9298.0 sentences: 455.0 pages: flesch: 47.0 cache: ./cache/cord-290481-i2ppvsh5.txt txt: ./txt/cord-290481-i2ppvsh5.txt summary: It was concluded that, at least in part, viral pathogenicity is due to interference of silencing suppressors with developmental function of plant small RNAs. Despite their mechanistic similarity, p21 and p19 appear to be structurally and evolutionarily unrelated and neither has detectable homologues outside the respective virus genera (Vargason et al., 2003; Ye and Patel, 2005) . Although Citrus tristeza virus (CTV) encodes p20, a p21like suppressor of RNA silencing, screening of the CTV genome revealed an additional suppressor, p23, that has no homologues in other closteroviruses (Fig. 2) (Lu et al., 2004) . A comparison of TMV and BYV, which both evolved from the alphavirus-like ancestors, shows that the large part of the ∼9 kb genomic surplus of BYV is dedicated to facilitating the synthesis of the virion RNA and multiple sgRNAs. The rest of the surplus was invested in the formation of the complex virion tail that empowers virus transport within and transmission between the host plants and in suppression of RNA silencing (Fig. 1) . abstract: The largest extant RNA genomes are found in two diverse families of positive-strand RNA viruses, the animal Coronaviridae and the plant Closteroviridae. Comparative analysis of the viruses from the latter family reveals three levels of gene conservation. The most conserved gene module defines RNA replication and is shared with plant and animal viruses in the alphavirus-like superfamily. A module of five genes that function in particle assembly and transport is a hallmark of the family Closteroviridae and was likely present in the ancestor of all three closterovirus genera. This module includes a homologue of Hsp70 molecular chaperones and three diverged copies of the capsid protein gene. The remaining genes show dramatic variation in their numbers, functions, and origins among closteroviruses within and between the genera. Proteins encoded by these genes include suppressors of RNA silencing, RNAse III, papain-like proteases, the AlkB domain implicated in RNA repair, Zn-ribbon-containing protein, and a variety of proteins with no detectable homologues in the current databases. The evolutionary processes that have shaped the complex and fluid genomes of the large RNA viruses might be similar to those that have been involved in evolution of genomic complexity in other divisions of life. url: https://www.ncbi.nlm.nih.gov/pubmed/16529837/ doi: 10.1016/j.virusres.2006.02.002 id: cord-270670-cubh9jxc author: Domingo, E. title: Viruses as Quasispecies: Biological Implications date: 2006 words: 10489.0 sentences: 453.0 pages: flesch: 39.0 cache: ./cache/cord-270670-cubh9jxc.txt txt: ./txt/cord-270670-cubh9jxc.txt summary: a Upon infection with an RNA virus (even with a single particle, as depicted here, enlarged about 10 6 times), viral replication leads to a mutant spectrum of related genomes, termed viral quasispecies. As further discussed in the text, in real infections multiple mutant spectra that can amount to a large number of replicating (or potentially replicating) genomes (up to 10 9 or even 10 12 per infected individual) provide highly dynamic mutant repertoire viral yields in cell culture, have been immensely powerful in characterizing the population dynamics of RNA viruses (see references in the reviews by Domingo and Holland 1997; Quiñones-Mateu and Arts 2002; Novella 2003; and the chapters by Quiñones-Mateu and Arts and Escarmís et al., this volume) . Despite these limitations, determination of nucleotide sequence heterogeneities in virus populations using correct reagents and adequate controls has consistently documented that most RNA viruses (and also some DNA viruses) consist of complex mutant spectra, with an average number of 1-100 mutations per genome (Sect. abstract: During viral infections, the complex and dynamic distributions of variants, termed viral quasispecies, play a key role in the adaptability of viruses to changing environments and the fate of the population as a whole. Mutant spectra are continuously and avoidably generated during RNA genome replication, and they are not just a by-product of error-prone replication, devoid of biological relevance. On the contrary, current evidence indicates that mutant spectra contribute to viral pathogenesis, can modulate the expression of phenotypic traits by subpopulations of viruses, can include memory genomes that reflect the past evolutionary history of the viral lineage, and, furthermore, can participate in viral extinction through lethal mutagenesis. Also, mutant spectra are the target on which selection and random drift act to shape the long-term evolution of viruses. The biological relevance of mutant spectra is the central topic of this chapter. url: https://www.ncbi.nlm.nih.gov/pubmed/16568896/ doi: 10.1007/3-540-26397-7_3 id: cord-022128-r8el8nqm author: Domingo, Esteban title: Molecular basis of genetic variation of viruses: error-prone replication date: 2019-11-08 words: 17663.0 sentences: 798.0 pages: flesch: 39.0 cache: ./cache/cord-022128-r8el8nqm.txt txt: ./txt/cord-022128-r8el8nqm.txt summary: In the case of viral genomes, mutations can result from different mechanisms: (i) template miscopying (direct incorporation of an incorrect nucleotide); (ii) primer-template misalignments that include miscoding followed by realignment, and misalignment of the template relative to the growing chain (polymerase "slippage" or "stuttering"); (iii) activity of cellular enzymes (i.e., deaminases), or (iv) chemical damage to the viral nucleic acids (deamination, depurination, depyrimidination, reactions with oxygen radicals, direct and indirect effects of ionizing radiation, photochemical reactions, etc.) (Naegeli, 1997; Bloomfield et al., 2000; Friedberg et al., 2006) . In addition to the general environmental and sequence context consequences for templatecopying fidelity that may affect any genome type, mutation rates for DNA viruses will also be influenced by: (i) whether the DNA polymerase that catalyzes viral DNA synthesis includes or lacks a functional proofreading-repair activity. abstract: Genetic variation is a necessity of all biological systems. Viruses use all known mechanisms of variation; mutation, several forms of recombination, and segment reassortment in the case of viruses with a segmented genome. These processes are intimately connected with the replicative machineries of viruses, as well as with fundamental physical-chemical properties of nucleotides when acting as template or substrate residues. Recombination has been viewed as a means to rescue viable genomes from unfit parents or to produce large modifications for the exploration of phenotypic novelty. All types of genetic variation can act conjointly as blind processes to provide the raw materials for adaptation to the changing environments in which viruses must replicate. A distinction is made between mechanistically unavoidable and evolutionarily relevant mutation and recombination. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153327/ doi: 10.1016/b978-0-12-816331-3.00002-7 id: cord-280048-b4dz1lnn author: Domingo, Esteban title: Viral quasispecies date: 2019-10-17 words: 7955.0 sentences: 411.0 pages: flesch: 36.0 cache: ./cache/cord-280048-b4dz1lnn.txt txt: ./txt/cord-280048-b4dz1lnn.txt summary: Research on quasispecies has proceeded through several theoretical and experimental avenues that include continuing studies on evolutionary optimization and the origin of life, RNA-RNA interactions and replicator networks, the error threshold in variable fitness landscapes, consideration of chemical mutagenesis and proofreading mechanisms, evolution of tumor cells, bacterial populations or stem cells, chromosomal instability, drug resistance, and conformation distributions in prions (a class of proteins with conformation-dependent pathogenic potential; in this case the quasispecies is defined by a distribution of conformations) [16, 20] . Adaptability of RNA viruses is linked to parameters that facilitate exploration of sequence space: genome size (1.8 to 33 Kb), population size (variable but that can attain an impressive 10 12 individual genomes in an infected host at a given time), replication rate, mutation rate, fecundity (yield of viral particles per cell), and number of mutations required for a phenotypic change (surprisingly low for several relevant traits) (see [49] ). abstract: Viral quasispecies refers to a population structure that consists of extremely large numbers of variant genomes, termed mutant spectra, mutant swarms or mutant clouds. Fueled by high mutation rates, mutants arise continually, and they change in relative frequency as viral replication proceeds. The term quasispecies was adopted from a theory of the origin of life in which primitive replicons) consisted of mutant distributions, as found experimentally with present day RNA viruses. The theory provided a new definition of wild type, and a conceptual framework for the interpretation of the adaptive potential of RNA viruses that contrasted with classical studies based on consensus sequences. Standard clonal analyses and deep sequencing methodologies have confirmed the presence of myriads of mutant genomes in viral populations, and their participation in adaptive processes. The quasispecies concept applies to any biological entity, but its impact is more evident when the genome size is limited and the mutation rate is high. This is the case of the RNA viruses, ubiquitous in our biosphere, and that comprise many important pathogens. In virology, quasispecies are defined as complex distributions of closely related variant genomes subjected to genetic variation, competition and selection, and that may act as a unit of selection. Despite being an integral part of their replication, high mutation rates have an upper limit compatible with inheritable information. Crossing such a limit leads to RNA virus extinction, a transition that is the basis of an antiviral design termed lethal mutagenesis. url: https://www.ncbi.nlm.nih.gov/pubmed/31622336/ doi: 10.1371/journal.pgen.1008271 id: cord-298033-kzdp9edn author: Domingo, Esteban title: Quasispecies dynamics in disease prevention and control date: 2019-11-08 words: 16346.0 sentences: 735.0 pages: flesch: 37.0 cache: ./cache/cord-298033-kzdp9edn.txt txt: ./txt/cord-298033-kzdp9edn.txt summary: Quasispecies dynamics in disease prevention and control following statement will be obvious to the reader: "If a single mutation is able to confer resistance to an antiviral agent, and the mutation does not cause a significant selective disadvantage to the virus (fitness decrease) in the considered environment, a drug-resistant virus mutant will be present in most, if not all, virus populations" (Domingo, 1989) . The phenotypic barrier to drug resistance is equivalent to the fitness cost inflicted upon the virus by the mutations and corresponding amino acid substitution(s) required for resistance [Fitness cost is treated in Chapter 4 (Section 4.6) and in Chapter 7 (Section 7.4.2) in connection with the frequency of monoclonal antibody-or cytotoxic T-cell-escape mutants in viral populations]. For viruses that replicate in cell culture, it is possible to estimate the minimal viral population size needed to select a drug-resistant mutant which is generally positively correlated with the genetic barrier ( Fig. 8.5 ). abstract: Medical interventions to prevent and treat viral disease constitute evolutionary forces that may modify the genetic composition of viral populations that replicate in an infected host and influence the genomic composition of those viruses that are transmitted and progress at the epidemiological level. Given the adaptive potential of viruses in general and the RNA viruses in particular, the selection of viral mutants that display some degree of resistance to inhibitors or vaccines is a tangible challenge. Mutant selection may jeopardize control of the viral disease. Strategies intended to minimize vaccination and treatment failures are proposed and justified based on fundamental features of viral dynamics explained in the preceding chapters. The recommended use of complex, multiepitopic vaccines, and combination therapies as early as possible after initiation of infection falls under the general concept that complexity cannot be combated with simplicity. It also follows that sociopolitical action to interrupt virus replication and spread as soon as possible is as important as scientifically sound treatment designs to control viral disease on a global scale. url: https://www.sciencedirect.com/science/article/pii/B9780128163313000088 doi: 10.1016/b978-0-12-816331-3.00008-8 id: cord-303265-v6ci69n0 author: Domingo, Esteban title: Introduction to virus origins and their role in biological evolution date: 2019-11-08 words: 15685.0 sentences: 764.0 pages: flesch: 42.0 cache: ./cache/cord-303265-v6ci69n0.txt txt: ./txt/cord-303265-v6ci69n0.txt summary: Topics covered include molecular mechanisms of genetic variation, with emphasis on high mutation rates, Darwinian principles acting on viruses, quasispecies dynamics and its implications, consequences for virus-host interactions, fitness as a relevant parameter, experimental model systems in cell culture, ex-vivo and in vivo, long-term virus evolution, the current situation of antiviral strategies to confront quasispecies swarms, and conceptual extensions of quasispecies to nonviral systems. With regard to the concepts of genome stability versus variation addressed in this book, it is helpful to divide viruses into four groups, depending on whether it is DNA or RNA the type of genetic material, which acts as a replicative intermediate in the infected cell (bottom gray shaded boxes in Fig. 1.1 ). They were selected for replicability, stability, and evolvability with trade-offs 1.4 Origin of life: a brief historical account and current views (acquisition of benefits for one of the three traits at some cost for another trait) likely play a role at this stage (see Chapter 4 for trade-offs in virus evolution). abstract: Viruses are diverse parasites of cells and extremely abundant. They might have arisen during an early phase of the evolution of life on Earth dominated by ribonucleic acid or RNA-like macromolecules, or when a cellular world was already well established. The theories of the origin of life on Earth shed light on the possible origin of primitive viruses or virus-like genetic elements in our biosphere. Some features of present-day viruses, notably error-prone replication, might be a consequence of the selective forces that mediated their ancestral origin. Two views on the role of viruses in our biosphere predominate; viruses considered as opportunistic, selfish elements, and viruses considered as active participants in the construction of the cellular world via the lateral transfer of genes. These two models have a bearing on viruses being considered predominantly as disease agents or predominantly as cooperators in the shaping of differentiated cellular organisms. url: https://www.sciencedirect.com/science/article/pii/B9780128163313000015 doi: 10.1016/b978-0-12-816331-3.00001-5 id: cord-252147-bvtchcbt author: Domingo-Espín, Joan title: Engineered Biological Entities for Drug Delivery and Gene Therapy: Protein Nanoparticles date: 2011-11-15 words: 17193.0 sentences: 888.0 pages: flesch: 39.0 cache: ./cache/cord-252147-bvtchcbt.txt txt: ./txt/cord-252147-bvtchcbt.txt summary: Modular protein engineering, virus-like particles (VLPs), and other self-assembling entities are envisioned as modulatable novel protein nanoparticles able to include many desirable properties in the correct delivery of drugs and nucleic acids. 120 Modular fusion proteins that combine distinct functions required for cell type-specific uptake and intracellular delivery of DNA or drugs present an attractive approach for the development of self-assembling vectors for targeted gene or drug delivery. 215, 216 Although VLP-based vaccines have been primarily developed for their use against the corresponding virus, in the last decades genetic engineering or chemical modifications have been applied in order to generate chimeric VLPs. Thus, on the one hand, commonly short heterologous peptide epitopes or full proteins that are unable to form VLPs or that are unsafe for vaccination have been presented on surface-exposed loops or fused to N-or C-exposed termini of structural viral capsid proteins on VLPs. 154, 161, 210 Different HPV, 217-219 HBV, 220,221 parvovirus, 222, 223 and chimeric polyoma VLPs have been engineered 170, 175 and tested for different applications including vaccination against viral or bacterial diseases, against virus-induced tumors, and more recently, for immunotherapy of nonviral cancer. abstract: The development of genetic engineering techniques has speeded up the growth of the biotechnological industry, resulting in a significant increase in the number of recombinant protein products on the market. The deep knowledge of protein function, structure, biological interactions, and the possibility to design new polypeptides with desired biological activities have been the main factors involved in the increase of intensive research and preclinical and clinical approaches. Consequently, new biological entities with added value for innovative medicines such as increased stability, improved targeting, and reduced toxicity, among others have been obtained. Proteins are complex nanoparticles with sizes ranging from a few nanometers to a few hundred nanometers when complex supramolecular interactions occur, as for example, in viral capsids. However, even though protein production is a delicate process that imposes the use of sophisticated analytical methods and negative secondary effects have been detected in some cases as immune and inflammatory reactions, the great potential of biodegradable and tunable protein nanoparticles indicates that protein-based biotechnological products are expected to increase in the years to come. url: https://doi.org/10.1016/b978-0-12-416020-0.00006-1 doi: 10.1016/b978-0-12-416020-0.00006-1 id: cord-006892-n2ncamqh author: Donaldson, Braeden title: Virus-like particle vaccines: immunology and formulation for clinical translation date: 2018-09-19 words: 9775.0 sentences: 456.0 pages: flesch: 31.0 cache: ./cache/cord-006892-n2ncamqh.txt txt: ./txt/cord-006892-n2ncamqh.txt summary: For example, chemical conjugation of mannoside-based saccharides on the surface of Rabbit hemorrhagic disease virus (RHDV) VLP selectively targets the mannose receptor expressed on the surface of APCs, inducing increased uptake and alteration of antigen cross-presentation in murine dendritic cells [57] . While the induction of a potent humoral immune response and the subsequent production of anti-VLP antibodies is the primary desired outcome of most commercial VLP vaccines, these is increasing appreciation for the role of vaccine-induced cell-mediated immunity [123] [124] [125] . Novel Epstein-Barr virus-like particles incorporating gH/gL-EBNA1 or gB-LMP2 induce high neutralizing antibody titers and EBV-specific T-cell responses in immunized mice Induction of immune memory following administration of a prophylactic quadrivalent human papillomavirus (HPV) types 6/11/16/18 L1 virus-like particle (VLP) vaccine. Antigen incorporated in virus-like particles is delivered to specific dendritic cell subsets that induce an effective antitumor immune response in vivo abstract: Introduction: Virus-like particle (VLP) vaccines face significant challenges in their translation from laboratory models, to routine clinical administration. While some VLP vaccines thrive and are readily adopted into the vaccination schedule, others are restrained by regulatory obstacles, proprietary limitations, or finding their niche amongst the crowded vaccine market. Often the necessity to supplant an existing vaccination regimen possesses an immediate obstacle for the development of a VLP vaccine, despite any preclinical advantages identified over the competition. Novelty, adaptability and formulation compatibility may prove invaluable in helping place VLP vaccines at the forefront of vaccination technology. Areas covered: The purpose of this review is to outline the diversity of VLP vaccines, VLP-specific immune responses, and to explore how modern formulation and delivery techniques can enhance the clinical relevance and overall success of VLP vaccines. Expert commentary: The role of formation science, with an emphasis on the diversity of immune responses induced by VLP, is underrepresented amongst clinical trials for VLP vaccines. Harnessing such diversity, particularly through the use of combinations of select excipients and adjuvants, will be paramount in the development of VLP vaccines. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103734/ doi: 10.1080/14760584.2018.1516552 id: cord-318725-09a32vyg author: Dong, Rui title: Virus Database and Online Inquiry System Based on Natural Vectors date: 2017-12-17 words: 3379.0 sentences: 204.0 pages: flesch: 52.0 cache: ./cache/cord-318725-09a32vyg.txt txt: ./txt/cord-318725-09a32vyg.txt summary: The database stores all viral genomes, their corresponding natural vectors, and the classification information of the single/multiple-segmented viral reference sequences downloaded from National Center for Biotechnology Information. The online inquiry system serves the purpose of computing natural vectors and their distances based on submitted genomes, providing an online interface for accessing and using the database for viral classification and prediction, and back-end processes for automatic and manual updating of database content to synchronize with GenBank. Using the natural vector representation, if a viral genome consists of a single-nucleotide sequence, known as single-segmented, then the virus will be represented by a 12-dimensional numerical vector in the database. As natural vector can reflect core information stored in sequences and genomes, we use it to construct the virus classification system introduced in this article. abstract: We construct a virus database called VirusDB (http://yaulab.math.tsinghua.edu.cn/VirusDB/) and an online inquiry system to serve people who are interested in viral classification and prediction. The database stores all viral genomes, their corresponding natural vectors, and the classification information of the single/multiple-segmented viral reference sequences downloaded from National Center for Biotechnology Information. The online inquiry system serves the purpose of computing natural vectors and their distances based on submitted genomes, providing an online interface for accessing and using the database for viral classification and prediction, and back-end processes for automatic and manual updating of database content to synchronize with GenBank. Submitted genomes data in FASTA format will be carried out and the prediction results with 5 closest neighbors and their classifications will be returned by email. Considering the one-to-one correspondence between sequence and natural vector, time efficiency, and high accuracy, natural vector is a significant advance compared with alignment methods, which makes VirusDB a useful database in further research. url: https://doi.org/10.1177/1176934317746667 doi: 10.1177/1176934317746667 id: cord-003122-a3f4l6iu author: Dou, Dan title: Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement date: 2018-07-20 words: 10272.0 sentences: 565.0 pages: flesch: 43.0 cache: ./cache/cord-003122-a3f4l6iu.txt txt: ./txt/cord-003122-a3f4l6iu.txt summary: The segmentation of the influenza genome makes these additional trafficking requirements especially challenging, as each viral RNA (vRNA) gene segment must navigate the network of cellular membrane barriers during the processes of entry and assembly. To accomplish this goal, influenza A viruses (IAVs) utilize a combination of viral and cellular mechanisms to coordinate the transport of their proteins and the eight vRNA gene segments in and out of the cell. Influenza A viruses (IAVs) and type B viruses (IBVs) contain 8, negative-sense, single-stranded viral RNA (vRNA) gene segments ( Figure 1A ) (3, 4) , which encode transcripts for 10 essential viral proteins, as well as several strain-dependent accessory proteins ( Figure 1B) . In contrast to the early steps in IAV entry, vRNP trafficking to the nucleus following the fusion event is highly dependent on the host cell machinery and transport pathways [reviewed in Ref. abstract: Influenza viruses replicate within the nucleus of the host cell. This uncommon RNA virus trait provides influenza with the advantage of access to the nuclear machinery during replication. However, it also increases the complexity of the intracellular trafficking that is required for the viral components to establish a productive infection. The segmentation of the influenza genome makes these additional trafficking requirements especially challenging, as each viral RNA (vRNA) gene segment must navigate the network of cellular membrane barriers during the processes of entry and assembly. To accomplish this goal, influenza A viruses (IAVs) utilize a combination of viral and cellular mechanisms to coordinate the transport of their proteins and the eight vRNA gene segments in and out of the cell. The aim of this review is to present the current mechanistic understanding for how IAVs facilitate cell entry, replication, virion assembly, and intercellular movement, in an effort to highlight some of the unanswered questions regarding the coordination of the IAV infection process. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6062596/ doi: 10.3389/fimmu.2018.01581 id: cord-312964-vsrqmmv7 author: Doyle, William J. title: Prevention of otitis media caused by viral upper respiratory tract infection: Vaccines, antivirals, and other approaches date: 2003 words: 6376.0 sentences: 259.0 pages: flesch: 29.0 cache: ./cache/cord-312964-vsrqmmv7.txt txt: ./txt/cord-312964-vsrqmmv7.txt summary: Past studies show that new episodes of OM are usually a complication of viral upper respiratory infection (vURI), and therefore, a rational approach to achieving that goal is to develop intervention strategies that target vURIassociated OM. Past studies show that new episodes of OM are usually a complication of viral upper respiratory infection (vURI), and therefore, a rational approach to achieving that goal is to develop intervention strategies that target vURIassociated OM. Active synergy between certain upper respiratory viruses and nasopharyngeal pathogens was demonstrated for OM pathogenesis in chinchillas and humans [27] [28] [29] , and pre-existing or concurrent vURI in infants and children with acute, bacterial OM is frequently observed [24, 25] . In one double-blind clinical study, intranasal steroid (fluticasone propionate) was administered for 7 days immediately after onset of vURI symptoms in an attempt to decrease nasopharyngeal inflammation (and possible eustachian-tube obstruction), but was not efficacious in preventing AOM and might have increased OM incidence during rhinovirus infection [69] . abstract: Otitis media (OM) imposes significant morbidity on the pediatric age group and a large financial burden on the general population. Because standard medical treatments are not highly efficacious in resolving the accompanying middle ear (ME) inflammation, a goal of current research is OM prevention. Past studies show that new episodes of OM are usually a complication of viral upper respiratory infection (vURI), and therefore, a rational approach to achieving that goal is to develop intervention strategies that target vURIassociated OM. However, past experiences with antibiotics show that, in the absence of well-defined treatment protocols that maximize expected efficacy, the adoption of prophylactic or active treatments for OM can have negative consequences for the patient and for the general population. In this review, we discuss the hypothesized mechanisms by which a vURI is translated into an acute OM episode and describe different strategies for aborting that process. Limitations to deployment of each strategy are outlined. url: https://www.ncbi.nlm.nih.gov/pubmed/12791210/ doi: 10.1007/s11882-003-0093-7 id: cord-293540-45awgabp author: Drancourt, Michel title: Point-of-care testing for community-acquired pneumonia date: 2013-07-23 words: 1697.0 sentences: 97.0 pages: flesch: 50.0 cache: ./cache/cord-293540-45awgabp.txt txt: ./txt/cord-293540-45awgabp.txt summary: The rate and timing of pandemic A H1N1 virus infections might have revealed the diff erences in H7N9 disease outcome, by contrast with historical infections with seasonal infl uenza A H3N2 viruses. To avoid this delay, we introduced point-of-care (POC) microbiology laboratories near emergency departments where patients with community-acquired pneumonia are seen fi rst. However, it should be noted that not all pathogens that can cause community-acquired pneumonia can be detected by POC tests, and molecular tests for Staphylococus aureus have not been approved by the US Food and Drug Administration (FDA) or the European Conformity (CE). 9 This new capacity of POC tests increases the number of diagnoses 11 and underscores that community-acquired pneumonia can result from co-infection with several pathogens, 10 which will challenge common notions about causation and management. Furthermore, detection by POC testing of an abnormal increase in group A streptococci might suggest co-infection with infl uenza. abstract: nan url: https://api.elsevier.com/content/article/pii/S1473309913701658 doi: 10.1016/s1473-3099(13)70165-8 id: cord-286719-1xjmlwqr author: Draz, Mohamed Shehata title: Applications of gold nanoparticles in virus detection date: 2018-02-15 words: 18990.0 sentences: 901.0 pages: flesch: 37.0 cache: ./cache/cord-286719-1xjmlwqr.txt txt: ./txt/cord-286719-1xjmlwqr.txt summary: The developed AuNP-based detection techniques are reported for various groups of clinically relevant viruses with a special focus on the applied types of bio-AuNP hybrid structures, virus detection targets, and assay modalities and formats. These techniques represent the majority of molecular techniques applied in virus detection and include various types of target amplification techniques (e.g., PCR, loop-mediated isothermal amplification (LAMP), transcription-mediated amplification, and nucleic acid sequence-based amplification), signal amplification techniques (e.g., branched DNA and hybrid capture), and probe amplification techniques (e.g., ligase chain reaction and strand-displacement amplification). [70] developed an impedimetric electrochemical assay for the detection of AIV M gene sequences based on measuring changes in the impedimetric behavior of the electrode when the target DNA hybridizes with the capture DNA probes immobilized onto its surface and is subsequently labeled by AuNPs via streptavidin/ biotin interaction (Fig. 12C) . abstract: Viruses are the smallest known microbes, yet they cause the most significant losses in human health. Most of the time, the best-known cure for viruses is the innate immunological defense system of the host; otherwise, the initial prevention of viral infection is the only alternative. Therefore, diagnosis is the primary strategy toward the overarching goal of virus control and elimination. The introduction of a new class of nanoscale materials with multiple unique properties and functions has sparked a series of breakthrough applications. Gold nanoparticles (AuNPs) are widely reported to guide an impressive resurgence in biomedical and diagnostic applications. Here, we review the applications of AuNPs in virus testing and detection. The developed AuNP-based detection techniques are reported for various groups of clinically relevant viruses with a special focus on the applied types of bio-AuNP hybrid structures, virus detection targets, and assay modalities and formats. We pay particular attention to highlighting the functional role and activity of each core Au nanostructure and the resultant detection improvements in terms of sensitivity, detection range, and time. In addition, we provide a general summary of the contributions of AuNPs to the mainstream methods of virus detection, technical measures, and recommendations required in guidance toward commercial in-field applications. url: https://doi.org/10.7150/thno.23856 doi: 10.7150/thno.23856 id: cord-279557-hk77e3pp author: Drosten, Christian title: Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection date: 2013-06-17 words: 4214.0 sentences: 243.0 pages: flesch: 55.0 cache: ./cache/cord-279557-hk77e3pp.txt txt: ./txt/cord-279557-hk77e3pp.txt summary: BACKGROUND: The Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging virus involved in cases and case clusters of severe acute respiratory infection in the Arabian Peninsula, Tunisia, Morocco, France, Italy, Germany, and the UK. [4] [5] [6] Here, we provide a full description of a fatal case of MERS-CoV infection imported to Munich, Germany, from Abu Dhabi, including a chronological profi le of virus concentrations in diverse body compartments. We subjected all available MERS-CoV genome sequences to phylogenetic analysis, including a correlation and regression analysis of known dates of virus isolation versus tree branch lengths (fi gure 3). Without quantitative laboratory data from well documented cases of MERS-CoV infection, most considerations had been made on the basis of an assumed analogy to severe acute respiratory syndrome (SARS). The recorded viral load profi le, with highest RNA concentrations in bronchoalveolar lavage and tracheobronchial aspirates, confi rms suggestions made in another report about the preferential use of lower-respiratory-tract samples for virus diagnostic tests. abstract: BACKGROUND: The Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging virus involved in cases and case clusters of severe acute respiratory infection in the Arabian Peninsula, Tunisia, Morocco, France, Italy, Germany, and the UK. We provide a full description of a fatal case of MERS-CoV infection and associated phylogenetic analyses. METHODS: We report data for a patient who was admitted to the Klinikum Schwabing (Munich, Germany) for severe acute respiratory infection. We did diagnostic RT-PCR and indirect immunofluorescence. From time of diagnosis, respiratory, faecal, and urine samples were obtained for virus quantification. We constructed a maximum likelihood tree of the five available complete MERS-CoV genomes. FINDINGS: A 73-year-old man from Abu Dhabi, United Arab Emirates, was transferred to Klinikum Schwabing on March 19, 2013, on day 11 of illness. He had been diagnosed with multiple myeloma in 2008, and had received several lines of treatment. The patient died on day 18, due to septic shock. MERS-CoV was detected in two samples of bronchoalveolar fluid. Viral loads were highest in samples from the lower respiratory tract (up to 1·2 × 10(6) copies per mL). Maximum virus concentration in urine samples was 2691 RNA copies per mL on day 13; the virus was not present in the urine after renal failure on day 14. Stool samples obtained on days 12 and 16 contained the virus, with up to 1031 RNA copies per g (close to the lowest detection limit of the assay). One of two oronasal swabs obtained on day 16 were positive, but yielded little viral RNA (5370 copies per mL). No virus was detected in blood. The full virus genome was combined with four other available full genome sequences in a maximum likelihood phylogeny, correlating branch lengths with dates of isolation. The time of the common ancestor was halfway through 2011. Addition of novel genome data from an unlinked case treated 6 months previously in Essen, Germany, showed a clustering of viruses derived from Qatar and the United Arab Emirates. INTERPRETATION: We have provided the first complete viral load profile in a case of MERS-CoV infection. MERS-CoV might have shedding patterns that are different from those of severe acute respiratory syndrome and so might need alternative diagnostic approaches. FUNDING: European Union; German Centre for Infection Research; German Research Council; and German Ministry for Education and Research. url: https://doi.org/10.1016/s1473-3099(13)70154-3 doi: 10.1016/s1473-3099(13)70154-3 id: cord-304850-9xetsc2c author: Drosten, Christian title: Virus ecology: a gap between detection and prediction date: 2013-05-22 words: 1500.0 sentences: 95.0 pages: flesch: 51.0 cache: ./cache/cord-304850-9xetsc2c.txt txt: ./txt/cord-304850-9xetsc2c.txt summary: 7, 8 These and other recent findings remind us of an important issue in viral reservoir ecology: non-persisting viruses are maintained on a social level, requiring large, dense and interconnected host groups for their perpetual transmission. 13 There are prominent examples of bat-borne viruses that can be passed between humans, including Ebola virus, Marburg virus, Nipah virus and the severe acute respiratory syndrome agent. However, there remains a large gap between the many studies describing novel reservoir-borne viruses and our capabilities to use this knowledge to predict or prevent future human disease outbreaks. 13 As we dig deeper into viral reservoir ecology, including its man-made modifications, we may find that changes in host populations affect the transmission and maintenance of viruses with possible consequences for their potential to infect humans (Figure 1 ). Habitat fragmentation Resource abundance Change of social structure Risk Virus replication / transmission Duration of excretion / infectivity Figure 1 Modification of viral maintenance optimum. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/26038466/ doi: 10.1038/emi.2013.25 id: cord-260690-h5pjv2dw author: Druce, Julian title: Laboratory diagnosis and surveillance of human respiratory viruses by PCR in Victoria, Australia, 2002–2003 date: 2004-11-12 words: 3803.0 sentences: 201.0 pages: flesch: 45.0 cache: ./cache/cord-260690-h5pjv2dw.txt txt: ./txt/cord-260690-h5pjv2dw.txt summary: A total of 333 additional respiratory specimens, including 20 from asymptomatic laboratory staff was used to validate the PCR assays for influenza A virus (H1 and H3 subtypes), influenza B virus, RSV, parainfluenza viruses (at least one of types 1-3), picornaviruses (a mixture of enteroviruses and rhinoviruses), and adenoviruses (each of different serotype) (Table III) . The process included the design and evaluation of primers; optimization of nucleic acid extraction conditions; establishment of optimum PCR amplification conditions; evaluation of applicable specimen types; determination of assay sensitivity compared to conventional assays; specificity testing using clinical material likely to be negative (including asymptomatic staff volunteers); or material previously shown to be positive for respiratory viruses by conventional assays or by sequencing of an amplified product where no other confirmatory method was available. abstract: Respiratory viruses were identified by the polymerase chain reaction (PCR) in more than 4,200 specimens collected during 2002 and 2003 in Victoria, Australia from patients admitted to hospitals or participating in an influenza surveillance program. Influenza viruses and picornaviruses were important causes of morbidity in both years. Additional testing of picornavirus‐positive samples suggested that rhinoviruses but not enteroviruses were more likely to be associated with respiratory symptoms, irrespective of the season in which they circulated. Detection of influenza viruses was strongly associated with the clinical symptoms of cough, fever, and fatigue; but each of the other respiratory viruses occasionally caused these symptoms or was responsible for symptoms severe enough to require hospitalization. Human coronaviruses HCoV‐OC43 and HCoV‐229E circulated at low levels throughout the study period with peak activity in winter, but overall did not circulate as widely as has often been reported for these agents. Evidence for the human metapneumovirus (hMPV) was only sought in the second year of the study and revealed low‐level circulation of this virus, mainly in the cooler months among the very young and adult populations. The detection rate of all viruses declined with increasing age of the patient, particularly in hospital patients. Infection with more than one respiratory virus occurred in a small number of patients; picornaviruses were most commonly implicated in these dual infections. J. Med. Virol. 75:122–129, 2005. © 2005 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/15543580/ doi: 10.1002/jmv.20246 id: cord-294108-uvnh0s9r author: Dube, Taru title: Repurposed Drugs, Molecular Vaccines, Immune‐Modulators, and Nanotherapeutics to Treat and Prevent COVID‐19 Associated with SARS‐CoV‐2, a Deadly Nanovector date: 2020-10-25 words: 13885.0 sentences: 845.0 pages: flesch: 44.0 cache: ./cache/cord-294108-uvnh0s9r.txt txt: ./txt/cord-294108-uvnh0s9r.txt summary: [2, [8] [9] [10] This article discusses SARS-CoV-2 nanostructure, the virus biology in connection to its epidemiology, clinical manifestations, and potential and future therapeutic options including repurposed drugs, vaccine/protein therapies, immune therapies, and nanotherapeutics. Mechanisms such as inhibition of viral enzymes (DNA and RNA polymerases, 3CL pro, TMPRSS2, reverse transcriptase, neuraminidase, endonucleases, and other proteases) or processes such as ACE2 cellular receptor inhibitors and endosomal acidification mediators prohibiting viral fusion; molecules interfering with glycosylation of the viral protein, viral assembly, new viral particle transport, and release, and immunomodulation of cytokine release can be potential targets in developing various antiviral drugs for the SARS-CoV-2. [85] A randomized, placebo-controlled, Phase IV clinical trial assessing the safety and efficacy of umifenovir as an adjuvant therapy to the combined therapeutic regimen of IFN 1a, lopinavir/ritonavir and hydroxychloroquine in moderate to severe COVID-19 patients (NCT04350684) is underway. abstract: The deadly pandemic, coronavirus disease 2019 (COVID‐19), caused due to the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), has paralyzed the world. Although significant methodological advances have been made in the field of viral detection/diagnosis with 251 in vitro diagnostic tests receiving emergency use approval by the US‐FDA, little progress has been made in identifying curative or preventive therapies. This review discusses the current trends and potential future approaches for developing COVID‐19 therapeutics, including repurposed drugs, vaccine candidates, immune‐modulators, convalescent plasma therapy, and antiviral nanoparticles/nanovaccines/combinatorial nanotherapeutics to surmount the pandemic viral strain. Many potent therapeutic candidates emerging via drug‐repurposing could significantly reduce the cost and duration of anti‐COVID‐19 drug development. Gene/protein‐based vaccine candidates that could elicit both humoral and cell‐based immunity would be on the frontlines to prevent the disease. Many emerging nanotechnology‐based interventions will be critical in the fight against the deadly virus by facilitating early detection and enabling target oriented multidrug therapeutics. The therapeutic candidates discussed in this article include remdesivir, dexamethasone, hydroxychloroquine, favilavir, lopinavir/ritonavir, antibody therapeutics like gimsilumab and TJM2, anti‐viral nanoparticles, and nanoparticle‐based DNA and mRNA vaccines. url: https://doi.org/10.1002/adtp.202000172 doi: 10.1002/adtp.202000172 id: cord-313301-7mkadtp9 author: Duffy, Siobain title: EVOLUTION OF HOST SPECIFICITY DRIVES REPRODUCTIVE ISOLATION AMONG RNA VIRUSES date: 2007-08-23 words: 6091.0 sentences: 273.0 pages: flesch: 45.0 cache: ./cache/cord-313301-7mkadtp9.txt txt: ./txt/cord-313301-7mkadtp9.txt summary: In particular, the high pernucleotide mutation rates of RNA viruses (Drake 1993) provide extensive genetic variation that fuels evolution by natural selection, making the study of reproductive isolation and speciation especially feasible (Holmes 2004) . We tested the plausibility of the no-gene mechanism of speciation by examining the consequences of adaptation to a novel host in laboratory populations of the RNA phage 6, which infects a number of Pseudomonas species. The same microevolutionary processes of mutation and natural selection, which led to the adaptation of 6 populations to a novel host also resulted in a macroevolutionary event: the evolution of a new virus species that is reproductively isolated from the ancestral phage 6 wt . Beyond uniquely demonstrating the evolution of reproductive isolation in the laboratory, our study extends the literature describing the evolutionary genetics of narrowed host range when viruses adapt to a single host. abstract: Ecological speciation hypotheses claim that assortative mating evolves as a consequence of divergent natural selection for ecologically important traits. Reproductive isolation is expected to be particularly likely to evolve by this mechanism in species such as phytophagous insects that mate in the habitats in which they eat. We tested this expectation by monitoring the evolution of reproductive isolation in laboratory populations of an RNA virus that undergoes genetic exchange only when multiple virus genotypes coinfect the same host. We subjected four populations of the RNA bacteriophage φ6 to 150 generations of natural selection on a novel host. Although there was no direct selection acting on host range in our experiment, three of the four populations lost the ability to infect one or more alternative hosts. In the most extreme case, one of the populations evolved a host range that does not contain any of the hosts infectible by the wild‐type φ6. Whole genome sequencing confirmed that the resulting reproductive isolation was due to a single nucleotide change, highlighting the ease with which an emerging RNA virus can decouple its evolutionary fate from that of its ancestor. Our results uniquely demonstrate the evolution of reproductive isolation in allopatric experimental populations. Furthermore, our data confirm the biological credibility of simple “no‐gene” mechanisms of assortative mating, in which this trait arises as a pleiotropic effect of genes responsible for ecological adaptation. url: https://www.ncbi.nlm.nih.gov/pubmed/17908251/ doi: 10.1111/j.1558-5646.2007.00226.x id: cord-269975-1ebmq7t8 author: Duplantier, Allen J. title: Combating biothreat pathogens: ongoing efforts for countermeasure development and unique challenges date: 2020-05-27 words: 12963.0 sentences: 580.0 pages: flesch: 32.0 cache: ./cache/cord-269975-1ebmq7t8.txt txt: ./txt/cord-269975-1ebmq7t8.txt summary: None of the filoviruses or henipaviruses has any FDA-approved therapeutics or vaccines available for prevention or treatment of human disease, and while ribavirin is sometimes used to treat Lassa fever, it is not a terribly effective drug against this viral infection [28] . Many of the therapeutics that are in different stages of either preclinical or clinical development for select biothreat pathogens include small molecule antivirals (Tables 7.3 and 7.4), antibody (or antibody cocktails) against viruses or bacteria/virulence factors (Table 7 .5), and combination drug therapy (Table 7 .6). Although no FDA-approved HDT therapies are yet available for treating infectious diseases, we have summarized in this section the antimicrobial Primary screening of small molecule chemical libraries in the phenotypic HCI assay will identify compounds that inhibit pathogen infection as well as those that may contribute to cellular toxicity. abstract: Research to discover and develop antibacterial and antiviral drugs with potent activity against pathogens of biothreat concern presents unique methodological and process-driven challenges. Herein, we review laboratory approaches for finding new antibodies, antibiotics, and antiviral molecules for pathogens of biothreat concern. Using high-throughput screening techniques, molecules that directly inhibit a pathogen’s entry, replication, or growth can be identified. Alternatively, molecules that target host proteins can be interesting targets for development when countering biothreat pathogens, due to the modulation of the host immune response or targeting proteins that interfere with the pathways required by the pathogen for replication. Monoclonal and cocktail antibody therapies approved by the Food and Drug Administration for countering anthrax and under development for treatment of Ebola virus infection are discussed. A comprehensive tabular review of current in vitro, in vivo, pharmacokinetic and efficacy datasets has been presented for biothreat pathogens of greatest concern. Finally, clinical trials and animal rule or traditional drug approval pathways are also reviewed. Opinions; interpretations; conclusions; and recommendations are those of the authors and are not necessarily endorsed by the US Army. url: https://api.elsevier.com/content/article/pii/B9780128184806000072 doi: 10.1016/b978-0-12-818480-6.00007-2 id: cord-323987-gh1m05gi author: Dziąbowska, Karolina title: Detection Methods of Human and Animal Influenza Virus—Current Trends date: 2018-10-18 words: 11112.0 sentences: 760.0 pages: flesch: 46.0 cache: ./cache/cord-323987-gh1m05gi.txt txt: ./txt/cord-323987-gh1m05gi.txt summary: RIDTs with digital readout systems showed many similarities to conventional assays like small sample volume (less than 150 µL) and short analysis time (around 15 min) but exhibited much better sensitivities, even one order of magnitude lower limits of detection (LODs). Among methods mentioned, general diagnostic tests for influenza base on virus culture (conventional and shellvial), detection of viral nucleic acid (PCR) or antigens (by neuraminidase enzymatic activity, fluorescent antibody or enzyme/optical immunoassay) and serologic tests. Main trends for influenza virus detection are: (I) modifications of traditional ''gold star'' methods like PCR, RIDTs, ELISA what results in analysis time shortening, costs lowering, LOD and limit of quantification (LOQ) improvement, (II) conjugating of traditional methods and creating new platforms, micro-biochips and others, (III) introducing known solutions to new ones, like smartphone-based analysis control with results data insertion into Google Maps, (IV) reuse of the functions of known devices, like glucometer, smartphone cameras, (V) the most common used detection methods: spectral/optical, electrical, (VI) and entirely new approaches. abstract: The basic affairs connected to the influenza virus were reviewed in the article, highlighting the newest trends in its diagnostic methods. Awareness of the threat of influenza arises from its ability to spread and cause a pandemic. The undiagnosed and untreated viral infection can have a fatal effect on humans. Thus, the early detection seems pivotal for an accurate treatment, when vaccines and other contemporary prevention methods are not faultless. Public health is being attacked with influenza containing new genes from a genetic assortment between animals and humankind. Unfortunately, the population does not have immunity for mutant genes and is attacked in every viral outbreak season. For these reasons, fast and accurate devices are in high demand. As currently used methods like Rapid Influenza Diagnostic Tests lack specificity, time and cost-savings, new methods are being developed. In the article, various novel detection methods, such as electrical and optical were compared. Different viral elements used as detection targets and analysis parameters, such as sensitivity and specificity, were presented and discussed. url: https://doi.org/10.3390/bios8040094 doi: 10.3390/bios8040094 id: cord-022393-s26d54ew author: E. Newcomer, Christian title: Zoonoses and Other Human Health Hazards date: 2007-09-02 words: 17040.0 sentences: 872.0 pages: flesch: 42.0 cache: ./cache/cord-022393-s26d54ew.txt txt: ./txt/cord-022393-s26d54ew.txt summary: Wild caught mice that are maintained in naturalistic housing environments in the laboratory, laboratory mice that have contact with wild or feral mice, and mice kept as pets in the home environment are examples of animal management conditions that would be conducive to the expression and transmission of zoonotic diseases and other mouse-associated implications in the New World serocomplex group are present among the wild rodents endemic to the United States such as Neotoma spp. Many published reports of human LCM infection are associated with laboratory animal and pet contact, particularly mice and hamsters, and these studies now span many decades (Armstrong and Lillie 1934; Bowen et al. The apparent ease with which LCMV is transmitted to humans also occurs in a variety of other laboratory animal species; hamsters, guinea pigs, swine, dogs, and nonhuman primates, especially callitrichids, which readily sustain natural infections. akari infections depend on the prevention of wild mice and the mite vector from entering laboratory animal facilities and human dwellings. abstract: Zoonoses refers to the infectious diseases and infestations that are transmissible directly from an animal host to humans. The biomedical literature contains numerous reports of zoonotic diseases and parasitic infestations from laboratory mice and their wild counterparts. The extended maintenance of the laboratory mouse over a number of generations under controlled and increasingly sophisticated laboratory animal housing conditions with veterinary oversight and effective infection control measures has markedly reduced the likelihood that zoonotic agents would be encountered in a modem animal care and use environment. Wild caught mice that are maintained in naturalistic housing environments in the laboratory, laboratory mice that have contact with wild or feral mice, and mice kept as pets in the home environment are examples of animal management conditions that would be conducive to the expression and transmission of zoonotic diseases and other mouse-associated hazards. In addition to the zoonoses, mice are capable of inflicting bites on inadequately trained personnel and are a rich source of allergens for a substantial number of persons predisposed to develop mouse-associated allergic sensitivities. This chapter discusses the mouse-associated zoonotic diseases and other health hazards and explains the strategies that are helpful for reducing or eliminating the risk of personnel exposure to these conditions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155645/ doi: 10.1016/b978-012369454-6/50054-6 id: cord-255217-l2ak5ygj author: Eccles, Ronald title: Why is temperature sensitivity important for the success of common respiratory viruses? date: 2020-08-10 words: 3861.0 sentences: 200.0 pages: flesch: 40.0 cache: ./cache/cord-255217-l2ak5ygj.txt txt: ./txt/cord-255217-l2ak5ygj.txt summary: 34 It has been known for some time that human influenza viruses vary in their temperature sensitivity with those adapted to the cooler human airway causing mild disease and those adapted to higher temperatures causing more serious lower respiratory tract infections. 44, 45 The common cold syndrome is a mild disease because the respiratory viruses have a permissive temperature sensitivity close to that found in the human upper airways 30 C-34 C and a restrictive temperature sensitivity that conThe acquisition of temperature sensitivity is key to the success of a respiratory virus and this is well illustrated with emerging avian influenza H5N1. The temperature sensitivity of respiratory viruses should be considered as an important factor in determining their success as parasites of the human airway. Journal of clinical virology: the official publication of the Pan American Society for Clinical Virology abstract: This review explores the idea that temperature sensitivity is an important factor in determining the success of respiratory viruses as human parasites. The review discusses several questions. What is viral temperature sensitivity? At what range of temperatures are common respiratory viruses sensitive? What is the mechanism for their temperature sensitivity? What is the range of temperature along the human airway? What is it that makes respiratory viruses such successful parasites of the human airway? What is the role of temperature sensitivity in respiratory zoonoses? A definition of temperature sensitivity is proposed, as “the property of a virus to replicate poorly or not at all, at the normal body temperature of the host (restrictive temperature), but to replicate well at the lower temperatures found in the upper airway of the host (permissive temperature).” Temperature sensitivity may influence the success of a respiratory virus in several ways. Firstly; by restricting the infection to the upper airways and reducing the chance of systemic infection that may reduce host mobility and increase mortality, and thus limit the spread of the virus. Secondly; by causing a mild upper airway illness with a limited immune response compared to systemic infection, which means that persistent herd immunity does not develop to the same extent as with systemic infections, and re‐infection may occur later. Thirdly; infection of the upper airway triggers local reflex rhinorrhea, coughing and sneezing which aid the exit of the virus from the host and the spread of infection in the community. url: https://www.ncbi.nlm.nih.gov/pubmed/32776651/ doi: 10.1002/rmv.2153 id: cord-342412-azkamnpa author: Ecker, David J title: The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents date: 2005-04-25 words: 7206.0 sentences: 409.0 pages: flesch: 42.0 cache: ./cache/cord-342412-azkamnpa.txt txt: ./txt/cord-342412-azkamnpa.txt summary: This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. For example, the Centers for Disease Control and Prevention (CDC) maintains an ever-changing list of notifiable diseases, the National Institute of Allergy and Infectious Disease (NIAID) lists agents with potential for use in bioterrorist attacks, and the Department of Health and Human Services (HHS) maintains a list of critical human pathogens. This article focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. It provides a compilation of lists, taken from the database, of important and/or regulated biological agents from a number of agencies including HHS, the United States Department of Agriculture (USDA), the CDC, the World Health Organization (WHO), the NIAID, and other sources. abstract: BACKGROUND: Thousands of different microorganisms affect the health, safety, and economic stability of populations. Many different medical and governmental organizations have created lists of the pathogenic microorganisms relevant to their missions; however, the nomenclature for biological agents on these lists and pathogens described in the literature is inexact. This ambiguity can be a significant block to effective communication among the diverse communities that must deal with epidemics or bioterrorist attacks. RESULTS: We have developed a database known as the Microbial Rosetta Stone. The database relates microorganism names, taxonomic classifications, diseases, specific detection and treatment protocols, and relevant literature. The database structure facilitates linkage to public genomic databases. This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. CONCLUSION: The Microbial Rosetta Stone is available at . The database provides public access to up-to-date taxonomic classifications of organisms that cause human diseases, improves the consistency of nomenclature in disease reporting, and provides useful links between different public genomic and public health databases. url: https://www.ncbi.nlm.nih.gov/pubmed/15850481/ doi: 10.1186/1471-2180-5-19 id: cord-289406-54vyzxjf author: Edwards, Suzanne title: An Experimental Model for Myocarditis and Congestive Heart Failure after Rabbit Coronavirus Infection date: 1992-01-17 words: 3503.0 sentences: 217.0 pages: flesch: 48.0 cache: ./cache/cord-289406-54vyzxjf.txt txt: ./txt/cord-289406-54vyzxjf.txt summary: In a model for virus-induced myocarditis and congestive heart failure, rabbit coronavirus infection was divided into acute (days 2–5) and subacute (days 6–12) phases on the basis of day of death and pathologic findings. Both Coxsackie Band encephalomyocarditis virus infections in mice may progress to myocarditis and congestive heart failure, and some survi-vors may progress to a dilated cardiomyopathy later in life [5, [14] [15] [16] . Rabbits that died on days 10-12 had pleural effusion, pulmonary edema, ascites, enlarged hearts, dilated right and left ventricular cavities, and congestion in the lungs and liver. It seems likely that pleural effusion disease virus infection also results in a significant percentage of animals dying from heart failure, since degeneration and necrosis of myocytes, pulmonary edema, pleural effusion, dilated ventricles, and congestion of the lungs, liver, and spleen are common [18, 26] . abstract: In a model for virus-induced myocarditis and congestive heart failure, rabbit coronavirus infection was divided into acute (days 2–5) and subacute (days 6–12) phases on the basis of day of death and pathologic findings. During the acute phase, the principal histologic lesions were degeneration and necrosis of myocytes, myocytolysis, interstitial edema, and hemorrhage. The severity of these changes increased in the subacute phase. Pleural effusion and congestion of the lungs and liver were also present at this time. Myocarditis was detected by day 9 and peaked by day 12. Heart weights and heart weight-to-body weight ratios were increased, and dilation of the right ventricular cavity became prominent early in infection and persisted. In contrast, dilation of the left ventricle occurred late in the subacute stage. Virus was isolated from infected hearts between days 2 and 12. These data suggest that rabbit coronavirus infection progresses to myocarditis and congestive heart failure. url: https://www.ncbi.nlm.nih.gov/pubmed/1309370/ doi: 10.1093/infdis/165.1.134 id: cord-318686-we6pveus author: Ehlen, Lukas title: Epithelial cell lines of the cotton rat (Sigmodon hispidus) are highly susceptible in vitro models to zoonotic Bunya-, Rhabdo-, and Flaviviruses date: 2016-05-04 words: 5608.0 sentences: 284.0 pages: flesch: 53.0 cache: ./cache/cord-318686-we6pveus.txt txt: ./txt/cord-318686-we6pveus.txt summary: CONCLUSION: In the current study, we showed that newly established cell lines from the cotton rat can serve as host-specific in vitro models for viral infection experiments. The cotton rat (Sigmodon hispidus) is a unique example of a rodent species that is a well-established animal model to study viral pathogenesis and is also associated with a large range of zoonotic viruses in the wild [20] [21] [22] . To evaluate whether the broad viral susceptibility seen in both animalmodel and wild cotton rats was also reflected in in vitro cell culture models, we generated continuous cell lines from the respiratory and renal tracts of a cotton rat, and assessed their use for virus replication studies of known and potentially novel zoonotic viruses. In the work presented herein, we generated epithelial cell lines from the respiratory and renal tracts of a cotton rat due to its susceptibility to a broad range of human viruses, as well as the association of multiple important and emerging zoonotic viruses with this species. abstract: BACKGROUND: Small mammals such as bats and rodents have been increasingly recognized as reservoirs of novel potentially zoonotic pathogens. However, few in vitro model systems to date allow assessment of zoonotic viruses in a relevant host context. The cotton rat (Sigmodon hispidus) is a New World rodent species that has a long-standing history as an experimental animal model due to its unique susceptibility to human viruses. Furthermore, wild cotton rats are associated with a large variety of known or potentially zoonotic pathogens. METHODS: A method for the isolation and culture of airway epithelial cell lines recently developed for bats was applied for the generation of rodent airway and renal epithelial cell lines from the cotton rat. Continuous cell lines were characterized for their epithelial properties as well as for their interferon competence. Susceptibility to members of zoonotic Bunya-, Rhabdo-, and Flaviviridae, in particular Rift Valley fever virus (RVFV), vesicular stomatitis virus (VSV), West Nile virus (WNV), and tick-borne encephalitis virus (TBEV) was tested. Furthermore, novel arthropod-derived viruses belonging to the families Bunya-, Rhabdo-, and Mesoniviridae were tested. RESULTS: We successfully established airway and kidney epithelial cell lines from the cotton rat, and characterized their epithelial properties. Cells were shown to be interferon-competent. Viral infection assays showed high-titre viral replication of RVFV, VSV, WNV, and TBEV, as well as production of infectious virus particles. No viral replication was observed for novel arthropod-derived members of the Bunya-, Rhabdo-, and Mesoniviridae families in these cell lines. CONCLUSION: In the current study, we showed that newly established cell lines from the cotton rat can serve as host-specific in vitro models for viral infection experiments. These cell lines may also serve as novel tools for virus isolation, as well as for the investigation of virus-host interactions in a relevant host species. url: https://www.ncbi.nlm.nih.gov/pubmed/27142375/ doi: 10.1186/s12985-016-0531-5 id: cord-337914-1hwnxkdd author: Ehlkes, L. title: Epidemiologie des Ebolafiebers und anderer, in Deutschland seltener hochkontagiöser, lebensbedrohlicher Erkrankungen date: 2015-05-22 words: 2987.0 sentences: 373.0 pages: flesch: 54.0 cache: ./cache/cord-337914-1hwnxkdd.txt txt: ./txt/cord-337914-1hwnxkdd.txt summary: Hochsicherheitsbetten für die Versorgung von Patienten mit Ebolafieber gibt es -anders als in industrialisierten Ländern -in den Ausbruchsgebieten in der Regel nicht. Subsequent human-to-human transmission can lead to epidemics, such as the current outbreak of Ebola virus disease in West Africa. Subsequent human-to-human transmission can lead to epidemics, such as the current outbreak of Ebola virus disease in West Africa. Ebola virus disease · Highly contagious · Outbreak · Epidemic · Viral hemorrhagic fever laufen derzeit z. Die Epidemiologie von Lassa-Fieber ist eng geknüpft an das zeitliche und räumliche Auftreten des wichtigsten Reservoirtiers, der Vielzitzenmaus (Mastomys natalensis), in der Nähe des Menschen. Neben intensivmedizinischen Maßnahmen wird Ribavirin zur antiviralen Therapie gegen das Lassa-Virus eingesetzt [42] , das bei Behandlung in den ersten sechs Tagen nach Beginn der Symptomatik die Letalität bei Lassa-Fieber von 60-80 % auf 10 % senken kann [43] . Die Falldetektion mit anschließender Isolierung ist auch bei SARS das Rückgrat der Ausbruchs-Kontrolle. abstract: Apart from sporadic exported cases, the occurrence of Ebola, Marburg and Lassa virus diseases is limited to the African continent. Crimean-Congo Hemorrhagic Fever occurs in Southeastern Europe but, so far, not in Germany. Other hemorrhagic fever disease-viruses occur in distinct regions in South America. Pulmonary plague is the bacterial infectious disease with the most contagious and lethal course and it is endemic to Madagascar and East Africa, but also occurs in other countries (e.g. India, USA). Monkey pox epidemics have occurred in remote areas of the Congo Basin. Such outbreaks could potentially become more common with the discontinuation of the cross-protective smallpox vaccination. The Severe Acute Respiratory Syndrome (SARS) that emerged in 2002/2003 is another pathogen with significant epidemic potential. Typical for these diseases is a natural circulation between reservoir animals in remote areas. Sporadic transmission to humans can occur through contact with an infected animal. Subsequent human-to-human transmission can lead to epidemics, such as the current outbreak of Ebola virus disease in West Africa. url: https://doi.org/10.1007/s00103-015-2165-y doi: 10.1007/s00103-015-2165-y id: cord-302529-43pd2qsp author: El Moussi, Awatef title: Virological Surveillance of Influenza Viruses during the 2008–09, 2009–10 and 2010–11 Seasons in Tunisia date: 2013-09-19 words: 3251.0 sentences: 163.0 pages: flesch: 45.0 cache: ./cache/cord-302529-43pd2qsp.txt txt: ./txt/cord-302529-43pd2qsp.txt summary: METHOD: We describe in this report the findings of laboratory-based surveillance of human cases of influenza virus and other respiratory viruses'' infection during three seasons in Tunisia. A subset of sentinel primary care physicians participating in virological surveillance schemes in the community submits respiratory samples for virological testing from patients presenting in primary health care with an ILI, as well as all regional emergency centres and hospitals that take on surveillance of influenza from community, hospitalized and fatal cases. Phylogenetic analysis of the HA1 nucleotid sequence of 23 influenza A(H1N1)pdm09 viruses from mild, severe (patients hospitalized with severe pneumonia and severe acute respiratory syndrome) and fatal cases, shows that all viruses characterised in Tunisia during season 2009-2010 were outside the seven genetic groups described in the European Centre for Disease Prevention and Control (ECDC) report [19] . abstract: BACKGROUND: The data contribute to a better understanding of the circulation of influenza viruses especially in North-Africa. OBJECTIVE: The objective of this surveillance was to detect severe influenza cases, identify their epidemiological and virological characteristics and assess their impact on the healthcare system. METHOD: We describe in this report the findings of laboratory-based surveillance of human cases of influenza virus and other respiratory viruses' infection during three seasons in Tunisia. RESULTS: The 2008–09 winter influenza season is underway in Tunisia, with co-circulation of influenza A/H3N2 (56.25%), influenza A(H1N1) (32.5%), and a few sporadic influenza B viruses (11.25%). In 2010–11 season the circulating strains are predominantly the 2009 pandemic influenza A(H1N1)pdm09 (70%) and influenza B viruses (22%). And sporadic viruses were sub-typed as A/H3N2 and unsubtyped influenza A, 5% and 3%, respectively. Unlike other countries, highest prevalence of influenza B virus Yamagata-like lineage has been reported in Tunisia (76%) localised into the clade B/Bangladesh/3333/2007. In the pandemic year, influenza A(H1N1)pdm09 predominated over other influenza viruses (95%). Amino acid changes D222G and D222E were detected in the HA gene of A(H1N1)pdm09 virus in two severe cases, one fatal case and one mild case out of 50 influenza A(H1N1)pdm09 viruses studied. The most frequently reported respiratory virus other than influenza in three seasons was RSV (45.29%). CONCLUSION: This article summarises the surveillance and epidemiology of influenza viruses and other respiratory viruses, showing how rapid improvements in influenza surveillance were feasible by connecting the existing structure in the health care system for patient records to electronic surveillance system for reporting ILI cases. url: https://www.ncbi.nlm.nih.gov/pubmed/24069267/ doi: 10.1371/journal.pone.0074064 id: cord-003598-m2fsrwvw author: Elbahesh, Husni title: Response Modifiers: Tweaking the Immune Response Against Influenza A Virus date: 2019-04-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Despite causing pandemics and yearly epidemics that result in significant morbidity and mortality, our arsenal of options to treat influenza A virus (IAV) infections remains limited and is challenged by the virus itself. While vaccination is the preferred intervention strategy against influenza, its efficacy is reduced in the elderly and infants who are most susceptible to severe and/or fatal infections. In addition, antigenic variation of IAV complicates the production of efficacious vaccines. Similarly, effectiveness of currently used antiviral drugs is jeopardized by the development of resistance to these drugs. Like many viruses, IAV is reliant on host factors and signaling-pathways for its replication, which could potentially offer alternative options to treat infections. While host-factors have long been recognized as attractive therapeutic candidates against other viruses, only recently they have been targeted for development as IAV antivirals. Future strategies to combat IAV infections will most likely include approaches that alter host-virus interactions on the one hand or dampen harmful host immune responses on the other, with the use of biological response modifiers (BRMs). In principle, BRMs are biologically active agents including antibodies, small peptides, and/or other (small) molecules that can influence the immune response. BRMs are already being used in the clinic to treat malignancies and autoimmune diseases. Repurposing such agents would allow for accelerated use against severe and potentially fatal IAV infections. In this review, we will address the potential therapeutic use of different BRM classes to modulate the immune response induced after IAV infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6473099/ doi: 10.3389/fimmu.2019.00809 id: cord-007784-fq2urilg author: Elderfield, Ruth title: Influenza Pandemics date: 2011-09-22 words: 10484.0 sentences: 539.0 pages: flesch: 51.0 cache: ./cache/cord-007784-fq2urilg.txt txt: ./txt/cord-007784-fq2urilg.txt summary: H5N1 virus has been responsible for over 500 cases of human infection and 300 deaths (as of 31st August 2010 according to the World Health Organisation avian influenza surveillance system) but thankfully has not yet reassorted with a human-adapted influenza virus, nor given rise to a pandemic outbreak [45] . For avian influenza viruses to adapt to and transmit between humans, it is now apparent that in addition to the reassortment events that occur during antigenic shift, their HA proteins must also undergo modifications that alter their fine receptor binding specificity. However, the human seasonal virus had changed so dramatically that it shared only 79% amino acids with the 1918 HA protein, and this did not allow for any antigenic cross protection for humans who had been infected with seasonal H1 in recent years against the novel 2009 pandemic strain. abstract: The recent H1N1 pandemic that emerged in 2009 has illustrated how swiftly a new influenza virus can circulate the globe. Here we explain the origins of the 2009 pandemic virus, and other twentieth century pandemics. We also consider the impact of the 2009 pandemic in the human population and the use of vaccines and antiviral drugs. Thankfully this outbreak was much less severe than that associated with Spanish flu in 1918. We describe the viral factors that affect virulence of influenza and speculate on the future course of this virus in humans and animals. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123151/ doi: 10.1007/978-1-4614-0204-6_8 id: cord-317851-lj07947c author: Elena, S F title: Experimental evolution of plant RNA viruses date: 2008-02-06 words: 4184.0 sentences: 191.0 pages: flesch: 42.0 cache: ./cache/cord-317851-lj07947c.txt txt: ./txt/cord-317851-lj07947c.txt summary: In this review, we will focus on recent studies that used plant viruses to address evolutionary questions of general interest, such as the rate and fitness effects of deleterious mutations and the role of neutrality as a source of mutational robustness, the evolution of generalist viruses, or the effect of vertical versus horizontal transmission on virulence. Despite mutation rate is still high compared to that of DNA-based microorganisms, a classic field observation is that natural plant virus populations generally exhibit limited genetic variation (García-Arenal et al., 2001) , which may imply either that purifying selection may be strong or that genome replication occurs mainly by Luria''s stamping machine model (Luria, 1951) rather than exponentially (French and Stenger, 2003) , the two hypotheses being nonexclusive. abstract: Undoubtedly, viruses represent a major threat faced by human and veterinary medicines and by agronomy. The rapid evolution of viruses enables them to escape from natural immunities and from state-of-the-art antiviral treatments, with new viruses periodically emerging with deadly consequences. Viruses have also become powerful and are increasingly used tools in the field of experimental evolution. A growing body of evidence points that the evolution of viruses is mainly determined by key features such as their compacted genomes, enormous population sizes, and short generation times. In addition, RNA viruses also present large selection coefficients, antagonistic epistasis, and high mutation rates. Most of this knowledge comes from studies that have used either bacteriophages or animal viruses in cell cultures as experimental systems. However, plant viruses provide almost identical advantages for evolutionary studies and, in addition, offer an invaluable tool for studying the interplay between viruses and pluricellular hosts. Without seeking to be exhaustive, here we summarize some peculiarities of plant viruses and review recent experiments that have explored important questions on evolution, such as the role of deleterious mutation and neutrality, the effect of different transmission modes in the evolution of virulence, and the heterogeneous selective constraints imposed by multiple hosts. url: https://doi.org/10.1038/sj.hdy.6801088 doi: 10.1038/sj.hdy.6801088 id: cord-301064-ex6qb6zj author: Elena, Santiago F. title: Editorial: A home for virology, ecology, epidemiology, and evolutionary biology date: 2015-03-26 words: 1316.0 sentences: 66.0 pages: flesch: 42.0 cache: ./cache/cord-301064-ex6qb6zj.txt txt: ./txt/cord-301064-ex6qb6zj.txt summary: Although genetic diversity is an essential part of virus biology, classical approaches to virus control often ignore evolutionary processes and focus on understanding in great detail the molecular bases of pathogenesis, virus-host interaction, and drug-virus interference. Although many studies appear in evolutionary biology journals, particularly those on viral experimental evolution, mathematical modeling, molecular evolution, and phylogenetics, a large proportion are submitted to journals that focus on virology and pathogenesis. We have established the journal Virus Evolution with this aim in mind, and we hope that it will grow into a successful and dynamic inter-disciplinary community of researchers interested in understanding why and how viruses have and continue to evolve. The Board has expertise in animal, plant, and bacterial viruses and in a wide range of techniques, including experimental evolutionary biology, molecular epidemiology, metagenomics, structural biology, population genetics, ecology, and molecular virology. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/27774275/ doi: 10.1093/ve/vev001 id: cord-336510-qzm9wgde author: Ellermann-Eriksen, Svend title: Macrophages and cytokines in the early defence against herpes simplex virus date: 2005-08-03 words: 20036.0 sentences: 986.0 pages: flesch: 46.0 cache: ./cache/cord-336510-qzm9wgde.txt txt: ./txt/cord-336510-qzm9wgde.txt summary: In a first wave of responses, cytokines, primarily type I interferons (IFN) and tumour necrosis factor are produced and exert a direct antiviral effect and activate the macrophages themselves. Generally the type I IFNs exhibit a huge range of biological effects, such as antiviral and antiproliferative effects, stimulation of immune cells such as T cells, natural killer (NK) cells, monocytes, macrophages, and dendritic cells, increased expression of MHC-I, activation of pro-apoptotic genes and inhibition of anti-apoptotic mechanisms, modulation of cellular differentiation, and inhibition of angiogenesis [171] . Effect of IL-4 and IL-13 on IFN-gamma-induced production of nitric oxide in mouse macrophages infected with herpes simplex virus type 2 Herpes Simplex virus type 1-induced interferon production and activation of natural killer cells in mice NF-kappaB activation is responsible for the synergistic effect of herpes simplex virus type 2 infection on interferon-gamma-induced nitric oxide production in macrophages abstract: Herpes simplex virus (HSV) type 1 and 2 are old viruses, with a history of evolution shared with humans. Thus, it is generally well-adapted viruses, infecting many of us without doing much harm, and with the capacity to hide in our neurons for life. In rare situations, however, the primary infection becomes generalized or involves the brain. Normally, the primary HSV infection is asymptomatic, and a crucial element in the early restriction of virus replication and thus avoidance of symptoms from the infection is the concerted action of different arms of the innate immune response. An early and light struggle inhibiting some HSV replication will spare the host from the real war against huge amounts of virus later in infection. As far as such a war will jeopardize the life of the host, it will be in both interests, including the virus, to settle the conflict amicably. Some important weapons of the unspecific defence and the early strikes and beginning battle during the first days of a HSV infection are discussed in this review. Generally, macrophages are orchestrating a multitude of anti-herpetic actions during the first hours of the attack. In a first wave of responses, cytokines, primarily type I interferons (IFN) and tumour necrosis factor are produced and exert a direct antiviral effect and activate the macrophages themselves. In the next wave, interleukin (IL)-12 together with the above and other cytokines induce production of IFN-γ in mainly NK cells. Many positive feed-back mechanisms and synergistic interactions intensify these systems and give rise to heavy antiviral weapons such as reactive oxygen species and nitric oxide. This results in the generation of an alliance against the viral enemy. However, these heavy weapons have to be controlled to avoid too much harm to the host. By IL-4 and others, these reactions are hampered, but they are still allowed in foci of HSV replication, thus focusing the activity to only relevant sites. So, no hero does it alone. Rather, an alliance of cytokines, macrophages and other cells seems to play a central role. Implications of this for future treatment modalities are shortly considered. url: https://www.ncbi.nlm.nih.gov/pubmed/16076403/ doi: 10.1186/1743-422x-2-59 id: cord-022947-ruizhgwh author: Elliot, Elisa L title: Indicator organisms for estuarine and marine waters date: 2006-03-27 words: 10565.0 sentences: 551.0 pages: flesch: 43.0 cache: ./cache/cord-022947-ruizhgwh.txt txt: ./txt/cord-022947-ruizhgwh.txt summary: These bacteria and other coliforms were used in the past as indicators of water-borne pathogens, that is, the presence of fecal contamination being correlated with the occurrence of pathogens, for which direct detection methods were not available. Total coliforms are the most universally used indicator group, but include bacteria, in addition to Escherichia coil, that are not specifically associated with fecal pollution, i.e., Klebsiella spp., Citrobacter spp., and Enterobacter spp. Finding an appropriate indicator for the presence of enteric viruses, i.e., poliovirus, coxsackievirus A, coxsackievirus B, and echovirus [50, 147] , in sea water, is a vexing problem, especially for those responsible for regulating the use of sewage-contamined sites, including fresh, estuarine, and marine water and sediment, and shellfish harvested from these waters. Correlations between the number of fecal bacterial pathogens and indicator bacteria and their respective bacteriophages in fresh and marine water have been reported [185] . abstract: Abstract The use of indicator organisms for estuarine and coastal waters has been reviewed. The natural flora of the environment must be considered in selecting an indicator organism, but, more importantly, recent work which shows a viable but non‐recoverable stage of pathogens entering the marine environment demonstrates that the conventional detection of indicator microorganisms is misleading, if not inaccurate. Results suggest that the newly developed epifluorescent/immunofluorescent direct detection of pathogens in the environment may be the most reliable method for determining public health hazards in marine and estuarine waters. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164043/ doi: 10.1111/j.1574-6968.1985.tb01183.x id: cord-320055-6ycp8m89 author: Elliot, Elisa L title: Indicator organisms for estuarine and marine waters date: 1985-07-31 words: 10567.0 sentences: 551.0 pages: flesch: 43.0 cache: ./cache/cord-320055-6ycp8m89.txt txt: ./txt/cord-320055-6ycp8m89.txt summary: These bacteria and other coliforms were used in the past as indicators of water-borne pathogens, that is, the presence of fecal contamination being correlated with the occurrence of pathogens, for which direct detection methods were not available. Total coliforms are the most universally used indicator group, but include bacteria, in addition to Escherichia coil, that are not specifically associated with fecal pollution, i.e., Klebsiella spp., Citrobacter spp., and Enterobacter spp. Finding an appropriate indicator for the presence of enteric viruses, i.e., poliovirus, coxsackievirus A, coxsackievirus B, and echovirus [50, 147] , in sea water, is a vexing problem, especially for those responsible for regulating the use of sewage-contamined sites, including fresh, estuarine, and marine water and sediment, and shellfish harvested from these waters. Correlations between the number of fecal bacterial pathogens and indicator bacteria and their respective bacteriophages in fresh and marine water have been reported [185] . abstract: Abstract The use of indicator organisms for estuarine and coastal waters has been reviewed. The natural flora of the environment must be considered in selecting an indicator organism, but, more importantly, recent work which shows a viable but non-recoverable stage of pathogens entering the marine environment demonstrates that the conventional detection of indicator microorganisms is misleading, if not inaccurate. Results suggest that the newly developed epifluorescent/immunofluorescent direct detection of pathogens in the environment may be the most reliable method for determining public health hazards in marine and estuarine waters. url: https://api.elsevier.com/content/article/pii/0378109785900576 doi: 10.1016/0378-1097(85)90057-6 id: cord-298862-8bijio30 author: Eltom, Kamal H. title: Buffalopox Virus: An Emerging Virus in Livestock and Humans date: 2020-08-20 words: 4318.0 sentences: 231.0 pages: flesch: 47.0 cache: ./cache/cord-298862-8bijio30.txt txt: ./txt/cord-298862-8bijio30.txt summary: Buffalopox was first described in India, later in other countries, and has become an emerging contagious viral zoonotic disease infecting milkers with high morbidity among affected domestic buffalo and cattle. Over time, VACV evolved into BPXV by establishing itself in buffaloes to be increasingly pathogenic to this host and to make infections in cattle and humans. The full-length sequences of these four genes of BPXVs-obtained from outbreaks in buffaloes, cattle, and humans in India-were analyzed, to investigate their evolutionary relationship to other OPXVs circulating in the world vis-à The full-length sequences of these four genes of BPXVs-obtained from outbreaks in buffaloes, cattle, and humans in India-were analyzed, to investigate their evolutionary relationship to other OPXVs circulating in the world vis-à-vis the vaccine strains. Sequence and phylogenetic analysis of host-range (E3L, K3L, and C7L) and structural protein (B5R) genes of buffalopox virus isolates from buffalo, cattle, and human in India abstract: Buffalopox virus (BPXV) is the cause of buffalopox, which was recognized by the FAO/WHO Joint Expert Committee on Zoonosis as an important zoonotic disease. Buffalopox was first described in India, later in other countries, and has become an emerging contagious viral zoonotic disease infecting milkers with high morbidity among affected domestic buffalo and cattle. BPXV is a member of the genus Orthopoxvirus and a close variant of the vaccinia virus (VACV). Recent genome data show that BPXV shares a most recent common ancestor of VACV Lister strain, which had been used for inoculating buffalo calves to produce a Smallpox vaccine. Over time, VACV evolved into BPXV by establishing itself in buffaloes to be increasingly pathogenic to this host and to make infections in cattle and humans. Together with the current pandemic of SARS-COV2/COVID 19, BPXV infections illustrate how vulnerable the human population is to the emergence and re-emergence of viral pathogens from unsuspected sources. In view that majority of the world population are not vaccinated against smallpox and are most vulnerable in the event of its re-emergence, reviewing and understanding the biology of vaccinia-like viruses are necessary for developing a new generation of safer smallpox vaccines in the smallpox-free world. url: https://doi.org/10.3390/pathogens9090676 doi: 10.3390/pathogens9090676 id: cord-326719-p1ma4akz author: Enjuanes, Luis title: Virus-based vectors for gene expression in mammalian cells: Coronavirus date: 2003-12-31 words: 5923.0 sentences: 282.0 pages: flesch: 52.0 cache: ./cache/cord-326719-p1ma4akz.txt txt: ./txt/cord-326719-p1ma4akz.txt summary: Coronaviruses have several advantages as vectors over other viral expression systems: (1) coronaviruses are single-stranded RNA viruses that replicate within the cytoplasm without a DNA intermediary, making integration of the virus genome into the host cell chromosome unlikely, (2) these viruses have the largest RNA virus genome and, in principle, have room for the insertion of large foreign genes, (3) a pleiotropic secretory immune response is best induced by the stimulation of gut-associated lymphoid tissues, (4) the tropism of coronaviruses may be modified by manipulation of the spike (S) protein allowing engineering of the tropism of the vector, (5) non-pathogenic coronavirus strains infecting most species of interest (human, porcine, bovine, canine, feline, and avian) are available to develop expression systems, and (6) infectious coronavirus cDNA clones are available to design expression systems. abstract: Publisher Summary The coronavirus and the torovirus genera form the Coronaviridae family, which is closely related to the Arteriviridae family. Both families are included in the Nidovirales order. Recently, a new group of invertebrate viruses, the Roniviridae, with a genetic structure and replication strategy similar to those of coronaviruses, has been described. This new virus family has been included within the Nidovirales. Coronaviruses have several advantages as vectors over other viral expression systems: (1) coronaviruses are single-stranded RNA viruses that replicate within the cytoplasm without a DNA intermediary, making integration of the virus genome into the host cell chromosome unlikely, (2) these viruses have the largest RNA virus genome and, in principle, have room for the insertion of large foreign genes, (3) a pleiotropic secretory immune response is best induced by the stimulation of gut-associated lymphoid tissues, (4) the tropism of coronaviruses may be modified by manipulation of the spike (S) protein allowing engineering of the tropism of the vector, (5) non-pathogenic coronavirus strains infecting most species of interest (human, porcine, bovine, canine, feline, and avian) are available to develop expression systems, and (6) infectious coronavirus cDNA clones are available to design expression systems. Within the coronavirus two types of expression vectors have been developed: one requires two components (helper–dependent expression system) and the other a single genome that is modified either by targeted recombination or by engineering a cDNA encoding an infectious RNA. This chapter focuses on the advantages and limitations of these coronavirus expression systems, the attempts to increase their expression levels by studying the transcription-regulating sequences (TRSs), and the proven possibility of modifying their tissue and species-specificity. url: https://www.sciencedirect.com/science/article/pii/S016773060338010X doi: 10.1016/s0167-7306(03)38010-x id: cord-021805-2j07zw6q author: Epstein, Jonathan H. title: Emerging Diseases in Bats date: 2018-09-28 words: 4160.0 sentences: 214.0 pages: flesch: 50.0 cache: ./cache/cord-021805-2j07zw6q.txt txt: ./txt/cord-021805-2j07zw6q.txt summary: 6, 7 Bats have been associated with several zoonotic viruses that have recently been discovered and linked to significant human and animal disease, including severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), Ebola and Marburg viruses, and Nipah virus (NiV) 8 (see also Chapters 19, 34, and 42 ). Viral discovery has, however, significantly expanded our understanding of the phylogenetic breadth of important viral families such as filoviruses (e.g., Ebola virus), paramyxoviruses (e.g., NiV), and coronaviruses (e.g., SARS coronavirus [CoV]), which is necessary for both better understanding what makes viruses pathogenic and also for recognizing wildlife reservoirs of viral pathogens, once they do emerge, more rapidly. Data are mounting to support bats as important reservoirs compared with other mammals, and large-scale surveillance efforts like PREDICT and the recently launched Global Virome Project, a 10-year effort to identify the majority of viruses in key wildlife species in emerging disease hot spots, 73 will shed more light on the total diversity of viruses in bat species and the types of human-animal interfaces that exist in different geographic and cultural contexts. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152049/ doi: 10.1016/b978-0-323-55228-8.00040-0 id: cord-338400-30vl2hks author: Epstein, Jonathan H. title: Identification of GBV-D, a Novel GB-like Flavivirus from Old World Frugivorous Bats (Pteropus giganteus) in Bangladesh date: 2010-07-01 words: 4653.0 sentences: 246.0 pages: flesch: 50.0 cache: ./cache/cord-338400-30vl2hks.txt txt: ./txt/cord-338400-30vl2hks.txt summary: Phylogenetic analysis indicates that this first GBV-like flavivirus reported in bats constitutes a distinct species within the Flaviviridae family and is ancestral to the GBV-A and -C virus clades. GBV-A viruses have been described in New World primates and are not known to infect humans [17] [18] [19] , while GBV-C (also known as Hepatitis G virus (HGV)) have frequently been isolated from humans in many regions of the World, including India and Bangladesh [19] [20] [21] [22] [23] , and from wild chimpanzees (Pan troglodytes) in Africa [24, 25] . Our findings provide new insight into the range of known hosts for GB-like viruses and demonstrate the power of unbiased sequencing to characterize the diversity of potentially zoonotic pathogens carried by bats and other reservoirs. Molecular analyses of sera from Pteropus giganteus bats from Faridpur, Bangladesh led to the identification of a 9,633 nt sequence consistent in genomic organization with known GBV and other species within the family Flaviviridae [16] . abstract: Bats are reservoirs for a wide range of zoonotic agents including lyssa-, henipah-, SARS-like corona-, Marburg-, Ebola-, and astroviruses. In an effort to survey for the presence of other infectious agents, known and unknown, we screened sera from 16 Pteropus giganteus bats from Faridpur, Bangladesh, using high-throughput pyrosequencing. Sequence analyses indicated the presence of a previously undescribed virus that has approximately 50% identity at the amino acid level to GB virus A and C (GBV-A and -C). Viral nucleic acid was present in 5 of 98 sera (5%) from a single colony of free-ranging bats. Infection was not associated with evidence of hepatitis or hepatic dysfunction. Phylogenetic analysis indicates that this first GBV-like flavivirus reported in bats constitutes a distinct species within the Flaviviridae family and is ancestral to the GBV-A and -C virus clades. url: https://doi.org/10.1371/journal.ppat.1000972 doi: 10.1371/journal.ppat.1000972 id: cord-001616-9sc2xmqr author: Erdem, Hakan title: New global viral threats date: 2015 words: 3085.0 sentences: 249.0 pages: flesch: 58.0 cache: ./cache/cord-001616-9sc2xmqr.txt txt: ./txt/cord-001616-9sc2xmqr.txt summary: In March 2014, the Ministry of Health of Guinea reported a disease outbreak characterized by fever, severe diarrhea, vomiting, and a high case-fatality rate. 31 One avian influenza case was detected in Taiwan due to H6N1 subtype, whereas 2 of 3 H10N8 human infections observed in China were lethal. In late March 2013, novel human infections due to avian influenza A H7N9 virus were reported from China. Frequently Asked Questions on human infection caused by the avian influenza A(H7N9) virus Comparative epidemiology of human infections with avian influenza A H7N9 and H5N1 viruses in China: a populationbased study of laboratory-confirmed cases Human infections with avian influenza A(H7N9) virus Human infection with avian influenza A(H7N9) virus -update Human infection with a novel avian-origin influenza A (H7N9) virus Epidemiology of human infections with avian influenza A(H7N9) virus in China abstract: Infectious diseases have caused great catastrophes in human history, as in the example of the plague, which wiped out half of the population in Europe in the 14th century. Ebola virus and H7N9 avian influenza virus are 2 lethal pathogens that we have encountered in the second decade of the 21st century. Ebola infection is currently being seen in West Africa, and H7N9 avian flu appears to have settled in Southeast Asia. This article focuses on the current situation and the future prospects of these potential infectious threats to mankind. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4404471/ doi: 10.15537/smj.2015.4.10089 id: cord-015871-1tuf4zxi author: Ergonul, Onder title: Treatment of Crimean-Congo Hemorrhagic Fever date: 2007 words: 8234.0 sentences: 474.0 pages: flesch: 44.0 cache: ./cache/cord-015871-1tuf4zxi.txt txt: ./txt/cord-015871-1tuf4zxi.txt summary: In contrast, a dose of ribavirin at least nine times greater was required to induce a comparable inhibitory effect on the yields of Rift Valley fever virus, for which the drug has been shown to inhibit replication in monkeys and rodents [104] . However hemorrhagic fever virus infections can be approached by the following different therapeutic strategies [6] : (i) administration of high-titered neutralizing antibodies and/or (ii) treatment with antiviral drugs. In recent times, several groups have studied the antiviral activities of interferons against hemorrhagic fever viruses. Human MxA protein inhibits the replication of Crimean-Congo hemorrhagic fever virus Type I interferon inhibits Crimean-Congo hemorrhagic fever virus in human target cells Genotoxic effect of ribavirin in patients with Crimean-Congo hemorrhagic fever Ribavirin efficacy in an in vivo model of Crimean-Congo hemorrhagic fever virus (CCHF) infection Inhibition of Crimean-Congo hemorrhagic fever viral infectivity yields in vitro by ribavirin abstract: Ribavirin is a synthetic purine nucleoside analog with a modified base and D-ribose sugar, also known as virazol, first synthesized by Sidwell and colleagues in 1972 [43, 49] (Fig. 19-1). It is of particular interest, because it was the first synthetic nucleoside to exhibit broad spectrum antiviral activity, and it is one of few antiviral drugs in clinical use effective against agents other than HIV and herpesviruses [43]. It inhibits the replication of a wide range of RNA and DNA viruses in vitro, including orthomyxo, paramyxo, arena, bunya, flavi, herpes, adeno, pox, and retroviruses [49]. In current clinical practice, ribavirin is commonly used for certain viral infections (Table 19-1). Most notably, it is used in combination with interferon-α for treatment of HCV infection [66]. Ribavirin aerosol is used for treatment of pediatric infection by respiratory syncytial virus [19]. It is the only antiviral drug that could be also used in viral hemorrhagic fever syndromes. Besides Crimean- Congo hemorrhagic fever (CCHF), it is used in Lassa fever [70]. Viruses in the Bunyaviridae family are generally sensitive to ribavirin [92]. A prospective, randomized, double-blind, placebo-controlled trial of 242 patients with serologically confirmed Hantaan virus in the People’s Republic of China found a sevenfold decrease in mortality among ribavirin-treated patients [54], other studies did not confirm these benefits. Ribavirin was found to be effective against CCHF virus (CCHFV) in vitro [99, 104]. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119965/ doi: 10.1007/978-1-4020-6106-6_19 id: cord-334941-6uattdti author: Espmark, Åke title: Other viruses date: 2014-06-27 words: 3579.0 sentences: 210.0 pages: flesch: 54.0 cache: ./cache/cord-334941-6uattdti.txt txt: ./txt/cord-334941-6uattdti.txt summary: Of the orbiviruses, the Colorado tick fever virus is the only one known to cause disease in man. Of the orbiviruses, the Colorado tick fever virus is the only one known to cause disease in man. It has recently been demonstrated that its aetiological agent probably is a bunyavirus which is antigenically related to haemorrhagic fever virus, and is endemic in the Soviet Union and large parts of Asia {Korean haemorrhagic fevery see also Chapter 34). In non-endemic areas units for the hospital care of imported cases of Lassa fever are needed as are the high-risk units of the national virological laboratories permitting work with highly contagious viruses like that of the Lassa fever. In 1967 a number of cases of a haemorrhagic disease with a considerable mortality rate was reported from laboratories at Marburg in the Federal Republic of Germany. Rabies virus causes an acute CNS disease which is lethal for man. abstract: This chapter discusses the characteristics of other viruses. The reovirus family is composed of three groups—reovirus, orbivirus, and rotavirus—and can cause infections in both man and animals. Other reoviruses are pathogenic to insects and plants. The orbivirus group consists of a large number of members, some of which are transmitted by vectors and, therefore, belong to the heterogenic arboviruses. Of the orbiviruses, the Colorado tick fever virus is the only one known to cause disease in man. As indicated by its name, the vector is a tick and the virus produces a febrile illness with myalgia. Arboviruses, that is, viruses borne by arthropod vectors and multiplying both in the arthropod and in the animal on which the arthropod is parasitic, show markedly variable morphological and biochemical characteristics. Coronavirus-like particles have been observed in fecal specimens of patients with gastroenteritis symptoms in India, Australia, Gambia, West Germany, and other countries. url: https://www.sciencedirect.com/science/article/pii/B9780407002531500384 doi: 10.1016/b978-0-407-00253-1.50038-4 id: cord-288348-b10e023s author: Estes, Mary Kolb title: Epidemic viral gastroenteritis date: 1979-06-30 words: 4523.0 sentences: 232.0 pages: flesch: 39.0 cache: ./cache/cord-288348-b10e023s.txt txt: ./txt/cord-288348-b10e023s.txt summary: Of the many viruses identified in stools, only two groups have met the criteria as definite etiologic agents of epidemic gastroenteritis in human subjects: rotaviruses and the small 27 nm agents [Norwalk-like agents) ( of investigations which began with an epidemic of gastroenteritis occurring in the newborn in the Baltimore-Washington area in the fall of 1941. Rotaviruses have been established as enteritis viruses by isolation and purification from stools of subjects suffering from gastroenteritis, and by induction of disease and seroconversion in both animals and volunteer subjects with purified preparations, Epidemiologic studies on the prevalence of rotavirus infections have shown these ubiquitous agents to be a major cause of gastroenteritis in children. Local immune factors, such as secretory immunoglobulin A or interferon, may therefore be important in protection against rotavirus infection, Alternatively, reinfection in the presence of circulating antibody could reflect the presence of multiple serotypes of virus [37] ; at least four agents in human subjects have been characterized to date [38-411. abstract: Abstract Epidemic viral gastroenteritis is a significant world wide problem. In developed countries, gastroenteritis accounts for significant morbidity and loss of time from work; in the Third World it is the leading cause of mortality among infants and children. Recent technologic advances have been associated with an explosion of research activity. Two virus groups, the Norwalk-like agents and the rotaviruses, are currently accepted as causative agents of viral gastroenteritis in man. The problem of viral gastroenteritis is reviewed both from a current and a historic perspective. url: https://api.elsevier.com/content/article/pii/0002934379904571 doi: 10.1016/0002-9343(79)90457-1 id: cord-291946-kq0rsuxj author: Etienne, Lucie title: The Mongoose, the Pheasant, the Pox, and the Retrovirus date: 2013-08-27 words: 2911.0 sentences: 132.0 pages: flesch: 46.0 cache: ./cache/cord-291946-kq0rsuxj.txt txt: ./txt/cord-291946-kq0rsuxj.txt summary: The genomes of two species of mongooses and an egg-laying mammal called an echidna show that a virus currently present in poultry, the reticuloendotheliosis virus (REV), is actually of ancient exotic mammalian origin. The genomes of two species of mongooses and an egg-laying mammal called an echidna show that a virus currently present in poultry, the reticuloendotheliosis virus (REV), is actually of ancient exotic mammalian origin. Although REV may still exist somewhere in a mammalian host, its modern form links an 8 million-year-old infection of the ancestor of a mongoose to a virus that now is circulating in wild birds through malaria studies in the mid-20 th century. Although REV may still exist somewhere in a mammalian host, its modern form links an 8 million-year-old infection of the ancestor of a mongoose to a virus that now is circulating in wild birds through malaria studies in the mid-20 th century. abstract: Paleovirology is the study of ancient viruses. The existence of a paleovirus can sometimes be detected by virtue of its accidental insertion into the germline of different animal species, which allows one to date when the virus actually existed. However, the ancient and the modern often connect, as modern viruses have unexpected origins that can be traced to ancient infections. The genomes of two species of mongooses and an egg-laying mammal called an echidna show that a virus currently present in poultry, the reticuloendotheliosis virus (REV), is actually of ancient exotic mammalian origin. REV apparently spread to poultry through a circuitous route involving the isolation of malaria parasites from a pheasant from Borneo housed at the Bronx Zoo that was contaminated with REV. Repeated passage of this virus in poultry adapted the virus to its new host. At some point, the virus got inserted into another virus, called fowlpox virus, which has spread back into the wild. Although REV may still exist somewhere in a mammalian host, its modern form links an 8 million-year-old infection of the ancestor of a mongoose to a virus that now is circulating in wild birds through malaria studies in the mid-20(th) century. These lessons of ancient and modern viruses have implications for modern human pandemics from viral reservoirs and for human interventions that may come with unintended consequences. url: https://www.ncbi.nlm.nih.gov/pubmed/24013523/ doi: 10.1371/journal.pbio.1001641 id: cord-008686-9ybxuy00 author: Everett, Tom title: Poor transmission of seasonal cold viruses in a British Antarctic Survey base date: 2019-03-14 words: 6924.0 sentences: 362.0 pages: flesch: 54.0 cache: ./cache/cord-008686-9ybxuy00.txt txt: ./txt/cord-008686-9ybxuy00.txt summary: However, in the acute infection stage respiratory viruses are generally present in relatively high copy numbers, with median values of mostly 4-8 log 10 (i.e. 10,0 0 0-10 0,0 0 0,0 0 0 copies/ml) for adeno-, corona-, hMPV, influenza, PIV and RSV, as reported in one comprehensive paediatric study. 2 A 26-year-old male ( index case of the outbreak report 2 ) from Kerala''s Perambra town died undiagnosed with fever, en-cephalitis and respiratory distress in Government Medical College Kozhikode(GMCK), after being transferred from Taluk Hospital, Perambra(THP). 6 Along with the wound cleansing and post-exposure rabies immunoglobulin (RIG) and vaccination, any risk of SHBV requires that high dose acyclovir (preferably valaciclovir 1 g TDS PO; or acyclovir 800 mg 5 times daily PO, for adults) PEP for at least 14 days should be considered. After the first dengue-fever epidemic in China, which occurred in May 1978 in Foshan, Guangdong Province, there have been regional outbreaks of dengue every year and the number of cases has increased. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133657/ doi: 10.1016/j.jinf.2019.03.007 id: cord-001120-fxd533b4 author: Everitt, Aaron R. title: Defining the Range of Pathogens Susceptible to Ifitm3 Restriction Using a Knockout Mouse Model date: 2013-11-21 words: 4874.0 sentences: 252.0 pages: flesch: 47.0 cache: ./cache/cord-001120-fxd533b4.txt txt: ./txt/cord-001120-fxd533b4.txt summary: We showed that Ifitm3 does not impact on the restriction or pathogenesis of bacterial (Salmonella typhimurium, Citrobacter rodentium, Mycobacterium tuberculosis) or protozoan (Plasmodium berghei) pathogens, despite in vitro evidence. Here we sought therefore to expand and define the role of Ifitm3 in pathogen restriction by assessing the susceptibility of Ifitm3-deficient (Ifitm3 -/-) mice to bacteria (Salmonella Typhimurium, Citrobacter rodentium, Mycobacterium tuberculosis), a parasite (Plasmodium berghei) and a virus (respiratory syncytial virus, RSV) to determine the specificity of this crucial antimicrobial protein. Similarly, bacterial counts revealed no significant differences between wild type and Ifitm3 -/-mice; together showing that Ifitm3 does not play a role in resistance or susceptibility to Salmonella infection. The experimental challenge revealed there to be no significant difference in phenotype seen in Ifitm3 -/-mice compared with wild type littermate controls, with both showing susceptibility to ECM ( Figure 5A ). abstract: The interferon-inducible transmembrane (IFITM) family of proteins has been shown to restrict a broad range of viruses in vitro and in vivo by halting progress through the late endosomal pathway. Further, single nucleotide polymorphisms (SNPs) in its sequence have been linked with risk of developing severe influenza virus infections in humans. The number of viruses restricted by this host protein has continued to grow since it was first demonstrated as playing an antiviral role; all of which enter cells via the endosomal pathway. We therefore sought to test the limits of antimicrobial restriction by Ifitm3 using a knockout mouse model. We showed that Ifitm3 does not impact on the restriction or pathogenesis of bacterial (Salmonella typhimurium, Citrobacter rodentium, Mycobacterium tuberculosis) or protozoan (Plasmodium berghei) pathogens, despite in vitro evidence. However, Ifitm3 is capable of restricting respiratory syncytial virus (RSV) in vivo either through directly restricting RSV cell infection, or by exerting a previously uncharacterised function controlling disease pathogenesis. This represents the first demonstration of a virus that enters directly through the plasma membrane, without the need for the endosomal pathway, being restricted by the IFITM family; therefore further defining the role of these antiviral proteins. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836756/ doi: 10.1371/journal.pone.0080723 id: cord-345848-s84lxe6l author: Everitt, Aaron R. title: IFITM3 restricts the morbidity and mortality associated with influenza date: 2012-03-25 words: 4570.0 sentences: 278.0 pages: flesch: 52.0 cache: ./cache/cord-345848-s84lxe6l.txt txt: ./txt/cord-345848-s84lxe6l.txt summary: We find that a statistically significant number of hospitalized subjects show enrichment for a minor IFITM3 allele (SNP rs12252-C) that alters a splice acceptor site, and functional assays show the minor CC genotype IFITM3 has reduced influenza virus restriction in vitro. We find that a statistically significant number of hospitalised subjects show enrichment for a minor IFITM3 allele (SNP rs12252-C) that alters a splice acceptor site, and functional assays show the minor CC genotype IFITM3 has reduced influenza virus restriction in vitro. Given the higher viral load in Ifitm3 −/− mice and increased replication of influenza A virus in Ifitm3 deleted cells in vitro (Fig. 1d) , we examined both viral nucleic acid and protein distribution in the lung. Analysis of cell populations resident in the lung tissue on day 6 post-infection showed that Ifitm3 −/− mice displayed significantly reduced proportions of CD4+ (p=0.004) and CD8+ Tcells (p=0.02) and natural killer (NK) cells (p=0.0001) but an elevated proportion of neutrophils (p=0.007) (Fig. 3a) . abstract: The 2009 H1N1 influenza pandemic showed the speed with which a novel respiratory virus can spread and the ability of a generally mild infection to induce severe morbidity and mortality in a subset of the population. Recent in vitro studies show that the interferon-inducible transmembrane (IFITM) protein family members potently restrict the replication of multiple pathogenic viruses. Both the magnitude and breadth of the IFITM proteins' in vitro effects suggest that they are critical for intrinsic resistance to such viruses, including influenza viruses. Using a knockout mouse model, we now test this hypothesis directly and find that IFITM3 is essential for defending the host against influenza A virus in vivo. Mice lacking Ifitm3 display fulminant viral pneumonia when challenged with a normally low-pathogenicity influenza virus, mirroring the destruction inflicted by the highly pathogenic 1918 'Spanish' influenza. Similar increased viral replication is seen in vitro, with protection rescued by the re-introduction of Ifitm3. To test the role of IFITM3 in human influenza virus infection, we assessed the IFITM3 alleles of individuals hospitalized with seasonal or pandemic influenza H1N1/09 viruses. We find that a statistically significant number of hospitalized subjects show enrichment for a minor IFITM3 allele (SNP rs12252-C) that alters a splice acceptor site, and functional assays show the minor CC genotype IFITM3 has reduced influenza virus restriction in vitro. Together these data reveal that the action of a single intrinsic immune effector, IFITM3, profoundly alters the course of influenza virus infection in mouse and humans. url: https://www.ncbi.nlm.nih.gov/pubmed/22446628/ doi: 10.1038/nature10921 id: cord-325827-492xi3ee author: Evermann, J. F. title: Biological and pathological consequences of feline infectious peritonitis virus infection in the cheetah date: 1988 words: 4215.0 sentences: 178.0 pages: flesch: 38.0 cache: ./cache/cord-325827-492xi3ee.txt txt: ./txt/cord-325827-492xi3ee.txt summary: Subsequent observations based upon seroepidemiological surveys and electron microscopy of fecal material verified that cheetahs were indeed capable of being infected by coronaviruses, which were antigenically related to coronaviruses affecting domestic cats, i.e. feline infectious peritonitis virus/feline enteric coronavirus. The purpose of this review is to present desciptions of the various forms of coronaviral infections in the cheetah relying upon studies of both natural infections, as well as experimental infections in other species with coronaviruses, such as mouse hepatitis virus (MHV), canine coronavirus (CCV), transmissible gastroenteritis virus (TGEV) of swine, and bovine coronavirus (BCV) of neonatal calves [28, 36, 39, 49, 57, 60, 61, 75, 79, 92] . The occurrence of coronaviral infections of the cheetah have now been documented based on serology, electron microscopy of fecal contents, and the occurrence of fatal forms of infectious peritonitis compatible with the clinicopathologic signs observed in domestic cats with FIP [7, 10, 26, 29, 38, 43, 56, 72] . abstract: An epizootic of feline infectious peritonitis in a captive cheetah population during 1982–1983 served to focus attention on the susceptibility of the cheetah (Acinoyx jubatus) to infectious disease. Subsequent observations based upon seroepidemiological surveys and electron microscopy of fecal material verified that cheetahs were indeed capable of being infected by coronaviruses, which were antigenically related to coronaviruses affecting domestic cats, i.e. feline infectious peritonitis virus/feline enteric coronavirus. Coincident with the apparent increased susceptibility of the cheetah to infectious diseases, were observations that the cheetah was genetically unusual insofar as large amounts of enzyme-encoding loci were monomorphic, and that unrelated cheetahs were capable of accepting allogenic skin grafts. These data provided the basis for a hypothesis that the cheetah, through intensive inbreeding, had become more susceptible to viral infections as a result of genetic homogeneity. url: https://www.ncbi.nlm.nih.gov/pubmed/2849387/ doi: 10.1007/bf01310822 id: cord-048368-wm4c7rk6 author: Evseenko, Vasily A title: Experimental infection of H5N1 HPAI in BALB/c mice date: 2007-07-27 words: 2880.0 sentences: 202.0 pages: flesch: 55.0 cache: ./cache/cord-048368-wm4c7rk6.txt txt: ./txt/cord-048368-wm4c7rk6.txt summary: Serological analysis showed wide cross-reactivity of this virus with sera produced to H5N1 HPAI viruses isolated earlier in South-East Asia. Earlier HPAI viruses were investigated in mice [4, 5] and murine models were successively used for reverse genetics made influenza vaccines [6] . Sequence comparison of the NA protein of A/duck/Tuva/01/06 aligned with the NA of N2 subtype of A/Wuhan/359/95 (H3N2) influenza virus showed phenotype potentially sensitive to neuraminidase inhibitors. Despite powerful anti-influenza virus effects of TNF-α in lung tissue, as it was described previously [28] , we consider that elevated production of the cytokines seems to be crucial in the pathogenesis of HPAI infection. Summing up, in our study BALB/c mice infected with HPAI, strain A/duck/Tuva/01/06, appeared to be able to produce the innate immune response, which culminated to the development of shock and subsequent multiple organ failure. abstract: BACKGROUND: In 2005 huge epizooty of H5N1 HPAI occurred in Russia. It had been clear that territory of Russia becoming endemic for H5N1 HPAI. In 2006 several outbreaks have occurred. To develop new vaccines and antiviral therapies, animal models had to be investigated. We choose highly pathogenic strain for these studies. RESULTS: A/duck/Tuva/01/06 belongs to Quinghai-like group viruses. Molecular markers – cleavage site, K627 in PB2 characterize this virus as highly pathogenic. This data was confirmed by direct pathogenic tests: IVPI = 3.0, MLD(50 )= 1,4Log10EID(50). Also molecular analysis showed sensivity of the virus to adamantanes and neuraminidase inhibitors. Serological analysis showed wide cross-reactivity of this virus with sera produced to H5N1 HPAI viruses isolated earlier in South-East Asia. Mean time to death of infected animals was 8,19+/-0,18 days. First time acute delayed hemorrhagic syndrome was observed in mice lethal model. Hypercytokinemia was determined by elevated sera levels of IFN-gamma, IL-6, IL-10. CONCLUSION: Assuming all obtained data we can conclude that basic model parameters were characterized and virus A/duck/Tuva/01/06 can be used to evaluate anti-influenza vaccines and therapeutics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1973068/ doi: 10.1186/1743-422x-4-77 id: cord-022196-1tionxun author: FENNER, FRANK title: The Nature and Classification of Animal Viruses date: 2013-11-17 words: 9588.0 sentences: 406.0 pages: flesch: 46.0 cache: ./cache/cord-022196-1tionxun.txt txt: ./txt/cord-022196-1tionxun.txt summary: With most isometric particles and in all complex virions, the capsid encloses another protein structure containing the viral genome, called the core. All animal viruses with tubular nucleocapsids are enveloped, and in these the lipid layer from which glycoprotein peplomers project is probably applied to a protein shell (the membrane protein; see Fig. 1 -1), which may be relatively rigid, as in Rhabdovirus, or readily distorted (as in the myxoviruses) so that in negatively stained electron micrographs the virions appear to be pleomorphic. The RNA viruses that have the largest (single-stranded) genomes, those of the Leukovirus genus, also have a highly complex structure with an envelope enclosing an icosahedral capsid that, in turn, surrounds a tubular nucleocapsid. The conventional physicochemical criteria [(a) nucleic acid: type, strandedness, fragmentation, and molecular weight; (b) virion: shape, size, and symmetry] are suitable for classification at this level of family/genus, perhaps assisted by the serological cross-reactivity of "group" antigens where these have been recognized. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155428/ doi: 10.1016/b978-0-12-253040-1.50006-3 id: cord-023705-3q9yr6np author: FENNER, FRANK title: Viral Replication date: 2014-06-27 words: 8331.0 sentences: 424.0 pages: flesch: 51.0 cache: ./cache/cord-023705-3q9yr6np.txt txt: ./txt/cord-023705-3q9yr6np.txt summary: Many important biochemical phenomena such as the splicing and other types of posttranscriptional processing of RNA, the posttranslational cleavage and glycosylation of proteins, the replication of RNA, reverse transcription, integration, and the transposition of viral genes and cellular oncogenes were first elucidated by virologists and have general application in cell biology. Many important biochemical phenomena, such as splicing and other types of posttranscriptional processing of RNA, posttranslational cleavage and glycosylation of proteins, replica tion of RNA, reverse transcription, integration, and transposition of viral genes and cellular oncogenes, were first elucidated by virologists and have general application in cell biology. The proteins translated from the early transcripts of DNA viruses include enzymes and other proteins required for the replication of viral nucleic acid, as well as proteins that suppress host cell RNA and protein synthesis. abstract: Viral replication is the central focus of much experimental virology and is a significant part of molecular biology. Studies with bacteriophages in their prokaryotic host cells in the 1940s and 1950s provided the first insights into the complexities of viral replication. With the development of mammalian cell culture procedures, the techniques used for the study of bacteriophages were adapted to animal viruses. Progress has been such that the basic mechanisms of transcription, translation, and nucleic acid replication have been characterized for all the major families of animal viruses and the strategy of gene expression and its regulation clarified. Many important biochemical phenomena such as the splicing and other types of posttranscriptional processing of RNA, the posttranslational cleavage and glycosylation of proteins, the replication of RNA, reverse transcription, integration, and the transposition of viral genes and cellular oncogenes were first elucidated by virologists and have general application in cell biology. The chapter provides a general overview on viral replication for understanding pathogenesis, immunity, chemotherapy, and the role of viruses in cancer. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173495/ doi: 10.1016/b978-0-12-253055-5.50008-6 id: cord-023731-jqgervt7 author: FENNER, FRANK title: Laboratory Diagnosis of Viral Diseases date: 2014-06-27 words: 6992.0 sentences: 320.0 pages: flesch: 39.0 cache: ./cache/cord-023731-jqgervt7.txt txt: ./txt/cord-023731-jqgervt7.txt summary: Having allocated it to a particular family (e.g., Adenoviridae), one can then go on to determine the species or serotype (e.g., canine Immunodiffusion Antibody neutralizes infectivity of virion; inhibits cytopathology, reduces plaques, or protects animals Antibody inhibits viral hemagglutination Antigen-antibody complex binds complement, which is thereafter unavailable for the lysis of hemolysissensitized sheep red blood cells Antibody-aggregated virions are visible by electron microscopy Antibody labeled with fluorochrome binds to intracellular antigen; fluoresces by UV microscopy Peroxidase-labeled antibody binds to intracellular antigen; colored precipitate forms on adding substrate Enzyme-labeled antibody (or antigen) binds to antigen (or antibody); substrate changes color Radiolabeled antibody (or antigen) binds to antigen (or antibody), e.g., attached to solid phase Antibodies and soluble antigens produce visible lines of precipitate in a gel adenovirus 1) by more discriminating serological procedures. abstract: Tests for the specific diagnosis of a viral infection in an animal are of two general types: (1) those that demonstrate the presence of the virus and (2) those that demonstrate the presence of specific viral antibody. The provision, by a single laboratory, of a comprehensive service for the diagnosis of viral infections of domestic animals is a formidable undertaking. There are about 200 individual viral species in some 20 different viral families that infect the eight major domestic animal species. If antigenic types within an individual viral species are considered and the number of animal species is broadened to include turkey, duck, and zoo and laboratory animals, then the number of individual viruses exceeds 1000. It is, therefore, not surprising that few single laboratories could have available the necessary specific reagents, skills, and experience for the diagnosis of such a large number of infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173550/ doi: 10.1016/b978-0-12-253055-5.50017-7 id: cord-354109-mli0c97c author: Faezi, Nasim Asadi title: Viral infections in patients with acute respiratory infection in Northwest of Iran date: 2017-01-22 words: 3171.0 sentences: 166.0 pages: flesch: 47.0 cache: ./cache/cord-354109-mli0c97c.txt txt: ./txt/cord-354109-mli0c97c.txt summary: The aim of this study was to determine the frequency, mortality and association with clinical entities of influenza virus type A, influenza virus type B, respiratory syncytial virus (RSV), coronavirus, and adenoviruses in patients with ARI. Aim of the present study was to determine the frequency and mortality of the viral respiratory infections including influenza virus type A, influenza virus type B, respiratory syncytial virus (RSV), coronavirus, and adenoviruses in patients with ARI that referred to central Hospital in Northwest of Iran during September 2014 till May 2015. In another study that conducted in a Tehran hospital on children with acute respiratory infection, influenza A virus, RSV, and adenovirus were detected in 4.4, 5.7, and 6.3%, respectively [15] . Diagnosis of the adenovirus, RSV, and influenza virus by rapid detection test (immunochromatography) in children with acute respiratory infection, Iran abstract: INTRODUCTION: Acute respiratory infection (ARI) is one of the main causes of morbidity and mortality all around the world. The aim of this study was to determine the frequency, mortality and association with clinical entities of influenza virus type A, influenza virus type B, respiratory syncytial virus (RSV), coronavirus, and adenoviruses in patients with ARI. MATERIALS AND METHODS: During September 2014 till May 2015, 143 respiratory inpatients samples for viral testing collected from central Hospital in Northwest of Iran. A real-time reverse transcription-PCR (RT-PCR) assay was done to allow in one test the detection of influenza A and B viruses. Also, RSV and adenovirus were identified by Immunochromatography test. RESULTS: Twenty-four (46%) cases were positive for influenza A, which 11 (46%) of them were subtype H1N1 and 13 (54%) cases were subtype H3N2. Also, 21 (40%) cases were positive for influenza B, 5 (10%) cases were positive for RSV, and 2 (4%) cases were positive for adenovirus. One of the patients was positive for both influenza A and adenovirus. Two of the patients were positive for both influenza A and RSV. None of the patients were positive for coronavirus. CONCLUSIONS: Our findings show the importance of influenza virus type A, influenza virus type B, RSV, and adenoviruses associated with ARI in hospitalized patient and the different epidemiological patterns of the viruses in Tabriz, Iran. url: https://doi.org/10.3103/s0891416816030046 doi: 10.3103/s0891416816030046 id: cord-334027-xhfmio7k author: Fagre, Anna C. title: Can Bats Serve as Reservoirs for Arboviruses? date: 2019-03-03 words: 8738.0 sentences: 492.0 pages: flesch: 43.0 cache: ./cache/cord-334027-xhfmio7k.txt txt: ./txt/cord-334027-xhfmio7k.txt summary: No demonstrable pathologic effects noted during infection of three bat species [big brown bats (Eptesicus fuscus), little brown bats (Myotis lucifigus) and Mexican free-tailed bats (Tadarida brasiliensie mexicana) with various strains of JBEV or St. Louis encephalitis virus (SLEV) [69] . While experimental data demonstrated that some bat species can sustain JBEV infections and support mosquito-borne transmission of this virus, the epidemiological significance of these observations in the field remains unclear. To truly elucidate the role of bats as reservoirs for arboviruses, field surveillance studies documenting natural infection and transmission dynamics among vector and vertebrate species must be supplemented with experimental infections to characterize viremia profiles and infectiousness to vectors, virus-induced pathology, and immune kinetics following infection. The isolation of Marburg virus from Egyptian rousette bats in Uganda in addition to experimental infections demonstrating viremia and shedding in the absence of overt pathology support the role of this bat species as the reservoir for Marburg virus [6, 7, 208] . abstract: Bats are known to harbor and transmit many emerging and re-emerging viruses, many of which are extremely pathogenic in humans but do not cause overt pathology in their bat reservoir hosts: henipaviruses (Nipah and Hendra), filoviruses (Ebola and Marburg), and coronaviruses (SARS-CoV and MERS-CoV). Direct transmission cycles are often implicated in these outbreaks, with virus shed in bat feces, urine, and saliva. An additional mode of virus transmission between bats and humans requiring further exploration is the spread of disease via arthropod vectors. Despite the shared ecological niches that bats fill with many hematophagous arthropods (e.g., mosquitoes, ticks, biting midges, etc.) known to play a role in the transmission of medically important arboviruses, knowledge surrounding the potential for bats to act as reservoirs for arboviruses is limited. To this end, a comprehensive literature review was undertaken examining the current understanding and potential for bats to act as reservoirs for viruses transmitted by blood-feeding arthropods. Serosurveillance and viral isolation from either free-ranging or captive bats are described in relation to four arboviral groups (Bunyavirales, Flaviviridae, Reoviridae, Togaviridae). Further, ecological associations between bats and hematophagous viral vectors are characterized (e.g., bat bloodmeals in mosquitoes, ingestion of mosquitoes by bats, etc). Lastly, knowledge gaps related to hematophagous ectoparasites (bat bugs and bed bugs (Cimicidae) and bat flies (Nycteribiidae and Streblidae)), in addition to future directions for characterization of bat-vector-virus relationships are described. url: https://doi.org/10.3390/v11030215 doi: 10.3390/v11030215 id: cord-023200-3caevjvh author: Falanga, Annarita title: Membranotropic peptides mediating viral entry date: 2018-02-13 words: 6062.0 sentences: 270.0 pages: flesch: 41.0 cache: ./cache/cord-023200-3caevjvh.txt txt: ./txt/cord-023200-3caevjvh.txt summary: The discovery of short, membrane interacting, amphipathic or hydrophobic sequences (known as membranotropic peptides) in both enveloped and non‐enveloped viruses suggests that these small peptides are strongly involved in breaching the host membrane and in the delivery of the viral genome into the host cell. [3, 4] The molecular details of the interactions at the interface of virus and cell surfaces are quite complex and highly variable, but there is a common idea that only a limited number of pathways allowing viruses to reach the sites of penetration exist, with enveloped and non-enveloped viruses presenting different and unrelated processes, but with general principles driving all fusion events. [16, 17] Viral fusion proteins undergo significant rearrangements from the pre-fusion to the post-fusion conformations which are triggered by either receptor binding, proteolytic cleavage or low endosomal pH, and eventually determine the exposure of previously sequestered hydrophobic peptides, loops, or patches, able to interact with and destabilize one or both the opposing membranes. abstract: The means used by enveloped viruses to bypass cellular membranes are well characterized; however, the mechanisms used by non‐enveloped viruses to deliver their genome inside the cell remain unresolved and poorly defined. The discovery of short, membrane interacting, amphipathic or hydrophobic sequences (known as membranotropic peptides) in both enveloped and non‐enveloped viruses suggests that these small peptides are strongly involved in breaching the host membrane and in the delivery of the viral genome into the host cell. Thus, in spite of noticeable differences in entry, this short stretches of membranotropic peptides are probably associated with similar entry‐related events. This review will uncover the intrinsic features of viral membranotropic peptides involved in viral entry of both naked viruses and the ones encircled with a biological membrane with the objective to better elucidate their different functional properties and possible applications in the biomedical field. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167733/ doi: 10.1002/pep2.24040 id: cord-014796-6rw2wk1q author: Fayyadh, Thaer Kadhim title: Simultaneous detection of multiple viruses in their co-infected cells using multicolour imaging with self-assembled quantum dot probes date: 2017-05-06 words: 4741.0 sentences: 239.0 pages: flesch: 54.0 cache: ./cache/cord-014796-6rw2wk1q.txt txt: ./txt/cord-014796-6rw2wk1q.txt summary: title: Simultaneous detection of multiple viruses in their co-infected cells using multicolour imaging with self-assembled quantum dot probes The authors introduce a method for simultaneous imaging, detection and quantitative evaluation of multiple viruses in single cells by using multicolor quantum dot (QD) probes and in a single staining cycle. In this study, by using the multicolour QD-probes and a single staining procedure cycle, we have realized the simultaneous detection and quantitative evaluation of multiple viruses in their infected cells. As shown in Fig. 2a , there is obvious QD fluorescent signal in the cells infected with H1N1 virus incubated with fully assembly QD625-SpA-MAb as a Bone-step procedure^. As shown in Fig. 5 , by using the one-step staining procedure with a cocktail of QD625-SpA-MAb, QD525-SpA-MAb and QD705-SpA-MAb probes, the three influenza A virus subtypes H1N1, H3N2 and H9N2 were detected in the same co-infected MDCK cells with three types of corresponding QD signals (Fig. 5a) . abstract: The simultaneous detection and evaluation of the coinfection of a cell by multiple viruses or even multiple subtypes still is a difficult challenge. The authors introduce a method for simultaneous imaging, detection and quantitative evaluation of multiple viruses in single cells by using multicolor quantum dot (QD) probes and in a single staining cycle. The multicolor QD probes were fabricated via interaction between QDs conjugated to Staph. aureus protein A (SpA-QDs) and virus-specific antibodies. A cocktail of differently colored QD-SpA-MAbs probes were loaded into the same cells containing multiple viruses, and this enabled the different viruses to be fluorescently imaged and analyzed simultaneously. Specifically, influenza A viruses of type H1N1, H3N2, and H9N2, as well as human adenovirus species B type 3 (HAdV-B3) were imaged and detected in virus-infected cells or in their co-infected cells. In our perception, the method provides a flexible platform for simultaneous detection of multiple viruses in co-infected cells. Hence, it offers new opportunities for the molecular diagnosis of virus coinfection and for studies on virus-cell interactions. [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00604-017-2300-6) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088048/ doi: 10.1007/s00604-017-2300-6 id: cord-344970-ud1lhkyi author: Fecchi, Katia title: Coronavirus Interplay With Lipid Rafts and Autophagy Unveils Promising Therapeutic Targets date: 2020-08-11 words: 5433.0 sentences: 276.0 pages: flesch: 43.0 cache: ./cache/cord-344970-ud1lhkyi.txt txt: ./txt/cord-344970-ud1lhkyi.txt summary: Lipid rafts are specialized plasma membrane microdomains involved in important processes of the virus infections and of the host target cells (Rosenberger et al., 2000) . This minireview reports on the available knowledge about the interplay between coronaviruses, including the SARS-CoV-2, with lipid rafts and autophagic pathways, in order to focus the attention to novel potential targets to inhibit coronavirus infections. As outlined in this review, lipid rafts and autophagic pathways play a pivotal role in coronavirus infection, being critical for viral entry and replication, as well as for viral release from the host cells. In fact, different drugs described as inhibitors or inducers of the autophagy that control host cell pathways process involved in coronavirus infection, have sparked interest for their potential antiviral activity (Shakya et al., 2018; Liu et al., 2019; Xu et al., 2020; Yang et al., 2020 ; Table 1 ). abstract: Coronaviruses are enveloped, single-stranded, positive-sense RNA viruses that can infect animal and human hosts. The infection induces mild or sometimes severe acute respiratory diseases. Nowadays, the appearance of a new, highly pathogenic and lethal coronavirus variant, SARS-CoV-2, responsible for a pandemic (COVID-19), represents a global problem for human health. Unfortunately, only limited approaches are available to treat coronavirus infections and a vaccine against this new coronavirus variant is not yet available. The plasma membrane microdomain lipid rafts have been found by researchers to be involved in the replication cycle of numerous viruses, including coronaviruses. Indeed, some pathogen recognition receptors for coronaviruses as for other viruses cluster into lipid rafts, and it is therefore conceivable that the first contact between virus and host cells occurs into these specialized regions, representing a port of cell entry for viruses. Recent data highlighted the peculiar pro-viral or anti-viral role played by autophagy in the host immune responses to viral infections. Coronaviruses, like other viruses, were reported to be able to exploit the autophagic machinery to increase their replication or to inhibit the degradation of viral products. Agents known to disrupt lipid rafts, such as metil-β-cyclodextrins or statins, as well as autophagy inhibitor agents, were shown to have an anti-viral role. In this review, we briefly describe the involvement of lipid rafts and autophagy in coronavirus infection and replication. We also hint how lipid rafts and autophagy may represent a potential therapeutic target to be investigated for the treatment of coronavirus infections. url: https://www.ncbi.nlm.nih.gov/pubmed/32849425/ doi: 10.3389/fmicb.2020.01821 id: cord-003302-vxk7uqlc author: Fedson, David S title: Influenza, evolution, and the next pandemic date: 2018-10-03 words: 6378.0 sentences: 324.0 pages: flesch: 41.0 cache: ./cache/cord-003302-vxk7uqlc.txt txt: ./txt/cord-003302-vxk7uqlc.txt summary: These studies help explain the lower mortality in children compared with adults seen in the 1918 influenza pandemic and in many other types of acute illness. They agree with Worobey et al that early life antigenic imprinting might have led to a dysregulated T-cell response that increased the risk of death following infection in 1918 with a new and antigenically dissimilar influenza virus. In trying to understand the ''mystery'' of greater mortality among young adults during the 1918 pandemic, scientists have studied influenza viruses and the human response to previous infection. Considered with evidence from endotoxemic mice [28] and other studies [4] [5] [6] [7] [8] [9] , their findings suggest that the mortality impact of pandemic and seasonal influenza and other forms of acute critical illness might be reduced by treating the host response. abstract: Mortality rates in influenza appear to have been shaped by evolution. During the 1918 pandemic, mortality rates were lower in children compared with adults. This mortality difference occurs in a wide variety of infectious diseases. It has been replicated in mice and might be due to greater tolerance of infection, not greater resistance. Importantly, combination treatment with inexpensive and widely available generic drugs (e.g. statins and angiotensin receptor blockers) might change the damaging host response in adults to a more tolerant response in children. These drugs might work by modifying endothelial dysfunction, mitochondrial biogenesis and immunometabolism. Treating the host response might be the only practical way to reduce global mortality during the next influenza pandemic. It might also help reduce mortality due to seasonal influenza and other forms of acute critical illness. To realize these benefits, we need laboratory and clinical studies of host response treatment before and after puberty. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6234328/ doi: 10.1093/emph/eoy027 id: cord-287851-9p0dr7rl author: Fedson, David S title: Confronting an influenza pandemic with inexpensive generic agents: can it be done? date: 2008-09-30 words: 4878.0 sentences: 277.0 pages: flesch: 46.0 cache: ./cache/cord-287851-9p0dr7rl.txt txt: ./txt/cord-287851-9p0dr7rl.txt summary: The investigators commented that because of the functional redundancy of many cytokines and chemokines, deleting more than one of these genes might have had a greater (presumably more adverse) eff ect on the course of disease, and concluded that mice are suitable for evaluating agents that "modulate the infl ammatory response induced by H5N1 viruses, either alone or in combination with antiviral therapy". 18 More recently, a study of acute infl uenza pneumonia showed that compared with normal mice, Toll-like receptor (TLR) 3 knockout mice had reduced levels of several proinfl ammatory cytokines and chemokines and high pulmonary virus titres, yet mortality was unexpectedly low. For reasons of global public health it is crucially important for investigators to undertake experimental studies to determine whether these or other generic agents (or several of them in combination) could be eff ective in treating H5N1 and other potentially pandemic infl uenza virus infections. abstract: Summary Avian influenza A H5N1 presents a serious and possibly imminent pandemic threat. In such an event, adequate supplies of affordable vaccines and antiviral agents will be unavailable to most people in the world. In view of the overwhelming need for effective alternatives, generic agents that target the host immune response or the pandemic virus should be considered. Many scientists doubt the effectiveness of these agents. Nonetheless, several studies suggest that statins improve outcomes in patients with bacteraemia and pneumonia and might be similarly effective against influenza. An experimental study has shown that the fibrate gemfibrozil, a peroxisome proliferator-activated receptor (PPAR) α agonist, reduces mortality in H2N2 influenza virus-infected mice. There is substantial molecular cross-talk between statins and PPAR agonists, and their clinical effects are additive in patients with cardiovascular diseases. Chloroquine increases endosomal pH, impairing influenza virus release into the cytosol. Statins, fibrates, and chloroquine are produced as generic medications in developing countries. They are inexpensive, could be stockpiled, and would be available on the first pandemic day. With a lack of realistic alternatives for confronting the next pandemic, research is urgently needed to determine whether these and other generic agents could mitigate the effects of what might otherwise become an unprecedented global public-health crisis. url: https://doi.org/10.1016/s1473-3099(08)70070-7 doi: 10.1016/s1473-3099(08)70070-7 id: cord-006640-25ykas09 author: Fedson, David S. title: What treating Ebola means for pandemic influenza date: 2018-07-16 words: 5824.0 sentences: 278.0 pages: flesch: 43.0 cache: ./cache/cord-006640-25ykas09.txt txt: ./txt/cord-006640-25ykas09.txt summary: Physicians should be prepared to undertake clinical trials of widely available generic drugs to determine whether they improve survival in patients with seasonal influenza, other emerging virus diseases, and other forms of acute critical illness. An experience during the recent Ebola outbreak in Sierra Leone (2014-2016) suggests that inexpensive generic drugs might be used to treat patients with pandemic influenza and other emerging virus diseases. Several new investigational treatments targeting the Ebola virus were tested in clinical trials in West Africa (Guinea, Liberia, Sierra Leone): antiviral agents, convalescent plasma, and monoclonal antibody preparations [3, 4] . The Ebola treatment experience in Sierra Leone suggests that generic drugs targeting the host response might be used to treat patients who develop severe illness due to pandemic influenza, other emerging virus diseases, and everyday diseases like seasonal influenza, bacterial sepsis, and community-acquired pneumonia [11] . abstract: Almost all new treatments being developed for the next influenza pandemic target the virus. During the Ebola crisis in West Africa, patients were treated with an inexpensive generic statin/angiotensin receptor blocker combination that appeared to greatly improve survival. These drugs target the host response, not the virus, and probably reverse endothelial dysfunction. Scientists and health officials have shown little interest in this idea. Yet, during the early months of the next pandemic, vaccines will be unavailable and treatment options will be limited. Physicians should be prepared to undertake clinical trials of widely available generic drugs to determine whether they improve survival in patients with seasonal influenza, other emerging virus diseases, and other forms of acute critical illness. Public health officials should give these studies their strong support. If successful, they will suggest a ‘bottom up’ approach to patient care that could be implemented worldwide on the first pandemic day. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102163/ doi: 10.1057/s41271-018-0138-8 id: cord-326960-9phlylce author: Felberbaum, Rachael S. title: The baculovirus expression vector system: A commercial manufacturing platform for viral vaccines and gene therapy vectors date: 2015-03-20 words: 7289.0 sentences: 374.0 pages: flesch: 43.0 cache: ./cache/cord-326960-9phlylce.txt txt: ./txt/cord-326960-9phlylce.txt summary: This combination of features and product approvals has previously attracted interest from academic researchers, and more recently from industry leaders, to utilize BEVS to develop next generation vaccines, vectors for gene therapy, and other biopharmaceutical complex proteins. expresSF+ cells are used to manufacture three licensed products: Flublok ® influenza vaccine (Protein Sciences Corporation), Glybera ® gene therapy for the treatment of familial lipoprotein lipase deficiency (uniQure), and Ingelvac CircoFLEX ® veterinary vaccine to protect against porcine circovirus type 2 (Boehringer Ingelheim Vetmedica). Recombinant AAV-based gene therapies have been in development and shown promise for some time; however, a major limitation to their implementation had been the inability to scale up the manufacturing process to produce sufficient quantities of rAAVs. The original rAAV vectors were produced in mammalian tissue culture using adherent cells such as HEK293 cells, which required about 5000 175-cm 2 flasks to produce enough material for a large animal study or human clinical trial (~10 15 rAAV particles) [55] . abstract: The baculovirus expression vector system (BEVS) platform has become an established manufacturing platform for the production of viral vaccines and gene therapy vectors. Nine BEVS‐derived products have been approved – four for human use (Cervarix®, Provenge®, Glybera® and Flublok®) and five for veterinary use (Porcilis® Pesti, BAYOVAC CSF E2®, Circumvent® PCV, Ingelvac CircoFLEX® and Porcilis® PCV). The BEVS platform offers many advantages, including manufacturing speed, flexible product design, inherent safety and scalability. This combination of features and product approvals has previously attracted interest from academic researchers, and more recently from industry leaders, to utilize BEVS to develop next generation vaccines, vectors for gene therapy, and other biopharmaceutical complex proteins. In this review, we explore the BEVS platform, detailing how it works, platform features and limitations and important considerations for manufacturing and regulatory approval. To underscore the growth in opportunities for BEVS‐derived products, we discuss the latest product developments in the gene therapy and influenza vaccine fields that follow in the wake of the recent product approvals of Glybera® and Flublok®, respectively. We anticipate that the utility of the platform will expand even further as new BEVS‐derived products attain licensure. Finally, we touch on some of the areas where new BEVS‐derived products are likely to emerge. url: https://doi.org/10.1002/biot.201400438 doi: 10.1002/biot.201400438 id: cord-017249-la5sum39 author: Feldblyum, Tamara V. title: Seasonal and Pandemic Influenza Surveillance and Disease Severity date: 2015-05-12 words: 11430.0 sentences: 516.0 pages: flesch: 39.0 cache: ./cache/cord-017249-la5sum39.txt txt: ./txt/cord-017249-la5sum39.txt summary: With the growing focus of the US health care system on the meaningful use of electronic medical records, one of the practical applications is expanding biosurveillance and preparedness capabilities, such as surveillance of infl uenza severity and associated risk factors during seasonal epidemics and pandemics [ 18 , 22 ] . EHR-based surveillance systems such as Electronic Medical Record Support for Public Health (ESP) implemented in Ohio and Massachusetts and BioSense were successfully used for analyzing ICD-9 diagnosis codes, reporting notifi able disease cases, surveillance of ILI, identifi cation of infl uenza or upper respiratory infection risk factors among hospitalized patients, and for monitoring diabetes prevalence, risk factors, and disease severity [ 13 , 19 ] . Pregnancy has been reported as a risk factor for seasonal and pandemic infl uenza infections and severe disease outcomes using historical and current data. abstract: Continuous investments in influenza research, surveillance, and prevention efforts are critical to mitigate the consequences of annual influenza epidemics and pandemics. New influenza viruses emerge due to antigenic drift and antigenic shift evading human immune system and causing annual epidemics and pandemics. Three pandemics with varying disease severity occurred in the last 100 years. The disease burden and determinants of influenza severity depend on circulating viral strains and individual demographic and clinical factors. Surveillance is the most effective strategy for appropriate public health response. Active and passive surveillance methods are utilized to monitor influenza epidemics and emergence of novel viruses. Meaningful use of electronic health records could be a cost-effective approach to improved influenza surveillance url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121762/ doi: 10.1007/978-1-4939-2410-3_29 id: cord-339744-xrit0w5i author: Feng, Bo title: Investigation of antiviral state mediated by interferon-inducible transmembrane protein 1 induced by H9N2 virus and inactivated viral particle in human endothelial cells date: 2017-11-03 words: 6309.0 sentences: 408.0 pages: flesch: 52.0 cache: ./cache/cord-339744-xrit0w5i.txt txt: ./txt/cord-339744-xrit0w5i.txt summary: Our previous microarray analysis showed that H9N2 virus infection and inactivated viral particle inoculation increased the expression of interferon-inducible transmembrane protein 1 (IFITM1) in human umbilical vein endothelial cells (HUVECs). In present study, we deeply investigated the expression patterns of IFITM1 and IFITM1-mediated antiviral response induced by H9N2 virus infection and inactivated viral particle inoculation in HUVECs. Epithelial cells that are considered target cells of the influenza virus were selected as a reference control. The results indicated that the cellular interaction between intracellular molecules and viral particles might be involved in the induction of IFITM1 expression in HUVECs. To determine the antiviral activity of IFITM1 protein induced by H9N2 virus infection, HUVECs or BEAS-2Bs were infected with H9N2 virus at MOI of 5 and incubated for 1 h, then cells were transfected with IFITM1 specific siRNA or control siRNA for 36 h. abstract: BACKGROUND: Endothelial cells are believed to play an important role in response to virus infection. Our previous microarray analysis showed that H9N2 virus infection and inactivated viral particle inoculation increased the expression of interferon-inducible transmembrane protein 1 (IFITM1) in human umbilical vein endothelial cells (HUVECs). In present study, we deeply investigated the expression patterns of IFITM1 and IFITM1-mediated antiviral response induced by H9N2 virus infection and inactivated viral particle inoculation in HUVECs. Epithelial cells that are considered target cells of the influenza virus were selected as a reference control. METHODS: First, we quantified the expression levels of IFITM1 in HUVECs induced by H9N2 virus infection or viral particle inoculation using quantitative real-time PCR and western blot. Second, we observed whether hemagglutinin or neuraminidase affected IFITM1 expression in HUVECs. Finally, we investigated the effect of induced-IFITM1 on the antiviral state in HUVECs by siRNA and activation plasmid transfection. RESULTS: Both H9N2 virus infection and viral particle inoculation increased the expression of IFITM1 without elevating the levels of interferon-ɑ/β in HUVECs. HA or NA protein binding alone is not sufficient to increase the levels of IFITM1 and interferon-ɑ/β in HUVECs. IFITM1 induced by viral particle inoculation significantly decreased the virus titers in culture supernatants of HUVECs. CONCLUSIONS: Our results showed that inactivated viral particle inoculation increased the expression of IFITM1 at mRNA and protein levels. Moreover, the induction of IFITM1 expression mediated the antiviral state in HUVECs. url: https://www.ncbi.nlm.nih.gov/pubmed/29100522/ doi: 10.1186/s12985-017-0875-5 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: 4930.0 sentences: 240.0 pages: flesch: 45.0 cache: ./cache/cord-294568-12eyo13f.txt txt: ./txt/cord-294568-12eyo13f.txt summary: Influenza viruses are one of the main causative agents of ARIs worldwide; however, many other respiratory viruses for which insufficient epidemiological information is available can also cause ARIs. Studies performed at the international level have frequently identified human respiratory syncytial virus (HRSV), human parainfluenza virus (HPIV), influenza virus (flu), human mastadenovirus (HMdV), rhinovirus (RV), and enterovirus (EV) and less frequently identified human metapneumovirus (HMPV), primate bocaparvovirus (PBpV), and human coronavirus (HCoV) [12] . Therefore, the objective of this study was to determine the viral aetiology of these infections and to analyse the behaviour of non-influenza respiratory viruses in the Mexican population. The importance of the differential diagnosis of other respiratory viruses in samples with negative influenza results becomes apparent when we observe the prevalence of the three main viruses identified in this study as well as their associations with severe cases and deaths, especially in the child population. 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-305807-n3fs7533 author: Ferreira, T B title: Use of adenoviral vectors as veterinary vaccines date: 2005-10-18 words: 8466.0 sentences: 437.0 pages: flesch: 40.0 cache: ./cache/cord-305807-n3fs7533.txt txt: ./txt/cord-305807-n3fs7533.txt summary: 11 Then recognition that purified replication-defective Ads could be propagated on 293 cells without helper viruses paved the way toward intentional production of genetically modified Ads. 12 The popularity of Ad as a recombinant viral vector is largely due to the successful and safe immunization of millions of US military recruits in 1971 with enterically coated Ad4 and Ad7 as a prevention against acute respiratory disease (ARD) outbreaks. Gonin et al, 37 10 years ago, constructed a replicationdefective HAd5, containing the envelope protein ENV gene of FIV; however, despite the fact that an antibody response to pseudorabies virus in cats showed the potential of rHAd5 vectors to be used in this species, cats injected with 10 10.8 -10 11.8 of 50% tissue culture infectious dose (TCID 50 ) adjuvanted with montanide ISA 708 (water in nonmineral oil) or with montanide ISA 206 (double water/mineral oil/water) of this rAd did not develop detectable antibody response against ENV. abstract: Vaccines are the most effective and inexpensive prophylactic tool in veterinary medicine. Ideally, vaccines should induce a lifelong protective immunity against the target pathogen while not causing clinical or pathological signs of diseases in the vaccinated animals. However, such ideal vaccines are rare in the veterinary field. Many vaccines are either of limited effectiveness or have harmful side effects. In addition, there are still severe diseases with no effective vaccines. A very important criterion for an ideal vaccine in veterinary medicine is low cost; this is especially important in developing countries and even more so for poultry vaccination, where vaccines must sell for a few cents a dose. Traditional approaches include inactivated vaccines, attenuated live vaccines and subunit vaccines. Recently, genetic engineering has been applied to design new, improved vaccines. Adenovirus vectors are highly efficient for gene transfer in a broad spectrum of cell types and species. Moreover, adenoviruses often induce humoral, mucosal and cellular immune responses to antigens encoded by the inserted foreign genes. Thus, adenoviruses have become a vector of choice for delivery and expression of foreign proteins for vaccination. Consequently, the market requirements for adenovirus vaccines are increasing, creating a need for production methodologies of concentrated vectors with warranted purity and efficacy. This review summarizes recent developments and approaches of adenovirus production and purification as the application of these vectors, including successes and failures in clinical applications to date. url: https://www.ncbi.nlm.nih.gov/pubmed/16231058/ doi: 10.1038/sj.gt.3302618 id: cord-008454-8brxpotx author: Field, Anne M. title: Diagnostic Virology Using Electron Microscopic Techniques date: 2008-04-09 words: 18793.0 sentences: 981.0 pages: flesch: 50.0 cache: ./cache/cord-008454-8brxpotx.txt txt: ./txt/cord-008454-8brxpotx.txt summary: The morphology of negatively stained virus particles is sufficient for grouping purposes but it is necessary to use immune electron microscopy (IEM) to differentiate morphologically identical but antigenically distinct viruses. Virus particles are sometimes present in such large numbers in clinical specimens that they can be detected directly by electron microscopy and negative staining methods in particular can be used to provide a rapid diagnosis. Immune electron microscopy on sectioned material presents considerable technical difficulties and viral content of tissue homogenates may be too low for negative stain IEM so a virus seen in the tissue cannot always be sufficiently well identified for diagnostic purposes. Similarly, thin section studies on livers of marmosets infected with hepatitis A virus showed cytoplasmic picornavirus-like particles which could be extracted for use as antigen to detect antibodies by negative stain IEM (Provost et al., 197513) and by complement fixation (Provost et al., 1975a) . abstract: This chapter illustrates the development of the use of electron microscopy in viral diagnosis. The field covered is confined to medical viral diagnosis, but parallel developments have taken place in both veterinary and botanical fields and techniques derived from both these sources are also included where relevant. It is reported that the scanning transmission mode of operation, which can induce image contrast changes electronically, may enhance studies with unstained sections and perhaps facilitate thin section immune electron microscopy (IEM). The application of negative stain IEM has been particularly useful for the study of the antigenic nature of some of the newly discovered noncultivable viruses. Viral antigens can also be detected in thin sections of infected cells by IEM with suitably labeled specific antibodies. Confirmation of viral infection by electron microscopy on tissues originally processed for light microscopy is also frequently useful. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7131171/ doi: 10.1016/s0065-3527(08)60432-7 id: cord-298745-3rrlap70 author: Field, H. E. title: Henipaviruses: Emerging Paramyxoviruses Associated with Fruit Bats date: 2007 words: 8409.0 sentences: 419.0 pages: flesch: 46.0 cache: ./cache/cord-298745-3rrlap70.txt txt: ./txt/cord-298745-3rrlap70.txt summary: The apparent temporally clustered emergence of Hendra virus and Nipah virus in Australia and Malaysia, respectively, and the identification of species of fruit bats ( Pteropus spp., commonly known as flying foxes) as likely reservoir hosts, poses a number of important questions on the ecology of henipaviruses. Hendra virus was first described in 1994 in Australia when it caused an outbreak of severe acute respiratory disease with high mortality in thoroughbred horses in a training stable in the city of Brisbane (Murray et al. The negative surveillance findings (based on a highly sensitive serum neutralisation test) provided a high level of confidence that Hendra virus was not being sustained by in-contact domestic animal transmission, was not established in the Queensland horse population, and that the outbreak was unlikely to have originated from domestic species. giganteus , Nipah virus infection dynamics in the species, potential modes of transmission to humans, and identification of factors precipitating emergence. abstract: Two related, novel, zoonotic paramyxoviruses have been described recently. Hendra virus was first reported in horses and thence humans in Australia in 1994; Nipah virus was first reported in pigs and thence humans in Malaysia in 1998. Human cases of Nipah virus infection, apparently unassociated with infection in livestock, have been reported in Bangladesh since 2001. Species of fruit bats (genus Pteropus ) have been identified as natural hosts of both agents. Anthropogenic changes (habitat loss, hunting) that have impacted the population dynamics of Pteropus species across much of their range are hypothesised to have facilitated emergence. Current strategies for the management of henipaviruses are directed at minimising contact with the natural hosts, monitoring identified intermediate hosts, improving biosecurity on farms, and better disease recognition and diagnosis. Investigation of the emergence and ecology of henipaviruses warrants a broad, cross-disciplinary ecosystem health approach that recognises the critical linkages between human activity, ecological change, and livestock and human health. url: https://www.ncbi.nlm.nih.gov/pubmed/17848064/ doi: 10.1007/978-3-540-70962-6_7 id: cord-018393-5jlqn7wq author: Finke, Ernst-Jürgen title: Bioterrorismus, infektiologische Aspekte date: 2011-12-14 words: 25008.0 sentences: 3876.0 pages: flesch: 44.0 cache: ./cache/cord-018393-5jlqn7wq.txt txt: ./txt/cord-018393-5jlqn7wq.txt summary: Wenn sie sich jedoch verstärkt, kann man sie leicht erkennen, aber nur schwer heilen." (Nicolo Macchiavelli, 1449 -1527 Es ist wenig wahrscheinlich, dass biologische Anschläge rechtzeitig als solche erkannt werden, sofern kein automatisches Monitoring mit einem zuverlässigen Echtzeit-Nachweis von B-Agenzien existiert. B. Enzephalitiden viraler Genese sowie die Frühstadien von nvCJD und möglicherweise auch die Frühsymptomatik der Alzheimer-Krankheit; außerdem die Borreliose-Infektion (Neuroborreliose), bei der ein heterogenes Symptomenbild angenommen wird, das sich wenig mit der Ausprägung einer (BDV-spezifischen) Dysfunktion im limbischen System deckt. Unklar ist jedoch, wie häufig sich aus initial milden Infektionen der oberen Luftwege eine Bronchitis oder eine Pneumonie entwickelt und was die auslösenden Faktoren dafür sind. Beim Nachweis hoch positiver (häufig mit anderen Chlamydienspezies kreuzreagierender) Antikörper ist bei entsprechender klinischer Symptomatik die gezielte Erhebung der Anamnese hinsichtlich einer möglichen Exposition des Patienten gegenüber den natürlichen Wirten diagnostisch wegweisend. Aus Patientenseren wurden Cyclospora-spezifische Antikörper isoliert, jedoch sind die Vorgänge der Immunantwort auf Cyclospora noch nicht vollständig geklärt und ob sich eine Immunität entwickelt, ist fraglich. abstract: Infektionskrankheiten sind ständige Begleiter und gefürchtete Geißeln der Menschheit. Pest und Pocken versetzen als todbringende Seuchen die Menschen nicht erst seit dem Altertum in Schrecken (lat.: terror). Archaische Ängste und vor allem eine hohe Medienaufmerksamkeit sorgen immer wieder für Panik und irrationale Reaktionen: Im indischen Surat setzte im Herbst 1994 während eines ungewöhnlichen Pestausbruchs eine Massenflucht ein, nachdem die Presse den Verdacht auf Lungenpest und terroristische Anschläge verbreitet hatte. Über 800.000 Menschen, darunter auch zahlreiche Ärzte und Pflegekräfte, verließen daraufhin ihre Arbeitsplätze und Wohnorte. Allein die drastischen Flug- und Handelsbeschränkungen brachten Indien einen ökonomischen Schaden von etwa 3 Milliarden US $. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123253/ doi: 10.1007/978-3-642-17158-1_3 id: cord-313356-ninzeazy author: Fiorillo, Luca title: COVID-19 Surface Persistence: A Recent Data Summary and Its Importance for Medical and Dental Settings date: 2020-04-30 words: 3803.0 sentences: 248.0 pages: flesch: 53.0 cache: ./cache/cord-313356-ninzeazy.txt txt: ./txt/cord-313356-ninzeazy.txt summary: title: COVID-19 Surface Persistence: A Recent Data Summary and Its Importance for Medical and Dental Settings Recently, due to the coronavirus pandemic, many guidelines and anti-contagion strategies continue to report unclear information about the persistence of coronavirus disease 2019 (COVID-19) in the environment. The purpose of this article is to highlight all the sources currently present in the literature concerning the persistence of the different coronaviruses in the environment as well as in medical and dental settings. The aim of this article is to evaluate, through the analysis of the current literature, how long this virus can remain active on different surfaces. On average, the different coronaviruses persist in an infectious state on surfaces for several days, even up to nine. Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72314 Cases From the Chinese Center for Disease Control and Prevention abstract: Recently, due to the coronavirus pandemic, many guidelines and anti-contagion strategies continue to report unclear information about the persistence of coronavirus disease 2019 (COVID-19) in the environment. This certainly generates insecurity and fear in people, with an important psychological component that is not to be underestimated at this stage of the pandemic. The purpose of this article is to highlight all the sources currently present in the literature concerning the persistence of the different coronaviruses in the environment as well as in medical and dental settings. As this was a current study, there are still not many sources in the literature, and scientific strategies are moving towards therapy and diagnosis, rather than knowing the characteristics of the virus. Such an article could be an aid to summarize virus features and formulate new guidelines and anti-spread strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/32365891/ doi: 10.3390/ijerph17093132 id: cord-316682-4360s2yu author: Fischer, William A. title: Personal Protective Equipment: Protecting Health Care Providers in an Ebola Outbreak date: 2015-11-01 words: 5052.0 sentences: 241.0 pages: flesch: 47.0 cache: ./cache/cord-316682-4360s2yu.txt txt: ./txt/cord-316682-4360s2yu.txt summary: Given that the Ebola virus is primarily transmitted through direct contact of mucous membranes and cuts in the skin with infected patients and/or their bodily fluids, it is necessary to cover these potential portals of infection with PPE as part of a structured and instructed donning and doffing procedure. Personal protective equipment (PPE) plays a critical role in mitigating the risk of health care personnel (HCP) exposure to contaminated body fluids in the care of patients with communicable infectious diseases, including EVD. 5 In the PAPR PPE set HCP wore a Tyvek (DuPont, Wilmington, Delaware) suit, shoe covers, a surgical gown, and a large hood, whereas the enhanced respiratory and contact precautions system included only a surgical gown, indicating that a second covering significantly reduced exposure to contaminated body fluids and provided evidence for the use of aprons on top of gowns or coveralls in the care of Ebola-infected patients. abstract: Abstract Purpose The recent Ebola epidemic that devastated West Africa has infected and killed more health care providers than any other outbreak in the history of this virus. An improved understanding of pathogen transmission and the institution of strategies to protect health care providers against infection are needed in infectious disease outbreaks. This review connects what is known about Ebola virus transmission with personal protective equipment (PPE) designed to arrest nosocomial transmission. Methods Articles pertaining to filovirus transmission and PPE in filovirus outbreaks were reviewed and findings are presented. In addition, studies that evaluated PPE and donning and doffing strategies are presented. Findings PPE is one step in a comprehensive infection prevention and control strategy that is required to protect health care providers. Given that the Ebola virus is primarily transmitted through direct contact of mucous membranes and cuts in the skin with infected patients and/or their bodily fluids, it is necessary to cover these potential portals of infection with PPE as part of a structured and instructed donning and doffing procedure. Implications Current recommendations about PPE and the donning and doffing processes are based on anecdotal experience. However, the use of non-human viruses can help provide evidence-based guidelines on both PPE and donning and doffing processes. url: https://doi.org/10.1016/j.clinthera.2015.07.007 doi: 10.1016/j.clinthera.2015.07.007 id: cord-330852-n7j0c4ne author: Fischer, Wolfgang B. title: Mechanism of Function of Viral Channel Proteins and Implications for Drug Development date: 2012-02-23 words: 23680.0 sentences: 1178.0 pages: flesch: 53.0 cache: ./cache/cord-330852-n7j0c4ne.txt txt: ./txt/cord-330852-n7j0c4ne.txt summary: By adding data from functional studies like Cys scanning and electrophysiological measurements as mentioned as well as computational modeling data (Sansom and Kerr, 1993; Sansom et al., 1997; Zhong et al., 1998) , an approximate structural model of the tetrameric assembly of the TMDs of M2 with the histidines and tryptophans as important pore lining residues has been generated. Amiloride derivatives block ion channel activity and enhancement of virus-like particle budding caused by HIV-1 protein Vpu Backbone structure of the amantadine-blocked trans-membrane domain M2 protein channel from influenza A virus Molecular dynamics investigation of membrane-bound bundles of the channel-forming transmembrane domain of viral protein U from the Human Immunodeficiency Virus HIV-1 Influenza B virus BM2 protein has ion channel activity that conducts protons across membranes Three-dimensional structure of the channel-forming trans-membrane domain of virus protein "u" (Vpu) from HIV-1 abstract: Viral channel-forming proteins comprise a class of viral proteins which, similar to their host companions, are made to alter electrochemical or substrate gradients across lipid membranes. These proteins are active during all stages of the cellular life cycle of viruses. An increasing number of proteins are identified as channel proteins, but the precise role in the viral life cycle is yet unknown for the majority of them. This review presents an overview about these proteins with an emphasis on those with available structural information. A concept is introduced which aligns the transmembrane domains of viral channel proteins with those of host channels and toxins to give insights into the mechanism of function of the viral proteins from potential sequence identities. A summary of to date investigations on drugs targeting these proteins is given and discussed in respect of their mode of action in vivo. url: https://doi.org/10.1016/b978-0-12-394305-7.00006-9 doi: 10.1016/b978-0-12-394305-7.00006-9 id: cord-290509-56pfww0l author: Fleet, Graham H title: Foodborne viral illness - status in Australia date: 2000-07-25 words: 4915.0 sentences: 281.0 pages: flesch: 50.0 cache: ./cache/cord-290509-56pfww0l.txt txt: ./txt/cord-290509-56pfww0l.txt summary: Norwalk-like virus contamination of oysters and orange juice, and hepatitis A virus contamination of oysters have been responsible for large outbreaks of foodborne viral disease in Australia. However, 1973, and were found in the faeces and duodenal genuine interest in food or waterborne viral diseases mucosal epithelial cells of children who had been did not develop in Australia until 1978 when oysters hospitalised with acute, non-bacterial gastroenteritis were found to be responsible for a very large (Bishop et al., 1974) . Oysters harvested Victoria, by examining for the virus in faecal specifrom an estuary in northern NSW and supposedly mens that had been submitted for suspected viral depurated were suspected of causing an outbreak of gastroenteritis over the period 1980-1996. A recent report has suggested that Norwalk virus was not detected in the juice but the outbreak and Norwalk-like viruses probably account for the terminated when the juice was withdrawn from the greatest incidence of foodborne disease in Australia market. abstract: Norwalk-like virus contamination of oysters and orange juice, and hepatitis A virus contamination of oysters have been responsible for large outbreaks of foodborne viral disease in Australia. Rotavirus, adenovirus, astrovirus, parvovirus and other enteroviruses also contribute to the incidence of gastroenteritis in this country but the role of foods and waters in transmitting these viruses is unclear. Protocols for the investigation, surveillance and reporting of foodborne viral illness require further development to enable a more accurate description of the problem. Few laboratories have the capability to analyse foods for viruses and specific training in this technology is needed. Management of food safety in Australia largely relies on the implementation of HACCP principles, but these need to be adapted to address the specific risks from viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/10946844/ doi: 10.1016/s0168-1605(00)00249-x id: cord-103135-nly9vojr author: Fletcher, Nicola F. title: A novel antiviral formulation inhibits a range of enveloped viruses date: 2020-03-30 words: 6468.0 sentences: 329.0 pages: flesch: 47.0 cache: ./cache/cord-103135-nly9vojr.txt txt: ./txt/cord-103135-nly9vojr.txt summary: ViroSAL had no effect on the infectivity of a non-enveloped virus, norovirus, which is in agreement with previous studies demonstrating that free fatty acids are ineffective against nonenveloped viruses (Thormar et al., 1987 , Kohn et al., 1980 . In this study, ViroSAL at the indicated concentrations was mixed with an equal volume of viral inoculum (MeV:original TCID50 = 4.48 7 /mL, HSV-1: 100 PFU/mL, EBV: MOI=10, Zika: MOI=10, Orf: 4 PFU/mL) or pseudoviruses bearing VSV, Ebola, Lassa or SARS-CoV-1 envelope glycoproteins, and incubated at room temperature for 2 minutes. Virus/ViroSAL or control treated virus was inoculated onto appropriate target cells and incubated for 48h at 37°C, then fixed and infection enumerated, or, for pseudovirus assays, lysed and luciferase activity quantified as previously described (Fletcher et al., 2015) . Milk-based free fatty acids, as well as fatty acid emulsions, have been shown to inhibit infection of Vero cells with VSV and HSV-1, with no antiviral effect on poliovirus, a non-enveloped virus (Thormar et al., 1987) . abstract: Some free fatty acids derived from milk and vegetable oils are known to have potent antiviral and antibacterial properties. However, therapeutic applications of short to medium chain fatty acids are limited by physical characteristics such as immiscibility in aqueous solutions. We evaluated a novel proprietary formulation based on an emulsion of short chain caprylic acid, ViroSAL, for its ability to inhibit a range of viral infections in vitro and in vivo. In vitro, ViroSAL inhibited the enveloped viruses Epstein-Barr, measles, herpes simplex, Zika and orf parapoxvirus, together with Ebola, Lassa, vesicular stomatitis and SARS-CoV-1 pseudoviruses, in a concentration- and time-dependent manner. Evaluation of the components of ViroSAL revealed that caprylic acid was the main antiviral component; however, the ViroSAL formulation significantly inhibited viral entry compared with caprylic acid alone. In vivo, ViroSAL significantly inhibited Zika and Semliki Forest Virus replication in mice following the inoculation of these viruses into mosquito bite sites. In agreement with studies investigating other free fatty acids, ViroSAL had no effect on norovirus, a non-enveloped virus, indicating that its mechanism of action may be via surfactant disruption of the viral envelope. We have identified a novel antiviral formulation that is of great interest for prevention and/or treatment of a broad range of enveloped viruses. url: https://doi.org/10.1101/2020.03.29.009464 doi: 10.1101/2020.03.29.009464 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-017758-zfudssm9 author: Fong, I. W. title: Emergence of New Tickborne Infections date: 2017-02-08 words: 8054.0 sentences: 353.0 pages: flesch: 45.0 cache: ./cache/cord-017758-zfudssm9.txt txt: ./txt/cord-017758-zfudssm9.txt summary: These include new phleboviruses of the Bunyaviridae family, exemplified by severe fever with thrombocytopenia syndrome virus [SFTSV] recognized in China in 2010, and the Heartland virus, a closely related but distinct virus, presenting with similar clinical features and discovered in Missouri in 2012. Other newly recognized tickborne infections include a novel spirochete of the relapsing fever group, Borrelia miyamotoi, first reported to cause human infection in Russia in 2011 and subsequently discovered to cause clinical disease in the Netherlands, Japan, and the United States, with transmission by the black-legged deer tick Ixodes scapularis. Transmission of SFTSV is considered mainly from tick bites, but there is also evidence from multiple reports that the virus can be transmitted from human to human by direct contact with blood of infected patients [67] [68] [69] [70] [71] . Severe fever with thrombocytopenia syndrome virus in ticks collected from humans, South Korea abstract: Several tickborne infectious diseases such as Lyme borreliosis, ehrlichiosis, anaplasmosis, babesiosis, and others have been expanding to new endemic regions in the world for over a decade. Moreover, new pathogens transmitted by ticks have recently been recognized in animals and humans from diverse regions of the globe, widely separated in distance. These include new phleboviruses of the Bunyaviridae family, exemplified by severe fever with thrombocytopenia syndrome virus [SFTSV] recognized in China in 2010, and the Heartland virus, a closely related but distinct virus, presenting with similar clinical features and discovered in Missouri in 2012. Other newly recognized tickborne infections include a novel spirochete of the relapsing fever group, Borrelia miyamotoi, first reported to cause human infection in Russia in 2011 and subsequently discovered to cause clinical disease in the Netherlands, Japan, and the United States, with transmission by the black-legged deer tick Ixodes scapularis. In Europe a new tickborne disease, neoehrlichiosis caused by Candidatus neoehrlichia mikurensis belonging to the Anaplasmataceae family, has been described recently. Furthermore, new tickborne rickettsial infections continue to be recognized in Europe such as tickborne lymphadenopathy identified in 1997 and caused by Rickettsia slovaca. Novel tickborne infectious diseases will continue to emerge worldwide for the foreseeable future and be a challenge to the health of human populations. Innovative methods of prevention for a broad variety of tick-transmitted diseases are needed, and one approach is to develop a universal tick vaccine that can be given to animal hosts or humans. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122411/ doi: 10.1007/978-3-319-50890-0_5 id: cord-000113-d0eur1hq author: Fooks, Anthony R. title: Emerging Technologies for the Detection of Rabies Virus: Challenges and Hopes in the 21st Century date: 2009-09-29 words: 6937.0 sentences: 319.0 pages: flesch: 38.0 cache: ./cache/cord-000113-d0eur1hq.txt txt: ./txt/cord-000113-d0eur1hq.txt summary: The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. Another method for the detection of rabies virus antigen from postmortem samples is a recently developed rapid immunodiagwww.plosntds.org nostic test (RIDT) based on the principles of immunochromatography [13] . Development of RT-LAMP assays for use in diagnosis and surveillance is challenged by the considerable sequence variation observed within the rabies virus genome [44] that can frustrate specific primer design. Currently, high-throughput rabies virus molecular detection methods augment standard diagnostic tests or are in the process of development and refinement for use alone. abstract: The diagnosis of rabies is routinely based on clinical and epidemiological information, especially when exposures are reported in rabies-endemic countries. Diagnostic tests using conventional assays that appear to be negative, even when undertaken late in the disease and despite the clinical diagnosis, have a tendency, at times, to be unreliable. These tests are rarely optimal and entirely dependent on the nature and quality of the sample supplied. In the course of the past three decades, the application of molecular biology has aided in the development of tests that result in a more rapid detection of rabies virus. These tests enable viral strain identification from clinical specimens. Currently, there are a number of molecular tests that can be used to complement conventional tests in rabies diagnosis. Indeed the challenges in the 21st century for the development of rabies diagnostics are not of a technical nature; these tests are available now. The challenges in the 21st century for diagnostic test developers are two-fold: firstly, to achieve internationally accepted validation of a test that will then lead to its acceptance by organisations globally. Secondly, the areas of the world where such tests are needed are mainly in developing regions where financial and logistical barriers prevent their implementation. Although developing countries with a poor healthcare infrastructure recognise that molecular-based diagnostic assays will be unaffordable for routine use, the cost/benefit ratio should still be measured. Adoption of rapid and affordable rabies diagnostic tests for use in developing countries highlights the importance of sharing and transferring technology through laboratory twinning between the developed and the developing countries. Importantly for developing countries, the benefit of molecular methods as tools is the capability for a differential diagnosis of human diseases that present with similar clinical symptoms. Antemortem testing for human rabies is now possible using molecular techniques. These barriers are not insurmountable and it is our expectation that if such tests are accepted and implemented where they are most needed, they will provide substantial improvements for rabies diagnosis and surveillance. The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745658/ doi: 10.1371/journal.pntd.0000530 id: cord-252974-pwx27kdi author: Fornek, Jamie L. title: Use of Functional Genomics to Understand Influenza–Host Interactions date: 2007-08-31 words: 6755.0 sentences: 331.0 pages: flesch: 42.0 cache: ./cache/cord-252974-pwx27kdi.txt txt: ./txt/cord-252974-pwx27kdi.txt summary: We will explore increasingly complex models for studying influenza-host interactions using functional genomics, including cell culture systems, murine models of infection, and nonhuman primates (Fig. 1) . These studies, led by John Kash, revealed that genes related to various immune cells, notably NK cells, neutrophils, macrophages, and T helper 1 (Th1) cells, were upregulated in mice infected with the fully reconstructed 1918 virus as early as 1 day postinfection. To expand upon the above study, we have also employed functional genomics to assess the effect of influenza infection on the early innate immune response in the lungs of pigtailed macaques, how genes related to this response were regulated over time, and whether gene expression signatures of infection could also be detected in the blood. Global host immune response: Pathogenesis and transcriptional profiling of type A influenza viruses expressing the hemagglutinin and neuraminidase genes from the 1918 pandemic virus abstract: Infection with influenza typically results in mild‐to‐moderate illness in healthy individuals; however, it is responsible for 30,000–40,000 deaths each year in the United States. In extreme cases, such as the influenza pandemic of 1918, tens of millions of people have died from the infection. To prepare for future influenza outbreaks, it is necessary to understand how the virus interacts with the host and to determine what makes certain strains of influenza highly pathogenic. Functional genomics provides a unique approach to this effort by allowing researchers to examine the effect of influenza infection on global host mRNA levels. Researchers are making increasing use of this approach to study virus–host interactions using a variety of model systems. For example, data obtained using microarray technology, in combination with mouse and macaque infection models, is providing exciting new insights into the pathogenicity of the 1918 virus. These studies suggest that the lethality associated with this virus is in part due to an aberrant and unchecked immune response. Progress is also being made toward using functional genomics in the diagnosis and prognosis of acute lung infections and in the development of more effective influenza vaccines and antivirals. url: https://www.ncbi.nlm.nih.gov/pubmed/17765704/ doi: 10.1016/s0065-3527(07)70003-9 id: cord-001528-33f94doo author: Fouchier, Ron A. M. title: Studies on Influenza Virus Transmission between Ferrets: the Public Health Risks Revisited date: 2015-01-23 words: 3522.0 sentences: 141.0 pages: flesch: 40.0 cache: ./cache/cord-001528-33f94doo.txt txt: ./txt/cord-001528-33f94doo.txt summary: Initial calculations of the potential risks associated with research on influenza virus transmission via respiratory droplets or aerosols between ferrets (1-4) used reports on select agent theft, loss, and release collected by the U.S. Centers for Disease Control and Prevention (CDC) from 2004 to 2010 (7) to calculate the probability of occurrence of LAIs. Although these reports have limitations (1, 4, 7) , they provide the most recent account of LAIs in the United States and probably reflect the current state of the art in biosafety and biosecurity practices better than older studies on laboratory incidents (8, 9) , e.g., as a consequence of the implementation of the U.S. select agent program and best practices developed in biosafety and biosecurity in general over the last decades. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4323420/ doi: 10.1128/mbio.02560-14 id: cord-291294-w5ecsht4 author: Foulongne, V. title: Le bocavirus humain (HBoV) date: 2008-03-17 words: 2784.0 sentences: 259.0 pages: flesch: 62.0 cache: ./cache/cord-291294-w5ecsht4.txt txt: ./txt/cord-291294-w5ecsht4.txt summary: Dans le domaine des infections respiratoires, le recourt extensif à la biologie moléculaire a également apporté des progrès très significatifs, avec les découvertes respectives depuis 2001 du metapneumovirus humain (HMPV) [3] , du SARS-Co [4, 5] , des nouveaux coronavirus humains HCoV-NL63 et HCoV-HKU1 [6] [7] [8] et du bocavirus humain (HBoV) [9] . Des observations récentes en microscopie électronique, conduites sur des prélèvements respiratoires dans lesquels l''ADN du virus avait pu être détecté, ont confirmé que le bocavirus humain présentait toutes les caractéristiques structurales des Parvoviridae. Cette prévalence place le HBoV selon les études et les régions au deuxième ou troisième rang des agents viraux détectés dans ces prélèvements, derrière le virus respiratoire syncytial mais à une fréquence comparable avec les rhinovirus ou le HMPV. Enfin, certaines études décrivent une phase virémique chez quelques patients, notamment en phase aiguë de l''infection, [35] suggérant que le HBoV puisse induire des infection systémiques comme cela est d''ailleurs observé avec les autres parvovirus [35, 36] . abstract: The human bocavirus (HBoV) has been recently identified by means of molecular screening techniques in respiratory tract secretions from children with acute respiratory tract disease. This virus, which belongs to the Parvoviridae family, has been detected worldwide with a 5 to 10% prevalence among children with upper or lower respiratory tract infections, essentially during the winter period. A seroepidemiological study has shown that almost all the children have antibodies to HBoV by the age of five years, and HBoV infection seems to be rare in adults. HBoV is often detected in association with other respiratory viruses. This virus has also been detected in stools, but its role in gastroenteritis has not been yet established. Virological diagnostic of HBoV infection is based on the detection of viral DNA by PCR. Viral load determination by viral DNA quantitation in respiratory tract secretions could be a tool to differentiate between symptomatic HBoV infection and virus carriage. url: https://doi.org/10.1016/j.patbio.2008.01.001 doi: 10.1016/j.patbio.2008.01.001 id: cord-355685-wgad0eoh author: Francesconi, Valeria title: Synthesis and Biological Evaluation of Novel (thio)semicarbazone-Based Benzimidazoles as Antiviral Agents against Human Respiratory Viruses date: 2020-03-25 words: 6010.0 sentences: 322.0 pages: flesch: 45.0 cache: ./cache/cord-355685-wgad0eoh.txt txt: ./txt/cord-355685-wgad0eoh.txt summary: Compounds 6, 8, 16 and 17, bearing the 5-(thio)semicarbazone and 5-hydrazone functionalities in combination with the 2-benzyl ring on the benzimidazole core structure, acted as dual inhibitors of influenza A virus and human coronavirus. For respiratory syncytial virus (RSV), activity is limited to the 5-thiosemicarbazone (25) and 5-hydrazone (22) compounds carrying the 2-[(benzotriazol-1/2-yl)methyl]benzimidazole scaffold. The herein-investigated benzimidazole-based derivatives may represent valuable hit compounds, deserving subsequent structural improvements towards more efficient antiviral agents for the treatment of pathologies caused by these human respiratory viruses. For RSV, activity is restricted to the 5-(thio)semicarbazone (25) and hydrazone (22) compounds carrying the 2-[(benzotriazol-1/2-yl)methyl]benzimidazole scaffold, in line with the previously synthesized analogues (see above), which show comparable potency in the low micromolar range. In summary, this study reports the synthesis of a series of (thio)semicarbazone-and hydrazone-containing benzimidazoles for the development of novel antiviral agents which have shown the ability to inhibit the replication of three human respiratory viruses. abstract: Respiratory RNA viruses are responsible for recurrent acute respiratory illnesses that still represent a major medical need. Previously we developed a large variety of benzimidazole derivatives able to inhibit these viruses. Herein, two series of (thio)semicarbazone- and hydrazone-based benzimidazoles have been explored, by derivatizing 5-acetyl benzimidazoles previously reported by us, thereby evaluating the influence of the modification on the antiviral activity. Compounds 6, 8, 16 and 17, bearing the 5-(thio)semicarbazone and 5-hydrazone functionalities in combination with the 2-benzyl ring on the benzimidazole core structure, acted as dual inhibitors of influenza A virus and human coronavirus. For respiratory syncytial virus (RSV), activity is limited to the 5-thiosemicarbazone (25) and 5-hydrazone (22) compounds carrying the 2-[(benzotriazol-1/2-yl)methyl]benzimidazole scaffold. These molecules proved to be the most effective antiviral agents, able to reach the potency profile of the licensed drug ribavirin. The molecular docking analysis explained the SAR of these compounds around their binding mode to the target RSV F protein, revealing the key contacts for further assessment. The herein-investigated benzimidazole-based derivatives may represent valuable hit compounds, deserving subsequent structural improvements towards more efficient antiviral agents for the treatment of pathologies caused by these human respiratory viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32218301/ doi: 10.3390/molecules25071487 id: cord-300189-gsp1dozg author: Franci, Gianluigi title: Infectivity inhibition by overlapping synthetic peptides derived from the gH/gL heterodimer of herpes simplex virus type 1 date: 2017-02-14 words: 6345.0 sentences: 322.0 pages: flesch: 50.0 cache: ./cache/cord-300189-gsp1dozg.txt txt: ./txt/cord-300189-gsp1dozg.txt summary: To date, few peptide molecules outside the well-known inhibitory regions of Class 1 viral fusion proteins, the heptad repeats, should be as fusion; therefore, a brute force approach to the identification of peptide entry inhibitors may help in the dissection of HSV-1 glycoproteins domains. Previous works using a physico-chemical algorithm, the Wimley-White Interfacial Hydrophobicity Scale (WWIHS), in combination with other structural data allowed us to predict regions in gH potentially involved in membrane interactions during the entry and fusion process, and some of them were found to possess HSV antiviral activity in dose-dependent inhibition assays [66] . [76] used a phage display methodology to identify a peptide (named P1) to inhibit West Nile virus (WNV) infectivity, possibly by binding to the envelope glycoprotein (E protein) necessary for membrane fusion. Substitution of herpes simplex virus 1 entry glycoproteins with those of saimiriine herpesvirus 1 reveals a gD-gH/gL functional interaction and a region within the gD profusion domain that is critical for fusion abstract: Herpes simplex virus (HSV) is a human pathogen that infects epithelial cells. The cutaneous lesions, caused by the virus, spread to the nervous system creating several complications. Fusion of host membranes with the viral envelope is mandatory and mediated by a group of glycoproteins conserved in all Herpesviridae subfamilies, such as the glycoproteins B (gB), H (gH), L (gL) and D (gD). We investigated the inhibitory activity mediated by synthetic overlapping peptides spanning the entire ectodomains of gH and gL glycoproteins. We have performed a brute analysis of the complete gH/gL heterodimer in order to explore the inhibitory activity of peptides modelled on these glycoproteins against HSV‐1 infection. Twenty‐four of the gH peptides at a concentration of 150 μM reached the 50% of inhibition cut‐off. Interestingly, they are mainly located in the gH carboxy‐terminal domain. None of the gL peptides had a clear inhibiting effect. No peptide toxicity was observed by lactate dehydrogenase assay at the concentrations used in our experimental conditions. HSV‐1 therapy is based on acyclovir treatment, but some resistant strains are emerging. In this scenario, innovative approaches for HSV‐1 treatment are necessary. Our data support the direct involvement of the described domains in the process of virus penetration; therefore, these results are of relevance to the potential development of novel therapeutic compounds to prevent HSV‐1 infections. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd. url: https://doi.org/10.1002/psc.2979 doi: 10.1002/psc.2979 id: cord-266136-81sx505i author: Freymuth, F. title: Les virus des bronchiolites aiguës date: 2010-06-16 words: 3458.0 sentences: 336.0 pages: flesch: 66.0 cache: ./cache/cord-266136-81sx505i.txt txt: ./txt/cord-266136-81sx505i.txt summary: In Normandy (France), human respiratory syncytial virus (hRSV) was detected in 64.1% of acute bronchiolitis in hospitalized children, rhinovirus in 26.8%, human metapneumovirus (hMPV) in 7.6%, and parainfluenza virus (PIV) in 3.4%. Une étude américaine a estimé à 18 % la fréquence des infections à hRSV chez les enfants de moins de 5 ans atteints d''une infection respiratoire aiguë ; 20 % de ces infections conduisant à une hospitalisation, 18 % à une consultation dans un service d''urgence pédiatrique et 15 % à la visite d''un médecin [7] . Une étude caennaise a été menée entre septembre 1998 et octobre 2000 chez 211 enfants hospitalisés pour une infection respiratoire aiguë dans laquelle seul un rhinovirus était détecté dans les voies respiratoires, alors que la recherche des virus influenza, PIV, hRSV, adénovirus était négative [31] . abstract: In Normandy (France), human respiratory syncytial virus (hRSV) was detected in 64.1% of acute bronchiolitis in hospitalized children, rhinovirus in 26.8%, human metapneumovirus (hMPV) in 7.6%, and parainfluenza virus (PIV) in 3.4%. The viruses causing acute bronchiolitis in the community were hRSV (42%), rhinovirus (19.5%), coronavirus (8%), PIV (3.5%), and hMPV (2.5%). In 53.7% of the cases, hRSV infected infants (86.9%), 53.7% being less than 6 months of age. Of the hRSV cases, 48.2% were detected in November and December and 44.5% in January and February. The hRSV epidemic started the 1st or 2nd week of October but it varied from one year to another and from one region to another. hRSV acute bronchiolitis increased from 261 cases in epidemics from 1999–2003 to 341 cases from 2004–2009. Rhinoviruses gave acute bronchiolitis in 38.4% of cases. A rate of 54.6% of viruses was detected in September and October and 38.5% in March and April. A total of 34.2% of infected infants were under 6 months of age, 37.8% between 6 months and 2 years, and 19.5% were between 2 and 5 years old. hMPV epidemics coincided with hRSV epidemics, but they accounted for one-sixth the number of cases. HMPV infected infants (74%) who were older than those infected with hRSV, and the diagnosis was bronchiolitis (59%) and pneumonia (17%). PIV infections (about 100 cases per year) included PIV3 (62.7%), PIV1 (25.3%), and PIV2 (7.3%). PIV1 infections occurred every 2 years in the fall. PIV3 infections were observed every year during the fall and winter, with peaks of infections in the spring in the years without PIV1. There were acute cases of bronchiolitis in 29.8% of PIV3 infections and 18.3% in PIV1 infections. url: https://www.ncbi.nlm.nih.gov/pubmed/20558050/ doi: 10.1016/j.arcped.2010.05.006 id: cord-354068-4qlk6y7h author: Friedrich, Brian M. title: Potential Vaccines and Post-Exposure Treatments for Filovirus Infections date: 2012-09-21 words: 10605.0 sentences: 540.0 pages: flesch: 44.0 cache: ./cache/cord-354068-4qlk6y7h.txt txt: ./txt/cord-354068-4qlk6y7h.txt summary: Due to the difficulties in evaluating wild-type filovirus infection in small animals and the generally high level of immune protection correlates derived from non-human primate (NHP) models of infection, therapeutics and vaccines are ultimately evaluated in NHP species for efficacy against filovirus. In their study, a heterologous prime/boost strategy with recombinant adenovirus serotypes 26 and 35 carrying GP (Z) and GP (S/G) demonstrated complete protection among NHPs. Each of these vectors was capable of stimulating humoral and cell-mediated immune responses in the context of NHPs pre-vaccinated with rAd5 as evidenced by antibody titers reaching an order of magnitude above those achieved in rAd5 vaccinated subjects (1:32,000 compared to 1:6,800), and CD8 + intracellular cytokine staining was 4.7-fold greater among heterologous prime/boosted subjects (0.41% compared to 0.09%) [59] . This GP-Fc fusion protein induced both cell-mediated and humoral immune responses, and mice vaccinated with ZEBOVGP-Fc demonstrated 90% protection against a lethal EBOV challenge. abstract: Viruses of the family Filoviridae represent significant health risks as emerging infectious diseases as well as potentially engineered biothreats. While many research efforts have been published offering possibilities toward the mitigation of filoviral infection, there remain no sanctioned therapeutic or vaccine strategies. Current progress in the development of filovirus therapeutics and vaccines is outlined herein with respect to their current level of testing, evaluation, and proximity toward human implementation, specifically with regard to human clinical trials, nonhuman primate studies, small animal studies, and in vitro development. Contemporary methods of supportive care and previous treatment approaches for human patients are also discussed. url: https://doi.org/10.3390/v4091619 doi: 10.3390/v4091619 id: cord-353869-l53ms3q8 author: Friesen, Robert H. E. title: New Class of Monoclonal Antibodies against Severe Influenza: Prophylactic and Therapeutic Efficacy in Ferrets date: 2010-02-08 words: 4680.0 sentences: 202.0 pages: flesch: 44.0 cache: ./cache/cord-353869-l53ms3q8.txt txt: ./txt/cord-353869-l53ms3q8.txt summary: METHODOLOGY/PRINCIPAL FINDINGS: We evaluated the prophylactic and therapeutic efficacy of the human monoclonal antibody CR6261 against lethal challenge with the highly pathogenic avian H5N1 virus in ferrets, the optimal model of human influenza infection. CONCLUSIONS/SIGNIFICANCE: These data demonstrate the prophylactic and therapeutic efficacy of this new class of human monoclonal antibodies in a highly stringent and clinically relevant animal model of influenza and justify clinical development of this approach as intervention for both seasonal and pandemic influenza. Mean decline in body weight at the end of the experiment was 6.2% in the group of ferrets that received CR6261 4 hours after challenge ( Figure 2B) , which was significantly less (p = 0.025) than the 10.1% observed in control animals. These findings were in accordance with the observation that the mean lung weights of ferrets treated with CR6261 at 4 hours post challenge were lower compared to the control group (5.7 g versus 14.9 g, p,0.001; Figure 2F ). abstract: BACKGROUND: The urgent medical need for innovative approaches to control influenza is emphasized by the widespread resistance of circulating subtype H1N1 viruses to the leading antiviral drug oseltamivir, the pandemic threat posed by the occurrences of human infections with highly pathogenic avian H5N1 viruses, and indeed the evolving swine-origin H1N1 influenza pandemic. A recently discovered class of human monoclonal antibodies with the ability to neutralize a broad spectrum of influenza viruses (including H1, H2, H5, H6 and H9 subtypes) has the potential to prevent and treat influenza in humans. Here we report the latest efficacy data for a representative antibody of this novel class. METHODOLOGY/PRINCIPAL FINDINGS: We evaluated the prophylactic and therapeutic efficacy of the human monoclonal antibody CR6261 against lethal challenge with the highly pathogenic avian H5N1 virus in ferrets, the optimal model of human influenza infection. Survival rates, clinically relevant disease signs such as changes in body weight and temperature, virus replication in lungs and upper respiratory tract, as well as macro- and microscopic pathology were investigated. Prophylactic administration of 30 and 10 mg/kg CR6261 prior to viral challenge completely prevented mortality, weight loss and reduced the amount of infectious virus in the lungs by more than 99.9%, abolished shedding of virus in pharyngeal secretions and largely prevented H5N1-induced lung pathology. When administered therapeutically 1 day after challenge, 30 mg/kg CR6261 prevented death in all animals and blunted disease, as evidenced by decreased weight loss and temperature rise, reduced lung viral loads and shedding, and less lung damage. CONCLUSIONS/SIGNIFICANCE: These data demonstrate the prophylactic and therapeutic efficacy of this new class of human monoclonal antibodies in a highly stringent and clinically relevant animal model of influenza and justify clinical development of this approach as intervention for both seasonal and pandemic influenza. url: https://www.ncbi.nlm.nih.gov/pubmed/20161706/ doi: 10.1371/journal.pone.0009106 id: cord-001974-wjf3c7a7 author: Friis-Nielsen, Jens title: Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers date: 2016-02-19 words: 5773.0 sentences: 348.0 pages: flesch: 48.0 cache: ./cache/cord-001974-wjf3c7a7.txt txt: ./txt/cord-001974-wjf3c7a7.txt summary: Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. The datasets went through a sequential pipeline with modules (in order) of preprocessing, computational subtraction of host sequences, low-complexity sequence removal, sequence assembly, clustering, association to metadata features, and taxonomical annotation. Associations from the shortest mode tended to have higher dispersion in the range of ORs. Furthermore, one block of clustering results using global alignment mode, alignment length based on the shortest contig, and a minimum sequence identity of 90% (c09ˆaSyG1), had an overall high range of ORs as well as the highest minimum values. The clusters are significantly associated with lowest p-values to biological features and the species annotations are described by HMP. abstract: Virus discovery from high throughput sequencing data often follows a bottom-up approach where taxonomic annotation takes place prior to association to disease. Albeit effective in some cases, the approach fails to detect novel pathogens and remote variants not present in reference databases. We have developed a species independent pipeline that utilises sequence clustering for the identification of nucleotide sequences that co-occur across multiple sequencing data instances. We applied the workflow to 686 sequencing libraries from 252 cancer samples of different cancer and tissue types, 32 non-template controls, and 24 test samples. Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. We provide examples of identified inhabitants of the healthy tissue flora as well as experimental contaminants. Unmapped sequences that co-occur with high statistical significance potentially represent the unknown sequence space where novel pathogens can be identified. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776208/ doi: 10.3390/v8020053 id: cord-003523-byxuruk1 author: Fritsch, Annemarie title: Influenza C virus in pre-school children with respiratory infections: retrospective analysis of data from the national influenza surveillance system in Germany, 2012 to 2014 date: 2019-03-07 words: 4287.0 sentences: 211.0 pages: flesch: 48.0 cache: ./cache/cord-003523-byxuruk1.txt txt: ./txt/cord-003523-byxuruk1.txt summary: title: Influenza C virus in pre-school children with respiratory infections: retrospective analysis of data from the national influenza surveillance system in Germany, 2012 to 2014 METHODS: A total of 1,588 samples from 0 to 4 year-old children presenting as outpatients with influenza-like illness (ILI) or acute respiratory infection were analysed retrospectively. In Germany, no surveillance data and no sequence information on circulating influenza C viruses have ever been reported. We furthermore sequenced the haemagglutinin esterase (HE) gene from influenza C-positive samples to phylogenetically characterise the detected viruses. To extend the basis for the co-infection data, all influenza C-positive samples were additionally tested for human parainfluenza viruses types 1-4 and coronaviruses OC43, NL63, HKU1 and 229E. Thereby, the low detection rates in the general population were confirmed, but a higher clinical impact for paediatric patients was indicated, as influenza C was described to also cause lower respiratory tract disease [6] [7] [8] [9] [10] . abstract: INTRODUCTION: Recent data on influenza C virus indicate a possible higher clinical impact in specified patient populations than previously thought. AIM: We aimed to investigate influenza C virus circulation in Germany. METHODS: A total of 1,588 samples from 0 to 4 year-old children presenting as outpatients with influenza-like illness (ILI) or acute respiratory infection were analysed retrospectively. The samples represented a subset of all samples from the German national surveillance system for influenza in this age group in 2012–14. The presence of influenza C virus was investigated by real-time PCR. For positive samples, information on symptoms as well as other respiratory virus co-infections was considered. Retrieved influenza C viral sequences were phylogenetically characterised. RESULTS: Influenza C viral RNA was detected in 20 (1.3% of) samples, including 16 during the 2012/13 season. The majority (18/20) of influenza C-positive patients had ILI according to the European Union definition, one patient had pneumonia. Viruses belonged to the C/Sao Paulo and C/Kanagawa lineages. Most (11/20) samples were co-infected with other respiratory viruses. CONCLUSION: Our data are the first on influenza C virus circulation in Germany and notably from a European national surveillance system. The low detection frequency and the identified virus variants confirm earlier observations outside a surveillance system. More virus detections during the 2012/13 season indicate a variable circulation intensity in the different years studied. Influenza C virus can be considered for ILI patients. Future studies addressing its clinical impact, especially in patients with severe disease are needed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6415498/ doi: 10.2807/1560-7917.es.2019.24.10.1800174 id: cord-004761-cgby8bhz author: Fuchs, N. title: Virus isolation and titration at 33‡ and 37‡ C date: 1975 words: 1157.0 sentences: 81.0 pages: flesch: 52.0 cache: ./cache/cord-004761-cgby8bhz.txt txt: ./txt/cord-004761-cgby8bhz.txt summary: Various prototype viruses and original specimens were comparatively titrated in cell cultures at 33‡ and 37‡ C. g. Lennette and Schmidt, 1969) recommend an incubation temperature of 33 ~ rather than 37~ for the isolation of viruses from the human respiratory tract. Original specimens (stool suspensions, throat and conjunetival swabs, vesicular fluid) containing the following virus types were inoculated: adenovirus I, 2, 3, 5, 7, 8, herpesvirus hominis, poliovirus 1 and 3, coxsackievirus A9 and B5, eehovirus types 6, 9, 11, 18 and 30. To our knowledge influenza viruses are the only ones of the viruses occurring in the human respiratory tract, in which a comparative testing of original specimens (in embryonated eggs) has demonstrated the superiority of the lower temperature (Stern and Tippett, 1963) . Both temperatures appear satisfactory for vaccinia virus, herpesvirus, enteroviruses and parainfluenza viruses. abstract: Various prototype viruses and original specimens were comparatively titrated in cell cultures at 33‡ and 37‡ C. Higher titers at 37‡ were consistently obtained with adenoviruses; for other viruses (enteroviruses, herpesvirus hominis, vaccinia virus, parainfluenza viruses) the titers were mostly identical at either temperature. Original specimens and prototype strains showed the same behavior. The habit to cultivate viruses from throat swabs at 33‡ C is unsatisfactory for adenoviruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086892/ doi: 10.1007/bf02121753 id: cord-271091-ffn59sgf author: Galao, Rui P title: Saccharomyces cerevisiae: a versatile eukaryotic system in virology date: 2007-10-10 words: 6539.0 sentences: 318.0 pages: flesch: 42.0 cache: ./cache/cord-271091-ffn59sgf.txt txt: ./txt/cord-271091-ffn59sgf.txt summary: These include the analysis of the function of individual proteins from important pathogenic viruses, the elucidation of key processes in viral replication through the development of systems that allow the replication of higher eukayotic viruses in yeast, and the use of yeast in antiviral drug development and vaccine production. Although the expression of viral proteins in yeast not always necessarily reflects their role in higher eukaryotes, here we selected some examples in which the analysis in yeast of their effect on highly conserved cellular processes such as cell cycle control, apoptosis or mRNA degradation have contributed to the current understanding of the pathogenesis of important viral pathogens such as HIV-1 and HCV. The identification of the host factors involved in viral RNA replication is a priority area of research in virology because it can provide new targets for antiviral drug development. abstract: The yeast Saccharomyces cerevisiae is a well-established model system for understanding fundamental cellular processes relevant to higher eukaryotic organisms. Less known is its value for virus research, an area in which Saccharomyces cerevisiae has proven to be very fruitful as well. The present review will discuss the main achievements of yeast-based studies in basic and applied virus research. These include the analysis of the function of individual proteins from important pathogenic viruses, the elucidation of key processes in viral replication through the development of systems that allow the replication of higher eukayotic viruses in yeast, and the use of yeast in antiviral drug development and vaccine production. url: https://www.ncbi.nlm.nih.gov/pubmed/17927824/ doi: 10.1186/1475-2859-6-32 id: cord-254194-962vynwk author: Galdiero, Stefania title: Silver Nanoparticles as Potential Antiviral Agents date: 2011-10-24 words: 10034.0 sentences: 447.0 pages: flesch: 38.0 cache: ./cache/cord-254194-962vynwk.txt txt: ./txt/cord-254194-962vynwk.txt summary: Silver nanoparticles have mainly been studied for their antimicrobial potential against bacteria, but have also proven to be active against several types of viruses including human imunodeficiency virus, hepatitis B virus, herpes simplex virus, respiratory syncytial virus, and monkey pox virus. Theoretically, any metal could be analysed for antiviral activity, however, little effort has been done to determine the interactions of metal nanoparticles with viruses, and only recently some studies have emerged showing that metal nanoparticles can be effective antiviral agents against HIV-1 [37] [38] [39] [40] , hepatitis B virus [41] , respiratory syncytial virus [42] , herpes simplex virus type 1 [43, 44] , monkeypox virus [45] , influenza virus [46] and Tacaribe virus [47] . abstract: Virus infections pose significant global health challenges, especially in view of the fact that the emergence of resistant viral strains and the adverse side effects associated with prolonged use continue to slow down the application of effective antiviral therapies. This makes imperative the need for the development of safe and potent alternatives to conventional antiviral drugs. In the present scenario, nanoscale materials have emerged as novel antiviral agents for the possibilities offered by their unique chemical and physical properties. Silver nanoparticles have mainly been studied for their antimicrobial potential against bacteria, but have also proven to be active against several types of viruses including human imunodeficiency virus, hepatitis B virus, herpes simplex virus, respiratory syncytial virus, and monkey pox virus. The use of metal nanoparticles provides an interesting opportunity for novel antiviral therapies. Since metals may attack a broad range of targets in the virus there is a lower possibility to develop resistance as compared to conventional antivirals. The present review focuses on the development of methods for the production of silver nanoparticles and on their use as antiviral therapeutics against pathogenic viruses. url: https://doi.org/10.3390/molecules16108894 doi: 10.3390/molecules16108894 id: cord-298019-gf2asni1 author: Galdiero, Stefania title: gH625: A milestone in understanding the many roles of membranotropic peptides date: 2014-10-12 words: 8586.0 sentences: 354.0 pages: flesch: 37.0 cache: ./cache/cord-298019-gf2asni1.txt txt: ./txt/cord-298019-gf2asni1.txt summary: While they have been initially discovered in viral fusion proteins and have been involved in the mechanism of viral entry, it is now clear that their features and their mode of interaction with membrane bilayers can be exploited to design viral inhibitors as well as to favor delivery of cargos across the cell membrane and across the blood–brain barrier. Peptides with a propensity for membrane binding can also interfere with enveloped virus entry by direct physical interaction with the hydrophobic surfaces present on cell membranes and/or fusion proteins. Since not all membranotropic peptides are able to cross the membrane bilayer, it is essential to identify structural characteristics of hydrophobic peptides know to enter the cell membrane to highlight any feature that is involved in the penetration which may help in the design of novel delivery tools. Dendrimer functionalization with a membrane-interacting domain of herpes simplex virus type 1: towards intracellular delivery abstract: Here, we review the current knowledge about viral derived membranotropic peptides, and we discuss how they may be used for many therapeutic applications. While they have been initially discovered in viral fusion proteins and have been involved in the mechanism of viral entry, it is now clear that their features and their mode of interaction with membrane bilayers can be exploited to design viral inhibitors as well as to favor delivery of cargos across the cell membrane and across the blood–brain barrier. The peptide gH625 has been extensively used for all these purposes and provides a significant contribution to the field. We describe the roles of this sequence in order to close the gap between the many functions that are now emerging for membranotropic peptides. url: https://api.elsevier.com/content/article/pii/S0005273614003411 doi: 10.1016/j.bbamem.2014.10.006 id: cord-266985-9qwttt2y author: Gale, P. title: Applications of omics approaches to the development of microbiological risk assessment using RNA virus dose–response models as a case study date: 2014-11-04 words: 8073.0 sentences: 341.0 pages: flesch: 43.0 cache: ./cache/cord-266985-9qwttt2y.txt txt: ./txt/cord-266985-9qwttt2y.txt summary: At present, the great strength of gene sequence data appears to be in giving information on the distribution and proportion of susceptible genotypes (for example due to the presence of the appropriate pathogen‐binding receptor) in the host population rather than in predicting specificities from the amino acid sequences concurrently obtained. The nature of the mutant spectrum in RNA viruses greatly complicates the application of omics approaches to the development of mechanistic dose–response models and prevents prediction of risks of disease progression (given infection has occurred) at the level of the individual host. The binding of NoV capsid protein to its HBGA receptor Table 1 Breakdown of the initial infection process into four steps for building a mechanistic dose-response relationship for RNA viruses through the oral route: information needs Host glycans play a central role in the pathogen infection process including binding of virus to specific receptors in steps 1 and 2 and also in the immune system. abstract: T e in the amount of ‘omics’ data available and in our ability to interpret those data. The aim of this paper was to consider how omics techniques can be used to improve and refine microbiological risk assessment, using dose–response models for RNA viruses, with particular reference to norovirus through the oral route as the case study. The dose–response model for initial infection in the gastrointestinal tract is broken down into the component steps at the molecular level and the feasibility of assigning probabilities to each step assessed. The molecular mechanisms are not sufficiently well understood at present to enable quantitative estimation of probabilities on the basis of omics data. At present, the great strength of gene sequence data appears to be in giving information on the distribution and proportion of susceptible genotypes (for example due to the presence of the appropriate pathogen‐binding receptor) in the host population rather than in predicting specificities from the amino acid sequences concurrently obtained. The nature of the mutant spectrum in RNA viruses greatly complicates the application of omics approaches to the development of mechanistic dose–response models and prevents prediction of risks of disease progression (given infection has occurred) at the level of the individual host. However, molecular markers in the host and virus may enable more broad predictions to be made about the consequences of exposure in a population. In an alternative approach, comparing the results of deep sequencing of RNA viruses in the faeces/vomitus from donor humans with those from their infected recipients may enable direct estimates of the average probability of infection per virion to be made. url: https://doi.org/10.1111/jam.12656 doi: 10.1111/jam.12656 id: cord-012582-k1mjik27 author: Gallego, Iván title: Stronger Together: Multivalent Phage Capsids Inhibit Virus Entry date: 2020-08-27 words: 1579.0 sentences: 95.0 pages: flesch: 44.0 cache: ./cache/cord-012582-k1mjik27.txt txt: ./txt/cord-012582-k1mjik27.txt summary: This report highlights a phage capsid scaffold strategy that can be used to precisely position sialic acid moieties to inhibit influenza A virus replication. This report highlights a phage capsid scaffold strategy that can be used to precisely position sialic acid moieties to inhibit influenza A virus replication. In this work, the authors have selected the icosahedral capsid of the bacteriophage Qβ as the rigid scaffold for the attachment of the sialic acid to achieve a structurally defined presentation of the ligands that matches the binding sites of the trimeric hemagglutinin. All these findings demonstrate that these phage capsid nanoparticles can be employed as efficient inhibitors of influenza A virus and may be the first step towards the development of a new group of antivirals based on protein scaffolds for the treatment of influenza. This new approach from the Hackenberger group represents a promising example of how controlled protein assemblies can be used as precise multivalent scaffolds in the development of innovative antiviral therapeutics. abstract: Antivirals are now more important than ever. To efficiently inhibit virus replication, antiviral multivalent strategies need sufficient affinity to overcome the excellent matching between the virus and its receptor. This report highlights a phage capsid scaffold strategy that can be used to precisely position sialic acid moieties to inhibit influenza A virus replication url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7461183/ doi: 10.1002/cbic.202000536 id: cord-312431-de7zhswl author: Ganesh, Atheesha title: Detecting Virus‐Like Particles from the Umgeni River, South Africa date: 2013-08-30 words: 7112.0 sentences: 376.0 pages: flesch: 48.0 cache: ./cache/cord-312431-de7zhswl.txt txt: ./txt/cord-312431-de7zhswl.txt summary: These results indicate the potential of viruses in the water samples especially from the lower catchment areas of the Umgeni River to infect human hosts throughout the year. It is well recognised that monitoring the presence of enteric viruses could be challenging due to the relatively low level of infectious viral particles towards the respective host species and small viral particle size existing in environmental waters, thus making it essential to start with a large water sample volume and concentrate it to several orders of magnitude [27] [28] [29] [30] [31] . The present study was conducted to optimise procedures to extract and enumerate indigenous virus-like particles (VLPs) and to determine the community structures and infectivity of these viruses from river water. Canonical correspondence analysis (CCA) was used to reveal the association amongst the bacteriophages, VLPs and the physical and chemical water quality variables, which were measured from the same sites and seasons in concurrent studies performed in this laboratory [46] , with a view to defining the significant variables accountable for the observed spatial and temporal distribution of the communities. abstract: It is important to consider viruses in water quality because of their incidence as causal agents for diarrhoeal disease, and due to their characteristics, which allow them to survive in changing environmental conditions indefinitely. This study assessed the viral quality of the Umgeni River in South Africa seasonally. A two‐step tangential flow filtration process was setup to remove the bacteria and to concentrate the virus populations from large volume water samples. The concentrated water samples contained up to 659 and 550 pfu/mL of somatic and F‐RNA coliphages, respectively. Several virus families including Adenoviridae, Herpesviridae, Orthomyxoviridae, Picornaviridae, Poxviridae and Reoviridae were found in the river based on the morphologies examined under transmission electron microscopy. All concentrated water samples produced substantial cytopathic effects on the Vero, HEK 293, Hela and A549 cell lines. These results indicate the potential of viruses in the water samples especially from the lower catchment areas of the Umgeni River to infect human hosts throughout the year. The present study highlights the importance of routine environmental surveillance of human enteric viruses in water sources. This can contribute to a better understanding of the actual burden of disease on those who might be using the water directly without treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/32313584/ doi: 10.1002/clen.201200564 id: cord-000265-llilwq1u author: Gao, Rongbao title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case date: 2010-10-12 words: 4896.0 sentences: 253.0 pages: flesch: 46.0 cache: ./cache/cord-000265-llilwq1u.txt txt: ./txt/cord-000265-llilwq1u.txt summary: Autopsy studies have shown that human highly pathogenic avian influenza virus (H5N1) can infect multiple human organs other than just the lungs, and that possible causes of organ damage are either viral replication and/or dysregulation of cytokines and chemokines. Although H5N1 virus infection of humans is primarily one of the lower respiratory tract, more recent reports suggested that influenza A H5N1 may in rare, severe cases, disseminate beyond the lungs and infect brain [26, 27] , intestines [20, 27] and lymphoid tissues [27] , and result in extra-pulmonary clinical manifestations including encephalopathy or encephalitis [15, 28] . To better understand the pathogenesis of human H5N1 virus infection, and investigate the route of virus dissemination in vivo, we report on the use of different techniques to detect virus distribution and infection of 5 organ systems in a laboratory confirmed fatal human H5N1 virus infection, and analyze the relationship between viral load in tissues and host response. abstract: Autopsy studies have shown that human highly pathogenic avian influenza virus (H5N1) can infect multiple human organs other than just the lungs, and that possible causes of organ damage are either viral replication and/or dysregulation of cytokines and chemokines. Uncertainty still exists, partly because of the limited number of cases analysed. In this study, a full autopsy including 5 organ systems was conducted on a confirmed H5N1 human fatal case (male, 42 years old) within 18 hours of death. In addition to the respiratory system (lungs, bronchus and trachea), virus was isolated from cerebral cortex, cerebral medullary substance, cerebellum, brain stem, hippocampus ileum, colon, rectum, ureter, aortopulmonary vessel and lymph-node. Real time RT-PCR evidence showed that matrix and hemagglutinin genes were positive in liver and spleen in addition to positive tissues with virus isolation. Immunohistochemistry and in-situ hybridization stains showed accordant evidence of viral infection with real time RT-PCR except bronchus. Quantitative RT-PCR suggested that a high viral load was associated with increased host responses, though the viral load was significantly different in various organs. Cells of the immunologic system could also be a target for virus infection. Overall, the pathogenesis of HPAI H5N1 virus was associated both with virus replication and with immunopathologic lesions. In addition, immune cells cannot be excluded from playing a role in dissemination of the virus in vivo. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953511/ doi: 10.1371/journal.pone.0013315 id: cord-281429-6lv3di4x author: García-Nicolás, Obdulio title: Targeting of the Nasal Mucosa by Japanese Encephalitis Virus for Non-Vector-Borne Transmission date: 2018-11-27 words: 7414.0 sentences: 396.0 pages: flesch: 49.0 cache: ./cache/cord-281429-6lv3di4x.txt txt: ./txt/cord-281429-6lv3di4x.txt summary: Using nasal mucosal tissue explants and primary porcine nasal epithelial cells (NEC) at the air-liquid interface (ALI) and macrophages as ex vivo and in vitro models, we determined that the nasal epithelium could represent the route of entry and exit for JEV in pigs. Porcine NEC at the ALI exposed to with JEV resulted in apical and basolateral virus shedding and release of monocyte recruiting chemokines, indicating infection and replication in macrophages. Using nasal mucosa tissue explants and three-dimensional porcine nasal epithelial cells cultures and macrophages as ex vivo and in vitro models, we determined that the nasal epithelium could be a route of entry as well as exit for the virus. In fact, our data demonstrate that JEV has the ability of infecting apically, resulting in both apical and basolateral virus shedding in swine nasal epithelial cells and indicating that the porcine nasal mucosa could represent a gateway for JEV entry and exit in pigs. abstract: The mosquito-borne Japanese encephalitis virus (JEV) causes severe central nervous system diseases and cycles between Culex mosquitoes and different vertebrates. For JEV and some other flaviviruses, oronasal transmission is described, but the mode of infection is unknown. Using nasal mucosal tissue explants and primary porcine nasal epithelial cells (NEC) at the air-liquid interface (ALI) and macrophages as ex vivo and in vitro models, we determined that the nasal epithelium could represent the route of entry and exit for JEV in pigs. Porcine NEC at the ALI exposed to with JEV resulted in apical and basolateral virus shedding and release of monocyte recruiting chemokines, indicating infection and replication in macrophages. Moreover, macrophages stimulated by alarmins, including interleukin-25, interleukin-33, and thymic stromal lymphopoietin, were more permissive to the JEV infection. Altogether, our data are important to understand the mechanism of non-vector-borne direct transmission of Japanese encephalitis virus in pigs. IMPORTANCE JEV, a main cause of severe viral encephalitis in humans, has a complex ecology composed of a mosquito-waterbird cycle and a cycle involving pigs, which amplifies virus transmission to mosquitoes, leading to increased human cases. JEV can be transmitted between pigs by contact in the absence of arthropod vectors. Moreover, virus or viral RNA is found in oronasal secretions and the nasal epithelium. Using nasal mucosa tissue explants and three-dimensional porcine nasal epithelial cells cultures and macrophages as ex vivo and in vitro models, we determined that the nasal epithelium could be a route of entry as well as exit for the virus. Infection of nasal epithelial cells resulted in apical and basolateral virus shedding and release of monocyte recruiting chemokines and therefore infection and replication in macrophages, which is favored by epithelial-cell-derived cytokines. The results are relevant to understand the mechanism of non-vector-borne direct transmission of JEV. url: https://doi.org/10.1128/jvi.01091-18 doi: 10.1128/jvi.01091-18 id: cord-284479-75zgljet author: García-Serradilla, Moisés title: Drug repurposing for new, efficient, broad spectrum antivirals date: 2019-04-15 words: 7574.0 sentences: 416.0 pages: flesch: 43.0 cache: ./cache/cord-284479-75zgljet.txt txt: ./txt/cord-284479-75zgljet.txt summary: Thus, the antiviral activity of cyclosporine A (CsA) and some of its nonimmunosuppressive analogs against these viruses has been shown to be related to its ability to bind cellular cyclophilins and inhibiting the interaction with the viral proteins (Bienkowska-Haba et al., 2009; Bose et al., 2003; Damaso and Moussatche, 1998; Franke et al., 1994; Kaul et al., 2009; Nakagawa et al., 2004; Thali et al., 1994; Wainberg et al., 1988; Yang et al., 2008) . CsA has also been reported to inhibit the propagation of several strains of influenza A virus in cell cultures blocking a late step of the replication cycle by mechanisms that might implicate CypA-dependent and -independent pathways (Hamamoto et al., 2013; Liu et al., 2012a; Ma et al., 2016) . Therefore, further studies are needed to better understand the mode of action of AgNPs, their cell specificity and toxicological issues in order to generate new and more effective compounds as well as the use in combination with other drugs in the treatment of different viral diseases. abstract: Emerging viruses are a major threat to human health. Recent outbreaks have emphasized the urgent need for new antiviral treatments. For several pathogenic viruses, considerable efforts have focused on vaccine development. However, during epidemics infected individuals need to be treated urgently. High-throughput screening of clinically tested compounds provides a rapid means to identify undiscovered, antiviral functions for well-characterized therapeutics. Repurposed drugs can bypass part of the early cost and time needed for validation and authorization. In this review we describe recent efforts to find broad spectrum antivirals through drug repurposing. We have chosen several candidates and propose strategies to understand their mechanism of action and to determine how resistance to antivirals develops in infected cells. url: https://doi.org/10.1016/j.virusres.2019.02.011 doi: 10.1016/j.virusres.2019.02.011 id: cord-016798-tv2ntug6 author: Gautam, Ablesh title: Bioinformatics Applications in Advancing Animal Virus Research date: 2019-06-06 words: 6978.0 sentences: 405.0 pages: flesch: 44.0 cache: ./cache/cord-016798-tv2ntug6.txt txt: ./txt/cord-016798-tv2ntug6.txt summary: The chapter further provides information on the tools that can be used to study viral epidemiology, phylogenetic analysis, structural modelling of proteins, epitope recognition and open reading frame (ORF) recognition and tools that enable to analyse host-viral interactions, gene prediction in the viral genome, etc. This chapter will introduce virologists to some of the common as well virus-specific bioinformatics tools that the researches can use to analyse viral sequence data to elucidate the viral dynamics, evolution and preventive therapeutics. Novel virus types comprise of new CDSs that are different than previously known CDSs. There are multiple databases and tools available for analysis of human viruses; however, there are still only a limited number of resources designed specifically for veterinary viruses. VIRsiRNAdb is an online curated repository that stores experimentally validated research data of siRNA and short hairpin RNA (shRNA) targeting diverse genes of 42 important human viruses, including influenza virus (Tyagi et al. abstract: Viruses serve as infectious agents for all living entities. There have been various research groups that focus on understanding the viruses in terms of their host-viral relationships, pathogenesis and immune evasion. However, with the current advances in the field of science, now the research field has widened up at the ‘omics’ level. Apparently, generation of viral sequence data has been increasing. There are numerous bioinformatics tools available that not only aid in analysing such sequence data but also aid in deducing useful information that can be exploited in developing preventive and therapeutic measures. This chapter elaborates on bioinformatics tools that are specifically designed for animal viruses as well as other generic tools that can be exploited to study animal viruses. The chapter further provides information on the tools that can be used to study viral epidemiology, phylogenetic analysis, structural modelling of proteins, epitope recognition and open reading frame (ORF) recognition and tools that enable to analyse host-viral interactions, gene prediction in the viral genome, etc. Various databases that organize information on animal and human viruses have also been described. The chapter will converse on overview of the current advances, online and downloadable tools and databases in the field of bioinformatics that will enable the researchers to study animal viruses at gene level. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121192/ doi: 10.1007/978-981-13-9073-9_23 id: cord-014397-7b88ycv8 author: Gavora, JS title: Resistance of livestock to viruses: mechanisms and strategies for genetic engineering date: 1996-12-15 words: 11583.0 sentences: 528.0 pages: flesch: 41.0 cache: ./cache/cord-014397-7b88ycv8.txt txt: ./txt/cord-014397-7b88ycv8.txt summary: Thus introduction of new mechanisms of disease resistance in livestock by gene transfer may be viewed as a logical continuation of the creative influence of humans on the evolution of farm animals and birds that could benefit mankind by improvements in food safety and production efficiency. As background for the discussion of the subject, the article deals briefly with coevolution of hosts and parasites and principal elements of virus-host interactions, and reviews past improvement of disease resistance in plants and livestock by conventional breeding and genetic engineering, as well as the potential ''biological cost'' of genetic manipulation. Basic understanding of the parallel evolution of viruses and their hosts provides a useful starting point for the consideration of strategies for genetic engineering of new mechanisms of resistance. Genetic engineering strategies that prevent entry of viruses into host cells would be effective against all three types of viral infection. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2708302/ doi: 10.1186/1297-9686-28-5-385 id: cord-304747-ojyxs3cp author: Gaynor, Anne M title: Identification of a Novel Polyomavirus from Patients with Acute Respiratory Tract Infections date: 2007-05-04 words: 6665.0 sentences: 328.0 pages: flesch: 51.0 cache: ./cache/cord-304747-ojyxs3cp.txt txt: ./txt/cord-304747-ojyxs3cp.txt summary: Screening of 2,135 patients with acute respiratory tract infections in Brisbane, Queensland, Australia, and St. Louis, Missouri, United States, using WU virus–specific PCR primers resulted in the detection of 43 additional specimens that contained WU virus. The virus was detected in the respiratory secretions from an additional 43 patients in two continents, and the complete genomes of multiple isolates were sequenced. In the early region, an unspliced open reading frame of 194 amino acids was detected that possibly encodes for the STAg. As the paradigm in other polyomaviruses is that STAg is expressed from a spliced message, analysis of potential splice sites revealed the presence of a putative splice donor sequence just one nucleotide 59 of the initially predicted The initial screen used primers targeting the VP2 region, which possessed less than 20% amino acid homology to JC and BK virus to minimize the possibility of cross reactivity with the known human polyomaviruses. abstract: We report the identification of a novel polyomavirus present in respiratory secretions from human patients with symptoms of acute respiratory tract infection. The virus was initially detected in a nasopharyngeal aspirate from a 3-year-old child from Australia diagnosed with pneumonia. A random library was generated from nucleic acids extracted from the nasopharyngeal aspirate and analyzed by high throughput DNA sequencing. Multiple DNA fragments were cloned that possessed limited homology to known polyomaviruses. We subsequently sequenced the entire virus genome of 5,229 bp, henceforth referred to as WU virus, and found it to have genomic features characteristic of the family Polyomaviridae. The genome was predicted to encode small T antigen, large T antigen, and three capsid proteins: VP1, VP2, and VP3. Phylogenetic analysis clearly revealed that the WU virus was divergent from all known polyomaviruses. Screening of 2,135 patients with acute respiratory tract infections in Brisbane, Queensland, Australia, and St. Louis, Missouri, United States, using WU virus–specific PCR primers resulted in the detection of 43 additional specimens that contained WU virus. The presence of multiple instances of the virus in two continents suggests that this virus is geographically widespread in the human population and raises the possibility that the WU virus may be a human pathogen. url: https://www.ncbi.nlm.nih.gov/pubmed/17480120/ doi: 10.1371/journal.ppat.0030064 id: cord-002423-1u44tdrj author: Geoghegan, Jemma L. title: Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families date: 2017-02-08 words: 6186.0 sentences: 267.0 pages: flesch: 44.0 cache: ./cache/cord-002423-1u44tdrj.txt txt: ./txt/cord-002423-1u44tdrj.txt summary: While this method does not explicitly model host-switching events, it does provide a simple means to compare multiple topologies of virus-host pairs, and accounts for differences in sample size and the fact that several viruses from a specific family can infect a single host species. Across the data set as a whole we found that all virus families displayed relatively large tree topological distances with nPH85 values of !0.6, suggesting that cross-species transmission is widespread, at least at the family-level (Fig 2; S3 Table) . As with the analysis of topological distances, this revealed that cross-species transmission was the most common evolutionary event in all virus families studied here, with co-divergence consistently less frequent (with the possible exception of the Hepadnaviridae-see below), and lineage duplication and extinction playing a much more minor role. To investigate the comparative prevalence of cross-species transmission among viruses we measured the congruence between virus and host phylogenetic trees using a normalized tree topological distance-based approach (nPH85, [14] ). abstract: The cross-species transmission of viruses from one host species to another is responsible for the majority of emerging infections. However, it is unclear whether some virus families have a greater propensity to jump host species than others. If related viruses have an evolutionary history of co-divergence with their hosts there should be evidence of topological similarities between the virus and host phylogenetic trees, whereas host jumping generates incongruent tree topologies. By analyzing co-phylogenetic processes in 19 virus families and their eukaryotic hosts we provide a quantitative and comparative estimate of the relative frequency of virus-host co-divergence versus cross-species transmission among virus families. Notably, our analysis reveals that cross-species transmission is a near universal feature of the viruses analyzed here, with virus-host co-divergence occurring less frequently and always on a subset of viruses. Despite the overall high topological incongruence among virus and host phylogenies, the Hepadnaviridae, Polyomaviridae, Poxviridae, Papillomaviridae and Adenoviridae, all of which possess double-stranded DNA genomes, exhibited more frequent co-divergence than the other virus families studied here. At the other extreme, the virus and host trees for all the RNA viruses studied here, particularly the Rhabdoviridae and the Picornaviridae, displayed high levels of topological incongruence, indicative of frequent host switching. Overall, we show that cross-species transmission plays a major role in virus evolution, with all the virus families studied here having the potential to jump host species, and that increased sampling will likely reveal more instances of host jumping. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319820/ doi: 10.1371/journal.ppat.1006215 id: cord-277417-f71jwdzj author: Geoghegan, Jemma L. title: The phylogenomics of evolving virus virulence date: 2018-10-10 words: 10443.0 sentences: 468.0 pages: flesch: 44.0 cache: ./cache/cord-277417-f71jwdzj.txt txt: ./txt/cord-277417-f71jwdzj.txt summary: Our current understanding of virulence evolution is based on insights drawn from two perspectives that have developed largely independently: long-standing evolutionary theory based on limited real data examples that often lack a genomic basis, and experimental studies of virulence-determining mutations using cell culture or animal models. Such a phylogenomic approach to studying virulence evolution is timely because of the rapidity with which virus genome sequence data are now being generated, including during ongoing disease outbreaks of emerging viruses [19] [20] [21] , and because of the development of new phylogeny-based methods for studying and visualizing genomic data [22] [23] [24] . For example, the repeated evolution of the same amino acid changes following the cross-species transmission of avian influenza virus to humans strongly suggests that they directly affect host range 66 , and a similar approach has been used to elucidate the nature of the evolutionary arms race between viruses and their hosts 67, 68 . abstract: How virulence evolves after a virus jumps to a new host species is central to disease emergence. Our current understanding of virulence evolution is based on insights drawn from two perspectives that have developed largely independently: long-standing evolutionary theory based on limited real data examples that often lack a genomic basis, and experimental studies of virulence-determining mutations using cell culture or animal models. A more comprehensive understanding of virulence mutations and their evolution can be achieved by bridging the gap between these two research pathways through the phylogenomic analysis of virus genome sequence data as a guide to experimental study. url: https://doi.org/10.1038/s41576-018-0055-5 doi: 10.1038/s41576-018-0055-5 id: cord-017748-xy26tk0t author: Georgiev, Vassil St. title: Influenza date: 2009 words: 11757.0 sentences: 536.0 pages: flesch: 39.0 cache: ./cache/cord-017748-xy26tk0t.txt txt: ./txt/cord-017748-xy26tk0t.txt summary: This, coupled with the difficulty to predict which subtype of avian influenza virus will cause the next human pandemic means that an ideal vaccine would elicit an immune response that protects the host from infection with a broad range of influenza viruses from the same or different subtypes (14) . Therefore, if a virus with a new HA and/or NA glycoprotein emerges in the human population, cell-mediated immunity directed against the highly conserved internal proteins could have a role in protection at the time of a pandemic (14) . Although most influenza vaccines are designed to induce HA-specific antibody responses to protect the host from infection, the biology of avian influenza viruses presents several unique challenges compared with human influenza viruses. DNA vaccines encoding the HA and NA glycoproteins of avian influenza viruses or conserved internal virus proteins, such as matrix proteins and nucleoproteins, induced protective immunity in mice and chickens (90) (91) (92) (93) . abstract: Influenza is a highly contagious, acute respiratory illness afflicting humans. Although influenza epidemics occur frequently, their severity varies (1). Not until 1933, when the first human influenza virus was isolated, was it possible to define with certainty which pandemics were caused by influenza viruses. In general, influenza A viruses are more pathogenic than are influenza B viruses. Influenza A virus is a zoonotic infection, and more than 100 types of influenza A viruses infect most species of birds, pigs, horses, dogs, and seals. It is believed that the 1918–1919 pandemic originated from a virulent strain of H1N1 from pigs and birds. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122397/ doi: 10.1007/978-1-60327-297-1_13 id: cord-025995-nxeg03xj author: Gerba, Charles P. title: Pathogen Removal from Wastewater during Groundwater Recharge date: 2013-11-17 words: 10527.0 sentences: 533.0 pages: flesch: 53.0 cache: ./cache/cord-025995-nxeg03xj.txt txt: ./txt/cord-025995-nxeg03xj.txt summary: Studies indicate that bacteria and viruses are not removed effectively from wastewaters during primary treatment [19] ; removal of viruses during secondary treatment (active sludge) is dependent largely on virus adsorption to solids. [40] with cores of sandy forest soil receiving poliovirus in sewage effluent at various pH levels between 5.5 and 9.0, virus retention was best at pH 5.5, and the release and migration of retained viruses by subsequent distilled water applications was lower from the cores that re ceived sewage effluent having lower pH values. [57] on virus survival and movement in a rapid-infiltration system for wastewater, the rate of inactivation of indigenous viruses was greater in the fall than in the winter, possibly due in part to the effects of higher temperatures in the former season. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7271151/ doi: 10.1016/b978-0-250-40549-7.50015-1 id: cord-290851-1e5e033r author: Gerlier, Denis title: Emerging zoonotic viruses: new lessons on receptor and entry mechanisms date: 2011-06-12 words: 2742.0 sentences: 153.0 pages: flesch: 45.0 cache: ./cache/cord-290851-1e5e033r.txt txt: ./txt/cord-290851-1e5e033r.txt summary: Here I review the receptors and mode of entry of three emerging zoonotic viruses, responsible for rare but deadly diseases, whose natural reservoir is the bat: severe acute respiratory syndrome coronavirus (SARS-CoV), Hendra (HeV), Nipah (NiV), Ebola (EboV), and Marburg (MarV) viruses. S mediates binding to the cellular receptor Angiotensin Converting Enzyme 2 (ACE2) [4 ] , and ensures the viral-cell membrane fusion that allows virus entry. The EboV (and MarV) entry process lasts for about 1 h [94, 95] and can be schematized as follows ( Figure 3) : Firstly, (i) EboV attaches to the cells via the GP1/GP2 interaction with DC-SIGN/R and/or LECStin and is (ii) immediately internalized by constitutive and/or virus-contact-induced macropinocytosis. Cell adhesion promotes ebola virus envelope glycoprotein-mediated binding and infection abstract: Viruses enter the host cell by binding cellular receptors that allow appropriate delivery of the viral genome. Although the horizontal propagation of viruses feeds the continuous emergence of novel pathogenic viruses, the genetic variation of cellular receptors can represent a challenging barrier. The SARS coronavirus, henipaviruses and filoviruses are zoonotic RNA viruses that use bats as their reservoir. Their lethality for man has fostered extensive research both on the cellular receptors they use and their entry pathways. These studies have allowed new insights into the diversity of the molecular mechanisms underlying both virus entry and pathogenesis. url: https://doi.org/10.1016/j.coviro.2011.05.014 doi: 10.1016/j.coviro.2011.05.014 id: cord-298736-9bvyp21d author: Gerold, Gisa title: Decoding protein networks during virus entry by quantitative proteomics date: 2016-06-15 words: 12159.0 sentences: 626.0 pages: flesch: 38.0 cache: ./cache/cord-298736-9bvyp21d.txt txt: ./txt/cord-298736-9bvyp21d.txt summary: In the past decade mass spectrometry based proteomics methods have reached sensitivities and high throughput compatibilities of genomics methods and now allow the reliable quantitation of proteins in complex samples from limited material. Since then technological developments like antibody based affinity purification (AP), mass spectrometry (MS) of proteins, DNA mediated transformation and molecular cloning led to the discovery of dozens of receptors for human pathogenic viruses (Fig. 1) . While transcriptomics can reveal long-term alterations of the cellular state, virus entry usually occurs within minutes and typically relies on rapid changes of protein conformation, localization, interactions and post-translational modifications (PTM). Of note, high resolution proteomics can not only reveal transient interactions of VAP with enzymes, but also has the potential to identify proteolytic cleavage sites and redox modifications in VAPs. It is conceivable that virus induced protein interactions during entry not only serve to promote the virus uptake pathway, but can also help cloak viruses and lead to immune evasion. abstract: Abstract Virus entry into host cells relies on interactions between viral and host structures including lipids, carbohydrates and proteins. Particularly, protein–protein interactions between viral surface proteins and host proteins as well as secondary host protein–protein interactions play a pivotal role in coordinating virus binding and uptake. These interactions are dynamic and frequently involve multiprotein complexes. In the past decade mass spectrometry based proteomics methods have reached sensitivities and high throughput compatibilities of genomics methods and now allow the reliable quantitation of proteins in complex samples from limited material. As proteomics provides essential information on the biologically active entity namely the protein, including its posttranslational modifications and its interactions with other proteins, it is an indispensable method in the virologist's toolbox. Here we review protein interactions during virus entry and compare classical biochemical methods to study entry with novel technically advanced quantitative proteomics techniques. We highlight the value of quantitative proteomics in mapping functional virus entry networks, discuss the benefits and limitations and illustrate how the methodology will help resolve unsettled questions in virus entry research in the future. url: https://api.elsevier.com/content/article/pii/S0168170215300617 doi: 10.1016/j.virusres.2015.09.006 id: cord-321053-lgae22f8 author: Gerold, Gisa title: Opportunities and Risks of Host-targeting Antiviral Strategies for Hepatitis C date: 2013-10-04 words: 9393.0 sentences: 470.0 pages: flesch: 42.0 cache: ./cache/cord-321053-lgae22f8.txt txt: ./txt/cord-321053-lgae22f8.txt summary: Numerous in vitro studies in combination with a growing number of HCV sequencing data from patients undergoing DAA treatment underline that the virus can develop drug-resistance and fitness restoring compensatory mutations [11] . An emerging third group of antivirals, so called hosttargeting antivirals (HTA), may be part of such future combination therapies, in particular as HTAs hold the promise of overcoming some of the caveats of DAAs. HTAs are antibodies, RNAs or small molecules, which interfere with host factors needed for HCV propagation. On the one hand, this demonstrates that HCV can in theory evade HTA therapy by mutating the viral binding partner of the targeted host factor and in fact suggests a low genetic barrier to resistance. Targeting HCV RNA Replication: Phosphatidylinositol 4-kinase III alpha (PI4KIIIα) Genome wide RNA interference screens and in depth cell culture replication assays with HCV replicons and full length infectious virus have revealed numerous additional host dependency factors, that could in principle serve as antiviral targets [99] [100] [101] [102] [103] [104] [105] [106] [107] . abstract: Hepatitis C virus (HCV) infects more than 2 % of the world population with highest prevalence in parts of Africa and Asia. Past standard of care using interferon α and ribavirin had adverse effects and showed modest efficacy for some HCV genotypes spurring the development of direct acting antivirals (DAAs). Such DAAs target viral proteins and are thus better tolerated but they suffer from emergence of vial resistance. Furthermore, DAAs are often HCV genotype specific. Novel drug candidates targeting host factors required for HCV propagation, so called host-targeting antivirals (HTAs), promise to overcome both caveats. The genetic barrier to resistance is usually considered to be high for HTAs and all HCV genotypes presumably use the same host factors. Recent data, however, challenge these assumptions, at least for some HTAs. Here, we highlight the most important host-targeting strategies against hepatitis C and critically discuss their opportunities and risks. url: https://www.ncbi.nlm.nih.gov/pubmed/32214912/ doi: 10.1007/s11901-013-0187-1 id: cord-292075-t9z7zqz4 author: Gessain, Antoine title: Mécanismes d’émergence virale et transmission interespèces : l’exemple des rétrovirus Foamy simiens chezl’Homme en Afrique Centrale date: 2013-12-31 words: 2159.0 sentences: 133.0 pages: flesch: 52.0 cache: ./cache/cord-292075-t9z7zqz4.txt txt: ./txt/cord-292075-t9z7zqz4.txt summary: After reviewing the current available data on the discovery, cross-species transmission from monkeys and apes to humans of the simian foamy retroviruses, we will report the results of our study. These populations are living nearby the habitats of several monkeys and apes, often naturally infected by different retroviruses including SIV, STLV and simian foamy virus. These populations are living nearby the habitats of several monkeys and apes, often naturally infected by different retroviruses including SIV, STLV and simian foamy virus. After reviewing the current available data on the discovery, cross-species transmission from monkeys and apes to humans of the simian foamy INTRODUCTION L''espèce humaine est en contact permanent avec l''environnement qui contient une multitude d''agents infectieux (virus, bactéries, parasites, champignons). Cross-species transmission of simian retroviruses, how and why they could lead to the emergence of new diseases in the human population Two distinct variants of simian foamy virus in naturally infected mandrills (Mandrillus sphinx) and cross-species transmission to humans abstract: SUMMARY A large proportion of viral pathogens that have emerged during the last decades in humans are considered to have originated from various animal species. This is well exemplified by several recent epidemics such as those of Nipah, Severe Acute Respiratory Syndrome, Avian flu, Ebola, Monkeypox, and Hantaviruses. After the initial interspecies transmission per se, the viruses can disseminate into the human population through various and distinct mechanisms. Some of them are well characterized and understood, thus allowing a certain level of risk control and prevention. Surprisingly and in contrast, the initial steps that lead to the emergence of several viruses, and of their associated diseases, remain still poorly understood. Epidemiological field studies conducted in certain specific high-risk populations are thus necessary to obtain new insights into the early events of this emergence process. Human infections by simian viruses represent increasing public health concerns. Indeed, by virtue of their genetic and physiological similarities, non-human primates (NHPs) are considered to be likely the sources of viruses that can infect humans and thus may pose a significant threat to human population. This is well illustrated by retroviruses, which have the ability to cross species, adapt to a new host and sometimes spread within these new species. Sequence comparison and phylogenetic studies have thus clearly showed that the emergence of human immunodeficiency virus type 1 (HIV-1) and HIV-2 in humans have resulted from several independent interspecies transmissions of different SIV types from Chimpanzees and African monkeys (including sooty mangabeys), respectively, probably during the first part of the last century. The situation for Human T cell Lymphotropic virus type 1 (HTLV-1) is, for certain aspects, quite comparable. Indeed, the origin of most HTLV-1 subtypes appears to be linked to interspecies transmission between STLV-1-infected monkeys and humans, followed by variable periods of evolution in the human host. In this review, after an introduction on emerging viruses, we will briefly present the results of a large epidemiological study performed in groups of Bantus and Pygmies living in villages and settlements located in the rain forest of the South region of Cameroon. These populations are living nearby the habitats of several monkeys and apes, often naturally infected by different retroviruses including SIV, STLV and simian foamy virus. Most of the persons included in this study were hunters of such NHPs, thus at high risk of contact with infected body fluids (blood, saliva,...) during hunting activities. After reviewing the current available data on the discovery, cross-species transmission from monkeys and apes to humans of the simian foamy retroviruses, we will report the results of our study. Such infection is a unique natural model to study the different mechanisms of restriction of retroviral emergence in Humans. url: https://www.ncbi.nlm.nih.gov/pubmed/26137812/ doi: 10.1016/s0001-4079(19)31387-1 id: cord-305302-go87uu06 author: Gessain, Antoine title: Editorial overview: Emerging viruses: interspecies transmission date: 2015-02-28 words: 2482.0 sentences: 112.0 pages: flesch: 45.0 cache: ./cache/cord-305302-go87uu06.txt txt: ./txt/cord-305302-go87uu06.txt summary: Furthermore, some of these diseases, associated with emerging viruses, had recent major public health impact, as exemplified in humans by the AIDS [1] , hepatitis C pandemics [2] , or the current Ebola disease epidemic, or in crops by cassava mosaic disease, which seriously compromises food security in East Africa [3] . The emergence of a new viral associated disease or of a new virus is indeed the result of a sequence of successive steps, sometimes complex, and is often related to the entanglement of several factors: socioeconomic or particular cultural activities, increased mobility of human, animal and plant mobility (''the world is a global village''), human exploitation of the environment as deforestation or increase of agricultural or otherwise human managed land, resulting in loss of biodiversity or ecosystem simplification, disruption of human, animal and plant health systems in armed conflict, urbanization with development of huge slums of great poverty and basic hygiene, decreased interest in the surveillance and control of infectious diseases, use of unsterile medical equipment as part of therapeutic and/or mass vaccination and, finally, the ability of certain viruses to adapt quickly to a changing environment. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1879625715000243 doi: 10.1016/j.coviro.2015.02.001 id: cord-276583-j8bf0eme author: Ghalyanchi Langeroudi, Arash title: Full-length characterization and phylogenetic analysis of hemagglutinin gene of H9N2 virus isolated from broilers in Iran during 1998–2007 date: 2012-01-21 words: 5360.0 sentences: 266.0 pages: flesch: 53.0 cache: ./cache/cord-276583-j8bf0eme.txt txt: ./txt/cord-276583-j8bf0eme.txt summary: The results showed that all nine representative H9N2 isolates belong to low pathogenic AIVs since none of the amino acid sequences at the cleavage site of the HA of the isolates possessed the basic motif required for highly pathogenic viruses (R-X-R/K-R). Amino acid sequences at the cleavage site of the HA of the isolates possessed -P-A-R-S-S-R-G-L-motif, except for two isolated: TH85 (A to T) and Fig. 1 Phylogenetic relationships of HA genes of representative influenza A viruses isolated in Iran, Middle Eastern, Eurasian countries, and USA. In the present study, seven from nine H9N2 Iranian isolates possessed amino acid 226-L (numbered according to H3) at the receptor binding site, indicating its potential to infect humans. Sequence and phylogenetic analysis of the haemagglutinin genes of H9N2 avian influenza viruses isolated from commercial chickens in Iran Sequence analysis and phylogenetic study of hemagglutinin Gene of H9N2 subtype of avian influenza virus isolated during 1998-2002 in Iran abstract: H9N2 avian influenza A viruses (AIV) have become panzootic in Eurasia over the last decade and are endemic in Iran since 1998, and inactivated vaccine has been used in chickens to control the disease. The hemagglutinin (HA), one of eight protein-coding genes, plays an important role during the early stage of infection. To study their evolution and zoonotic potential, we conducted an in silico analysis of H9N2 viruses that have infected broiler in Tehran Province, Iran between 1998 and 2007. The complete coding region of HA genes from nine H9N2 subtypes isolated from chicken flocks in Tehran Province during 1998–2007 was amplified and sequenced. Sequence analysis and phylogenetic studies of H9N2 subtype viruses on the basis of data of 9 viruses in this study and 30 selected strains are available in the GenBank. Sequence and phylogenetic analyses revealed a large number of similar substitution mutations and close evolutionary relation among sequences of HA. The isolates possessed two types of amino acid motif –R–S-S-R/G-L- and -R-S-N-R/G-L- at the cleavage site of HA. The results showed that all nine representative H9N2 isolates belong to low pathogenic AIVs since none of the amino acid sequences at the cleavage site of the HA of the isolates possessed the basic motif required for highly pathogenic viruses (R-X-R/K-R). Six out of these nine isolates possessed leucine at position 226, which prevails in the sequences found in human strains. Phylogenetic analysis showed that all our isolates belonged to the G1-like sublineage. Also, these isolates showed some degree of homology with other H9N2 isolates, e.g., 89.46–93.93.39% with qu/HK/G1/97 and 93.39–98.39% with pa/Narita/92A/98. The available evidence indicates that HA genes of H9 influenza virus circulating in Iran during the past years were not well conserved. Our finding emphasizes the importance of reinforcing AIV surveillance, especially after the emergence of high pathogenicity in poultry in Iran. url: https://www.ncbi.nlm.nih.gov/pubmed/32214973/ doi: 10.1007/s00580-012-1405-x id: cord-317198-mean7sj9 author: Giamberardin, Heloisa I.G. title: Clinical and epidemiological features of respiratory virus infections in preschool children over two consecutive influenza seasons in southern Brazil date: 2016-02-09 words: 3534.0 sentences: 183.0 pages: flesch: 48.0 cache: ./cache/cord-317198-mean7sj9.txt txt: ./txt/cord-317198-mean7sj9.txt summary: title: Clinical and epidemiological features of respiratory virus infections in preschool children over two consecutive influenza seasons in southern Brazil This study reports the results of a systematic screening for respiratory viruses in pediatric outpatients from an emergency department (ED) in southern Brazil during two consecutive influenza seasons. © 2016 Wiley Periodicals, Inc. Viral acute respiratory infections (ARIs) in pediatric outpatients represent a significant burden on emergency departments (EDs) and the patients'' families, mainly during influenza seasons, being associated with around 20% of all deaths in pre-school children worldwide, with 90% of these deaths due to pneumonia. This study reports, the results of a laboratory-based surveillance for respiratory viruses in preschool children who were treated in the ED of a pediatric referral hospital during two consecutive influenza seasons. abstract: This study reports the results of a systematic screening for respiratory viruses in pediatric outpatients from an emergency department (ED) in southern Brazil during two consecutive influenza seasons. Children eligible for enrollment in this study were aged 24–59 months and presented with acute respiratory symptoms and fever. Naso‐ and oropharyngeal swabs were collected and multiplex reverse transcription PCR (RT‐PCR) was performed to identify the respiratory viruses involved. In total, 492 children were included in this study: 248 in 2010 and 244 in 2011. In 2010, 136 samples (55%) were found to be positive for at least one virus and the most frequently detected viruses were human rhinovirus (HRV) (18%), adenovirus (AdV) (13%), and human coronavirus (CoV) (5%). In 2011, 158 samples (65%) were found to be positive for at least one virus, and the most frequently detected were HRV (29%), AdV (12%), and enterovirus (9%). Further, the presence of asthma (OR, 3.17; 95% CI, 1.86–5.46) was independently associated with HRV infection, whereas fever was associated with AdV (OR, 3.86; 95% CI, 1.31–16.52) and influenza infections (OR, 3.74; 95% CI, 1.26–16.06). Ten patients (2%) were diagnosed with pneumonia, and six of these tested positive for viral infection (4 HRV, 1 RSV, and 1 AdV). Thus, this study identified the most common respiratory viruses found in preschool children in the study region and demonstrated their high frequency, highlighting the need for improved data collection, and case management in order to stimulate preventive measures against these infections. J. Med. Virol. 88:1325–1333, 2016. © 2016 Wiley Periodicals, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/26773605/ doi: 10.1002/jmv.24477 id: cord-268999-6748c617 author: Gibson, Kristen E title: Viral pathogens in water: occurrence, public health impact, and available control strategies date: 2014-01-14 words: 4052.0 sentences: 197.0 pages: flesch: 41.0 cache: ./cache/cord-268999-6748c617.txt txt: ./txt/cord-268999-6748c617.txt summary: Although there have been advances in both drinking water treatment technologies and source water protection strategies, waterborne disease outbreaks (WBDOs) due to viral pathogens still occur each year worldwide. Although there have been advances in both drinking water treatment technologies and source water protection strategies, waterborne disease outbreaks (WBDOs) due to viral pathogens still occur each year worldwide. The current review ( Figure 1 ) focuses on (1) the occurrence of viral pathogens of primary concern in various water sources; (2) virus-related WBDOS by water type reported worldwide over the past decade (from approximately 2000 to 2012); and (3) DW treatment options for the inactivation or removal of viruses. This paucity of available data for viruses in DW can most likely be attributed to the need for very large volumes (>100 to 6000 L) of water to be concentrated followed by subsequent recovery and detection of virus targets -a process that is challenging often Viral pathogens in water Gibson 51 Treatment options specific to removal/inactivation of viruses: -Many options available though implementation varies worldwide due to availability of technology. abstract: The public health impact of the transmission of viruses in water is significant worldwide. Waterborne viruses can be introduced into our recreational and finished drinking water sources through a variety of pathways ultimately resulting in the onset of illness in a portion of the exposed population. Although there have been advances in both drinking water treatment technologies and source water protection strategies, waterborne disease outbreaks (WBDOs) due to viral pathogens still occur each year worldwide. By highlighting the prevalence of viral pathogens in water as well as (1) the dominant viruses of concern, (2) WBDOs due to viruses, and (3) available water treatment technologies, the goal of this review is to provide insight into the public health impact of viruses in water. url: https://www.sciencedirect.com/science/article/pii/S1879625713002083 doi: 10.1016/j.coviro.2013.12.005 id: cord-346916-jj4l9ydl author: Girardi, Erika title: Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell date: 2020-08-23 words: 13119.0 sentences: 728.0 pages: flesch: 45.0 cache: ./cache/cord-346916-jj4l9ydl.txt txt: ./txt/cord-346916-jj4l9ydl.txt summary: Moreover, despite the molecular mimicry set by RNA viruses to resemble cellular mRNAs and escape host recognition, the viral nucleic acid still needs to embark on a long journey through a hostile cell environment and must overcome the obstacles put in place by the host antiviral system in order to be translated and replicated. Another example, is the zinc-finger antiviral protein (ZAP), which binds vRNAs containing a ZAP response element (ZRE) and induces RNA degradation via interaction of its N-terminal domain with host decay machinery mediated [75] (Fig. 1 ). In fact, IRES elements present in the genome of different families of RNA viruses lack overall conserved features [146, 147] .The classification of viral IRESs in four types stems from their structural organization, their respective dependence on sets of translation initiation factors, and whether they use scanning or instead directly recruit ribosomes to the start codon [148] (Fig. 2) . abstract: As obligate intracellular parasites with limited coding capacity, RNA viruses rely on host cells to complete their multiplication cycle. Viral RNAs (vRNAs) are central to infection. They carry all the necessary information for a virus to synthesize its proteins, replicate and spread and could also play essential non-coding roles. Regardless of its origin or tropism, vRNA has by definition evolved in the presence of host RNA Binding Proteins (RBPs), which resulted in intricate and complicated interactions with these factors. While on one hand some host RBPs recognize vRNA as non-self and mobilize host antiviral defenses, vRNA must also co-opt other host RBPs to promote viral infection. Focusing on pathogenic RNA viruses, we will review important scenarios of RBP-vRNA interactions during which host RBPs recognize, modify or degrade vRNAs. We will then focus on how vRNA hijacks the largest ribonucleoprotein complex (RNP) in the cell, the ribosome, to selectively promote the synthesis of its proteins. We will finally reflect on how novel technologies are helping in deepening our understanding of vRNA-host RBPs interactions, which can be ultimately leveraged to combat everlasting viral threats. url: https://api.elsevier.com/content/article/pii/S1084952120300914 doi: 10.1016/j.semcdb.2020.08.006 id: cord-273019-hbpfz8rt author: Glingston, R. Sahaya title: Organelle dynamics and viral infections: at cross roads date: 2018-06-25 words: 9513.0 sentences: 486.0 pages: flesch: 35.0 cache: ./cache/cord-273019-hbpfz8rt.txt txt: ./txt/cord-273019-hbpfz8rt.txt summary: Studies on the herpes simplex virus-1 (HSV-1) infection on Vero, BHK-21 and PtK 2 cells reported transportation of viral tegument-capsid by dynein to the cytoplasmic side of NPC [22, 23] . In order to construct these compartments, viruses alter host''s fatty acid metabolism, induce rearrangement of the membrane constituents and also recruit cellular machinery to produce proteins essential for its replication [59, 60] . Upregulation of mitophagy and degradation of the mitochondrial antiviral signalling protein (MAVS) in order to attenuate the antiviral immune response in non-small cell lung cancer (NSCLC) cells was reported upon measles virus infection [83] . The expression of matrix protein (M) of human parainfluenza virus type 3 (HPIV3) in HEK293T and HeLa cells was reported to induce mitophagy resulting in the suppression of type1 interferon response [84] . Many viruses or viral proteins are reported to localize to peroxisomes and/or exploit their functions to facilitate their replication in the host cells [108] . abstract: Viruses are obligate intracellular parasites of the host cells. A commonly accepted view is the requirement of internal membranous structures for various aspects of viral life cycle. Organelles enable favourable intracellular environment for several viruses. However, studies reporting organelle dynamics upon viral infections are scant. In this review, we aim to summarize and highlight modulations caused to various organelles upon viral infection or expression of its proteins. url: https://api.elsevier.com/content/article/pii/S1286457918301412 doi: 10.1016/j.micinf.2018.06.002 id: cord-350747-5t5xthk6 author: Gmyl, A. P. title: Diverse Mechanisms of RNA Recombination date: 2005 words: 8187.0 sentences: 463.0 pages: flesch: 41.0 cache: ./cache/cord-350747-5t5xthk6.txt txt: ./txt/cord-350747-5t5xthk6.txt summary: It was believed until recently that the only possible mechanism of RNA recombination is replicative template switching, with synthesis of a complementary strand starting on one viral RNA molecule and being completed on another. An illustrative example of deletions is provided by defective interfering (DI) genomes, which accumulate in a virus population upon high-multiplicity infections and lack a fragment of the sequence coding for viral proteins [5] [6] [7] . A special role in the variation of RNA viruses is played by recombination, the generation of new genomes from two or more parental RNAs. Recombination between viral RNA molecules was observed for the first time as early as in the 1960s in the poliovirus [14, 15] . In other words, it is possible to assume that some of the mechanisms of nonreplicative RNA recombination play an important role in the evolution of not only viral, but also cell genomes [51, 90] . abstract: Recombination is widespread among RNA viruses, but many molecular mechanisms of this phenomenon are still poorly understood. It was believed until recently that the only possible mechanism of RNA recombination is replicative template switching, with synthesis of a complementary strand starting on one viral RNA molecule and being completed on another. The newly synthesized RNA is a primary recombinant molecule in this case. Recent studies have revealed other mechanisms of replicative RNA recombination. In addition, recombination between the genomes of RNA viruses can be nonreplicative, resulting from a joining of preexisting parental molecules. Recombination is a potent tool providing for both the variation and conservation of the genome in RNA viruses. Replicative and nonreplicative mechanisms may contribute differently to each of these evolutionary processes. In the form of trans splicing, nonreplicative recombination of cell RNAs plays an important role in at least some organisms. It is conceivable that RNA recombination continues to contribute to the evolution of DNA genomes. url: https://doi.org/10.1007/s11008-005-0069-x doi: 10.1007/s11008-005-0069-x id: cord-308857-otsrexqu author: Goel, Saurav title: Resilient and Agile Engineering Solutions to Address Societal Challenges such as Coronavirus Pandemic date: 2020-05-28 words: 10608.0 sentences: 526.0 pages: flesch: 47.0 cache: ./cache/cord-308857-otsrexqu.txt txt: ./txt/cord-308857-otsrexqu.txt summary: This newly identified disease is caused by a new strain of the virus being referred to as Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS CoV-2; formerly called 2019-nCoV). We review the current medical and manufacturing response to COVID-19, including advances in instrumentation, sensing, use of lasers, fumigation chambers and development of novel tools such as lab-on-the-chip using combinatorial additive and subtractive manufacturing techniques and use of molecular modelling and molecular docking in drug and vaccine discovery. However, the coronavirus isolated from pangolins is 99% similar in a specific region of the Spike protein, which corresponds to the 74 amino acids involved in the Angiotensin-Converting Enzyme 2 (ACE 2) receptor binding domain, which allows the virus to enter human cells to infect them as shown in Figure 2 (b). (figures reprinted with permission) Our nasal lining tissue contains a rich number of cell receptors called angiotensinconverting enzyme 2 (ACE2), which are favourable sites for the SARS CoV-2 to attach its spiked protein to, thus paving way for the entrance of the virus inside the body. abstract: The world is witnessing tumultuous times as major economic powers including the US, UK, Russia, India, and most of Europe continue to be in a state of lockdown. The worst-hit sectors due to this lockdown are sales, production (manufacturing), transport (aerospace and automotive) and tourism. Lockdowns became necessary as a preventive measure to avoid the spread of the contagious and infectious “Coronavirus Disease 2019” (COVID-19). This newly identified disease is caused by a new strain of the virus being referred to as Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS CoV-2; formerly called 2019-nCoV). We review the current medical and manufacturing response to COVID-19, including advances in instrumentation, sensing, use of lasers, fumigation chambers and development of novel tools such as lab-on-the-chip using combinatorial additive and subtractive manufacturing techniques and use of molecular modelling and molecular docking in drug and vaccine discovery. We also offer perspectives on future considerations on climate change, outsourced versus indigenous manufacturing, automation, and antimicrobial resistance. Overall, this paper attempts to identify key areas where manufacturing can be employed to address societal challenges such as COVID-19. url: https://www.sciencedirect.com/science/article/pii/S2468519420300604?v=s5 doi: 10.1016/j.mtchem.2020.100300 id: cord-310171-1fmsxx2s author: Goffard, Anne title: Virus and cystic fibrosis: Rhinoviruses are associated with exacerbations in adult patients() date: 2014-02-25 words: 3325.0 sentences: 176.0 pages: flesch: 41.0 cache: ./cache/cord-310171-1fmsxx2s.txt txt: ./txt/cord-310171-1fmsxx2s.txt summary: Since the sensitive molecular methods for detection of viruses are more and more common, several recent studies highlight the clinical importance of respiratory viruses especially during exacerbation of asthma, chronic obstructive pulmonary disease (COPD) or CF [3] [4] [5] [6] [7] [8] [9] . In the present study, we reported detection of respiratory viruses from adult patients with CF during either routine visit or acute pulmonary exacerbation. To conclude, we have reported a relatively high frequency of respiratory viruses in a cohort of CF adult patients from France, and demonstrated for the first time that rhinovirus detection including newly identified HRV-Ca variants are the most frequent and significantly associated with respiratory exacerbations. Respiratory viruses in children with cystic fibrosis: viral detection and clinical findings Association of respiratory viral infections with pulmonary deterioration in patients with cystic fibrosis abstract: BACKGROUND: Few studies have suggested the potential role of respiratory viruses in cystic fibrosis (CF) exacerbation, but their real impact is probably underestimated. METHOD: Sixty-four sputum samples collected from 46 adult patients were included in the study: 33 samples were collected during exacerbation of CF, and 31 during the stable phase. After extraction, nucleic acids were tested for the presence of respiratory viruses. When rhinovirus (HRV) was detected, the 5′UTR and VP4/2 regions were sequenced, and phylogenetically analyzed. The characteristics of patients in exacerbation and stable phase were compared. RESULTS: Viruses were found in 25% of samples. The HRV viruses were the most frequently detected followed by coronaviruses. Only the HRV detection was significantly associated with the occurrence of CF pulmonary exacerbation (p < 0.027). Characterization of 5′UTR and VP4/2 regions of the HRV genome specified that HRV-A, -B, -C were detected. All HRV-C were recombinant HRV-Ca. CONCLUSIONS: HRV were the most frequently detected viruses; their detection was significantly associated with the occurrence of an exacerbation. The reality of viral recombination between HRV was demonstrated in CF patients for the first time, raising the role of viruses in lung microbiota. Further studies are now warranted to decipher virus impact in CF. url: https://doi.org/10.1016/j.jcv.2014.02.005 doi: 10.1016/j.jcv.2014.02.005 id: cord-323700-5awng7h1 author: Goggin, Rachel K. title: Comparative Viral Sampling in the Sinonasal Passages; Different Viruses at Different Sites date: 2018-09-19 words: 3528.0 sentences: 197.0 pages: flesch: 49.0 cache: ./cache/cord-323700-5awng7h1.txt txt: ./txt/cord-323700-5awng7h1.txt summary: The aim of the study here presented was to establish differences in viral detection and species sampled from different sinonasal sites, in an effort to validate and standardise viral collection techniques, and facilitate further investigation of the sinonasal virome. All DNA extracts first underwent an endogenous retrovirus 3 (ERV3) assay (present as two copies per human diploid cell) in order to confirm respiratory sample collection quality. Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control High rates of detection of respiratory viruses in the nasal washes and mucosae of patients with chronic rhinosinusitis Detection of herpesviruses 1-6 and community-acquired respiratory viruses in patients with chronic rhinosinusitis with nasal polyposis Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions Real-time quantitative PCR assays for detection and monitoring of pathogenic human viruses in immunosuppressed pediatric patients abstract: Background: With the emergence of the microbiome as an important factor in health and disease in the respiratory tract standardised, validated techniques are required for its accurate characterisation. No standardised technique has been reported specifically for viral sampling in the sinonasal passages. Aim: To optimise viral sampling techniques from the sinonasal cavity. Methods: Sterile cytology brushes were used under endoscopic guidance to sample the sinonasal mucosa at time of endoscopic sinus surgery at both the middle and inferior meatuses (MM and IM). DNA and RNA were extracted from the samples and underwent PCR or RT-PCR testing, respectively, for a panel of 15 common upper respiratory tract viruses. Results: Twenty-four adult patients were recruited for this study. 18/24 (75%) patients were positive for virus in at least one site, while 8/24 (33%) were positive for virus at both sites. The mean number of viruses identified at the two sites were similar (0.875 ± 0.899 at the MM vs. 0.750 ± 1.032 at the IM). 6/24 (25%) of patients showed no virus at either site, while 3/24 (12.5%) demonstrated the same viral species at both sites. Conclusion: Although the number of viruses present at different sites with the nasal cavity are similar, discord exists in the viral species between sites. It is therefore recommended that both sites are sampled in the clinical and research setting better to characterise the viral species within the nasal cavity. url: https://doi.org/10.3389/fcimb.2018.00334 doi: 10.3389/fcimb.2018.00334 id: cord-315167-ph15z424 author: Goka, E. A. title: Pan-human coronavirus and human bocavirus SYBR Green and TaqMan PCR assays; use in studying influenza A viruses co-infection and risk of hospitalization date: 2014-12-05 words: 3311.0 sentences: 185.0 pages: flesch: 52.0 cache: ./cache/cord-315167-ph15z424.txt txt: ./txt/cord-315167-ph15z424.txt summary: title: Pan-human coronavirus and human bocavirus SYBR Green and TaqMan PCR assays; use in studying influenza A viruses co-infection and risk of hospitalization This study investigated the association between influenza A viruses co-infection with hBoV and hCoV and severity and the sensitivity of a real-time polymerase chain reaction (RT-PCR) assay for identification of 15 coronaviruses. A series of 217 samples from patients aged 37.7 (SD ± 30.4)] with seasonal influenza A viruses (SeasFluA) identified between 06/2011 and 06/2012 in NW England were tested for hCoV and hBoV using RT-PCR. RESULTS: The limit of detection of hCoV RT-PCR assay was 2 copies/µl of human coronavirus RNA template, a sensitivity comparable to a previously published SYBR green assay for human coronaviruses. This study did not find a significant association between seasonal influenza A viruses co-infection with hCoV and hBoV and severe disease. abstract: PURPOSE: Influenza A viruses, human coronaviruses (hCoV) and human bocavirus (hBoV) are emerging respiratory viruses. This study investigated the association between influenza A viruses co-infection with hBoV and hCoV and severity and the sensitivity of a real-time polymerase chain reaction (RT-PCR) assay for identification of 15 coronaviruses. METHODOLOGY: Published sequences for the 15 human coronaviruses were used to design a consensus PCR targeting the replicase open reading frame 1b. A previously published PCR targeting the NS1 Gene of all known human bocavirus strains was also utilized. A series of 217 samples from patients aged 37.7 (SD ± 30.4)] with seasonal influenza A viruses (SeasFluA) identified between 06/2011 and 06/2012 in NW England were tested for hCoV and hBoV using RT-PCR. Association between co-infection and disease outcome was assessed using logistic regression. RESULTS: The limit of detection of hCoV RT-PCR assay was 2 copies/µl of human coronavirus RNA template, a sensitivity comparable to a previously published SYBR green assay for human coronaviruses. A total of 12 hCoV and 17 hBoV were identified in the 217 influenza A positive samples. A higher proportion (61.5 %; 8/13) of SeasFluA/hBoV co-infections were identified in patients that were admitted either to a general ward or the intensive care unit compared to 44.3 % (66/149) of single SeasFlu A virus infections (OR 2.5 95 % CI 0.67–9.34, p = 0.17). In a stratified analysis, there was a trend towards higher association between FluA, hCoV and hBoV with increasing age (especially in patients aged 24–45 years and >65 year old). CONCLUSION: Our hCoV RT-PCR protocol appeared to be of adequate analytical sensitivity for diagnosis. More and larger studies are needed to confirm the role of hCoV, hBoV in causing severe disease when they co-infect with influenza A viruses. url: https://doi.org/10.1007/s15010-014-0710-5 doi: 10.1007/s15010-014-0710-5 id: cord-305742-wf6qxplf author: Gomez, Santiago A. title: Binding of SARS–CoV–2 to cell receptors: a tale of molecular evolution date: 2020-09-28 words: 3457.0 sentences: 176.0 pages: flesch: 53.0 cache: ./cache/cord-305742-wf6qxplf.txt txt: ./txt/cord-305742-wf6qxplf.txt summary: In addition to the formal quantum characterization of bonding interactions, computation of absorption spectra for the specific virus· · · cell interacting residues yields significant shifts of ∆λ max = 47 and 66 nm in the wavelength for maximum absorption in the complex with respect to the isolated host and virus, respectively. In this work, we are interested in two crucial aspects of the initial virus· · · cell interaction problem: to pinpoint the specific residue to residue binding sites between the structurally known spike proteins of the virus [6] and the structurally known ACE2 receptor in cell membranes, [5] and to understand, from a fundamental, quantum perspective, the molecular factors driving the virus· · · cell binding. Therefore, we characterize the virus· · · cell binding as due to a large number of non-covalent contacts between the two proteins, enhanced by the water molecules, acting in conjunction with the specific residue to residue hydrogen bonds. abstract: The magnified infectious power of the SARS–CoV–2 virus compared to its precursor SARS–CoV is intimately linked to an enhanced ability in the mutated virus to find available hydrogen bond sites in the host cells. This characteristic is acquired during virus evolution because of the selective pressure exerted at the molecular level. We pinpoint the specific residue (in the virus) to residue (in the cell) contacts during the initial recognition and binding and show that the virus· · · cell interaction is mainly due to an extensive network of hydrogen bonds and to a large surface of non–covalent interactions. In addition to the formal quantum characterization of bonding interactions, computation of absorption spectra for the specific virus· · · cell interacting residues yields significant shifts of ∆λ max = 47 and 66 nm in the wavelength for maximum absorption in the complex with respect to the isolated host and virus, respectively. url: https://doi.org/10.1002/cbic.202000618 doi: 10.1002/cbic.202000618 id: cord-305327-hayhbs5u author: Gonzalez, Jean-Paul title: Global Spread of Hemorrhagic Fever Viruses: Predicting Pandemics date: 2017-09-19 words: 10210.0 sentences: 424.0 pages: flesch: 37.0 cache: ./cache/cord-305327-hayhbs5u.txt txt: ./txt/cord-305327-hayhbs5u.txt summary: Other pathogens that are remarkable for their epidemic expansions include the arenavirus hemorrhagic fevers and hantavirus diseases carried by rodents over great geographic distances and the arthropod-borne viruses (West Nile, chikungunya and Zika) enabled by ecology and vector adaptations. Emergence from a sporadic case to an outbreak, to an epidemic, and ultimately to a pandemic depends upon effective transmission among nonimmune hosts, host availability (density), characteristics of the vector (natural or human made) that would enable it to circumvent distances, and the pathogen infectiousness. Although MARV expansion appears to be limited to a few countries in Africa, the recent emergence (estimated at a few decades ago) of a second human pathogenic marburgvirus known as Ravn virus, and the widely distributed Old World rousette fruit bats (Rousettus spp.) serving as reservoir for both viruses [45] , are two factors that favor pandemic risk. abstract: As successive epidemics have swept the world, the scientific community has quickly learned from them about the emergence and transmission of communicable diseases. Epidemics usually occur when health systems are unprepared. During an unexpected epidemic, health authorities engage in damage control, fear drives action, and the desire to understand the threat is greatest. As humanity recovers, policy-makers seek scientific expertise to improve their “preparedness” to face future events. Global spread of disease is exemplified by the spread of yellow fever from Africa to the Americas, by the spread of dengue fever through transcontinental migration of mosquitos, by the relentless influenza virus pandemics, and, most recently, by the unexpected emergence of Ebola virus, spread by motorbike and long haul carriers. Other pathogens that are remarkable for their epidemic expansions include the arenavirus hemorrhagic fevers and hantavirus diseases carried by rodents over great geographic distances and the arthropod-borne viruses (West Nile, chikungunya and Zika) enabled by ecology and vector adaptations. Did we learn from the past epidemics? Are we prepared for the worst? The ultimate goal is to develop a resilient global health infrastructure. Besides acquiring treatments, vaccines, and other preventive medicine, bio-surveillance is critical to preventing disease emergence and to counteracting its spread. So far, only the western hemisphere has a large and established monitoring system; however, diseases continue to emerge sporadically, in particular in Southeast Asia and South America, illuminating the imperfections of our surveillance. Epidemics destabilize fragile governments, ravage the most vulnerable populations, and threaten the global community. Pandemic risk calculations employ new technologies like computerized maintenance of geographical and historical datasets, Geographic Information Systems (GIS), Next Generation sequencing, and Metagenomics to trace the molecular changes in pathogens during their emergence, and mathematical models to assess risk. Predictions help to pinpoint the hot spots of emergence, the populations at risk, and the pathogens under genetic evolution. Preparedness anticipates the risks, the needs of the population, the capacities of infrastructure, the sources of emergency funding, and finally, the international partnerships needed to manage a disaster before it occurs. At present, the world is in an intermediate phase of trying to reduce health disparities despite exponential population growth, political conflicts, migration, global trade, urbanization, and major environmental changes due to global warming. For the sake of humanity, we must focus on developing the necessary capacities for health surveillance, epidemic preparedness, and pandemic response. url: https://doi.org/10.1007/978-1-4939-6981-4_1 doi: 10.1007/978-1-4939-6981-4_1 id: cord-009577-29u7pdpk author: Gonzalez‐Scarano, F. title: Molecular pathogenesis of neurotropic viral infections date: 2004-10-08 words: 6374.0 sentences: 294.0 pages: flesch: 41.0 cache: ./cache/cord-009577-29u7pdpk.txt txt: ./txt/cord-009577-29u7pdpk.txt summary: To cause systemic illness, a virus must first enter the host animal, undergo primary replication at a site near its portal of entry, and then ultimately spread to distant target tissues, such as the central nervous system (CNS). An infecting animal virus faces two main blocks to penetration of the CNS or any other specific target organ: (1) a variety of barriers prevent the free access of viruses to target cells, and (2) even when these barriers are ineffective, only certain cell types will support the internalization and replication of a particular virus. Monoclonal antibody variants have been used to map the antigenic sites of the influenza hemagglutinin 122, 76, 771 and have been used successfully to define important regions of the cellular binding proteins of rabies virus, reovirus, coronaviruses, and the California serogroup-all CNS pathogens. Viruses bind to the plasma membrane of susceptible target cells through specific receptors which may be proteins (HIV), lipids (vesicular stomatitis virus), or contain sialic acid (reovirus, influenza) [21, 641. abstract: Classical virologists defined a number of viruses that affect the nervous system and identified tissue tropism, extraneural replication, and viremia as important parameters that determine whether viral infections will affect the central nervous system. Molecular techniques are expanding this knowledge by permitting us to relate specific genes and gene products to two defined phenotypes: neuroinvasion and neurovirulence. Two converging situations make this knowledge particularly useful: (1) the development of antiviral drugs and subunit vaccines, which mandate that pathogenesis be related to specific regions of the viral genome; and (2) the expanding problem of central nervous system infections in immunodeficient states. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159691/ doi: 10.1002/ana.410220502 id: cord-278684-txlvla0j author: Gonzalez–Dunia, Daniel title: Borna Disease Virus and the Brain date: 1998-01-30 words: 13952.0 sentences: 784.0 pages: flesch: 43.0 cache: ./cache/cord-278684-txlvla0j.txt txt: ./txt/cord-278684-txlvla0j.txt summary: The BDV paradigm is amenable to study virus–cell interactions in the CNS that can lead to neurodevelopmental abnormalities, immune-mediated damage, as well as alterations in cell differentiated functions that affect brain homeostasis. Evidence provided by epidemiological and clinical data, together with virological studies, have led to the hypothesis that chronic viral infections of the CNS contribute to human mental disorders of unknown etiology. Therefore, neuronal damage seen in BD appears to be mediated by the cytotoxic activity of CD8 ϩ T-cells present in the brain parenchyma of BDV-infected rats. Studies on PTI-NB rats may provide valuable information regarding the contribution of CNS resident cells to disturbances in cytokine gene expression caused by BDV. Borna disease virus replicates in astrocytes, Schwann cells and ependymal cells in persistently infected rats: Location of viral genomic and messenger RNAs by in situ hybridization Expression of tissue factor is increased in astrocytes within the central nervous system during persistent infection with Borna disease virus abstract: Viruses with the ability to establish persistent infection in the central nervous system (CNS) can induce progressive neurologic disorders associated with diverse pathological manifestations. Clinical, epidemiological, and virological evidence supports the hypothesis that viruses contribute to human mental diseases whose etiology remains elusive. Therefore, the investigation of the mechanisms whereby viruses persist in the CNS and disturb normal brain function represents an area of research relevant to clinical and basic neurosciences. Borna disease virus (BDV) causes CNS disease in several vertebrate species characterized by behavioral abnormalities. Based on its unique features, BDV represents the prototype of a new virus family. BDV provides an important model for the investigation of the mechanisms and consequences of viral persistence in the CNS. The BDV paradigm is amenable to study virus–cell interactions in the CNS that can lead to neurodevelopmental abnormalities, immune-mediated damage, as well as alterations in cell differentiated functions that affect brain homeostasis. Moreover, seroepidemiological data and recent molecular studies indicate that BDV is associated with certain neuropsychiatric diseases. The potential role of BDV and of other yet to be uncovered BDV-related viruses in human mental health provides additional impetus for the investigation of this novel neurotropic infectious agent. url: https://api.elsevier.com/content/article/pii/S0361923097002761 doi: 10.1016/s0361-9230(97)00276-1 id: cord-334365-idjvbcy4 author: Gooding, J. Justin title: Virus Detection: What Were We Doing before COVID-19 Changed the World? date: 2020-05-29 words: 969.0 sentences: 69.0 pages: flesch: 55.0 cache: ./cache/cord-334365-idjvbcy4.txt txt: ./txt/cord-334365-idjvbcy4.txt summary: The papers in this virtual issue are by some of the researchers that have been developing tests to detect viruses. It is clear that a rapid, portable test that could detect the virus directly, with high sensitivity and specificity, would be a brilliant advance. In this virtual issue we concentrate on the development of molecular tests for viruses, a focus not surprising for two chemistry journals dealing with analytical measurement. The issue leads with a review on detection of biothreats (Mother Nature is an accomplished bioterrorist!), and then covers a range of innovative technologies 1 that focus on assays for point of care testing, 2−4 faster diagnostic testing, 5−8 more sensitive diagnostic testing, 9−17 characterizing the response to the virus, 18−21 and highly sensitive methods for biologically tracking and characterizing the virus. Development of an Electrochemical Paper-Based Analytical Device for Trace Detection of Virus Particles abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32469511/ doi: 10.1021/acssensors.0c01029 id: cord-343918-5yk1j4ms author: Gorbalenya, A.E. title: Phylogeny of Viruses date: 2008-07-30 words: 3892.0 sentences: 182.0 pages: flesch: 40.0 cache: ./cache/cord-343918-5yk1j4ms.txt txt: ./txt/cord-343918-5yk1j4ms.txt summary: For inferring phylogeny, the differences between aligned sequences of genomes and proteins are quantified and depicted in the form of a tree, in which contemporary species and their intermediate and common ancestors occupy, respectively, the terminal nodes, internal nodes, and the root. Phylogenetic analysis is used in a wide range of studies to address both applied and fundamental issues of virus research, including epidemiology, diagnostics, forensic studies, phylogeography, origin, evolution, and taxonomy of viruses. With the latter virus, poor sampling of the coronavirus diversity in the SARS-CoV lineage at the time, some uncertainty over the relationship between phylogeny and taxonomy of coronaviruses, and the complexity of phylogenetic analysis of a virus data set including isolated distant lineages led to considerable controversy over the exact evolutionary position of SARS-CoV among coronaviruses. abstract: Biological species, including viruses, change through generations and over time in the process known as evolution. Viruses may evolve at high, uneven, and fluctuating rates among genome sites. The accumulated changes, through either mutation or recombination with other species, are first fixed in the genome of successful individuals that give rise to genetic lineages. The relationship between biological lineages related by common descent is called ‘phylogeny’. For inferring phylogeny, the differences between aligned sequences of genomes and proteins are quantified and depicted in the form of a tree, in which contemporary species and their intermediate and common ancestors occupy, respectively, the terminal nodes, internal nodes, and the root. The tree is characterized by a topology, length of branches, shape, and the root position. A complex mathematical apparatus has been developed for phylogeny inference that can evaluate inter-species differences, facilitate tree building and comparison of trees, and assess the fit between data and tree through, typically, computationally intensive calculations. A reconstructed tree is an approximation of the true phylogeny that practically remains unknown. The phylogenetic analysis is used in applied and fundamental virus research, including epidemiology, diagnostics, forensic studies, phylogeography, evolutionary studies, and virus taxonomy. It can provide an evolutionary perspective on variation of any trait that can be measured for a group of viruses. url: https://www.sciencedirect.com/science/article/pii/B9780123744104007123 doi: 10.1016/b978-012374410-4.00712-3 id: cord-338081-ggw5l1qm author: Gorbalenya, Alexander E. title: Phylogeny of Viruses date: 2017-06-26 words: 3638.0 sentences: 154.0 pages: flesch: 41.0 cache: ./cache/cord-338081-ggw5l1qm.txt txt: ./txt/cord-338081-ggw5l1qm.txt summary: For inferring phylogeny, the differences between aligned sequences of genomes and proteins are quantified and depicted in the form of a tree, in which contemporary species and their intermediate and common ancestors occupy, respectively, the terminal nodes, internal nodes, and the root. Bayesian methods have the highest computational cost due to their sampling approach and thus show the lowest speed, while realization of the similarly advanced ML algorithm may be largely comparable in speed to distance methods, allowing for the phylogenetic analysis of very large data sets like genome-wide tree reconstructions of cellular organisms or thousands of viruses. In the case of SARS-CoV, poor sampling of the coronavirus diversity in the lineage at the time, some uncertainty over the relationship between phylogeny and taxonomy of coronaviruses, and the complexity of phylogenetic analysis of a virus data set including isolated distant lineages led to considerable controversy over the exact evolutionary position of SARS-CoV among coronaviruses. abstract: Biological species, including viruses, change through generations and over time in the process known as evolution. Viruses may evolve at high, uneven, and fluctuating rates among genome sites. The accumulated changes, through either mutation or recombination with other species, are first fixed in the genome of successful individuals that give rise to genetic lineages. The relationship between biological lineages related by common descent is called ‘phylogeny’. For inferring phylogeny, the differences between aligned sequences of genomes and proteins are quantified and depicted in the form of a tree, in which contemporary species and their intermediate and common ancestors occupy, respectively, the terminal nodes, internal nodes, and the root. The tree is characterized by a topology, length of branches, shape, and the root position. A complex mathematical apparatus has been developed for phylogeny inference that can evaluate inter-species differences, facilitate tree building and comparison of trees, and assess the fit between data and tree through, typically, computationally intensive calculations. A reconstructed tree is an approximation of the true phylogeny that practically remains unknown. The phylogenetic analysis is used in applied and fundamental virus research, including epidemiology, diagnostics, forensic studies, phylogeography, evolutionary studies, and virus taxonomy. It can provide an evolutionary perspective on variation of any trait that can be measured for a group of viruses. url: https://api.elsevier.com/content/article/pii/B9780128012383957234 doi: 10.1016/b978-0-12-801238-3.95723-4 id: cord-307893-mvl0wrsj author: Goulter-Thorsen, R.M. title: Disciplines Associated with Food Safety: Food Virology date: 2014-01-13 words: 4993.0 sentences: 249.0 pages: flesch: 46.0 cache: ./cache/cord-307893-mvl0wrsj.txt txt: ./txt/cord-307893-mvl0wrsj.txt summary: Poliovirus was the first enteric virus to be widely recognized, causing foodborne disease outbreaks in the early 1900s associated with the consumption of contaminated raw milk. This method, as well as cultivation methods for the vaccine strain of poliovirus, eventually allowed for the quantification of infective virus plaque forming units and facilitated studies on detection and control of enteric viruses in water and foods, with a particular focus on molluscan shellfish. Although promising, the utility of these molecular amplification methods for virus detection in food and environmental samples was limited by low levels of contamination; high levels of matrix-associated inhibitory substances that interfered with nucleic acid amplification; and the lack of broadly reactive primers and probes for HuNoV. Recent epidemiological data continue to support the fact that viruses, particularly HuNoV, are the most common cause of foodborne disease of known etiology in USA. HEV is a positive-sense single-stranded RNA virus that is transmitted via the fecal-oral route, generally through the consumption of water and sometimes food that has become contaminated with human feces. abstract: Food virology is a relatively young but important field in food safety. Viruses in general and human noroviruses in particular, are the leading cause of foodborne disease of known etiology in developed countries. Hepatitis A virus is also important, as are a number of emerging viruses. This article identifies the relevant viruses, describes their structural characteristics and the diseases they cause, and what is known about their epidemiological significance. It also describes why their transmission is so difficult to control, their detection difficult to achieve, and future research needs that will facilitate their study by food safety scientists. url: https://www.sciencedirect.com/science/article/pii/B978012378612800024X doi: 10.1016/b978-0-12-378612-8.00024-x id: cord-007710-0u5ot5h4 author: Graham, Barney S. title: Challenges and Opportunities for Respiratory Syncytial Virus Vaccines date: 2013-05-24 words: 4113.0 sentences: 161.0 pages: flesch: 36.0 cache: ./cache/cord-007710-0u5ot5h4.txt txt: ./txt/cord-007710-0u5ot5h4.txt summary: Several technological and conceptual advances have recently occurred that make RSV vaccine development more feasible, and this collected knowledge is intended to help inform and organize the future contributions of funding agencies, scientists, regulatory agencies, and policy makers that will be needed to achieve the goal of a safe, effective, and accessible vaccine to prevent RSV-associated disease. Barik, this volume), and suggest that vaccines that elicit responses that block or avoid the immunomodulation associated with wild-type RSV infection without enhancing disease could provide more potent and durable immunity than natural infection. These include the need for improved animal models, better understanding of mucosal immunity, more definitive clinical endpoints to use in efficacy trials, alternate vaccination strategies to protect the young infant (e.g., vaccinating pregnant women) and other high risk populations for whom vaccination may have limited effectiveness, and remedies for liability concerns. abstract: Respiratory syncytial virus (RSV) causes a significant proportion of the global burden of respiratory disease. Here we summarize the conclusions of a series of chapters written by investigators describing and interpreting what is known about the virology, clinical manifestations, immunity, pathogenesis, and epidemiology of RSV relevant to vaccine development. Several technological and conceptual advances have recently occurred that make RSV vaccine development more feasible, and this collected knowledge is intended to help inform and organize the future contributions of funding agencies, scientists, regulatory agencies, and policy makers that will be needed to achieve the goal of a safe, effective, and accessible vaccine to prevent RSV-associated disease. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121045/ doi: 10.1007/978-3-642-38919-1_20 id: cord-349011-kxhpdvri author: Grandvaux, Nathalie title: CSV2018: The 2nd Symposium of the Canadian Society for Virology date: 2019-01-18 words: 8844.0 sentences: 375.0 pages: flesch: 42.0 cache: ./cache/cord-349011-kxhpdvri.txt txt: ./txt/cord-349011-kxhpdvri.txt summary: Invited keynote speakers included David Kelvin (Dalhousie University and Shantou University Medical College) who provided a historical perspective on influenza on the 100th anniversary of the 1918 pandemic; Sylvain Moineau (Université Laval) who described CRISPR-Cas systems and anti-CRISPR proteins in warfare between bacteriophages and their host microbes; and Kate O''Brien (then from Johns Hopkins University, now relocated to the World Health Organization where she is Director of Immunization, Vaccines and Biologicals), who discussed the underlying viral etiology for pneumonia in the developing world, and the evidence for respiratory syncytial virus (RSV) as a primary cause. The "Viral Subversion of Host Cell Processes" session also included presentations from the following trainees: Nichole McMullen (Dalhousie University) who reported the unconventional egress mechanisms of non-enveloped reoviruses, Justine Sitz (Université Laval) who described interactions between a human papillomavirus protein and a host DNA repair-specific E3 ubiquitin ligase, and Quentin Osseman (Université de Montréal) who described interactions between respiratory syncytial virus (RSV) and the host autophagy pathway. abstract: The 2nd Symposium of the Canadian Society for Virology (CSV2018) was held in June 2018 in Halifax, Nova Scotia, Canada, as a featured event marking the 200th anniversary of Dalhousie University. CSV2018 attracted 175 attendees from across Canada and around the world, more than double the number that attended the first CSV symposium two years earlier. CSV2018 provided a forum to discuss a wide range of topics in virology including human, veterinary, plant, and microbial pathogens. Invited keynote speakers included David Kelvin (Dalhousie University and Shantou University Medical College) who provided a historical perspective on influenza on the 100th anniversary of the 1918 pandemic; Sylvain Moineau (Université Laval) who described CRISPR-Cas systems and anti-CRISPR proteins in warfare between bacteriophages and their host microbes; and Kate O’Brien (then from Johns Hopkins University, now relocated to the World Health Organization where she is Director of Immunization, Vaccines and Biologicals), who discussed the underlying viral etiology for pneumonia in the developing world, and the evidence for respiratory syncytial virus (RSV) as a primary cause. Reflecting a strong commitment of Canadian virologists to science communication, CSV2018 featured the launch of Halifax’s first annual Soapbox Science event to enable public engagement with female scientists, and the live-taping of the 499th episode of the This Week in Virology (TWIV) podcast, hosted by Vincent Racaniello (Columbia University) and science writer Alan Dove. TWIV featured interviews of CSV co-founders Nathalie Grandvaux (Université de Montréal) and Craig McCormick (Dalhousie University), who discussed the origins and objectives of the new society; Ryan Noyce (University of Alberta), who discussed technical and ethical considerations of synthetic virology; and Kate O’Brien, who discussed vaccines and global health. Finally, because CSV seeks to provide a better future for the next generation of Canadian virologists, the symposium featured a large number of oral and poster presentations from trainees and closed with the awarding of presentation prizes to trainees, followed by a tour of the Halifax Citadel National Historic Site and an evening of entertainment at the historic Alexander Keith’s Brewery. url: https://doi.org/10.3390/v11010079 doi: 10.3390/v11010079 id: cord-000501-qz68gtd4 author: Greatorex, Jane S. title: Survival of Influenza A(H1N1) on Materials Found in Households: Implications for Infection Control date: 2011-11-22 words: 4311.0 sentences: 194.0 pages: flesch: 47.0 cache: ./cache/cord-000501-qz68gtd4.txt txt: ./txt/cord-000501-qz68gtd4.txt summary: METHODOLOGY AND PRINCIPAL FINDINGS: Influenza A/PuertoRico/8/34 (PR8) or A/Cambridge/AHO4/2009 (pandemic H1N1) viruses were inoculated onto a wide range of surfaces used in home and work environments, then sampled at set times following incubation at stabilised temperature and humidity. The potential for transmission of influenza by indirect contact (i.e. via fomites) is linked to the ability of virus to survive in transmissible titres on commonly touched surfaces; however few data exist on this subject. We evaluate the survival of influenza A (H1N1) viruses deliberately applied to a range of commonly touched household and workplace surfaces, using RT-PCR for genome detection and culture methods to determine viability. Our data are consistent with recent findings from a study of environmental deposition of pandemic H1N1 virus in the homes of infected patients, involving our laboratory, when almost 10% of tested surfaces yielded viable virus [15] . abstract: BACKGROUND: The majority of influenza transmission occurs in homes, schools and workplaces, where many frequently touched communal items are situated. However the importance of transmission via fomites is unclear since few data exist on the survival of virus on commonly touched surfaces. We therefore measured the viability over time of two H1N1 influenza strains applied to a variety of materials commonly found in households and workplaces. METHODOLOGY AND PRINCIPAL FINDINGS: Influenza A/PuertoRico/8/34 (PR8) or A/Cambridge/AHO4/2009 (pandemic H1N1) viruses were inoculated onto a wide range of surfaces used in home and work environments, then sampled at set times following incubation at stabilised temperature and humidity. Virus genome was measured by RT-PCR; plaque assay (for PR8) or fluorescent focus formation (for pandemic H1N1) was used to assess the survival of viable virus. CONCLUSIONS/SIGNIFICANCE: The genome of either virus could be detected on most surfaces 24 h after application with relatively little drop in copy number, with the exception of unsealed wood surfaces. In contrast, virus viability dropped much more rapidly. Live virus was recovered from most surfaces tested four hours after application and from some non-porous materials after nine hours, but had fallen below the level of detection from all surfaces at 24 h. We conclude that influenza A transmission via fomites is possible but unlikely to occur for long periods after surface contamination (unless re-inoculation occurs). In situations involving a high probability of influenza transmission, our data suggest a hierarchy of priorities for surface decontamination in the multi-surface environments of home and hospitals. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3222642/ doi: 10.1371/journal.pone.0027932 id: cord-287286-4l963z2q author: Green, Victoria A. title: Molecular mechanisms of viral infection and propagation: An overview of the second Advanced Summer School in Africa date: 2010-07-28 words: 7368.0 sentences: 363.0 pages: flesch: 43.0 cache: ./cache/cord-287286-4l963z2q.txt txt: ./txt/cord-287286-4l963z2q.txt summary: The main themes of discussion at the summer school were: 1) why viral infection can lead to cancer; 2) how a greater understanding of the mechanisms underpinning human immunodeficiency virus (HIV) propagation can inform new antiviral strategies; 3) the abilities of viruses to evade the immune system and the obstacles to the development of effective vaccines; and, 4) the potential afforded by viruses as research tools. The import of the host, including an ability to regulate viral gene expression in different tissues and to mount an effective immune response, is becoming increasingly apparent in determining the molecular basis of HPV-associated tumor progression. Advantages CoVs possess over other viruses as expression vectors include: 1) the possibility of spike protein manipulation, to engineer virus tropism (88, 89) ; 2) the replication of the RNA genome in the cytoplasm, side-stepping potential problems associated with integration (90); 3) the existence of nonpathogenic strains that infect a wide range of species of health and economic importance; 4) the ability to carry large genomes (27-30 kb) , which could favor the introduction of extensive foreign genes (91); and 5) the availability of cDNA clones derived from infectious strains (92, 93) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/20681023/ doi: 10.1002/iub.364 id: cord-337577-dqikrmk7 author: Greenberg, Harry B. title: Vaccination against Viruses date: 2016-05-09 words: 4789.0 sentences: 225.0 pages: flesch: 32.0 cache: ./cache/cord-337577-dqikrmk7.txt txt: ./txt/cord-337577-dqikrmk7.txt summary: In the elderly, measures of cell-mediated immunity, such as granzyme B levels in virus-stimulated peripheral blood mononuclear cells, may correlate better than serum antibody titers with vaccine-elicited protection (McElhaney et al., 2009 ). Whether cell-mediated effector mechanisms, mucosal antibody, or some other factor is primarily responsible for protection by live attenuated influenza vaccines or natural infection remains controversial despite several decades of study. A key finding has been that, among the neutralizing antibodies elicited in response to influenza virus, HIV, or RSV infection or immunization, some have remarkably broad specificity (Burton and Mascola 2015; Corti et al., 2013 Corti et al., , 2011 . The elucidation of Toll-like receptors as key sentry molecules that detect potential pathogens and recruit antigen-presenting cells for a subsequent antigen-specific response has enabled the rational design of a new generation of potential vaccine adjuvants (Wu et al., 2014) . abstract: Most vaccines in use today are the result of empirical development. The mechanism of action of many vaccines in common use remains incompletely understood. Understanding how such vaccines protect is an ongoing subject of study using increasingly sophisticated immunological tools, such as B cell and T cell repertoire and transcriptome analysis. Such tools are also being applied to the design of vaccines against those viral targets that have evaded vaccine-mediated protection thus far. As basic immunological science intersects with the practicalities of assuring vaccine safety, tolerability, efficacy, and consistency in the clinic, the practical utility of more sophisticated immunological measures for vaccine development may be determined by whether they can be reduced to simply executed, highly standardized, reproducible assays with outcomes that have clear interpretations for vaccine development and use. Basic immunology, empirical vaccine testing, and regulatory science are all necessary contributors to developing the next generation of vaccines, including vaccines effective against the pathogens for which vaccines are not currently available. url: https://api.elsevier.com/content/article/pii/B9780123742797140160 doi: 10.1016/b978-0-12-374279-7.14016-0 id: cord-304424-048xo7jn author: Greninger, Alexander L. title: A decade of RNA virus metagenomics is (not) enough date: 2018-01-15 words: 9606.0 sentences: 495.0 pages: flesch: 43.0 cache: ./cache/cord-304424-048xo7jn.txt txt: ./txt/cord-304424-048xo7jn.txt summary: That same year 36,789 colony sequences from DNase-treated RNA extracted from viral concentrates of human feces revealed a preponderance of pepper mild mottle virus and other plant viruses, but no new human viruses (Zhang et al., 2005) . While finding a new virus in the environment is not necessarily a problem in either DNA or RNA, the low fidelity of RNA polymerases and the sequence space they are capable of sampling, along with the possibility of recombination, lend themselves to new species and genera that are the trophies of metagenomic viral discovery. While metagenomics delivered on the promise of finding novel human viruses, viral discovery in humans has increasingly become a tragic story of patients interacting with the wrong squirrel or tick on the wrong day and most samples sequenced are frankly negative (Hoffmann et al., 2015; McMullan et al., 2012) . The greatest paradigm shifter in recent viral metagenomics work has been the sheer number and diversity of novel RNA viruses present in arthropods and invertebrates. abstract: It is hard to overemphasize the role that metagenomics has had on our recent understanding of RNA virus diversity. Metagenomics in the 21st century has brought with it an explosion in the number of RNA virus species, genera, and families far exceeding that following the discovery of the microscope in the 18th century for eukaryotic life or culture media in the 19th century for bacteriology or the 20th century for virology. When the definition of success in organism discovery is measured by sequence diversity and evolutionary distance, RNA viruses win. This review explores the history of RNA virus metagenomics, reasons for the successes so far in RNA virus metagenomics, and methodological concerns. In addition, the review briefly covers clinical metagenomics and environmental metagenomics and highlights some of the critical accomplishments that have defined the fast pace of RNA virus discoveries in recent years. Slightly more than a decade in, the field is exhausted from its discoveries but knows that there is yet even more out there to be found. url: https://www.ncbi.nlm.nih.gov/pubmed/29055712/ doi: 10.1016/j.virusres.2017.10.014 id: cord-325825-0lyt8gfq author: Griffiths, Samantha J. title: A Systematic Analysis of Host Factors Reveals a Med23-Interferon-λ Regulatory Axis against Herpes Simplex Virus Type 1 Replication date: 2013-08-08 words: 12504.0 sentences: 601.0 pages: flesch: 45.0 cache: ./cache/cord-325825-0lyt8gfq.txt txt: ./txt/cord-325825-0lyt8gfq.txt summary: Host factors (HFs) which positively or negatively regulate HSV-1 replication were identified by screening a druggable genome siRNA library (4 siRNAs per gene) targeting 7,237 human genes against a HSV-1 reporter virus expressing the enhanced green fluorescent protein (eGFP; HSV-1 strain C12) in the epithelial Hela cell line, due to their ease of transfection and susceptibility to HSV-1 infection [34] . Combined bioinformatic analyses of protein interaction and siRNA depletion screens found a significant functional enrichment for proteins involved in transcription, and identified multi-protein complexes enriched for pro-viral HFs which strongly inhibited HSV-1 upon depletion, including the RNA-polymerase II, eIF3 and Mediator complexes ( Figure 3a) . Furthermore, qPCR analysis found depletion of Med23 inhibited the induction of IFN-l expression following HSV-1 infection of A549 cells in comparison to cells transfected with the RSCF siRNA control ( Figure 4e ). abstract: Herpes simplex virus type 1 (HSV-1) is a neurotropic virus causing vesicular oral or genital skin lesions, meningitis and other diseases particularly harmful in immunocompromised individuals. To comprehensively investigate the complex interaction between HSV-1 and its host we combined two genome-scale screens for host factors (HFs) involved in virus replication. A yeast two-hybrid screen for protein interactions and a RNA interference (RNAi) screen with a druggable genome small interfering RNA (siRNA) library confirmed existing and identified novel HFs which functionally influence HSV-1 infection. Bioinformatic analyses found the 358 HFs were enriched for several pathways and multi-protein complexes. Of particular interest was the identification of Med23 as a strongly anti-viral component of the largely pro-viral Mediator complex, which links specific transcription factors to RNA polymerase II. The anti-viral effect of Med23 on HSV-1 replication was confirmed in gain-of-function gene overexpression experiments, and this inhibitory effect was specific to HSV-1, as a range of other viruses including Vaccinia virus and Semliki Forest virus were unaffected by Med23 depletion. We found Med23 significantly upregulated expression of the type III interferon family (IFN-λ) at the mRNA and protein level by directly interacting with the transcription factor IRF7. The synergistic effect of Med23 and IRF7 on IFN-λ induction suggests this is the major transcription factor for IFN-λ expression. Genotypic analysis of patients suffering recurrent orofacial HSV-1 outbreaks, previously shown to be deficient in IFN-λ secretion, found a significant correlation with a single nucleotide polymorphism in the IFN-λ3 (IL28b) promoter strongly linked to Hepatitis C disease and treatment outcome. This paper describes a link between Med23 and IFN-λ, provides evidence for the crucial role of IFN-λ in HSV-1 immune control, and highlights the power of integrative genome-scale approaches to identify HFs critical for disease progression and outcome. url: https://doi.org/10.1371/journal.ppat.1003514 doi: 10.1371/journal.ppat.1003514 id: cord-022262-ck2lhojz author: Gromeier, Matthias title: Genetics, Pathogenesis and Evolution of Picornaviruses date: 2007-09-02 words: 28035.0 sentences: 1423.0 pages: flesch: 46.0 cache: ./cache/cord-022262-ck2lhojz.txt txt: ./txt/cord-022262-ck2lhojz.txt summary: The following viruses have been recognized as picornaviruses on the basis of their genome sequences and physico-chemical properties as well as the result of comparative sequence analyses (see the section on Evolution): equine rhinovirus types I and 2, Aichi virus, porcine enterovirus, avian encephalomyelitis virus, infectious flacherie virus of silkworm Clusters of enteroviruses refer to groups of enteroviruses arranged predominantly according to genotypic kinship (Hyypia et al., 1997) . Briefly, when expression vectors ( Figure 12 .6E) consisting of a gag gene (encoding p17-p24; 1161 nt) of human immunodeficiency virus that was fused to the N-terminus of the poliovirus polyprotein (Andino et al., 1994; Mueller and Wimmer, 1998) were analysed after transfection into HeLa cells, the genomes were not only found to be severely impaired in viral replication but they were also genetically unstable (Mueller and Wimmer, 1997) . abstract: The discovery of viruses heralded an exciting new era for research in the medical and biological sciences. It has been realized that the cellular receptor guiding a virus to a target cell cannot be the sole determinant of a virus's pathogenic potential. Comparative analyses of the structures of genomes and their products have placed the picornaviruses into a large “picorna-like” virus family, in which they occupy a prominent place. Most human picornavirus infections are self-limiting, yet the enormously high rate of picornavirus infections in the human population can lead to a significant incidence of disease complications that may be permanently debilitating or even fatal. Picornaviruses employ one of the simplest imaginable genetic systems: they consist of single-stranded RNA that encodes only a single multidomain polypeptide, the polyprotein. The RNA is packaged into a small, rigid, naked, and icosahedral virion whose proteins are unmodified except for a myristate at the N-termini of VP4. The RNA itself does not contain modified bases. The key to ultimately understanding picornaviruses may be to rationalize the huge amount of information about these viruses from the perspective of evolution. It is possible that the replicative apparatus of picornaviruses originated in the precellular world and was subsequently refined in the course of thousands of generations in a slowly evolving environment. Picornaviruses cultivated the art of adaptation, which has allowed them to “jump” into new niches offered in the biological world. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155501/ doi: 10.1016/b978-012220360-2/50013-1 id: cord-006252-cbelsymu author: Gross, Peter A. title: Current Recommendations for the Prevention and Treatment of Influenza in the Older Population date: 2012-11-18 words: 7666.0 sentences: 466.0 pages: flesch: 49.0 cache: ./cache/cord-006252-cbelsymu.txt txt: ./txt/cord-006252-cbelsymu.txt summary: Other groups merit consideration (Recommendations of the Immunization Practices Advisory Committee 1990): (a) in the general population, anyone who wishes to reduce the chance of acquiring influenza infection; (b) anyone who provides essential community services and persons living or working in an institutional setting; (c) persons infected with HIV should be vaccinated, although they may not respond as well if their disease is far advanced; and (d) foreign travellers should be immunised when travelling to the trop-Prevention and Treatment of Influenza implication here is that B cell epitopes are intact external molecules such as haemagglutinins, while T cell epitopes appear to be linear sequences exposed by enzymatic breakdown of the original molecule. abstract: Influenza is a major cause of morbidity and mortality in the elderly. Influenza vaccine is recommended for people aged 65 years and older and those in long term care. Currently only 30% of high risk persons are vaccinated. Vaccination generally stimulates an adequate immune response, is well tolerated and is to be encouraged. Prophylactic amantadine 100 mg/day should be given for 2 weeks with influenza vaccine in the aged population when they have not been previously immunised. Broad application of these preventive measures would have a significant impact on reducing influenza prevalence in the elderly and other high risk groups. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7100770/ doi: 10.2165/00002512-199101060-00003 id: cord-260147-w19hl2vs author: Gröner, Albrecht title: Effective inactivation of a wide range of viruses by pasteurization date: 2017-11-16 words: 4285.0 sentences: 204.0 pages: flesch: 33.0 cache: ./cache/cord-260147-w19hl2vs.txt txt: ./txt/cord-260147-w19hl2vs.txt summary: STUDY DESIGN AND METHODS: The virus inactivation kinetics of pasteurization for a broad range of viruses were evaluated in the relevant intermediates from more than 15 different plasma manufacturing processes. The first reliable virus inactivation method, pasteurization (heat treatment in aqueous solution at 608C for 10 hr), to effectively inactivate HBV and HCV (at that time called non-A/non-B hepatitis virus) in coagulation factor concentrates was studied and implemented at Behringwerke (a predecessor company of CSL Behring) in the late 1970s and early 1980s by employing suitable stabilizers and conditions to permit pasteurization without modifying the product, for example, formation of neoantigens or activated factors. 11, 12 Virus validation guidelines were ultimately developed and issued by the European authorities, requiring manufacturers to carry out studies to demonstrate the capacity, reliability, and effectiveness of the manufacturing processes to inactivate and/or remove viruses potentially present in the starting material (plasma pool for fractionation). abstract: BACKGROUND: Careful selection and testing of plasma reduces the risk of blood‐borne viruses in the starting material for plasma‐derived products. Furthermore, effective measures such as pasteurization at 60°C for 10 hours have been implemented in the manufacturing process of therapeutic plasma proteins such as human albumin, coagulation factors, immunoglobulins, and enzyme inhibitors to inactivate blood‐borne viruses of concern. A comprehensive compilation of the virus reduction capacity of pasteurization is presented including the effect of stabilizers used to protect the therapeutic protein from modifications during heat treatment. STUDY DESIGN AND METHODS: The virus inactivation kinetics of pasteurization for a broad range of viruses were evaluated in the relevant intermediates from more than 15 different plasma manufacturing processes. Studies were carried out under the routine manufacturing target variables, such as temperature and product‐specific stabilizer composition. Additional studies were also performed under robustness conditions, that is, outside production specifications. RESULTS: The data demonstrate that pasteurization inactivates a wide range of enveloped and nonenveloped viruses of diverse physicochemical characteristics. After a maximum of 6 hours' incubation, no residual infectivity could be detected for the majority of enveloped viruses. Effective inactivation of a range of nonenveloped viruses, with the exception of nonhuman parvoviruses, was documented. CONCLUSION: Pasteurization is a very robust and reliable virus inactivation method with a broad effectiveness against known blood‐borne pathogens and emerging or potentially emerging viruses. Pasteurization has proven itself to be a highly effective step, in combination with other complementary safety measures, toward assuring the virus safety of final product. url: https://www.ncbi.nlm.nih.gov/pubmed/29148053/ doi: 10.1111/trf.14390 id: cord-260168-rb7j94dh author: Gu, Jiang title: H5N1 infection of the respiratory tract and beyond: a molecular pathology study date: 2007-09-27 words: 6291.0 sentences: 369.0 pages: flesch: 51.0 cache: ./cache/cord-260168-rb7j94dh.txt txt: ./txt/cord-260168-rb7j94dh.txt summary: Negative controls also included an unrelated antisense probe against the fragment of the polymerase gene (R1AB) of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV), 20 as well as H5N1 in-situ hybridisation probes to tissues (including lung and tracheal) obtained from seven adults who died from infectious lung diseases other than H5N1 infl uenza (four, SARS; one, purulent bronchitis; two, pneumonia), one adult who died from a non-infectious disease (gastric ulcer), one pregnant woman who died from an amniotic embolism, and one aborted fetus. Presence of viral sequences and antigens in the CNS is consistent with the recent isolation of H5N1 virus from cerebrospinal fl uid of a boy who died from encephalitis 6 with neurological symptoms commonly seen in patients with H5N1 infl uenza (Gao Zh, unpublished), including the two cases in this study. abstract: BACKGROUND: Human infection with avian influenza H5N1 is an emerging infectious disease characterised by respiratory symptoms and a high fatality rate. Previous studies have shown that the human infection with avian influenza H5N1 could also target organs apart from the lungs. METHODS: We studied post-mortem tissues of two adults (one man and one pregnant woman) infected with H5N1 influenza virus, and a fetus carried by the woman. In-situ hybridisation (with sense and antisense probes to haemagglutinin and nucleoprotein) and immunohistochemistry (with monoclonal antibodies to haemagglutinin and nucleoprotein) were done on selected tissues. Reverse-transcriptase (RT) PCR, real-time RT-PCR, strand-specific RT-PCR, and nucleic acid sequence-based amplification (NASBA) detection assays were also undertaken to detect viral RNA in organ tissue samples. FINDINGS: We detected viral genomic sequences and antigens in type II epithelial cells of the lungs, ciliated and non-ciliated epithelial cells of the trachea, T cells of the lymph node, neurons of the brain, and Hofbauer cells and cytotrophoblasts of the placenta. Viral genomic sequences (but no viral antigens) were detected in the intestinal mucosa. In the fetus, we found viral sequences and antigens in the lungs, circulating mononuclear cells, and macrophages of the liver. The presence of viral sequences in the organs and the fetus was also confirmed by RT-PCR, strand-specific RT-PCR, real-time RT-PCR, and NASBA. INTERPRETATION: In addition to the lungs, H5N1 influenza virus infects the trachea and disseminates to other organs including the brain. The virus could also be transmitted from mother to fetus across the placenta. url: https://www.sciencedirect.com/science/article/pii/S0140673607615153 doi: 10.1016/s0140-6736(07)61515-3 id: cord-267326-355q6k6k author: Gu, Xiaoqiong title: Geospatial distribution of viromes in tropical freshwater ecosystems date: 2018-06-15 words: 8426.0 sentences: 424.0 pages: flesch: 44.0 cache: ./cache/cord-267326-355q6k6k.txt txt: ./txt/cord-267326-355q6k6k.txt summary: This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems. However, up till now, studies of land use impacts on the virome community in freshwater ecosystems are still limited as they mainly rely on traditional methodology (culture-based method or qPCR/RT-qPCR), which focuses on limited human virus targets without considering the whole picture of the viral community in the water environment (Corsi et al., 2014; Lenaker et al., 2017) . Thus, the objectives of this study were to: 1) investigate the overall virome distribution and diversity in diverse freshwater ecosystems (reservoirs/tributaries) in a tropical environment, 2) compare the virome community based on the different land use patterns, 3) assess the extent of human-related pathogenic viruses in surface waters, especially emerging zoonotic and human-related viruses, which may have been undetected before. abstract: This study seeks to understand the general distribution of virome abundance and diversity in tropical freshwater ecosystems in Singapore and the geospatial distribution of the virome under different landuse patterns. Correlations between diversity, environmental parameters and land use patterns were analyzed and significant correlations were highlighted. Overall, the majority (65.5%) of the annotated virome belonged to bacteriophages. The percentage of Caudovirales was higher in reservoirs whereas the percentages of Dicistroviridae, Microviridae and Circoviridae were higher in tributaries. Reservoirs showed a higher Shannon-index virome diversity compared to upstream tributaries. Land use (urbanized, agriculture and parkland areas) influenced the characteristics of the virome distribution pattern. Dicistroviridae and Microviridae were enriched in urbanized tributaries while Mimiviridae, Phycodnaviridae, Siphoviridae and Podoviridae were enriched in parkland reservoirs. Several sequences closely related to the emerging zoonotic virus, cyclovirus, and the human-related virus (human picobirnavirus), were also detected. In addition, the relative abundance of PMMoV (pepper mild mottle virus) sequences was significantly correlated with RT-qPCR measurements (0.588 < r < 0.879, p < 0.05). This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems. url: https://www.ncbi.nlm.nih.gov/pubmed/29550725/ doi: 10.1016/j.watres.2018.03.017 id: cord-290231-4m9lj0uq author: Guirakhoo, Farshad title: The Murray Valley encephalitis virus prM protein confers acid resistance to virus particles and alters the expression of epitopes within the R2 domain of E glycoprotein date: 1992-12-31 words: 5738.0 sentences: 261.0 pages: flesch: 48.0 cache: ./cache/cord-290231-4m9lj0uq.txt txt: ./txt/cord-290231-4m9lj0uq.txt summary: Abstract To study the role of the precursor to the membrane protein (prM) in flavivirus maturation, we inhibited the proteolytic processing of the Murray Valley encephalitis (MVE) virus prM to membrane protein in infected cells by adding the acidotropic agent ammonium chloride late in the virus replication cycle. By using monoclonal antibodies (MAbs) and protease maps, we previously demonstrated that the E glycoprotein of tick-borne encephalitis (TBE) virus undergoes an irreversible conformational change, predominantly in the epitopes of domain A, at mildly acidic pH . To understand the role of prM protein in virus maturation and its interaction with the E glycoprotein, we investigated the effect that ammonium chloride had on MVE viruses grown in C6/36 mosquito cells. The reactivities of MAbs defining nine distinct epitopes on the MVE E glycoprotein were compared on M-and prMcontaining viruses using supernatants of ammonium chloride-treated or untreated virus-infected C6/36 cells. abstract: Abstract To study the role of the precursor to the membrane protein (prM) in flavivirus maturation, we inhibited the proteolytic processing of the Murray Valley encephalitis (MVE) virus prM to membrane protein in infected cells by adding the acidotropic agent ammonium chloride late in the virus replication cycle. Viruses purified from supernatants of ammonium chloride-treated cells contained prM protein and were unable to fuse C6/36 mosquito cells from without. When ammonium chloride was removed from the cells, both the processing of prM and the fusion activity of the purified viruses were partially restored. By using monoclonal antibodies (MAbs) specific for the envelope (E) glycoprotein of MVE virus, we found that at least three epitopes were less accessible to their corresponding antibodies in the prM-containing MVE virus particles. Amino-terminal sequencing of proteolytic fragments of the E protein which were reactive with sequence-specific peptide antisera or MAb enabled us to estimate the site of the E protein interacting with the prM to be within amino acids 200 to 327. Since prM-containing viruses were up to 400-fold more resistant to a low pH environment, we conclude that the E-prM interaction might be necessary to protect the E protein from irreversible conformational changes caused by maturation into the acidic vesicles of the exocytic pathway. url: https://www.ncbi.nlm.nih.gov/pubmed/1280384/ doi: 10.1016/0042-6822(92)90267-s id: cord-271692-60nlid3c author: Guo, Wen-Ping title: Phylogeny and Origins of Hantaviruses Harbored by Bats, Insectivores, and Rodents date: 2013-02-07 words: 6203.0 sentences: 305.0 pages: flesch: 51.0 cache: ./cache/cord-271692-60nlid3c.txt txt: ./txt/cord-271692-60nlid3c.txt summary: Notably, the phylogenetic histories of the viruses are not always congruent with those of their hosts, suggesting that cross-species transmission has played a major role during hantavirus evolution and at all taxonomic levels, although we also noted some evidence for virus-host co-divergence. Our phylogenetic analysis also suggests that hantaviruses might have first appeared in Chiroptera (bats) or Soricomorpha (moles and shrews), before emerging in rodent species. An evolutionary analysis of all known hantaviruses including the novel viruses described here reveals the existence of four distinct phylogenetic groups of viruses that infect a range of mammalian hosts, and which have sometimes exchanged genes through segment reassortment. Irrespective of this history of reassortment it is clear that there have been multiple cross-species transmission events in the evolutionary history of the hantaviruses with, for example, those viruses sampled Soricomorpha forming a paraphyletic group, as do those from bats shown in the L tree. abstract: Hantaviruses are among the most important zoonotic pathogens of humans and the subject of heightened global attention. Despite the importance of hantaviruses for public health, there is no consensus on their evolutionary history and especially the frequency of virus-host co-divergence versus cross-species virus transmission. Documenting the extent of hantavirus biodiversity, and particularly their range of mammalian hosts, is critical to resolving this issue. Here, we describe four novel hantaviruses (Huangpi virus, Lianghe virus, Longquan virus, and Yakeshi virus) sampled from bats and shrews in China, and which are distinct from other known hantaviruses. Huangpi virus was found in Pipistrellus abramus, Lianghe virus in Anourosorex squamipes, Longquan virus in Rhinolophus affinis, Rhinolophus sinicus, and Rhinolophus monoceros, and Yakeshi virus in Sorex isodon, respectively. A phylogenetic analysis of the available diversity of hantaviruses reveals the existence of four phylogroups that infect a range of mammalian hosts, as well as the occurrence of ancient reassortment events between the phylogroups. Notably, the phylogenetic histories of the viruses are not always congruent with those of their hosts, suggesting that cross-species transmission has played a major role during hantavirus evolution and at all taxonomic levels, although we also noted some evidence for virus-host co-divergence. Our phylogenetic analysis also suggests that hantaviruses might have first appeared in Chiroptera (bats) or Soricomorpha (moles and shrews), before emerging in rodent species. Overall, these data indicate that bats are likely to be important natural reservoir hosts of hantaviruses. url: https://doi.org/10.1371/journal.ppat.1003159 doi: 10.1371/journal.ppat.1003159 id: cord-276908-9jthjf24 author: Gupta, Akanksha title: COVID‐19: Emergence of Infectious Diseases, Nanotechnology Aspects, Challenges, and Future Perspectives date: 2020-07-06 words: 5174.0 sentences: 385.0 pages: flesch: 57.0 cache: ./cache/cord-276908-9jthjf24.txt txt: ./txt/cord-276908-9jthjf24.txt summary: In last two decades, entire world faced three major outbreaks of coronaviruses like Severe Acute respiratory syndrome (SARS), middle east respiratory syndrome (MERS) and novel coronavirus disease i.e., COVID-19. Previously, CoV causes an epidemic of SARS in humans and infected thousands viruses belong to family Coronaviridae, which shows crown-like appearances under an electron microscope. A recent study published, relied on this approach, using the predicted structure of all SARS-CoV-2 proteins based on their homology with other known coronavirus protein structures, and identified several compounds with potential antiviral activity. [39, 77] A biological preparation provides active acquired immunity against particular infectious disease like COVID19 [51, 68] 5 Shenzhen, China SARS-CoV, NL63, HKU1 The organosulfur in the essential garlic oil inhibit the ACE2 (host-receptor site of the virus) and main protease of the virus as well as to treat the infection due to SARS-CoV-2. abstract: Wuhan, a city of China, is the epicenter for the pandemic outbreak of coronavirus disease‐2019 (COVID‐19). It has become a severe public health challenge to the world and established a public health emergency of international worry. This infectious disease has pulled down the economy of almost all top developed nations. The coronaviruses (CoVs) known for various epidemics caused time to time. Infectious diseases such as severe acute respiratory syndrome (SARS) and middle east respiratory syndrome (MERS), followed by COVID‐19, are all coronaviruses led outbreaks that scourged the history of mankind. CoVs evolved themselves to more infectious, transmissible, and more pandemic with time. To prevent the spread of the SARS‐CoV‐2, many countries have ordered the complete lockdown to combat the outbreak. This paper briefly discussed the historical background of CoVs and the evolution of human coronaviruses (HCoVs), the case studies and the development of their antiviral medications. The viral infection encountered with present‐day challenges and futuristic approaches with the help of nanotechnology to minimize the spread of infectious viruses. The antiviral drugs and their clinical advances, along with herbal medicines for viral inhibition and immunity boosters, are described. Elaboration of tables related to CoVs for the compilation of the literature has been adopted for the better understanding. url: https://www.ncbi.nlm.nih.gov/pubmed/32835089/ doi: 10.1002/slct.202001709 id: cord-291534-c6cjxq07 author: Gwyer Findlay, Emily title: Cationic Host Defence Peptides: Potential as Antiviral Therapeutics date: 2013-05-07 words: 8778.0 sentences: 410.0 pages: flesch: 39.0 cache: ./cache/cord-291534-c6cjxq07.txt txt: ./txt/cord-291534-c6cjxq07.txt summary: In addition, various a-defensins are described as having additional, non-microbicidal properties, including chemotaxis for effector cells of the innate and adaptive immune systems [24, 25] , inhibition of macrophage pro-inflammatory cytokines [26] , modulation of the intestinal microbiome [27] and the formation of protective peptide nanonets [28] . In particular, it demonstrated direct antiviral activity of HNP1 against HSV-1 in a temperature-and pH-dependent manner, inhibited by serum, but interestingly less sensitive to the inhibitory effects of cations than the more broadly studied antibacterial properties. Thus, although b-defensins can inhibit influenza virus infectivity (albeit less potently than the a-defensins or LL-37) [89] , immunomodulatory properties, perhaps also including up-regulation of IAV uptake by neutrophils [84] , may prove to be key to their protective function against this virus in vivo and future therapeutic developments. Both rhesus h-defensins and retrocyclins (including RTD3, RC1 and RC2) have been found to inhibit HSV-1 and HSV-2 infection of human cervical epithelial cell lines following pre-incubation of virus and peptide [66] . abstract: There is a pressing need to develop new antiviral treatments; of the 60 drugs currently available, half are aimed at HIV-1 and the remainder target only a further six viruses. This demand has led to the emergence of possible peptide therapies, with 15 currently in clinical trials. Advancements in understanding the antiviral potential of naturally occurring host defence peptides highlights the potential of a whole new class of molecules to be considered as antiviral therapeutics. Cationic host defence peptides, such as defensins and cathelicidins, are important components of innate immunity with antimicrobial and immunomodulatory capabilities. In recent years they have also been shown to be natural, broad-spectrum antivirals against both enveloped and non-enveloped viruses, including HIV-1, influenza virus, respiratory syncytial virus and herpes simplex virus. Here we review the antiviral properties of several families of these host peptides and their potential to inform the design of novel therapeutics. url: https://doi.org/10.1007/s40259-013-0039-0 doi: 10.1007/s40259-013-0039-0 id: cord-007898-nky7bo6u author: HUGHES, C.S. title: Effects of certain stress factors on the re-excretion of infectious laryngotracheitis virus from latently infected carrier birds date: 2018-09-04 words: 2227.0 sentences: 112.0 pages: flesch: 60.0 cache: ./cache/cord-007898-nky7bo6u.txt txt: ./txt/cord-007898-nky7bo6u.txt summary: authors: HUGHES, C.S.; GASKELL, R.M.; JONES, R.C.; BRADBURY, J.M.; JORDAN, F.T.W. title: Effects of certain stress factors on the re-excretion of infectious laryngotracheitis virus from latently infected carrier birds Experiments were set up to assess the effects of ''natural'' and ''artificial'' stresses on the re-excretion of infectious laryngotracheitis (ilt) virus in latently infected chickens recovered from the acute phase of the disease. Experiments were set up to assess the effects of ''natural'' and ''artificial'' stresses on the re-excretion of infectious laryngotracheitis (In) virus in latently infected chickens recovered from the acute phase of the disease. It appears from these studies that the ''nat ural'' stress of rehousing and, or, the addition of a contact bird, and also the onset of lay may increase the shedding rate in the ILT virus carrier. Nine of the 10 birds shed virus after onset of lay compared with only two in the three-and-a-half weeks before, and there was a highly significant increase in the overall number of virus isolations during this period. abstract: Experiments were set up to assess the effects of ‘natural’ and ‘artificial’ stresses on the re-excretion of infectious laryngotracheitis (ilt) virus in latently infected chickens recovered from the acute phase of the disease. The stresses were rehousing with the addition of ilt-free contact birds, corticosteroid treatment and the onset of lay. The contact birds were also monitored for transmission of the virus from the carrier birds. Rehousing with unfamiliar birds induced ilt virus shedding in one of five birds and there was evidence of transmission from this bird to its mate. The onset of lay had a significant effect on the overall shedding rates of the carrier birds. Nine of 10 birds shed virus after onset of lay compared with only two in the three-and-a-half weeks before, and there was a highly significant increase (P<0·001) in the overall number of virus isolations during this period. Corticosteroid treatment did not affect virus shedding. These results may explain some of the apparently spontaneous outbreaks of ilt which occur in the field. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7126566/ doi: 10.1016/s0034-5288(18)31158-5 id: cord-022354-aqtceqqo author: HUNTER, ERIC title: Membrane Insertion and Transport of Viral Glycoproteins: A Mutational Analysis date: 2012-12-02 words: 17747.0 sentences: 697.0 pages: flesch: 44.0 cache: ./cache/cord-022354-aqtceqqo.txt txt: ./txt/cord-022354-aqtceqqo.txt summary: second apolar region in gp 37 consists of a 27 amino acid long stretch of hydrophobic residues near the carboxy terminus that functions during translation to stop the movement of the protein into the lumen of the rough endoplasmic reticulum (RER) and to anchor the complex in the membrane. In order to examine the role of the signal peptide in RSV glycoprotein biosynthesis we constructed a series of deletion mutations within the 5'' coding region of the env gene using the double-stranded exonuclease BaBl. Oligonucleotide linkers of the sequence CATCGATG were ligated to the ends of the truncated molecules to introduce a unique restriction endonuclease cleavage site and to replace the deleted in-frame AUG. We found that replacement of the nonconserved region of the cytoplasmic domain with a longer unrelated sequence of amino acids from SV40 vector sequences (mutant Cl) did not alter the rate of transport to the Golgi apparatus nor the appearance of the glycoprotein on the cell surface. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155604/ doi: 10.1016/b978-0-12-203460-2.50007-x id: cord-021552-6jbm869r author: HURST, CHRISTON J. title: Relationship Between Humans and Their Viruses date: 2007-05-09 words: 7828.0 sentences: 395.0 pages: flesch: 43.0 cache: ./cache/cord-021552-6jbm869r.txt txt: ./txt/cord-021552-6jbm869r.txt summary: Viral replication ~ at the individual host level, the primary tissue and organ tropisms are toward the cervix, conjunctiva, pharynx, small intestine, and urethra; the secondary tissue and organ tropisms are toward the brain, kidney, lungs, and lymph nodes; at the host population level, these viruses generally are endemic and initially acquired at a very early age, with the infections very often asymptomatic in young children. ~ral replication ~ at the individual host level, primary tissue and organ tropisms are toward the small intestine; secondary tissue and organ tropisms are toward the liver; at the host population level, these tend to be epidemic within human populations; for the hepatitis E virus it seems that acquisition occurs from swine, with the result being epidemics (often very widespread) of human disease; some acquisition from animals may come from eating infected animals; subsequent transmission of all caliciviruses within human populations is by fecally contaminated waste and thus can be very widespread. Alternate hosts: One species of viral family Hepadnaviridae (hepatitis B virus) is known to infect humans, and it seems naturally limited to humans. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7150212/ doi: 10.1016/b978-012362675-2/50015-x id: cord-288231-vg8bwed9 author: Haagmans, Bart L. title: The Application of Genomics to Emerging Zoonotic Viral Diseases date: 2009-10-26 words: 3406.0 sentences: 146.0 pages: flesch: 35.0 cache: ./cache/cord-288231-vg8bwed9.txt txt: ./txt/cord-288231-vg8bwed9.txt summary: Other viruses, such as influenza A viruses and severe acute respiratory syndrome coronavirus (SARS-CoV), may need multiple genetic changes to adapt successfully to humans as a new host species; these changes might include differential receptor usage, enhanced replication, evasion of innate and adaptive host immune defenses, and/or increased efficiency of transmission. New molecular techniques such as high-throughput sequencing, mRNA expression profiling, and array-based single nucleotide polymorphism (SNP) analysis provide ways to rapidly identify emerging pathogens (Nipah virus and SARS-CoV, for example) and to analyze the diversity of their genomes as well as the host responses against them. After introduction of a new influenza A virus from an avian or porcine reservoir into the human species, viral genomics studies are essential to identify critical mutations that enable the circulating virus to spread efficiently, interact with different receptors, and cause disease in the new host. abstract: Interspecies transmission of pathogens may result in the emergence of new infectious diseases in humans as well as in domestic and wild animals. Genomics tools such as high-throughput sequencing, mRNA expression profiling, and microarray-based analysis of single nucleotide polymorphisms are providing unprecedented ways to analyze the diversity of the genomes of emerging pathogens as well as the molecular basis of the host response to them. By comparing and contrasting the outcomes of an emerging infection with those of closely related pathogens in different but related host species, we can further delineate the various host pathways determining the outcome of zoonotic transmission and adaptation to the newly invaded species. The ultimate challenge is to link pathogen and host genomics data with biological outcomes of zoonotic transmission and to translate the integrated data into novel intervention strategies that eventually will allow the effective control of newly emerging infectious diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/19855817/ doi: 10.1371/journal.ppat.1000557 id: cord-256917-6h1ip37z author: Habibi-Yangjeh, Aziz title: Review on heterogeneous photocatalytic disinfection of waterborne, airborne, and foodborne viruses: Can we win against pathogenic viruses? date: 2020-07-15 words: 4781.0 sentences: 262.0 pages: flesch: 32.0 cache: ./cache/cord-256917-6h1ip37z.txt txt: ./txt/cord-256917-6h1ip37z.txt summary: suggested three mechanisms for viral disinfection in photocatalytic processes, which include physical damage of viruses, metal ion toxicity obtained from metal-including photocatalysts, and chemical oxidation by ROS generated over the photocatalysts [5] . Therefore, by considering the actual state of the review, this study focuses on a survey of the photocatalytic inactivation of waterborne, airborne, and foodborne viruses using semiconductor-assisted photocatalysis and the perspective of this important research field to tackle issues related to the spread of different viruses worldwide. In a research conducted by Kim and Jang [18] , the photocatalytic processes were investigated by V-UV with short illumination times to simultaneously disinfect MS2 as an airborne virus (nearly 90% disinfection efficiency at a VUV illumination time of 0.009 s) and remove the produced ozone toward an air inactivation system. After designing and fabricating more efficient photocatalysts, these photoactive materials could be used for inactivation of waterborne viruses in water decontamination plants and fabrication of more effective filters to disinfect airborne viruses. abstract: Microbial pathogenic contaminations have world widely represented a serious health hazard to humans. Viruses, as a member of microbial contaminants, seriously threaten human health due to their high environmental resistance, having small sizes, and causing an extensive range of diseases. Therefore, selecting an appropriate technology to remove viral contaminants from the air, water, and foods is of prominent significance. Traditional methods for viral disinfection have not proven to be highly practical and effective because they need high energy resources and operational expenses. In recent years, semiconductor-based photocatalysis has attracted more attention in the field of microorganism inactivation due to its outstanding performance and mild reaction conditions. Therefore, this review primarily concentrates on the recent development in viral inactivation/disinfection by heterogeneous photocatalysts. Moreover, the photocatalytic viral inactivation of waterborne, airborne, and foodborne viruses is discussed. Given the appealing merits of heterogeneous photocatalytic disinfection of viruses, there is no doubt that this technology will be an impressively active research field and a source of comfort and confidence to humans in battling against viruses. url: https://www.sciencedirect.com/science/article/pii/S0021979720309255?v=s5 doi: 10.1016/j.jcis.2020.07.047 id: cord-310920-itqwhi6a author: Haddad, Christina title: Integrated Approaches to Reveal Mechanisms by which RNA Viruses Reprogram the Cellular Environment date: 2020-07-02 words: 3698.0 sentences: 205.0 pages: flesch: 44.0 cache: ./cache/cord-310920-itqwhi6a.txt txt: ./txt/cord-310920-itqwhi6a.txt summary: Each of these techniques provide important vantage points to understand the complexities of virus-host interactions, but we attempt to make the case that by integrating these and similar methods, more vivid descriptions of how viruses reprogram the cellular environment emerges. Obtaining structural details of the UTRs and identifying functional binding sites of RBPs will be deeply insightful in elucidating how this virus replicates within host cells. Given the large number of RBPs known to interact with genomic and subgenomic viral RNAs to modulate translation, replication and the shift between these two stages, CLIP-seq can be employed to understand virology at the molecular level. Studying RNA structural interactions and the effects of viral-host RBPs on RNA structure and function are essential for understanding translation, replication, and transcription processes in order to better understand how viruses reprogram the cellular environment. abstract: RNA viruses are major threats to global society and mass outbreaks can cause long-lasting damage to international economies. RNA and related retro viruses represent a large and diverse family that contribute to the onset of human diseases such as AIDS; certain cancers like T cell lymphoma; severe acute respiratory illnesses as seen with COVID-19; and others. The hallmark of this viral family is the storage of genetic material in the form of RNA, and upon infecting host cells, their RNA genomes reprogram the cellular environment to favor productive viral replication. RNA is a multifunctional biomolecule that not only stores and transmits heritable information, but it also has the capacity to catalyze complex biochemical reactions. It is therefore no surprise that RNA viruses use this functional diversity to their advantage to sustain chronic or lifelong infections. Efforts to subvert RNA viruses therefore requires a deep understanding of the mechanisms by which these pathogens usurp cellular machinery. Here, we briefly summarize several experimental techniques that individually inform on key physicochemical features of viral RNA genomes and their interactions with proteins. Each of these techniques provide important vantage points to understand the complexities of virus-host interactions, but we attempt to make the case that by integrating these and similar methods, more vivid descriptions of how viruses reprogram the cellular environment emerges. These vivid descriptions should expedite the identification of novel therapeutic targets. url: https://api.elsevier.com/content/article/pii/S1046202320301249 doi: 10.1016/j.ymeth.2020.06.013 id: cord-279691-v5kpmk0b author: Hagemeijer, Marne C. title: Biogenesis and Dynamics of the Coronavirus Replicative Structures date: 2012-11-21 words: 9036.0 sentences: 483.0 pages: flesch: 43.0 cache: ./cache/cord-279691-v5kpmk0b.txt txt: ./txt/cord-279691-v5kpmk0b.txt summary: Upon infection, coronaviruses extensively rearrange cellular membranes into organelle-like replicative structures that consist of double-membrane vesicles and convoluted membranes to which the nonstructural proteins involved in RNA synthesis localize. This review will summarize the current knowledge on the biogenesis of the replicative structures, the membrane anchoring of the replication-transcription complexes, and the location of viral RNA synthesis, with particular focus on the dynamics of the coronavirus replicative structures and individual replication-associated proteins. A distinctive common feature of +RNA viruses is the replication of their genomes in the cytoplasm of the host cell in association with rearranged cellular membranes that are remodeled into organelle-like membranous structures to which the viral replication-transcription complexes (RTCs) localize. The first detectable membrane rearrangements in CoV-infected cells are 200 to 350 nm organelle-like structures that have been described for both MHV [47, 62] and the SARS-CoV [5, 63] and consist of spherical vesicles containing double lipid bilayers, termed DMVs ( Figure 2 ). abstract: Coronaviruses are positive-strand RNA viruses that are important infectious agents of both animals and humans. A common feature among positive-strand RNA viruses is their assembly of replication-transcription complexes in association with cytoplasmic membranes. Upon infection, coronaviruses extensively rearrange cellular membranes into organelle-like replicative structures that consist of double-membrane vesicles and convoluted membranes to which the nonstructural proteins involved in RNA synthesis localize. Double-stranded RNA, presumably functioning as replicative intermediate during viral RNA synthesis, has been detected at the double-membrane vesicle interior. Recent studies have provided new insights into the assembly and functioning of the coronavirus replicative structures. This review will summarize the current knowledge on the biogenesis of the replicative structures, the membrane anchoring of the replication-transcription complexes, and the location of viral RNA synthesis, with particular focus on the dynamics of the coronavirus replicative structures and individual replication-associated proteins. url: https://www.ncbi.nlm.nih.gov/pubmed/23202524/ doi: 10.3390/v4113245 id: cord-291561-sxvgue36 author: Haixu, Liang title: Detection of 20 respiratory viruses and bacteria by influenza-like illness surveillance in Beijing, China, 2016–2018 date: 2019-11-25 words: 10271.0 sentences: 543.0 pages: flesch: 50.0 cache: ./cache/cord-291561-sxvgue36.txt txt: ./txt/cord-291561-sxvgue36.txt summary: A full genome phylogenetic analysis of this 2019-nCoV indicates that it is closely related to bat SARS-like CoV ( Fig. 1 ) , compatible with a zoonotic origin for this virus, similar to SARS-CoV and MERS-CoV. 3 5 This study aim to assess the genetic diversity and potential role of genetic recombination in the evolutionary dynamics of FRCoVs. Genetic analyses were conducted with five complete genomes and 160 gene sequences of FRCoVs downloaded from the NIAID Virus Pathogen Database and Analysis Resource. 3 Ten years after the SARS, MERS emerged in 2012, have caused 2494 human infections with 858 deaths (as of November 2019) and remains a disease of global, and particularly Middle Eastern, public health concern. Relatively low detection rates have even been reported in studies conducted in other geographical areas, such as Gansu Province in China, 6 The discrepancies in the influenza detection rates among patients with ILI from different areas highlighted the geographical differences in virus burdens. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/31778686/ doi: 10.1016/j.jinf.2019.11.014 id: cord-343347-guciupc8 author: Hajj Hussein, Inaya title: Vaccines Through Centuries: Major Cornerstones of Global Health date: 2015-11-26 words: 12280.0 sentences: 573.0 pages: flesch: 47.0 cache: ./cache/cord-343347-guciupc8.txt txt: ./txt/cord-343347-guciupc8.txt summary: Consequently, this work tried to put together the major achievements through history stressing the importance, continuous vital role, and the need for immunization for health prevention and protection as well as its impact on human experience. A few years later, word of his success circulated among the public, and Jenner wrote "An Inquiry into the Causes and Effects of the Variolae Vaccinae, a Disease Discovered in some of the Western Counties of England, particularly Gloucestershire and Known by the Name of CowPox, " after adding several cases to his initial achievement with the boy Phipps. Takahashi was able to make this remarkable advance at a time when very few viruses had been attenuated to produce efficacious live-virus vaccines including yellow fever, polio, measles, mumps, and rubella as previously mentioned. As a result of these successful trials, the live varicella virus vaccine (Varivax) was licensed in 1995 for the active immunization of persons 12 months of age and older (51) . abstract: Multiple cornerstones have shaped the history of vaccines, which may contain live-attenuated viruses, inactivated organisms/viruses, inactivated toxins, or merely segments of the pathogen that could elicit an immune response. The story began with Hippocrates 400 B.C. with his description of mumps and diphtheria. No further discoveries were recorded until 1100 A.D. when the smallpox vaccine was described. During the eighteenth century, vaccines for cholera and yellow fever were reported and Edward Jenner, the father of vaccination and immunology, published his work on smallpox. The nineteenth century was a major landmark, with the “Germ Theory of disease” of Louis Pasteur, the discovery of the germ tubercle bacillus for tuberculosis by Robert Koch, and the isolation of pneumococcus organism by George Miller Sternberg. Another landmark was the discovery of diphtheria toxin by Emile Roux and its serological treatment by Emil Von Behring and Paul Ehrlih. In addition, Pasteur was able to generate the first live-attenuated viral vaccine against rabies. Typhoid vaccines were then developed, followed by the plague vaccine of Yersin. At the beginning of World War I, the tetanus toxoid was introduced, followed in 1915 by the pertussis vaccine. In 1974, The Expanded Program of Immunization was established within the WHO for bacille Calmette–Guerin, Polio, DTP, measles, yellow fever, and hepatitis B. The year 1996 witnessed the launching of the International AIDS Vaccine Initiative. In 1988, the WHO passed a resolution to eradicate polio by the year 2000 and in 2006; the first vaccine to prevent cervical cancer was developed. In 2010, “The Decade of vaccines” was launched, and on April 1st 2012, the United Nations launched the “shot@Life” campaign. In brief, the armamentarium of vaccines continues to grow with more emphasis on safety, availability, and accessibility. This mini review highlights the major historical events and pioneers in the course of development of vaccines, which have eradicated so many life-threatening diseases, despite the vaccination attitudes and waves appearing through history. url: https://doi.org/10.3389/fpubh.2015.00269 doi: 10.3389/fpubh.2015.00269 id: cord-292643-n6xp5mlz author: Hall, Richard J. title: Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery date: 2013-09-13 words: 4803.0 sentences: 219.0 pages: flesch: 44.0 cache: ./cache/cord-292643-n6xp5mlz.txt txt: ./txt/cord-292643-n6xp5mlz.txt summary: The relative abundance of a virus (or viral nucleic acid) in a sample, compared to that of other organisms such as bacteria or host cells (or their genomes), is a critical factor for the discovery of viruses when using metagenomics. A study on human liver tissue compared enrichment techniques of freeze-thaw, centrifugation and nuclease-treatment for the detection of Hepatitis C Virus using both Roche 454 and Illumina high-throughput sequencing platforms (Daly et al., 2011) . After an initial 10 min reverse transcription step at 45 • C and 10 min denaturation Table 1 Virus enrichment process prior to sequencing in metagenomic studies on human and animal samples. This artificial sample represents a starting point to evaluate simple and rapid viral enrichment methods for use in virus metagenomics studies that seek to detect a virus that is causing disease in humans or animals. abstract: The discovery of new or divergent viruses using metagenomics and high-throughput sequencing has become more commonplace. The preparation of a sample is known to have an effect on the representation of virus sequences within the metagenomic dataset yet comparatively little attention has been given to this. Physical enrichment techniques are often applied to samples to increase the number of viral sequences and therefore enhance the probability of detection. With the exception of virus ecology studies, there is a paucity of information available to researchers on the type of sample preparation required for a viral metagenomic study that seeks to identify an aetiological virus in an animal or human diagnostic sample. A review of published virus discovery studies revealed the most commonly used enrichment methods, that were usually quick and simple to implement, namely low-speed centrifugation, filtration, nuclease-treatment (or combinations of these) which have been routinely used but often without justification. These were applied to a simple and well-characterised artificial sample composed of bacterial and human cells, as well as DNA (adenovirus) and RNA viruses (influenza A and human enterovirus), being either non-enveloped capsid or enveloped viruses. The effect of the enrichment method was assessed by both quantitative real-time PCR and metagenomic analysis that incorporated an amplification step. Reductions in the absolute quantities of bacteria and human cells were observed for each method as determined by qPCR, but the relative abundance of viral sequences in the metagenomic dataset remained largely unchanged. A 3-step method of centrifugation, filtration and nuclease-treatment showed the greatest increase in the proportion of viral sequences. This study provides a starting point for the selection of a purification method in future virus discovery studies, and highlights the need for more data to validate the effect of enrichment methods on different sample types, amplification, bioinformatics approaches and sequencing platforms. This study also highlights the potential risks that may attend selection of a virus enrichment method without any consideration for the sample type being investigated. url: https://doi.org/10.1016/j.jviromet.2013.08.035 doi: 10.1016/j.jviromet.2013.08.035 id: cord-315131-4yb2b70g author: Hammerschmidt, Sven title: Threat of infection: Microbes of high pathogenic potential – strategies for detection, control and eradication date: 2005-06-28 words: 7177.0 sentences: 343.0 pages: flesch: 40.0 cache: ./cache/cord-315131-4yb2b70g.txt txt: ./txt/cord-315131-4yb2b70g.txt summary: This report highlights some of the lectures that were presented during the international symposium ''Threat of infection: Microbes of high potential -strategies for detection, control and eradication'' in July 2004 in Wu¨rzburg (Germany). E. Kaufmann (Max-Planck-Institute for Infection Biology (MPI), Berlin) suggested that the following vaccination strategies against intracellular bacteria deserve consideration: (i) attenuated viable strains, (ii) naked DNA encoding protective antigens and (iii) protective antigens expressed by recombinant viable vectors (bacteria or viruses). Based on the initial finding that several live-attenuated PrV vaccine strains lack a major surface antigen (glycoprotein E, gE) which is invariably present in all field strains (Mettenleiter et al., 1985) , a simple ELISA system has been developed that is able to specifically detect the presence or absence of anti-gE antibodies in the animal (van Oirschot et al., 1986) . abstract: Abstract Infectious diseases due to microbes of high pathogenic potential remain a constant and variable threat for human and animal health. The emergence of new diseases or the re-emergence of diseases that were previously under control complicates the situation to date. Infectious disease research, which has undergone a dramatic progress in understanding disease mechanisms such as host–pathogen interactions, is now focusing increasingly on new strategies for prevention and therapy. Significant progress has been achieved in the development of delivery systems for protective heterologous protein antigens and in veterinary vaccinology. A landmark of infectious diseases research is the chemical synthesis of genomes, a major new field of research referred to as “synthetic biology”, that to date has resulted in the chemical synthesis of the poliovirus and of phage φX174 genomes and their expression as infectious viruses. On the molecular level the evolution of pathogens and mechanisms of genome flexibility, which account for several pathogenic properties of infectious agents, have received increased attention. Bacterial toxins are an additional threat to human health and their interference with host cells and cellular functions is receiving more attention. url: https://www.sciencedirect.com/science/article/pii/S1438422105000457 doi: 10.1016/j.ijmm.2005.03.004 id: cord-292575-vsswxwdi author: Hammou, Rahma Ait title: Chapter 7 Scientific Advances in the Diagnosis of Emerging and Reemerging Viral Human Pathogens date: 2020-12-31 words: 8496.0 sentences: 402.0 pages: flesch: 39.0 cache: ./cache/cord-292575-vsswxwdi.txt txt: ./txt/cord-292575-vsswxwdi.txt summary: It is in this context that this chapter aims to discuss the various scientific advances, particularly molecular, in terms of diagnosis of these diseases; the new discoveries in the role of nanotechnologies and nanobiosensors; and also the implication of biomarkers, especially microRNAs (miRNAs), since it was reported that a single miRNA has the ultimate capacity to target multiple genes simultaneously. The availability of nucleic acidÀbased technology, such as real-time PCR, along with conventional staining and culture methods and immunoassays, can provide laboratories of many sizes with a comprehensive and responsible approach for the detection of both commonly encountered and emerging or reemerging pathogens. As is the case for SARS, agents of bioterrorism, and the other pathogens, rapid diagnostic methods, such as real-time PCR, and microarray will likely play a major role in the early and sensitive detection of emerging and reemerging infectious diseases encountered in the future. abstract: Abstract Despite scientific advances, the diagnosis of infectious diseases is primarily possible through vaccination and later by antibiotics. Emerging and reemerging pathologies are still considered to be dangerous to humanity because of the unique nature of these diseases: it is the encounter between two living organisms that have coexisted for millions of years within the people on the same planet without being previously recognized. These infectious agents, such as bacteria, viruses, fungi, or parasites, pose no threat to humans. In fact, only a few hundred are able to inflict damage to the human host. In addition, the spectrum of human disease caused by a particular pathogen varies considerably depending on the factors related to the ecological agent, the host, and the infectious agents. Several emerging or reemerging infectious agents are organisms that could be used in biological control. The differentiation of a natural epidemic from a bioterrorian event is based on several epidemiological indices as well as on the molecular characterization of the pathogen(s) involved. The role of pathologists is indeed very important. It is in this context that this chapter aims to discuss the various scientific advances, particularly molecular, in terms of diagnosis of these diseases; the new discoveries in the role of nanotechnologies and nanobiosensors; and also the implication of biomarkers, especially microRNAs (miRNAs), since it was reported that a single miRNA has the ultimate capacity to target multiple genes simultaneously. In a viral infection context, miRNAs have been connected with the interplay between host and pathogen and occupy a major role in the host–parasite interaction and pathogenesis. It is in this context that various molecular and nanomethods for the detection of emerging viruses and experimental validation of miRNAs during quelling viruses target transcripts will be discussed in this chapter. url: https://www.sciencedirect.com/science/article/pii/B978012814966900007X doi: 10.1016/b978-0-12-814966-9.00007-x id: cord-306948-wkisfz1m author: Han, Mingyuan title: Engineering the PRRS virus genome: Updates and perspectives date: 2014-12-05 words: 9514.0 sentences: 480.0 pages: flesch: 45.0 cache: ./cache/cord-306948-wkisfz1m.txt txt: ./txt/cord-306948-wkisfz1m.txt summary: Serologic marker candidates identified among B-cell linear epitopes of Nsp2 and structural proteins of a North American strain of porcine reproductive and respiratory syndrome virus A full-length cDNA infectious clone of North American type 1 porcine reproductive and respiratory syndrome virus: expression of green fluorescent protein in the Nsp2 region Identification of nonessential regions of the nsp2 replicase protein of porcine reproductive and respiratory syndrome virus strain VR-2332 for replication in cell culture Establishment of a DNA-launched infectious clone for a highly pneumovirulent strain of type 2 porcine reproductive and respiratory syndrome virus: identification and in vitro and in vivo characterization of a large spontaneous deletion in the nsp2 region Recovery of viable porcine reproductive and respiratory syndrome virus from an infectious clone containing a partial deletion within the Nsp2-encoding region Determination of the complete nucleotide sequence of a vaccine strain of porcine reproductive and respiratory syndrome virus and identification of the Nsp2 gene with a unique insertion abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) is endemic in most pig producing countries worldwide and causes enormous economic losses to the pork industry. Infectious clones for PRRSV have been constructed, and so far at least 14 different infectious clones are available representing both genotypes I and II. Two strategies have been taken for progeny reconstitution: RNA transfection and DNA transfection. Mutations, insertions, deletions, and replacements of the viral genome have been employed to study the structure function relationship, foreign gene expression, functional complementation, and virulence determinants. Essential regions and non-essential regions for viral replication have been identified in both the coding regions and non-encoding regions. Foreign sequences have successfully been inserted into the nsp2 and N regions and in the space between ORF1b and ORF2a. Chimeras between member viruses in the family Arteriviridae have also been constructed and utilized to study cell tropism and functional complementation. This review discusses the advances and utilization of PRRSV reverse genetics and its potential for future research. url: https://doi.org/10.1016/j.vetmic.2014.10.007 doi: 10.1016/j.vetmic.2014.10.007 id: cord-354536-c9v9kbw8 author: Han, Yan-Jie title: Advances and challenges in the prevention and treatment of COVID-19 date: 2020-07-09 words: 5268.0 sentences: 330.0 pages: flesch: 48.0 cache: ./cache/cord-354536-c9v9kbw8.txt txt: ./txt/cord-354536-c9v9kbw8.txt summary: This article introduced the origin, virological characteristics and epidemiological overview of SARS-CoV-2, reviewed the currently known drugs that may prevent and treat coronavirus, explained the characteristics of the new coronavirus and provided novel information for the prevention and treatment of COVID-19. 18 In view of the curative effect of ribavirin in the treatment of diseases caused by SARS-CoV and MERS-CoV, 21 it is expected to become one of the effective drugs to treat coronavirus. 16 The "Pneumonitis Diagnosis and Treatment Scheme for New Coronavirus Infection (Trial Version 7)" states that aerosolized interferon alpha can be used as a trial treatment against SARS-CoV-2 virus to improve the virus clearance effect of respiratory mucosa in patients. 64 It has been revealed that chlorpromazine is a broad-spectrum virus inhibitor that can inhibit HCV, alpha virus, and various coronaviruses including human coronavirus 229E, SARS-CoV and MERS-CoV in vitro. abstract: Since the end of 2019, a new type of coronavirus pneumonia (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has been spreading rapidly throughout the world. Previously, there were two outbreaks of severe coronavirus caused by different coronaviruses worldwide, namely Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV). This article introduced the origin, virological characteristics and epidemiological overview of SARS-CoV-2, reviewed the currently known drugs that may prevent and treat coronavirus, explained the characteristics of the new coronavirus and provided novel information for the prevention and treatment of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32714083/ doi: 10.7150/ijms.47836 id: cord-257569-36qx1sy9 author: Hanada, Kousuke title: A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes date: 2004-06-17 words: 3460.0 sentences: 156.0 pages: flesch: 43.0 cache: ./cache/cord-257569-36qx1sy9.txt txt: ./txt/cord-257569-36qx1sy9.txt summary: title: A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes In conclusion, the variation of mutation rates for RNA viruses is caused by different replication frequencies, which are affected strongly by the infection and transmission modes. First, we estimated the rates of synonymous substitution for 46 different species of RNA viruses except Puumala virus, human T-lymphotropic virus 1 (HTLV-1) and GB virus C/hepatitis G virus (HGV), using the time-serial sample data. This indicated that the transmission mode affected the replication frequency and that differences in the replication frequencies contributed to the variation of the rate of synonymous substitution for RNA viruses. Moreover, in the present study, we proved that the variation in the synonymous substitution rates among RNA viruses was caused by variation of the replication frequency, and that differences in the infection and transmission modes affected the variation of replication frequencies. abstract: RNA viruses successfully adapt to various environments by repeatedly producing new mutants, often through generating a number of nucleotide substitutions. To estimate the degree of variation in mutation rates of RNA viruses and to understand the source of such variation, we studied the synonymous substitution rate because synonymous substitution is exempt from functional constraints at the protein level, and its rate reflects the mutation rate to a great extent. We estimated the synonymous substitution rates for a total of 49 different species of RNA viruses, and we found that the rates had tremendous variation by 5 orders of magnitude (from 1.3 × 10(−7) to 6.2 × 10(−2) /synonymous site/year). Comparing the synonymous substitution rates with the replication frequencies and replication error rates for the RNA viruses, we found that the main source of the rate variation was differences in the replication frequency because the rates of replication error were roughly constant over different RNA viruses. Moreover, we examined a relationship between viral life strategies and synonymous substitution rates to understand which viral life strategies affect replication frequencies. The results show that the variation of synonymous substitution rates has been influenced most by either the difference in the infection modes or the differences in the transmission modes. In conclusion, the variation of mutation rates for RNA viruses is caused by different replication frequencies, which are affected strongly by the infection and transmission modes. url: https://www.ncbi.nlm.nih.gov/pubmed/15014142/ doi: 10.1093/molbev/msh109 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-273777-qb0vp9gr author: Happel, Anna-Ursula title: The Vaginal Virome—Balancing Female Genital Tract Bacteriome, Mucosal Immunity, and Sexual and Reproductive Health Outcomes? date: 2020-07-30 words: 6250.0 sentences: 279.0 pages: flesch: 30.0 cache: ./cache/cord-273777-qb0vp9gr.txt txt: ./txt/cord-273777-qb0vp9gr.txt summary: A range of vaginal DNA viruses infecting eukaryote cells have been identified by shotgun metagenomics of vaginal samples from generally healthy, asymptomatic women of reproductive age participating in the Human Microbiome Project (HMP) [9] , including double-stranded (ds) DNA (families Adenoviridae, Herpesviridae, Papillomaviridae and Polyomaviridae) and single-stranded (ss) DNA viruses (families Anelloviridae) ( Table 1 and Figure 1 ). Although prokaryotic-infecting viruses, from now on referred to as bacteriophages, are estimated to be amongst the most abundant living entities on Earth [24] and are thought to play an important role in shaping the bacterial microbiota and associated health outcomes in the human gut [5, [25] [26] [27] , oral cavity [28, 29] , skin [30, 31] and lungs [32] , their role in the lower reproductive tract is understudied. Observational studies have shown that the acquisition and transmission of viral sexually transmitted infections (STIs), including HSV-2, HPV and HIV, are more common in women with high diversity, nonoptimal vaginal bacterial microbiota [42] [43] [44] . abstract: Besides bacteria, fungi, protists and archaea, the vaginal ecosystem also contains a range of prokaryote- and eukaryote-infecting viruses, which are collectively referred to as the “virome”. Despite its well-described role in the gut and other environmental niches, the vaginal virome remains understudied. With a focus on sexual and reproductive health, we summarize the currently known components of the vaginal virome, its relationship with other constituents of the vaginal microbiota and its association with adverse health outcomes. While a range of eukaryote-infecting viruses has been described to be present in the female genital tract (FGT), few prokaryote-infecting viruses have been described. Literature suggests that various vaginal viruses interact with vaginal bacterial microbiota and host immunity and that any imbalance thereof may contribute to the risk of adverse reproductive health outcomes, including infertility and adverse birth outcomes. Current limitations of vaginal virome research include experimental and analytical constraints. Considering the vaginal virome may represent the missing link in our understanding of the relationship between FGT bacteria, mucosal immunity, and adverse sexual and reproductive health outcomes, future studies evaluating the vaginal microbiome and its population dynamics holistically will be important for understanding the role of the vaginal virome in balancing health and disease. url: https://doi.org/10.3390/v12080832 doi: 10.3390/v12080832 id: cord-262514-1e2bc0bi author: Harrison, Alyne K title: Visceral target organs in systemic St. Louis encephalitis virus infection of hamsters date: 1982-12-31 words: 3177.0 sentences: 169.0 pages: flesch: 45.0 cache: ./cache/cord-262514-1e2bc0bi.txt txt: ./txt/cord-262514-1e2bc0bi.txt summary: SLE virus causes a widespread infection in suckling mice and hamsters when it is inoculated by a peripheral route and involves numerous organs and tissues in addition to the CNS, the principal target when the virus is injected intracerebrally. Light microscopic observations were of little help in identifying major extraneural target organs and tissues in the clinically ill and moribund hamsters, but frozen-section immunofluorescence of all organ systems indicated significant virus growth in the pancreas, adrenal gland, small intestine, heart, skeletal muscle, and kidney. Immunofluorescence studies of mice experimentally infected with tick-borne encephalitis virus indicated that, in addition to the CNS, the peripheral nervous system, the special sensory nerve cells of the retina and olfactory mucosa, the secretory glands, the tubular epithelium of the kidney, and both striated and smooth muscle tissue were affected (Albrecht, 1960) . abstract: Abstract Ultrastructural aspects of St. Louis encephalitis virus infection of the major extraneutral organs and tissues of suckling hamsters were examined. In the pancreas, both the exocrine and endocrine portions were equally affected by the virus. A feature apparently unique to flaviviruses was the accumulation of virus particles in all types of secretory granules in this organ. Virus particles were seen within myocardial fibers and within the smooth muscle cells and endothelial cells of small blood vessels of the heart. In the intestines, the lamina propria was the most severely infected, with virus particles accumulated in all cell types. url: https://www.ncbi.nlm.nih.gov/pubmed/6891341/ doi: 10.1016/0014-4800(82)90043-0 id: cord-008013-blf57r7u author: Hartmann, K. title: Feline immunodeficiency virus infection: an overview date: 2005-03-02 words: 7164.0 sentences: 464.0 pages: flesch: 47.0 cache: ./cache/cord-008013-blf57r7u.txt txt: ./txt/cord-008013-blf57r7u.txt summary: Acquired immune dysfunction in cats with experimentally induced feline immunodeficiency virus infection: comparison of short-term and long-term infections Programmed cell death (apoptosis) as a mechanism of cell death in peripheral blood mononuclear cells from cats infected with feline immunodeficiency virus (FIV) Journal ¢![ the American VeteHna U Medical Association hnmunization-induced decrease of the CD4+ CD8+ ratio in cats experimentally infected ~,4th feline immunodeficiency virus, l/etm4na O, Immunolo~, and hnm u nopathoh~© Effects of incidental infections and immnne activation on disease progression in experimentally feline immunodeficiency virus-infected cats Characterization of mo''rphologic changes and lymphocyte subset distribution in lymph nodes from cats with naturally acquired feline immunodeficiency virus infection Gag-and em,-specific antibodies in cats after natural and experimental infection with feline immunodeficiency virus. Effect of 3''-acido-2'',3''-dideoxythymidine (AZT) on experimental feline immunodeficiency virus infection in domestic cats Progressive immune dysfunction in cats experimentally infected with feline immunodeficiency virus Pathogenesis of experimentally induced feline immunodeficiency virus infection in cats abstract: In 1987, Pedersen et al. (1987) reported the isolation of a T-lymphotropic virus possessing thecharacteristics of a lentivirus from pet cats in Davis, California. From the first report onwards, it was evident that in causing an acquired immunodeficiency syndrome in cats, the virus was of substantial veterinary importance. It shares many physical and biochemical properties with human immunodeficiency virus (HIV), and was therefore named feline immunodeficiency virus (FIV). This article reviews recent knowledge of the aetiology, epidemiology, pathogenesis, clinical signs, diagnosis, prevention, and treatment options of FIV infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7128420/ doi: 10.1016/s1090-0233(98)80008-7 id: cord-272052-8vvpm4tx author: Hartmann, Katrin title: Clinical aspects of feline immunodeficiency and feline leukemia virus infection date: 2011-10-15 words: 9582.0 sentences: 444.0 pages: flesch: 35.0 cache: ./cache/cord-272052-8vvpm4tx.txt txt: ./txt/cord-272052-8vvpm4tx.txt summary: In a survey study of 826 naturally FIV-infected cats examined at North American Veterinary Teaching Hospitals, the most common disease syndromes were stomatitis, neoplasia (especially lymphoma and cutaneous squamous cell carcinoma), ocular inflammation (uveitis and chorioretinitis), anemia and leukopenia, opportunistic infections, renal insufficiency, lower urinary tract disease, and endocrinopathies such as hyperthyroidism and diabetes mellitus (Levy, 2000a) . Causes of CD4 + cell loss include decreased production secondary to bone marrow or thymic infection, lysis of infected cells induced by FIV itself (cytopathic effects), destruction of virus-infected cells by the immune system, or death by apoptosis (cell death that follows receipt of a membrane signal initiating a series of programmed intracellular events) (Bishop et al., 1993; Ohno et al., 1993 Ohno et al., , 1994 Johnson et al., 1996; Guiot et al., 1997a,b; Mizuno et al., 1997; Mortola et al., 1998a,b; Piedimonte et al., 1999; Mizuno et al., 2001 Mizuno et al., , 2003b Tompkins et al., 2002) . abstract: Feline leukemia virus (FeLV) and feline immunodeficiency virus (FIV) are retroviruses with a global impact on the health of domestic cats. The two viruses differ in their potential to cause disease. FIV can cause an acquired immunodeficiency syndrome that increases the risk of developing opportunistic infections, neurological diseases, and tumors. In most naturally infected cats, however, FIV itself does not cause severe clinical signs, and FIV-infected cats may live many years without any health problems. FeLV is more pathogenic, and was long considered to be responsible for more clinical syndromes than any other agent in cats. FeLV can cause tumors (mainly lymphoma), bone marrow suppression syndromes (mainly anemia) and lead to secondary infectious diseases caused by suppressive effects of the virus on bone marrow and the immune system. Today, FeLV is less important as a deadly infectious agent as in the last 20 years prevalence has been decreasing in most countries. url: https://www.sciencedirect.com/science/article/pii/S0165242711002005 doi: 10.1016/j.vetimm.2011.06.003 id: cord-343690-rafvxgx1 author: Hartmann, Katrin title: Clinical Aspects of Feline Retroviruses: A Review date: 2012-10-31 words: 10289.0 sentences: 498.0 pages: flesch: 35.0 cache: ./cache/cord-343690-rafvxgx1.txt txt: ./txt/cord-343690-rafvxgx1.txt summary: Although FIV can cause an acquired immunodeficiency syndrome in cats ("feline AIDS") comparable to human immunodeficiency virus (HIV) infection in humans, with increased risk for opportunistic infections, neurologic diseases, and tumors, in most naturally infected cats, FIV does not cause a severe clinical syndrome. Experimental FIV infection also progresses through several stages, similar to HIV infection in people, including an acute phase, a clinically asymptomatic phase of variable duration, and a terminal phase sometimes called "feline acquired immunodeficiency syndrome" ("AIDS") [18, 19] . Of 8642 FeLV-infected cats presented to North American Veterinary Teaching Hospitals, various co-infections (including FIV infection, feline infectious peritonitis (FIP), upper respiratory infection, hemotropic mycoplasmosis, and stomatitis) were the most frequent findings (15%), followed by anemia (11%), lymphoma (6%), leukopenia or thrombocytopenia (5%), and leukemia or myeloproliferative diseases (4%) [20] . An early defect in primary and secondary t cell responses in asymptomatic cats during acute feline immunodeficiency virus (fiv) infection abstract: Feline leukemia virus (FeLV) and feline immunodeficiency virus (FIV) are retroviruses with global impact on the health of domestic cats. The two viruses differ in their potential to cause disease. FeLV is more pathogenic, and was long considered to be responsible for more clinical syndromes than any other agent in cats. FeLV can cause tumors (mainly lymphoma), bone marrow suppression syndromes (mainly anemia), and lead to secondary infectious diseases caused by suppressive effects of the virus on bone marrow and the immune system. Today, FeLV is less commonly diagnosed than in the previous 20 years; prevalence has been decreasing in most countries. However, FeLV importance may be underestimated as it has been shown that regressively infected cats (that are negative in routinely used FeLV tests) also can develop clinical signs. FIV can cause an acquired immunodeficiency syndrome that increases the risk of opportunistic infections, neurological diseases, and tumors. In most naturally infected cats, however, FIV itself does not cause severe clinical signs, and FIV-infected cats may live many years without any health problems. This article provides a review of clinical syndromes in progressively and regressively FeLV-infected cats as well as in FIV-infected cats. url: https://www.ncbi.nlm.nih.gov/pubmed/23202500/ doi: 10.3390/v4112684 id: cord-261417-4pf5nsw2 author: Harwig, Alex title: The Battle of RNA Synthesis: Virus versus Host date: 2017-10-21 words: 7864.0 sentences: 443.0 pages: flesch: 53.0 cache: ./cache/cord-261417-4pf5nsw2.txt txt: ./txt/cord-261417-4pf5nsw2.txt summary: Why the virus prefers to use these snRNAs as targets has yet to be experimentally established, but it has been proposed that the selective de-capping of U1 and U2 RNAs in combination with the binding of the viral NS1 protein to U6 snRNA may serve to inhibit host pre-mRNA splicing [66] . The folding of the TAR hairpin is key to the regulation of HIV-1 transcription [94] as it is used as a scaffold to recruit essential transcription factors, including the 86-101 amino acid (aa) viral trans-activator protein (Tat) [83] ( Figure 3C ). Interestingly, the human T-lymphotropic virus type 1 transcriptional activator Tax also utilizes P-TEFb for viral transcription and displaces P-TEFb from 7SK snRNP through binding CycT1 [101, 102] , suggesting that P-TEFb liberation from 7SK snRNP could be a common theme developed by different viruses to support their replication in host cells. abstract: Transcription control is the foundation of gene regulation. Whereas a cell is fully equipped for this task, viruses often depend on the host to supply tools for their transcription program. Over the course of evolution and adaptation, viruses have found diverse ways to optimally exploit cellular host processes such as transcription to their own benefit. Just as cells are increasingly understood to employ nascent RNAs in transcription regulation, recent discoveries are revealing how viruses use nascent RNAs to benefit their own gene expression. In this review, we first outline the two different transcription programs used by viruses, i.e., transcription (DNA-dependent) and RNA-dependent RNA synthesis. Subsequently, we use the distinct stages (initiation, elongation, termination) to describe the latest insights into nascent RNA-mediated regulation in the context of each relevant stage. url: https://www.ncbi.nlm.nih.gov/pubmed/29065472/ doi: 10.3390/v9100309 id: cord-341101-5yvjbr5q author: Hashem, Anwar M. title: Therapeutic use of chloroquine and hydroxychloroquine in COVID-19 and other viral infections: A narrative review date: 2020-05-06 words: 4823.0 sentences: 275.0 pages: flesch: 43.0 cache: ./cache/cord-341101-5yvjbr5q.txt txt: ./txt/cord-341101-5yvjbr5q.txt summary: While approved specific antiviral drugs against SARS-CoV-2 are still lacking, a large number of existing drugs are being explored as a possible treatment for COVID-19 infected patients. In general, studies showed no significant effect of CQ on CoVs including SARS-CoV and feline infectious peritonitis virus (FIPV) replication or clinical scores in mice and cats, respectively [105, 110] . There are very limited published clinical trials that studied the possible antiviral effect of CQ or HCQ in CoV and non-CoV infected patients (Table 5 ). Anti-malaria drug chloroquine is highly effective in treating avian influenza A H5N1 virus infection in an animal model In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro abstract: The rapidly spreading Coronavirus Disease (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus (SARS-CoV-2), represents an unprecedented serious challenge to the global public health community. The extremely rapid international spread of the disease with significant morbidity and mortality made finding possible therapeutic interventions a global priority. While approved specific antiviral drugs against SARS-CoV-2 are still lacking, a large number of existing drugs are being explored as a possible treatment for COVID-19 infected patients. Recent publications have re-examined the use of Chloroquine (CQ) and/or Hydroxychloroquine (HCQ) as a potential therapeutic option for these patients. In an attempt to explore the evidence that supports their use in COVID-19 patients, we comprehensively reviewed the previous studies which used CQ or HCQ as an antiviral treatment. Both CQ and HCQ demonstrated promising in vitro results, however, such data have not yet been translated into meaningful in vivo studies. While few clinical trials have suggested some beneficial effects of CQ and HCQ in COVID-19 patients, most of the reported data are still preliminary. Given the current uncertainty, it is worth being mindful of the potential risks and strictly rational the use of these drugs in COVID-19 patients until further high quality randomized clinical trials are available to clarify their role in the treatment or prevention of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32387694/ doi: 10.1016/j.tmaid.2020.101735 id: cord-348427-worgd0xu author: Hatcher, Eneida L. title: Virus Variation Resource – improved response to emergent viral outbreaks date: 2017-01-04 words: 5552.0 sentences: 258.0 pages: flesch: 48.0 cache: ./cache/cord-348427-worgd0xu.txt txt: ./txt/cord-348427-worgd0xu.txt summary: The resource now includes expanded data processing pipelines and analysis tools, and supports selection and retrieval of nucleotide and protein sequences from four new viral groups: Ebolaviruses, MERS coronavirus, rotavirus, and Zika virus ( Table 2 ). New processes have been added to parse source descriptor terms from Gen-Bank records and map these to controlled vocabulary, and the resource now supports retrieval of sequences based on standardized isolation source and host terms in addition to standardized gene and protein names. The resource includes data processing pipelines that retrieve sequences from GenBank, provide standardized gene and protein an-notation, and map sequence source descriptors (i.e. metadata) to uniform vocabularies. To resolve this issue, the Virus Variation database loading pipeline parses Gen-Bank records, identifies important metadata terms, such as sample isolation host, date, country and source, and maps these to a standardized vocabulary using a hierarchical approach. abstract: The Virus Variation Resource is a value-added viral sequence data resource hosted by the National Center for Biotechnology Information. The resource is located at http://www.ncbi.nlm.nih.gov/genome/viruses/variation/ and includes modules for seven viral groups: influenza virus, Dengue virus, West Nile virus, Ebolavirus, MERS coronavirus, Rotavirus A and Zika virus. Each module is supported by pipelines that scan newly released GenBank records, annotate genes and proteins and parse sample descriptors and then map them to controlled vocabulary. These processes in turn support a purpose-built search interface where users can select sequences based on standardized gene, protein and metadata terms. Once sequences are selected, a suite of tools for downloading data, multi-sequence alignment and tree building supports a variety of user directed activities. This manuscript describes a series of features and functionalities recently added to the Virus Variation Resource. url: https://doi.org/10.1093/nar/gkw1065 doi: 10.1093/nar/gkw1065 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-337712-ylqgraos author: Heinz, Franz X. title: Profile of SARS-CoV-2 date: 2020-10-30 words: 6028.0 sentences: 301.0 pages: flesch: 44.0 cache: ./cache/cord-337712-ylqgraos.txt txt: ./txt/cord-337712-ylqgraos.txt summary: Despite these similarities, distinguishing features were identified that are likely to contribute to the biological differences observed between the two viruses, including the significantly higher rate of subclinical and mild infections caused by SARS-CoV-2, which makes control of virus spread currently so difficult. If expectations were too optimistic and results obtained with some of the front runners are disappointing, windows of opportunity will open for an arsenal of alternative developments in progress [54, 59] (https:// www.who.int/publications/m/item/draft-landscapeof-covid-19-candidate-vaccines, accessed 2 October 2020) These include subunit vaccines with S proteins stabilized in their prefusion conformation in combination with potent adjuvants, use of the RBD only as an immunogen instead of the whole S protein [67, 68] , other rationally designed immunogens [69] , other (non-Adeno) vector vaccines including replication-competent vectors [55, 70] , self-amplifying RNA vaccines [71] , live-attenuated vaccines [55] , DNA vaccines [72] , and intranasally applied vaccines with the potential to induce local immunity at the site of virus entry [73] . abstract: The recent emergence of a new coronavirus (severe acute respiratory syndrome coronavirus‑2, SARS-CoV-2) that is transmitted efficiently among humans and can result in serious disease and/or death has become a global threat to public health and economy. In this article, we describe some of the most important characteristics of this new virus (including gaps in our understanding) and provide a perspective of ongoing activities for developing virus-specific countermeasures, such as vaccines and antiviral drugs. url: https://www.ncbi.nlm.nih.gov/pubmed/33125580/ doi: 10.1007/s00508-020-01763-1 id: cord-338804-nreqluol author: Heise, M.T. title: Viral Pathogenesis date: 2014-11-28 words: 6413.0 sentences: 232.0 pages: flesch: 35.0 cache: ./cache/cord-338804-nreqluol.txt txt: ./txt/cord-338804-nreqluol.txt summary: Viral interactions with these receptors can have a significant impact upon several aspects of viral pathogenesis, including determining the cell or tissue tropism of a virus or even whether a virus can efficiently infect and cause disease in a specific host species. Therefore, viruses that are defective in their ability to antagonize the host type I interferon system are often unable to replicate and spread efficiently within the host, illustrating the importance of viral immune evasion strategies in determining whether a virus will be pathogenic ( Figure 2) . (b) If the virus effectively interferes with the type I interferon response, interferon will be prevented from inducing a robust antiviral state within the host, and the virus is able to replicate to higher levels, will spread more efficiently, and may cause more severe disease. Therefore, like other aspects of viral pathogenesis, a complex series of virus-host interactions determines whether infection with cancer associated viruses ultimately results in disease development. abstract: Viral pathogenesis describes the processes by which viral infections cause diseases and involves virus–host interactions at the cellular and systemic level that determine whether a virus will cause a disease, what form that disease takes, and how severe the disease will be. Though the pathogenesis of each virus is unique, there are several common points in the virus life cycle that are shared between all pathogenic viruses, and by considering these common aspects of the virus-induced disease process, we can explore some general concepts in viral pathogenesis while illustrating some of the virus specific processes that shape disease outcomes. url: https://www.sciencedirect.com/science/article/pii/B9780128012383000799 doi: 10.1016/b978-0-12-801238-3.00079-9 id: cord-254890-4ynsgu6c author: Heldens, J.G.M. title: Veterinary vaccine development from an industrial perspective date: 2008-03-03 words: 9217.0 sentences: 443.0 pages: flesch: 39.0 cache: ./cache/cord-254890-4ynsgu6c.txt txt: ./txt/cord-254890-4ynsgu6c.txt summary: Live vaccine: Low passage lot for safety (GLP) on target species including pregnant animals in case indication is required High passage lot for efficacy: Onset of immunity and duration of immunity Inactivated vaccine: High passage lot for safety (GLP) and efficacy Licensing batches (10% commercial scale, GMP) -Consistency of production, process validation -Transfer of production process and control tests to manufacturing departments and quality control departments -Stability studies on antigen and final product in final container Field studies (GCP) -Safety -Efficacy derived from treated animals from which food is derived, and the consumer. The likely approach to develop vaccines would be, first, the cloning and site directed mutagenesis to turn the HA-gene into a non-pathogenic form, and, second, the production of so-called high growth re-assortants producing considerable amounts of the new HA protein, which is, among others, the protective antigen in influenza virus. abstract: Veterinary vaccines currently available in Europe and in other parts of the world are developed by the veterinary pharmaceutical industry. The development of a vaccine for veterinary use is an economic endeavour that takes many years. There are many obstacles along the path to the successful development and launch of a vaccine. The industrial development of a vaccine for veterinary use usually starts after the proof of concept that is based on robust academic research. A vaccine can only be made available to the veterinary community once marketing authorisation has been granted by the veterinary authorities. This review gives a brief description of the regulatory requirements which have to be fulfilled before a vaccine can be admitted to the market. Vaccines have to be produced in a quality controlled environment to guarantee delivery of a product of consistent quality with well defined animal and consumer safety and efficacy characteristics. The regulatory and manufacturing legislative framework in which the development takes place is described, as well as the trend in developments in production systems. Recent developments in bacterial, viral and parasite vaccine research and development are also addressed and the development of novel adjuvants that use the expanding knowledge of immunology and disease pathology are described. url: https://api.elsevier.com/content/article/pii/S1090023307003930 doi: 10.1016/j.tvjl.2007.11.009 id: cord-005885-r3qtoqu1 author: Hellmich, Luisa title: Exantheme nach Auslandsreisen date: 2019-10-09 words: 2645.0 sentences: 362.0 pages: flesch: 50.0 cache: ./cache/cord-005885-r3qtoqu1.txt txt: ./txt/cord-005885-r3qtoqu1.txt summary: Auch wenn die jährlich übermittelten Zika-Virus-Infektionen insgesamt zurückgehen (2016: 222 Fälle, 2017: 69 Fälle, 2018: 18 Fälle), ist aufgrund der häufig symptomlosen Infektion von einer beträchtlichen Dunkelziffer auszugehen (RKI [Robert Koch-Institut]) [8] . Typisch für eine Zika-Virus-Infektion ist eine meist gleichzeitig mit dem Exanthem auftretende Konjunktivitis, die im Schnitt etwas länger als das Exanthem anhält (Median 4 bis 6 Tage) [9] . Bei der Erstinfektion mit einer der 4 DENV-Typen kann sich nach einer Inkubationszeit von 4 bis 7, maximal 14 Tagen ein klassisches Dengue-Fieber mit plötzlichem (häufig biphasischem) Fieber (>38°C), einem hämmernden Retrobulbärschmerz, starken muskuloskelettalen Schmerzen ("break-bone-fever") und Konjunktivitis entwickeln. Bei der Infektion mit dem zu den Togaviridae gehörenden RNA-Virus kommt es nach einer Inkubationszeit von 3 bis 12 Tagen zu einem plötzlichen Fieberanstieg, starken Kopfschmerzen und sehr heftigen bilateralen Arthralgien (v. abstract: In view of globalization and the associated transport of goods as well as rising travel activity, imported infections with subtropical and tropical pathogens are increasing in Germany. In returning travelers presenting with fever, general symptoms and skin rash, a number of diseases need to be considered. The clinical appearance of the skin rash, accurate travel history and epidemiological information on country-specific risks are helpful in making the correct diagnosis. In this article we provide an overview of the most common exanthemas in travelers who have returned, associated symptoms, diagnostic methods, therapies, as well as prevention strategies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095896/ doi: 10.1007/s00105-019-04489-y id: cord-286298-pn9nwl64 author: Helmy, Yosra A. title: The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control date: 2020-04-24 words: 9290.0 sentences: 516.0 pages: flesch: 51.0 cache: ./cache/cord-286298-pn9nwl64.txt txt: ./txt/cord-286298-pn9nwl64.txt summary: Another group of researchers reported that the virus originated from bats based on the genome sequence of SARS-CoV-2, which is 96% identical to bat coronavirus RaTG13. These factors include, but are not limited to: (1) travel to or contact with individuals who have recently visited Wuhan, China, or other places experiencing an outbreak; (2) close contact with persons who are diagnosed positive for the disease, such as healthcare workers caring for patients with SARS-CoV-2; (3) contact with droplets and secretions (produced by sneezing or coughing) from an infected person and eating or handling wild animals native to China such as bats. These factors include, but are not limited to: (1) travel to or contact with individuals who have recently visited Wuhan, China, or other places experiencing an outbreak; (2) close contact with persons who are diagnosed positive for the disease, such as healthcare workers caring for patients with SARS-CoV-2; (3) contact with droplets and secretions (produced by sneezing or coughing) from an infected person and eating or handling wild animals native to China such as bats. abstract: A pneumonia outbreak with unknown etiology was reported in Wuhan, Hubei province, China, in December 2019, associated with the Huanan Seafood Wholesale Market. The causative agent of the outbreak was identified by the WHO as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), producing the disease named coronavirus disease-2019 (COVID-19). The virus is closely related (96.3%) to bat coronavirus RaTG13, based on phylogenetic analysis. Human-to-human transmission has been confirmed even from asymptomatic carriers. The virus has spread to at least 200 countries, and more than 1,700,000 confirmed cases and 111,600 deaths have been recorded, with massive global increases in the number of cases daily. Therefore, the WHO has declared COVID-19 a pandemic. The disease is characterized by fever, dry cough, and chest pain with pneumonia in severe cases. In the beginning, the world public health authorities tried to eradicate the disease in China through quarantine but are now transitioning to prevention strategies worldwide to delay its spread. To date, there are no available vaccines or specific therapeutic drugs to treat the virus. There are many knowledge gaps about the newly emerged SARS-CoV-2, leading to misinformation. Therefore, in this review, we provide recent information about the COVID-19 pandemic. This review also provides insights for the control of pathogenic infections in humans such as SARS-CoV-2 infection and future spillovers. url: https://www.ncbi.nlm.nih.gov/pubmed/32344679/ doi: 10.3390/jcm9041225 id: cord-006129-5rog0s98 author: Hemida, Maged Gomaa title: Exploiting the Therapeutic Potential of MicroRNAs in Viral Diseases: Expectations and Limitations date: 2012-08-16 words: 7443.0 sentences: 508.0 pages: flesch: 50.0 cache: ./cache/cord-006129-5rog0s98.txt txt: ./txt/cord-006129-5rog0s98.txt summary: [12] Answering back, certain host miRNAs alter the cell gene expression to defend the cells against the viral infection by interfering with viral proteins or other cellular factors as a type of immune response against these particular viruses. [40] These virus-encoded miRNAs play important roles in the establishment of latent infection, as well as the pathogenesis of virally induced diseases. According to the most recent studies, herpesviruses utilize their encoded miRNAs in a wide range of biologic functions, such as inhibition of apoptosis, immune evasion, control of cellular proliferation, and regulation of viral replication. [58] Downregulation of UL114 protein, using miR-UL112-1, results in inhibition of viral DNA replication and subsequently triggers the latent phase of infection, making the virus able to evade the host immune system. abstract: New therapeutic approaches are urgently needed for serious diseases, including cancer, cardiovascular diseases, viral infections, and others. A recent direction in drug development is the utilization of nucleic acidbased therapeutic molecules, such as antisense oligonucleotides, ribozymes, short interfering RNA (siRNA), and microRNA (miRNA). miRNAs are endogenous, short, non-coding RNA molecules. Some viruses encode their own miRNAs, which play pivotal roles in viral replication and immune evasion strategies. Conversely, viruses that do not encode miRNAs may manipulate host cell miRNAs for the benefits of their replication. miRNAs have therefore become attractive tools for the study of viral pathogenesis. Lately, novel therapeutic strategies based on miRNA technology for the treatment of viral diseases have been progressing rapidly. Although this new generation of molecular therapy is promising, there are still several challenges to face, such as targeting delivery to specific tissues, avoiding off-target effects of miRNAs, reducing the toxicity of the drugs, and overcoming mutations and drug resistance. In this article, we review the current knowledge of the role and therapeutic potential of miRNAs in viral diseases, and discuss the limitations of these therapies, as well as strategies to overcome them to provide safe and effective clinical applications of these new therapeutics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7099301/ doi: 10.1007/bf03256383 id: cord-252456-971d0sir author: Hemida, Maged Gomaa title: The SARS-CoV-2 outbreak from a one health perspective date: 2020-03-16 words: 4824.0 sentences: 244.0 pages: flesch: 55.0 cache: ./cache/cord-252456-971d0sir.txt txt: ./txt/cord-252456-971d0sir.txt summary: The SARS-CoV-2 is a new human coronavirus candidate recently detected in China that is now reported in people on inhabited continents. Currently, the case fatality rate is relatively low (⁓3.6%) compared to infections with severe acute respiratory syndrome coronavirus (SARS-CoV, (10%) and MERS-CoV (32%) [11] . Based on the previous emergence history of SARS-CoV, the presence of a large number of mammals and birds overcrowded in one place may give a chance for pathogens, particularly those with RNA genomes such as coronaviruses and influenza viruses, to emerge. Based on the previous experience from the other emerging diseases, particularly SARS-CoV and influenza viruses, avoiding the mixing of various species of animals, birds, and mammals, is highly suggested [51, 65, 66] . The process of decontamination of the virus-contaminated surfaces by the appropriate disinfectants or virucidal agents was successful in case of other respiratory viruses such as SARS-CoV and avian influenza [59] . abstract: The SARS-CoV-2 is a new human coronavirus candidate recently detected in China that is now reported in people on inhabited continents. The virus shares a high level of identity with some bat coronaviruses and is recognised as a potentially zoonotic virus. We are utilizing the One Health concept to understand the emergence of the virus, as well as to point to some possible control strategies that might reduce the spread of the virus across the globe; thus, containment of such virus would be possible. url: https://api.elsevier.com/content/article/pii/S2352771420300185 doi: 10.1016/j.onehlt.2020.100127 id: cord-325875-93krp81r author: Henao-Diaz, Alexandra title: Guidelines for oral fluid-based surveillance of viral pathogens in swine date: 2020-10-19 words: 6151.0 sentences: 289.0 pages: flesch: 43.0 cache: ./cache/cord-325875-93krp81r.txt txt: ./txt/cord-325875-93krp81r.txt summary: (2020) showed that the probability of detecting porcine reproductive and respiratory syndrome virus (PRRSV) ribonucleic acid (RNA) in serum by reverse transcription polymerase chain reaction (RT-PCR) at 98 days post infection (DPI) was~2% versus~30% in lymphoid tissues (tonsil) by bioassay [16] . Similarly, differences in detection rates have been reported for pen-based oral fluids versus individual Table 1 provides examples of the detection of virus-specific nucleic acids and/or antibody in swine oral fluids, i.e., is not comprehensive b Acronyms defined in the list of abbreviations and terms pig buccal or nasal swabs for animals inoculated with FMDV, IAV, Senecavirus A (SVA), and swine vesicular disease virus (SVDV) [45, 62, 63, 68] . Diagnosis of the Lelystad strain of porcine reproductive and respiratory syndrome virus infection in individually housed pigs: comparison between serum and oral fluid samples for viral nucleic acid and antibody detection abstract: Recent decades have seen both rapid growth and extensive consolidation in swine production. As a collateral effect, these changes have exacerbated the circulation of viruses and challenged our ability to prevent, control, and/or eliminate impactful swine diseases. Recent pandemic events in human and animal health, e.g., SARS-CoV-2 and African swine fever virus, highlight the fact that clinical observations are too slow and inaccurate to form the basis for effective health management decisions: systematic processes that provide timely, reliable data are required. Oral fluid-based surveillance reflects the adaptation of conventional testing methods to an alternative diagnostic specimen. The routine use of oral fluids in commercial farms for PRRSV and PCV2 surveillance was first proposed in 2008 as an efficient and practical improvement on individual pig sampling. Subsequent research expanded on this initial report to include the detection of ≥23 swine viral pathogens and the implementation of oral fluid-based surveillance in large swine populations (> 12,000 pigs). Herein we compile the current information regarding oral fluid collection methods, testing, and surveillance applications in swine production. url: https://www.ncbi.nlm.nih.gov/pubmed/33082999/ doi: 10.1186/s40813-020-00168-w id: cord-267003-k7eo2c26 author: Hendaus, Mohamed A title: Virus-induced secondary bacterial infection: a concise review date: 2015-08-24 words: 3468.0 sentences: 238.0 pages: flesch: 36.0 cache: ./cache/cord-267003-k7eo2c26.txt txt: ./txt/cord-267003-k7eo2c26.txt summary: 7 The human body is usually capable of eliminating respiratory viral infections with no sequelae; however, in some cases, viruses bypass the immune response of the airways, causing conceivable severe respiratory diseases. 49, 50 virus effect on the immune system Post-viral sustained desensitization of lung sentinel cells to TLR signals may be one possible contributor to the common secondary bacterial pneumonia associated with viral infection. Hendaus et al human-alveolar basal-epithelial cells) during a respiratory viral infection by increasing the expression of ICAM-1. It has been recommended that treatment or prevention of a viral disease may be a superior method for diminishing 62 It has also been published that live attenuated influenza vaccine is effective in reducing the incidence of all-cause AOM [86] [87] [88] and pneumonia 89 compared to placebo in children. Effects of rhinovirus infection on the adherence of Streptococcus pneumoniae to cultured human airway epithelial cells 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-017527-ylng1us2 author: Herman, Philippe title: Biosafety Recommendations on the Handling of Animal Cell Cultures date: 2014-11-05 words: 10237.0 sentences: 453.0 pages: flesch: 38.0 cache: ./cache/cord-017527-ylng1us2.txt txt: ./txt/cord-017527-ylng1us2.txt summary: While biosafety recommendations (as outlined hereafter) are principally aimed at providing maximal protection of human health (including laboratory workers) and the environment, it is recognised that many of the precautionary measures will also directly benefit the quality of research activities involving animal cell cultures. The methodology of biological risk assessment of contained use activities involving pathogenic and/or genetically modified organisms (GMO) identifies and takes into account the probability of occurrence and the severity of a potential negative effect on public health (including the exposed workers) and/or the environment. The risk assessment applied to animal cell cultures relies on a thorough evaluation of both the intrinsic properties of the cell culture -including subsequent properties acquired as a result of genetic modification(s) -and the possibility that the cell culture may inadvertently be contaminated or deliberately infected with pathogenic micro-organisms. abstract: The first steps in tissue culture are dating back to the beginning of the nineteenth century when biosafety measures did not yet exist. Later on, animal cell culture became essential for scientific research, diagnosis and biotechnological activities. Along with this development, biosafety concerns have emerged pointing to the risks for human health and in a lesser extent for the environment associated to the handling of animal cell cultures. The management of these risks requires a thorough risk assessment of both the cell cultures and the type of manipulation prior the start of any activity. It involves a case-by-case evaluation of both the intrinsic properties of the cell culture genetically modified or not and the probability that it may inadvertently or intentionally become infected with pathogenic micro-organisms. The latter hazard is predominant when adventitious contaminants are pathogenic or have a better capacity to persist in unfavourable conditions. Consequently, most of the containment measures primarily aim at protecting cells from adventitious contamination. Cell cultures known to harbour an infectious etiologic agent should be manipulated in compliance with containment measures recommended for the etiologic agent itself. The manipulation of cell cultures from human or primate origin necessitates the use of a type II biosafety cabinet. The scope of this chapter is to highlight aspects relevant for the risk assessment and to summarize the main biosafety recommendations and the recent technological advances allowing a mitigation of the risk for the handling of animal cell cultures. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122109/ doi: 10.1007/978-3-319-10320-4_22 id: cord-326027-58whwspe author: Hernaez, Bruno title: Visualization of the African swine fever virus infection in living cells by incorporation into the virus particle of green fluorescent protein-p54 membrane protein chimera date: 2006-06-20 words: 7885.0 sentences: 372.0 pages: flesch: 45.0 cache: ./cache/cord-326027-58whwspe.txt txt: ./txt/cord-326027-58whwspe.txt summary: title: Visualization of the African swine fever virus infection in living cells by incorporation into the virus particle of green fluorescent protein-p54 membrane protein chimera To track the behavior of African swine fever virus (ASFV) in the infected cells in real time, we produced an infectious recombinant ASFV (B54GFP-2) that expresses and incorporates into the virus particle a chimera of the p54 envelope protein fused to the enhanced green fluorescent protein (EGFP). To determine that protein p54, a major component of the external envelope of ASFV, fused to EGFP protein remains incorporated to the viral particle, BA71V and B54GFP-2 virions were Percoll purified and analyzed by SDS-PAGE and Western blotting using specific antibodies (Fig. 2a) . This new role for p54 in morphogenesis supports the selection of p54 as viral fusion protein and suggests that studies about p54-EGFP trafficking during infection in live cells would be helpful to analyze the acquisition of ASFV envelopes from ER during virus assembly. abstract: Many stages of African swine fever virus infection have not yet been studied in detail. To track the behavior of African swine fever virus (ASFV) in the infected cells in real time, we produced an infectious recombinant ASFV (B54GFP-2) that expresses and incorporates into the virus particle a chimera of the p54 envelope protein fused to the enhanced green fluorescent protein (EGFP). The incorporation of the fusion protein into the virus particle was confirmed immunologically and it was determined that p54-EGFP was fully functional by confirmation that the recombinant virus made normal-sized plaques and presented similar growth curves to the wild-type virus. The tagged virus was visualized as individual fluorescent particles during the first stages of infection and allowed to visualize the infection progression in living cells through the viral life cycle by confocal microscopy. In this work, diverse potential applications of B54GFP-2 to study different aspects of ASFV infection are shown. By using this recombinant virus it was possible to determine the trajectory and speed of intracellular virus movement. Additionally, we have been able to visualize for first time the ASFV factory formation dynamics and the cytophatic effect of the virus in live infected cells. Finally, we have analyzed virus progression along the infection cycle and infected cell death as time-lapse animations. url: https://api.elsevier.com/content/article/pii/S0042682206000353 doi: 10.1016/j.virol.2006.01.021 id: cord-304807-j2k1oel2 author: Herrera-Rodriguez, José title: Inactivated or damaged? Comparing the effect of inactivation methods on influenza virions to optimize vaccine production date: 2019-03-14 words: 5758.0 sentences: 274.0 pages: flesch: 43.0 cache: ./cache/cord-304807-j2k1oel2.txt txt: ./txt/cord-304807-j2k1oel2.txt summary: The properties of the viral formulation, such as successful inactivation, preservation of hemagglutinin (HA) binding ability, fusion capacity and the potential to stimulate a Toll-like receptor 7 (TLR7) reporter cell line were then assessed and compared to the properties of the untreated virus. Hemagglutination and fusion ability were highly affected by those treatments that conferred higher inactivation, with BPL-treated virus binding and fusing at a lower degree compared to FA-inactivated samples. Our aim was to compare the effects of these procedures on the key properties, namely residual infectivity, receptor binding, fusion, and Toll-like receptor 7 (TLR7) mediated activation of innate immune mechanisms, and to determine whether these effects are similar for different virus strains. Previous studies show that BPL is capable of complete inactivation of influenza virus; however, the effectivity might vary depending on the incubation time and temperature. abstract: The vast majority of commercially available inactivated influenza vaccines are produced from egg-grown or cell-grown live influenza virus. The first step in the production process is virus inactivation with β-propiolactone (BPL) or formaldehyde (FA). Recommendations for production of inactivated vaccines merely define the maximal concentration for both reagents, leaving the optimization of the process to the manufacturers. We assessed the effect of inactivation with BPL and FA on 5 different influenza virus strains. The properties of the viral formulation, such as successful inactivation, preservation of hemagglutinin (HA) binding ability, fusion capacity and the potential to stimulate a Toll-like receptor 7 (TLR7) reporter cell line were then assessed and compared to the properties of the untreated virus. Inactivation with BPL resulted in undetectable infectivity levels, while FA-treated virus retained very low infectious titers. Hemagglutination and fusion ability were highly affected by those treatments that conferred higher inactivation, with BPL-treated virus binding and fusing at a lower degree compared to FA-inactivated samples. On the other hand, BPL-inactivated virus induced higher levels of activation of TLR7 than FA-inactivated virus. The alterations caused by BPL or FA treatments were virus strain dependent. This data shows that the inactivation procedures should be tailored on the virus strain, and that many other elements beside the concentration of the inactivating agent, such as incubation time and temperature, buffer and virus concentration, have to be defined to achieve a functional product. url: https://www.sciencedirect.com/science/article/pii/S0264410X19301847 doi: 10.1016/j.vaccine.2019.01.086 id: cord-348141-eskefcwk author: Herrington, CS title: Viruses and disease: emerging concepts for prevention, diagnosis and treatment date: 2014-12-11 words: 2120.0 sentences: 93.0 pages: flesch: 41.0 cache: ./cache/cord-348141-eskefcwk.txt txt: ./txt/cord-348141-eskefcwk.txt summary: Articles on emerging diseases caused by Ebola virus, Marburg virus, coronaviruses such as SARS and MERS, Nipah virus and noroviruses are followed by reviews of enteroviruses, HIV infection, measles, mumps, human respiratory syncytial virus (RSV), influenza, cytomegalovirus (CMV) and varicella zoster virus (VZV). The issue concludes with a series of articles reviewing the relationship between viruses and cancer, including the role played by Epstein–Barr virus (EBV) in the pathogenesis of lymphoma and carcinoma; how human papillomaviruses (HPVs) are involved in the development of skin cancer; the involvement of hepatitis B virus infection in hepatocellular carcinoma; and the mechanisms by which Kaposi''s sarcoma‐associated herpesvirus (KSHV) leads to Kaposi''s sarcoma. Nevertheless, in this new era, pathology will continue to be a vital component of identifying the true relationships between viruses and human disease, and we hope that this Annual Review Issue will serve as a blueprint for future studies in the diagnosis, treatment and prevention of virus-related conditions through an improved understanding of the processes involved. abstract: Viruses cause a wide range of human diseases, ranging from acute self‐resolving conditions to acute fatal diseases. Effects that arise long after the primary infection can also increase the propensity for chronic conditions or lead to the development of cancer. Recent advances in the fields of virology and pathology have been fundamental in improving our understanding of viral pathogenesis, in providing improved vaccination strategies and in developing newer, more effective treatments for patients worldwide. The reviews assembled here focus on the interface between virology and pathology and encompass aspects of both the clinical pathology of viral disease and the underlying disease mechanisms. Articles on emerging diseases caused by Ebola virus, Marburg virus, coronaviruses such as SARS and MERS, Nipah virus and noroviruses are followed by reviews of enteroviruses, HIV infection, measles, mumps, human respiratory syncytial virus (RSV), influenza, cytomegalovirus (CMV) and varicella zoster virus (VZV). The issue concludes with a series of articles reviewing the relationship between viruses and cancer, including the role played by Epstein–Barr virus (EBV) in the pathogenesis of lymphoma and carcinoma; how human papillomaviruses (HPVs) are involved in the development of skin cancer; the involvement of hepatitis B virus infection in hepatocellular carcinoma; and the mechanisms by which Kaposi's sarcoma‐associated herpesvirus (KSHV) leads to Kaposi's sarcoma. We hope that this collection of articles will be of interest to a wide range of scientists and clinicians at a time when there is a renaissance in the appreciation of the power of pathology as virologists dissect the processes of disease. Copyright © 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/25366544/ doi: 10.1002/path.4476 id: cord-023678-9q68ftr9 author: Hierholzer, J.C. title: Virus isolation and quantitation date: 2007-09-02 words: 7674.0 sentences: 425.0 pages: flesch: 61.0 cache: ./cache/cord-023678-9q68ftr9.txt txt: ./txt/cord-023678-9q68ftr9.txt summary: The method conserves the virus and viral antigens, because the supernatant fluid is decanted from the cell culture into a sterile tube at the end of the incubation period (7-10 days); the monolayer is washed twice with 2-3 ml of plain Hanks Balanced Salt Solution (HBSS) at room temperature; 1 ml of fresh HBSS followed by 0.2 ml of 0.4% mammalian erythrocyte suspension from the appropriate species is added to the monolayer; the tube is incubated stationary with the fluid covering the monolayer; and the test is read 3 times at 20-min intervals by agitating the tube in a sideways motion and then observing the monolayer at 40-100x magnification to see if the erythrocytes are firmly attached to the cultured cells or are floating free in the fluid (see Fig. 15 .4). abstract: This chapter outlines the two most commonly used methods of virus isolation—namely, tissue cultures and embryonated eggs. The chapter describes the methodology involved for the predominant virus groups that cover the majority of viruses encountered in the clinical situation. The chapter also describes selected methods of virus assay and the calculation of virus titers. Nasal swabs are the easiest specimens to collect for respiratory viruses and are also the best specimens for the majority of the respiratory viruses described in the chapter. Hemadsorption is a fast and convenient method of detecting orthomyxoviruses and non respiratory syncytial virus paramyxoviruses in cell cultures in which the cytopathic effect vary from obvious to minimal. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173433/ doi: 10.1016/b978-012465330-6/50003-8 id: cord-269519-8hr8wyrr author: Hirotsu, Yosuke title: Analysis of Covid-19 and non-Covid-19 viruses, including influenza viruses, to determine the influence of intensive preventive measures in Japan date: 2020-07-07 words: 1599.0 sentences: 113.0 pages: flesch: 54.0 cache: ./cache/cord-269519-8hr8wyrr.txt txt: ./txt/cord-269519-8hr8wyrr.txt summary: Other viruses in addition to SARS-CoV-2 cause cold-like symptoms and spread in the winter. However, the extent to which SARS-CoV-2, influenza viruses and other causative viruses have prevailed since implementing preventive measures is unclear. RESULTS: FilmArray Respiratory Panel analysis detected at least one virus in 32 of 191 patients with cold-like symptoms (21%). RT-PCR analysis detected SARS-CoV-2 (4.2%, n=8) in patients who were not infected with the aforementioned respiratory viruses. This epidemiologic study shows the infectability of each virus after implementing social preventive measures against SARS-CoV-2. The respiratory panel detected that 17% of the cohort (32/191 patients) were infected with causative viruses. At the start of the coronavirus epidemic, the infectivity of SARS-CoV-2 was unknown compared to that of influenza viruses. This study evaluated the differences in infectivity between SARS-CoV-2 and influenza viruses. The This study showed that taking stringent measures may prevent influenza viruses, which have more strongly affected human life for a longer time. abstract: BACKGROUND: Severe acute respiratory coronavirus 2 (SARS-CoV-2) has spread and caused death worldwide. Preventive measures and infection control are underway, and some areas show signs of convergence. Other viruses in addition to SARS-CoV-2 cause cold-like symptoms and spread in the winter. However, the extent to which SARS-CoV-2, influenza viruses and other causative viruses have prevailed since implementing preventive measures is unclear. OBJECTIVES: We aim to investigate the incidence of causative viruses and pathogens in patients. STUDY DESIGN: We collected 191 nasopharyngeal swabs from patients with cold-like symptoms in Japan. All samples were subjected to multiplex PCR with the FilmArray Respiratory Panel and reverse transcription PCR (RT-PCR) to detect SARS-CoV-2. RESULTS: FilmArray Respiratory Panel analysis detected at least one virus in 32 of 191 patients with cold-like symptoms (21%). Of these, we frequently identified human rhinoviruses/enteroviruses (5.8%, n=11), human metapneumovirus (3.7%, n=7), coronavirus 229E (2.1%, n=4) and coronavirus OC43 (1.6%, n=3); while no influenza viruses were detected. RT-PCR analysis detected SARS-CoV-2 (4.2%, n=8) in patients who were not infected with the aforementioned respiratory viruses. CONCLUSIONS: Co-infection with SARS-CoV-2 and other viruses was not observed. Causative viruses remain prevalent after implementing preventive measures. SARS-CoV-2 differs from influenza viruses in its infectivity. url: https://doi.org/10.1016/j.jcv.2020.104543 doi: 10.1016/j.jcv.2020.104543 id: cord-269426-82g5eiyg author: Holman, David H. title: Viral Vectors date: 2009-01-30 words: 8734.0 sentences: 420.0 pages: flesch: 40.0 cache: ./cache/cord-269426-82g5eiyg.txt txt: ./txt/cord-269426-82g5eiyg.txt summary: Abstract Traditional vaccine development platforms such as live-attenuated virus, killed virus, or recombinant subunit-based vaccines are often effective in eliciting long-term immunity to a number of infectious human pathogens. Finally, it is suggested that vaccination by alternate routes of administration (such as oral or intranasal) rather than injection can overcome pre-existing vector immunity ( Appaiahgari et al., 2006 ; Xiang et al., 2003 ) , which is supported by data from a human clinical trial ( Van Kampen et al., 2005 Lusky et al., 1998 ; Moorhead et al., 1999 ) or the E4 region ( Dedieu et al., 1997 ; Gao et al., 1996 ) of the Ad genome, which reduced or eliminated the expression of E2 or E4 proteins. High-level primary CD8( ϩ ) T-cell response to human immunodeficiency virus type 1 gag and env generated by vaccination with recombinant vesicular stomatitis viruses abstract: Abstract Traditional vaccine development platforms such as live-attenuated virus, killed virus, or recombinant subunit-based vaccines are often effective in eliciting long-term immunity to a number of infectious human pathogens. However, for many human pathogens, vaccine platforms such as these are unsuitable for human use due to safety concerns, poor efficacy, or simple impracticality. As a result, much work has focused on the use of recombinant virus vectors as a means for vaccination against human pathogens. Viral vectors can express foreign proteins at high levels in host cells, resulting in strong, long-lasting immune responses against the target proteins. This chapter describes the use of virus vectors in the context of vaccination against human pathogens. Various vector platforms are discussed, compared, and contrasted. url: https://api.elsevier.com/content/article/pii/B978012369408900007X doi: 10.1016/b978-0-12-369408-9.00007-x id: cord-346853-0c1qdjb5 author: Holmes, E. C. title: The Evolutionary Genetics of Viral Emergence date: 2007 words: 6123.0 sentences: 261.0 pages: flesch: 45.0 cache: ./cache/cord-346853-0c1qdjb5.txt txt: ./txt/cord-346853-0c1qdjb5.txt summary: Despite the wealth of data describing the ecological factors that underpin viral emergence, little is known about the evolutionary processes that allow viruses to jump species barriers and establish productive infections in new hosts. We also emphasize the current lack of convincing data as to whether viral emergence requires adaptation to the new host species during the early stages of infection, or whether it is largely a chance process involving the transmission of a viral strain with the necessary genetic characteristics. For example, one model of viral emergence posits that adaptation to a new host species during the early period of an epidemic is of fundamental importance, because this raises the basic reproductive rate of the virus, R 0 , to greater than 1, so that sustained transmission networks can be established (Anita et al. abstract: Despite the wealth of data describing the ecological factors that underpin viral emergence, little is known about the evolutionary processes that allow viruses to jump species barriers and establish productive infections in new hosts. Understanding the evolutionary basis to virus emergence is therefore a key research goal and many of the debates in this area can be considered within the rigorous theoretical framework established by evolutionary genetics. In particular, the respective roles played by natural selection and genetic drift in shaping genetic diversity are also of fundamental importance for understanding the nature of viral emergence. Herein, we discuss whether there are evolutionary rules to viral emergence, and especially whether certain types of virus, or those that infect a particular type of host species, are more likely to emerge than others. We stress the complex interplay between rates of viral evolution and the ability to recognize cell receptors from phylogenetically divergent host species. We also emphasize the current lack of convincing data as to whether viral emergence requires adaptation to the new host species during the early stages of infection, or whether it is largely a chance process involving the transmission of a viral strain with the necessary genetic characteristics. url: https://www.ncbi.nlm.nih.gov/pubmed/17848060/ doi: 10.1007/978-3-540-70962-6_3 id: cord-286137-4cbh3u3z author: Honce, Rebekah title: They are what you eat: Shaping of viral populations through nutrition and consequences for virulence date: 2020-08-13 words: 1928.0 sentences: 119.0 pages: flesch: 33.0 cache: ./cache/cord-286137-4cbh3u3z.txt txt: ./txt/cord-286137-4cbh3u3z.txt summary: In mineral-and vitamin-deficient mice, genetic mutations arise in coxsackie B and influenza virus populations that promote virulence even in well-nourished hosts [36] [37] [38] [39] [40] . Experimental evolution of CA/09 virus through two models of murine obesity resulted in a viral population displaying increased virulence upon inoculation of a wild-type host. Interestingly, arbovirus-infected obese or protein-deficient mice showed higher morbidity but lower viral diversity, and both malnourished models transmitted virus less efficiently, highlighting that the effects of nutrition may vary based on the natural life cycles of viral families [42] . In our studies with influenza virus, we linked the emergence of a more diverse and virulent viral population with blunted interferon responses in obese hosts. Interferon treatment of obese mice restricted the emergence of a diverse quasispecies and attenuated the virulence of the resulting viral population, strengthening the claim that a robust innate immune response restricts subsequent infection severity, possibly through reduced viral replication and acquisition of a genetically diverse viral population [8, 20, 41] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32790755/ doi: 10.1371/journal.ppat.1008711 id: cord-022399-66mzbynu author: Hopkins, Graham title: Basic microbiology date: 2009-05-15 words: 8602.0 sentences: 552.0 pages: flesch: 52.0 cache: ./cache/cord-022399-66mzbynu.txt txt: ./txt/cord-022399-66mzbynu.txt summary: Bacteria are important because of their ubiquity -that is, their ability to infect and multiply in varied environments -and the ability of many types of bacteria to cause disease -their pathogenicity. To reduce problems caused by bacteria, it is important to understand something of their structure, growth, environmental and metabolic requirements, classification, relationship with disease and the particular problems they can cause to the eye. The result is that the cells tend to grow and divide at a slower rate but are more resistant to antibacterial chemicals, viruses (bacteriophages), phagocytes and other adverse agents. As causative organisms of disease, fungi are less important than bacteria and viruses. • Sterilization: the killing or removal of all viable organisms (including bacterial spores) from an object or pharmaceutical product by the use of chemical or physical agents. Developments have led to the introduction of agents that are more effective against the infecting organism and less toxic to the host. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155651/ doi: 10.1016/b978-0-7506-8864-2.50005-2 id: cord-298905-c2uuvfm5 author: Horzinek, M. C. title: Molecular pathogenesis of virus infections date: 1987 words: 3888.0 sentences: 193.0 pages: flesch: 40.0 cache: ./cache/cord-298905-c2uuvfm5.txt txt: ./txt/cord-298905-c2uuvfm5.txt summary: Using coronaviruses as examples the changes in virulence have been traced back to single mutational events; recombination, however, is likely to be an alternative mechanism by which virus-host interactions (e.g. the cell-, organor animal species-spectrum) can dramatically change. Parainfluenzaviruses, for example, attach to neuraminic acid-containing receptors; since glycolipids and glycoproteins containing neuraminic acid abound in vertebrate cell membranes the adsorption/penetration process lacks the specificity required to explain the restrictions in host range and tissue tropism of paramyxoviruses 29. Also in influenza virus infection cap structures are essential: these are cannibalized from host cell nuclear RNA precursor molecules and used as primers for viral RNA replication and synthesis 28. Autoimmune phenomena involving both the humoral and cellular limbs of the immune response have been identified in neurological conditions following infections with e.g. canine distemper virus3; invasion of brain tissue is supposed to cause changes in the molecular constitution of myelin and membrane components, making them recognizable as ''nonself''. abstract: Although a very wide range of viral diseases exists in vertebrates, certain generalizations can be made regarding pathogenetic pathways on the molecular level. The presentation will focus on interactions of virions and their components with target cells. Using coronaviruses as examples the changes in virulence have been traced back to single mutational events; recombination, however, is likely to be an alternative mechanism by which virus-host interactions (e.g. the cell-, organ- or animal species-spectrum) can dramatically change. Receptor molecules are essential for the early interactions during infection and some ot these have been identified. Events in the target cell and the host organism are discussed, and wherever possible, aspects of virus evolution and cooperation between infectious agents are highlighted. url: https://www.ncbi.nlm.nih.gov/pubmed/2826215/ doi: 10.1007/bf01945522 id: cord-023092-unjv71qv author: Horzinek, Prof. Dr Marian C. title: Feline leukaemia prophylaxis date: 2008-04-10 words: 2407.0 sentences: 140.0 pages: flesch: 50.0 cache: ./cache/cord-023092-unjv71qv.txt txt: ./txt/cord-023092-unjv71qv.txt summary: The humoral immune response against FeLV is directed mainly against the viral surface structure gp70/85 and against the so-called ''feline oncornavirus-associated membrane antigen'' (FOCMA). The numerous experiments to develop an efficient vaccine against FeLV infection have recently shown their first success: in the U.S.A. a preparation is presently being marketed for use by the small animal practitioner. (1) cells (virus-producing, live or inactivated) (2) virus (live or inactivated) (3) split products (viral or cellular surface structures; gp7O/gp85, FOCMA) (4) synthetic antigens ( 5 ) products obtained by genetic engineering (antigens from pro-or eukaryotic Each of the above-mentioned strategies has been followed with varying success, cells after cloning of the respective viral genes) and the hope for the future is directed towards development of synthetic and genetically engineered vaccines. Vaccination against feline leukaemia virus using a cell membrane antigen system Feline leukemia virus envelope glycoprotein vaccine: preparation and evaluation of immunizing potency in guinea pig and cat abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7166725/ doi: 10.1111/j.1748-5827.1986.tb02146.x id: cord-296309-i1mpov7k author: Houldcroft, Charlotte J. title: Clinical and biological insights from viral genome sequencing date: 2017-01-16 words: 9050.0 sentences: 389.0 pages: flesch: 35.0 cache: ./cache/cord-296309-i1mpov7k.txt txt: ./txt/cord-296309-i1mpov7k.txt summary: We will also explore two areas in which viral WGS has recently proven its clinical utility: metagenomic sequencing to identify viruses that cause encephalitis (BOX 1) ; and the role of WGS in molecular epidemiology and public health management of the Pan-American Zika virus outbreak (BOX 2) . However, the increasing number of resistance genes that are located across viral genomes, together with decreasing costs of sequencing and the use of sequence data for transmission studies, are driving a reappraisal of the need for WGS. The numerous phylogenetically informative variant sites that can be obtained from full-length or near full-length genomes removes the need for high-quality sequences, which enabled the robust linking of cases of Ebola virus infection and public health interventions in real time during the 2015 epidemic 39 . There are several methods that are available to achieve WGS of viruses from clinical samples; amplicon sequencing, target enrichment or metagenomics. abstract: Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages. Although there are only partially addressed technical, financial and ethical issues in regard to the clinical application of viral WGS, this technique provides important insights into virus transmission, evolution and pathogenesis. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nrmicro.2016.182) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1038/nrmicro.2016.182 doi: 10.1038/nrmicro.2016.182 id: cord-320693-de1lmzl1 author: Hu, Han title: Antiviral activity of Piscidin 1 against pseudorabies virus both in vitro and in vivo date: 2019-07-31 words: 5052.0 sentences: 320.0 pages: flesch: 52.0 cache: ./cache/cord-320693-de1lmzl1.txt txt: ./txt/cord-320693-de1lmzl1.txt summary: METHODS: In this study, we evaluated the activities of five broad-spectrum antimicrobial peptides (AMPs) against several important swine-origin pathogenic viruses by TCID(50) assay. The pathogenic viruses isolated from pigs including pseudorabies virus (PRV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and rotavirus (RV) are commonly observed in China. In this study, we investigated the activity of five AMPs including piscidin, caerin, maculatin, lactoferricin B, and indolicidin against several porcine-origin viruses. The antiviral effects of the peptides (maculatin, caerin, piscidin, lactoferricin B, indolicidin) were investigated in vitro against several viral pathogens that severely threaten the porcine industry. Three peptides (caerin, piscidin, maculatin) exhibited inhibitory activity against PRV, PEDV, TGEV, PRRSV, and rotavirus. Our plaque reduction assay result indicated that piscidin, caerin, and maculatin could inhibit PRV by directly interacting with the virus. abstract: BACKGROUND: Swine-origin virus infection spreading widely could cause significant economic loss to porcine industry. Novel antiviral agents need to be developed to control this situation. METHODS: In this study, we evaluated the activities of five broad-spectrum antimicrobial peptides (AMPs) against several important swine-origin pathogenic viruses by TCID(50) assay. Plaque reduction assay and cell apoptosis assay were also used to test the activity of the peptides. Protection effect of piscidin against pseudorabies virus (PRV) was also examined in mouse model. RESULTS: Piscidin (piscidin 1), caerin (caerin 1.1) and maculatin (maculatin 1.1) could inhibit PRV by direct interaction with the virus particles in a dose-dependent manner and they could also protect the cells from PRV-induced apoptosis. Among the peptides tested, piscidin showed the strongest activity against PRV. Moreover, in vivo assay showed that piscidin can reduce the mortality of mice infected with PRV. CONCLUSION: In vitro and in vivo experiments indicate that piscidin has antiviral activity against PRV. url: https://doi.org/10.1186/s12985-019-1199-4 doi: 10.1186/s12985-019-1199-4 id: cord-016576-1yqwci0y author: Hu, Xiaohua title: Mining Candidate Viruses as Potential Bio-terrorism Weapons from Biomedical Literature date: 2005 words: 2659.0 sentences: 148.0 pages: flesch: 56.0 cache: ./cache/cord-016576-1yqwci0y.txt txt: ./txt/cord-016576-1yqwci0y.txt summary: In this paper we present a semantic-based data mining approach to identify candidate viruses as potential bio-terrorism weapons from biomedical literature. If a virus is found in the different document sets obtained by several search keywords, the virus should be considered as suspicious and treated as candidate viruses for bio-terrorism. We propose an automated, semantic-based data mining system to identify viruses that can be used as potential weapons in bio-terrorism. Following the criteria established by Geissler and the similar ideas used by Swanson [10] , in the mining procedure, we consider many important properties of the virus such as the genetic aspects of virulence; airbone transmission of viral disease; and stability of viruses in air or aerosol mixtures etc.. We introduce an automated semantic-based search system, called Combinational Search based Virus Seeker (CSbVS), to identify viruses that can be used as potential weapons in bio-terrorism. abstract: In this paper we present a semantic-based data mining approach to identify candidate viruses as potential bio-terrorism weapons from biomedical literature. We first identify all the possible properties of viruses as search key words based on Geissler’s 13 criteria; the identified properties are then defined using MeSH terms. Then, we assign each property an importance weight based on domain experts’ judgment. After generating all the possible valid combinations of the properties, we search the biomedical literature, retrieving all the relevant documents. Next our method extracts virus names from the downloaded documents for each search keyword and identifies the novel connection of the virus according to these 4 properties. If a virus is found in the different document sets obtained by several search keywords, the virus should be considered as suspicious and treated as candidate viruses for bio-terrorism. Our findings are intended as a guide to the virus literature to support further studies that might then lead to appropriate defense and public health measures. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120915/ doi: 10.1007/11427995_6 id: cord-002937-7xauocti author: Huang, Chung-Guei title: A pilot study on primary cultures of human respiratory tract epithelial cells to predict patients’ responses to H7N9 infection date: 2018-02-20 words: 6238.0 sentences: 293.0 pages: flesch: 46.0 cache: ./cache/cord-002937-7xauocti.txt txt: ./txt/cord-002937-7xauocti.txt summary: We aimed to investigate whether primary cultures of human respiratory tract epithelial cells are helpful to understand H7N9 virus pathogenesis and tissue tropism, and to evaluate how patient-related characteristics can affect the host''s response to infection. In this scenario, primary cultures of human respiratory tract epithelial cells would be invaluable to understand H7N9 virus tissue tropism and pathogenesis, as well as to evaluate how patient-related characteristics can modulate the host''s response to infection. With regard to virus tropism, viral RNA quantities were significantly higher in epithelial cells obtained from the upper anatomical locations than from the lower anatomical locations, without adjustment (P = 0.030); however, the difference lost significance after adjustment for age, sex, medical comorbidities, and obesity (P = 0.490; Figure 2B ). abstract: Avian influenza A(H7N9) virus infections frequently lead to acute respiratory distress syndrome and death in humans. We aimed to investigate whether primary cultures of human respiratory tract epithelial cells are helpful to understand H7N9 virus pathogenesis and tissue tropism, and to evaluate how patient-related characteristics can affect the host's response to infection. Normal human bronchial epithelial cells (isolated from two different donors) and primary epithelial cells (harvested from 27 patients undergoing airway surgery) were experimentally infected with H7N9 and/or H1N1pdm for 72 h. After virus infection, the culture media were collected for viral RNA quantitation and cytokine detection. Both H7N9 and H1N1pdm viruses replicated and induced a cytokine response differently for each donor in the normal human bronchial epithelial model. H7N9 replicated equivalently in epithelial cells harvested from the inferior turbinate and paranasal sinus, and those from the larynx and bronchus, at 72 h post-infection. Viral RNA quantity at 72 h was significantly higher in patients aged 21–64 years than in patients aged ≥ 65 years; however, no effects of sex, medical comorbidities, and obesity were noted. H7N9-infected cultured cells released multiple cytokines within 72 h. Levels of interleukin-1β, interleukin-6, interleukin-8, interferon-γ, and tumor necrosis factor-α were associated differently with patient-related characteristics (such as age, sex, obesity, and medical comorbidities). In the era of precision medicine, these findings illustrate the potential utility of this primary culture approach to predict a host's response to H7N9 infection or to future infection by newly emerging viral infections, and to dissect viral pathogenesis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5865685/ doi: 10.18632/oncotarget.24537 id: cord-259627-8stewshp author: Huang, Qing title: Inactivation of dengue virus by methylene blue/narrow bandwidth light system date: 2004-12-02 words: 2690.0 sentences: 132.0 pages: flesch: 47.0 cache: ./cache/cord-259627-8stewshp.txt txt: ./txt/cord-259627-8stewshp.txt summary: Because photodynamic virus inactivation with methylene blue (MB)/light system has proven effective in blood banking, MB was selected as a photosensitizing agent, dengue virus as a model virus for enveloped RNA viruses, and an in-house fabricated narrow bandwidth light system overlapping the absorption spectrum of MB as the light source. Results showed that the concentration of MB working solution, illumination intensity of light source, illumination distance and time were four key factors affecting efficiency of virus inactivation using the MB/narrow bandwidth light system. The results indicate that MB concentration, illumination time and distance are three key factors affecting efficiency of virus inactivation when the illumination intensity of the light source was held constant. MB working concentration and illumination intensity, time and distance are the four key factors affecting the inactivation efficiency of the MB/narrow bandwidth light system. abstract: Abstract Peracetic acid was one of the most commonly used disinfectants on solid surfaces in hospitals or public places. However, peracetic acid is an environmental toxin. Therefore, safer, alternative disinfectants or disinfectant systems should be developed. Because photodynamic virus inactivation with methylene blue (MB)/light system has proven effective in blood banking, MB was selected as a photosensitizing agent, dengue virus as a model virus for enveloped RNA viruses, and an in-house fabricated narrow bandwidth light system overlapping the absorption spectrum of MB as the light source. Dengue virus was mixed with different concentrations of MB, and illuminated by the narrow bandwidth light system under different illumination distances and times. The amount of dengue virus remaining was evaluated by plaque forming assays. Results showed that the concentration of MB working solution, illumination intensity of light source, illumination distance and time were four key factors affecting efficiency of virus inactivation using the MB/narrow bandwidth light system. Dengue virus could be completely inactivated at 2.5 m in 5 min when MB⩾1.0 μg/ml. However, when the distance reached 3.0 m, only greater concentrations of MB (2.0 μg/ml) could completely inactivate virus in a reasonably short time (20 min), and smaller concentrations of MB (1.0 μg/ml) could only completely inactivate virus using longer times (25 min). The results of this virus inactivation model indicate that our MB/narrow bandwidth light system provides a powerful, easy way to inactivate dengue viruses. url: https://www.sciencedirect.com/science/article/pii/S1011134404001186 doi: 10.1016/j.jphotobiol.2004.08.005 id: cord-336493-ggo9wsrm author: Huang, Stephen S. H. title: Immunity toward H1N1 influenza hemagglutinin of historical and contemporary strains suggests protection and vaccine failure date: 2013-04-23 words: 6444.0 sentences: 342.0 pages: flesch: 46.0 cache: ./cache/cord-336493-ggo9wsrm.txt txt: ./txt/cord-336493-ggo9wsrm.txt summary: In our present study, we investigated the clinical characteristics and immune cross-reactivity of significant H1N1 influenza strains in the past 100 years in ferrets to determine the immunogenicity of important H1N1 viruses. Ferrets show respiratory illness similar to humans and clinical features of disease are easily observed where fevers can persist days following infection of viruses such as 2009 H1N1pdm influenza 21, 23, 30 . As well as fever, nasal discharge and sneezing can also be observed in animals infected with influenza viruses 21 These influenza A viruses were chosen due to their emergence and influence in H1N1 genetic history (Fig. 1 , strains used in this study are marked with an asterisks) as covered in the introduction. The immunogenic findings showed antisera produced from ferret infection with Taiwan/86 was not able to inhibit hemagglutination with the other viruses on our virus panel, which compliments the literature describing the 1986 strain. abstract: Evolution of H1N1 influenza A outbreaks of the past 100 years is interesting and significantly complex and details of H1N1 genetic drift remains unknown. Here we investigated the clinical characteristics and immune cross-reactivity of significant historical H1N1 strains. We infected ferrets with H1N1 strains from 1943, 1947, 1977, 1986, 1999, and 2009 and showed each produced a unique clinical signature. We found significant cross-reactivity between viruses with similar HA sequences. Interestingly, A/FortMonmouth/1/1947 antisera cross-reacted with A/USSR/90/1977 virus, thought to be a 1947 resurfaced virus. Importantly, our immunological data that didn't show cross-reactivity can be extrapolated to failure of past H1N1 influenza vaccines, ie. 1947, 1986 and 2009. Together, our results help to elucidate H1N1 immuno-genetic alterations that occurred in the past 100 years and immune responses caused by H1N1 evolution. This work will facilitate development of future influenza therapeutics and prophylactics such as influenza vaccines. url: https://doi.org/10.1038/srep01698 doi: 10.1038/srep01698 id: cord-017429-3evwlfac author: Hubálek, Zdenek title: Vertebrates as Hosts and Reservoirs of Zoonotic Microbial Agents date: 2010-11-10 words: 4952.0 sentences: 630.0 pages: flesch: 57.0 cache: ./cache/cord-017429-3evwlfac.txt txt: ./txt/cord-017429-3evwlfac.txt summary: VIRUSES: Lyssavirus s.s. Colonial species distributed in southern USA; roosts in caves, also mine tunnels, hollow trees, buildings, and migrates up to 70 km. Noctule Bat (Nyctalus noctula: Photo 7.12) A large Eurasian species, living in deciduous and mixed forests, and roosting in tree hollows (e.g., woodpecker holes), feeds on large insects. Extensive home range (usually up to 15 km, occasionally 160 km recorded North-American, medium-sized (about that of a small dog) species living near wooded areas, closely to streams and lakes, rock cliffs, but also in urban areas. Comparatively large (25-40 cm long plus tail 7-12 cm; weight about 1 kg) rodent, living in steppe habitat (dry upland prairies) of central and southern areas of USA, and forming extensive colonies ("towns") with deep burrows. BACTERIA: Leptospira grippotyphosa, Francisella tularensis, Borrelia burgdorferi s.s. North-Eurasian species of flying nocturnal squirrel. abstract: This chapter presents a survey of zoonotic microorganisms that have been isolated from vertebrates (Vertebrata), and are potentially transmissible to humans. It is intended as an aid for microbiologists, zoologists and epidemiologists, making possible better orientation among hosts (and reservoirs) of zoonoses. A great number of sources have been used in this compilation, e.g. Davis et al. (1970), Kucheruk (1979, 1989), Karabatsos (1985–1995), Hubálek (1994), etc. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121989/ doi: 10.1007/978-90-481-9657-9_7 id: cord-332205-ydijp66b author: Hufsky, Franziska title: Virologists—Heroes need weapons date: 2018-02-08 words: 1165.0 sentences: 69.0 pages: flesch: 53.0 cache: ./cache/cord-332205-ydijp66b.txt txt: ./txt/cord-332205-ydijp66b.txt summary: Nowadays, nearly everyone in the life sciences has used BLAST [8] at least once, or made an alignment, or asked a bioinformatician to analyze high-throughput sequencing data. Bioinformaticians routinely have to develop tailored, study-specific algorithms and tools used by a wide variety of scientists, including biochemists, biologists, geneticists, and molecular life scientists; but we rarely find virus-specific tools used by virologists. But astonishingly, we now know that the human genome consists of 8%-60% virus-derived sequences (depending on how this is measured: 8% can be directly traced back to viruses, whereas a figure of 60% includes LINEs and SINEs that are thought to be of viral origin [12] ). The EVBC aims to develop bioinformatical tools for nearly all areas: (1) for detection of viruses, e.g., from high-throughput sequencing data; (2) virus assembly; (3) quasispecies reconstruction; (4) intraviral interactions; (5) virus entry, i.e., protein-protein interaction; (6) virus -host interactions; (7) phylogeny/cophylogeny; and (8) therapy. abstract: nan url: https://doi.org/10.1371/journal.ppat.1006771 doi: 10.1371/journal.ppat.1006771 id: cord-295531-zojb3cew author: Huggett, Kathryn D. title: Influenza A date: 2008-01-10 words: 2094.0 sentences: 141.0 pages: flesch: 50.0 cache: ./cache/cord-295531-zojb3cew.txt txt: ./txt/cord-295531-zojb3cew.txt summary: Subtypes of influenza A viruses that are prominent in one species may on occasion infect and cause disease in another. Influenza A is a single-stranded RNA virus that causes an acute and highly contagious upper respiratory disease. It was approved in 1966 for chemoprophylaxis and in 1976 for treatment and chemoprophylaxis of influenza type A virus in both adults and children 1 year of age. It was approved in 1993 for the treatment and chemoprophylaxis of influenza A infections in adults and prophylaxis in children. It was approved in 1999 for the treatment of uncomplicated influenza infections in patients aged 1 year. It was approved in 1999 for the treatment of uncomplicated influenza infections in patients aged 1 year. Basic information on the diagnosis, clinical findings, complications, prevention and treatment of influenza, including vaccine safety recommendations, can be found at: http://www3.accessmedicine.com/content.aspx?aID=17572#17572 Information on the common cold and flu can be located at: http://familydoctor.org/517. abstract: The influenza viruses, which contain single-stranded RNA, are classified into 3 types, A, B, and C … url: https://www.sciencedirect.com/science/article/pii/B9780080552323609225 doi: 10.1016/b978-008055232-3.60922-5 id: cord-334560-1j9zmuub author: Hunt, Catherine L. title: Filovirus Entry: A Novelty in the Viral Fusion World date: 2012-02-07 words: 6445.0 sentences: 301.0 pages: flesch: 48.0 cache: ./cache/cord-334560-1j9zmuub.txt txt: ./txt/cord-334560-1j9zmuub.txt summary: Details of the molecular events following cathepsin-dependent trimming of GP(1) are currently incomplete; however, the processed GP(1) specifically interacts with endosomal/lysosomal membranes that contain the Niemann Pick C1 (NPC1) protein and expression of NPC1 is required for productive infection, suggesting that GP/NPC1 interactions may be an important late step in the entry process. However, for reasons that are not entirely clear, this type of study has not been successful in identifying cell surface proteins that directly interact with EBOV GP to mediate virus entry [41, 42] . However, as both of these regions can be deleted from EBOV GP 1 without loss of viral transduction efficiency [16, [50] [51] [52] , it is likely that C-type lectins increase filovirus attachment to cells rather than serving as cellular receptors that mediate internalization of the virus into endosomes [53] . abstract: Ebolavirus (EBOV) and Marburgvirus (MARV) that compose the filovirus family of negative strand RNA viruses infect a broad range of mammalian cells. Recent studies indicate that cellular entry of this family of viruses requires a series of cellular protein interactions and molecular mechanisms, some of which are unique to filoviruses and others are commonly used by all viral glycoproteins. Details of this entry pathway are highlighted here. Virus entry into cells is initiated by the interaction of the viral glycoprotein(1) subunit (GP(1)) with both adherence factors and one or more receptors on the surface of host cells. On epithelial cells, we recently demonstrated that TIM-1 serves as a receptor for this family of viruses, but the cell surface receptors in other cell types remain unidentified. Upon receptor binding, the virus is internalized into endosomes primarily via macropinocytosis, but perhaps by other mechanisms as well. Within the acidified endosome, the heavily glycosylated GP(1) is cleaved to a smaller form by the low pH-dependent cellular proteases Cathepsin L and B, exposing residues in the receptor binding site (RBS). Details of the molecular events following cathepsin-dependent trimming of GP(1) are currently incomplete; however, the processed GP(1) specifically interacts with endosomal/lysosomal membranes that contain the Niemann Pick C1 (NPC1) protein and expression of NPC1 is required for productive infection, suggesting that GP/NPC1 interactions may be an important late step in the entry process. Additional events such as further GP(1) processing and/or reducing events may also be required to generate a fusion-ready form of the glycoprotein. Once this has been achieved, sequences in the filovirus GP(2) subunit mediate viral/cellular membrane fusion via mechanisms similar to those previously described for other enveloped viruses. This multi-step entry pathway highlights the complex and highly orchestrated path of internalization and fusion that appears unique for filoviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/22470835/ doi: 10.3390/v4020258 id: cord-022674-90g0461f author: Hurst, Christon J. title: Detecting Viruses in Water date: 1989-09-01 words: 7260.0 sentences: 398.0 pages: flesch: 39.0 cache: ./cache/cord-022674-90g0461f.txt txt: ./txt/cord-022674-90g0461f.txt summary: Subsequent recovery of the adsorbed viruses can occur either by dissolving the filter material, if it is composed of alginate,"" or by exposing the adsorbent to a volume of eluant that is smaller than the original water sample and facilitates a reversal of the virus adsorption process. Of the many different types and configurations of virus adsorbents, those now preferred for use in recovering viruses from large volumes of water are wound cartridge filters*'' and pleated cartridge filter@ based on either glass fiber or nylon, including types that are positively charged, and columns of glass powder.26 Also of interest is the use of sheet filter material that has been modified in situ either by a precipitation of metal hydroxides within the filter ma-trix2" or by coating the filter with cationic 74 RESEARCHANDTECHNOLOGY Cultures of mammalian cells were prepared using a laminar-flow filtered air hood. abstract: Various and divergent approaches that have been used to concentrate and assay viruses from tap water and environmental freshwaters are summarized and briefly explained. The basic principles behind the different methodologies and descriptions of the most recent developments are emphasized. Comparisons help demonstrate the relative sensitivities of different concentration and assay techniques. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159604/ doi: 10.1002/j.1551-8833.1989.tb03273.x id: cord-348163-9q1rt8i7 author: Hussein, Hosni A. M. title: Beyond RGD: virus interactions with integrins date: 2015-09-01 words: 5945.0 sentences: 301.0 pages: flesch: 36.0 cache: ./cache/cord-348163-9q1rt8i7.txt txt: ./txt/cord-348163-9q1rt8i7.txt summary: Integrins are a family of receptor molecules that serve as entry receptors for a variety of different viruses, including foot-and-mouth disease virus (FMDV) [97] , Kaposi''s sarcoma-associated herpesvirus (KSHV) [5], herpes simplex virus-2 (HSV-2) [31], adenovirus [168] , human papillomavirus-16 (HPV-16) [3] , reovirus [40] , and others. On the other hand, interactions of viruses with cellular integrins induce conformational changes in the viral surface proteins, helping to expose the essential domains required for virus entry into a host cell [107] . Similarly, several human herpesviruses, including HSV [147] , KSHV [4], and CMV [93] , make their initial contact with cells by binding to cellsurface HSPGs. In general, binding of viruses to carbohydrate moieties on the surface of cells is the key step that induces conformational changes in the viral structure that are critical for interactions with entry-promoting receptors such as integrins. abstract: Viruses successfully infect host cells by initially binding to the surfaces of the cells, followed by an intricate entry process. As multifunctional heterodimeric cell-surface receptor molecules, integrins have been shown to usefully serve as entry receptors for a plethora of viruses. However, the exact role(s) of integrins in viral pathogen internalization has yet to be elaborately described. Notably, several viruses harbor integrin-recognition motifs displayed on viral envelope/capsid-associated proteins. The most common of these motifs is the minimal peptide sequence for binding integrins, RGD (Arg-Gly-Asp), which is known for its role in virus infection via its ability to interact with over half of the more than 20 known integrins. Not all virus-integrin interactions are RGD-dependent, however. Non-RGD-binding integrins have also been shown to effectively promote virus entry and infection as well. Such virus-integrin binding is shown to facilitate adhesion, cytoskeleton rearrangement, integrin activation, and increased intracellular signaling. Also, we have attempted to discuss the role of carbohydrate moieties in virus interactions with receptor-like host cell surface integrins that drive the process of internalization. As much as possible, this article examines the published literature regarding the role of integrins in terms of virus infection and virus-encoded glycosylated proteins that mediate interactions with integrins, and it explores the idea of targeting these receptors as a therapeutic treatment option. url: https://www.ncbi.nlm.nih.gov/pubmed/26321473/ doi: 10.1007/s00705-015-2579-8 id: cord-292353-z86rjwle author: Hussein, Islam T.M. title: Recent Advances in Hantavirus Molecular Biology and Disease date: 2011-04-01 words: 13579.0 sentences: 708.0 pages: flesch: 47.0 cache: ./cache/cord-292353-z86rjwle.txt txt: ./txt/cord-292353-z86rjwle.txt summary: Hantaviruses pose a serious threat to human health because their infection causes two highly fatal diseases, hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS). The sequences at both the 3 0 and 5 0 termini of each RNA segment are complementary forming ''''panhandle'''' structures that are specifically recognized by the N protein and were shown to be important for viral transcription and replication. Further studies revealed that cellular 5 0capped mRNA oligoribonucleotides are rescued by N in virus-infected cells and stored in P-bodies for the later use as primers by the viral RdRp during transcription initiation . The UTRs are encapsidated by nucleocapsid protein and associate with RdRp both in the host cells and in the virion, and only these nucleocapsids are believed to be functional templates for mRNA synthesis and RNA replication by the viral RdRp. c. abstract: Hantaviruses are emerging zoonotic pathogens that belong to the Bunyaviridae family. They have been classified as category A pathogens by CDC (centers for disease control and prevention). Hantaviruses pose a serious threat to human health because their infection causes two highly fatal diseases, hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS). These pathogens are transmitted to humans through aerosolized excreta of their infected rodent hosts. Hantaviruses have a tripartite-segmented negative-sense RNA genome. The three genomic RNA segments, S, M, and L, encode a nucleocapsid protein (N), a precursor glycoprotein that is processed into two envelope glycoproteins (Gn and Gc) and the viral RNA-dependent RNA polymerase (RdRp), respectively. N protein is the major structural component of the virus, its main function is to protect and encapsidate the three genomic RNAs forming three viral ribonucleocapsids. Recent studies have proposed that N in conjunction with RdRp plays important roles in the transcription and replication of viral genome. In addition, N preferentially facilitates the translation of viral mRNA in cells. Glycoproteins, Gn and Gc, play major roles in viral attachment and entry to the host cells, virulence, and assembly and packaging of new virions in infected cells. RdRp functions as RNA replicase and transcriptase to replicate and transcribe the viral RNA and is also thought to have endonuclease activity. Currently, no antiviral therapy or vaccine is available for the treatment of hantavirus-associated diseases. Understanding the molecular details of hantavirus life cycle will help in the identification of targets for antiviral therapeutics and in the design of potential antiviral drug for the treatment of HFRS and HCPS. Due to the alarming fatality of hantavirus diseases, development of an effective vaccine against hantaviruses is a necessity. url: https://www.sciencedirect.com/science/article/pii/B9780123870223000069 doi: 10.1016/b978-0-12-387022-3.00006-9 id: cord-322206-roxa3ix6 author: I. Sardi, Silvia title: High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics date: 2020-07-21 words: 4199.0 sentences: 212.0 pages: flesch: 46.0 cache: ./cache/cord-322206-roxa3ix6.txt txt: ./txt/cord-322206-roxa3ix6.txt summary: Herein, we used RNA-based metatranscriptomics associated with Ion Torrent deep sequencing to allow for the high-quality reconstitution of an outbreak-related Zika virus (ZIKV) genome (10,739 nt), with extended 5′-UTR and 3′-UTR regions, using a newly-implemented bioinformatics approach. Besides allowing for the assembly of one of the largest complete ZIKV genomes to date, our strategy also yielded high-quality complete genomes of two arthropod-infecting viruses co-infecting C6/36 cell lines, namely: Alphamesonivirus 1 strain Salvador (20,194 nt) and Aedes albopictus totivirus-like (4618 nt); the latter likely represents a new viral species. Altogether, our results demonstrate that our bioinformatics approach associated with Ion Torrent sequencing allows for the high-quality reconstruction of known and unknown viral genomes, overcoming the main limitation of RNA deep sequencing for virus identification. Here, we applied RNA-based metatranscriptomics associated with Ion Torrent deep sequencing and a newly developed Bioinformatics approach to the high-quality reconstitution of viral genomes. abstract: Arboviruses, including the Zika virus, have recently emerged as one of the most important threats to human health. The use of metagenomics-based approaches has already proven valuable to aid surveillance of arboviral infections, and the ability to reconstruct complete viral genomes from metatranscriptomics data is key to the development of new control strategies for these diseases. Herein, we used RNA-based metatranscriptomics associated with Ion Torrent deep sequencing to allow for the high-quality reconstitution of an outbreak-related Zika virus (ZIKV) genome (10,739 nt), with extended 5′-UTR and 3′-UTR regions, using a newly-implemented bioinformatics approach. Besides allowing for the assembly of one of the largest complete ZIKV genomes to date, our strategy also yielded high-quality complete genomes of two arthropod-infecting viruses co-infecting C6/36 cell lines, namely: Alphamesonivirus 1 strain Salvador (20,194 nt) and Aedes albopictus totivirus-like (4618 nt); the latter likely represents a new viral species. Altogether, our results demonstrate that our bioinformatics approach associated with Ion Torrent sequencing allows for the high-quality reconstruction of known and unknown viral genomes, overcoming the main limitation of RNA deep sequencing for virus identification. url: https://www.ncbi.nlm.nih.gov/pubmed/32708079/ doi: 10.3390/v12070782 id: cord-272099-26nhza2s author: IKEDA, KEIKO title: Survival of influenza A virus on contaminated student clothing date: 2015-02-09 words: 2903.0 sentences: 137.0 pages: flesch: 49.0 cache: ./cache/cord-272099-26nhza2s.txt txt: ./txt/cord-272099-26nhza2s.txt summary: The amount of infectious virus recovered from the nine types of clothing decreased with time and was shown to differ widely between clothing samples, when the contaminated clothing samples were maintained in uncovered glass Petri dishes in a safety cabinet under air blowing. At the indicated time points after virus deposition, one piece of the contaminated cloth was transferred into a glass test tube, immediately followed by the addition of 1,000 µl ice-cold Dulbecco''s phosphate-buffered saline (PBS) without Ca 2+ and Mg 2+ , but containing 0.1% BSA. After leaving for 20 min in air, the cloths were transferred to glass test tubes, the contaminated virus was extracted with PBS containing 0.1% BSA by vigorous mixing with a Vortex mixer, and the amount of infectious virus recovered in the extract was measured. These observations support the importance of water in the deposit for the maintenance of the infectivity and transmissibility of influenza virus on contaminated clothes. abstract: The role of contaminated clothing in the transmission of influenza A virus during an epidemic period was investigated by examining the recovery of infectious influenza virus from experimentally virus-contaminated clothing, which had been subejected to routine wearing and washing for several months or years. The amount of infectious virus recovered from the nine types of clothing decreased with time and was shown to differ widely between clothing samples, when the contaminated clothing samples were maintained in uncovered glass Petri dishes in a safety cabinet under air blowing. These results indicate a dependence of virus transmissibility on the nature of the contaminated clothes. The difference in recovery was shown to have no significant correlation with the thickness or the materials of the clothing; however, a correlation was observed with the residual amount of water in the deposited virus preparation on the test clothing. url: https://www.ncbi.nlm.nih.gov/pubmed/25780410/ doi: 10.3892/etm.2015.2278 id: cord-292830-gcfx1095 author: Ianevski, Aleksandr title: Novel activities of safe-in-human broad-spectrum antiviral agents date: 2018-04-23 words: 5511.0 sentences: 298.0 pages: flesch: 45.0 cache: ./cache/cord-292830-gcfx1095.txt txt: ./txt/cord-292830-gcfx1095.txt summary: Here, we reviewed all approved, investigational and experimental antiviral agents, which are safe in man, and identified 59 compounds that target at least three viral diseases. Here, we hypothesised that some of the identified safe-in-human BSAs could possess novel antiviral activities and, therefore, could be used for treatment of many different viral infections. Fig. 1 shows BSAs and other approved antiviral drugs linked to viral and host targets through viruses they inhibit. Thus, we tested several known BSA agents against (−)ssRNA, (+) ssRNA, ssRNA-RT and dsDNA viruses and identified novel activities for dalbavancin against EV1, ezetimibe against ZIKV and HIV-1, as well as azacitidine, cyclosporine, minocycline, oritavancin and ritonavir against RVFV. We identified novel antiviral activities for dalbavancin (against EV1), ezetimibe (against HIV-1 and ZIKV), azacitidine, cyclosporine, minocycline, oritavancin and ritonavir (against RVFV) (Fig. 4) . abstract: According to the WHO, there is an urgent need for better control of viral diseases. Re-positioning existing safe-in-human antiviral agents from one viral disease to another could play a pivotal role in this process. Here, we reviewed all approved, investigational and experimental antiviral agents, which are safe in man, and identified 59 compounds that target at least three viral diseases. We tested 55 of these compounds against eight different RNA and DNA viruses. We found novel activities for dalbavancin against echovirus 1, ezetimibe against human immunodeficiency virus 1 and Zika virus, as well as azacitidine, cyclosporine, minocycline, oritavancin and ritonavir against Rift valley fever virus. Thus, the spectrum of antiviral activities of existing antiviral agents could be expanded towards other viral diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/29698664/ doi: 10.1016/j.antiviral.2018.04.016 id: cord-259260-qcfgigga author: Ibrahim, Ibrahim M. title: GRP78: A cell''s response to stress date: 2019-06-01 words: 6837.0 sentences: 393.0 pages: flesch: 50.0 cache: ./cache/cord-259260-qcfgigga.txt txt: ./txt/cord-259260-qcfgigga.txt summary: GRP78 expression is increased in cases of ER stressors like when the cell is abridged from sugar, treated with reagents that inhibit the process of protein glycosylation or disturb the intercellular calcium storage [5] . In the standard conditions of balance in the cell (homeostasis) GRP78 is bounded in an inactive form to Activating transcription factor 6 (ATF6), protein kinase RNA-like endoplasmic reticulum kinase (PERK), and Inositol-requiring enzyme 1 (IRE1) which are UPR transmembrane stress sensors. According to the ligand or the peptide that bind to CS-GRP78, it will be activated in a defined signaling pathway that affects Besides, if the cell is cancerous, CS GRP78 will induce resistance to chemotherapy. Glucose regulated protein 78 (GRP78) inhibits apoptosis and attentinutes chemosensitivity of gemcitabine in breast cancer cell via AKT/mitochondrial apoptotic pathway De-regulation of GRP stress protein expression in human breast cancer cell lines Kringle 5 of human plasminogen induces apoptosis of endothelial and tumor cells through surface-expressed glucose-regulated protein 78 abstract: Abstract Background Glucose-Regulated Protein 78 (GRP78) is a chaperone heat shock protein that has been intensely studied in the last two decades. GRP78 is the master of the unfolded protein response (UBR) in the Endoplasmic Reticulum (ER) in normal cells. GRP78 force the unfolded proteins to refold or degrade using cellular degradation mechanisms. Scope Under stress, the overexpression of GRP78 on the cell membrane mediates the vast amount of disordered proteins. Unfortunately, this makes it a tool for pathogens (bacterial, fungal and viral) to enter the cell and to start different pathways leading to pathogenesis. Additionally, GRP78 is overexpressed on the membranes of various cancer cells and increase the aggressiveness of the disease. Major conclusions The current review summarizes structure, function, and different mechanisms GRP78 mediate in response to normal or stress conditions. General significance GRP78 targeting and possible inhibition mechanisms are also covered in the present review aiming to prevent the virulence of pathogens and cancer. url: https://doi.org/10.1016/j.lfs.2019.04.022 doi: 10.1016/j.lfs.2019.04.022 id: cord-035163-tqh5wv12 author: Ijaz, M. Khalid title: Combating SARS-CoV-2: leveraging microbicidal experiences with other emerging/re-emerging viruses date: 2020-09-08 words: 6841.0 sentences: 345.0 pages: flesch: 46.0 cache: ./cache/cord-035163-tqh5wv12.txt txt: ./txt/cord-035163-tqh5wv12.txt summary: In the present review, we suggest that approaches for infection prevention and control (IPAC) for SARS-CoV-2 and future emerging/re-emerging viruses can be invoked based on pre-existing data on microbicidal and hygiene effectiveness for related and unrelated enveloped viruses. These therefore included coronaviruses, Lassa virus, SFTSV, Hantaan virus, MERS-CoV, SARS-CoV, SARS-CoV-2, Ebola virus, influenza H5N1, Nipah virus, EV-D68, particle size, reservoir species, tissue tropism, mode of transmission, transmissibility, virus shedding, minimal infectious dose, infectious dose 50 , mortality, survival on surfaces, persistence on surfaces, stability on surfaces, survival in aerosols, persistence in aerosols, stability in aerosols, microbicidal efficacy, virucidal efficacy, disinfectant efficacy, antiseptic efficacy, emerging/re-emerging enveloped viruses, UVC susceptibility, zoonoses, and personal hygiene for SARS-CoV-2. As mentioned in Table 2 , the most common modes of transmission for the emerging/ re-emerging viruses discussed in this review are contact with infected bodily secretions/ excretions and contaminated fomites, especially high-touch environmental surfaces (HITES), and inhalation of respiratory droplets/aerosols containing infectious virus (Fig. 1) . abstract: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan City, China, late in December 2019 is an example of an emerging zoonotic virus that threatens public health and international travel and commerce. When such a virus emerges, there is often insufficient specific information available on mechanisms of virus dissemination from animal-to-human or from person-to-person, on the level or route of infection transmissibility or of viral release in body secretions/excretions, and on the survival of virus in aerosols or on surfaces. The effectiveness of available virucidal agents and hygiene practices as interventions for disrupting the spread of infection and the associated diseases may not be clear for the emerging virus. In the present review, we suggest that approaches for infection prevention and control (IPAC) for SARS-CoV-2 and future emerging/re-emerging viruses can be invoked based on pre-existing data on microbicidal and hygiene effectiveness for related and unrelated enveloped viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7485481/ doi: 10.7717/peerj.9914 id: cord-337285-t6qr41wc author: Ikeda, Masanori title: Modulation of host metabolism as a target of new antivirals() date: 2007-10-10 words: 8180.0 sentences: 466.0 pages: flesch: 46.0 cache: ./cache/cord-337285-t6qr41wc.txt txt: ./txt/cord-337285-t6qr41wc.txt summary: Using cell culture systems, several cellular proteins have been identified as effective molecules for HCV RNA replication (Table 1) . [66] reported that lovastatin (LOV), one of the HMG-CoA reductase inhibitors, inhibited HCV RNA replication in HCV replicon-harboring cells. Depletion of the GGPP by statins may inhibit the geranylgeranylation of cellular proteins such as FBL2 and cause the anti-HCV effect in the cells. During the development of IFN therapy for patients with CH-C, the lack of a robust method of HCV RNA replication in cell culture has hampered research into the HCV life cycle and the discovery of potent new anti-HCV reagents. VX-950, a novel hepatitis C virus (HCV) NS3-4A protease inhibitor, exhibits potent antiviral activities in HCV replicon cells Selectable subgenomic and genome-length dicistronic RNAs derived from an infectious molecular clone of the HCV-N strain of hepatitis C virus replicate efficiently in cultured Huh7 cells abstract: The therapy for chronic hepatitis C (CH–C) started with interferon (IFN) monotherapy in the early 1990s and this therapy was considered effective in about 10% of cases. The present standard therapy of pegylated IFN with ribavirin achieves a sustained virologic response in about 50% of patients. However, about half of the CH–C patients are still at risk of fatal liver cirrhosis and hepatocellular carcinoma. The other significant event in hepatitis C virus (HCV) research has been the development of a cell culture system. The subgenomic replicon system enables robust HCV RNA replication in hepatoma cells. And recently, the complete life cycle of HCV has been achieved using a genotype 2a strain, JFH1. These hallmarks have provided much information about the mechanisms of HCV replication, including information on the host molecules required for the replication. Anti-HCV reagents targeting HCV proteins have been developed, and some of them are now in clinical trials. However, the RNA-dependent RNA polymerase frequently causes mutations in the HCV genome, which lead to the emergence of drug-resistant HCV mutants. Some of the cellular proteins essential for HCV RNA replication have already been discovered using the HCV cell culture system. These host molecules are also candidate targets for antivirals. Here, we describe the recent progress regarding the anti-HCV reagents targeting host metabolism. url: https://www.sciencedirect.com/science/article/pii/S0169409X07001317 doi: 10.1016/j.addr.2007.03.021 id: cord-346836-6jyv0q5e author: Ikegami, Tetsuro title: The Pathogenesis of Rift Valley Fever date: 2011-05-06 words: 10419.0 sentences: 483.0 pages: flesch: 46.0 cache: ./cache/cord-346836-6jyv0q5e.txt txt: ./txt/cord-346836-6jyv0q5e.txt summary: RVFV infection in humans usually causes a self-limiting, acute and febrile illness; however, a small number of cases progress to neurological disorders, partial or complete blindness, hemorrhagic fever, or thrombosis. This review describes the pathology of RVF in human patients and several animal models, and summarizes the role of viral virulence factors and host factors that affect RVFV pathogenesis. RVFV infection in humans primarily causes a self-limiting febrile illness; however, some patients develop hemorrhagic fever, neurological disorders, or blindness after the febrile period [5, 7, 8] . Inbred rat strains mimic the disparate human response to rift valley fever virus infection Clinical, virological and serological response of the west african dwarf sheep to experimental infection with different strains of rift valley fever virus abstract: Rift Valley fever (RVF) is an emerging zoonotic disease distributed in sub-Saharan African countries and the Arabian Peninsula. The disease is caused by the Rift Valley fever virus (RVFV) of the family Bunyaviridae and the genus Phlebovirus. The virus is transmitted by mosquitoes, and virus replication in domestic ruminant results in high rates of mortality and abortion. RVFV infection in humans usually causes a self-limiting, acute and febrile illness; however, a small number of cases progress to neurological disorders, partial or complete blindness, hemorrhagic fever, or thrombosis. This review describes the pathology of RVF in human patients and several animal models, and summarizes the role of viral virulence factors and host factors that affect RVFV pathogenesis. url: https://www.ncbi.nlm.nih.gov/pubmed/21666766/ doi: 10.3390/v3050493 id: cord-003092-3owcqt3d author: Iketani, Sho title: Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation date: 2018-07-03 words: 8948.0 sentences: 392.0 pages: flesch: 46.0 cache: ./cache/cord-003092-3owcqt3d.txt txt: ./txt/cord-003092-3owcqt3d.txt summary: These results utilize a method for identifying genome-wide changes associated with brief adaptation to culture to highlight the notion that even brief exposure to immortalized cells may affect key viral properties and underscore the balance of features of the HN-F complex required for fitness by circulating viruses. Deep genomic sequencing of nine sets of paired clinical samples (primary nasal swabs in viral transport medium) and culture isolates (culture harvest from zero passage virus) led to discovery of a number of HN mutations associated with rapid evolution in culture. To assess the frequency of mutations identified earlier, we also performed deep sequencing of 118 HPIV-3 clinical samples and culture isolates from the University of Washington Virology Laboratory, allowing us to confirm that the alterations associated with brief exposure to culture for viral isolation were almost entirely found in the sequences of culture isolates and found commonly within populations of viruses in those isolates. abstract: Human parainfluenza viruses cause a large burden of human respiratory illness. While much research relies upon viruses grown in cultured immortalized cells, human parainfluenza virus 3 (HPIV-3) evolves in culture. Cultured viruses differ in their properties compared to clinical strains. We present a genome-wide survey of HPIV-3 adaptations to culture using metagenomic next-generation sequencing of matched pairs of clinical samples and primary culture isolates (zero passage virus). Nonsynonymous changes arose during primary viral isolation, almost entirely in the genes encoding the two surface glycoproteins—the receptor binding protein hemagglutinin-neuraminidase (HN) or the fusion protein (F). We recovered genomes from 95 HPIV-3 primary culture isolates and 23 HPIV-3 strains directly from clinical samples. HN mutations arising during primary viral isolation resulted in substitutions at HN’s dimerization/F-interaction site, a site critical for activation of viral fusion. Alterations in HN dimer interface residues known to favor infection in culture occurred within 4 days (H552 and N556). A novel cluster of residues at a different face of the HN dimer interface emerged (P241 and R242) and imply a role in HPIV-3-mediated fusion. Functional characterization of these culture-associated HN mutations in a clinical isolate background revealed acquisition of the fusogenic phenotype associated with cultured HPIV-3; the HN-F complex showed enhanced fusion and decreased receptor-cleaving activity. These results utilize a method for identifying genome-wide changes associated with brief adaptation to culture to highlight the notion that even brief exposure to immortalized cells may affect key viral properties and underscore the balance of features of the HN-F complex required for fitness by circulating viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030562/ doi: 10.1128/mbio.00898-18 id: cord-338727-1kodz527 author: Ilinskaya, O. N. title: Ribonucleases as antiviral agents date: 2014-10-11 words: 4605.0 sentences: 227.0 pages: flesch: 44.0 cache: ./cache/cord-338727-1kodz527.txt txt: ./txt/cord-338727-1kodz527.txt summary: Many ribonucleases (RNases) are able to inhibit the reproduction of viruses in infected cell cultures and laboratory animals, but the molecular mechanisms of their antiviral activity remain unclear. Therefore, the formation of RNA fragments enhanced by RNase L, followed by their interaction with RIG I and MDA5, activates transcription factor NF κB and triggers transcription of interferon β gene, which prevents virus replication and stimulates the growth of immune system cells [9] . Previously, onconase, an RNases from oocytes of the leopard frog Rana pipiens, efficiently suppresses the replication of HIV 1 due to the selective degrada tion of viral RNA, which exhibits no pronounced cytotoxic effect on infected human cells [22] . At the first stage, when binase meets the virus outside cell, its catalytic activity is not inhibited by the natural RNase and it may destroy viral RNA (Fig. 3, C) . Ribonucleases in HIV type 1 inhibition: Effect of recombinant RNases on infection of primary T cells and immune activation induced RNase gene and protein expression abstract: Many ribonucleases (RNases) are able to inhibit the reproduction of viruses in infected cell cultures and laboratory animals, but the molecular mechanisms of their antiviral activity remain unclear. The review discusses the well-known RNases that possess established antiviral effects, including both intracellular RNases (RNase L, MCPIP1 protein, and eosinophil-associated RNases) and exogenous RNases (RNase A, BS-RNase, onconase, binase, and synthetic RNases). Attention is paid to two important, but not always obligatory, aspects of molecules of RNases that have antiviral properties, i.e., catalytic activity and ability to dimerize. The hypothetic scheme of virus elimination by exogenous RNases that reflects possible types of interaction of viruses and RNases with a cell is proposed. The evidence for RNases as classical components of immune defense and thus perspective agents for the development of new antiviral therapeutics is proposed. url: https://doi.org/10.1134/s0026893314040050 doi: 10.1134/s0026893314040050 id: cord-018040-k0h5ejjt author: Ilyinskii, P. title: Aspects of Microparticle Utilization for Potentiation of Novel Vaccines: Promises and Risks date: 2009 words: 6930.0 sentences: 309.0 pages: flesch: 41.0 cache: ./cache/cord-018040-k0h5ejjt.txt txt: ./txt/cord-018040-k0h5ejjt.txt summary: Many recombinant vaccines against novel (HIV, HCV) or ever-changing (influenza) infectious agents require the presence of adjuvants/delivery vehicles to induce strong immune responses. Cationic and anionic polylactide co-glycolide (PLG) microparticles have been successfully used to adsorb a variety of agents, which include plasmid DNA, recombinant proteins and adjuvant active oligonucleotides and are also currently tested in several vaccine applications. The size of these vectors is generally within 10-1000 nm and it is a specific mechanism by which our immune system recognizes such particles that underlies their adjuvant potencies (in addition, many carriers protect proteins/NA from rapid degradation in vivo and release them into the organism during prolonged periods of time, which also results in higher immunogenicity). Several VLPbased vaccines have been licensed for general use, many of them against HBV, which are composed of HBV surface antigen (HBsAg), which is a main component of currently used protein-based, alum adjuvant-potentiated vaccine. abstract: Many recombinant vaccines against novel (HIV, HCV) or ever-changing (influenza) infectious agents require the presence of adjuvants/delivery vehicles to induce strong immune responses. The necessity of their improvement led to the major effort towards development of vaccine delivery systems that are generally particulate (e.g., nano- and microparticles) and have comparable dimensions to the pathogens (viruses or bacteria). The mode of action of these adjuvants is not fully understood but implies the stimulation of the innate or antigen-specific immune responses, and/or the increase of antigen uptake or processing by antigen-presenting cells (APC). Moreover, enhancement of adjuvant activity through the use of micro- and nanoparticulate delivery systems often resulted from the synergistic effects producing immune responses stronger than those elicited by the adjuvant or delivery system alone. Among particulate adjuvants, biodegradable micro- and nanoparticles of poly(D,L-lactide-co-glycoside) (PLGA) or poly(D,L-lactide) (PLA) have been reported to enhance both humoral and cellular immune responses against an encapsulated protein antigen. Cationic and anionic polylactide co-glycolide (PLG) microparticles have been successfully used to adsorb a variety of agents, which include plasmid DNA, recombinant proteins and adjuvant active oligonucleotides and are also currently tested in several vaccine applications. Another approach envisions specific targeting of APC, especially peripheral DC and exploitation of particulate systems that are small enough for lymphatic uptake (polystyrene nanobeads). Micro- and nanoparticles offer the possibility of enhancement of their uptake by appropriate cells through manipulation of their surface properties. Still, questions regarding toxicity and molecular interaction between micro- and nano-particles and immune cells, tissues and whole organisms remain to be addressed. These risks and other possible side effects should be assessed in detail especially if mass-production and massive administration of such preparations is to be considered. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122810/ doi: 10.1007/978-90-481-2523-4_26 id: cord-289360-h6wvx7gw author: Imperiale, Michael J. title: The Importance of Virology at a Time of Great Need and Great Jeopardy date: 2015-03-10 words: 1290.0 sentences: 59.0 pages: flesch: 51.0 cache: ./cache/cord-289360-h6wvx7gw.txt txt: ./txt/cord-289360-h6wvx7gw.txt summary: journal: mBio Viruses account for up to 20% of all human cancers, and although a large percentage of new human papillomavirus (HPV) and HBV infections can now be prevented by vaccination, many are already infected, and the vaccines are not being used to their full potential. The tremendous reduction in mortality from such diseases as variola, measles, and rubella came about only because the causative viruses were identified, cultivated, attenuated, and made into effective vaccines by biomedical research. While we scientists cannot directly control funding or regulations, we can take charge of some aspects of the research enterprise in a way to ensure that it continues to benefit society. This requires engaging our elected officials both directly and indirectly by continuing to educate them and the public at large about the importance of fundamental research in infectious diseases. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/25759503/ doi: 10.1128/mbio.00236-15 id: cord-298036-2zurc60t author: Imre, Gergely title: Cell death signalling in virus infection date: 2020-09-12 words: 8002.0 sentences: 414.0 pages: flesch: 37.0 cache: ./cache/cord-298036-2zurc60t.txt txt: ./txt/cord-298036-2zurc60t.txt summary: Subsequently, granzyme-B induces mitochondrial apoptosis by performing cleavage of the BCL-2 homology domain-3 (BH3)-only protein, BH3 interacting domain death agonist (BID), which then leads to BAX/BAK-mediated MOMP and the initiation of the caspase-9-driven apoptotic pathway [16] . Still, the mechanism, by which IRF-3 triggers cell death signalling pathways is only partially understood and the studies indicate a strong cell type specificity in the apoptosis sensitivity in response to viral PAMPs Z-RNA and z-DNA fragments, which are distinct from the B-structure of eukaryotic RNA and DNA are recognized by z-DNA/RNA binding protein-1 (ZBP1; also: DAI). Necroptosis initiation takes place upon TNFR ligation, which, however, primarily leads to NFkB activation via the assembly of so called complex-I, including adaptor proteins TNFRSF1A associated via death domain (TRADD), TRAF2, cellular IAP (cIAP) and ubiquitinated receptor interacting serine/threonine kinase 1 (RIPK1) [10] . abstract: Apoptosis, necroptosis and pyroptosis represent three major regulated cell death modalities. Apoptosis features cell shrinkage, nuclear fragmentation and cytoplasm-blebbing. Necroptosis and pyroptosis exhibit osmotic imbalances in the cell accompanied by early membrane ruptures, which morphologically resembles necrosis. Importantly, these two lytic cell death forms facilitate the release of damage associated molecular patterns into the extracellular space leading to inflammatory response. Whereas, during apoptosis, the membrane integrity is preserved and the apoptotic cell is removed by neighbouring cells ensuring the avoidance of immune-stimulation. Viruses comprise a versatile group of intracellular pathogens, which elicit various strategies to infect and to propagate. Viruses are recognized by a myriad of pathogen recognition receptors in the human cells, which consequently lead to activation of the immune system and in certain circumstances cell-autonomous cell death. Importantly, the long-standing view that a cell death inducing capacity of a virus is equal to its pathogenic potential seems to be only partially valid. The altruistic cell death of an infected cell may serve the whole organism by ultimately curbing the way of virus manufacturing. In fact, several viruses express “anti-cell death” proteins to avoid this viral-defence mechanism. Conversely, some viruses hijack cell death pathways to selectively destroy cell populations in order to compromise the immune system of the host. This review discusses the pros and cons of virus induced cell death from the perspective of the host cells and attempts to provide a comprehensive overview of the complex network of cell death signalling in virus infection. url: https://api.elsevier.com/content/article/pii/S0898656820302497 doi: 10.1016/j.cellsig.2020.109772 id: cord-271105-eyigl0wz author: Ionidis, Georgios title: Development and virucidal activity of a novel alcohol-based hand disinfectant supplemented with urea and citric acid date: 2016-02-11 words: 4990.0 sentences: 252.0 pages: flesch: 48.0 cache: ./cache/cord-271105-eyigl0wz.txt txt: ./txt/cord-271105-eyigl0wz.txt summary: Under the Guideline of Deutsche Vereinigung zur Bekämpfung der Viruskrankeiten e.V. and the Robert Koch-Institute (DVV/RKI Guideline) [22] , disinfectants achieving at least 4 log 10 titer reduction factor (RF of 4) against vaccinia virus and bovine viral diarrhea virus (BVDV) are active against all enveloped viruses (limited spectrum virucidal) [23, 24] . The different formulations of the new hand rub based on ethanol, citric acid and urea were screened undiluted (80.0 % due to the addition of test virus suspension and interfering substance) against PV, AdV and polyomavirus SV40 as non-enveloped test viruses of the Guideline of DVV/RKI in the presence of FCS with a fixed exposure time of 60 s. Consequently, the formulation with the sufficient virucidal activity containing 69.39 % w/w ethanol, 3.69 % w/w 2-propanol, 2.0 % urea and 2.0 % citric acid was tested against several non-enveloped (MNV, AdV, PV, polyomavirus SV40) and enveloped viruses (BVDV, vaccinia virus strain Elstree) in the presence or absence of FCS according to Guideline of DVV/RK or in clean conditions according to EN 14476. abstract: BACKGROUND: Hand disinfectants are important for the prevention of virus transmission in the health care system and environment. The development of broad antiviral spectrum hand disinfectants with activity against enveloped and non-enveloped viruses is limited due to a small number of permissible active ingredients able to inactivate viruses. METHODS: A new hand disinfectant was developed based upon 69.39 % w/w ethanol and 3.69 % w/w 2-propanol. Different amounts of citric acid and urea were added in order to create a virucidal claim against poliovirus (PV), adenovirus type 5 (AdV) and polyomavirus SV40 (SV40) as non-enveloped test viruses in the presence of fetal calf serum (FCS) as soil load. The exposure time was fixed to 60 s. RESULTS: With the addition of 2.0 % citric acid and 2.0 % urea an activity against the three test viruses was achieved demonstrating a four log(10) reduction of viral titers. Furthermore, this formulation was able to inactivate PV, AdV, SV40 and murine norovirus (MNV) in quantitative suspension assays according to German and European Guidelines within 60 s creating a virucidal claim. For inactivation of vaccinia virus and bovine viral diarrhea virus 15 s exposure time were needed to demonstrate a 4 log(10) reduction resulting in a claim against enveloped viruses. Additionally, it is the first hand disinfectant passing a carrier test with AdV and MNV. CONCLUSIONS: In conclusion, this new formulation with a low alcohol content, citric acid and urea is capable of inactivating all enveloped and non-enveloped viruses as indicated in current guidelines and thereby contributing as valuable addition to the hand disinfection portfolio. url: https://doi.org/10.1186/s12879-016-1410-9 doi: 10.1186/s12879-016-1410-9 id: cord-288703-wdh1jiry author: Ishtiaq, Farah title: A Call to Introduce Structured Zika Surveillance in India date: 2017-11-15 words: 3042.0 sentences: 149.0 pages: flesch: 47.0 cache: ./cache/cord-288703-wdh1jiry.txt txt: ./txt/cord-288703-wdh1jiry.txt summary: India has the climatic conditions conducive to year-round transmission of Zika virus, and a structured disease surveillance program should be implemented to prevent an outbreak. Farah Ishtiaq 1, * India has the climatic conditions conducive to year-round transmission of Zika virus, and a structured disease surveillance program should be implemented to prevent an outbreak. In fact, India is an ideal place to explore the coevolutionary dynamics of this host-parasite system because of several factors: (i) the high volume of human movements [5] , (ii) the apparent immunity to Zika from circulating strains of the virus [1] , and (iii) the possibility of transmission in less immunocompetent hosts, such as pregnant women and the elderly viii , and (iv) adults with a prior history of malaria or dengue infections, which may help facilitate transmission and pathogenesis of Zika, potentially resulting in a positive feedback loop [12] . abstract: India has the climatic conditions conducive to year-round transmission of Zika virus, and a structured disease surveillance program should be implemented to prevent an outbreak. Such a program should (i) start screening before an outbreak arises; (ii) collect baseline data to assess future disease risk and monitor potential birth defects; and (iii) provide new insights into the ecology of the disease and inform public health policy following the one health concept. url: https://www.ncbi.nlm.nih.gov/pubmed/29153262/ doi: 10.1016/j.pt.2017.10.008 id: cord-016754-6fv8mjld author: Iturriza-Gómara, Miren title: Gastroenteric Viruses date: 2007 words: 4900.0 sentences: 269.0 pages: flesch: 41.0 cache: ./cache/cord-016754-6fv8mjld.txt txt: ./txt/cord-016754-6fv8mjld.txt summary: Enzyme immunosorbent assays (EIA) and passive particle agglutination tests (PPAT), some of which are available commercially, provide sensitivity comparable to, or better than, EM for the detection of RVs, NVs, ASVs, and ADVs. More recently, molecular methods, reverse-transcription polymerase chain reaction (RT-PCR), PCR, or nucleic acid-based sequence amplification (NASBA) assays have been developed for the detection of enteric viruses. Testing for the presence of viruses in food, water, or environmental samples has only been possible since the development of very sensitive molecular methods, which include virus elution from the foodstuff, followed by concentration (36) efficient nucleic acid extraction methods for the removal of inhibitors of amplification. Multiple enteric viruses, SVs, ADVs, NVs, and RVs were detected in symptomatic patients suggesting the ingestion of fecally contaminated food or water (unpublished data). Polymerase chain reaction detection of small round-structured viruses from two related hospital outbreaks of gastroenteritis using inosine-containing primers The development of polymerase chain reaction assays for detection of small round structured and other human enteric viruses in molluscan shellfish abstract: In recent years, viruses have been recognized increasingly as an important cause of foodborne infections. More than 160 enteric viruses are excreted in the feces of infected individuals, and some may also be present in the vomitus. Food and water are directly contaminated with fecal material, through the use of sewage sludge in agriculture, sewage pollution of shellfish culture beds, or may be contaminated by infected food-handlers. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121132/ doi: 10.1007/978-1-59745-501-5_8 id: cord-301592-n5ns3m34 author: Ivaska, Lauri title: Aetiology of febrile pharyngitis in children: Potential of myxovirus resistance protein A (MxA) as a biomarker of viral infection date: 2017-01-07 words: 4142.0 sentences: 249.0 pages: flesch: 47.0 cache: ./cache/cord-301592-n5ns3m34.txt txt: ./txt/cord-301592-n5ns3m34.txt summary: We aimed to document the viral and bacterial aetiology of pharyngitis and to assess the pathogenic role of viruses by determining the myxovirus resistance protein A (MxA) in the blood as a marker of interferon response. We aimed to document the viral and bacterial aetiology of pharyngitis and to assess the pathogenic role of viruses by determining the myxovirus resistance protein A (MxA) in the blood as a marker of interferon response. Methods: In this prospective observational study, throat swabs and blood samples were collected from children (age 1e16 years) presenting to the emergency department with febrile pharyngitis. Methods: In this prospective observational study, throat swabs and blood samples were collected from children (age 1e16 years) presenting to the emergency department with febrile pharyngitis. 23e25 The aim of this study was to document the microbial causes of acute pharyngitis in children and adolescents in an outpatient setting and to evaluate the causative role of viruses by determining myxovirus resistance protein A (MxA) and other biomarker levels. abstract: OBJECTIVES: Besides group A streptococcus (GAS), microbial causes of pharyngitis in children are not well known. We aimed to document the viral and bacterial aetiology of pharyngitis and to assess the pathogenic role of viruses by determining the myxovirus resistance protein A (MxA) in the blood as a marker of interferon response. METHODS: In this prospective observational study, throat swabs and blood samples were collected from children (age 1–16 years) presenting to the emergency department with febrile pharyngitis. Microbial cause was sought by bacterial culture, polymerase chain reaction, and serology. Blood MxA level was determined. RESULTS: A potential pathogen was detected in 88% of 83 patients: GAS alone in 10%, GAS and viruses in 13%, group C or G streptococci alone in 2% and together with viruses in 3%, and viruses alone in 59% of cases. Enteroviruses, rhinoviruses, and adenoviruses were the most frequently detected viruses. Blood MxA levels were higher in children with viral (880 [245–1250] μg/L; median [IQR]) or concomitant GAS-viral (340 [150–710] μg/L) than in those with sole GAS (105 [80–160] μg/L) infections. CONCLUSIONS: Detection of respiratory viruses simultaneously with elevated blood MxA levels supports the causative role of viruses in the majority of children with pharyngitis. url: https://doi.org/10.1016/j.jinf.2017.01.002 doi: 10.1016/j.jinf.2017.01.002 id: cord-018017-c8myq6bi author: Iversen, Patrick L. title: The Threat from Viruses date: 2018-09-30 words: 11563.0 sentences: 615.0 pages: flesch: 51.0 cache: ./cache/cord-018017-c8myq6bi.txt txt: ./txt/cord-018017-c8myq6bi.txt summary: Numerous emerging infections caused by viral agents have imposed high impact on human survival (Table 3 .3). The apparent success of these viruses is that as they move from reservoir hosts to humans and as humans become immune to the initial infection, the population of diverse genomes offers multiple chances to adapt by finding a "fit" genome version which can propagate until the next transition requiring adaption. Human T-cell Lymphotropic Virus (HTLV-1) HTLV-1 is a single-stranded RNA retrovirus, defined by their use of reverse transcriptase, a polymerase, that makes a DNA copy of the RNA 7 kb viral genome. If we combine cardiovascular events and neoplasia caused by infection, then infectious disease is the most significant threat to human life and qualifies as the area of greatest impact. Adeno-associated Virus (AAV) is a single stranded DNA virus that infects humans but are not known to cause disease. is a 5229 base double-stranded DNA virus infecting less than 5 percent of the human population. abstract: Infectious disease represent the most significant threat to human health. Significant geologic cataclysmic events have caused the extinction of countless species, but these “Wrath of God” events predate the emergence of Homo sapiens. Pandemic infections have accompanied the rise of human civilization frequently re-occurring leaving a lasting imprint on human history punctuated by profound loss of life. Emerging infections become endemic and are here to stay marking their presence with an annual death toll. Each decade brings a new onslaught of emerging infectious agents. We are surprised again and again but are never prepared. The long-term consequences often remain unrecognized and are always inconvenient including cancer, cardiovascular disease and immune associated diseases that threaten our health. Reliance on clusters of clinical symptoms in the face of diverse and non-descriptive viral infection symptoms is a foolhardy form of crisis management. Viral success is based on rapid replication resulting in large numbers. Single-stranded RNA viruses with their high replication error rate represent a paradigm for resilience. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122756/ doi: 10.1007/978-3-319-98164-2_3 id: cord-276009-p98wjtjb author: Iyer, Arun V. title: Recombinant vesicular stomatitis virus-based west Nile vaccine elicits strong humoral and cellular immune responses and protects mice against lethal challenge with the virulent west Nile virus strain LSU-AR01 date: 2009-02-05 words: 7538.0 sentences: 406.0 pages: flesch: 45.0 cache: ./cache/cord-276009-p98wjtjb.txt txt: ./txt/cord-276009-p98wjtjb.txt summary: title: Recombinant vesicular stomatitis virus-based west Nile vaccine elicits strong humoral and cellular immune responses and protects mice against lethal challenge with the virulent west Nile virus strain LSU-AR01 These results suggest that VSV-vectored vaccines administered intranasally can efficiently induce protective humoral and cellular immune responses against WNV infections. The salient features of this vaccine study are: (1) A prime-boost intranasal vaccination approach with recombinant VSVs expressing the WNV E glycoprotein produced robust CD8 + IFN␥ + T cell responses; (2) This vaccine approach produced strong neutralizing titers against the WNV; (3) Vaccinated mice were protected against lethal challenge and they were free of neuronal necrosis, while unvaccinated mice There was no statistically significant difference observed between these two groups. These results suggest that a prime-boost VSV-vectored intranasal vaccine approach induces strong humoral and cellular immune responses that protect mice against WNV-induced neuronal necrosis. abstract: Vesicular stomatitis virus (VSV) has been extensively utilized as a viral vector system for the induction of protective immune responses against a variety of pathogens. We constructed recombinant VSVs specifying either the Indiana or Chandipura virus G glycoprotein and expressing the West Nile virus (WNV) envelope (E) glycoprotein. Mice were intranasally vaccinated using a prime (Indiana)-boost (Chandipura) immunization approach and challenged with the virulent WNV-LSU-AR01. Ninety-percent (9 of 10) of the vaccinated mice survived as compared to 10% of the mock-vaccinated mice after WNV lethal challenge. Histopathological examination of brain tissues revealed neuronal necrosis in mock-vaccinated mice but not in vaccinated mice, and vaccinated, but not mock-vaccinated mice developed a strong neutralizing antibody response against WNV. Extensive immunological analysis using polychromatic flow cytometry staining revealed that vaccinated, but not mock-vaccinated mice developed robust cellular immune responses as evidenced by up-regulation of CD4(+) CD154(+) IFNγ(+) T cells in vaccinated, but not mock-vaccinated mice. Similarly, vaccinated mice developed robust E-glycoprotein-specific CD8(+) T cell immune responses as evidenced by the presence of a high percentage of CD8(+) CD62L(low) IFNγ(+) cells. In addition, a sizeable population of CD8(+) CD69(+) cells was detected indicating E-specific activation of mature T cells and CD4(+) CD25(+) CD127(low) T regulatory (T reg) cells were down-regulated. These results suggest that VSV-vectored vaccines administered intranasally can efficiently induce protective humoral and cellular immune responses against WNV infections. url: https://www.ncbi.nlm.nih.gov/pubmed/19070640/ doi: 10.1016/j.vaccine.2008.11.087 id: cord-341968-uc8i9h0m author: Izaguirre, Gonzalo title: The Proteolytic Regulation of Virus Cell Entry by Furin and Other Proprotein Convertases date: 2019-09-09 words: 7870.0 sentences: 410.0 pages: flesch: 45.0 cache: ./cache/cord-341968-uc8i9h0m.txt txt: ./txt/cord-341968-uc8i9h0m.txt summary: A wide variety of viruses exploit furin and other proprotein convertases (PCs) of the constitutive protein secretion pathway in order to regulate their cell entry mechanism and infectivity. Like other enveloped viruses that rely on surface glycoproteins for binding and fusion, coronaviruses have the Spike (S) protein, which is cleaved by proteases during virion biosynthesis, as well as during entry into target cells [53] . The location of furin and related PCs in the vesicles of the constitutive protein secretion pathway, where viruses are assembled during morphogenesis or disassembled during cell entry, explains why a diversity of virus types have evolutionarily converged to depend on PCs. Viruses also use other types of proteases for the proteolytic regulation of the binding and fusion functions; however, proteases are restricted to specific cell types, which limits the range of the viral infection, so when some viruses mutate and acquire PC reactivity, they may expand their cell tropism and become more pathogenic. abstract: A wide variety of viruses exploit furin and other proprotein convertases (PCs) of the constitutive protein secretion pathway in order to regulate their cell entry mechanism and infectivity. Surface proteins of enveloped, as well as non-enveloped, viruses become processed by these proteases intracellularly during morphogenesis or extracellularly after egress and during entry in order to produce mature virions activated for infection. Although viruses also take advantage of other proteases, it is when some viruses become reactive with PCs that they may develop high pathogenicity. Besides reacting with furin, some viruses may also react with the PCs of the other specificity group constituted by PC4/PC5/PACE4/PC7. The targeting of PCs for inhibition may result in a useful strategy to treat infections with some highly pathogenic viruses. A wide variety of PC inhibitors have been developed and tested for their antiviral activity in cell-based assays. url: https://doi.org/10.3390/v11090837 doi: 10.3390/v11090837 id: cord-003792-v48xeqdz author: Izquierdo-Suzán, Mónica title: Natural Vertical Transmission of Zika Virus in Larval Aedes aegypti Populations, Morelos, Mexico date: 2019-08-17 words: 4017.0 sentences: 182.0 pages: flesch: 47.0 cache: ./cache/cord-003792-v48xeqdz.txt txt: ./txt/cord-003792-v48xeqdz.txt summary: We characterized natural vertical transmission of Zika virus in pools of Aedes aegypti larvae hatched from eggs collected in Jojutla, Morelos, Mexico. We characterized natural vertical transmission of Zika virus in pools of Aedes aegypti larvae hatched from eggs collected in Jojutla, Morelos, Mexico. Several studies carried out under laboratory conditions have demonstrated that Zika virus can infect many different Aedes mosquito species (3) ; still, the key species for the transmission of Zika virus to humans are Ae. aegypti and Ae. albopictus (4) (5) (6) . In this study, we sought to demonstrate natural vertical transmission in Ae. aegypti mosquitoes by detecting viral RNA and isolating infectious Zika virus from larvae hatched from field-collected eggs. In this work, we were also able to demonstrate the natural vertical transmission of Zika virus in Ae. aegypti mosquitoes by the successful isolation of infectious Zika virus (31N) from larvae raised from field-collected eggs. abstract: We characterized natural vertical transmission of Zika virus in pools of Aedes aegypti larvae hatched from eggs collected in Jojutla, Morelos, Mexico. Of the 151 pools analyzed, 17 tested positive for Zika virus RNA; infectious Zika virus was successfully isolated from 1 of the larvae pools (31N) in C6/36 cells. Real-time quantitative PCR and indirect immunofluorescence assays confirmed the identity of the isolate, named Zika virus isolate 31N; plaque assays in Vero cells demonstrated the isolate’s infectivity in a mammalian cell line. We obtained the complete genome of Zika virus isolate 31N by next-generation sequencing and identified 3 single-nucleotide variants specific to Zika virus isolate 31N using the meta-CATS tool. These results demonstrate the occurrence of natural vertical transmission of Zika virus in wild Ae. aegypti mosquitoes and suggest that this transmission mode could aid in the spread and maintenance of Zika virus in nature. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6649329/ doi: 10.3201/eid2508.181533 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-271568-qgpi2kcs author: Jackwood, M.W. title: Avian coronavirus infectious bronchitis virus susceptibility to botanical oleoresins and essential oils in vitro and in vivo date: 2010-01-21 words: 7596.0 sentences: 351.0 pages: flesch: 57.0 cache: ./cache/cord-271568-qgpi2kcs.txt txt: ./txt/cord-271568-qgpi2kcs.txt summary: Genomic diversity and the Abbreviations: CPE, cytopathic effects; EID50, 50% embryo infectious dose; ELISA, enzyme linked immunosorbent assay; HMA, hexamethylene amiloride; IBV, infectious bronchitis virus; MHV, mouse hepatitis virus; PBS, phosphate buffered saline; RFLP, restriction fragment length polymorphism; RT-PCR, reverse transcriptasepolymerase chain reaction; SARS-CoV, Severe Acute Respiratory Syndrome virus; SPF, specific pathogen free; TCID50, 50% tissue culture infectious dose. Clinical signs were observed in all of the Mass41 virus challenged groups of birds regardless of treatment but in the intranasal and spray treated groups, fewer birds had signs and the signs were milder, as reflected by lower average scores (Table 1) . Virus was detected in 1 of 5 vaccinated birds in the treated group at 7 days post-vaccination Table 3 Experiment 4: clinical signs a in broiler chickens challenged with IBV at various times after treatment with QR448(a) at 1 day of age. abstract: Anti-coronaviral activity of a mixture of oleoresins and essential oils from botanicals, designated QR448(a), was examined in vitro and in vivo. Treatment of avian infectious bronchitis virus (IBV) with QR448(a) reduced the virus titer as measured in two laboratory host systems, Vero E6 cells and embryonating eggs. The effect of QR448(a) on IBV in chickens was also investigated. Administering QR448(a) to chickens at a 1:20 dilution by spray, 2 h before challenge with IBV was determined to be the most effective treatment. Treatment decreased the severity of clinical signs and lesions in the birds, and lowered the amount of viral RNA in the trachea. Treatment with QR448(a) protected chickens for up to 4 days post-treatment from clinical signs of disease (but not from infection) and decreased transmission of IBV over a 14-day period. Anti-IBV activity of QR448(a) was greater prior to virus attachment and entry indicating that the effect is virucidal. In addition, QR448(a) had activity against both Massachusetts and Arkansas type IB viruses, indicating that it can be expected to be effective against IBV regardless of serotype. To our knowledge, this is the first report on the in vivo use of a virucidal mixture of compounds effective against the coronavirus IBV. url: https://doi.org/10.1016/j.virusres.2010.01.006 doi: 10.1016/j.virusres.2010.01.006 id: cord-009144-3slh1nbk author: Jacobs, J.W. title: RESPIRATORY SYNCYTIAL AND OTHER VIRUSES ASSOCIATED WITH RESPIRATORY DISEASE IN INFANTS date: 1971-05-01 words: 3288.0 sentences: 218.0 pages: flesch: 60.0 cache: ./cache/cord-009144-3slh1nbk.txt txt: ./txt/cord-009144-3slh1nbk.txt summary: Diagnosis by virus isolation and serology was attempted in 377 cases of respiratory-tract infection in infants under one year of age admitted to hospital during two winters. THERE have been few intensive studies of respiratoryvirus infections of infants.1-5 To prevent these infections, it is necessary to know which viruses cause the most severe illness and whether maternal antibody plays any part in their prevention. We report here the results of a survey of respiratory-virus infections in infants under one year of age in hospital. In this survey, as in others, R.s. virus was the commonest cause of respiratory illness requiring admission at this age (40°0), and the illnesses were more severe than those associated with other viruses (table iv). 23 Effect of Maternal Antibody The few parainfluenza virus infections observed in this survey occurred only in infants more than four months of age. abstract: Diagnosis by virus isolation and serology was attempted in 377 cases of respiratory-tract infection in infants under one year of age admitted to hospital during two winters. A diagnosis of infection with respiratory syncytial (R.S.) virus was made in 40%, rhinovirus in 6·1%, adenovirus in 3·7%, parainfluenza in 2·1%, enterovirus in 1·9%, and influenza in 1·3%. R.S.-virus infections were more severe than others and occurred mostly in the first five months of life, with a peak at two months. Rhinovirus infections occurred at all ages, and often involved the lower respiratory tract. Of the 12 deaths, only 1 (due to R.S. virus) was not associated with a contributory cause. Maternal antibody to R.S. virus did not notably affect the incidence or severity of R.S.-virus infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7135715/ doi: 10.1016/s0140-6736(71)92440-8 id: cord-022305-uvor9rts author: Jacoby, Robert O. title: Viral Diseases date: 2013-11-17 words: 15852.0 sentences: 898.0 pages: flesch: 46.0 cache: ./cache/cord-022305-uvor9rts.txt txt: ./txt/cord-022305-uvor9rts.txt summary: The number of viruses known to be naturally infectious for laboratory rats is small, and most cause inapparent infections which usually are detected by serological monitoring (Table I) . Significance: Latent, vertically-transmissible agent isolated from submaxillary gland; no signs or lesions; induces HAI antibody; unre lated antigenically to rat coronaviruses or cytomegalovirus; must dif ferentiate isolates from coronaviruses, cytomegaloviruses C. Infected rats excrete virus from the respiratory tract for about 7 days, at which time anti-SDAV antibody is first detectable in serum by either NT or CF tests ( Fig. 30 and Table V) (61) . Infections of SDAV or RCV can be diagnosed on the basis of clinical signs, lesions, and serological profiles of NT and CF antibody and confirmed by isolation of the causative virus. The pathogenesis and lesions of natural and experimental Sendai virus infection have been well described for mice (2, 132, 160) , but only limited information on rats is available. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155549/ doi: 10.1016/b978-0-12-074901-0.50018-6 id: cord-295041-5vpawtef author: Jakhmola, Shweta title: SARS-CoV-2, an Underestimated Pathogen of the Nervous System date: 2020-09-28 words: 5012.0 sentences: 310.0 pages: flesch: 39.0 cache: ./cache/cord-295041-5vpawtef.txt txt: ./txt/cord-295041-5vpawtef.txt summary: Numerous clinical studies have reported neurological symptoms in COVID-19 patients since the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), apart from the atypical signs of pneumonia. Angiotensin-converting enzyme-2 (ACE-2), a potential receptor for SARS-CoV-2 entry, is expressed on various brain cells and cerebral parts, i.e., subfornical organ, paraventricular nucleus, nucleus of the tractus solitarius, and rostral ventrolateral medulla, as well as in non-cardiovascular areas such as the motor cortex and raphe. The resident CNS cells like astrocytes and microglia also express ACE-2, thus highlighting the vulnerability of the nervous system to SARS-CoV-2 infection. Furthermore, the presence of SARS-CoV-2 in cerebrospinal fluid (CSF) of COVID-19 patients is confirmed through genome sequencing [4] ; however, experimental evidence is needed to validate virusmediated neurological damage. Furthermore, the interaction of SARS-CoV-2 and ACE-2-expressing neuronal/glial cells may facilitate virus entry into the nervous system through different routes. abstract: Numerous clinical studies have reported neurological symptoms in COVID-19 patients since the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), apart from the atypical signs of pneumonia. Angiotensin-converting enzyme-2 (ACE-2), a potential receptor for SARS-CoV-2 entry, is expressed on various brain cells and cerebral parts, i.e., subfornical organ, paraventricular nucleus, nucleus of the tractus solitarius, and rostral ventrolateral medulla, as well as in non-cardiovascular areas such as the motor cortex and raphe. The resident CNS cells like astrocytes and microglia also express ACE-2, thus highlighting the vulnerability of the nervous system to SARS-CoV-2 infection. Additionally, transmembrane serine protease 2 (TMPRSS2) and furin facilitate virus entry into the host. Besides, the probable routes of virus entry into the nervous system include the hematogenic pathway, through the vagus, the olfactory nerve, or the enteric nervous system. However, the trajectory of SARS-CoV-2 to the brain needs investigation. Furthermore, a Th17-mediated cytokine storm is seen in COVID-19 cases with higher levels of IL-1β/2/7/8/9/10/17, GM-CSF, IFN-γ, TNF-α, CXCL-10, MCP1, and MIP1α/β. Some cytokines can cross the blood-brain barrier and activate the brain’s immune cells to produce neural cytokines, leading to neuronal dysfunctions. Nonetheless, most of the neurological conditions developed due to viral infections may not have effective and registered treatments. Although, some antivirals may inhibit the virus-mediated pathogenesis and prove to be suitable in COVID-19 treatment. Therefore, clinicians’ and researchers’ collective expertise may unravel the potential of SARS-CoV-2 infection to prevent short-term and long-term CNS damage. url: https://doi.org/10.1007/s42399-020-00522-7 doi: 10.1007/s42399-020-00522-7 id: cord-002274-6rddtogo author: James, Joe title: Influenza A virus PB1-F2 protein prolongs viral shedding in chickens lengthening the transmission window date: 2016-10-13 words: 6599.0 sentences: 311.0 pages: flesch: 52.0 cache: ./cache/cord-002274-6rddtogo.txt txt: ./txt/cord-002274-6rddtogo.txt summary: Here we report that the presence of a full-length PB1-F2 protein, from a low pathogenicity H9N2 avian influenza virus, prolongs infectious virus shedding from directly inoculated chickens, thereby enhancing transmission of the virus by lengthening the transmission window to contact birds. Spillover of these viruses into domesticated poultry populations has resulted in the evolution of highly pathogenic avian influenza (HPAI) subtypes such as the Asian-lineage H5N1 which has been circulating continuously in birds since 2003 and has caused upwards of 700 human infections . To ascertain if the presence of a full-length PB1-F2 protein effected in vivo virus replication in chickens, we determined the level of infectious virus shed from both the buccal and cloacal cavities of birds inoculated with both high and low doses for 10 days following infection. We assessed viral infectivity, pathogenicity and transmissibility between chickens of isogenic viruses differing only by the presence of a full-length PB1-F2 protein. abstract: Avian influenza is a significant economic burden on the poultry industry in geographical regions where it is enzootic. It also poses a public health concern when avian influenza subtypes infect humans, often with high mortality. Understanding viral genetic factors which positively contribute to influenza A virus (IAV) fitness – infectivity, spread and pathogenesis – is of great importance both for human and livestock health. PB1-F2 is a small accessory protein encoded by IAV and in mammalian hosts has been implicated in a wide range of functions that contribute to increased pathogenesis. In the avian host, the protein has been understudied despite high-level full-length conservation in avian IAV isolates, which is in contrast to the truncations of the PB1-F2 length frequently found in mammalian host isolates. Here we report that the presence of a full-length PB1-F2 protein, from a low pathogenicity H9N2 avian influenza virus, prolongs infectious virus shedding from directly inoculated chickens, thereby enhancing transmission of the virus by lengthening the transmission window to contact birds. As well as extending transmission, the presence of a full-length PB1-F2 suppresses pathogenicity evidenced by an increased minimum lethal dose in embryonated chicken eggs and increasing survival in directly infected birds when compared to a virus lacking an ORF for PB1-F2. We propose that there is a positive pressure to maintain a full-length functional PB1-F2 protein upon infection of avian hosts as it contributes to the effective transmission of IAV in the field. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5078828/ doi: 10.1099/jgv.0.000584 id: cord-256370-cz88t29n author: Jansen van Vuren, Petrus title: Isolation of a Novel Fusogenic Orthoreovirus from Eucampsipoda africana Bat Flies in South Africa date: 2016-02-29 words: 5529.0 sentences: 263.0 pages: flesch: 49.0 cache: ./cache/cord-256370-cz88t29n.txt txt: ./txt/cord-256370-cz88t29n.txt summary: This is the first report on isolation of an orthoreovirus from an arthropod host associated with bats, and phylogenetic and sequence data suggests that MAHLV constitutes a new species within the Orthoreovirus genus. Maximum Likelihood trees were prepared using amino acid sequences of all open reading frames from all segments, showing the placement of Mahlapitsi virus (MAHLV) in the Orthoreovirus genus relative to other viruses in this genus for which sequence is available on Genbank. A Maximum Likelihood tree, constructed with nucleic acid sequence data for the RNA-dependent RNA polymerase (RdRp) encoding segments of representative viruses from the different genera within Reoviridae (Figure 7) shows the placement of both isolates amongst other orthoreoviruses in the family. Maximum Likelihood trees were prepared using the deduced amino acid sequences from the open reading frames (ORF''s) of all the virus'' segments and those of other viruses in the Orthoreovirus genus (Figures 8-10) . abstract: We report on the isolation of a novel fusogenic orthoreovirus from bat flies (Eucampsipoda africana) associated with Egyptian fruit bats (Rousettus aegyptiacus) collected in South Africa. Complete sequences of the ten dsRNA genome segments of the virus, tentatively named Mahlapitsi virus (MAHLV), were determined. Phylogenetic analysis places this virus into a distinct clade with Baboon orthoreovirus, Bush viper reovirus and the bat-associated Broome virus. All genome segments of MAHLV contain a 5' terminal sequence (5'-GGUCA) that is unique to all currently described viruses of the genus. The smallest genome segment is bicistronic encoding for a 14 kDa protein similar to p14 membrane fusion protein of Bush viper reovirus and an 18 kDa protein similar to p16 non-structural protein of Baboon orthoreovirus. This is the first report on isolation of an orthoreovirus from an arthropod host associated with bats, and phylogenetic and sequence data suggests that MAHLV constitutes a new species within the Orthoreovirus genus. url: https://doi.org/10.3390/v8030065 doi: 10.3390/v8030065 id: cord-276006-mjjnkqv6 author: Jarach, Natanel title: Polymers in the Medical Antiviral Front-Line date: 2020-07-31 words: 12573.0 sentences: 738.0 pages: flesch: 41.0 cache: ./cache/cord-276006-mjjnkqv6.txt txt: ./txt/cord-276006-mjjnkqv6.txt summary: Those anions show antiviral properties by affecting Larson studied modified PEI composed of N,N-Dodecylmethyl-PEI that exhibited antiviral effect on HSV-1 and HSV-2 viruses (see also Figure 6 ) [98] , influenza A virus [99] and on poliovirus and rotavirus [100] . Larson studied modified PEI composed of N,N-Dodecylmethyl-PEI that exhibited antiviral effect on HSV-1 and HSV-2 viruses (see also Figure 6 ) [98] , influenza A virus [99] and on poliovirus and rotavirus [100] . Xiao and Xue examined the antiviral effect of quaternary pyridinium containing co-polymers on several Influenza viruses (A, PR8, 8, 34) , as demonstrated in Figure 11 [35]. Xiao and Xue examined the antiviral effect of quaternary pyridinium containing co-polymers on several Influenza viruses (A, PR8, 8, 34) , as demonstrated in Figure 11 [35]. abstract: Antiviral polymers are part of a major campaign led by the scientific community in recent years. Facing this most demanding of campaigns, two main approaches have been undertaken by scientists. First, the classic approach involves the development of relatively small molecules having antiviral properties to serve as drugs. The other approach involves searching for polymers with antiviral properties to be used as prescription medications or viral spread prevention measures. This second approach took two distinct directions. The first, using polymers as antiviral drug-delivery systems, taking advantage of their biodegradable properties. The second, using polymers with antiviral properties for on-contact virus elimination, which will be the focus of this review. Anti-viral polymers are obtained by either the addition of small antiviral molecules (such as metal ions) to obtain ion-containing polymers with antiviral properties or the use of polymers composed of an organic backbone and electrically charged moieties like polyanions, such as carboxylate containing polymers, or polycations such as quaternary ammonium containing polymers. Other approaches include moieties hybridized by sulphates, carboxylic acids, or amines and/or combining repeating units with a similar chemical structure to common antiviral drugs. Furthermore, elevated temperatures appear to increase the anti-viral effect of ions and other functional moieties. url: https://doi.org/10.3390/polym12081727 doi: 10.3390/polym12081727 id: cord-010159-uo47oab1 author: Jartti, Tuomas title: Respiratory viruses and acute asthma in children date: 2007-04-02 words: 571.0 sentences: 41.0 pages: flesch: 56.0 cache: ./cache/cord-010159-uo47oab1.txt txt: ./txt/cord-010159-uo47oab1.txt summary: title: Respiratory viruses and acute asthma in children We read with great interest the article by Khetsuriani et al 1 on the prevalence of respiratory tract viruses in children with asthma. The results of PCR analysis of combined nasopharyngeal and throat swabs for 13 different viruses were positive in 63% of patients with asthma exacerbation in the 1-year study. We disagree with the low virus detection rate reported by Khetsuriani et al 1 because many studies in wheezing children have shown virus detection rates of close to 90%. 1 Interestingly, 2 or more viruses were detected in 43% of the children compared with 7% in the study by Khetsuriani et al. Our findings suggest that nearly all exacerbations of asthma in children necessitating hospitalization are associated with viral infection. Prevalence of viral respiratory tract infections in children with asthma Human bocavirus and acute wheezing in children abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172149/ doi: 10.1016/j.jaci.2007.02.025 id: cord-004211-58x3nnsc author: Javelle, Emilie title: The challenging management of Rift Valley Fever in humans: literature review of the clinical disease and algorithm proposal date: 2020-01-22 words: 6929.0 sentences: 348.0 pages: flesch: 43.0 cache: ./cache/cord-004211-58x3nnsc.txt txt: ./txt/cord-004211-58x3nnsc.txt summary: title: The challenging management of Rift Valley Fever in humans: literature review of the clinical disease and algorithm proposal Clinicians need to consider RVF in the differential diagnosis for febrile illnesses in a suitable context, however manifestations of RVFV in humans are varied and unspecific including hepatitis, encephalitis, hemorrhagic disease, and retinitis with potential dramatic consequences. during the major outbreak in Egypt in 1977, it is considered that less than 5% of symptomatic cases will present complications including ocular, neurologic and hemorrhagic symptoms, while favorable outcome will occur within 1 week for the others [17] . Epidemic Rift Valley fever in Saudi Arabia: a clinical study of severe illness in humans Pathologic studies on suspect animal and human cases of Rift Valley fever from an outbreak in Eastern Africa Severe human illness caused by Rift Valley Fever Virus in Mauritania abstract: Rift Valley Fever (RVF) is an emerging zoonotic arbovirus with a complex cycle of transmission that makes difficult the prediction of its expansion. Recent outbreaks outside Africa have led to rediscover the human disease but it remains poorly known. The wide spectrum of acute and delayed manifestations with potential unfavorable outcome much complicate the management of suspected cases and prediction of morbidity and mortality during an outbreak. We reviewed literature data on bio-clinical characteristics and treatments of RVF human illness. We identified gaps in the field and provided a practical algorithm to assist clinicians in the cases assessment, determination of setting of care and prolonged follow-up. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6977312/ doi: 10.1186/s12941-020-0346-5 id: cord-307744-wbr84taq author: Jayadevan, Rajeev title: Does a younger host make the virus weaker? Presenting a new hypothesis date: 2020-09-13 words: 573.0 sentences: 46.0 pages: flesch: 69.0 cache: ./cache/cord-307744-wbr84taq.txt txt: ./txt/cord-307744-wbr84taq.txt summary: RESULTS: Virus become more virulent as it passes through weaker hosts and vice versa. CONCLUSIONS: Viruses become more virulent when it passes through weaker and older hosts. While compiling the data about doctors'' deaths in India during the COVID-19 pandemic, the case of a 50-year-old doctor who contracted the infection while taking care of his mother at home was observed. Did the son get a more virulent selection of virus after it passed through his mother, who was an older and weaker host? Coxsackie virus CVB3 is known to become more virulent as it passes through weaker and older mice hosts [4] . In the study of 108 COVID-related deaths among doctors in India, nearly half were general practitioners, who saw older patients [5]. It will be worth analysing the transmission chain of COVID-19 from this perspective, specifically to see if the age and frailty of the donor of the virus made a difference in the outcome in the host. abstract: BACKGROUND: COVID-19 is a pandemic, resulting in large number of deaths all over the world. METHODS: The risk factors for mortality are not clearly understood. We are presenting a new hypothesis. RESULTS: Virus become more virulent as it passes through weaker hosts and vice versa. CONCLUSIONS: Viruses become more virulent when it passes through weaker and older hosts. It will be worth analysing the transmission chain of COVID-19 from this perspective. url: https://www.sciencedirect.com/science/article/pii/S187140212030360X?v=s5 doi: 10.1016/j.dsx.2020.09.011 id: cord-269126-d81z6t0a author: Jayaseelan, Vijayashree Priyadharsini title: Repurposing calcium channel blockers as antiviral drugs date: 2020-08-19 words: 1141.0 sentences: 68.0 pages: flesch: 45.0 cache: ./cache/cord-269126-d81z6t0a.txt txt: ./txt/cord-269126-d81z6t0a.txt summary: As convincing reports on calcium channel blockers mediated increase in ACE2 expression has not been documented so far, these drugs can be a safe alternative for treating CoVID patients with hypertension. Host cells are found to modulate calcium signalling in response to viral infection and the viruses in-turn harness this environment for their own survival and propagation. Interestingly, in an attempt made to identify genetic variants associated with susceptibility to neuro-invasive disease caused by West Nile virus, CASNA1H (Calcium Voltage-Gated Channel Subunit Alpha1 H) achieved a genome-wide significance implying the fact that ionchannels could be as important as other immuno-modulatory proteins controlling host response to viral infections (Long et al. Extensive research on existing calcium channel blockers intended for use as anti-hypertensives might as well aid in repurposing these drugs into the anti-viral regimen. Host calcium channels and pumps in viral infections Calcium ions directly interact with the Ebola virus fusion peptide to promote structure-function changes that enhance infection abstract: The current pandemic caused by the SARS-CoV-2 has claimed over a half a million lives within a very short span of time. A therapeutic drug which could prevent the entry and propagation of the virus is the need of the hour. Several lines of evidence collected from experimental studies older than three decades have pointed out the fact that inhibiting calcium entry into cells can affect vital steps in the lifecycle of viruses. Hence, calcium channel blockers may be considered as an effective measure in the containment of the viruses. This commentary throws light two scientific papers although with divergent facts converging at a point by suggesting a promising treatment option for CoVID-19 (Fang et al. Lancet Respir Med 8:e21, 2020; Straus et al. J Virol 94:e00426, 2020). url: https://doi.org/10.1007/s12079-020-00579-y doi: 10.1007/s12079-020-00579-y 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-324984-ojrpsdt9 author: Ji, Xingyue title: Medicinal chemistry strategies toward host targeting antiviral agents date: 2020-02-14 words: 16814.0 sentences: 825.0 pages: flesch: 43.0 cache: ./cache/cord-324984-ojrpsdt9.txt txt: ./txt/cord-324984-ojrpsdt9.txt summary: In addition, host proteins are not under the genetic control of viral genome, and hence HTAs possess much higher genetic barrier to drug resistance as compared with DAAs. In recent years, much progress has been made to the development of HTAs with the approval of chemokine receptor type 5 antagonist maraviroc for human immunodeficiency virus treatment and more in the pipeline for other viral infections. 3 Altogether, targeting host factors is a very promising strategy with possibility to address the critical challenges faced with the DAAs. In this review, we summarize the recent advances made in HTAs from a medicinal chemistry standpoint, and the host targets are generally classified into three different categories based on the development stage of their corresponding inhibitors/modulators, namely the ones which reached Food and Drug Administration (FDA) approval, that have entered clinical trials and those in preclinical studies. abstract: Direct‐acting antiviral agents (DAAs) represent a class of drugs targeting viral proteins and have been demonstrated to be very successful in combating viral infections in clinic. However, DAAs suffer from several inherent limitations, including narrow‐spectrum antiviral profiles and liability to drug resistance, and hence there are still unmet needs in the treatment of viral infections. In comparison, host targeting antivirals (HTAs) target host factors for antiviral treatment. Since host proteins are probably broadly required for various viral infections, HTAs are not only perceived, but also demonstrated to exhibit broad‐spectrum antiviral activities. In addition, host proteins are not under the genetic control of viral genome, and hence HTAs possess much higher genetic barrier to drug resistance as compared with DAAs. In recent years, much progress has been made to the development of HTAs with the approval of chemokine receptor type 5 antagonist maraviroc for human immunodeficiency virus treatment and more in the pipeline for other viral infections. In this review, we summarize various host proteins as antiviral targets from a medicinal chemistry prospective. Challenges and issues associated with HTAs are also discussed. url: https://doi.org/10.1002/med.21664 doi: 10.1002/med.21664 id: cord-252397-qlu7dilh author: Johnson, Reed F. title: Intratracheal exposure of common marmosets to MERS-CoV Jordan-n3/2012 or MERS-CoV EMC/2012 isolates does not result in lethal disease date: 2015-11-01 words: 5024.0 sentences: 255.0 pages: flesch: 49.0 cache: ./cache/cord-252397-qlu7dilh.txt txt: ./txt/cord-252397-qlu7dilh.txt summary: Results from a natural history study of MERS-CoV-infected rhesus monkeys indicated that intratracheal inoculation induced a non-lethal disease with limited pathology observed in recovering animals at 28 days post-inoculation and infectious virus could be recovered from lung but not other tissues assayed (Yao et al., 2014) . One subject in the MERS-EMC inoculated group appeared to develop a secondary infection observed by CT that increased to study end, day 25 post-exposure. With the use of CT, we observed that IT inoculation of common marmosets with MERS-JOR or MERS-EMC isolates resulted in a non-lethal disease characterized by limited clinical signs and moderate consolidative lung pathology that did not completely resolve by study end. In this experiment, we sought to determine if there were virus specific differences in disease progression following intratracheal inoculation of common marmosets with Middle Eastern Respiratory Syndrome Coronavirus, commonly known as MERS-CoV, with two common laboratory viral isolates (MERS-EMC and MERS-Jordan). abstract: Middle East Respiratory Syndrome Coronavirus (MERS-CoV) continues to be a threat to human health in the Middle East. Development of countermeasures is ongoing; however, an animal model that faithfully recapitulates human disease has yet to be defined. A recent study indicated that inoculation of common marmosets resulted in inconsistent lethality. Based on these data we sought to compare two isolates of MERS-CoV. We followed disease progression in common marmosets after intratracheal exposure with: MERS-CoV-EMC/2012, MERS-CoV-Jordan-n3/2012, media, or inactivated virus. Our data suggest that common marmosets developed a mild to moderate non-lethal respiratory disease, which was quantifiable by computed tomography (CT), with limited other clinical signs. Based on CT data, clinical data, and virological data, MERS-CoV inoculation of common marmosets results in mild to moderate clinical signs of disease that are likely due to manipulations of the marmoset rather than as a result of robust viral replication. url: https://www.sciencedirect.com/science/article/pii/S0042682215003323 doi: 10.1016/j.virol.2015.07.013 id: cord-009561-pg4jmvw4 author: Johnson, Richard T. title: The virology of demyelinating diseases date: 2004-10-08 words: 3602.0 sentences: 204.0 pages: flesch: 34.0 cache: ./cache/cord-009561-pg4jmvw4.txt txt: ./txt/cord-009561-pg4jmvw4.txt summary: The possible role of a virus or viruses is supported by data that (1) a childhood exposure is involved and "viral" infections may precipitate exacerbations of disease, (2) experimental infections in animals and natural infections in humans can cause diseases with long incubation periods, remitting and relapsing courses, and demyelination, and (3) patients with multiple sclerosis have abnormal immune responses to viruses. Thud, studies of patients with multiple sclerosis consistently have shown higher levels of antibody against measles virus in serum and cerebrospinal fluid (CSF) than in controls and in some studies antibodies have been elevated to other viral agents as well (Table 2) . In studies of CSF we found no intrathecal synthesis of antibody in posuneasles encephalomyelitis to suggest antigenic stimulation Subsequently, a variety of diseases of the central and peripheral nervous system and muscle have been described as complications of HIV infection [58, 591. abstract: Infectious agents have been postulated as causes of multiple sclerosis for over a century. The possible role of a virus or viruses is supported by data that (1) a childhood exposure is involved and “viral” infections may precipitate exacerbations of disease, (2) experimental infections in animals and natural infections in humans can cause diseases with long incubation periods, remitting and relapsing courses, and demyelination, and (3) patients with multiple sclerosis have abnormal immune responses to viruses. The pathogenesis of three human demyelinating diseases of known viral etiology is discussed. In progressive multifocal leukoencephalopathy, a papovavirus selectively infects oligodendrocytes and causes focal areas of demyelination. In postmeasles encephalomyelitis, the virus is lymphotrophic and disrupts immune regulation that can result in an autoimmune perivenular demyelinating illness without evidence of infection of the central nervous system. In human immunodeficiency virus‐encephalopathy and myelopathy virus is present in macrophages and microglia and the myelin abnormalities apparently are caused by soluble factors such as viral proteins, cytokines, or neurotoxins. These findings may have implications on how, when, and where to seek viruses in multiple sclerosis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159614/ doi: 10.1002/ana.410360715 id: cord-285367-jxlt0gby author: Johnson, Richard T. title: Emerging Issues in Neurovirology: New Viruses, Diagnostic Tools, and Therapeutics date: 2008-08-31 words: 3296.0 sentences: 158.0 pages: flesch: 41.0 cache: ./cache/cord-285367-jxlt0gby.txt txt: ./txt/cord-285367-jxlt0gby.txt summary: In the current era of escalating globalization with rapid transport, changing climate, and an ever growing human population with associated changes in lifestyle, poverty, and war, the emergence of new neurologic infections is accelerated. In the 1960s and 1970s, this emergence was foreshadowed by the appearance of new recombinant (duck-human) influenza viruses, legionnaires'' disease, toxic shock syndrome, Lyme disease, and the neurovirulent La Crosse strains of California encephalitis virus. Some have been due to the evolution of more virulent agents (eg, enterovirus 71, chikunqunya virus, and drug-resistant microbes), some to geographic relocation of agents (eg, Dengue type 3 in Sri Lanka and West Nile virus in North America), and some to contact with animals and crossing of species barriers (eg, bovine spongiform encephalopathy, variant Creutzfeldt-Jakob disease, Nipah virus, and the severe acute respiratory syndrome [SARS] virus). abstract: In the current era of escalating globalization with rapid transport, changing climate, and an ever growing human population with associated changes in lifestyle, poverty, and war, the emergence of new neurologic infections is accelerated. Understanding their origins using epidemiologic and molecular tools will contribute to improved control of agent spread throughout vulnerable populations. Although few interventions are effective in acute epidemics, the prompt identification of new infectious agents and the roll-out of vaccines together with new antiviral and neuroprotective drugs are promising for the management of future epidemics. url: https://doi.org/10.1016/j.ncl.2008.04.003 doi: 10.1016/j.ncl.2008.04.003 id: cord-015023-ishxfinx author: Jones, David title: Hard water date: 1995 words: 1154.0 sentences: 70.0 pages: flesch: 57.0 cache: ./cache/cord-015023-ishxfinx.txt txt: ./txt/cord-015023-ishxfinx.txt summary: divert the search for environmental clues away from specific uncommon viruses to a broader category of events occurring early in life which are applicable to regional populations"; this comment is presumably aimed at Kurtzke and those sharing his view 3 that existing epidemiological data point to a specific infectious (presumably viral) agent as a direct cause of MS. Aircraft and rockets, for example, have to be very light but stiff structures; they also depend on liquid fuels pumped at high velocities. Many aircraft already store their fuel in compartments in their wings, and little modification should be needed to pump it to the engines through the hollow spars of the wing structure. More cunning still, its stiffness and damping could even be altered in flight by redistributing the fuel flow between different spars of the structure. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095081/ doi: 10.1038/377106a0 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-254527-zddwajzg author: Junter, Guy-Alain title: Polysaccharide-based chromatographic adsorbents for virus purification and viral clearance date: 2020-01-13 words: 16940.0 sentences: 907.0 pages: flesch: 42.0 cache: ./cache/cord-254527-zddwajzg.txt txt: ./txt/cord-254527-zddwajzg.txt summary: Table 2 gathers a variety of packed-bed column chromatography procedures applied to viral particle purification in which the stationary phase consists of AG -essentially Sepharose® ("Separation-Pharmacia-AG"; GE Healthcare, Chicago, Ill.) (Seph) -or CELe.g., Cellufine™ (JNC Corporation, Tokyo, Japan) -gel beads, modified to fulfill varying separation modes, i.e., ion exchange, size exclusion and affinity (Table 3 [77] [78] [79] [80] [81] ). For instance, the purification process for Nuwiq®, a recombinant coagulation factor VIII (a blood-clotting protein whose deficiency is associated with hemophilia A) patented by Octapharma AG (Lachen, Switzerland) [195] , includes solvent/detergent (S/D) treatment, Planova NF, and five chromatography steps using PS-based stationary phases, i.e., MMC (Capto MMC), CEC (SP Seph FF), AFC (VIIISelect, a Capto matrix with factor VIIIselective ligand), AEC (Q Seph FF) and SEC (Superdex 200). abstract: Viruses still represent a significant threat to human and animal health worldwide. In the fight against viral infections, high-purity viral stocks are needed for manufacture of safer vaccines. It is also a priority to ensure the viral safety of biopharmaceuticals such as blood products. Chromatography techniques are widely implemented at both academic and industrial levels in the purification of viral particles, whole viruses and virus-like particles, and to remove viral contaminants from biopharmaceutical products. This paper focuses on polysaccharide adsorbents, particulate resins and membrane adsorbers, used in virus purification/removal chromatography processes. Different chromatographic modes are surveyed, with particular attention on ion exchange and affinity/pseudo-affinity adsorbents among which commercially available agarose-based resins (Sepharose®) and cellulose-based membrane adsorbers (Sartobind®) occupy a dominant position. Mainly built on the development of new ligands coupled to conventional agarose/cellulose matrices, the development perspectives of polysaccharide-based chromatography media in this antiviral area are stressed in a conclusive part. url: https://www.sciencedirect.com/science/article/pii/S209517791930838X?v=s5 doi: 10.1016/j.jpha.2020.01.002 id: cord-287711-gw8mgg4m author: Junter, Guy-Alain title: Cellulose-based virus-retentive filters: a review date: 2017-06-01 words: 11711.0 sentences: 582.0 pages: flesch: 40.0 cache: ./cache/cord-287711-gw8mgg4m.txt txt: ./txt/cord-287711-gw8mgg4m.txt summary: Data from spiking studies quantifying the viral filtration performance of cellulosic filters are detailed, i.e., first, the virus reduction capacity of regenerated cellulose hollow fiber filters in the manufacturing process of blood products and, second, the efficiency of virus recovery/concentration from water samples by the viradel (virus adsorption–elution) method using charge modified, electropositive cellulosic filters or conventional electronegative cellulose ester microfilters. Data from spiking studies quantifying the viral filtration performance of cellulosic filters are detailed, i.e., first, the virus reduction capacity of regenerated cellulose hollow fiber filters in the manufacturing process of blood products and, second, the efficiency of virus recovery/concentration from water samples by the viradel (virus adsorption-elution) method using charge modified, electropositive cellulosic filters or conventional electronegative cellulose ester microfilters. abstract: Viral filtration is a critical step in the purification of biologics and in the monitoring of microbiological water quality. Viral filters are also essential protection elements against airborne viral particles. The present review first focuses on cellulose-based filter media currently used for size-exclusion and/or adsorptive filtration of viruses from biopharmaceutical and environmental water samples. Data from spiking studies quantifying the viral filtration performance of cellulosic filters are detailed, i.e., first, the virus reduction capacity of regenerated cellulose hollow fiber filters in the manufacturing process of blood products and, second, the efficiency of virus recovery/concentration from water samples by the viradel (virus adsorption–elution) method using charge modified, electropositive cellulosic filters or conventional electronegative cellulose ester microfilters. Viral analysis of field water samples by the viradel technique is also surveyed. This review then describes cellulose-based filter media used in individual protection equipment against airborne viral pathogens, presenting innovative filtration media with virucidal properties. Some pros and cons of cellulosic viral filters and perspectives for cellulose-based materials in viral filtration are underlined in the review. url: https://www.ncbi.nlm.nih.gov/pubmed/32214924/ doi: 10.1007/s11157-017-9434-1 id: cord-319210-yqimufdh author: KENNEDY, P.G.E. title: On the possible viral aetiology of multiple sclerosis date: 1994-09-17 words: 3980.0 sentences: 181.0 pages: flesch: 42.0 cache: ./cache/cord-319210-yqimufdh.txt txt: ./txt/cord-319210-yqimufdh.txt summary: 1 The presence of inflammatory histological changes in the MS lesions such as perivenular lymphocytic infiltration, and the raised cerebrospinal fluid (CSF) immunoglobulins in an oligoclonal pattern detected in most MS patients are very suggestive of an immune basis for the disease, 23 one that may possibly be related to some kind of viral infection. Although by their very nature animal models of virus-induced demyelination only produce a form of indirect evidence for the viral aetiology of MS, nevertheless they can reveal important insights into the possible mechanisms by which a virus can initiate a pathogenetic cascade leading to CNS myelin destruction. 36 In the brains, only a small percentage of the oligodendrocytes are infected with the virus, so the main mechanism of demyelination is almost certainly indirect, presumably via the generation of Class II antigen-induced T cell responses and release of cytokines and/or toxic viral proteins. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/7953500/ doi: 10.1093/oxfordjournals.qjmed.a068963 id: cord-010001-u0d5jkp1 author: KOTWAL, GIRISH J. title: Anti‐HIV, Anti‐Poxvirus, and Anti‐SARS Activity of a Nontoxic, Acidic Plant Extract from the Trifollium Species Secomet‐V/anti‐Vac Suggests That It Contains a Novel Broad‐Spectrum Antiviral date: 2006-01-22 words: 2608.0 sentences: 123.0 pages: flesch: 51.0 cache: ./cache/cord-010001-u0d5jkp1.txt txt: ./txt/cord-010001-u0d5jkp1.txt summary: With a well-established infrastructure and the methodology to cultivate and to titer viruses accurately 6 to evaluate antiviral effects, it was possible to show that indeed a small volume of the plant extract termed Secomet-V was able to inactivate approximately 1 million virus particles of the attenuated recombinant vaccinia virus vGK5 7 in 1 minute consistently and reproducibly. Secomet-V, an extract of an African plant also found elsewhere in Asia, has been found to have potent antiviral activity against a poxvirus (vaccinia virus), rendering about 1 million particles noninfectious in 1 min with a 50th of a milliliter in in vitro assays (FIG. HIV-infected cells treated with plant extract showed no significant effect on the viral levels (TABLE 1) . There was no difference in the effectiveness of the plant extract in rendering vaccinia virus noninfectious whether it was autoclaved or not, suggesting that the bioactive agent is most likely but not necessarily a heat-stable compound and not a small peptide. abstract: Enveloped animal viruses such as human immunodeficiency virus (HIV), hepatitis B virus, hepatitis C virus, human papillomavirus, Marburg, and influenza are major public health concerns around the world. The prohibitive cost of antiretroviral (ARV) drugs for most HIV‐infected patients in sub‐Saharan Africa and the serious side effects in those who have access to ARV drugs make a compelling case for the study of complementary and alternative therapies. Such therapies should have scientifically proved antiviral activity and minimal toxic effects. A plant extract, Secomet‐V, with an anecdotal indication in humans for promise as an anti‐HIV treatment, was investigated. Using a previously described attenuated vaccinia virus vGK5, we established the antiviral activity of Secomet‐V. Chemical analysis showed that it has an acidic pH, nontoxic traces of iron (<10 ppm), and almost undetectable levels of arsenic (<1.0 ppm). The color varies from colorless to pale yellow to dark brown. The active agent is heat stable at least up to sterilizing temperature of 121°C. The crude plant extract is a mixture of several small molecules separable by high‐pressure liquid chromatography. The HIV viral loads were significantly reduced over several months in a few patients monitored after treatment with Secomet‐V. Secomet‐V was also found to have antiviral activity against the SARS virus but not against the West Nile virus. Secomet‐V, therefore, is a broad‐spectrum antiviral, which possibly works by neutralizing viral infectivity, resulting in the prevention of viral attachment. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167892/ doi: 10.1196/annals.1352.014 id: cord-026641-eemp6b5j author: Kabiljo, Julijan title: From threat to cure: understanding of virus-induced cell death leads to highly immunogenic oncolytic influenza viruses date: 2020-06-11 words: 6689.0 sentences: 373.0 pages: flesch: 37.0 cache: ./cache/cord-026641-eemp6b5j.txt txt: ./txt/cord-026641-eemp6b5j.txt summary: In the absence of NS1 apoptosis appears to be induced through the viral-RNA-mediated induction of retinoic acidinducible gene I (RIG-I) and interferon (IFN) signaling including protein kinase R (PKR) and eukaryotic initiation factor 2 alpha (eIF2α) activation and subsequent block of translation [39] [40] [41] . Another study screened a variety of wild-type influenza A viruses for their infectivity in pancreatic carcinoma cell lines and showed oncolytic effectiveness in a mouse model of human pancreatic cancer 67 . expressed a recombinant humanized cytotoxic T-lymphocyte-associated protein 4 (CTLA4) immune checkpoint inhibiting antibody from two different RNA fragments of the influenza A virus genome in order to enhance its anti-cancer effectiveness in a murine B16 melanoma model 96 . Further effects of oncolytic influenza A viruses on the cancer-immune microenvironment shown in murine models include activation of NK-cells and macrophage polarization towards immuno-stimulatory M1 phenotypes 66, 114 . abstract: Oncolytic viruses constitute an emerging strategy in immunomodulatory cancer treatment. The first oncolytic virus, Talimogene laherparepvec (T-VEC), based on herpes simplex virus 1 (HSV-1), was approved by the Food and Drug Administration (FDA) and European Medicines Agency (EMA) in 2015. The field of oncolytic virotherapy is still in its beginnings, since many promising viruses remain only superficially explored. Influenza A virus causes a highly immunogenic acute infection but never leads to a chronic disease. While oncolytic influenza A viruses are in preclinical development, they have not made the transition into clinical practice yet. Recent insights into different types of cell death caused by influenza A virus infection illuminate novel possibilities of enhancing its therapeutic effect. Genetic engineering and experience in influenza A virus vaccine development allow safe application of the virus in patients. In this review we give a summary of efforts undertaken to develop oncolytic influenza A viruses. We discuss strategies for targeting viral replication to cancerous lesions and arming them with immunogenic transgenes. We furthermore describe which modes of cell death are induced by influenza A virus infection and how these insights may be utilized to optimize influenza A virus-based oncolytic virus design. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7288254/ doi: 10.1038/s41420-020-0284-1 id: cord-323311-xl2fv0qx author: Kahn, R. E. title: 6th International Conference on Emerging Zoonoses date: 2012-09-07 words: 19161.0 sentences: 802.0 pages: flesch: 41.0 cache: ./cache/cord-323311-xl2fv0qx.txt txt: ./txt/cord-323311-xl2fv0qx.txt summary: The three key characteristics of this integrated approach to so many infectious diseases are as follows: (i) to use cell culture, primary cells, nonhuman primate and human clinical models to study viral infection; (ii) to combine traditional histopathological, virological and biochemical approaches with functional genomics, proteomics and computational biology (Haagmans et al., 2009); and (iii) to obtain signatures of virulence and insights into mechanisms of host defense response, viral evasion and pathogenesis (Casadevaill et al., 2011) . The unity of human, animal and ecosystem health outlined by Professor Aguirre, as well as the interactions among multiple tick-borne pathogens in a natural reservoir host set out by Professor Fish and his research team, both summarized in Topic 1 above, highlight the necessity of cross-disciplinary collaboration in studying zoonotic bacterial diseases (Daszak et al., 2007, pp. abstract: The 6th International Conference on Emerging Zoonoses, held at Cancun, Mexico, 24–27 February 2011, offered 84 participants from 18 countries, a snapshot of current research in numerous zoonoses caused by viruses, bacteria or prions. Co‐chaired by Professors Heinz Feldmann and Jürgen Richt, the conference explored 10 topics: (i) The ecology of emerging zoonotic diseases; (ii) The role of wildlife in emerging zoonoses; (iii) Cross‐species transmission of zoonotic pathogens; (iv) Emerging and neglected influenza viruses; (v) Haemorrhagic fever viruses; (vi) Emerging bacterial diseases; (vii) Outbreak responses to zoonotic diseases; (viii) Food‐borne zoonotic diseases; (ix) Prion diseases; and (x) Modelling and prediction of emergence of zoonoses. Human medicine, veterinary medicine and environmental challenges are viewed as a unity, which must be considered under the umbrella of ‘One Health’. Several presentations attempted to integrate the insights gained from field data with mathematical models in the search for effective control measures of specific zoonoses. The overriding objective of the research presentations was to create, improve and use the tools essential to address the risk of contagions in a globalized society. In seeking to fulfil this objective, a three‐step approach has often been applied: (i) use cultured cells, model and natural animal hosts and human clinical models to study infection; (ii) combine traditional histopathological and biochemical approaches with functional genomics, proteomics and computational biology; and (iii) obtain signatures of virulence and insights into mechanisms of host defense response, immune evasion and pathogenesis. This meeting review summarizes 39 of the conference presentations and mentions briefly the 16 articles in this Special Supplement, most of which were presented at the conference in earlier versions. The full affiliations of all presenters and many colleagues have been included to facilitate further inquiries from readers. url: https://www.ncbi.nlm.nih.gov/pubmed/22958247/ doi: 10.1111/j.1863-2378.2012.01539.x id: cord-311748-yr2ep7uf author: Kahyaoglu, L. N. title: 11 New approaches in microbial pathogen detection date: 2013-12-31 words: 8020.0 sentences: 381.0 pages: flesch: 48.0 cache: ./cache/cord-311748-yr2ep7uf.txt txt: ./txt/cord-311748-yr2ep7uf.txt summary: In recent years, polymerase chain reaction (PCR)-based methods in particular, have become the gold standard for virus detection in food due to their high sensitivity, specifi city and potential to detect even a single virus particle (Bosch et al. In recent years, qRT-PCR has been widely used in food virology as the most promising nucleic acid detection method, since it offers several advantages over conventional RT-PCR, including high sensitivity, the possibility of simultaneous amplifi cation, detection and quantifi cation of the target nucleic acids in a single step, and with minimum risk of carry-over contamination through the use of a closed system (Mackay et al. The challenges associated with the detection of foodborne viruses, such as PCR inhibitors and low virus concentrations in foods, affect the effi ciency of realtime assay adversely, therefore, for process control (PC) an internal amplifi cation control (IAC), which is extracted and amplifi ed with the target sequence, is crucial in the evaluation of PCR and to prevent false negatives (Di Pasquale et al. abstract: Abstract: Viruses are common causes of foodborne outbreaks. Viral diseases have low fatality rates but transmission to humans via food is important due to the high probability of consuming fecally contaminated food or water because of poor food handling. Because of the low infectious doses of some foodborne viruses, there is a need for standardization and the development of new sensitive methods for detecting viruses. The focus is on molecular and non-molecular approaches, and emerging methods for the detection of foodborne viruses. The detection of noroviruses, hepatitis A and E viruses, rotaviruses and adenoviruses will be discussed. The chapter will conclude with insights into future research directions. url: https://api.elsevier.com/content/article/pii/B978085709438450011X doi: 10.1533/9780857098740.3.202 id: cord-270940-acwkh6ed author: Kallio-Kokko, Hannimari title: Viral zoonoses in Europe date: 2005-06-29 words: 14695.0 sentences: 733.0 pages: flesch: 46.0 cache: ./cache/cord-270940-acwkh6ed.txt txt: ./txt/cord-270940-acwkh6ed.txt summary: Recently, during an outbreak in Finland in 2002, the causative agent of Pogosta disease was isolated for the first time in Europe from skin biopsies and a blood sample of patients [115] ; the virus strains were most closely related to SINV strains isolated from mosquitoes in Sweden and Russia 20 years previously. The genus Nairovirus (family Bunyaviridae) is composed of 34 predominantly tick-borne viruses that have been divided into seven serogroups [154] including several associated with severe human and livestock diseases (especially Crimean-Congo hemorrhagic fever virus (CCHFV) and Nairobi sheep disease virus). Rift Valley fever virus (RVFV), which is the type species of the genus and is transmitted by mosquitoes, causing an influenza-like disease that affects domestic animals and humans. abstract: A number of new virus infections have emerged or re-emerged during the past 15 years. Some viruses are spreading to new areas along with climate and environmental changes. The majority of these infections are transmitted from animals to humans, and thus called zoonoses. Zoonotic viruses are, as compared to human-only viruses, much more difficult to eradicate. Infections by several of these viruses may lead to high mortality and also attract attention because they are potential bioweapons. This review will focus on zoonotic virus infections occurring in Europe. url: https://www.ncbi.nlm.nih.gov/pubmed/16024128/ doi: 10.1016/j.femsre.2005.04.012 id: cord-274643-vjb2yt93 author: Kang, G. title: Viral Diarrhea date: 2008-08-26 words: 5682.0 sentences: 282.0 pages: flesch: 39.0 cache: ./cache/cord-274643-vjb2yt93.txt txt: ./txt/cord-274643-vjb2yt93.txt summary: Of the ''non-group A'' rotaviruses, group B rotavirus has been identified in epidemic outbreaks of severe diarrhea in adults in China and in symptomatic infections in children. Between 20% and 50% of cases of gastroenteritis caused by rotavirus in hospitals are considered to be of nosocomial origin, and nosocomial viral enteric infections have been documented in up to 6% of children admitted for more than 72 hours in both developed and developing countries. Rotaviruses induce a clinical illness characterized by vomiting, diarrhea, abdominal discomfort, fever, and dehydration (or a combination of some of these symptoms) that occurs primarily in infants and young children and may lead to hospitalization for rehydration therapy. Studies in adult volunteers indicate that people with detectable levels of antibodies do not develop the illness, although epidemiological observations suggest that human astrovirus infections do not induce heterotypic immunity, as an episode of astrovirus diarrhea is not associated with a reduced incidence of a subsequent episode. abstract: Viral gastroenteritis is among the most common illnesses affecting humans and has greatest impact at the extremes of age. The spectrum of disease can range from asymptomatic infections to severe disease with dehydration. Intensive investigation of enteric infections in the past three decades has made it increasingly clear that viruses cause a significant proportion of enteric illnesses worldwide. In contrast to bacterial pathogens, enteric viruses cannot multiply outside their host; hence, the original inoculum into the common source determines infectivity. Prevention of contamination of food and water will help control primary cases, whereas careful nursing and handwashing prevent secondary cases. url: https://www.sciencedirect.com/science/article/pii/B9780123739605005712 doi: 10.1016/b978-012373960-5.00571-2 id: cord-314390-q36ye9ff author: Kang, Gagandeep title: Viral Diarrhea date: 2016-10-24 words: 6020.0 sentences: 281.0 pages: flesch: 39.0 cache: ./cache/cord-314390-q36ye9ff.txt txt: ./txt/cord-314390-q36ye9ff.txt summary: Of the ''non-group A'' rotaviruses, group B rotavirus has been identified in epidemic outbreaks of severe diarrhea in adults in China and in symptomatic infections in children. Between 20% and 50% of cases of gastroenteritis caused by rotavirus in hospitals are considered to be of nosocomial origin, and nosocomial viral enteric infections have been documented in up to 6% of children admitted for >72 h in both developed and developing countries. Rotaviruses induce a clinical illness characterized by vomiting, diarrhea, abdominal discomfort, fever, and dehydration (or a combination of some of these symptoms) that occurs primarily in infants and young children and may lead to hospitalization for rehydration therapy. Studies in adult volunteers indicate that people with detectable levels of antibodies do not develop the illness, although epidemiological observations suggest that human astrovirus infections may not induce heterotypic immunity, as an episode of astrovirus diarrhea is not associated with a reduced incidence of a subsequent episode. abstract: Viral gastroenteritis is among the most common illnesses affecting humans and has greatest impact at the extremes of age. The spectrum of disease can range from asymptomatic infections to severe disease with dehydration. In contrast to bacterial pathogens, enteric viruses cannot multiply outside their host; hence, the original inoculum into the common source determines infectivity. Prevention of contamination of food and water control primary cases, whereas careful nursing and handwashing prevent secondary cases. Effective vaccines are available and widely used to prevent rotaviral gastroenteritis, but vaccines for other causes of viral gastroenteritis are not yet available. url: https://www.sciencedirect.com/science/article/pii/B9780128036785004860 doi: 10.1016/b978-0-12-803678-5.00486-0 id: cord-277970-sb1wjd3b author: Kang, Qianli title: Screening for Anti-Influenza Actives of Prefractionated Traditional Chinese Medicines date: 2020-10-14 words: 2817.0 sentences: 165.0 pages: flesch: 43.0 cache: ./cache/cord-277970-sb1wjd3b.txt txt: ./txt/cord-277970-sb1wjd3b.txt summary: It''s therefore of great value to discover novel antivirals from TCMs. In this paper, One hundred medicinal plants which have been included in TCM prescriptions for antiviral treatment were selected and prefractionated into 5 fractions each by sequentially using cyclohexane, dichloromethane, ethyl acetate, n-butanol, and water. As a result, ten TCM fractions were identified to have antiviral potency against IAV, deserving further analysis for novel anti-influenza lead drugs. To this end, 100 medicinal plants which have been recorded as antiviral formula compositions were fractionated with cyclohexane, dichloromethane, ethyl acetate, n-butanol, and water sequentially, generating a library consisting of 500 prefractionated TCM extracts (Figure 1, Table S1 ). By using a HTS approach based on recombinant reporter influenza PR8-PB2-Gluc virus, the antiviral activity of each fraction against IAV was evaluated, and 10 simplified extracts were identified as anti-influenza actives ( Figure 3 ). abstract: Traditional Chinese medicines (TCMs) have proven to possess advantages in counteracting virus infections according to clinical practices. It's therefore of great value to discover novel antivirals from TCMs. In this paper, One hundred medicinal plants which have been included in TCM prescriptions for antiviral treatment were selected and prefractionated into 5 fractions each by sequentially using cyclohexane, dichloromethane, ethyl acetate, n-butanol, and water. 500 TCM-simplified extracts were then subjected to a phenotypic screening using a recombinant IAV expressing Gaussia luciferase. Ten TCM fractions were identified to possess antiviral activities against influenza virus. The IC50's of the hit fractions range from 1.08 to 6.45 μg/mL, while the SIs, from 7.52 to 98.40. Furthermore, all the ten hit fractions inhibited the propagation of progeny influenza virus significantly at 20 μg/mL. The hit TCM fractions deserve further isolation for responsible constituents leading towards anti-influenza drugs. Moreover, a library consisting of 500 simplified TCM extracts was established, facilitating antiviral screening in quick response to emerging and re-emerging viruses such as Ebola virus and current SARS-CoV-2 pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/33123207/ doi: 10.1155/2020/4979850 id: cord-267831-uu883ofc author: Kang, Yuan-Lin title: Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2 date: 2020-06-15 words: 1257.0 sentences: 80.0 pages: flesch: 44.0 cache: ./cache/cord-267831-uu883ofc.txt txt: ./txt/cord-267831-uu883ofc.txt summary: We describe here potent inhibitory effects on content release and infection by chimeric VSV containing the envelope proteins of Zaire ebolavirus (VSV-ZEBOV) or SARS-CoV-2 (VSV-SARS-CoV-2) elicited by Apilimod and Vacuolin-1, small molecule inhibitors of the main endosomal Phosphatidylinositol-3-Phosphate/Phosphatidylinositol 5-Kinase, PIKfyve. 143 All of these viruses require low pH to trigger viral membrane fusion with the endosomal 144 membranes, and as expected, infection was fully blocked by Bafilomycin A1, which 145 inhibits the vacuolar type H + -ATPase (V-ATPase) acidification activity (Fig. 1C) . Mammalian cell morphology and 671 endocytic membrane homeostasis require enzymatically active phosphoinositide 672 5-kinase PIKfyve The phosphatidylinositol-3-phosphate 5-kinase inhibitor 710 apilimod blocks filoviral entry and infection A transmembrane serine protease is linked to the severe 735 acute respiratory syndrome coronavirus receptor and activates virus entry Characterization of severe acute respiratory syndrome-744 associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry abstract: Virus entry is a multistep process. It initiates when the virus attaches to the host cell and ends when the viral contents reach the cytosol. Genetically unrelated viruses can subvert analogous subcellular mechanisms and use similar trafficking pathways for successful entry. Antiviral strategies targeting early steps of infection are therefore appealing, particularly when the probability for successful interference through a common step is highest. We describe here potent inhibitory effects on content release and infection by chimeric VSV containing the envelope proteins of Zaire ebolavirus (VSV-ZEBOV) or SARS-CoV-2 (VSV-SARS-CoV-2) elicited by Apilimod and Vacuolin-1, small molecule inhibitors of the main endosomal Phosphatidylinositol-3-Phosphate/Phosphatidylinositol 5-Kinase, PIKfyve. We also describe potent inhibition of SARS-CoV-2 strain 2019-nCoV/USA-WA1/2020 by Apilimod. These results define new tools for studying the intracellular trafficking of pathogens elicited by inhibition of PIKfyve kinase and suggest the potential for targeting this kinase in developing small-molecule antivirals against SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32511398/ doi: 10.1101/2020.04.21.053058 id: cord-351377-xorj8tnz author: Kao, Chi-Fei title: The Characterization of Immunoprotection Induced by a cDNA Clone Derived from the Attenuated Taiwan Porcine Epidemic Diarrhea Virus Pintung 52 Strain date: 2018-10-04 words: 5936.0 sentences: 234.0 pages: flesch: 48.0 cache: ./cache/cord-351377-xorj8tnz.txt txt: ./txt/cord-351377-xorj8tnz.txt summary: Moreover, inoculation with iPEDVPT-P96 elicited comparable levels of anti-PEDV specific plasma IgG and fecal/salivary IgA, neutralizing antibody titers, and similar but less effective immunoprotection against the virulent PEDVPT-P5 challenge compared to the parental PEDVPT-P96. In the present study, an infectious cDNA clone of an attenuated G2b PEDV strain was successfully generated for the first time, and the in vitro and in vivo data indicate that iPEDVPT-P96 is further attenuated but remains immunogenic compared to its parental PEDVPT-P96 viral stock. While one piglet in the PEDVPT-P96 group showed intermittent loose diarrhea (score = 1) and viral shedding at 6 to 11 days post-inoculation (DPI) with the peak viral titer of 1.45 ± 3.24 log 10 RNA copies/mL at 8 DPI (Figure 4) , no evidence of PEDV-associated clinical signs and fecal viral shedding were demonstrated in both iPEDVPT-P96 and mock groups. abstract: The porcine epidemic diarrhea virus (PEDV) poses a great threat to the global swine industries and the unreliable protection induced by the currently available vaccines remains a major challenge. We previously generated a genogroup 2b (G2b) PEDV Taiwan Pintung 52 (PEDVPT) strain, PEDVPT-P96, and determined its promising host immune response against the virulent PEDVPT-P5 strain. To study the attenuation determinants of PEDVPT-P96 and establish a PEDVPT-P96-based recombinant vector as a vaccine platform for further antigenicity modification, iPEDVPT-P96, a full-length cDNA clone of PEDVPT-P96, was established. Comparing to the parental PEDVPT-P96 virus, the iPEDVPT-P96 virus showed efficient replication kinetics with a delayed decline of viral load and similar but much more uniform plaque sizes in Vero cells. In the 5-week-old piglet model, fecal viral shedding was observed in the PEDVPT-P96-inoculated piglets, whereas those inoculated with iPEDVPT-P96 showed neither detectable fecal viral shedding nor PEDV-associated clinical signs. Moreover, inoculation with iPEDVPT-P96 elicited comparable levels of anti-PEDV specific plasma IgG and fecal/salivary IgA, neutralizing antibody titers, and similar but less effective immunoprotection against the virulent PEDVPT-P5 challenge compared to the parental PEDVPT-P96. In the present study, an infectious cDNA clone of an attenuated G2b PEDV strain was successfully generated for the first time, and the in vitro and in vivo data indicate that iPEDVPT-P96 is further attenuated but remains immunogenic compared to its parental PEDVPT-P96 viral stock. The successful development of the iPEDVPT-P96 cDNA clone could allow for the manipulation of the viral genome to study viral pathogenesis and facilitate the rapid development of effective vaccines. url: https://www.ncbi.nlm.nih.gov/pubmed/30287770/ doi: 10.3390/v10100543 id: cord-258783-ev0h95b9 author: Kapil, Sanjay title: Canine Distemper Spillover in Domestic Dogs from Urban Wildlife date: 2011-11-30 words: 7346.0 sentences: 390.0 pages: flesch: 42.0 cache: ./cache/cord-258783-ev0h95b9.txt txt: ./txt/cord-258783-ev0h95b9.txt summary: Canine distemper virus (CDV) causes a major disease of domestic dogs that develops as a serious systemic infection in unvaccinated or improperly vaccinated dogs. 68 In addition to domestic dogs, urban wildlife in the United States such as raccoons, foxes, and skunks may play a role in direct transmission of distemper to large felids and other carnivores in zoos, wildlife parks, circuses, and captive breeding facilities. Canine distemper is a highly contagious disease of domestic dogs that also infects multiple wildlife hosts, some that serve as secondary or amplifying reservoirs of the virus. Because canine distemper is an RNA virus, a potential for emergence of antigenic variants exists, particularly in situations where wildlife that are infected with a strain of CDV that has adapted to that host spills back to domestic dogs. Introduction of novel canine distemper viruses in improperly vaccinated dog populations with insufficient immunity can cause new outbreaks of CDV. abstract: Canine distemper virus (CDV) causes a major disease of domestic dogs that develops as a serious systemic infection in unvaccinated or improperly vaccinated dogs. Domesticated dogs are the main reservoir of CDV, a multihost pathogen. This virus of the genus Morbillivirus in the family Paramyxoviridae occurs in other carnivorous species including all members of the Canidae and Mustelidae families and in some members of the Procyonidae, Hyaenidae, Ursidae, and Viverridae families. Canine distemper also has been reported in the Felidae family and marine mammals. The spread and incidences of CDV epidemics in dogs and wildlife here and worldwide are increasing. url: https://doi.org/10.1016/j.cvsm.2011.08.005 doi: 10.1016/j.cvsm.2011.08.005 id: cord-294478-3ickafd3 author: Kapil, Sanjay title: Diagnostic Investigation of Emerging Viruses of Companion Animals date: 2008-05-22 words: 7330.0 sentences: 328.0 pages: flesch: 38.0 cache: ./cache/cord-294478-3ickafd3.txt txt: ./txt/cord-294478-3ickafd3.txt summary: Variants of a known virus that has gained enhanced virulence or that is able to infect completely vaccinated animals A known virus that has reappeared in the population after a decline in incidence Novel or previously unidentified viral agents detected for the first time because of improved diagnostic capabilities ''''Mystery diseases'''' with large numbers of naive animals involved that are caused by previously uncharacterized viruses Spread of an emerging virus among small companion animals is multifactorial and includes animal health and sanitation practices; migration of a pathogen from a wild reservoir to domestic animals because of changes in populations, trade, climate, land use, and the introduction of invasive species (eg, plant, animal, insect); and, finally, globalization, as was the case with West Nile virus (WNV). Detecting emerging viral diseases of companion animals requires interaction and discussion among clinicians, pathologists, and virologists, and practicing small animal veterinarians must stay engaged in communication with these specialists through their state diagnostic laboratories or nearby colleges of veterinary medicine. abstract: In this article, the authors are specifically concerned with the timely and accurate detection of emerging diseases of small animals that are viral in origin. Veterinarians are bound to encounter emerging viruses in their practice. The problem is unavoidable, because viruses are highly mutagenic. Even the immune response dictates the nature of virus that evolves in a host. If the clinical signs and diagnostic methods fail to correlate, the veterinarian should work with the diagnostic laboratory to solve the diagnostic puzzle. url: https://www.ncbi.nlm.nih.gov/pubmed/18501276/ doi: 10.1016/j.cvsm.2008.02.009 id: cord-297494-6yxmaihl author: Katsurada, Naoko title: The impact of virus infections on pneumonia mortality is complex in adults: a prospective multicentre observational study date: 2017-12-06 words: 4336.0 sentences: 217.0 pages: flesch: 38.0 cache: ./cache/cord-297494-6yxmaihl.txt txt: ./txt/cord-297494-6yxmaihl.txt summary: However, influenza virus A and B were associated with three-fold higher mortality in patients with chronic respiratory disease but not with other comorbidities (ARR 3.38, 95% CI 1.54–7.42). We conducted this prospective multicentre study to determine the distribution of viruses associated with pneumonia in adults and to establish their virus-specific effects on pneumonia mortality stratified by age group and comorbidity status. To the best of our knowledge, this study is the first to systematically investigate virus-specific effects on pneumonia mortality by age group and comorbidity status among adults. In our study, multiple viruses were identified in 5.1% of virus-associated pneumonia and were associated with higher mortality than single viral infection in patients with chronic respiratory disease and other comorbidities. Systematic reviews have shown that multiple viral infections in patients with respiratory disease are not associated with disease severity [27, 28] ; however, the majority of previous studies included young children but not adults. abstract: BACKGROUND: Various viruses are known to be associated with pneumonia. However, the impact of viral infections on adult pneumonia mortality remains unclear. This study aimed to clarify the effect of virus infection on pneumonia mortality among adults stratified by virus type and patient comorbidities. METHODS: This multicentre prospective study enrolled pneumonia patients aged ≥15 years from September 2011 to August 2014. Sputum samples were tested by in-house multiplex polymerase chain reaction assays to identify 13 respiratory viruses. Viral infection status and its effect on in-hospital mortality were examined by age group and comorbidity status. RESULTS: A total of 2617 patients were enrolled in the study and 77.8% was aged ≥65 years. 574 (21.9%) did not have comorbidities, 790 (30.2%) had chronic respiratory disease, and 1253 (47.9%) had other comorbidities. Viruses were detected in 605 (23.1%) patients. Human rhinovirus (9.8%) was the most frequently identified virus, followed by influenza A (3.9%) and respiratory syncytial virus (3.9%). Respiratory syncytial virus was more frequently identified in patients with chronic respiratory disease (4.7%) than those with other comorbidities (4.2%) and without comorbidities (2.1%) (p = 0.037). The frequencies of other viruses were almost identical between the three groups. Virus detection overall was not associated with increased mortality (adjusted risk ratio (ARR) 0.76, 95% CI 0.53–1.09). However, influenza virus A and B were associated with three-fold higher mortality in patients with chronic respiratory disease but not with other comorbidities (ARR 3.38, 95% CI 1.54–7.42). Intriguingly, paramyxoviruses were associated with dramatically lower mortality in patients with other comorbidities (ARR 0.10, 95% CI 0.01–0.70) but not with chronic respiratory disease. These effects were not affected by age group. CONCLUSIONS: The impact of virus infections on pneumonia mortality varies by virus type and comorbidity status in adults. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-017-2858-y) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12879-017-2858-y doi: 10.1186/s12879-017-2858-y id: cord-300435-vs0ntcsb author: Katz, Al title: Heteroaggregation of an enveloped bacteriophage with colloidal sediments and effect on virus viability date: 2018-10-01 words: 5297.0 sentences: 295.0 pages: flesch: 46.0 cache: ./cache/cord-300435-vs0ntcsb.txt txt: ./txt/cord-300435-vs0ntcsb.txt summary: Four sediments in the colloidal size range: goethite, montmorillonite, illite, and kaolinite, were suspended with the bacteriophage φ6, a model enveloped virus, to determine relative rates of heteroaggregation and the effect of aggregation on virus viability. A study of heteroaggregation of the non-enveloped cowpea mosaic virus with colloidal hematite revealed that at pH 6, at which hematite carries a positive surface charge and the virus a negative charge, the aggregates accumulated four times as many viruses as hematite particles Vilker et al. In this work, we employ turbidity measurements to investigate the heteroaggregation of a model envelope virus, the bacteriophage φ6, with colloidal goethite and three clay minerals: illite, kaolinite and montmorillonite. Although imprecise knowledge of doublet shape complicates calculations of heteroaggregation rates, analysis of the turbidity slope coupled with particle concentrations allows one to determine relative aggregation rates between φ6 and the four sediment types, elucidating the nature of the interaction. abstract: Four sediments in the colloidal size range: goethite, montmorillonite, illite, and kaolinite, were suspended with the bacteriophage φ6, a model enveloped virus, to determine relative rates of heteroaggregation and the effect of aggregation on virus viability. Turbidity was measured on combinations of virus and each sediment type at low concentration to determine aggregation rates. Aggregation of sediment with virus occurred regardless of mineral type, and larger fraction of virus is expected to aggregate with increasing sediment concentration leading to higher deposition rates. The negatively charged sediments, aggregated with φ6 (also negatively charged at neutral pH) at a faster rate than the positively charged sediments, yielding turbidity slopes of 4.94 × 10(−3) s(−1) and 7.50 × 10(−4) s(−1) for φ6-montmorillonite and φ6-illite aggregates, respectively, and 2.98 × 10(−5) s(−1) and 2.84 × 10(−5) s(−1), for φ6-goethite and φ6-kaolinite, respectively. This indicates that the interaction between sediments and virus is hydrophobic, rather than electrostatic. Large numbers of virions remained viable post-aggregation, despite the fragility of the viral envelope, indicating that small-sized aggregates, which may travel more readily through porous media, may pose an infection risk. The fraction of φ6 that remained viable varied with sediment type, with montmorillonite-φ6 aggregates experiencing the greatest reduction in infectivity at 35%. TEM analyses reveal that in all sediment-φ6 combinations, infectivity loss was likely due to disassembly of the viral envelope as a result of aggregation. url: https://doi.org/10.1016/j.scitotenv.2018.04.425 doi: 10.1016/j.scitotenv.2018.04.425 id: cord-311823-85wj08gr author: Katze, Michael G. title: Innate immune modulation by RNA viruses: emerging insights from functional genomics date: 2008 words: 9154.0 sentences: 392.0 pages: flesch: 36.0 cache: ./cache/cord-311823-85wj08gr.txt txt: ./txt/cord-311823-85wj08gr.txt summary: In this section, we review recent studies in which genomic approaches have been used to provide new information on how viruses trigger and regulate innate immune pathways, and to evaluate the use of type I IFN-based therapy as a means to enhance the innate immune response to HCV. In RIg-I-deficient cells, influenza virus fails to elicit the expression of IFNβ and of many ISgs, including key antiviral mediators such as IRF3, STAT1 (signal transducer and activator of transcription 1), IFIT1 (IFN-induced protein with tetratricopeptide repeats 1; also known as ISg56) and ISg54 (also known as IFIT2). Although these studies have provided considerable information regarding the genes activated downstream of TlR activation, it will be advantageous to extend genomic analyses in the context of viral infection using cells lacking the expression of specific TlRs. The ability of a virus to establish an infection depends, at least to some extent, on its ability to block the host innate immune response or to modulate the activity of antiviral effector proteins. abstract: Although often encoding fewer than a dozen genes, RNA viruses can overcome host antiviral responses and wreak havoc on the cells they infect. Some manage to evade host antiviral defences, whereas others elicit an aberrant or disproportional immune response. Both scenarios can result in the disruption of intracellular signalling pathways and significant pathology in the host. Systems-biology approaches are increasingly being used to study the processes of viral triggering and regulation of host immune responses. By providing a global and integrated view of cellular events, these approaches are beginning to unravel some of the complexities of virus–host interactions and provide new insights into how RNA viruses cause disease. url: https://doi.org/10.1038/nri2377 doi: 10.1038/nri2377 id: cord-301285-p83ondy8 author: Kautz, Tiffany F title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy date: 2018-03-06 words: 8836.0 sentences: 472.0 pages: flesch: 53.0 cache: ./cache/cord-301285-p83ondy8.txt txt: ./txt/cord-301285-p83ondy8.txt summary: To validate the safety of low-fidelity mutations to increase vaccine attenuation, several mutations in the RNA-dependent RNA-polymerase (RdRp) were tested in the live-attenuated Venezuelan equine encephalitis virus vaccine strain, TC-83. Due to the error-prone nature of the RNA-dependent RNApolymerase (RdRp), RNA virus replication is characterized by a high mutation rate that results in increased genetic diversity of progeny viruses (Domingo et al. When compared with unpassaged, wild-type (wt) viruses, fidelity mutants have similar growth kinetics in vitro, but are attenuated in vivo due to the alteration of diversity produced during replication, which hampers the ability of the virus to overcome bottlenecks in the host (Pfeiffer and Kirkegaard 2005; Vignuzzi et al. The 4x mutant, while exhibiting phenotypic similarities with other altered fidelity mutants, had no significant difference in virus diversity compared with the TC-83 parent after one cell culture passage. abstract: During RNA virus replication, there is the potential to incorporate mutations that affect virulence or pathogenesis. For live-attenuated vaccines, this has implications for stability, as replication may result in mutations that either restore the wild-type phenotype via reversion or compensate for the attenuating mutations by increasing virulence (pseudoreversion). Recent studies have demonstrated that altering the mutation rate of an RNA virus is an effective attenuation tool. To validate the safety of low-fidelity mutations to increase vaccine attenuation, several mutations in the RNA-dependent RNA-polymerase (RdRp) were tested in the live-attenuated Venezuelan equine encephalitis virus vaccine strain, TC-83. Next generation sequencing after passage in the presence of mutagens revealed a mutant containing three mutations in the RdRp, TC-83 3x, to have decreased replication fidelity, while a second mutant, TC-83 4x displayed no change in fidelity, but shared many phenotypic characteristics with TC-83 3x. Both mutants exhibited increased, albeit inconsistent attenuation in an infant mouse model, as well as increased immunogenicity and complete protection against lethal challenge of an adult murine model compared with the parent TC-83. During serial passaging in a highly permissive model, the mutants increased in virulence but remained less virulent than the parent TC-83. These results suggest that the incorporation of low-fidelity mutations into the RdRp of live-attenuated vaccines for RNA viruses can confer increased immunogenicity whilst showing some evidence of increased attenuation. However, while in theory such constructs may result in more effective vaccines, the instability of the vaccine phenotype decreases the likelihood of this being an effective vaccine strategy. url: https://www.ncbi.nlm.nih.gov/pubmed/29593882/ doi: 10.1093/ve/vey004 id: cord-344749-omzhhr0k author: Kaya, Sariye Irem title: Electrochemical virus detections with nanobiosensors date: 2020-02-14 words: 8402.0 sentences: 508.0 pages: flesch: 37.0 cache: ./cache/cord-344749-omzhhr0k.txt txt: ./txt/cord-344749-omzhhr0k.txt summary: Cell culture-based virus isolation has been accepted as a "gold standard" in the detection and identification of viruses and is the technique by which all other test methods have been compared [35] . A novel method for dengue virus detection and antibody screening using a graphene-polymer based electrochemical biosensor Chitosan-carbon nanofiber modified single-use graphite electrodes developed for electrochemical detection of DNA hybridization related to hepatitis B virus A sensitive electrochemical biosensor for specific DNA sequence detection based on flower-like VS2, graphene and Au nanoparticles signal amplification Electrochemical DNA biosensor based on a tetrahedral nanostructure probe for the detection of avian influenza A (H7N9) virus Electrochemical DNA biosensor based on gold nanorods for detecting hepatitis B virus Electrochemical-DNA biosensor development based on a modified carbon electrode with gold nanoparticles for influenza a (H1N1) detection: effect of spacer Magnetic nanoparticle-based immunosensor for electrochemical detection of hepatitis B surface antigen abstract: Infectious diseases are caused from pathogens, which need a reliable and fast diagnosis. Today, expert personnel and centralized laboratories are needed to afford much time in diagnosing diseases caused from pathogens. Recent progress in electrochemical studies shows that biosensors are very simple, accurate, precise, and cheap at virus detection, for which researchers find great interest in this field. The clinical levels of these pathogens can be easily analyzed with proposed biosensors. Their working principle is based on affinity between antibody and antigen in body fluids. The progress still continues on these biosensors for accurate, rapid, reliable sensors in future. url: https://www.sciencedirect.com/science/article/pii/B9780128198704000177 doi: 10.1016/b978-0-12-819870-4.00017-7 id: cord-264350-4zxp3uae author: Kelley, James L. title: Chapter 12. Antiviral Agents date: 1984-12-31 words: 2520.0 sentences: 167.0 pages: flesch: 46.0 cache: ./cache/cord-264350-4zxp3uae.txt txt: ./txt/cord-264350-4zxp3uae.txt summary: The focus of this year''s chapter is on agents with activity A brief update of this year''s advances More comprehensive reviews dealing VIRAL RESPIRATORY DISEASE RNA viruses are the major causative factors of the various forms of acute respiratory disease .8 respiratory tract are probably the most common cause of symptomatic human infections. Ribavirin (l-~-~-ribofuranosyl-1,2,~-triazole-3-carboxamide) -This nucleoside has activity against a broad range of DNA and RNA viruses in An tissue culture and in animal model systems.2 analysis of the status of ribavirin 3) as an is still unresolved but may involve guanosine nucleotides and inhibition of inosine monophosphate dehydrogenase.Z6 In a clinical trial against influenza A, oral ribavirin failed to alter clinical signs and symptoms of the disease.2 However, it OR OR has recently been reported to have a therapeutic effect against both influenza A and influenza B virus infections when administered to patients by inhalation of small-particle aerosol through a face m a s k . abstract: Publisher Summary This chapter discusses the agents with activity primarily against RNA viruses. The communicable diseases of the respiratory tract are probably the most common cause of symptomatic human infections. The viruses that are causative agents for human respiratory disease comprise the five taxonomically distinct families: orthomyxoviridae, paramyxoviridae, picornaviridae, coronaviridae, and adenoviridae. The influenza viruses, which consist of types A, B, and C, belong to the family orthomyxoviridae. Types A and B have been associated with significant increases in mortality during epidemics. The disease may be asymptomatic or cause symptoms ranging from the common cold to fatal pneumonia. Immunization against influenza has been recommended for high-risk groups and antiviral chemotherapy (amantadine) is available for the treatment and prophylaxis of all influenza A infections. There is both a great need for and interest in developing a chemotherapeutic agent for the treatment of these two viral, respiratory tract pathogens. The family picornaviridae contains the genus Rhinovirus that is composed of over a hundred distinct serotypes. Amantadine and rimantadine are specifically active against influenza A virus infections. The amantadine recipients reported a higher incidence of side effects largely attributed to the central nervous system (CNS) symptoms. This difference in side effects may be a pharmacokinetic phenomenon that results in higher plasma concentrations of amantadine. Significant progress continues to be made in the clinical use and development of agents active against DNA viruses. Acyclovir (9-(2-h droxyethoxymethyl)guanine) has been the subject of several reviews and of a syrnposium. Considerable progress has been made in evaluating the clinical promise of acyclovir; however, there remains much to be learned concerning the best use of this drug in clinical practice. Significant strides have been made in the development of clinically useful antiviral agents, especially against the DNA viruses of the herpes family. Most of these agents are directed against viral nucleic acid synthesis and require activation by a virus-induced thymidine kinase. Researchers have begun to focus on other strategies that may produce broader spectrum anti-viral agents with different mechanisms of action. url: https://api.elsevier.com/content/article/pii/S0065774308606880 doi: 10.1016/s0065-7743(08)60688-0 id: cord-331739-y1d0leic author: Kempf, Christoph title: Pathogen inactivation and removal procedures used in the production of intravenous immunoglobulins date: 2007-03-31 words: 5089.0 sentences: 287.0 pages: flesch: 42.0 cache: ./cache/cord-331739-y1d0leic.txt txt: ./txt/cord-331739-y1d0leic.txt summary: Since plasma pools from 250 to 2000 blood donations were being used to produce albumin, efforts were initiated to inactivate hepatitis virus in human serum albumin solutions [6] . The emergence of human immunodeficiency virus (HIV) and reports of non-A, non-B hepatitis transmission by some IVIG products [11, 12] but not others caused manufacturers and regulatory agencies to examine existing IVIG manufacturing processes for their capacity to eliminate viruses [13e22]. Studies of IVIG manufacturing procedures suggested that cold ethanol fractionation removes viruses by two mechanisms: 1) inactivation and 2) partitioning. Efficient elimination of TSE infectivity from IgG solutions by Table 3 Log 10 reduction factors of model viruses observed during laboratory experiments of IVIG production (Carimune NF Ò ) Process (step in Fig. 1 [53] . To date IVIG therapeutics have reached a high safety standard due to consequent blood and plasma testing and the introduction of virus elimination steps in the manufacturing process. abstract: Abstract Patients with immunodeficiencies or some types of autoimmune diseases rely on a safe therapy with intravenous immunoglobulins (IVIGs) manufactured from human plasma, the only available source for this therapeutic. Since plasma is predisposed to contamination by a variety of blood-borne pathogens, ascertaining and ensuring the pathogen safety of plasma-derived therapeutics is a priority among manufacturers. State-of-the-art manufacturing processes provide a high safety standard by incorporating virus elimination procedures into the manufacturing process. Based on their mechanism these procedures are grouped into three classes: partitioning, inactivation, and virusfiltration. url: https://www.ncbi.nlm.nih.gov/pubmed/16581263/ doi: 10.1016/j.biologicals.2006.01.002 id: cord-309067-aemjbkfj author: Kennedy, Melissa title: Methodology in diagnostic virology date: 2005-03-01 words: 5885.0 sentences: 370.0 pages: flesch: 49.0 cache: ./cache/cord-309067-aemjbkfj.txt txt: ./txt/cord-309067-aemjbkfj.txt summary: Detection of the virus that causes an infection uses one of several methods: The virus may be propagated in the laboratory and characterized; the virus may be visualized by electron microscopy; the viral proteins may be detected using specific antibody; the viral nucleic acid may be detected; or an activity of the virus, such as red blood cell agglutination, may be assayed. Antigen detection assays involve the use of virus-specific antibody to detect or bind to the viral protein or antigen in the sample. The assays vary in the sample substrate, how the binding of antibody to antigen is visualized, sensitivity, and specificity. Most use pathogen-specific antibody for capture and detection as for IFA assays (Fig. 4B) . Variations on this protocol may be found with different assays, but the underlying technique of pathogen-specific antibody binding the virus in the sample is similar in all (Fig. 4) [1, 3, 4] . abstract: Selection of proper assays and appropriate interpretation of results can be a challenge to the veterinary clinician. Assays vary in methodology, sensitivity, and specificity. These assays can be invaluable in attaining the correct diagnosis, but a clear understanding of the assay and the results is essential. To this end, communication with the laboratory personnel is crucial. Optimal sample selection, shipping recommendations, assay selection, and interpretation should be discussed with the laboratory staff. url: https://api.elsevier.com/content/article/pii/S1094919404000702 doi: 10.1016/j.cvex.2004.09.009 id: cord-316951-1swlhdz5 author: Kennedy, Melissa title: General concepts of virology date: 2005-03-01 words: 1643.0 sentences: 107.0 pages: flesch: 50.0 cache: ./cache/cord-316951-1swlhdz5.txt txt: ./txt/cord-316951-1swlhdz5.txt summary: Virus pathogenesis is defined as the mechanism by which a virus replicates in the cell, and in doing so, injures a cell and produces disease. The virus must first attach to a cell by way of a surface receptor, followed by entry or penetration into the cell The virus uncoats within the cell and releases its nucleic acid For most viruses, the next step is viral transcription to produce mRNA. Genetic characteristics of the host include species, breed, organ, tissue susceptibility, and function at the cellular level (eg, cell receptor types and intracellular hospitality to the virus). It is defined as the specific cells and tissue in the host in which the virus replicates in a natural infection. A basic understanding of viruses and how they replicate and produce disease can aid in the management of virus infections. A basic understanding of viruses and how they replicate and produce disease can aid in the management of virus infections. abstract: A basic understanding of viruses and how they replicate and produce disease can aid in the management of virus infections. Parameters, such as clinical signs, sample and test selection, prognosis, and control, are implicit in this understanding. Information increases almost daily about known and emerging viruses; this impacts our ability to manage and control infections. url: https://api.elsevier.com/content/article/pii/S1094919404000714 doi: 10.1016/j.cvex.2004.09.010 id: cord-288238-36hiiw91 author: Keshavarz, Mohsen title: Metabolic host response and therapeutic approaches to influenza infection date: 2020-03-05 words: 8134.0 sentences: 425.0 pages: flesch: 32.0 cache: ./cache/cord-288238-36hiiw91.txt txt: ./txt/cord-288238-36hiiw91.txt summary: It is also reported that influenza infection significantly increases ROS production by inducing Nox4, and the proliferation of this virus in lung epithelial cells is dependent on redox-sensitive pathways activated by Nox4-derived ROS [16] . IFN can also exert its function on metabolic changes by producing several mediators including indoleamine-2,3-dioxygenase (IDO) and nitric oxide (NO), both of which appear to have either an inducible or an inhibitory role in viral replication [33] . In addition, increased temperature of cells during infection (which could be the result of virus replication and fever) causes heat stress which in turn can considerably downregulate carnitine palmitoyltransferase II (CPT II) activity and reduce the β-oxidation and ATP levels in fibroblasts of influenza-associated encephalopathy patients and healthy volunteers [110] . Through enhancing the activity of the mTORC1 complex, the influenza virus strengthens several metabolic pathways, including glycolysis, glutaminolysis, pentose phosphate, and fatty acid synthesis, to provide more ATP and structural materials for viral replication. abstract: Based on available metabolomic studies, influenza infection affects a variety of cellular metabolic pathways to ensure an optimal environment for its replication and production of viral particles. Following infection, glucose uptake and aerobic glycolysis increase in infected cells continually, which results in higher glucose consumption. The pentose phosphate shunt, as another glucose-consuming pathway, is enhanced by influenza infection to help produce more nucleotides, especially ATP. Regarding lipid species, following infection, levels of triglycerides, phospholipids, and several lipid derivatives undergo perturbations, some of which are associated with inflammatory responses. Also, mitochondrial fatty acid β-oxidation decreases significantly simultaneously with an increase in biosynthesis of fatty acids and membrane lipids. Moreover, essential amino acids are demonstrated to decline in infected tissues due to the production of large amounts of viral and cellular proteins. Immune responses against influenza infection, on the other hand, could significantly affect metabolic pathways. Mainly, interferon (IFN) production following viral infection affects cell function via alteration in amino acid synthesis, membrane composition, and lipid metabolism. Understanding metabolic alterations required for influenza virus replication has revealed novel therapeutic methods based on targeted inhibition of these cellular metabolic pathways. url: https://www.ncbi.nlm.nih.gov/pubmed/32161622/ doi: 10.1186/s11658-020-00211-2 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-349358-leicos9j author: Ketzinel‐Gilad, Mali title: RNA interference for antiviral therapy date: 2006-06-16 words: 12734.0 sentences: 684.0 pages: flesch: 44.0 cache: ./cache/cord-349358-leicos9j.txt txt: ./txt/cord-349358-leicos9j.txt summary: During the past few years, it has been demonstrated that RNAi, induced by specifically designed double‐stranded RNA (dsRNA) molecules, can silence gene expression of human viral pathogens both in acute and chronic viral infections. Likewise, expression vectors of siRNAs specific for two different regions of the WNV genome protected 293T cells from WNV infection, and significantly reduced viral RNA replication and virus production [35] . From the reports on the use of siRNA against human viral pathogens causing acute disease, we could learn that for each specific pathogen infecting a specific cell lineage or tissue, we would probably need to perform an indepth assessment, with proper in vitro and in vivo models, and develop specific delivery systems. The most challenging part of RNAi approaches for chronic viral infections is to design the best delivery method that would facilitate the targeting of the specific organ/cells with the appropriate expression system, for durable intracellular levels of gene-silencing effect. abstract: Silencing gene expression through a process known as RNA interference (RNAi) has been known in the plant world for many years. In recent years, knowledge of the prevalence of RNAi and the mechanism of gene silencing through RNAi has started to unfold. It is now believed that RNAi serves in part as an innate response against invading viral pathogens and, indeed, counter silencing mechanisms aimed at neutralizing RNAi have been found in various viral pathogens. During the past few years, it has been demonstrated that RNAi, induced by specifically designed double‐stranded RNA (dsRNA) molecules, can silence gene expression of human viral pathogens both in acute and chronic viral infections. Furthermore, it is now apparent that in in vitro and in some in vivo models, the prospects for this technology in developing therapeutic applications are robust. However, many key questions and obstacles in the translation of RNAi into a potential therapeutic platform still remain, including the specificity and longevity of the silencing effect, and, most importantly, the delivery of the dsRNA that induces the system. It is expected that for the specific examples in which the delivery issue could be circumvented or resolved, RNAi may hold promise for the development of gene‐specific therapeutics. Copyright © 2006 John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/16779870/ doi: 10.1002/jgm.929 id: cord-252725-e3pazjdi author: Khalil, Ayman title: The upshot of Polyphenolic compounds on immunity amid COVID-19 pandemic and other emerging communicable diseases: An appraisal date: 2020-10-15 words: 8759.0 sentences: 338.0 pages: flesch: 30.0 cache: ./cache/cord-252725-e3pazjdi.txt txt: ./txt/cord-252725-e3pazjdi.txt summary: In fact, several studies and clinical trials increasingly proved the role of polyphenols in controlling numerous human pathogens including SARS and MERS, which are quite similar to COVID-19 through the enhancement of host immune response against viral infections by different biological mechanisms. Actually, data indicated that activation of the nuclear factor (NF)-κB transcription factor (NF-κB) signaling pathway represents a major contribution to the inflammation induced post SARS-CoV infection and that NF-κB inhibitors are promising antiviral drugs against infections caused by the virus and potentially other pathogenic human coronaviruses [8] . Moreover, it was found to reduce the reactive oxygenated species (ROS) produced during viral infection and subsequently decrease pro-inflammatory markers such as IL-8, TNF-α, IL-1β and IL-6 [25] and increases anti-inflammatory cytokines such as IL-10 [35] , indicating that it has clear antiviral effects on several respiratory and common cold viruses through its ability to reduce virus imputation, replication and viral load in vitro, as well as lung inflammation and airways hyper-responsiveness in vivo [29] . abstract: Polyphenols are a large family of more than 10,000 naturally occurring compounds, which exert countless pharmacological, biological and physiological benefits for human health including several chronic diseases such as cancer, diabetes, cardiovascular, and neurological diseases. Their role in traditional medicine, such as the use of a wide range of remedial herbs (thyme, oregano, rosemary, sage, mint, basil), has been well and long known for treating common respiratory problems and cold infections. This review reports on the most highlighted polyphenolic compounds present in up to date literature and their specific antiviral perceptive properties that might enhance the body immunity facing COVID-19, and other viral infectious diseases. In fact, several studies and clinical trials increasingly proved the role of polyphenols in controlling numerous human pathogens including SARS and MERS, which are quite similar to COVID-19 through the enhancement of host immune response against viral infections by different biological mechanisms. Thus, polyphenols ought to be considered as a potential and valuable source for designing new drugs that could be used effectively in the combat against COVID‐19 and other rigorous diseases. url: https://doi.org/10.1007/s13659-020-00271-z doi: 10.1007/s13659-020-00271-z id: cord-304343-m7tbdfri author: Khandia, Rekha title: A Comprehensive Review of Autophagy and Its Various Roles in Infectious, Non-Infectious, and Lifestyle Diseases: Current Knowledge and Prospects for Disease Prevention, Novel Drug Design, and Therapy date: 2019-07-03 words: 20281.0 sentences: 1088.0 pages: flesch: 32.0 cache: ./cache/cord-304343-m7tbdfri.txt txt: ./txt/cord-304343-m7tbdfri.txt summary: Similarly, inhibiting the mTOR signaling pathway can prevent apoptosis and even enhance necroptosis, whereas starvation, which induces autophagy, protects cells from zVAD-mediated necroptotic death [194] . For instance, autophagy has been demonstrated to be actively involved in the replication of influenza A virus (IAV), which induces autophagosome formation during the early phase of infection and later inhibits autophagosomal maturation by preventing autophagosomal-lysosomal fusion and promoting autophagosomes to accumulate in virus-infected cells [253] . (5) A novel anti-cancer molecule, HA15, which targets HSPA5/BIP was shown to induce endoplasmic reticulum stress and increase the unfolded protein response, resulting in cancer cell death through autophagy and apoptosis. (5) A novel anti-cancer molecule, HA15, which targets HSPA5/BIP was shown to induce endoplasmic reticulum stress and increase the unfolded protein response, resulting in cancer cell death through autophagy and apoptosis. In addition, the novel anti-cancer molecule HA15, which targets HSPA5/BIP, was shown to induce ER stress and increase the unfolded protein response, resulting in cancer cell death via autophagy and apoptosis [304] . abstract: Autophagy (self-eating) is a conserved cellular degradation process that plays important roles in maintaining homeostasis and preventing nutritional, metabolic, and infection-mediated stresses. Autophagy dysfunction can have various pathological consequences, including tumor progression, pathogen hyper-virulence, and neurodegeneration. This review describes the mechanisms of autophagy and its associations with other cell death mechanisms, including apoptosis, necrosis, necroptosis, and autosis. Autophagy has both positive and negative roles in infection, cancer, neural development, metabolism, cardiovascular health, immunity, and iron homeostasis. Genetic defects in autophagy can have pathological consequences, such as static childhood encephalopathy with neurodegeneration in adulthood, Crohn’s disease, hereditary spastic paraparesis, Danon disease, X-linked myopathy with excessive autophagy, and sporadic inclusion body myositis. Further studies on the process of autophagy in different microbial infections could help to design and develop novel therapeutic strategies against important pathogenic microbes. This review on the progress and prospects of autophagy research describes various activators and suppressors, which could be used to design novel intervention strategies against numerous diseases and develop therapeutic drugs to protect human and animal health. url: https://doi.org/10.3390/cells8070674 doi: 10.3390/cells8070674 id: cord-326177-zzsaf3bl author: Khatri, Mahesh title: Mesenchymal stem cell-derived extracellular vesicles attenuate influenza virus-induced acute lung injury in a pig model date: 2018-01-29 words: 6655.0 sentences: 370.0 pages: flesch: 49.0 cache: ./cache/cord-326177-zzsaf3bl.txt txt: ./txt/cord-326177-zzsaf3bl.txt summary: title: Mesenchymal stem cell-derived extracellular vesicles attenuate influenza virus-induced acute lung injury in a pig model In several animal models of human diseases, MSC-EVs mimic the beneficial effects of MSCs. Influenza viruses cause annual outbreaks of acute respiratory illness resulting in significant mortality and morbidity. Next, we examined the anti-influenza activity of MSC-EVs in vitro in lung epithelial cells and anti-viral and immunomodulatory properties in vivo in a pig model of influenza virus. The antiinfluenza activity of MSC-EVs was due to transfer of RNAs from EVs to epithelial cells since pre-incubation of MSC-EVs with RNase enzyme abrogated the anti-influenza activity of MSC-EVs. In a pig model of influenza virus, intratracheal administration of MSC-EVs 12 h after influenza virus infection significantly reduced virus shedding in the nasal swabs, influenza virus replication in the lungs, and virus-induced production of proinflammatory cytokines in the lungs of influenza-infected pigs. abstract: BACKGROUND: Mesenchymal stem (stromal) cells (MSCs) mediate their immunoregulatory and tissue repair functions by secreting paracrine factors, including extracellular vesicles (EVs). In several animal models of human diseases, MSC-EVs mimic the beneficial effects of MSCs. Influenza viruses cause annual outbreaks of acute respiratory illness resulting in significant mortality and morbidity. Influenza viruses constantly evolve, thus generating drug-resistant strains and rendering current vaccines less effective against the newly generated strains. Therefore, new therapies that can control virus replication and the inflammatory response of the host are needed. The objective of this study was to examine if MSC-EV treatment can attenuate influenza virus-induced acute lung injury in a preclinical model. METHODS: We isolated EVs from swine bone marrow-derived MSCs. Morphology of MSC-EVs was determined by electron microscopy and expression of mesenchymal markers was examined by flow cytometry. Next, we examined the anti-influenza activity of MSC-EVs in vitro in lung epithelial cells and anti-viral and immunomodulatory properties in vivo in a pig model of influenza virus. RESULTS: MSC-EVs were isolated from MSC-conditioned medium by ultracentrifugation. MSC-EVs were round-shaped and, similarly to MSCs, expressed mesenchymal markers and lacked the expression of swine leukocyte antigens I and II. Incubation of PKH-26-labeled EVs with lung epithelial cells revealed that MSC-EVs incorporated into the epithelial cells. Next, we examined the anti-influenza and anti-inflammatory properties of MSC-EVs. MSC-EVs inhibited the hemagglutination activity of avian, swine, and human influenza viruses at concentrations of 1.25–5 μg/ml. MSC-EVs inhibited influenza virus replication and virus-induced apoptosis in lung epithelial cells. The anti-influenza activity of MSC-EVs was due to transfer of RNAs from EVs to epithelial cells since pre-incubation of MSC-EVs with RNase enzyme abrogated the anti-influenza activity of MSC-EVs. In a pig model of influenza virus, intratracheal administration of MSC-EVs 12 h after influenza virus infection significantly reduced virus shedding in the nasal swabs, influenza virus replication in the lungs, and virus-induced production of proinflammatory cytokines in the lungs of influenza-infected pigs. The histopathological findings revealed that MSC-EVs alleviated influenza virus-induced lung lesions in pigs. CONCLUSIONS: Our data demonstrated in a relevant preclinical large animal model of influenza virus that MSC-EVs possessed anti-influenza and anti-inflammatory properties and that EVs may be used as cell-free therapy for influenza in humans. url: https://doi.org/10.1186/s13287-018-0774-8 doi: 10.1186/s13287-018-0774-8 id: cord-300837-d0a8y5qh author: Khetawat, Dimple title: A Functional Henipavirus Envelope Glycoprotein Pseudotyped Lentivirus Assay System date: 2010-11-12 words: 8988.0 sentences: 355.0 pages: flesch: 44.0 cache: ./cache/cord-300837-d0a8y5qh.txt txt: ./txt/cord-300837-d0a8y5qh.txt summary: To circumvent this problem, we have developed a henipavirus envelope glycoprotein pseudotyped lentivirus assay system using either a luciferase gene or green fluorescent protein (GFP) gene encoding human immunodeficiency virus type-1 (HIV-1) genome in conjunction with the HeV and NiV fusion (F) and attachment (G) glycoproteins. Pseudotyped virus particles generated with the NiV F and G glycoproteins were able to infect and produce luciferase reporter gene activity at various levels on all permissive receptor expressing cells ( Figure 1A ) while no signal was observed with the receptor negative HeLa-USU or with control virus particles generated by transfection with empty vector (pCAGGs). To confirm these findings and demonstrate an expanded utility of the henipavirus envelope glycoprotein pseudotyping systems, NiV and HeV F and G glycoprotein bearing lentivirus particles were prepared with the GFP reporter gene encoding construct pNL4-3-GFP-E-R + and used to infect receptor positive 293T cells ( Figure 2 ). abstract: BACKGROUND: Hendra virus (HeV) and Nipah virus (NiV) are newly emerged zoonotic paramyxoviruses discovered during outbreaks in Queensland, Australia in 1994 and peninsular Malaysia in 1998/9 respectively and classified within the new Henipavirus genus. Both viruses can infect a broad range of mammalian species causing severe and often-lethal disease in humans and animals, and repeated outbreaks continue to occur. Extensive laboratory studies on the host cell infection stage of HeV and NiV and the roles of their envelope glycoproteins have been hampered by their highly pathogenic nature and restriction to biosafety level-4 (BSL-4) containment. To circumvent this problem, we have developed a henipavirus envelope glycoprotein pseudotyped lentivirus assay system using either a luciferase gene or green fluorescent protein (GFP) gene encoding human immunodeficiency virus type-1 (HIV-1) genome in conjunction with the HeV and NiV fusion (F) and attachment (G) glycoproteins. RESULTS: Functional retrovirus particles pseudotyped with henipavirus F and G glycoproteins displayed proper target cell tropism and entry and infection was dependent on the presence of the HeV and NiV receptors ephrinB2 or B3 on target cells. The functional specificity of the assay was confirmed by the lack of reporter-gene signals when particles bearing either only the F or only G glycoprotein were prepared and assayed. Virus entry could be specifically blocked when infection was carried out in the presence of a fusion inhibiting C-terminal heptad (HR-2) peptide, a well-characterized, cross-reactive, neutralizing human mAb specific for the henipavirus G glycoprotein, and soluble ephrinB2 and B3 receptors. In addition, the utility of the assay was also demonstrated by an examination of the influence of the cytoplasmic tail of F in its fusion activity and incorporation into pseudotyped virus particles by generating and testing a panel of truncation mutants of NiV and HeV F. CONCLUSIONS: Together, these results demonstrate that a specific henipavirus entry assay has been developed using NiV or HeV F and G glycoprotein pseudotyped reporter-gene encoding retrovirus particles. This assay can be conducted safely under BSL-2 conditions and will be a useful tool for measuring henipavirus entry and studying F and G glycoprotein function in the context of virus entry, as well as in assaying and characterizing neutralizing antibodies and virus entry inhibitors. url: https://www.ncbi.nlm.nih.gov/pubmed/21073718/ doi: 10.1186/1743-422x-7-312 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-328252-dk54w8z9 author: Kikkert, Marjolein title: Innate Immune Evasion by Human Respiratory RNA Viruses date: 2019-10-14 words: 11552.0 sentences: 550.0 pages: flesch: 43.0 cache: ./cache/cord-328252-dk54w8z9.txt txt: ./txt/cord-328252-dk54w8z9.txt summary: Whether PA-X also degrades viral dsRNA species to prevent recognition by cytosolic RNA sensors is not entirely clear, but mutant viruses in which this PA-X protein was expressed in significantly lower amounts elicited higher levels of innate immune response; for example, IFN-beta production was much higher in these infections [71] . This indeed suggests that PA-X, besides having a role in the degradation of cellular mRNAs, may also degrade viral RNA to prevent recognition by innate immune sensors and activation of innate immune responses, similar to what was shown for the CoVs. To my knowledge, an endoribonuclease has not been identified in the RSV genome, so this virus may use alternative innate immune evasion strategies, as discussed elsewhere in this review. [91] suggested that RSV specifically targets mRNA encoding surfactant protein A, an innate immune factor with an important role in the epithelial tissue of the lung, which directly binds to virus particles to cause their destruction by host defense mechanisms. abstract: The impact of respiratory virus infections on the health of children and adults can be very significant. Yet, in contrast to most other childhood infections as well as other viral and bacterial diseases, prophylactic vaccines or effective antiviral treatments against viral respiratory infections are either still not available, or provide only limited protection. Given the widespread prevalence, a general lack of natural sterilizing immunity, and/or high morbidity and lethality rates of diseases caused by influenza, respiratory syncytial virus, coronaviruses, and rhinoviruses, this difficult situation is a genuine societal challenge. A thorough understanding of the virus-host interactions during these respiratory infections will most probably be pivotal to ultimately meet these challenges. This review attempts to provide a comparative overview of the knowledge about an important part of the interaction between respiratory viruses and their host: the arms race between host innate immunity and viral innate immune evasion. Many, if not all, viruses, including the respiratory viruses listed above, suppress innate immune responses to gain a window of opportunity for efficient virus replication and setting-up of the infection. The consequences for the host's immune response are that it is often incomplete, delayed or diminished, or displays overly strong induction (after the delay) that may cause tissue damage. The affected innate immune response also impacts subsequent adaptive responses, and therefore viral innate immune evasion often undermines fully protective immunity. In this review, innate immune responses relevant for respiratory viruses with an RNA genome will briefly be summarized, and viral innate immune evasion based on shielding viral RNA species away from cellular innate immune sensors will be discussed from different angles. Subsequently, viral enzymatic activities that suppress innate immune responses will be discussed, including activities causing host shut-off and manipulation of stress granule formation. Furthermore, viral protease-mediated immune evasion and viral manipulation of the ubiquitin system will be addressed. Finally, perspectives for use of the reviewed knowledge for the development of novel antiviral strategies will be sketched. url: https://doi.org/10.1159/000503030 doi: 10.1159/000503030 id: cord-327013-gc6o8ou3 author: Kim, Heui Man title: Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea date: 2020-07-06 words: 2361.0 sentences: 142.0 pages: flesch: 41.0 cache: ./cache/cord-327013-gc6o8ou3.txt txt: ./txt/cord-327013-gc6o8ou3.txt summary: title: Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea The Korea Centers for Disease Control and Prevention operates the Korea Influenza and Respiratory Viruses Surveillance System (KINRESS) to monitor epidemics of influenza and Severe Acute Respiratory Infection (SARI) to identify mutated influenza viruses affecting drug resistance, pathogenesis, and transmission. CONCLUSIONS: Our data indicate the utility of monitoring influenza-infected immunocompromised patients in general hospitals for the early detection of emerging neuraminidase inhibitor-resistant viruses and maintaining continuous laboratory surveillance of patients with influenza-like illness in sentinel clinics to monitor the spread of such new variants. If a drug resistance mutation is found in the NA gene, the KINRESS attempts to isolate the virus and perform phenotypic analysis (NA inhibition assay). Here, drug-resistant A(H1N1)pdm09 viruses were detected via the KINRESS in patients with acute hematologic cancer not exhibiting recovery despite oseltamivir and peramivir administration; these were characterized genetically and antigenically following isolation. abstract: BACKGROUND: The emergence of influenza viruses resistant to anti-influenza drugs is a threat to global public health. The Korea Centers for Disease Control and Prevention operates the Korea Influenza and Respiratory Viruses Surveillance System (KINRESS) to monitor epidemics of influenza and Severe Acute Respiratory Infection (SARI) to identify mutated influenza viruses affecting drug resistance, pathogenesis, and transmission. METHODS: Oropharyngeal swab samples were collected from KINRESS and SARI during the 2018–2019 season. The specimens confirmed influenza virus using real-time RT-PCR on inoculated MDCK cells. HA and NA sequences of the influenza viruses were analyzed for phylogeny and mutations. Neuraminidase inhibition and hemagglutination inhibition assays were utilized to characterize the isolates. RESULTS: Two A(H1N1)pdm09 isolates harboring an H275Y substitution in the neuraminidase sequence were detected in patients with acute hematologic cancer. They had prolonged respiratory symptoms, with the virus present in the respiratory tract despite oseltamivir and peramivir treatment. Through the neuraminidase inhibition assay, both viruses were found to be resistant to oseltamivir and peramivir, but not to zanamivir. Although hemagglutinin and neuraminidase phylogenetic analyses suggested that the 2 A(H1N1)pdm09 isolates were not identical, their antigenicity was similar to that of the 2018–19 influenza vaccine virus. CONCLUSIONS: Our data indicate the utility of monitoring influenza-infected immunocompromised patients in general hospitals for the early detection of emerging neuraminidase inhibitor-resistant viruses and maintaining continuous laboratory surveillance of patients with influenza-like illness in sentinel clinics to monitor the spread of such new variants. Finally, characterization of the virus can inform the risk assessment for future epidemics and pandemics caused by drug-resistant influenza viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32631440/ doi: 10.1186/s12985-020-01375-1 id: cord-000114-f0vud3gu author: Kim, Jeong‐Ki title: Ducks: The “Trojan Horses” of H5N1 influenza date: 2009-05-31 words: 5413.0 sentences: 313.0 pages: flesch: 51.0 cache: ./cache/cord-000114-f0vud3gu.txt txt: ./txt/cord-000114-f0vud3gu.txt summary: While the H5N1 HPAI viruses are 100% lethal to chickens and gallinaceous poultry, they often cause asymptomatic infection in some species of domestic and wild ducks. 37 The first indication of the spread of H5N1 HPAI viruses from domestic to wild species of aquatic birds occurred in Kowloon and Penfold Park in Hong Kong, 38 where 19 different duck species were infected. If these wild birds are migratory and experience limited morbidity, they in turn can disperse HPAI viruses widely (Figure 2) , as suggested by the high genetic similarity of HPAI isolates from Africa, Europe, and the Middle East to the Qinghai-H5N1 virus. There is consensus that the migratory waterfowl of the world (predominantly wild ducks) serve as the natural reservoirs of all influenza A viruses, which cause asymptomatic infection in these birds. 51 The continuing co-circulation of multiple subtypes of LPAI viruses in domestic poultry could explain why a small percentage of susceptible domestic species can appear healthy while shedding transmissible levels of H5N1 HPAI virus. abstract: Abstract Wild ducks are the main reservoir of influenza A viruses that can be transmitted to domestic poultry and mammals, including humans. Of the 16 hemagglutinin (HA) subtypes of influenza A viruses, only the H5 and H7 subtypes cause highly pathogenic (HP) influenza in the natural hosts. Several duck species are naturally resistant to HP Asian H5N1 influenza viruses. These duck species can shed and spread virus from both the respiratory and intestinal tracts while showing few or no disease signs. While the HP Asian H5N1 viruses are 100% lethal for chickens and other gallinaceous poultry, the absence of disease signs in some duck species has led to the concept that ducks are the “Trojan horses” of H5N1 in their surreptitious spread of virus. An important unresolved issue is whether the HP H5N1 viruses are maintained in the wild duck population of the world. Here, we review the ecology and pathobiology of ducks infected with influenza A viruses and ducks’ role in the maintenance and spread of HP H5N1 viruses. We also identify the key questions about the role of ducks that must be resolved in order to understand the emergence and control of pandemic influenza. It is generally accepted that wild duck species can spread HP H5N1 viruses, but there is insufficient evidence to show that ducks maintain these viruses and transfer them from one generation to the next. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2749972/ doi: 10.1111/j.1750-2659.2009.00084.x id: cord-282344-o1rkx2z4 author: Kim, Seung Won title: Effects of humidity and other factors on the generation and sampling of a coronavirus aerosol date: 2007-07-25 words: 5076.0 sentences: 277.0 pages: flesch: 54.0 cache: ./cache/cord-282344-o1rkx2z4.txt txt: ./txt/cord-282344-o1rkx2z4.txt summary: The airborne viruses were collected on heating, ventilating, and air conditioning (HVAC) filters in an experimental apparatus and also sampled upstream of these test filters using AGI-30 and BioSampler impinger samplers. To study the effects of relative humidity (RH) on TGEV collection by the filters and samplers, the virus was nebulized into air at 30, 50, 70, and 90% RH. To measure the degree to which the nebulizers generated airborne viruses that could be sampled and remain viable, aerosolization efficiency, g A , was calculated in the same way as Adams et al. The recovery of TGEV from the test filter can be calculated in two ways: (1) relative to the airborne virus concentration, R a , and (2) relative to the nebulizer suspension concentration, R n . TGEV was nebulized, then sampled using AGI-30 impingers and BioSamplers, and finally collected on an HVAC test filter to measure the effects of nebulization stress and the recovery of viable virus from the filter. abstract: Suspensions of transmissible gastroenteritis virus (TGEV), a porcine coronavirus, were nebulized at rates of 0.1–0.2 ml/min into moving air using a Collison nebulizer or a plastic medical nebulizer operating at pressures ranging from 7 to 15 psi. The airborne viruses were collected on heating, ventilating, and air conditioning (HVAC) filters in an experimental apparatus and also sampled upstream of these test filters using AGI-30 and BioSampler impinger samplers. To study the effects of relative humidity (RH) on TGEV collection by the filters and samplers, the virus was nebulized into air at 30, 50, 70, and 90% RH. There were no significant changes in virus titer in the nebulizer suspension before and after nebulization for either nebulizer at any of the pressures utilized. Aerosolization efficiency – the ratio of viable virus sampled with impingers to the quantity of viable virus nebulized – decreased with increasing humidity. BioSamplers detected more airborne virus than AGI-30 samplers at all RH levels. This difference was statistically significant at 30 and 50% RH. Nebulizer type and pressure did not significantly affect the viability of the airborne virus. Virus recovery from test filters relative to the concentration of virus in the nebulizer suspension was less than 10%. The most and the least virus were recovered from filter media at 30% and 90% RH, respectively. The results suggest that TGEV, and perhaps other coronaviruses, remain viable longer in an airborne state and are sampled more effectively at low RH than at high humidity. url: https://www.ncbi.nlm.nih.gov/pubmed/32214623/ doi: 10.1007/s10453-007-9068-9 id: cord-285935-5rsk6g7l author: Kinast, Volker title: Hepatitis E Virus Drug Development date: 2019-05-28 words: 6638.0 sentences: 364.0 pages: flesch: 46.0 cache: ./cache/cord-285935-5rsk6g7l.txt txt: ./txt/cord-285935-5rsk6g7l.txt summary: Cyclic peptides (CP) that had been developed to abrogate interaction of p6Gag and TSG101 and inhibited viral release of HIV Virus like particles (VLPs) [76] were tested for their activity against HEV [77] . The compounds RBV and mycophenolic acid (MPA), both of which target enzymes involved in nucleotide synthesis, are either already used as treatment against HEV or have been reported for their potential to inhibit the virus. So far, the antiviral activity against HEV of only four drugs (Sofosbuvir, pegIFN-α, Ribavirin and silvestrol) was approved in experimental settings beyond in vitro cell culture systems. Sofosbuvir Inhibits Hepatitis E Virus Replication In Vitro and Results in an Additive Effect When Combined With Ribavirin Sofosbuvir shows antiviral activity in a patient with chronic hepatitis E virus infection Zinc Salts Block Hepatitis E Virus Replication by Inhibiting the Activity of Viral RNA-Dependent RNA Polymerase The natural compound silvestrol inhibits hepatitis E virus (HEV) replication in vitro and in vivo abstract: Hepatitis E virus (HEV) is an underestimated disease, leading to estimated 20 million infections and up to 70,000 deaths annually. Infections are mostly asymptomatic but can reach mortality rates up to 25% in pregnant women or become chronic in immunocompromised patients. The current therapy options are limited to the unspecific antivirals Ribavirin (RBV) and pegylated Interferon-α (pegIFN-α). RBV leads to viral clearance in only 80% of patients treated, and is, similar to pegIFN-α, contraindicated in the major risk group of pregnant women, emphasizing the importance of new therapy options. In this review, we focus on the urgent need and current efforts in HEV drug development. We provide an overview of the current status of HEV antiviral research. Furthermore, we discuss strategies for drug development and the limitations of the approaches with respect to HEV. url: https://doi.org/10.3390/v11060485 doi: 10.3390/v11060485 id: cord-264699-l8db5gll author: Kino, Tomoshige title: Virus-mediated modulation of the host endocrine signaling systems: clinical implications date: 2007-06-30 words: 4723.0 sentences: 226.0 pages: flesch: 33.0 cache: ./cache/cord-264699-l8db5gll.txt txt: ./txt/cord-264699-l8db5gll.txt summary: For example, HIV-1-encoded gp120 molecules, which are located on the surface of the viral particle and have a major role in the entry of viruses into target cells, demonstrate amino acid sequence similarity to the growth hormone-releasing hormone (GHRH) receptor of the host and suppress the activation of this receptor by GHRH. In addition to their extracellular actions, many viral molecules act inside infected cells to modulate intracellular host signaling systems, including transcriptional regulation of target genes by hormones. In agreement with these findings, one of the HIV-1 proteins, Vpr, which is a 96-amino acid virion-associated accessory protein that has multiple functions (including influencing transcriptional activity and arresting the cell cycle), increases the effects of GR stimulation by several fold, functioning as a nuclear receptor coactivator in cooperation with a host cell coactivator complex containing p300 or its homolog CREB-binding protein (CBP) [29] [30] [31] [32] . abstract: Viruses, which are among the simplest infective pathogens, can produce characteristic endocrine manifestations in infected patients. In addition to the classic modification of the host endocrine system by either direct or indirect destruction of the endocrine organs and/or effects exerted by systemic production of inflammatory and/or stress mediators, recent progress in molecular virology and endocrinology has revealed that virus-encoded molecules might alter the host endocrine-signaling systems by affecting extracellular and/or intracellular signal transduction and hormone sensitivity of host target tissues. Here, we provide a brief overview of such viral-mediated modulation of host endocrine signaling systems. We propose that virus-encoded molecules and the signaling systems they influence are potential therapeutic targets for the treatment of disorders that are associated with some viral infections. url: https://api.elsevier.com/content/article/pii/S104327600700046X doi: 10.1016/j.tem.2007.03.003 id: cord-257064-iafm3pcc author: Kint, Joeri title: Quantification of Infectious Bronchitis Coronavirus by Titration In Vitro and In Ovo date: 2014-12-18 words: 1809.0 sentences: 156.0 pages: flesch: 63.0 cache: ./cache/cord-257064-iafm3pcc.txt txt: ./txt/cord-257064-iafm3pcc.txt summary: During a titration assay, tissue cultures or embryonated eggs are incubated with tenfold serial dilutions of a virus containing sample and several days later the cytopathic effect is scored. The virus titer is defined as the reciprocal of the dilution at which 50 % of the inoculated embryos or tissue cultures show CPE. Passaging of IBV in either embryonated eggs or primary cell cultures leads to attenuation of the virus in vivo [10] [11] [12] . IBV strains which have been adapted to grow in cultures of primary chicken cells can be titrated on these cells using either the TCID 50 method or plaque titration. Virus titers in the original sample, expressed as 10 log EID 50 /ml are calculated using the method described by Spearman and Kaerber [6, 7] , using the following formula: Plaque formation by infectious bronchitis virus in chicken embryo kidney cell cultures Growth kinetics of embryo-and organ-culture adapted Beaudette strain of infectious bronchitis virus in embryonated chicken eggs abstract: Quantification of the number of infectious viruses in a sample is a basic virological technique. In this chapter we provide a detailed description of three techniques to estimate the number of viable infectious avian coronaviruses in a sample. All three techniques are serial dilution assays, better known as titrations. url: https://doi.org/10.1007/978-1-4939-2438-7_9 doi: 10.1007/978-1-4939-2438-7_9 id: cord-011457-hqxybv1k author: Kirui, James title: Generation and validation of a highly sensitive bioluminescent HIV-1 reporter vector that simplifies measurement of virus release date: 2020-05-19 words: 5612.0 sentences: 249.0 pages: flesch: 46.0 cache: ./cache/cord-011457-hqxybv1k.txt txt: ./txt/cord-011457-hqxybv1k.txt summary: To enable simple and highly sensitive measurement of virus release from transfected cells, we generated HIV-1 reporter viruses in which Nanoluciferase (NanoLuc) was inserted between the MA and CA domains of Gag (Gag-iNanoLuc). We generated viruses using the pNL4-3 Gag-iNanoLuc vector complemented with different ratios of the WT HIV-1 molecular clone pNL4-3 and tested their infectivity by measuring the HIV-1 Tat-driven firefly luciferase activity in TZM-bl cells. These results demonstrate that the Gag-iNanoLuc vector provides a highly sensitive and quantitative tool for measuring the effects of Gag mutations, host cell restriction factors, and small-molecule inhibitors on HIV-1 particle assembly and release. The Gag-NanoLuc fusion protein is expressed in the cell and released at similar levels to WT Gag, thereby enabling simple yet highly sensitive quantification of viral gene expression and virus particle production by measurement of the NanoLuc reporter protein bioluminescent activity in the cell lysates and supernatants. abstract: BACKGROUND: The continued persistence of HIV-1 as a public health concern due to the lack of a cure calls for the development of new tools for studying replication of the virus. Here, we used NanoLuc, a small and extremely bright luciferase protein, to develop an HIV-1 bioluminescent reporter virus that simplifies functional measurement of virus particle production. RESULTS: The reporter virus encodes a Gag protein containing NanoLuc inserted between the matrix (MA) and capsid (CA) domains of Gag, thereby generating virus particles that package high levels of the NanoLuc reporter. We observe that inserting the NanoLuc protein within HIV-1 Gag has minimal impact on Gag expression and virus particle release. We show that the reporter virus recapitulates inhibition of HIV-1 particle release by Gag mutations, the restriction factor tetherin, and the small-molecule inhibitor amphotericin-B methyl ester. CONCLUSION: These results demonstrate that this vector will provide a simple and rapid tool for functional studies of virus particle assembly and release and high-throughput screening for cellular factors and small molecules that promote or inhibit HIV-1 particle production. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7235552/ doi: 10.1186/s12977-020-00521-5 id: cord-005081-kxrzv16n author: Kiselev, O. I. title: Progress in the development of pandemic influenza vaccines and their production technologies date: 2010-11-12 words: 7263.0 sentences: 340.0 pages: flesch: 44.0 cache: ./cache/cord-005081-kxrzv16n.txt txt: ./txt/cord-005081-kxrzv16n.txt summary: We are using the following approaches to the development of industrial production: use of nanoparticles and nanoemulsions as functional adjuvants, construction of totally-safe strains for live attenuated influenza vaccines with deletions of molecular determinants of pathogenicity, application of protein and chemical chaperones to provide self-assembly of haemagglutinin molecules of the H1N1v-2009 virus, and impregnation of whole-virion preparations with nanoparticles to enhance antigenicity. Europe and the United States agreed to allot grants and worked out programs for developing novel technologies and vaccine preparations with improved qualities: a new generation of LAIV, that is, delNS1 vaccines with a limited replicative potential, LAIV with deletions of pathogenicity factors in genes, latest variations of subunit vaccines enhanced by adju vants, and capsid nanovaccines and nanovaccines based on inactivated viruses and virus like particles [14] . A marked breakthrough in the construction of recombinant vaccines is related to the use of insect cells and the obtaining of virus like particles (VLPs) based on baculovirus expression vectors. abstract: This article analyzes the current situation in the field of construction and production of pandemic influenza vaccines. The main task of protecting the population against influenza pandemics requires state-of-the-art approaches to the construction of influenza vaccines to be based on reassortment and genetic engineering techniques, including the analysis of primary structures of influenza viral genes, synthesis and cloning of the main viral genes, reverse genetics techniques, and banks of plasmids bearing basic viral genes. Reassortant technologies are now giving way to new approaches for objective reasons. The state-of-the-art technologies provide safety not only at the laboratories where vaccine viruses are constructed but also make the production process wholly safe. We are using the following approaches to the development of industrial production: use of nanoparticles and nanoemulsions as functional adjuvants, construction of totally-safe strains for live attenuated influenza vaccines with deletions of molecular determinants of pathogenicity, application of protein and chemical chaperones to provide self-assembly of haemagglutinin molecules of the H1N1v-2009 virus, and impregnation of whole-virion preparations with nanoparticles to enhance antigenicity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088289/ doi: 10.1134/s0003683810090024 id: cord-004774-fvf671jn author: Kjeldsberg, Elisabeth title: Detection of astroviruses in gut contents of nude and normal mice date: 1985 words: 1607.0 sentences: 116.0 pages: flesch: 60.0 cache: ./cache/cord-004774-fvf671jn.txt txt: ./txt/cord-004774-fvf671jn.txt summary: Gut contents of nude and normal mice were examined by electron microscopy in association with an outbreak of diarrhea in a colony of nude mice. Gut contents of nude and normal mice were examined by electron microscopy in association with an outbreak of diarrhea in a colony of nude mice. Virus-like particles with a morphology consistent with previous descriptions of astroviruses of other species were demonstrated in a high percentage of the animals. Virus-like particles with a morphology consistent with previous descriptions of astroviruses of other species were demonstrated in a high percentage of the animals. In this note we report the detection of astrovirus-like partieles in gut contents from nude mice, with and without clinical signs of illness, and from normal symptomless mice in association with an outbreak of diarrhea. The morphology of the virus-like particles detected in gut contents of nude and normal mice corresponds to the previous description of astroviruses. abstract: Gut contents of nude and normal mice were examined by electron microscopy in association with an outbreak of diarrhea in a colony of nude mice. Virus-like particles with a morphology consistent with previous descriptions of astroviruses of other species were demonstrated in a high percentage of the animals. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086935/ doi: 10.1007/bf01310560 id: cord-326725-0jgw083h author: Klamroth, Robert title: Pathogen inactivation and removal methods for plasma‐derived clotting factor concentrates date: 2013-09-30 words: 5972.0 sentences: 303.0 pages: flesch: 41.0 cache: ./cache/cord-326725-0jgw083h.txt txt: ./txt/cord-326725-0jgw083h.txt summary: These measures include selection of donors, screening of donations and plasma pools for markers of infection with known viruses, and a manufacturing process with a high capacity to inactivate and/or remove viruses by selected steps validated for their virus reduction capacity. [7] [8] [9] Although screening for viral markers by serology and virus nucleic acid by nucleic acid testing (NAT) ensures that nearly all plasma units entering production are free of HBV, HCV, and HIV, inactivation and removal steps are necessary to reduce any viruses that may enter the plasma pool during a "window period" before markers can be detected. 46 Although B19V was reduced by dry heat in validation studies, the reduction factor may not be sufficient for complete inactivation of the virus load in the final product; asymptomatic B19V infection was detected in a patient who received FVIII concentrate treated at 80°C for 72 hours. abstract: Pathogen safety is crucial for plasma‐derived clotting factor concentrates used in the treatment of bleeding disorders. Plasma, the starting material for these products, is collected by plasmapheresis (source plasma) or derived from whole blood donations (recovered plasma). The primary measures regarding pathogen safety are selection of healthy donors donating in centers with appropriate epidemiologic data for the main blood‐transmissible viruses, screening donations for the absence of relevant infectious blood‐borne viruses, and release of plasma pools for further processing only if they are nonreactive for serologic markers and nucleic acids for these viruses. Despite this testing, pathogen inactivation and/or removal during the manufacturing process of plasma‐derived clotting factor concentrates is required to ensure prevention of transmission of infectious agents. Historically, hepatitis viruses and human immunodeficiency virus have posed the greatest threat to patients receiving plasma‐derived therapy for treatment of hemophilia or von Willebrand disease. Over the past 30 years, dedicated virus inactivation and removal steps have been integrated into factor concentrate production processes, essentially eliminating transmission of these viruses. Manufacturing steps used in the purification of factor concentrates have also proved to be successful in reducing potential prion infectivity. In this review, current techniques for inactivation and removal of pathogens from factor concentrates are discussed. Ideally, production processes should involve a combination of complementary steps for pathogen inactivation and/or removal to ensure product safety. Finally, potential batch‐to‐batch contamination is avoided by stringent cleaning and sanitization methods as part of the manufacturing process. url: https://doi.org/10.1111/trf.12423 doi: 10.1111/trf.12423 id: cord-294585-dl5v9p50 author: Klein, H. G. title: Pathogen‐reduction methods: advantages and limits date: 2009-02-13 words: 4519.0 sentences: 216.0 pages: flesch: 40.0 cache: ./cache/cord-294585-dl5v9p50.txt txt: ./txt/cord-294585-dl5v9p50.txt summary: However, because blood contains numerous labile proteins and fragile cells, and because there is a wide array of potentially infectious agents, no single method of pathogen-inactivation will likely preserve all blood components, yet effectively remove all viruses, bacteria, spores, protozoa and prions. Riboflavin/ultraviolet light treatment has been evaluated in preclinical studies and found to result in reduction of infectivity by many pathogens including west Nile virus, intracellular HIV, bacteria and protozoa. Therapeutic efficacy and safety of platelets treated with a photochemical process for pathogen inactivation: the SPRINT Trial Clinical safety of platelets photochemically treated with amotosalen HCl and ultraviolet A light for pathogen inactivation: the SPRINT trial Fresh frozen plasma prepared with amotosalen HCl (S-59) photochemical pathogen inactivation: transfusion of patients with congenital coagulation factor deficiencies Therapeutic efficacy and safety of red blood cells treated with a chemical process (S-303) for pathogen inactivation: a Phase III clinical trial in cardiac surgery patients abstract: Pathogen‐reduction (inactivation) provides a proactive approach to reducing transfusion‐transmitted infection. Pathogen‐reduction technologies have been successfully implemented by plasma fractionators resulting in no transmission of human immunodeficiency, hepatitis C, or hepatitis B viruses by US‐licensed plasma derivatives since 1987. Fractionation technologies cannot be used to treat cellular blood components. Although blood donor screening, deferral and disease testing have drastically reduced the incidence of transfusion‐transmitted diseases, the threat of new or re‐emerging pathogens remains. Of particular concern is the silent emergence of a new agent with a prolonged latent period in which asymptomatic infected carriers would donate and spread infection. The ultimate goal of pathogen‐inactivation is to reduce transmission of potential pathogens without significantly compromising the therapeutic efficacy of the cellular and protein constituents of blood. The acceptable technology must not introduce toxicities into the blood supply nor result in neoantigen formation and subsequent antibody production. Several promising pathogen‐inactivation technologies are being developed and tested, and others are currently in use, but all of them have limits. Pathogen‐reduction promises an additional ‘layer of protection’ from infectious agents and has the potential to impact the safety of blood transfusions worldwide. url: https://www.ncbi.nlm.nih.gov/pubmed/32328162/ doi: 10.1111/j.1751-2824.2009.01224.x id: cord-020789-slsfhrkx author: Kleines, Michael title: Virale Atemwegserkrankungen – Influenza, RSV und neue Viren date: 2017-10-27 words: 3370.0 sentences: 440.0 pages: flesch: 44.0 cache: ./cache/cord-020789-slsfhrkx.txt txt: ./txt/cord-020789-slsfhrkx.txt summary: Die Bedeutung der entsprechenden Viren ließ sich nur durch die Anwendung moderner molekularer Methoden erkennen, und sie werden auch am besten durch molekulare Verfahren diagnostisch erfasst. In den letzten Jahren hat es eine Weiterentwicklung der verfügbaren Technologien (ausgehend von der für ein einzelnes Virus spezifischen Standard-PCR mit einem Zeitbedarf von 2-3 h) in 2 Richtungen gegeben: Zum einen sind nun Multiplexverfahren verfügbar, die organsystemorientiert alle relevanten Erreger für ein definiertes Krankheitsbild in einem Reaktionsansatz nachweisen können, z. Aber auch für das Management von RSV-Infektionen und Infektio-nen mit anderen respiratorischen Viren deuten sich substanzielle Fortschritte an. Letzter wichtiger Vertreter dieser Reihe, die von Subtypen mit den Hämagglutininkomponenten H5, H7 und H9 dominiert wird, ist ein Influenza-A-Virus vom Subtyp H7N9, das 2013 in China nachgewiesen wurde und eine größere Zahl humaner Infektionen verursacht hat (▶ Tab. 1). Aufgrund von eingeschränkter Sensitivität und Spezifität der Antikörpernachweisverfahren ist der positive Vorhersagewert positiver Antikörpernachweise für eine frische RSV-Infektion gering. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147921/ doi: 10.1055/s-0043-114856 id: cord-339172-210dwhgj author: Knoops, Kèvin title: SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum date: 2008-09-16 words: 9930.0 sentences: 411.0 pages: flesch: 43.0 cache: ./cache/cord-339172-210dwhgj.txt txt: ./txt/cord-339172-210dwhgj.txt summary: Specific þRNA virus replicase subunits are targeted to the membranes of particular cell organelles that are subsequently modified into characteristic structures with which viral RNA synthesis is associated. We used electron microscopy and tomography for the three-dimensional imaging of the membrane alterations induced by severe acute respiratory syndrome (SARS)-coronavirus, a member of the virus group with the largest RNA genome known to date. The lumen of this unique membrane network contains numerous large (diameter 250-300 nm) ''''inner vesicles,'''' which were formerly thought to reside in isolated DMVs. Intriguingly, although the interior of these vesicles does not appear to be connected to the cytosol, it labels abundantly for double-stranded RNA, which presumably is present at the site of viral RNA synthesis. In some of our images, the SARS-CoV-induced CM appeared to be continuous with both DMV outer membranes ( Figure 2D ; inset) and ER cisternae, suggesting a link to the viral RTC also in coronaviruses. abstract: Positive-strand RNA viruses, a large group including human pathogens such as SARS-coronavirus (SARS-CoV), replicate in the cytoplasm of infected host cells. Their replication complexes are commonly associated with modified host cell membranes. Membrane structures supporting viral RNA synthesis range from distinct spherular membrane invaginations to more elaborate webs of packed membranes and vesicles. Generally, their ultrastructure, morphogenesis, and exact role in viral replication remain to be defined. Poorly characterized double-membrane vesicles (DMVs) were previously implicated in SARS-CoV RNA synthesis. We have now applied electron tomography of cryofixed infected cells for the three-dimensional imaging of coronavirus-induced membrane alterations at high resolution. Our analysis defines a unique reticulovesicular network of modified endoplasmic reticulum that integrates convoluted membranes, numerous interconnected DMVs (diameter 200–300 nm), and “vesicle packets” apparently arising from DMV merger. The convoluted membranes were most abundantly immunolabeled for viral replicase subunits. However, double-stranded RNA, presumably revealing the site of viral RNA synthesis, mainly localized to the DMV interior. Since we could not discern a connection between DMV interior and cytosol, our analysis raises several questions about the mechanism of DMV formation and the actual site of SARS-CoV RNA synthesis. Our data document the extensive virus-induced reorganization of host cell membranes into a network that is used to organize viral replication and possibly hide replicating RNA from antiviral defense mechanisms. Together with biochemical studies of the viral enzyme complex, our ultrastructural description of this “replication network” will aid to further dissect the early stages of the coronavirus life cycle and its virus-host interactions. url: https://www.ncbi.nlm.nih.gov/pubmed/18798692/ doi: 10.1371/journal.pbio.0060226 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-336212-ueh4q408 author: Koenig, Kristi L. title: Identify-Isolate-Inform: A Tool for Initial Detection and Management of Zika Virus Patients in the Emergency Department date: 2016-04-04 words: 3597.0 sentences: 207.0 pages: flesch: 52.0 cache: ./cache/cord-336212-ueh4q408.txt txt: ./txt/cord-336212-ueh4q408.txt summary: The identify-isolate-inform (3I) tool, originally conceived for initial detection and management of Ebola virus disease patients in the ED, and later adjusted for measles and Middle East Respiratory Syndrome, can be adapted for real-time use for any emerging infectious disease. This paper describes the adaptation of the identify-isolateinform (3I) tool (initially developed for Ebola virus disease 8, 9 and modified for measles 10 and Middle East Respiratory Syndrome (MERS)) 11 for use in the detection and management of potential Zika virus patients presenting to the ED, including women who are pregnant or contemplating pregnancy, and their partners. The identify-isolate-inform (3I) tool, initially developed for Ebola virus disease and subsequently adapted for measles and MERS, can be modified for the ED evaluation and management of patients under investigation for Zika ( Figure 3 ). The identify-isolate-inform (3I) tool is an instrument that can be used real-time on the front lines to rapidly detect and manage patients at risk for Zika virus disease presenting to the ED. abstract: First isolated in 1947 from a monkey in the Zika forest in Uganda, and from mosquitoes in the same forest the following year, Zika virus has gained international attention due to concerns for infection in pregnant women potentially causing fetal microcephaly. More than one million people have been infected since the appearance of the virus in Brazil in 2015. Approximately 80% of infected patients are asymptomatic. An association with microcephaly and other birth defects as well as Guillain-Barre Syndrome has led to a World Health Organization declaration of Zika virus as a Public Health Emergency of International Concern in February 2016. Zika virus is a vector-borne disease transmitted primarily by the Aedes aegypti mosquito. Male to female sexual transmission has been reported and there is potential for transmission via blood transfusions. After an incubation period of 2–7 days, symptomatic patients develop rapid onset fever, maculopapular rash, arthralgia, and conjunctivitis, often associated with headache and myalgias. Emergency department (ED) personnel must be prepared to address concerns from patients presenting with symptoms consistent with acute Zika virus infection, especially those who are pregnant or planning travel to Zika-endemic regions, as well as those women planning to become pregnant and their partners. The identify-isolate-inform (3I) tool, originally conceived for initial detection and management of Ebola virus disease patients in the ED, and later adjusted for measles and Middle East Respiratory Syndrome, can be adapted for real-time use for any emerging infectious disease. This paper reports a modification of the 3I tool for initial detection and management of patients under investigation for Zika virus. Following an assessment of epidemiologic risk, including travel to countries with mosquitoes that transmit Zika virus, patients are further investigated if clinically indicated. If after a rapid evaluation, Zika or other arthropod-borne diseases are the only concern, isolation (contact, droplet, airborne) is unnecessary. Zika is a reportable disease and thus appropriate health authorities must be notified. The modified 3I tool will facilitate rapid analysis and triggering of appropriate actions for patients presenting to the ED at risk for Zika. url: https://doi.org/10.5811/westjem.2016.3.30188 doi: 10.5811/westjem.2016.3.30188 id: cord-022383-pz0htccp author: Kohn, Dennis F. title: Biology and Diseases of Rats date: 2013-11-17 words: 20181.0 sentences: 1195.0 pages: flesch: 50.0 cache: ./cache/cord-022383-pz0htccp.txt txt: ./txt/cord-022383-pz0htccp.txt summary: The severity and prevalence of clinical disease within an infected colony are associated with environmental conditions that induce stress (e.g., experimental manipulation, overcrowding, fluctuations in ambient temperature and humid ity, and copathogens). Salmonellosis, which was once a major cause of disease in laboratory rat and mouse colonies, is rarely reported in either species today. Mycoplasma pulmonis recently has become recognized as an important pathogen in the female genital tract of rats, and thus is being treated here as a distinct disease rather than as a sequella to MRM. Sendai virus commonly infects laboratory rats, but its clinical significance is less than in mice. Infection is usually diagnosed retrospectively in rats, where pulmonary lesions are observed following seroconversion to PVM in the absence of other respiratory pathogens. This disease, which occurs more fre quently in females, has been reported in numerous strains of rats. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155635/ doi: 10.1016/b978-0-12-263620-2.50010-0 id: cord-352054-g7q2z4l5 author: Kolivoška, Viliam title: Electrophoresis on a microfluidic chip for analysis of fluorescence‐labeled human rhinovirus date: 2007-11-15 words: 3710.0 sentences: 190.0 pages: flesch: 55.0 cache: ./cache/cord-352054-g7q2z4l5.txt txt: ./txt/cord-352054-g7q2z4l5.txt summary: Resolution of the sample constituents (virions, a contaminant present in all virus preparations, and excess dye) was improved upon adaptation of the separation conditions, mainly by adjusting the SDS concentration of the BGE. As the applied instrumentation (a commercial microdevice) utilized a red laser at l ex 630 nm for high-sensitivity detection, virus particles were fluorescence (FL)-labeled prior to analysis and preseparated from the excess of dye by size-exclusion chromatography (SEC). Separation from a contaminant, which also becomes labeled upon reaction of the virus sample with reactive Cy5, and from the excess free dye was improved by addition of SDS and varying its concentration in the BGE. Chip electrophoresis with the finally selected BGE (100 mM borate buffer, pH 8.3, containing 3.1 mM SDS), enabled an extremely rapid assessment of virus purity, and the investigation of bioaffinity reactions of labeled virus with a number of soluble artificial receptor fragments. abstract: We report the analysis of human rhinovirus serotype 2 (HRV2) on a commercially available lab‐on‐a‐chip instrument. Due to lack of sufficient native fluorescence, the proteinaceous capsid of HRV2 was labeled with Cy5 for detection by the red laser (λ (ex) 630 nm) implemented in the instrument. On the microdevice, electrophoresis of the labeled virus was possible in a BGE without stabilizing detergents, which is in contrast to conventional CE; moreover, analysis times were drastically shortened to the few 10 s range. Resolution of the sample constituents (virions, a contaminant present in all virus preparations, and excess dye) was improved upon adaptation of the separation conditions, mainly by adjusting the SDS concentration of the BGE. Purity of fractions from size‐exclusion chromatography after labeling of virus was assessed, and affinity complex formation of the labeled virus with various recombinant very‐low‐density lipoprotein receptor derivatives differing in the number of concatenated V3 ligand binding repeats was monitored. Virus analysis on microchip devices is of particular interest for experiments with infectious material because of easy containment and disposal of samples. Thus, the employment of microchip devices in routine analysis of viruses appears to be exceptionally attractive. url: https://www.ncbi.nlm.nih.gov/pubmed/18008310/ doi: 10.1002/elps.200700397 id: cord-259505-7hiss0j3 author: Kong, Qingming title: Proteomic analysis of purified coronavirus infectious bronchitis virus particles date: 2010-06-09 words: 6907.0 sentences: 355.0 pages: flesch: 44.0 cache: ./cache/cord-259505-7hiss0j3.txt txt: ./txt/cord-259505-7hiss0j3.txt summary: It is an important prerequisite for the functional studies to know the protein composition of the purified viral particles, as it allows the analysis of specific proteins and their roles during the virus life cycle, resulting in better understanding of the infection process and the pathogenesis of viruses. To date, there have been no reports about TENP associated with virus, but it''s an enriched and abundant protein identified in purified infectious bronchitis particles which suggests to us that it may be a requisite host protein in IBV life cycles. The present study 1) provides the first proteomic analysis of infectious bronchitis particles, 2) establishes the most comprehensive proteomic index of IBV and 3) shows that most of the virion incorporated host proteins have central roles in virus life cycle. abstract: BACKGROUND: Infectious bronchitis virus (IBV) is the coronavirus of domestic chickens causing major economic losses to the poultry industry. Because of the complexity of the IBV life cycle and the small number of viral structural proteins, important virus-host relationships likely remain to be discovered. Toward this goal, we performed two-dimensional gel electrophoresis fractionation coupled to mass spectrometry identification approaches to perform a comprehensive proteomic analysis of purified IBV particles. RESULTS: Apart from the virus-encoded structural proteins, we detected 60 host proteins in the purified virions which can be grouped into several functional categories including intracellular trafficking proteins (20%), molecular chaperone (18%), macromolcular biosynthesis proteins (17%), cytoskeletal proteins (15%), signal transport proteins (15%), protein degradation (8%), chromosome associated proteins (2%), ribosomal proteins (2%), and other function proteins (3%). Interestingly, 21 of the total host proteins have not been reported to be present in virions of other virus families, such as major vault protein, TENP protein, ovalbumin, and scavenger receptor protein. Following identification of the host proteins by proteomic methods, the presence of 4 proteins in the purified IBV preparation was verified by western blotting and immunogold labeling detection. CONCLUSIONS: The results present the first standard proteomic profile of IBV and may facilitate the understanding of the pathogenic mechanisms. url: https://www.ncbi.nlm.nih.gov/pubmed/20534109/ doi: 10.1186/1477-5956-8-29 id: cord-253594-9gbo8viu author: Konieczny, Leszek title: The COVID-19 Puzzle date: 2020-05-31 words: 1366.0 sentences: 90.0 pages: flesch: 49.0 cache: ./cache/cord-253594-9gbo8viu.txt txt: ./txt/cord-253594-9gbo8viu.txt summary: From the epidemiological perspective, an important factor affecting the spread of the virus is the proximity between infection targets. The bacterial genome includes a repository of viral genetic sequences -effectively a "catalogue" of known viruses. Its effects appear to depend on the carrier''s age: many people, particularly young ones, remain asymptomatic, while older individuals frequently develop serious -even life-threateningsymptoms. Variable susceptibility to infection may be a consequence of the general state of health, which, of course, depends on the individual''s age and co-morbidities -particularly metabolic ones (e.g. diabetes). Since the virus preferentially attacks the lungs, we can point to tobacco smoking as a factor, which promotes infection by damaging lung tissue. One mechanism which exhibits clear susceptibility to external disruption (including the presence of unusual substances) is protein folding. Genetic polymorphism undoubtedly results in individual variability, including well-known differences in alcohol tolerance. abstract: Viral diseases have affected humans since the dawn of humanity. Smallpox-now eradicated by vaccinations-serves as a particularly poignant example. More recently, the Spanish flu outbreak claimed a heavy toll in the early 20th century. The ongoing coronavirus pandemic appears no less threatening. The possible reason of highly variable course of disease is discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/32831524/ doi: 10.6026/97320630016418 id: cord-315781-dejh8q22 author: Konishi, Tomokazu title: Re-evaluation of the evolution of influenza H1 viruses using direct PCA date: 2019-12-17 words: 4590.0 sentences: 308.0 pages: flesch: 65.0 cache: ./cache/cord-315781-dejh8q22.txt txt: ./txt/cord-315781-dejh8q22.txt summary: It should be noted that avian viruses showed lower PC values and appeared around the centre of the PCA, while swine and human viruses exhibited extreme values (Figs. Thus, avian viruses had sequences that were similar to the average among samples at amino acids that were characteristic to the three groups of human and swine viruses: R, M, and U. Avian samples also showed characteristic motifs at other positions, which may appear in lower PCs. The relationships observed among the strains presented here are different from the classic ones 4, [8] [9] [10] [11] [12] in several elements. www.nature.com/scientificreports www.nature.com/scientificreports/ One of the major differences observed was the direct shift from avian to swine or human viruses. Drifts and spreading: the genomes of the R group of human viruses have been changing yearly (Figs. abstract: The history of influenza H1 virus was re-evaluated by applying a new methodology to sequencing data; this objective method enables comparisons among viral types. The approach led to the segregation of all segments of swine and human viruses into three distinct groups: two of them included the pandemic 1977 and 2009 human viruses, and the remaining group may be new in humans. These three groups might have originated from avian viruses and drifted out independently. Genome shifts occurred occasionally among swine viruses; however, distances between avian and swine/human viruses negated the existence of direct shifts from avian viruses. In humans, only one or two viruses appeared each year, which suggests the presence of competition among viruses that migrated freely. All segments drifted continuously under certain rules and constant velocity. Viruses that had caused an outbreak did not appear again over subsequent decades, which may mean populations had become immune to such viruses. In contrast, the viruses in livestock were rather conserved and maintained unique strains in small, separate areas. Such collections of swine strains included human segments, which could become an epidemic in the future. url: https://doi.org/10.1038/s41598-019-55254-z doi: 10.1038/s41598-019-55254-z id: cord-257553-479x7av6 author: Kortepeter, Mark G. title: Health Care Workers and Researchers Traveling to Developing-World Clinical Settings: Disease Transmission Risk and Mitigation date: 2010-12-01 words: 3967.0 sentences: 217.0 pages: flesch: 39.0 cache: ./cache/cord-257553-479x7av6.txt txt: ./txt/cord-257553-479x7av6.txt summary: title: Health Care Workers and Researchers Traveling to Developing-World Clinical Settings: Disease Transmission Risk and Mitigation This review provides practical advice for this special population of travelers, targeted to specific health care-related risks (needlestick, hemorrhagic fever viruses, severe viral respiratory disease, and tuberculosis), with suggestions for risk mitigation. Although no prophylaxis for hepatitis C virus (HCV) exposure exists, the needlestick transmission risk is lower (1.8%), and up to 20% of transmitted infections resolve spontaneously. The Centers for Disease Control and Prevention (CDC) recommends a 3-drug PEP regimen if the source patient is known to be infected with HIV and the source device is a hollow-bore needle or has visible blood contamination. During the pandemic, transmission to HCWs occurred after close, unprotected contact with symptomatic persons and was significantly mitigated once infection-control precautions were implemented; the degree of risk was related to the type and intensity of exposure (endotracheal intubation was significantly associated with contracting SARS) [27, 28] . abstract: With the recent emphasis on funding and training opportunities for global health and humanitarian aid and the increased interest in the field, many health care workers and medical researchers are traveling from resource-replete to resource-limited settings. This type of travel brings unique disease risks not routinely considered for the business or vacationing traveler. This review provides practical advice for this special population of travelers, targeted to specific health care-related risks (needlestick, hemorrhagic fever viruses, severe viral respiratory disease, and tuberculosis), with suggestions for risk mitigation. url: https://doi.org/10.1086/657115 doi: 10.1086/657115 id: cord-008556-oetrdm8g author: Kozak, Marilyn title: Regulation of Protein Synthesis in Virus-Infected Animal Cells date: 2008-03-01 words: 23945.0 sentences: 1270.0 pages: flesch: 51.0 cache: ./cache/cord-008556-oetrdm8g.txt txt: ./txt/cord-008556-oetrdm8g.txt summary: One consequence of the scanning mechanism is that deleting the "ribosome binding site" (i.e., the normal initiator codon and flanking sequences) will not abolish translation; ribosomes will simply use the next AUG codon downstream, which, in some cases, has been shown to direct the synthesis of a biologically active, truncated protein (Downey et al., 1984; Halpern and Smiley, 1984; Katinka and Yaniv, 1982) . The best evidence for this is the ability of both EMC and SFV 26 S mRNA to be translated in EMC virus-infected cells, in which host translation is drastically inhibited by a mechanism that has not been difined, but that clearly does not involve cap binding protein (Mosenkis et al., 1985) . In wild-type adenovirus-infected cells, in which host protein synthesis is drastically reduced, both adenovirus and influenza virus mRNAs are translated efficiently. abstract: This chapter summarizes the structural features that govern the translation of viral mRNAs: where the synthesis of a protein starts and ends, how many proteins can be produced from one mRNA, and how efficiently. It focuses on the interplay between viral and cellular mRNAs and the translational machinery. That interplay, together with the intrinsic structure of viral mRNAs, determines the patterns of translation in infected cells. It also points out some possibilities for translational regulation that can only be glimpsed at present, but are likely to come into focus in the future. The mechanism of selecting the initiation site for protein synthesis appears to follow a single formula. The translational machinery displays a certain flexibility that is exploited more frequently by viral than by cellular mRNAs. Although some of the parameters that determine efficiency have been identified, how efficiently a given mRNA will be translated cannot be predicted by summing the known parameters. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7131717/ doi: 10.1016/s0065-3527(08)60265-1 id: cord-021413-1ht1xm88 author: Kraft, Lisbeth M. title: Viral Diseases of the Digestive System date: 2013-10-21 words: 14259.0 sentences: 882.0 pages: flesch: 51.0 cache: ./cache/cord-021413-1ht1xm88.txt txt: ./txt/cord-021413-1ht1xm88.txt summary: Runner and Palm (1953) , studying C3H mice, indicated that there was a higher incidence of diarrhea in December/January (Kraft, 1961; Blackwell et al., 1966) , complement fixation (Wilsnack et al., 1969; Kapikian et al, 1976; Thouless et al., 1977b) , direct immunofluorescent staining or precipitin (Wilsnack et al., 1969; Spence et al., 1975; Foster α/., 1975; Peterson α/., 1976) , immune electron microscopy (Kapikian et al., 1974; Bridger and Woode, 1975) , immunoelectroosmophoresis (Tufvesson and Johnsson, 1976; Middleton et al., 1976) , enzyme-linked im munosorbent assay (ELISA) (Scherrer and Bernard, 1977; El lens etal., 1978; Yolken etal., 1978a,b,c) , radioimmunoas say (Acres and Babiuk, 1978; Kalica et al., 1977; Middleton et al., 1977) , immunodiffusion (Woode et al., 1976) , hemagglutination inhibition (Fauvel et al., 1978) , enzymelinked fluorescence assay (ELISA) (Yolken and Stopa, 1979) , an unlabeled soluble enzyme peroxidase-antiperoxidase method , plaque reduction test (Estes and Graham, 1980) , serologic trapping on antibody-coated electron microscope grids (Nicolaieff et al., 1980) , a solid phase system (SPACE, solid phase aggregation of coupled erythrocytes) for detection of rotaviruses in feces (Bradbume et al., 1979) , and immune electron microscopy with serum in agar diffusion (Lamontagne et al., 1980) . abstract: This chapter discusses three virus infections affecting the digestive system of mice and their properties: (1) epizootic diarrhea of infant mice (EDIM), (2) reovirus 3 infection, and (3) murine hepatitis virus infection (MHV). All three infections may cause serious, debilitating, and sometimes fatal diarrheal disease in nursling and weanling mice. Mice of all ages can be infected by the EDIM virus but overt disease is restricted to animals up to about 12–13 days of age at the time of first exposure. The EDIM virus is worldwide in distribution. Its prevalence is difficult to estimate because serologic tests have not been readily available, and it is not customary to sacrifice animals for the purpose of examining the appearance of their intestinal tract or for electron microscopic visualization of fecal contents. The acute disease of reovirus 3 infection affects mainly sucklings and weanlings, whereas the chronic disease is encountered in animals over 28 days of age. The MHV virus, on the other hand, has been found to affect cotton rats, rats, and hamsters. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149642/ doi: 10.1016/b978-0-12-262502-2.50016-x id: cord-000933-nn9gj0z1 author: Krzyzaniak, Magdalena Anna title: Host Cell Entry of Respiratory Syncytial Virus Involves Macropinocytosis Followed by Proteolytic Activation of the F Protein date: 2013-04-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Respiratory Syncytial Virus (RSV) is a highly pathogenic member of the Paramyxoviridae that causes severe respiratory tract infections. Reports in the literature have indicated that to infect cells the incoming viruses either fuse their envelope directly with the plasma membrane or exploit clathrin-mediated endocytosis. To study the entry process in human tissue culture cells (HeLa, A549), we used fluorescence microscopy and developed quantitative, FACS-based assays to follow virus binding to cells, endocytosis, intracellular trafficking, membrane fusion, and infection. A variety of perturbants were employed to characterize the cellular processes involved. We found that immediately after binding to cells RSV activated a signaling cascade involving the EGF receptor, Cdc42, PAK1, and downstream effectors. This led to a series of dramatic actin rearrangements; the cells rounded up, plasma membrane blebs were formed, and there was a significant increase in fluid uptake. If these effects were inhibited using compounds targeting Na(+)/H(+) exchangers, myosin II, PAK1, and other factors, no infection was observed. The RSV was rapidly and efficiently internalized by an actin-dependent process that had all hallmarks of macropinocytosis. Rather than fusing with the plasma membrane, the viruses thus entered Rab5-positive, fluid-filled macropinosomes, and fused with the membranes of these on the average 50 min after internalization. Rab5 was required for infection. To find an explanation for the endocytosis requirement, which is unusual among paramyxoviruses, we analyzed the fusion protein, F, and could show that, although already cleaved by a furin family protease once, it underwent a second, critical proteolytic cleavage after internalization. This cleavage by a furin-like protease removed a small peptide from the F1 subunits, and made the virus infectious. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3623752/ doi: 10.1371/journal.ppat.1003309 id: cord-003232-nquw7qga author: Kuchipudi, Suresh V. title: Novel Flu Viruses in Bats and Cattle: “Pushing the Envelope” of Influenza Infection date: 2018-08-06 words: 3837.0 sentences: 214.0 pages: flesch: 45.0 cache: ./cache/cord-003232-nquw7qga.txt txt: ./txt/cord-003232-nquw7qga.txt summary: This review examines the recent discovery of novel influenza viruses in bats and cattle, the evolving complexity of influenza virus host range including the ability to cross species barriers and geographic boundaries, and implications to animal and human health. In addition, we discussed the growing complexity of influenza virus-host interactions and highlighted the key research questions that need to be answered for a better understanding of the emergence of pandemic influenza viruses. Ability to infect a wide range hosts is a key contributing factor to the complex and seemingly expanding genetic diversity of IAVs. It is now well established that IAVs infect domestic pets such as dogs and cats, adding to the list of host species that could potentially expose humans to influenza viruses. Although influenza viruses infect humans and a wide range of animals and birds, cattle were never considered to be susceptible to influenza virus infection. abstract: Influenza viruses are among the major infectious disease threats of animal and human health. This review examines the recent discovery of novel influenza viruses in bats and cattle, the evolving complexity of influenza virus host range including the ability to cross species barriers and geographic boundaries, and implications to animal and human health. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6165133/ doi: 10.3390/vetsci5030071 id: cord-329145-424vv8a8 author: Kuhn, Jens H. title: Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae date: 2012-09-23 words: 5519.0 sentences: 229.0 pages: flesch: 40.0 cache: ./cache/cord-329145-424vv8a8.txt txt: ./txt/cord-329145-424vv8a8.txt summary: Suffixes are proposed for individual names that clarify whether a given genetic variant has been characterized based on passage zero material (-wt), has been passaged in tissue/cell culture (-tc), is known from consensus sequence fragments only (-frag), or does (most likely) not exist anymore (-hist). Unfortunately, most ICTV Study Groups or other expert groups have not provided clear guidelines in the past, accepting strain and genetic variant names as they were suggested by different researchers in their publications rather than creating consistent nomenclature schemes that apply at least to all viruses of one family. To differentiate uncultured or passage 0 filoviruses for which near-complete genomic data are available from those that exist in culture, we propose to follow the suggestions of the Rotavirus Classification Working Group and to add the suffix ''''-wt'''' (for ''''wild-type'''') to their genetic variant names as outlined above. abstract: The task of international expert groups is to recommend the classification and naming of viruses. The International Committee on Taxonomy of Viruses Filoviridae Study Group and other experts have recently established an almost consistent classification and nomenclature for filoviruses. Here, further guidelines are suggested to include their natural genetic variants. First, this term is defined. Second, a template for full-length virus names (such as “Ebola virus H.sapiens-tc/COD/1995/Kikwit-9510621”) is proposed. These names contain information on the identity of the virus (e.g., Ebola virus), isolation host (e.g., members of the species Homo sapiens), sampling location (e.g., Democratic Republic of the Congo (COD)), sampling year, genetic variant (e.g., Kikwit), and isolate (e.g., 9510621). Suffixes are proposed for individual names that clarify whether a given genetic variant has been characterized based on passage zero material (-wt), has been passaged in tissue/cell culture (-tc), is known from consensus sequence fragments only (-frag), or does (most likely) not exist anymore (-hist). We suggest that these comprehensive names are to be used specifically in the methods section of publications. Suitable abbreviations, also proposed here, could then be used throughout the text, while the full names could be used again in phylograms, tables, or figures if the contained information aids the interpretation of presented data. The proposed system is very similar to the well-known influenzavirus nomenclature and the nomenclature recently proposed for rotaviruses. If applied consistently, it would considerably simplify retrieval of sequence data from electronic databases and be a first important step toward a viral genome annotation standard as sought by the National Center for Biotechnology Information (NCBI). Furthermore, adoption of this nomenclature would increase the general understanding of filovirus-related publications and presentations and improve figures such as phylograms, alignments, and diagrams. Most importantly, it would counter the increasing confusion in genetic variant naming due to the identification of ever more sequences through technological breakthroughs in high-throughput sequencing and environmental sampling. url: https://doi.org/10.1007/s00705-012-1454-0 doi: 10.1007/s00705-012-1454-0 id: cord-317501-yblzopc3 author: Kuhn, Philipp title: Recombinant antibodies for diagnostics and therapy against pathogens and toxins generated by phage display date: 2016-06-21 words: 11086.0 sentences: 593.0 pages: flesch: 35.0 cache: ./cache/cord-317501-yblzopc3.txt txt: ./txt/cord-317501-yblzopc3.txt summary: Panning against peptides, recombinant viral proteins, or complete virus particles has led to the identification of antibodies directed against human pathogenic viruses such as Sin nombre virus [100] , Dengue virus [101, 102] , Influenza virus [103, 104] , VEEV [105] , Norovirus [106] , SARS coronavirus [107] , or Hepatitis C [108] from naïve antibody gene libraries. A naïve human Fab-phage library was screened for NS5-specific antibody fragments using various NS5 variants from Dengue Virus serotypes 1-4 as antigens for panning and characterization [128] . [180] reported the isolation of a human monoclonal antibody against the Block 2 region of Plasmodium falciparum merozoite surface protein-1 (PfMSP-1) by phage display from a malaria patient derived scFv library. In this context, the antibody phage display offers a powerful tool for antibody selection and allows the isolation of neutralizing antibodies against complete active toxins or special domains by using different human naïve antibody libraries with high diversity [185] [186] [187] . Single chain variable fragment antibodies against Shiga toxins isolated from a human antibody phage display library abstract: Antibodies are valuable molecules for the diagnostic and treatment of diseases caused by pathogens and toxins. Traditionally, these antibodies are generated by hybridoma technology. An alternative to hybridoma technology is the use of antibody phage display to generate recombinant antibodies. This in vitro technology circumvents the limitations of the immune system and allows—in theory—the generation of antibodies against all conceivable molecules. Phage display technology enables obtaining human antibodies from naïve antibody gene libraries when either patients are not available or immunization is not ethically feasible. On the other hand, if patients or immunized/infected animals are available, it is common to construct immune phage display libraries to select in vivo affinity‐matured antibodies. Because the phage packaged DNA sequence encoding the antibodies is directly available, the antibodies can be smoothly engineered according to the requirements of the final application. In this review, an overview of phage display derived recombinant antibodies against bacterial, viral, and eukaryotic pathogens as well as toxins for diagnostics and therapy is given. url: https://www.ncbi.nlm.nih.gov/pubmed/27198131/ doi: 10.1002/prca.201600002 id: cord-327855-txryqil7 author: Kulka, M. title: The cytopathic 18f strain of Hepatitis A virus induces RNA degradation in FrhK4 cells date: 2003 words: 8706.0 sentences: 394.0 pages: flesch: 50.0 cache: ./cache/cord-327855-txryqil7.txt txt: ./txt/cord-327855-txryqil7.txt summary: Analysis of total cellular RNA from HM175/18f infected FrhK4 cells by denaturing agarose gel electrophoresis and Northern blot hybridization revealed extensive degradation of both the 28S and 18S ribosomal RNA (rRNA) molecules. In this study, we report that infection of FrhK4 cells with the HAV cp strain HM175/18f results in the degradation of ribosomal RNA (rRNA) and the reduction of several cellular mRNAs including β-actin and GAPDH. Degradation of rRNA is a feature of virus infection in interferon (IFN) treated cells and is believed to be due to the availability of double stranded RNA (dsRNA) during replication or transcription of the viral genome, resulting in the activation of the RNase L pathway [58, 59] . While the role of a viral protein in the activation of 2-5A/RNase L pathway in 18f or CBV1 infected FrhK4 cells cannot be ruled out, previous reports with EMC virus and the studies involving dsRNA clearly suggests a similar mechanism of rRNA degradation reported here. abstract: The mechanism responsible for the induction of apoptosis by the rapidly replicating HM175/18f strain of Hepatitis A virus (HAV) was investigated. Full length HAV RNA and viral capsid protein VP1 were detected in 18f infected cells at earlier times post-infection than in HM175/clone 1 infected cells. Analysis of total cellular RNA from HM175/18f infected FrhK4 cells by denaturing agarose gel electrophoresis and Northern blot hybridization revealed extensive degradation of both the 28S and 18S ribosomal RNA (rRNA) molecules. Similar degradation was observed when these cells were infected with Human coxsackievirus B1, a fast replicating enterovirus. In contrast, the parental strain of 18f, HM175/clone 1 did not induce RNA degradation. Inhibition of RNA degradation correlated with inhibition of virus replication. The pattern of rRNA degradation resembled degradation of rRNAs by RNase L, an enzyme activated in interferon-treated cells following infection with certain viruses. Ribosomal RNA degradation was accompanied by the reduction in the levels of several cellular RNAs including those for β-actin and glyceraldehyde-3-phosphate dehydrogenase, while the levels of c-myc and c-jun were higher. Interferon mRNAs could not be detected in either infected or mock-infected control cells, and STAT1, a key regulator of interferon action was not phosphorylated following virus infection. These results reveal a heretofore-undescribed pathway that involves the regulation of RNA degradation and apoptosis following HAV/18f replication in FrhK4 cells. url: https://www.ncbi.nlm.nih.gov/pubmed/12827461/ doi: 10.1007/s00705-003-0110-0 id: cord-283880-lrrkuist author: Kumar, Arvind title: Evolution of selective-sequencing approaches for virus discovery and virome analysis date: 2017-07-15 words: 5934.0 sentences: 286.0 pages: flesch: 38.0 cache: ./cache/cord-283880-lrrkuist.txt txt: ./txt/cord-283880-lrrkuist.txt summary: Use of sequence dependent (i.e; generic PCR assays and microarray) and sequence independent (i.e; single primer amplification (SISPA) and random priming) approaches for nucleic acid amplification combined with Sanger sequencing or HTS allowed the rapid identification of new viruses after 1980 (Bishop-Lilly et al., 2010; Chang et al., 1994; Day et al., 2010; Grard et al., 2012; Kapoor et al., 2015; Ladner et al., 2016; Linnen et al., 1996; Matsui et al., 1991; Mokili et al., 2012; Muerhoff et al., 1997; Nichol et al., 1993; Qin et al., 2014; Quan et al., 2010; Simons et al., 1995b) (Fig. 1) . For the virome analysis of clinical samples with an abundance of host cells, like blood or tissues, pre-extraction based enrichment is not appropriate as the virus genome itself can be present in its non-capsidated or transcribed form. In positive selection methods, samples are enriched for viral nucleic acids directly using probes targeting the viruses like in PCR assays, microarray or virus capture (in solution based hybridization) approaches. abstract: Abstract Recent advances in sequencing technologies have transformed the field of virus discovery and virome analysis. Once mostly confined to the traditional Sanger sequencing based individual virus discovery, is now entirely replaced by high throughput sequencing (HTS) based virus metagenomics that can be used to characterize the nature and composition of entire viromes. To better harness the potential of HTS for the study of viromes, sample preparation methodologies use different approaches to exclude amplification of non-viral components that can overshadow low-titer viruses. These virus-sequence enrichment approaches mostly focus on the sample preparation methods, like enzymatic digestion of non-viral nucleic acids and size exclusion of non-viral constituents by column filtration, ultrafiltration or density gradient centrifugation. However, recently a new approach of virus-sequence enrichment called virome-capture sequencing, focused on the amplification or HTS library preparation stage, was developed to increase the ability of virome characterization. This new approach has the potential to further transform the field of virus discovery and virome analysis, but its technical complexity and sequence-dependence warrants further improvements. In this review we discuss the different methods, their applications and evolution, for selective sequencing based virome analysis and also propose refinements needed to harness the full potential of HTS for virome analysis. url: https://www.sciencedirect.com/science/article/pii/S0168170216305986 doi: 10.1016/j.virusres.2017.06.005 id: cord-294323-mryiqmsw author: Kumar, Binod title: The emerging influenza virus threat: status and new prospects for its therapy and control date: 2018-01-10 words: 8201.0 sentences: 390.0 pages: flesch: 43.0 cache: ./cache/cord-294323-mryiqmsw.txt txt: ./txt/cord-294323-mryiqmsw.txt summary: The wide range of hosts provides influenza A viruses greater chances of genetic re-assortment, leading to the emergence of zoonotic strains and occasional pandemics that have a severe impact on human life. Here, we primarily discuss the pathogenesis of influenza virus type A, its epidemiology, pandemic potential, current status of antiviral drugs and vaccines, and ways to effectively manage the disease during a crisis. A genetic shift occurs when two or more different influenza virus strains infect the same cell in a host, leading to recombination of genetic materials, an event that occasionally generates a new strain with a novel combination of hemagglutinin and neuraminidase. The antiviral drugs currently available against influenza viruses are adamantane derivatives (amantadine and rimantadine) and neuraminidase (NA) inhibitors (zanamivir, oseltamivir and peramivir). Due to the increasing burden of vaccine formulations and cases of antiviral-drug-resistant influenza virus isolates turning up every year, it has become necessary to search for alternatives to the current treatment and prevention strategies. abstract: Influenza A viruses (IAVs) are zoonotic pathogens that cause yearly outbreaks with high rates of morbidity and fatality. The virus continuously acquires point mutations while circulating in several hosts, ranging from aquatic birds to mammals, including humans. The wide range of hosts provides influenza A viruses greater chances of genetic re-assortment, leading to the emergence of zoonotic strains and occasional pandemics that have a severe impact on human life. Four major influenza pandemics have been reported to date, and health authorities worldwide have shown tremendous progress in efforts to control epidemics and pandemics. Here, we primarily discuss the pathogenesis of influenza virus type A, its epidemiology, pandemic potential, current status of antiviral drugs and vaccines, and ways to effectively manage the disease during a crisis. url: https://doi.org/10.1007/s00705-018-3708-y doi: 10.1007/s00705-018-3708-y id: cord-320935-3n157yl4 author: Kumar, Manish title: Making Waves Perspectives of Modelling and Monitoring of SARS-CoV-2 in Aquatic Environment for COVID-19 Pandemic date: 2020-09-12 words: 6613.0 sentences: 346.0 pages: flesch: 44.0 cache: ./cache/cord-320935-3n157yl4.txt txt: ./txt/cord-320935-3n157yl4.txt summary: This paper aims to collate information on recent developments on WBE in monitoring the trend of community-scale SARS-CoV-2 prevalence as well as models to predict virus spread and transmission among populations. While several studies have identified the presence of SARS-CoV-2 in the faecal matter of corona-infected patients [35, 36] , there is a growing concern on the transmission of the virus through water treatment plants (WTPs) and WWTPs. Several studies also detected the genetic material of the virus in raw wastewater across the globe [22, 26, 27] . These studies provided enough excellent reasons for modelling the spread of 2019-nCoV with the external environmental conditions, assuming that the cases of infection will decrease through secondary infection routes due to the inactivation of the virus on different surfaces; however, the possibility of transmission via direct contact remains unchanged. abstract: Prevalence of SARS-CoV-2 in the aquatic environment pertaining to the COVID-19 pandemic has been a global concern. Though SARS-CoV-2 is known as a respiratory virus, its detection in faecal matter and wastewater demonstrates its enteric involvement resulting in vulnerable aquatic environment. Here, we provide the latest updates on wastewater-based epidemiology, which is gaining interest in the current situation as a unique tool of surveillance and monitoring of the disease. Transport pathways with its migration through wastewater to surface and subsurface waters, probability of infectivity and ways of inactivation of SARS-CoV-2 are discussed in detail. Epidemiological models, especially compartmental projections, have been explained with an emphasis on its limitation and the assumptions on which the future predictions of disease propagation are based. Besides, this review covers various predictive models to track and project disease spread in the future and gives an insight into the probability of a future outbreak of the disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32953402/ doi: 10.1007/s40726-020-00161-5 id: cord-278099-ypov9ha3 author: Kumar, Surender title: Molecular characterization of a novel cryptic virus infecting pigeonpea plants date: 2017-08-03 words: 11403.0 sentences: 622.0 pages: flesch: 55.0 cache: ./cache/cord-278099-ypov9ha3.txt txt: ./txt/cord-278099-ypov9ha3.txt summary: The four dsRNAs eluted from the agarose gel were purified and have been used as templates for RT-PCR amplification employed in SISPA to generate fulllength cDNAs. It is of interest to examine if ArCV-1 RNA dependent RNA polymerase (RdRp) structurally resembles the known RdRp of the dsRNA bacteriophage Փ-6, reovirus, or with other viruses like calciviruses and picornaviruses [12] [13] [14] [15] [16] . We report here the results of elaborated computer-assisted analysis of ArCV-1 replicase which revealed the presence of conserved sequence motifs (A to G) present in the fingers and palm subdomains of the polymerase that are shared in most of the RdRps. Interestingly, ArCV-1 replicase has more structural resemblances with several members of ssRNA (+) mono-partite Picornaviruses (viral replication by primer-dependent initiation), than the de novo dsRNA bacteriophage Փ-6 and reovirus polymerases. Possible functions of the residues of the A to G motifs described for identical RdRps was conserved with respect to the ArCV-1 3Dpol structure and was discussed in structural analysis of ArCVTable 1 ) and the 3'' terminus contained the sequence "GCA CCCATATTC". abstract: A new member of the genus Deltapartitivirus was identified containing three dsRNAs with an estimated size of 1.71, 1.49 and 1.43 kb. The dsRNAs were extracted from symptomless pigeonpea [Cajanus cajan (L.) Millspaugh] plants cv. Erra Kandulu. This new virus with 4.64 kb genome was tentatively named Arhar cryptic virus-1 (ArCV-1). The genomic RNAs were amplified and characterized by sequence independent single primer amplification. The dsRNAs shared a highly conserved 16 nt 5’ non-coding region (5’-GATAATGATCCAAGGA-3’). The largest dsRNA (dsRNA-1) was identified as the viral RNA dependent RNA polymerase (replicase), predicted to encode a putative 55.34 kDa protein (P1). The two other smaller dsRNAs (dsRNA-2 and dsRNA-3) predicted to encode for putative capsid proteins of 38.50kDa (P2) and 38.51kDa (P3), respectively. Phylogenetic analysis indicated that ArCV-1 formed a clade together with Fragaria chiloensis cryptic virus, Rosa multiflora cryptic virus and Rose cryptic virus-1, indicating that ArCV-1 could be a new member of the genus Deltapartitivirus. ArCV-1 3D(pol) structure revealed several interesting features. The 3D(pol) in its full-length shares structural similarities with members of the family Caliciviridaeand family Picornaviridae. In addition, fourth dsRNA molecule (dsRNA-2A), not related to ArCV-1 genome, was found in the same plant tissue. The dsRNA-2A (1.6 kb) encodes a protein (P4), with a predicted size of 44.5 kDa. P4 shares similarity with coat protein genes of several cryptic viruses, in particular the bipartite cryptic viruses including Raphanus sativus cryptic virus-3. This is the first report of occurrence of a cryptic virus in pigeonpea plants. url: https://doi.org/10.1371/journal.pone.0181829 doi: 10.1371/journal.pone.0181829 id: cord-280854-cxpgwwjd author: Kumarasamy, Dhanabal title: Synthesis and in vitro antiviral evaluation of 4-substituted 3,4-dihydropyrimidinones date: 2017-01-15 words: 1649.0 sentences: 99.0 pages: flesch: 53.0 cache: ./cache/cord-280854-cxpgwwjd.txt txt: ./txt/cord-280854-cxpgwwjd.txt summary: The compounds were evaluated in vitro for their antiviral activity against a broad range of DNA and RNA viruses, along with assessment for potential cytotoxicity in diverse mammalian cell lines. The compounds were evaluated in vitro for their antiviral activity against a broad range of DNA and RNA viruses, along with assessment for potential cytotoxicity in diverse mammalian cell lines. The present work was aimed to synthesize 4-substituted 3,4-dihydropyrimidin-2(1H)-ones using various aromatic and aliphatic aldehydes and evaluate their antiviral activity against a broad range of DNA and RNA viruses, along with their cytotoxicity assessment in diverse mammalian cell lines. The antiviral activities and cytotoxicity of the synthesized compounds (4a-m and 5) were determined in CPE reduction assays with a broad and diverse panel of DNA and RNA viruses and using relevant mammalian cell lines. Compound 4m was found to be a selective and potent inhibitor of Punta Toro virus (PTV), a member of the family Bunyaviridae and the genus Phlebovirus. abstract: Abstract A series of 4-substituted 3,4-dihydropyrimidine-2-ones (DHPM) was synthesized, characterized by IR, 1H NMR, 13C NMR and HRMS spectra. The compounds were evaluated in vitro for their antiviral activity against a broad range of DNA and RNA viruses, along with assessment for potential cytotoxicity in diverse mammalian cell lines. Compound 4m, which possesses a long lipophilic side chain, was found to be a potent and selective inhibitor of Punta Toro virus, a member of the Bunyaviridae. For Rift Valley fever virus, which is another Bunyavirus, the activity of 4m was negligible. DHPMs with a C-4 aryl moiety bearing halogen substitution (4b, 4c and 4d) were found to be cytotoxic in MT4 cells. url: https://api.elsevier.com/content/article/pii/S0960894X1631277X doi: 10.1016/j.bmcl.2016.12.010 id: cord-018639-0g1ov96t author: Kurpiers, Laura A. title: Bushmeat and Emerging Infectious Diseases: Lessons from Africa date: 2015-09-21 words: 14563.0 sentences: 713.0 pages: flesch: 51.0 cache: ./cache/cord-018639-0g1ov96t.txt txt: ./txt/cord-018639-0g1ov96t.txt summary: Here we review the literature on bushmeat and EIDs for sub-Saharan Africa, summarizing pathogens (viruses, fungi, bacteria, helminths, protozoan, and prions) by bushmeat taxonomic group to provide for the first time a comprehensive overview of the current state of knowledge concerning zoonotic disease transmission from bushmeat into humans. In this review, we explore the links between bushmeat-related activities and EIDs in sub-Saharan Africa, where the vast majority of African emerging infectious zoonotic diseases occur (Jones et al. Although research has focused largely on mammals and, to a lesser extent, birds, theoretically any wildlife species harvested for bushmeat could be a potential source of zoonotic disease that can spillover during the hunting, butchering, and preparation process (Wolfe et al. With the increasing prevalence of zoonotic disease emergence and the associated risk for public health, we have to improve our understanding of the dynamics of spillover events of pathogens from animal to human hosts (Rostal et al. abstract: Zoonotic diseases are the main contributor to emerging infectious diseases (EIDs) and present a major threat to global public health. Bushmeat is an important source of protein and income for many African people, but bushmeat-related activities have been linked to numerous EID outbreaks, such as Ebola, HIV, and SARS. Importantly, increasing demand and commercialization of bushmeat is exposing more people to pathogens and facilitating the geographic spread of diseases. To date, these linkages have not been systematically assessed. Here we review the literature on bushmeat and EIDs for sub-Saharan Africa, summarizing pathogens (viruses, fungi, bacteria, helminths, protozoan, and prions) by bushmeat taxonomic group to provide for the first time a comprehensive overview of the current state of knowledge concerning zoonotic disease transmission from bushmeat into humans. We conclude by drawing lessons that we believe are applicable to other developing and developed regions and highlight areas requiring further research to mitigate disease risk. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123567/ doi: 10.1007/978-3-319-22246-2_24 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-345689-5ns1onkw author: Kusters, Inca C. title: Manufacturing Vaccines for an Emerging Viral Infection–Specific Issues Associated with the Development of a Prototype SARS Vaccine date: 2009-01-30 words: 6218.0 sentences: 287.0 pages: flesch: 42.0 cache: ./cache/cord-345689-5ns1onkw.txt txt: ./txt/cord-345689-5ns1onkw.txt summary: Taking into account all the uncertainties and anticipating the worst-case scenario, many laboratories and vaccine manufacturers started working on a vaccine approach against SARS infection, largely based on what was known from animal CoVs. In this chapter, we will discuss the necessity for international cooperation and the importance of discretionary funding for rapidly developing a prototype vaccine candidate. When the laboratory work on the SARS-CoV vaccine development started, no data were available on the inactivation characteristics of the virus. The results from the experiments performed to evaluate the viral loss of the SARS-CoV due to drying on glass surface were also surprising: 35 -42 days were necessary to inactivate the virus to the detection limit of the technique. Based on our experience to date, the inactivated, adjuvanted SARS-CoV prototype vaccine seems to be a good candidate for further evaluation in Phase 1 studies. abstract: Abstract The world was struck by surprise when a Severe Acute Respiratory Syndrome (SARS) epidemic started in 2003 in China. This disease had never been observed in man before; the SARS-Coronavirus causing the disease was unknown. With the uncertainty about the future impact of this epidemic, an important international collaboration started spontaneously sharing scientific knowledge and reagents. Resources became quickly available, and public and private efforts were undertaken to develop rapidly a vaccine. We will discuss here the importance of the international collaboration and the availability of funding. Moreover, we will review the most important and challenging steps during the industrial development of the SARS vaccine highlighting the difficulties in terms of safety working with such a highly pathogenic, unknown virus. We will emphasize the industrial perspectives on inactivation and decontamination experiments, the selection of the most promising vaccine candidate, the production process and the choice and use of animal models in such a pressing and difficult situation. Finally, we will briefly review the unique regulatory environment created during this period for the development of a SARS vaccine. url: https://www.sciencedirect.com/science/article/pii/B9780123694089000111 doi: 10.1016/b978-0-12-369408-9.00011-1 id: cord-353290-1wi1dhv6 author: Kustin, Talia title: Biased mutation and selection in RNA viruses date: 2020-09-28 words: 7611.0 sentences: 402.0 pages: flesch: 52.0 cache: ./cache/cord-353290-1wi1dhv6.txt txt: ./txt/cord-353290-1wi1dhv6.txt summary: We investigated possible reasons for the advantage of A-rich sequences including weakened RNA secondary structures, codon usage bias, and selection for a particular amino-acid composition, and conclude that host immune pressures may have led to similar biases in coding sequence composition across very divergent RNA viruses. Nevertheless, RNA viruses do share several common features that drive their evolution: (a) their ultimate dependence on the cell, (b) their high mutation rates, (c) strong purifying selection derived from constraints operating on a small and densely coding genome, and (d) sporadic but powerful positive selection driven by an evolutionary arms race with the host they infect. Two non-mutually exclusive hypotheses may be put forth to explain the consistent pattern of A-richness that we observe: there is selection for more A in viral sequences, and/or there is a mutational bias that leads to more A in genomes of viruses. abstract: RNA viruses are responsible for some of the worst pandemics known to mankind, including outbreaks of Influenza, Ebola, and the recent COVID-19. One major challenge in tackling RNA viruses is the fact they are extremely genetically diverse. Nevertheless, they share common features that include their dependence on host cells for replication, and high mutation rates. We set out to search for shared evolutionary characteristics that may aid in gaining a broader understanding of RNA virus evolution, and constructed a phylogeny-based dataset spanning thousands of sequences from diverse single-stranded RNA viruses of animals. Strikingly, we found that the vast majority of these viruses have a skewed nucleotide composition, manifested as adenine rich (A-rich) coding sequences. In order to test whether A-richness is driven by selection or by biased mutation processes, we harnessed the effects of incomplete purifying selection at the tips of virus phylogenies. Our results revealed consistent mutational biases towards U rather than A in genomes of all viruses. In +ssRNA viruses we found that this bias is compensated by selection against U and selection for A, which leads to A-rich genomes. In -ssRNA viruses the genomic mutational bias towards U on the negative strand manifests as A-rich coding sequences, on the positive strand. We investigated possible reasons for the advantage of A-rich sequences including weakened RNA secondary structures, codon usage bias, and selection for a particular amino-acid composition, and conclude that host immune pressures may have led to similar biases in coding sequence composition across very divergent RNA viruses. url: https://doi.org/10.1093/molbev/msaa247 doi: 10.1093/molbev/msaa247 id: cord-263764-2ewz8ok4 author: Kutter, Jasmin S title: Transmission routes of respiratory viruses among humans date: 2018-01-17 words: 4392.0 sentences: 242.0 pages: flesch: 40.0 cache: ./cache/cord-263764-2ewz8ok4.txt txt: ./txt/cord-263764-2ewz8ok4.txt summary: 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. Our observations underscore the urgent need for new knowledge on respiratory virus transmission routes and the implementation of this knowledge in infection control guidelines to advance intervention strategies for currently circulating and newly emerging viruses and to improve public health. Increasing numbers of studies focused on the detection and quantification of influenza viruses contained in droplets and aerosols expelled into the air through breathing, sneezing and coughing of infected individuals The SARS outbreak was primarily linked to healthcare settings, with 49% of the cases linked to hospitals [71] , most probably caused by aerosol-generating procedures on severely ill patients [72, 73] . 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-262722-cz3ce29n author: Kuzmanovic, Deborah A. title: A novel application of small-angle scattering techniques: Quality assurance testing of virus quantification technology date: 2008-03-31 words: 5479.0 sentences: 271.0 pages: flesch: 50.0 cache: ./cache/cord-262722-cz3ce29n.txt txt: ./txt/cord-262722-cz3ce29n.txt summary: Abstract Small-angle scattering (SAS) techniques, like small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS), were used to measure and thus to validate the accuracy of a novel technology for virus sizing and concentration determination. Additionally, scattering methods such as classical light scattering, small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) have also been employed to measure the concentration of samples when the molecular weight of the virus is known (Guinier, 1939; Guinier and Fournet, 1955; Jacrot and Zaccai, 1981; Koch et al., 2003) . The primary goal of this study is to explore the utility of using small-angle scattering (SAS) techniques, such as SAXS and SANS, as a general approach to the evaluation and quality assurance testing of virus characterization technology, using the integrated virus detection system (IVDS) instrument as a test technology. Specifically, it was determined using SAXS and SANS that the virus sizing and concentration technology, IVDS, can accurately measure the size of synthetic latex microspheres. abstract: Abstract Small-angle scattering (SAS) techniques, like small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS), were used to measure and thus to validate the accuracy of a novel technology for virus sizing and concentration determination. These studies demonstrate the utility of SAS techniques for use in quality assurance measurements and as novel technology for the physical characterization of viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32288383/ doi: 10.1016/j.radphyschem.2007.10.004 id: cord-274765-3wzht843 author: Kweon, Chang-Hee title: Derivation of attenuated porcine epidemic diarrhea virus (PEDV) as vaccine candidate date: 1999-06-04 words: 2518.0 sentences: 133.0 pages: flesch: 55.0 cache: ./cache/cord-274765-3wzht843.txt txt: ./txt/cord-274765-3wzht843.txt summary: The field isolate of porcine epidemic diarrhea virus (PEDV) was serially passaged in Vero cells. The cell passaged PEDV, designated KPEDV-9, was tested for its pathogenicity in the neonatal pigs, immunogenicity and safety in the pregnant sows. The results of this study supported that the attenuated virus derived from serial passage could be applied as vaccine for protecting suckling piglets against PEDV infection. In this study, we investigated the attenuation of PEDV through serial passages in Vero cell cultures and its prophylactic eect in pregnant sows. Nevertheless, when compared with the wild PEDV, the animals inoculated with the high passage level of virus did not show any severe signs of diarrhea or death in piglets, supporting attenuation. Development of an Elispot for the detection of antibody secreting cells against the porcine epidemic diarrhea virus (PEDV) in dierent tissues abstract: The field isolate of porcine epidemic diarrhea virus (PEDV) was serially passaged in Vero cells. The cell passaged PEDV, designated KPEDV-9, was tested for its pathogenicity in the neonatal pigs, immunogenicity and safety in the pregnant sows. The result indicated that KPEDV-9 at the 93rd passage revealed reduced pathogenicity in the neonatal pigs. Pregnant sows inoculated with the attenuated virus showed increased immune responses by ELISA. In addition, delivered piglets were protected from challenge of wild type PEDV. The safety test in pregnant sows indicated that all inoculated animals farrowed the average numbers of litters of piglets. The results of this study supported that the attenuated virus derived from serial passage could be applied as vaccine for protecting suckling piglets against PEDV infection. url: https://www.sciencedirect.com/science/article/pii/S0264410X99000596 doi: 10.1016/s0264-410x(99)00059-6 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-018364-b06084r1 author: LaBrunda, Michelle title: The Emerging Threat of Ebola date: 2019-06-07 words: 13502.0 sentences: 795.0 pages: flesch: 57.0 cache: ./cache/cord-018364-b06084r1.txt txt: ./txt/cord-018364-b06084r1.txt summary: Transmission of Ebola disease is still being studied, but it is known that person-toperson contact is the most common form of spread. One study found the risk of developing EVD for healthcare workers to be 100 times that of the general community during an outbreak of Ebola in Sierra Leone [67] . After the outbreak of SARS in 2003 many countries starting using boarder screening to try to identify possibly ill people in hopes of limiting spread of infectious disease, others jumped on board after the 2009 H1N1 influenza pandemic. An article by the CDC, published around the same time as the article recommending travel restriction for high-risk individuals, concludes that border screens are expensive and not effective in preventing the spread of disease [100] . Infection Prevention and Control Recommendations for Hospitalized Patients Under Investigation (PUIs) for Ebola Virus Disease (EVD) in U abstract: Ebola is one of the deadliest infectious disease of the modern era. Over 50% of those infected die. Prior to 1976, the disease was unknown. No one knows exactly where it came from, but it is postulated that a mutation in an animal virus allowed it to jump species and infect humans. In 1976 simultaneous outbreaks of Ebola occurred in what is now South Sudan and the Democratic Republic of the Congo (DRC). For 20 years, only sporadic cases were seen, but in 1995 a new outbreak occurred killing hundreds in the DRC. Since that time the frequency of these outbreaks has been increasing. It is uncertain why this is occurring, but many associate it with increasing human encroachment into forested areas bringing people and animals into more intimate contact and increased mobility of previously remote population. This chapter will navigate Ebola in the context of global health and security. There are multiple objectives of this chapter. First is to provide a basic understanding of Ebola disease processes and outbreak patterns. Second, is to explore the interplay between social determinants of health and Ebola. The role of technology in spreading Ebola outbreaks will be explained as will Ebola’s potential as a bioweapon. Readers will gain understanding of the link between environmental degradation and Ebola outbreaks. This chapter will be divided into five main sections. These are (1) a case study; (2) Ebola Disease process; (3) Social determinants of health and Ebola; (4) Ebola in the modern era, and (5) the link between Ebola and environmental degradation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123219/ doi: 10.1007/978-3-030-23491-1_6 id: cord-013526-6fip93l2 author: Labadie, Thomas title: A non-enveloped arbovirus released in lysosome-derived extracellular vesicles induces super-infection exclusion date: 2020-10-19 words: 8084.0 sentences: 379.0 pages: flesch: 51.0 cache: ./cache/cord-013526-6fip93l2.txt txt: ./txt/cord-013526-6fip93l2.txt summary: Here we used Bluetongue virus (BTV) as a model of a non-enveloped arthropod-borne virus and discovered that the majority of viruses are released in EVs. Based on the cellular proteins detected in these EVs, and use of inhibitors targeting the cellular degradation process, we demonstrated that these extracellular vesicles are derived from secretory lysosomes, in which the acidic pH is neutralized upon the infection. Virus released in secretory lysosomes infectious EVs. However, inhibition of autophagosome-lysosome fusion with chloroquine (CQ), led to a significant reduction of infectious EVs released as compared to the control ( Fig 2B) , indicating that the late steps of autophagy are necessary for infectious EVs. In addition, inhibition of MVBs regulator protein HSP90 using geldanamycin in BTV-infected cells (MOI = 10) also led to a significant reduction of infectivity measured in the EVs fraction, as compared to the control, indicating a possible role for MVBs in the release of infectious EVs. In contrast, GW4869, a drug that inhibits the release of exosomes (small vesicles~200nm) derived from MVBs, did not affect the secretion levels of EVs containing BTV ( Fig 2B) . abstract: Recent developments on extracellular vesicles (EVs) containing multiple virus particles challenge the rigid definition of non-enveloped viruses. However, how non-enveloped viruses hijack cell machinery to promote non-lytic release in EVs, and their functional roles, remain to be clarified. Here we used Bluetongue virus (BTV) as a model of a non-enveloped arthropod-borne virus and discovered that the majority of viruses are released in EVs. Based on the cellular proteins detected in these EVs, and use of inhibitors targeting the cellular degradation process, we demonstrated that these extracellular vesicles are derived from secretory lysosomes, in which the acidic pH is neutralized upon the infection. Moreover, we report that secreted EVs are more efficient than free-viruses for initiating infections, but that they trigger super-infection exclusion that only free-viruses can overcome. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7595637/ doi: 10.1371/journal.ppat.1009015 id: cord-263484-afcgqjwq author: Ladner, Jason T. title: Precision epidemiology for infectious disease control date: 2019-02-06 words: 3990.0 sentences: 179.0 pages: flesch: 29.0 cache: ./cache/cord-263484-afcgqjwq.txt txt: ./txt/cord-263484-afcgqjwq.txt summary: With sufficient sampling, relevant metadata (such as location and date) and an appropriate statistical framework, pathogen genomes can reveal patterns of epidemic transmission at a fine-scale resolution, thus enabling the design of targeted interventions that are more precise than those based on traditional epidemiological data alone. Through near-real-time genome sequencing and public data deposition of clinical, environmental, and foodrelated bacterial isolates, this network is streamlining the process of recognizing, investigating, and reducing the impact of foodborne disease outbreaks 42, 43 . This includes changes to research practice regarding the benefits for rapid and open sharing of data and results as well as a focus on building capacity for sequencing and analysis within public health agencies and the regions most severely impacted by infectious disease 57, 58 . One important approach to accelerating responses in the future is to build genome sequencing and analysis capabilities within public health agencies and hospitals as well as in developing countries disproportionately impacted by infectious disease outbreaks. abstract: Advances in genomics and computing are transforming the capacity for the characterization of biological systems, and researchers are now poised for a precision-focused transformation in the way they prepare for, and respond to, infectious diseases. This includes the use of genome-based approaches to inform molecular diagnosis and individual-level treatment regimens. In addition, advances in the speed and granularity of pathogen genome generation have improved the capability to track and understand pathogen transmission, leading to potential improvements in the design and implementation of population-level public health interventions. In this Perspective, we outline several trends that are driving the development of precision epidemiology of infectious disease and their implications for scientists’ ability to respond to outbreaks. url: https://www.ncbi.nlm.nih.gov/pubmed/30728537/ doi: 10.1038/s41591-019-0345-2 id: cord-300810-a1skdp67 author: Lafay, F. title: Spread of the CVS strain of rabies virus and of the avirulent mutant AvO1 along the olfactory pathways of the mouse after intranasal inoculation date: 1991-07-31 words: 5731.0 sentences: 292.0 pages: flesch: 54.0 cache: ./cache/cord-300810-a1skdp67.txt txt: ./txt/cord-300810-a1skdp67.txt summary: title: Spread of the CVS strain of rabies virus and of the avirulent mutant AvO1 along the olfactory pathways of the mouse after intranasal inoculation Abstract After intranasal instillation in the mouse, rabies virus (CVS strain) selectively infected olfactory receptor cells. On the other hand, other neuronal cells permissive for CVS, such as mitral cells or the anterior olfactory nucleus, are completely free of infection with the mutant, indicating that restriction is related to the ability of AvO1 to penetrate several categories of neurons. The G protein plays a pivotal role in the pathogenicity of the virus because of its interaction with the host cells '' Abbreviations used: AON, anterior olfactory nucleus; CNS, central nervous system; GABA, Gamma aminobutyric acid; HDB, horizontal limb of the diagonal band; HRP, horseradish peroxidase; HSVl, herpes simplex type 1; IPL, internal plexiform layer: LC, locus coeruleus; LD50, lethal dose 50%; LPA. abstract: Abstract After intranasal instillation in the mouse, rabies virus (CVS strain) selectively infected olfactory receptor cells. In the main olfactory bulb (MOB), infection was observed in periglomerular, tufted, and mitral cells and in interneurons located in the internal plexiform layer. Beyond the MOB, CVS spread into the brain along the olfactory pathways. This infection is specific to chains of functionally related neurons but at the death of the animal some nuclei remain uninfected. CVS also penetrated the trigeminal system. The avirulent mutant AvOl, carrying a mutation in position 333 of the glycoprotein, infected the olfactory epithelium and the trigeminal nerve as efficiently as CVS. During the second cycle of infection, the mutant was able to infect efficiently periglomerular cells in the MOB and neurons of the horizontal limb of the diagonal band, which indicates that maturation of infective particles is not affected in primarily infected neuronal cells. On the other hand, other neuronal cells permissive for CVS, such as mitral cells or the anterior olfactory nucleus, are completely free of infection with the mutant, indicating that restriction is related to the ability of AvO1 to penetrate several categories of neurons. From these observations, we concluded that CVS should be able to bind several different receptors to penetrate neurons, while the mutant would be unable to recognize some of them. url: https://api.elsevier.com/content/article/pii/0042682291901452 doi: 10.1016/0042-6822(91)90145-2 id: cord-328753-qwdxgk4z author: Lafaye, Pierre title: Use of camel single-domain antibodies for the diagnosis and treatment of zoonotic diseases date: 2018-09-25 words: 4624.0 sentences: 251.0 pages: flesch: 42.0 cache: ./cache/cord-328753-qwdxgk4z.txt txt: ./txt/cord-328753-qwdxgk4z.txt summary: The antigen-binding region of such homodimeric heavy-chain only antibodies consists of one single domain, called VHH. VHHs provide many advantages over conventional full-sized antibodies and currently used antibody-based fragments (Fab, scFv), including high specificity, stability and solubility, and small size, allowing them to recognize unusual antigenic sites and deeply penetrate tissues. The active antigen-binding fragment of heavy chain antibodies can be cloned and expressed in the form of VHH, which consists of only one domain (Fig. 1) . Gene therapy with an adenoviral vector expressing a bispecific VHH, consisting of two linked VHHs targeting different PA-neutralizing epitopes, was tested in mice, and found to protect them from anthrax toxin challenge and anthrax spore infection [55] . [92] have been found in the sera of infected camels, whereas antibodies against rabies virus, vesicular stomatitis virus, and FMD virus have been detected in llamas [93] and could lead to the possible isolation of specific broadly neutralizing VHHs. Many neutralizing VHHs that bind to different sites on the same target, including hidden antigenic sites, can be isolated from immunized or infected camelids. abstract: Camelids produce both conventional heterotetrameric antibodies and homodimeric heavy-chain only antibodies. The antigen-binding region of such homodimeric heavy-chain only antibodies consists of one single domain, called VHH. VHHs provide many advantages over conventional full-sized antibodies and currently used antibody-based fragments (Fab, scFv), including high specificity, stability and solubility, and small size, allowing them to recognize unusual antigenic sites and deeply penetrate tissues. Since their discovery, VHHs have been used extensively in diagnostics and therapy. In recent decades, the number of outbreaks of diseases transmissible from animals to humans has been on the rise. In this review, we evaluate the status of VHHs as diagnostic and therapeutic biomolecular agents for the detection and treatment of zoonotic diseases, such as bacterial, parasitic, and viral zoonosis. VHHs show great adaptability to inhibit or neutralize pathogenic agents for the creation of multifunctional VHH-based diagnostic and therapeutic molecules against zoonotic diseases. url: https://doi.org/10.1016/j.cimid.2018.09.009 doi: 10.1016/j.cimid.2018.09.009 id: cord-303665-l57e54hu author: Lahrich, S. title: Review on the contamination of wastewater by COVID-19 virus: Impact and treatment date: 2020-09-10 words: 5849.0 sentences: 329.0 pages: flesch: 48.0 cache: ./cache/cord-303665-l57e54hu.txt txt: ./txt/cord-303665-l57e54hu.txt summary: Under these circumstances, the passive, but effective, method of sewage or wastewater monitoring can be used to trace and track the presence of SARS-CoV-2, through their genetic material RNA, and screen entire community. Since wastewater contains viruses that are repelled by everyone, regardless of their health, monitoring for viruses in wastewater and environmental waters that receive effluent from wastewater treatment plants (WWTPs) can determine the true prevalence and molecular epidemiology of gastroenteritis viruses and the risks to human health (Guan et al., 2020; Huang et al., 2020; Wang et al., 2020a) in a given geographical area rather than clinical research (Prevost et al., 2015; Kazama et al., 2017) . Therefore, the safety of drinking water and wastewater depends on the appropriate selection of the disinfectant dose and contact time in the treated environment, which are very important analytical techniques and methods that can detect viruses. Understanding how the virus breaks down in the aquatic environment is also critical to assessing risks to human health at present; the stability of the SARS-CoV-2 genome in wastewater is unclear. abstract: Emerging viruses are a major public health problem. Most zoonotic pathogens originate in wildlife, including human immunodeficiency virus (HIV), influenza, Ebola, and coronavirus. Severe acute respiratory syndrome (SARS) is a viral respiratory illness caused by a coronavirus called SARS-associated coronavirus (SARS-CoV). Viruses are charged colloidal particles that have the ability to adsorb on surfaces depending on pH. Their sorptive interaction with solid particles has important implications for their behavior in aquatic environments, soils, sewage sludge, and other solid materials and their removal or concentration by water treatment processes. Current state of knowledge on the potential of wastewater surveillance to understand the COVID-19 pandemic is reviewed. This study also identified wastewater irrigation systems with a higher risk of COVID-19 transmission. Emphasis was placed on methodologies for the detection and quantification of SARS-CoV-2 in wastewater. url: https://doi.org/10.1016/j.scitotenv.2020.142325 doi: 10.1016/j.scitotenv.2020.142325 id: cord-001542-f089bs8r author: Lai, Kang Yiu title: Human Ebola virus infection in West Africa: a review of available therapeutic agents that target different steps of the life cycle of Ebola virus date: 2014-11-28 words: 11274.0 sentences: 604.0 pages: flesch: 42.0 cache: ./cache/cord-001542-f089bs8r.txt txt: ./txt/cord-001542-f089bs8r.txt summary: These may include monoclonal antibody (mAbs)-based therapies (e.g. ZMapp), anti-sense phosphorodiamidate morpholino oligomers (PMO AVI-6002), lipid nanoparticle small interfering RNA (LNP-siRNA: TKM-Ebola), and an EBOV glycoprotein-based vaccine using live-attenuated recombinant vesicular stomatitis virus (rVSV-EBOGP) or a chimpanzee adenovirus (rChAd-EBOGP)-based vector. The GP2 of the EBOV is able to counter the interferon (IFN)-inducible antiviral protein tetherin which restricts the VP40-dependent budding of the progeny viral particles from infected cells [16] [17] [18] . Currently available therapeutic agents that are effective in targeting the EBOV infection in cell or animal studies may include convalescent plasma, favipiravir, chloroquine, amiodarone, dronedarone, verapamil, clomiphene, toremifene, IFN-β, Na + /K + exchangers, Na + /K + -ATPase pump inhibitors, and antioxidants. The anti-EBOV activity of clomiphene and toremifene is dependent not on its estrogen receptor antagonistic action but upon the ability of both drugs to induce a Niemann-Pick C-like phenotype to inhibit viral entry at late endosome. abstract: The recent outbreak of the human Zaire ebolavirus (EBOV) epidemic is spiraling out of control in West Africa. Human EBOV hemorrhagic fever has a case fatality rate of up to 90%. The EBOV is classified as a biosafety level 4 pathogen and is considered a category A agent of bioterrorism by Centers for Disease Control and Prevention, with no approved therapies and vaccines available for its treatment apart from supportive care. Although several promising therapeutic agents and vaccines against EBOV are undergoing the Phase I human trial, the current epidemic might be outpacing the speed at which drugs and vaccines can be produced. Like all viruses, the EBOV largely relies on host cell factors and physiological processes for its entry, replication, and egress. We have reviewed currently available therapeutic agents that have been shown to be effective in suppressing the proliferation of the EBOV in cell cultures or animal studies. Most of the therapeutic agents in this review are directed against non-mutable targets of the host, which is independent of viral mutation. These medications are approved by the Food and Drug Administration (FDA) for the treatment of other diseases. They are available and stockpileable for immediate use. They may also have a complementary role to those therapeutic agents under development that are directed against the mutable targets of the EBOV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/2049-9957-3-43) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4334593/ doi: 10.1186/2049-9957-3-43 id: cord-352379-q5inrxcm author: Lai, Michael M. C. title: SARS virus: The beginning of the unraveling of a new coronavirus date: 2003-10-17 words: 7004.0 sentences: 376.0 pages: flesch: 49.0 cache: ./cache/cord-352379-q5inrxcm.txt txt: ./txt/cord-352379-q5inrxcm.txt summary: Nevertheless, the lack of a firm association of coronaviruses with any serious human illnesses had dampened the public''s interest in this virus family until the sudden emergence of the SARS coronavirus [24, 41, 62] , which caused the first new infectious disease of this millennium. In the SARS virus genome, the organization of gene la-lb, which accounts for more than two-thirds of the viral RNA, is very similar to that of the murine coronavirus MHV, except that it contains only one papain-like protease (PLpro-2) ( fig. Based on the predicted cleavage site specificity, the SARS virus gene la-lb is likely processed into thirteen final protein products. However, the published sequence analysis indicated that the entire SARS virus RNA resembled that of group II viruses; no evidence of recombination was noted [55, 66] . Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection abstract: Severe acute respiratory syndrome (SARS) virus caused a severe outbreak in several regions of the world in 2003. The virus is a novel coronavirus, which may have an origin in wild animals such as civet cats in southern China. Its genome structure, gene expression pattern and protein profiles are similar to those of other coronaviruses. However, distinct patterns of several open reading frames in the SARS virus genome may contribute to its severe virulence. The potential mutability of the coronavirus genome may pose problems in the control of future SARS outbreaks. The mechanism of SARS pathogenesis may involve both direct viral cytocidal effects on the target cells and immune-mediated mechanisms. The life cycle of the SARS virus is largely unknown; however, based on the analogy with other coronaviruses, several potential targets for antiviral development are identified. Vaccines offer an important preventive measure for possible future recurrences of SARS, but the prospect for their development is still unknown because of the uncertainty regarding the role of immune responses in SARS virus pathogenesis. The comparative studies of other coronaviruses offer insights into the understanding of SARS virus. url: https://www.ncbi.nlm.nih.gov/pubmed/14631105/ doi: 10.1007/bf02256318 id: cord-003917-bswndfvk author: Lalle, Eleonora title: Pulmonary Involvement during the Ebola Virus Disease date: 2019-08-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: 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-076082-4kpkhz0o author: Lam, Tommy Tsan-Yuk title: Evolutionary and Transmission Dynamics of Reassortant H5N1 Influenza Virus in Indonesia date: 2008-08-22 words: 6973.0 sentences: 312.0 pages: flesch: 44.0 cache: ./cache/cord-076082-4kpkhz0o.txt txt: ./txt/cord-076082-4kpkhz0o.txt summary: The H5N1 highly pathogenic avian influenza (HPAI) virus was originally isolated from a farmed goose in Guangdong province of China in 1996 [1] , and soon spread to live-poultry markets in Hong Kong [2] , resulting in 18 cases of human infection in 1997, 6 of which were fatal [3, 4] . We found previously unrecognized phylogenetic discordance between gene trees involving human and cat isolates (n = 25, denoted in red in Figures 1, S1-S3)-the main focus of our study-suggesting that they are reassortant viruses descending from group 2 and 3 lineages. To further investigate the putative reassortant human and cat viruses, a selected dataset (n = 24) of manually concatenated full genomes (Figure 2A ; see Methods) of Indonesian H5N1 HPAI viruses were analyzed using more sophisticated analysis methods, including similarity plots, bootscan analyses and GARD analyses (genetic algorithm for recombination detection). abstract: H5N1 highly pathogenic avian influenza (HPAI) viruses have seriously affected the Asian poultry industry since their recurrence in 2003. The viruses pose a threat of emergence of a global pandemic influenza through point mutation or reassortment leading to a strain that can effectively transmit among humans. In this study, we present phylogenetic evidences for the interlineage reassortment among H5N1 HPAI viruses isolated from humans, cats, and birds in Indonesia, and identify the potential genetic parents of the reassorted genome segments. Parsimony analyses of viral phylogeography suggest that the reassortant viruses may have originated from greater Jakarta and surroundings, and subsequently spread to other regions in the West Java province. In addition, Bayesian methods were used to elucidate the genetic diversity dynamics of the reassortant strain and one of its genetic parents, which revealed a more rapid initial growth of genetic diversity in the reassortant viruses relative to their genetic parent. These results demonstrate that interlineage exchange of genetic information may play a pivotal role in determining viral genetic diversity in a focal population. Moreover, our study also revealed significantly stronger diversifying selection on the M1 and PB2 genes in the lineages preceding and subsequent to the emergence of the reassortant viruses, respectively. We discuss how the corresponding mutations might drive the adaptation and onward transmission of the newly formed reassortant viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2515348/ doi: 10.1371/journal.ppat.1000130 id: cord-016171-17ut32bu author: Lane, J. Michael title: Smallpox as a Weapon for Bioterrorism date: 2009 words: 8404.0 sentences: 512.0 pages: flesch: 51.0 cache: ./cache/cord-016171-17ut32bu.txt txt: ./txt/cord-016171-17ut32bu.txt summary: Following September 11, 2001, the United States rebuilt its supplies of vaccine and Vaccinia Immune Globulin (VIG), expanded the network of laboratories capable of testing for variola virus, and engaged in a broad education campaign to help health care workers and the general public understand the disease (Centers for Disease Control and Prevention, 2003a) . Following September 11, 2001, the United States rebuilt its supplies of vaccine and Vaccinia Immune Globulin (VIG), expanded the network of laboratories capable of testing for variola virus, and engaged in a broad education campaign to help health care workers and the general public understand the disease (Centers for Disease Control and Prevention, 2003a) . If this algorithm indicates that a patient is high risk to be smallpox, local and national public health authorities should be immediately notified by telephone, and laboratory specimens taken for polymerase chain reaction (PCR), electron photomicroscopy (EM), and viral culture. abstract: Smallpox, the only disease ever eradicated, is one of the six pathogens considered a serious threat for biological terrorism (Henderson et al., 1999; Mahy, 2003; Whitley, 2003). Smallpox has several attributes that make it a potential threat. It can be grown in large amounts. It spreads via the respiratory route. It has a 30% mortality rate. The potential for an attack using smallpox motivated President Bush to call for phased vaccination of a substantial number of American health care and public health workers (Grabenstein and Winkenwerder, 2003; Stevenson and Stolberg, 2002). Following September 11, 2001, the United States rebuilt its supplies of vaccine and Vaccinia Immune Globulin (VIG), expanded the network of laboratories capable of testing for variola virus, and engaged in a broad education campaign to help health care workers and the general public understand the disease (Centers for Disease Control and Prevention, 2003a). This chapter summarizes the scientific and theoretical bases for use of smallpox as a bioweapon and options for preparation for defense against it. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120382/ doi: 10.1007/978-1-4419-1266-4_5 id: cord-336045-8qcj5uiy author: Langlois, Isabelle title: Viral diseases of ferrets date: 2005-03-01 words: 7196.0 sentences: 424.0 pages: flesch: 41.0 cache: ./cache/cord-336045-8qcj5uiy.txt txt: ./txt/cord-336045-8qcj5uiy.txt summary: A tentative diagnosis of canine distemper is based on the presence of typical clinical signs, severe leukopenia, a history of potential exposure to the virus, and questionable vaccination. The severity of disease depends on the origin (mink or ferret) of the ADV strain that is involved as well as the immune status and genotype of the infected individual [25] . Ferrets are used extensively as an animal model for influenza virus pathogenesis and immunity studies because their biologic response to influenza infection is similar to that of humans [53, 54] . Neurologic symptoms, including ataxia, hind-limb paresis, and torticollis, were reported in ferrets that were infected experimentally with avian influenza A (H5N1) viruses that were isolated from the 1997 outbreaks of disease in domestic poultry markets in Hong Kong [50, 65] . Detection of Aleutian disease virus DNA in tissues of naturally infected mink abstract: Distemper and rabies vaccination are highly recommended because of the almost invariable fatal outcome of these conditions. Vaccination should constitute an important part of a ferret's preventative medicine program. With the current and anticipated development and licensing of new vaccines, practitioners are invited to gain awareness of the latest vaccine information. Establishment of a practice vaccination protocol with regards to the site of administration of rabies and distemper vaccines is paramount to document any future abnormal tissue reactions. Influenza is the most common zoonotic disease that is seen in ferrets. Although it generally is benign in most ferrets, veterinarians must take this condition seriously. The characteristic continuous antigenic variation of this virus may lead to more virulent strains; the recent emergence of avian influenza virus outbreaks; and the increased susceptibility of elderly, young, and immunosuppressed individuals. url: https://www.ncbi.nlm.nih.gov/pubmed/15585193/ doi: 10.1016/j.cvex.2004.09.008 id: cord-328621-3jda0k2u author: Laporte, Manon title: Airway proteases: an emerging drug target for influenza and other respiratory virus infections date: 2017-04-14 words: 4302.0 sentences: 213.0 pages: flesch: 38.0 cache: ./cache/cord-328621-3jda0k2u.txt txt: ./txt/cord-328621-3jda0k2u.txt summary: Since the catalytic sites of the diverse serine proteases linked to influenza, parainfluenzaand coronavirus activation are structurally similar, active site inhibitors of these airway proteases could have broad therapeutic applicability against multiple respiratory viruses. Since the catalytic sites of the diverse serine proteases linked to influenza, parainfluenza-and coronavirus activation are structurally similar, active site inhibitors of these airway proteases could have broad therapeutic applicability against multiple respiratory viruses. The best inhibitor (92 in Table 2 ) had a K i value of 0.9 nM and, interestingly, produced clear inhibition of HA0 cleavage and virus replication in Calu-3 cells, which endogenously express HA0-activating proteases like TMPRSS2. Trypsin-like proteases of the human airways represent unique targets to suppress infections with influenza or other respiratory viruses which rely on these enzymes for their replication. Proteolytic activation of influenza viruses by serine proteases TMPRSS2 and HAT from human airway epithelium abstract: To enter into airway epithelial cells, influenza, parainfluenza- and coronaviruses rely on host cell proteases for activation of the viral protein involved in membrane fusion. One protease, transmembrane protease serine 2 (TMPRSS2) was recently proven to be crucial for hemagglutinin cleavage of some human influenza viruses. Since the catalytic sites of the diverse serine proteases linked to influenza, parainfluenza- and coronavirus activation are structurally similar, active site inhibitors of these airway proteases could have broad therapeutic applicability against multiple respiratory viruses. Alternatively, superior selectivity could be achieved with allosteric inhibitors of TMPRSS2 or another critical protease. Though still in its infancy, airway protease inhibition represents an attractive host-cell targeting approach to combat respiratory viruses such as influenza. url: https://api.elsevier.com/content/article/pii/S1879625716302103 doi: 10.1016/j.coviro.2017.03.018 id: cord-260708-l9w5jhsw author: Lasecka, Lidia title: The molecular biology of nairoviruses, an emerging group of tick-borne arboviruses date: 2013-12-11 words: 10690.0 sentences: 446.0 pages: flesch: 46.0 cache: ./cache/cord-260708-l9w5jhsw.txt txt: ./txt/cord-260708-l9w5jhsw.txt summary: The nairoviruses are a rapidly emerging group of tick-borne bunyaviruses that includes pathogens of humans (Crimean-Congo hemorrhagic fever virus [CCHFV]) and livestock (Nairobi sheep disease virus [NSDV], also known as Ganjam virus), as well as a large number of viruses for which the normal vertebrate host has not been established. As several potential cysteine-protease-like cleavage sites have been identified in the L protein sequence of nairoviruses [94] and some viral proteins containing an OTU-like protease domain have also been shown to undergo autoproteolytic cleavage to generate multiple mature proteins, e.g., the replicase of BlScV [98] , it has been suggested that the L proteins of nairoviruses may also be autoproteolytically cleaved into an active RNA polymerase and protein(s) with additional function [85] . Role of actin filaments in targeting of Crimean Congo hemorrhagic fever virus nucleocapsid protein to perinuclear regions of mammalian cells Structural analysis of a viral ovarian tumor domain protease from the Crimean-Congo hemorrhagic fever virus in complex with covalently bonded ubiquitin Induction of caspase activation and cleavage of the viral nucleocapsid protein in different cell types during Crimean-Congo hemorrhagic fever virus infection abstract: The nairoviruses are a rapidly emerging group of tick-borne bunyaviruses that includes pathogens of humans (Crimean-Congo hemorrhagic fever virus [CCHFV]) and livestock (Nairobi sheep disease virus [NSDV], also known as Ganjam virus), as well as a large number of viruses for which the normal vertebrate host has not been established. Studies on this group of viruses have been fairly limited, not least because CCHFV is a BSL4 human pathogen, restricting the number of labs able to study the live virus, while NSDV, although highly pathogenic in naive animals, is not seen as a threat in developed countries, making it a low priority. Nevertheless, recent years have seen significant progress in our understanding of the biology of these viruses, particularly that of CCHFV, and this article seeks to draw together our existing knowledge to generate an overall picture of their molecular biology, underlining areas of particular ignorance for future studies. url: https://www.ncbi.nlm.nih.gov/pubmed/24327094/ doi: 10.1007/s00705-013-1940-z id: cord-275570-i9fw0afj author: Lau, Susanna K. P. title: Molecular Research on Emerging Viruses: Evolution, Diagnostics, Pathogenesis, and Therapeutics date: 2018-01-30 words: 1475.0 sentences: 84.0 pages: flesch: 42.0 cache: ./cache/cord-275570-i9fw0afj.txt txt: ./txt/cord-275570-i9fw0afj.txt summary: The recent epidemics caused by Zika virus and Middle East respiratory syndrome coronavirus (MERS-CoV) clearly illustrate the ability of emerging viruses to pose huge public health problems within a short time. In this special issue, "Molecular Research on Emerging Viruses: Evolution, Diagnostics, Pathogenesis, and Therapeutics", insights into advances and discoveries in understanding the different aspects of various emerging viruses are given by eight original studies and four review articles. Three articles focus on arthropod-borne viruses (arboviruses) which are important emerging pathogens having caused various epidemics in recent years. In the systematic review and meta-analysis study by Coelho et al., the prevalence of microcephaly in infants born to Zika virus-infected women among all pregnancies was estimated [6] , which may contribute to the understanding of the public health impact of this emerging arbovirus. Two articles report on the virus-host interaction during porcine reproductive and respiratory syndrome virus (PRRSV) infection which causes severe losses in the swine industry worldwide. abstract: Viruses are increasingly recognized as emerging infectious disease agents in both humans and animals.[...]. url: https://doi.org/10.3390/ijms19020398 doi: 10.3390/ijms19020398 id: cord-297339-et2305rz author: Lauber, Chris title: Genetics-Based Classification of Filoviruses Calls for Expanded Sampling of Genomic Sequences date: 2012-08-31 words: 4480.0 sentences: 235.0 pages: flesch: 46.0 cache: ./cache/cord-297339-et2305rz.txt txt: ./txt/cord-297339-et2305rz.txt summary: In DEmARC, virus clusters are delimited objectively by devising a universal family-wide threshold on intra-cluster genetic divergence of viruses that is specific for each level of the classification. Based on our experience with other virus families, we conclude that the current sampling of filovirus genomic sequences needs to be considerably expanded in order to resolve these uncertainties in the framework of genetics-based classification. The DEmARC specifics include (i) the use of pairwise evolutionary distances (PEDs) instead of uncorrected p-distances, and (ii) a quantitative method to devise taxon levels and associated PED thresholds for virus clustering in a systematic and family-wide manner. The first selected threshold (PED of 0.120) results in seven clusters ( Figure 1B ) that match the official or tentative ICTV species of the family Filoviridae. In the high-sampling case of picornaviruses, no PED values with zero frequency are observed which suggests that the current sampling of filovirus genome sequences may strongly underestimate the natural genetic diversity in the family. abstract: We have recently developed a computational approach for hierarchical, genome-based classification of viruses of a family (DEmARC). In DEmARC, virus clusters are delimited objectively by devising a universal family-wide threshold on intra-cluster genetic divergence of viruses that is specific for each level of the classification. Here, we apply DEmARC to a set of 56 filoviruses with complete genome sequences and compare the resulting classification to the ICTV taxonomy of the family Filoviridae. We find in total six candidate taxon levels two of which correspond to the species and genus ranks of the family. At these two levels, the six filovirus species and two genera officially recognized by ICTV, as well as a seventh tentative species for Lloviu virus and prototyping a third genus, are reproduced. DEmARC lends the highest possible support for these two as well as the four other levels, implying that the actual number of valid taxon levels remains uncertain and the choice of levels for filovirus species and genera is arbitrary. Based on our experience with other virus families, we conclude that the current sampling of filovirus genomic sequences needs to be considerably expanded in order to resolve these uncertainties in the framework of genetics-based classification. url: https://www.ncbi.nlm.nih.gov/pubmed/23170166/ doi: 10.3390/v4091425 id: cord-000937-8vk89i4h author: Law, John title: Identification of Hepatotropic Viruses from Plasma Using Deep Sequencing: A Next Generation Diagnostic Tool date: 2013-04-17 words: 6644.0 sentences: 332.0 pages: flesch: 50.0 cache: ./cache/cord-000937-8vk89i4h.txt txt: ./txt/cord-000937-8vk89i4h.txt summary: RNA and DNA libraries were sequenced from plasma filtrates enriched in viral particles to catalog virus populations. Seven RNA libraries (aihP01, hbvP02, hcvP02, hcvP03, hcvP05, nshP01, norP01) and seven DNA libraries (aihP01D, hbvP02D, hcvP02D, hcvP03D, hcvP05D, nshP01D, norP01D) were constructed from patients with autoimmune hepatitis (AIH), hepatitis B virus (HBV) chronic infection, hepatitis C virus (HCV) chronic infection, non-alcoholic steatohepatitis (NASH), and healthy subjects (NOR). Plasma samples were obtained from patients with autoimmune hepatitis (AIH), chronic hepatitis B virus (HBV) infection, chronic hepatitis C virus (HCV) infection, non-alcoholic steatohepatitis (NASH), and healthy subjects (NOR); each RNA library was named by diagnosis (e.g. aihP01) and a suffix ''D'' was added for each DNA library (e.g. aihP01D). To a lesser extent (about one read per million), we also detected sequences resembling RNA viruses in our DNA libraries (Supplemental Tables S15-S28 ). Assembly of viral sequences was also possible for all viruses shown in Figure 2 as the most abundant virus in each library (data not shown). abstract: We conducted an unbiased metagenomics survey using plasma from patients with chronic hepatitis B, chronic hepatitis C, autoimmune hepatitis (AIH), non-alcoholic steatohepatitis (NASH), and patients without liver disease (control). RNA and DNA libraries were sequenced from plasma filtrates enriched in viral particles to catalog virus populations. Hepatitis viruses were readily detected at high coverage in patients with chronic viral hepatitis B and C, but only a limited number of sequences resembling other viruses were found. The exception was a library from a patient diagnosed with hepatitis C virus (HCV) infection that contained multiple sequences matching GB virus C (GBV-C). Abundant GBV-C reads were also found in plasma from patients with AIH, whereas Torque teno virus (TTV) was found at high frequency in samples from patients with AIH and NASH. After taxonomic classification of sequences by BLASTn, a substantial fraction in each library, ranging from 35% to 76%, remained unclassified. These unknown sequences were assembled into scaffolds along with virus, phage and endogenous retrovirus sequences and then analyzed by BLASTx against the non-redundant protein database. Nearly the full genome of a heretofore-unknown circovirus was assembled and many scaffolds that encoded proteins with similarity to plant, insect and mammalian viruses. The presence of this novel circovirus was confirmed by PCR. BLASTx also identified many polypeptides resembling nucleo-cytoplasmic large DNA viruses (NCLDV) proteins. We re-evaluated these alignments with a profile hidden Markov method, HHblits, and observed inconsistencies in the target proteins reported by the different algorithms. This suggests that sequence alignments are insufficient to identify NCLDV proteins, especially when these alignments are only to small portions of the target protein. Nevertheless, we have now established a reliable protocol for the identification of viruses in plasma that can also be adapted to other patient samples such as urine, bile, saliva and other body fluids. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3629200/ doi: 10.1371/journal.pone.0060595 id: cord-023488-jf2xl3vl author: Le Duc, James W. title: Emerging Viral Diseases: Why We Need to Worry about Bats, Camels, and Airplanes date: 2016-02-12 words: 9385.0 sentences: 464.0 pages: flesch: 49.0 cache: ./cache/cord-023488-jf2xl3vl.txt txt: ./txt/cord-023488-jf2xl3vl.txt summary: On occasion, a virus that is already widespread in a population can emerge as a cause of epidemic or endemic disease, due to an increase in the ratio of cases to infections. Although many zoonotic viruses can be transmitted to humans on occasion, their relative ability to spread from human to human determines whether or not they emerge as significant new virus diseases of mankind (Table 2 ). In the history of modern virology (the last 50 years) there are very few documented instances where zoonotic viruses have established themselves in the human population and emerged as new viral diseases of mankind (Table 2 ). Rarely, as in the case of HIV, SARS coronavirus, and Ebola filovirus, a zoonotic virus becomes established in humans, causing a disease that is truly new to the human species. abstract: The emergence of a new viral disease is one of the most dramatic aspects of virology, which often receives widespread attention from the scientific community and the lay public. Considering that the discipline of animal virology was established over 100 years ago, it may seem surprising that new virus diseases are still being discovered. How this happens is the subject of this chapter. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7170184/ doi: 10.1016/b978-0-12-800964-2.00016-1 id: cord-290034-4b0mshqa author: Le, Yen H. title: Virus detections among patients with severe acute respiratory illness, Northern Vietnam date: 2020-05-12 words: 2833.0 sentences: 145.0 pages: flesch: 43.0 cache: ./cache/cord-290034-4b0mshqa.txt txt: ./txt/cord-290034-4b0mshqa.txt summary: To examine evidence for select viral infections among patients with SARI in northern Vietnam, we studied 348 nasopharyngeal samples from military and civilian patients admitted to 4 hospitals in the greater Hanoi area from 2017–2019. Initial screening for human respiratory viral pathogens was performed in Hanoi, Vietnam at the National Institute of Hygiene and Epidemiology (NIHE) or the Military Institute of Preventative Medicine (MIPM), and an aliquot was shipped to Duke-NUS Medical School in Singapore for validation. There was one case of co-infection with enterovirus and coronavirus 229E including a female military hospital patient 28 years of age. Additionally, our results display enterovirus, adenovirus and coronavirus infections among the SARI cases, suggesting that cities in northern Vietnam could benefit also from local surveillance of non-influenza respiratory viruses. abstract: Severe acute respiratory illness (SARI) is a major cause of death and morbidity in low- and middle-income countries, however, the etiologic agents are often undetermined due to the lack of molecular diagnostics in hospitals and clinics. To examine evidence for select viral infections among patients with SARI in northern Vietnam, we studied 348 nasopharyngeal samples from military and civilian patients admitted to 4 hospitals in the greater Hanoi area from 2017–2019. Initial screening for human respiratory viral pathogens was performed in Hanoi, Vietnam at the National Institute of Hygiene and Epidemiology (NIHE) or the Military Institute of Preventative Medicine (MIPM), and an aliquot was shipped to Duke-NUS Medical School in Singapore for validation. Patient demographics were recorded and used to epidemiologically describe the infections. Among military and civilian cases of SARI, 184 (52.9%) tested positive for one or more respiratory viruses. Influenza A virus was the most prevalent virus detected (64.7%), followed by influenza B virus (29.3%), enterovirus (3.8%), adenovirus (1.1%), and coronavirus (1.1%). Risk factor analyses demonstrated an increased risk of influenza A virus detection among military hospital patients (adjusted OR, 2.0; 95% CI, 1.2–3.2), and an increased risk of influenza B virus detection among patients enrolled in year 2017 (adjusted OR, 7.9; 95% CI, 2.7–22.9). As influenza A and B viruses were commonly associated with SARI and are treatable, SARI patients entering these hospitals would benefit if the hospitals were able to adapt onsite molecular diagnostics. url: https://doi.org/10.1371/journal.pone.0233117 doi: 10.1371/journal.pone.0233117 id: cord-013412-gj443yei author: Lebedeva, Natalya Sh. title: The Application of Porphyrins and Their Analogues for Inactivation of Viruses date: 2020-09-23 words: 13428.0 sentences: 626.0 pages: flesch: 46.0 cache: ./cache/cord-013412-gj443yei.txt txt: ./txt/cord-013412-gj443yei.txt summary: The purpose of this review paper is to summarize the main approaches developed to date in the chemical and photodynamic inactivation of human and animal viruses using porphyrins and their analogues and to analyze and discuss the information on viral targets and antiviral activity of porphyrins, chlorins, of their conjugates with organic/inorganic compounds obtained in the last 10–15 years in order to identify the most promising areas. A cationic substituent is necessary to increase the solubility of porphyrins and their analogues in aqueous media, and three nitro groups provide linking of the gp120 protein with the glycoprotein ( Figure 3 ) and thereby inhibit fusion between the virus and the cell membrane. A cationic substituent is necessary to increase the solubility of porphyrins and their analogues in aqueous media, and three nitro groups provide linking of the gp120 protein with the glycoprotein ( Figure 3 ) and thereby inhibit fusion between the virus and the cell membrane. abstract: The problem of treating viral infections is extremely relevant due to both the emergence of new viral diseases and to the low effectiveness of existing approaches to the treatment of known viral infections. This review focuses on the application of porphyrin, chlorin, and phthalocyanine series for combating viral infections by chemical and photochemical inactivation methods. The purpose of this review paper is to summarize the main approaches developed to date in the chemical and photodynamic inactivation of human and animal viruses using porphyrins and their analogues and to analyze and discuss the information on viral targets and antiviral activity of porphyrins, chlorins, of their conjugates with organic/inorganic compounds obtained in the last 10–15 years in order to identify the most promising areas. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7583985/ doi: 10.3390/molecules25194368 id: cord-350948-oog6m4h3 author: Leclercq, Loïc title: How to improve the chemical disinfection of contaminated surfaces by viruses, bacteria and fungus? date: 2020-09-17 words: 4571.0 sentences: 256.0 pages: flesch: 51.0 cache: ./cache/cord-350948-oog6m4h3.txt txt: ./txt/cord-350948-oog6m4h3.txt summary: The disinfectants, based on equimolar mixtures of didecyldimethylammonium chloride ([DiC(10)][Cl]), dodecyloctaglycol (C(12)E(8)), and cyclodextrin (CD), show synergistic effects against enveloped viruses (RSV, HSV-1, VACV) and fungi (C. In this context, the didecyldimethylammonium chloride ([DiC 10 ] [Cl] ), one of the most widely used quaternary ammonium compounds in healthcare systems to prevent and control viral infections due to its ability to disorganize and to disrupt the envelopes of viruses (Leclercq et al., 2010) , is associated with detergents, such as dodecyloctaglycol (C 12 E 8 ), making the detergent-disinfectant combination ideal for general sanitation purposes (Rauwel et al., 2012) . As, some ethoxylated surfactants (e.g. Triton X-100, Nonoxynol-9 or Brij-97) have been shown to exhibit a virucidal activity due to their ability to solubilize the viral envelope of Epstein-Barr or herpes simplex viruses (Qualtiere and Pearson, 1979; Asculai et al., 1978) , and, as, CDs "are able to participate in the attack of viruses, and specifically SARS-CoV-2, in a large range of different ways" (Garrido et al., 2020) , we have investigated [DiC 10 ][Cl]/C 12 E 8 /CD ternary systems to obtain synergistic effects against enveloped viruses such as RSV instead of hazardous SARS-CoV-2. abstract: In response to the current pandemic situation, we present the development of an effective virucidal and biocidal solution to prevent from the spread of infectious diseases through contact with contaminated surfaces. The disinfectants, based on equimolar mixtures of didecyldimethylammonium chloride ([DiC(10)][Cl]), dodecyloctaglycol (C(12)E(8)), and cyclodextrin (CD), show synergistic effects against enveloped viruses (RSV, HSV-1, VACV) and fungi (C. albicans), and additive responses against bacteria (P. aeruginosa). These synergistic mixtures could then be highly helpful for prevention of respiratory illnesses, since a boosted activity allows: (i) a faster eradication of pathogens, (ii) a shorter contact time, and (iii) a complete and broad-spectrum eradication to avoid spread of resistant strains (including bacteria and fungi). url: https://api.elsevier.com/content/article/pii/S092809872030347X doi: 10.1016/j.ejps.2020.105559 id: cord-347039-eap592i7 author: Lee, Seung-Hwan title: Maneuvering for advantage: the genetics of mouse susceptibility to virus infection date: 2003-08-31 words: 6177.0 sentences: 299.0 pages: flesch: 38.0 cache: ./cache/cord-347039-eap592i7.txt txt: ./txt/cord-347039-eap592i7.txt summary: Receptors are recognized as important determinants of virus host range and tissue tropism; and some host resistance/susceptibility loci encode molecules that are expressed on the cell surface. Another example of natural host resistance is the restriction of ecotropic Murine LEUKEMIA VIRUS (MuLV) infection by the mouse Fv4 gene. The effort to understand the genetic basis of susceptibility to viral disease is driven by three considerations: (1) the increased public awareness of the toll imposed by viruses on the host; (2) the increase in susceptible human populations because of longer life expectancy, frequently accompanied by chronic illness, and the consequences of advances in medical technology, including immunosuppressive therapies for organ transplantation or treatment of malignancy; and (3) the need to develop new therapies for infections caused by multidrug-resistant Human killer-cell immunoglobulin-type receptor (KIR) is considered to be a functional homolog of mouse Ly49. Mouse genetics has also demonstrated that recognition and destruction of virus-infected cells by NK cells is mediated by specific interactions between activating NKcell receptors and viral target molecules. abstract: Abstract Genetic studies of host susceptibility to infection contribute to our understanding of an organism's response to pathogens at the immunological, cellular, and molecular levels. In this review we describe how the study of host genetics in mouse models has helped our understanding of host defense mechanisms against viral infection, and how this knowledge can be extended to human infections. We focus especially on the innate mechanisms that function as the host's first line of defense against infection. We also discuss the main issues that confront this field, as well as its future. url: https://www.sciencedirect.com/science/article/pii/S0168952503001720 doi: 10.1016/s0168-9525(03)00172-0 id: cord-102905-rlee32x7 author: Leis, Jonathan title: Ilaprazole and other novel prazole-based compounds that bind Tsg101 inhibit viral budding of HSV-1/2 and HIV from cells date: 2020-05-04 words: 5755.0 sentences: 297.0 pages: flesch: 51.0 cache: ./cache/cord-102905-rlee32x7.txt txt: ./txt/cord-102905-rlee32x7.txt summary: In this report we show that tenatoprazole and a related prazole drug, ilaprazole, effectively block infectious Herpes Simplex Virus (HSV)-1/2 release from Vero cells in culture. Our results indicate that prazole-based compounds may represent a class of drugs with potential to be broad-spectrum antiviral agents against multiple enveloped viruses, by interrupting cellular Tsg101 interaction with maturing virus, thus blocking the budding process that releases particles from the cell. Tenatoprazole and esomeprazole were shown to quantitatively inhibit the release of infectious HIV-1 from 293T cells in culture, and it was suggested that these effects may be mediated via changes in viral interaction with Tsg101, a key component of the cellular ESCRT complex (5, 33) . Given multiple reports suggesting that herpes viruses also use cellular ESCRT proteins in their replication process (20) (21) (22) (23) we tested if the Tsg101-binding prazole drugs, which blocked budding of HIV-1, would also block the release of herpes viruses from cells. abstract: In many enveloped virus families, including HIV and HSV, a crucial, yet unexploited, step in the viral life cycle is releasing particles from the infected cell membranes. This release process is mediated by host ESCRT complex proteins, which is recruited by viral structural proteins and provides the mechanical means for membrane scission and subsequent viral budding. The prazole drug, tenatoprazole, was previously shown to bind to ESCRT complex member Tsg101 and quantitatively block the release of infectious HIV-1 from cells in culture. In this report we show that tenatoprazole and a related prazole drug, ilaprazole, effectively block infectious Herpes Simplex Virus (HSV)-1/2 release from Vero cells in culture. By electron microscopy, we found that both prazole drugs block the release of HSV particles from the cell nuclear membrane resulting in their accumulation in the nucleus. Ilaprazole also quantitatively blocks the release of HIV-1 from 293T cells with an EC50 of 0.8 μM, which is more potent than tenatoprazole. Finally, we synthesized and tested multiple novel prazole-based analogs that demonstrate both binding to Tsg101 and inhibition of viral egress in the nanomolar range of HIV-1 from 293T cells. Our results indicate that prazole-based compounds may represent a class of drugs with potential to be broad-spectrum antiviral agents against multiple enveloped viruses, by interrupting cellular Tsg101 interaction with maturing virus, thus blocking the budding process that releases particles from the cell. Importance These results provide the basis for the development of drugs that target enveloped virus budding that can be used ultimately to control multiple virus infections in humans. url: https://doi.org/10.1101/2020.05.04.075036 doi: 10.1101/2020.05.04.075036 id: cord-333810-57d4oopv author: Leroy, Éric Maurice title: L’Émergence du virus EBOLA chez l’homme: un long processus pas totalement élucidé date: 2015-05-31 words: 4845.0 sentences: 439.0 pages: flesch: 66.0 cache: ./cache/cord-333810-57d4oopv.txt txt: ./txt/cord-333810-57d4oopv.txt summary: Plusieurs études ont montré que la contamination de l''homme s''est parfois produite lors de la manipulation de carcasses infectées de gorilles, chimpanzés et de céphalophes [21, 41] Les grands singes se contamineraient eux-mêmes probablement directement auprès des chauves-souris, en particulier lorsque les animaux de ces espèces animales consomment en même temps les fruits d''un même arbre. Cette diversité génétique des souches virales observées chez les carcasses d''animaux morts exclut par conséquent une transmission du virus d''un individu à l''autre et suggère au contraire que l''infection des grands singes résulterait de contaminations simultanées mais indépendantes à partir de sources animales distinctes, probablement le réservoir naturel du virus Ébola [21, 45] . Je pense que cette impression est purement factuelle, et est amplifiée par la couverture médiatique des maladies dues à certains virus dont les chauves-souris sont réservoirs (SARS, Ébola, Marburg ...). abstract: SUMMARY Since 1976 Ebola virus regularly has caused small deadly outbreaks in Central Africa, usually controlled in a few months. For the first time, an Ebola epidemic of exceptional magnitude dramatically engulfed several countries in West Africa since December 2013. Major failures of implementing measures to prevent human-to-human transmissions are the main cause of this large-scale Ebola outbreak. After about one-week incubation period, the Ebola virus disease is characterized by a sudden onset of high fever leading to multiple hemorrhages and to widespread organ failure. Several bat species constitute the main reservoirs of Ebola viruses. Human contamination would occur either directly from bats, widely consumed by the local populations, or through animal species susceptible to Ebola infection, such as chimpanzees and gorillas. Alongside this “natural cycle”, an “epidemic cycle” involving domestic animals living in villages such as dogs or pigs, is seriously suggested. Thus, according to the diversity of concerned animals and their clinical infection form, modalities of human contamination can be multiple and are still largely unknown. In this context, all efforts that could be made to unravel the mystery of the Ebola virus emergence in humans and clarify modalities of the virus transmission, would allow for predicting or for anticipating the future occurrence of epidemics. This review aims to provide an exhaustive inventory of the Ebola ecology to highlight events governing the virus transmission to humans that still remain unsolved. url: https://api.elsevier.com/content/article/pii/S0001407919309409 doi: 10.1016/s0001-4079(19)30940-9 id: cord-346906-1wmp43ti author: Lewandowski, Kuiama title: Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples date: 2019-12-23 words: 6766.0 sentences: 328.0 pages: flesch: 43.0 cache: ./cache/cord-346906-1wmp43ti.txt txt: ./txt/cord-346906-1wmp43ti.txt summary: We determine its sensitivity compared to that of existing diagnostic methods and its accuracy compared to short-read (Illumina) sequencing, using clinical samples from hospital patients during an influenza season and samples from a controlled laboratory infection in ferrets. During the study, respiratory samples submitted to the clinical diagnostic laboratory were routinely tested by a PCR-based test using the GeneXpert assay (Cepheid) to detect influenza A and B viruses and respiratory syncytial virus (RSV). Comparing this final method with our original protocol, using triplicate extractions from the pooled set of influenza A virus-positive samples demonstrated no significant loss in performance in the more rapid protocol (Fig. S3) , and we adopted this approach as our routine protocol, giving a wet-lab processing time of ϳ8 h. Future application of this method will involve real-time laboratory testing of respiratory samples, running the platform head to head with existing clinical diagnostics to further assess sensitivity and specificity, and using influenza virus sequence data to investigate transmission events. abstract: Influenza is a major global public health threat as a result of its highly pathogenic variants, large zoonotic reservoir, and pandemic potential. Metagenomic viral sequencing offers the potential for a diagnostic test for influenza virus which also provides insights on transmission, evolution, and drug resistance and simultaneously detects other viruses. We therefore set out to apply the Oxford Nanopore Technologies sequencing method to metagenomic sequencing of respiratory samples. We generated influenza virus reads down to a limit of detection of 10(2) to 10(3) genome copies/ml in pooled samples, observing a strong relationship between the viral titer and the proportion of influenza virus reads (P = 4.7 × 10(−5)). Applying our methods to clinical throat swabs, we generated influenza virus reads for 27/27 samples with mid-to-high viral titers (cycle threshold [C(T)] values, <30) and 6/13 samples with low viral titers (C(T) values, 30 to 40). No false-positive reads were generated from 10 influenza virus-negative samples. Thus, Nanopore sequencing operated with 83% sensitivity (95% confidence interval [CI], 67 to 93%) and 100% specificity (95% CI, 69 to 100%) compared to the current diagnostic standard. Coverage of full-length virus was dependent on sample composition, being negatively influenced by increased host and bacterial reads. However, at high influenza virus titers, we were able to reconstruct >99% complete sequences for all eight gene segments. We also detected a human coronavirus coinfection in one clinical sample. While further optimization is required to improve sensitivity, this approach shows promise for the Nanopore platform to be used in the diagnosis and genetic analysis of influenza virus and other respiratory viruses. url: https://doi.org/10.1128/jcm.00963-19 doi: 10.1128/jcm.00963-19 id: cord-022830-tvt58gtn author: Li, Dan title: Fate of Foodborne Viruses in the “Farm to Fork” Chain of Fresh Produce date: 2015-10-08 words: 12200.0 sentences: 520.0 pages: flesch: 44.0 cache: ./cache/cord-022830-tvt58gtn.txt txt: ./txt/cord-022830-tvt58gtn.txt summary: In order to supply a basis to identify possible prevention and control strategies, this review intends to demonstrate the fate of foodborne viruses in the farm to fork chain of fresh produce, which include the introduction routes (contamination sources), the viral survival abilities at different stages, and the reactions of foodborne viruses towards the treatments used in food processing of fresh produce. In order to determine a basis to identify possible prevention and control efforts, this article reviewed the transmission routes and viral persistence of foodborne viruses (mainly NoVs and HAV) during the farm-to-fork chain of fresh produce, as well as the effect of treatments used in food processing of fresh produce on viruses. In this section the effect of radiation, both nonionizing and ionizing radiation, and high-pressure processing (HPP) will be discussed as nonthermal inactivation treatment options for enteric viruses in fresh produce. abstract: Norovirus (NoV) and hepatitis A virus (HAV) are the most important foodborne viruses. Fresh produce has been identified as an important vehicle for their transmission. In order to supply a basis to identify possible prevention and control strategies, this review intends to demonstrate the fate of foodborne viruses in the farm to fork chain of fresh produce, which include the introduction routes (contamination sources), the viral survival abilities at different stages, and the reactions of foodborne viruses towards the treatments used in food processing of fresh produce. In general, the preharvest contamination comes mainly from soli fertilizer or irrigation water, while the harvest and postharvest contaminations come mainly from food handlers, which can be both symptomatic and asymptomatic. Foodborne viruses show high stabilities in all the stages of fresh produce production and processing. Low‐temperature storage and other currently used preservation techniques, as well as washing by water have shown limited added value for reducing the virus load on fresh produce. Chemical sanitizers, although with limitations, are strongly recommended to be applied in the wash water in order to minimize cross‐contamination. Alternatively, radiation strategies have shown promising inactivating effects on foodborne viruses. For high‐pressure processing and thermal treatment, efforts have to be made on setting up treatment parameters to induce sufficient viral inactivation within a food matrix and to protect the sensory and nutritional qualities of fresh produce to the largest extent. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162173/ doi: 10.1111/1541-4337.12163 id: cord-329902-db7hl770 author: Li, Desheng title: Influenza A(H1N1)pdm09 Virus Infection in Giant Pandas, China date: 2014-03-17 words: 1381.0 sentences: 74.0 pages: flesch: 41.0 cache: ./cache/cord-329902-db7hl770.txt txt: ./txt/cord-329902-db7hl770.txt summary: We confirmed infection with influenza A(H1N1)pdm09 in giant pandas in China during 2009 by using virus isolation and serologic analysis methods. We confirmed infection with influenza A(H1N1)pdm09 in giant pandas in China during 2009 by using virus isolation and serologic analysis methods. Analyses showed that each of the 8 gene segments of the virus we isolated were closely related to pH1N1 viruses circulating among humans, including a human representative strain (A/California/04/2009) and a contemporary strain (A/Sichuan/1/2009); these viruses showed 98.6%-100% nt identity to the panda strain (online Technical Appendix Table 1 , wwwnc.cdc.gov/EID/ article/20/3/13-1531-Techapp1.pdf). One panda (Zhangka) had detectable pH1N1 and H3 subtype HI antibodies before infection; this serum sample was collected before the display of overt clinical signs in the animal but after the onset of the human pH1N1 outbreak in China. abstract: We confirmed infection with influenza A(H1N1)pdm09 in giant pandas in China during 2009 by using virus isolation and serologic analysis methods. This finding extends the host range of influenza viruses and indicates a need for increased surveillance for and control of influenza viruses among giant pandas. url: https://doi.org/10.3201/eid2003.131531 doi: 10.3201/eid2003.131531 id: cord-278250-dwok857k author: Li, Heng title: The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites date: 2019-08-19 words: 7452.0 sentences: 379.0 pages: flesch: 44.0 cache: ./cache/cord-278250-dwok857k.txt txt: ./txt/cord-278250-dwok857k.txt summary: We performed metagenomic sequencing of fecal samples to detect the bacterial microbiome and virome composition of healthy one-year-old rhesus monkeys housed at the IMBCAMS (Fig. 1) . We comprehensively analyzed the interactions among the gut virome, bacterial microbiome and metabolomes based on the above results there were noticeable differences in bacterial β-diversity between control and experimental animals, as determined using principal component analysis (PCA), and the results showed good repeatability within a single group (Additional file 2: Figure S2F ). Briefly, the fecal virome composition was noticeably altered after depletion of the bacterial microbiome, and the abundances of many DNA viruses, bacteriophages and RNA viruses in the gut were clearly decreased. As expected, the whole gut bacterial microbiome, including gram-positive and gram-negative bacteria (Additional file 2: Figure S2E ), was depleted after treatment with the antibiotic cocktail, except for Escherichia-Shigella species belonging to Proteobacteria, which were resistant to the cocktail. abstract: BACKGROUND: The gut microbiome is closely associated with the health of the host; although the interaction between the bacterial microbiome and the whole virome has rarely been studied, it is likely of medical importance. Examination of the interactions between the gut bacterial microbiome and virome of rhesus monkey would significantly contribute to revealing the gut microbiome composition. METHODS: Here, we conducted a metagenomic analysis of the gut microbiome of rhesus monkeys in a longitudinal cohort treated with an antibiotic cocktail, and we documented the interactions between the bacterial microbiome and virome. The depletion of viral populations was confirmed at the species level by real-time PCR. We also detected changes in the gut metabolome by GC-MS and LC-MS. RESULTS: A majority of bacteria were depleted after treatment with antibiotics, and the Shannon diversity index decreased from 2.95 to 0.22. Furthermore, the abundance-based coverage estimator (ACE) decreased from 104.47 to 33.84, and the abundance of eukaryotic viruses also changed substantially. In the annotation, 6 families of DNA viruses and 1 bacteriophage family were present in the normal monkeys but absent after gut bacterial microbiome depletion. Intriguingly, we discovered that changes in the gut bacterial microbiome composition may promote changes in the gut virome composition, and tryptophan, arginine, and quinone may play roles in the interaction between the bacterial microbiome and virome. CONCLUSION: Our results indicated that the clearly altered composition of the virome was correlated with depletion in the bacterial community and that metabolites produced by bacteria possibly play important roles in the interaction. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12985-019-1211-z) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12985-019-1211-z doi: 10.1186/s12985-019-1211-z id: cord-305336-wxiazglk author: Li, Ji Lian title: Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera date: 2014-01-21 words: 6907.0 sentences: 319.0 pages: flesch: 50.0 cache: ./cache/cord-305336-wxiazglk.txt txt: ./txt/cord-305336-wxiazglk.txt summary: In the present study, we showed that a plant-pathogenic RNA virus, tobacco ringspot virus (TRSV), could replicate and produce virions in honeybees, Apis mellifera, resulting in infections that were found throughout the entire body. While intracellular life cycle, species-level genetic variation, and pathogenesis of the virus in honeybee hosts remain to be determined, the increasing prevalence of TRSV in conjunction with other bee viruses from spring toward winter in infected colonies was associated with gradual decline of host populations and winter colony collapse, suggesting the negative impact of the virus on colony survival. Conventional RT-PCR was performed on RNA samples extracted from adult bees, Varroa mites, different tissues, and bee bread collected from the same colony for the presence and distribution of TRSV. abstract: Emerging and reemerging diseases that result from pathogen host shifts are a threat to the health of humans and their domesticates. RNA viruses have extremely high mutation rates and thus represent a significant source of these infectious diseases. In the present study, we showed that a plant-pathogenic RNA virus, tobacco ringspot virus (TRSV), could replicate and produce virions in honeybees, Apis mellifera, resulting in infections that were found throughout the entire body. Additionally, we showed that TRSV-infected individuals were continually present in some monitored colonies. While intracellular life cycle, species-level genetic variation, and pathogenesis of the virus in honeybee hosts remain to be determined, the increasing prevalence of TRSV in conjunction with other bee viruses from spring toward winter in infected colonies was associated with gradual decline of host populations and winter colony collapse, suggesting the negative impact of the virus on colony survival. Furthermore, we showed that TRSV was also found in ectoparasitic Varroa mites that feed on bee hemolymph, but in those instances the virus was restricted to the gastric cecum of Varroa mites, suggesting that Varroa mites may facilitate the spread of TRSV in bees but do not experience systemic invasion. Finally, our phylogenetic analysis revealed that TRSV isolates from bees, bee pollen, and Varroa mites clustered together, forming a monophyletic clade. The tree topology indicated that the TRSVs from arthropod hosts shared a common ancestor with those from plant hosts and subsequently evolved as a distinct lineage after transkingdom host alteration. This study represents a unique example of viruses with host ranges spanning both the plant and animal kingdoms. url: https://www.ncbi.nlm.nih.gov/pubmed/24449751/ doi: 10.1128/mbio.00898-13 id: cord-262752-bwofzbwa author: Li, Qianqian title: Current status on the development of pseudoviruses for enveloped viruses date: 2017-12-07 words: 3268.0 sentences: 179.0 pages: flesch: 37.0 cache: ./cache/cord-262752-bwofzbwa.txt txt: ./txt/cord-262752-bwofzbwa.txt summary: Early work by Witte and colleagues showed that when they used VSV to infect the cells in which MLV is packaged, they were able to harvest pseudovirus for use in neutralization antibody assays. Development of in vitro and in vivo rabies virus neutralization assays based on a high-titer pseudovirus system Development of a pseudotyped-lentiviral-vector-based neutralization assay for chikungunya virus infection Second generation of pseudotype-based serum neutralization assay for Nipah virus antibodies: sensitive and high-throughput analysis utilizing secreted alkaline phosphatase Use of vesicular stomatitis virus pseudotypes bearing Hantaan or Seoul virus envelope proteins in a rapid and safe neutralization test A neutralization test for specific detection of Nipah virus antibodies using pseudotyped vesicular stomatitis virus expressing green fluorescent protein Truncation of the human immunodeficiency virus-type-2 envelope glycoprotein allows efficient pseudotyping of murine leukemia virus retroviral vector particles Cholesterol supplementation during production increases the infectivity of retroviral and Lentiviral vectors pseudotyped with the vesicular stomatitis virus glycoprotein (VSV-G) abstract: Emerging and reemerging infectious diseases have a strong negative impact on public health. However, because many of these pathogens must be handled in biosafety level, 3 or 4 containment laboratories, research and development of antivirals or vaccines against these diseases are often impeded. Alternative approaches to address this issue have been vigorously pursued, particularly the use of pseudoviruses in place of wild‐type viruses. As pseudoviruses have been deprived of certain gene sequences of the virulent virus, they can be handled in biosafety level 2 laboratories. Importantly, the envelopes of these viral particles may have similar conformational structures to those of the wild‐type viruses, making it feasible to conduct mechanistic investigation on viral entry and to evaluate potential neutralizing antibodies. However, a variety of challenging issues remain, including the production of a sufficient pseudovirus yield and the inability to produce an appropriate pseudotype of certain viruses. This review discusses current progress in the development of pseudoviruses and dissects the factors that contribute to low viral yields. url: https://doi.org/10.1002/rmv.1963 doi: 10.1002/rmv.1963 id: cord-327000-oyg3oyx1 author: Li, Shasha title: Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response date: 2020-05-11 words: 11098.0 sentences: 688.0 pages: flesch: 48.0 cache: ./cache/cord-327000-oyg3oyx1.txt txt: ./txt/cord-327000-oyg3oyx1.txt summary: This review highlights the immune evasion mechanisms employed by PEDV, which provides insights for the better understanding of PEDV-host interactions and developing effective vaccines and antivirals against CoVs. Porcine epidemic diarrhea virus (PEDV) is the etiological agent of porcine epidemic diarrhea (PED) that causes an acute and highly contagious enteric disease of swine characterized by vomiting, diarrhea, dehydration, and anorexia in pigs of all ages, especially resulting in severe diarrhea and high mortality rate in piglets. Nsp3 is the largest nsp protein, containing two papain-like protease (PLP1 and PLP2) domains, of which PEDV PLP2 acts as a viral deubiquitinase (DUB), to negatively regulate type I IFN signaling [80] . The evasive strategies utilized by PEDV are classified into four major types: (1) inhibition of RLRs-mediated IFN production pathways, (2) inhibition of the activation of transcription factors responsible for IFN induction, (3) disruption of the signal cascades induced by IFN, and (4) hiding its viral RNA to avoid the exposure of viral RNA to immune sensors. abstract: Porcine epidemic diarrhea virus (PEDV), a swine enteropathogenic coronavirus (CoV), is the causative agent of porcine epidemic diarrhea (PED). PED causes lethal watery diarrhea in piglets, which has led to substantial economic losses in many countries and is a great threat to the global swine industry. Interferons (IFNs) are major cytokines involved in host innate immune defense, which induce the expression of a broad range of antiviral effectors that help host to control and antagonize viral infections. PEDV infection does not elicit a robust IFN response, and some of the mechanisms used by the virus to counteract the host innate immune response have been unraveled. PEDV evades the host innate immune response by two main strategies including: 1) encoding IFN antagonists to disrupt innate immune pathway, and 2) hiding its viral RNA to avoid the exposure of viral RNA to immune sensors. This review highlights the immune evasion mechanisms employed by PEDV, which provides insights for the better understanding of PEDV-host interactions and developing effective vaccines and antivirals against CoVs. url: https://doi.org/10.3390/pathogens9050367 doi: 10.3390/pathogens9050367 id: cord-332046-ihc031ly author: Li, Yan‐Chao title: Neurotropic virus tracing suggests a membranous‐coating‐mediated mechanism for transsynaptic communication date: 2013-01-01 words: 4865.0 sentences: 236.0 pages: flesch: 47.0 cache: ./cache/cord-332046-ihc031ly.txt txt: ./txt/cord-332046-ihc031ly.txt summary: This study has systematically examined the assembly and dissemination of HEV 67N in the primary motor cortex of infected rats and provides additional evidence indicating that mem-branous-coating-mediated endo-/exocytosis can be used by HEV for its transsynaptic transfer. Consistent with the results in the previous experiments, the present study showed that at day 4 p.i. HEV-positive cells were observed in only a certain population of neurons with different sizes in layer V of the primary motor cortex (Fig. 1A,B) . Extracellular virions were not enclosed by any vesicular structures, whereas vesicle-enclosed virus particles were otherwise observed in the axonal terminals touching on the infected neurons, so it seemed that the virions within the synapses had acquired new vesicular membrane after entry. D shows a virion within a coated vesicle (arrow; see also the inset for details) in the axon terminal adjacent to an infected pyramidal cell. abstract: Swine hemagglutinating encephalomyelitis virus (HEV) has been shown to have a capability to propagate via neural circuits to the central nervous system after peripheral inoculation, resulting in acute deadly encephalomyelitis in natural host piglets as well as in experimental younger rodents. This study has systematically examined the assembly and dissemination of HEV 67N in the primary motor cortex of infected rats and provides additional evidence indicating that membranous‐coating‐mediated endo‐/exocytosis can be used by HEV for its transsynaptic transfer. In addition, our results suggested that this transsynaptic pathway could adapted for larger granular materials, such as viruses. These findings should help in understanding the mechanisms underlying coronavirus infections as well as the intercellular exchanges occurring at the synaptic junctions. J. Comp. Neurol. 521:203–212, 2013. © 2012 Wiley Periodicals, Inc. url: https://doi.org/10.1002/cne.23171 doi: 10.1002/cne.23171 id: cord-002076-7t4d4vvo author: Li, Yongfeng title: Applications of Replicating-Competent Reporter-Expressing Viruses in Diagnostic and Molecular Virology date: 2016-05-06 words: 4996.0 sentences: 229.0 pages: flesch: 36.0 cache: ./cache/cord-002076-7t4d4vvo.txt txt: ./txt/cord-002076-7t4d4vvo.txt summary: Commonly used tests based on wild-type viruses, such as immunostaining, cannot meet the demands for rapid detection of viral replication, high-throughput screening for antivirals, as well as for tracking viral proteins or virus transport in real time. This article reviews the applications of RCREVs in diagnostic and molecular virology, including rapid neutralization tests, high-throughput screening systems, identification of viral receptors and virus-host interactions, dynamics of viral infections in vitro and in vivo, vaccination approaches and others. Replicating-competent reporter-expressing viruses (RCREVs) are one type of artificially modified viruses that not only retain the viral genetic characteristics but also possess the new properties of the reporter genes, which represent a useful tool for quantitative analysis of viral replication and tracking viral protein transport in both living cells and animals. abstract: Commonly used tests based on wild-type viruses, such as immunostaining, cannot meet the demands for rapid detection of viral replication, high-throughput screening for antivirals, as well as for tracking viral proteins or virus transport in real time. Notably, the development of replicating-competent reporter-expressing viruses (RCREVs) has provided an excellent option to detect directly viral replication without the use of secondary labeling, which represents a significant advance in virology. This article reviews the applications of RCREVs in diagnostic and molecular virology, including rapid neutralization tests, high-throughput screening systems, identification of viral receptors and virus-host interactions, dynamics of viral infections in vitro and in vivo, vaccination approaches and others. However, there remain various challenges associated with RCREVs, including pathogenicity alterations due to the insertion of a reporter gene, instability or loss of the reporter gene expression, or attenuation of reporter signals in vivo. Despite all these limitations, RCREVs have become powerful tools for both basic and applied virology with the development of new technologies for generating RCREVs, the inventions of novel reporters and the better understanding of regulation of viral replication. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4885082/ doi: 10.3390/v8050127 id: cord-278973-82n0d1dh author: Li, Zhijie title: Characterization and pathogenicity of a novel mammalian orthoreovirus from wild short-nosed fruit bats date: 2016-05-31 words: 3737.0 sentences: 207.0 pages: flesch: 53.0 cache: ./cache/cord-278973-82n0d1dh.txt txt: ./txt/cord-278973-82n0d1dh.txt summary: This study describes the isolation, molecular characterization and analysis of pathogenicity of MRV variant B/03 from wild short-nosed fruit bats. BALB/c mice experimentally infected with B/03 virus by intranasal inoculation developed severe respiratory distress with tissue damage and inflammation. MRV isolates were obtained from hosts with or without clinical signs of disease, and the virus can infect a broad range of mammals (Dermody et al., 2013) . In this study, we report the characterization of a novel MRV strain (called "B/03") isolated from healthy, wild shortnosed fruit bats in Guangdong province, China. In this study, one strain of MRV, B/03, was isolated by in vitro cell culture from thirty wild short-nosed fruit bat samples from Shaoguan city of China''s Guangdong province. Based on sequence comparison and phylogenetic analysis, we conclude that the B/03 isolate is a novel type 1 bat orthoreovirus, and it might have originated from gene segment mixing during infection with more than one MRV strain in nature. abstract: Mammalian orthoreoviruses (MRVs) have a wide range of geographic distribution and have been isolated from humans and various animals. This study describes the isolation, molecular characterization and analysis of pathogenicity of MRV variant B/03 from wild short-nosed fruit bats. Negative stain electron microscopy illustrated that the B/03 strain is a non-enveloped icosahedral virus with a diameter of 70 nm. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) migration patterns showed that the B/03 viral genome contains 10 segments in a 3:3:4 arrangement. The isolate belongs to MRV serotype 1 based on S1 gene nucleotide sequence data. BALB/c mice experimentally infected with B/03 virus by intranasal inoculation developed severe respiratory distress with tissue damage and inflammation. Lastly, B/03 virus has an increased transmission risk between bats and humans or animals. url: https://doi.org/10.1016/j.meegid.2016.05.039 doi: 10.1016/j.meegid.2016.05.039 id: cord-342906-51296y8d author: Li, Zhiping title: Aerosolized avian influenza virus by laboratory manipulations date: 2012-08-06 words: 4489.0 sentences: 230.0 pages: flesch: 46.0 cache: ./cache/cord-342906-51296y8d.txt txt: ./txt/cord-342906-51296y8d.txt summary: Many of the routine procedures used to process influenza virus for laboratory research, such as centrifugation or mixing, have a high potential of producing aerosols [21] , and the particle load of each has been estimated to be up to 1-5 μm. To this end, this study was designed to monitor the presence of aerosolized H5N1 virus produced by normal procedures used to process the virus for experimental research and by the most frequently associated "accidents" for each, such as container breakage and accidental subcutaneous injection. None of the aerosol samples collected from any group at the time directly prior to processing of the experiment had detectable levels of H5N1, as evidenced by negative reverse transcription (Rt)-PCR and HA text results. Our results provide evidence that many of the laboratory techniques used to process influenza virus for experimental analysis produce aerosols and, thereby, represent significant risks of infection to laboratory personnel and potential spread beyond the laboratory. abstract: BACKGROUND: Avian H5N1 influenza viruses present a challenge in the laboratory environment, as they are difficult to collect from the air due to their small size and relatively low concentration. In an effort to generate effective methods of H5N1 air removal and ensure the safety of laboratory personnel, this study was designed to investigate the characteristics of aerosolized H5N1 produced by laboratory manipulations during research studies. RESULTS: Normal laboratory procedures used to process the influenza virus were carried out independently and the amount of virus polluting the on-site atmosphere was measured. In particular, zootomy, grinding, centrifugation, pipetting, magnetic stirring, egg inoculation, and experimental zoogenetic infection were performed. In addition, common accidents associated with each process were simulated, including breaking glass containers, syringe injection of influenza virus solution, and rupturing of centrifuge tubes. A micro-cluster sampling ambient air pollution collection device was used to collect air samples. The collected viruses were tested for activity by measuring their ability to induce hemagglutination with chicken red blood cells and to propagate in chicken embryos after direct inoculation, the latter being detected by reverse-transcription PCR and HA test. The results showed that the air samples from the normal centrifugal group and the negative-control group were negative, while all other groups were positive for H5N1. CONCLUSIONS: Our findings suggest that there are numerous sources of aerosols in laboratory operations involving H5N1. Thus, laboratory personnel should be aware of the exposure risk that accompanies routine procedures involved in H5N1 processing and take proactive measures to prevent accidental infection and decrease the risk of virus aerosol leakage beyond the laboratory. url: https://doi.org/10.1186/1743-422x-9-146 doi: 10.1186/1743-422x-9-146 id: cord-336157-aqc9zrrm author: Liang, Guodong title: Factors responsible for the emergence of arboviruses; strategies, challenges and limitations for their control date: 2015-03-25 words: 4111.0 sentences: 221.0 pages: flesch: 42.0 cache: ./cache/cord-336157-aqc9zrrm.txt txt: ./txt/cord-336157-aqc9zrrm.txt summary: Slave trading of Africans to the Americas, during the 16th to the 19th century was responsible for the first recorded emergence in the New World of two arthropod-borne viruses (arboviruses), yellow fever virus and dengue virus. [2] [3] Chikungunya virus (CHIKV), West Nile virus (WNV) and dengue virus (DENV) are three of a large number of neglected human pathogenic arthropod-borne viruses (arboviruses) whose combined figures for morbidity and mortality far exceed those for Ebola, severe acute respiratory syndrome and Middle East respiratory syndrome viruses. However, many other arthropod species, in which viruses have been identified, may be involved in perpetuating the virus life cycle without having been associated with overt disease in humans or animals. 55 However, implementation of temporary localized arthropod control measures during epidemics, for example in high density urbanized areas, can still play an important but transient role in reducing the impact on humans and animals of emerging arboviruses. abstract: Slave trading of Africans to the Americas, during the 16th to the 19th century was responsible for the first recorded emergence in the New World of two arthropod-borne viruses (arboviruses), yellow fever virus and dengue virus. Many other arboviruses have since emerged from their sylvatic reservoirs and dispersed globally due to evolving factors that include anthropological behaviour, commercial transportation and land-remediation. Here, we outline some characteristics of these highly divergent arboviruses, including the variety of life cycles they have developed and the mechanisms by which they have adapted to evolving changes in habitat and host availability. We cite recent examples of virus emergence that exemplify how arboviruses have exploited the consequences of the modern human lifestyle. Using our current understanding of these viruses, we also attempt to demonstrate some of the limitations encountered in developing control strategies to reduce the impact of future emerging arbovirus diseases. Finally, we present recommendations for development by an international panel of experts reporting directly to World Health Organization, with the intention of providing internationally acceptable guidelines for improving emerging arbovirus disease control strategies. Success in these aims should alleviate the suffering and costs encountered during recent decades when arboviruses have emerged from their sylvatic environment. url: https://www.ncbi.nlm.nih.gov/pubmed/26038768/ doi: 10.1038/emi.2015.18 id: cord-258489-pyfc7jde author: Lico, Chiara title: Viral vectors for production of recombinant proteins in plants date: 2008-03-10 words: 11091.0 sentences: 527.0 pages: flesch: 39.0 cache: ./cache/cord-258489-pyfc7jde.txt txt: ./txt/cord-258489-pyfc7jde.txt summary: In this review, we will focus on transient production strategies using plant viral expression systems, with a particular focus on the variety of proteins produced, and their applications. The unique properties of viruses such as ease of manipulation, high level amplification, site specific recombination, strong infectivity, enhanced translation and compact and repetitive morphological structure have enabled their broad application, from basic research to product development, including the generation of robust expression systems. From the discovery of viruses in 1898 (tobacco mosaic virus, TMV) (Bos, 1999) , to the first demonstration of RNAs role in virus replication by turnip yellow mosaic virus (TYMV) (Matthews, 1989) , to the very recent discovery of gene silencing and its implication in host response to infection, gene regulation and transgene expression (Baulcombe, 1999; Lu et al., 2003; Waterhouse and Helliwell, 2003) , plant virology has played a crucial role in the understanding of the most fundamental concepts of modern biology. Thanks to the recent improvements of viral-based vectors, mAbs have been produced with transient expression systems to quickly achieve much higher production levels along with other complex proteins. abstract: Global demand for recombinant proteins has steadily accelerated for the last 20 years. These recombinant proteins have a wide range of important applications, including vaccines and therapeutics for human and animal health, industrial enzymes, new materials and components of novel nano‐particles for various applications. The majority of recombinant proteins are produced by traditional biological “factories,” that is, predominantly mammalian and microbial cell cultures along with yeast and insect cells. However, these traditional technologies cannot satisfy the increasing market demand due to prohibitive capital investment requirements. During the last two decades, plants have been under intensive investigation to provide an alternative system for cost‐effective, highly scalable, and safe production of recombinant proteins. Although the genetic engineering of plant viral vectors for heterologous gene expression can be dated back to the early 1980s, recent understanding of plant virology and technical progress in molecular biology have allowed for significant improvements and fine tuning of these vectors. These breakthroughs enable the flourishing of a variety of new viral‐based expression systems and their wide application by academic and industry groups. In this review, we describe the principal plant viral‐based production strategies and the latest plant viral expression systems, with a particular focus on the variety of proteins produced and their applications. We will summarize the recent progress in the downstream processing of plant materials for efficient extraction and purification of recombinant proteins. J. Cell. Physiol. 216: 366–377, 2008. © 2008 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/18330886/ doi: 10.1002/jcp.21423 id: cord-288930-h13cxuh3 author: Lim, Faye J title: Viral Etiology and the Impact of Codetection in Young Children Presenting With Influenza-Like Illness date: 2016-07-20 words: 3429.0 sentences: 179.0 pages: flesch: 42.0 cache: ./cache/cord-288930-h13cxuh3.txt txt: ./txt/cord-288930-h13cxuh3.txt summary: METHODS: Children aged 6 to 59 months who presented to a tertiary pediatric hospital between influenza seasons 2008 and 2012 with fever and acute respiratory symptoms were enrolled, and nasal samples were collected. We compared demographics, presenting symptoms, and clinical outcomes of children with a single-virus infection and those in whom 2 or more viruses were detected (virus-virus codetection). With this study, we describe the virology of ARTI in children aged 6 months to 4 years who presented to a tertiary pediatric hospital in Australia with influenza-like illness during influenza season. We conclude that the impact of virus-virus codetection on disease severity in children who present with influenza-like illness is likely to be limited to those infected with specific pathogen pairs. Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children abstract: BACKGROUND: Children with acute respiratory tract infection (ARTI) frequently exhibit virus-virus codetection, yet the clinical significance of ARTI remains contentious. Using data from a prospective cohort of children with influenza-like illness, we examined the virology of ARTI and determined the clinical impact of virus-virus codetection. METHODS: Children aged 6 to 59 months who presented to a tertiary pediatric hospital between influenza seasons 2008 and 2012 with fever and acute respiratory symptoms were enrolled, and nasal samples were collected. Respiratory viruses were identified by culture and polymerase chain reaction. We compared demographics, presenting symptoms, and clinical outcomes of children with a single-virus infection and those in whom 2 or more viruses were detected (virus-virus codetection). We used logistic regression models and estimated marginal means to calculate the adjusted odds ratios and probabilities of symptom presentation, prescription of antibiotics, and hospitalization. RESULTS: Of 2356 children, a virus was detected in 1630 (69.2%) of them; rhinovirus (40.8%), influenza (29.5%), and respiratory syncytial virus (26.4%) were detected most commonly. Two or more viruses were detected in 25% of these children. After we adjusted for demographic factors, children with virus-virus codetection had greater odds of presenting with cough (adjusted odds ratio [aOR], 1.9; 95% confidence interval [CI], 1.2–3.1) and rhinorrhea (aOR, 1.8; 95% CI, 1.1–2.9) than those with a single-virus infection, although both symptoms were common. Children with influenza and respiratory syncytial virus combined had the highest probability of hospitalization (55%; 95% CI, 35%–73%), which was significantly greater than for those with influenza infection alone (22%; 95% CI, 16%–29%). CONCLUSIONS: Overall, virus-virus codetection has limited impact on clinical severity among children with influenza-like illness. However, infection with specific pathogen pairs might be associated with more severe outcomes. Routine diagnostics to identify specific viruses should be restricted to common pathogens. url: https://doi.org/10.1093/jpids/piw042 doi: 10.1093/jpids/piw042 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-269193-a647hwu9 author: Lin, Debby A. title: Evolutionary relatedness of the predicted gene product of RNA segment 2 of the Tick-Borne Dhori virus and the PB1 polymerase gene of influenza viruses date: 1991-05-31 words: 2946.0 sentences: 152.0 pages: flesch: 57.0 cache: ./cache/cord-269193-a647hwu9.txt txt: ./txt/cord-269193-a647hwu9.txt summary: Abstract The complete nucleotide sequence of the second largest RNA segment of Dhori/India/1313/61 virus was determined and the deduced amino acid sequence was compared with the polymerase (P) proteins of influenza A, B, and C viruses. The viral RNAs have been shown to encode information in the negative-sense (Clerx et al., 1983; Fuller et al., 1987; Freedman-Faulstich and Fuller, 1990) and it was previously shown that the Dhori nucleoprotein (encoded by RNA segment 5) shares conserved amino acid sequences with the influenza A, B, and C virus nucleoproteins (Fuller et al., 1987) . The PBl polymerase proteins are the most highly conserved among the proteins of the influenza A, B, and C viruses (Yamashita et a/,, 1989 ) and they are most likely required for nucleotide addition during viral RNA synthesis (Braam et al., 1983) . abstract: Abstract The complete nucleotide sequence of the second largest RNA segment of Dhori/India/1313/61 virus was determined and the deduced amino acid sequence was compared with the polymerase (P) proteins of influenza A, B, and C viruses. RNA segment 2 (2224 nucleotides) of Dhori virus contains a single long open reading frame that can encode a 716-amino amid polypeptide (81.3 kDa). The predicted polypeptide shares between 27 and 31% sequence identities with the PB1 polypeptides of influenza A, B, and C viruses. Among the regions most highly conserved are the sequences around the Asp-Asp motif common to many RNA polymerases. In spite of the high level of sequence identity between the Dhori RNA segment 2 gene product and the influenza A, B, and C virus PB1 proteins the amino acid composition of the Dhori protein indicates an acidic charge feature at pH 7.0 in contrast to the basic nature of the PB1 proteins of the influenza viruses. We suggest that the Dhori PB1-like protein be designated the Pα protein of this virus. url: https://www.ncbi.nlm.nih.gov/pubmed/2024457/ doi: 10.1016/0042-6822(91)90641-n id: cord-339423-5qym9dsf author: Lina, B. title: Virus émergents ou menaces à répétition date: 2005-05-31 words: 2886.0 sentences: 263.0 pages: flesch: 65.0 cache: ./cache/cord-339423-5qym9dsf.txt txt: ./txt/cord-339423-5qym9dsf.txt summary: L''analyse des mécanismes ayant permis l''apparition de ces virus montre que pour chaque virus émergent décrit, il ne s''agit en aucun cas de phénomènes purement aléatoires, mais bien de l''accumulation de facteurs qui permettent à ces agents infectieux de diffuser de l''animal vers l''homme. À chaque fois, cette émergence est considérée par le grand public comme un nouveau fléau pouvant potentiellement être responsable d''une mortalité très élevée, ce qui entraîne souvent des comportements irrationnels, ceci d''autant plus que l''importante mortalité autrefois liée aux infections virales et bactériennes a été oubliée (vaccinations et antibiotiques obligent) [2, 3] . Les années 2003 et 2004 ont été particulièrement instructives, permettant d''observer l''épidémie du Syndrome Respiratoire Aigu Sévère ou SRAS [4] , l''émergence de deux épidémies de grippe aviaire transmise à l''homme (influenza A H7N7 en Europe et A H5N1 en Asie) [5, 6] , l''apparition de cas de monkey pox [7] , et la diffusion du virus West Nile sur la quasi totalité du continent Nord Américain [8] . abstract: Résumé Les virus émergents ont défrayé la chronique durant les années 2003 et 2004. À cette occasion sont réapparues les peurs antiques concernant l’apparition d’un agent infectieux hautement pathogène, pouvant provoquer des épidémies associées à une mortalité élevée. Ces phénomènes sont clairement des menaces à répétition. L’analyse des mécanismes ayant permis l’apparition de ces virus montre que pour chaque virus émergent décrit, il ne s’agit en aucun cas de phénomènes purement aléatoires, mais bien de l’accumulation de facteurs qui permettent à ces agents infectieux de diffuser de l’animal vers l’homme. Différents modes d’infection existent, soit par transmission directe, soit par l’intermédiaire des vecteurs (moustiques, tiques ou autres animaux). La conjonction de facteurs écologiques, économiques et épidémiologiques font que ces épidémies naissent et éventuellement diffusent. Grâce au développement des réseaux de surveillance et à l’amélioration des techniques diagnostiques, les virus responsables de ces épidémies sont mieux identifiés. Les expériences récentes du SRAS et de la grippe aviaire en sont les meilleurs exemples. Abstract Emergent viruses have attracted attention during years 2003 and 2004. Ancient fears have reappeared regarding pathogenic agents, capable to result in epidemics with high mortality rates. Such events constitute really repeated threats. The analysis of mechanisms permitting emergence of these viruses has shown that they are not random phenomenons, but they result from accumulated factors leading to transmission from animals to men. Several modes of transmission of infection include: either direct transmission, or by intermediate vectors (mosquitoes, ticks and other (mammals) animals). Convergence of ecologic, economic and epidemiologic factors confer to the epidemics potential ability do spread widely. With the development of surveillance networks and improvement in diagnostic technologies, these “new” viruses are better identified. Recent occurrence of SARS and of the avian influenza are best examples of such experiences. url: https://api.elsevier.com/content/article/pii/S129455010580175X doi: 10.1016/s1294-5501(05)80175-x 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-003130-p2h8p5bm author: Lindqvist, Richard title: Tick-Borne Flaviviruses and the Type I Interferon Response date: 2018-06-21 words: 8350.0 sentences: 481.0 pages: flesch: 48.0 cache: ./cache/cord-003130-p2h8p5bm.txt txt: ./txt/cord-003130-p2h8p5bm.txt summary: There are more than 70 viruses in the genus flavivirus, and they are transmitted by arthropods such as mosquitoes (dengue virus (DENV), Japanese encephalitis virus (JEV) and West Nile virus (WNV), yellow fever virus (YFV), and Zika virus (ZIKV) and ticks (tick-borne encephalitis virus (TBEV), Langat virus (LGTV), Kyasanur forest disease virus (KFDV), Omsk hemorrhagic fever virus (OHFV), Powassan virus (POWV), and Louping-ill virus (LIV)) [1] [2] [3] [4] [5] . Two other ISGs which have been shown to be antivirally active against TBEV are virus inhibitory protein endoplasmic reticulum associated interferon inducible (viperin) and tripartite motif-79α (TRIM79α). The role of interferon in tick-borne encephalitis virus-infected l cells. A functional toll-like receptor 3 gene (tlr3) may be a risk factor for tick-borne encephalitis virus (tbev) infection Analysis of tick-borne encephalitis virus-induced host responses in human cells of neuronal origin and interferon-mediated protection abstract: Flaviviruses are globally distributed pathogens causing millions of human infections every year. Flaviviruses are arthropod-borne viruses and are mainly transmitted by either ticks or mosquitoes. Mosquito-borne flaviviruses and their interactions with the innate immune response have been well-studied and reviewed extensively, thus this review will discuss tick-borne flaviviruses and their interactions with the host innate immune response. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6071234/ doi: 10.3390/v10070340 id: cord-003004-iif2lnez author: Linster, Martin title: Clinical and Molecular Epidemiology of Human Parainfluenza Viruses 1–4 in Children from Viet Nam date: 2018-05-01 words: 4121.0 sentences: 223.0 pages: flesch: 49.0 cache: ./cache/cord-003004-iif2lnez.txt txt: ./txt/cord-003004-iif2lnez.txt summary: The present study describes species-specific clinical presentation, the genetic variability and HPIV circulation in Viet Nam. The outcome of RSV infection in hospitalized children under 2 years of age presenting with acute lower respiratory infection (ALRI) in Ho Chi Minh City was described previously 17 . Samples were sourced from two previous acute respiratory infection (ARI) cohorts among in-and outpatients, that were conducted at Children''s Hospital 1 and 2 in Ho Chi Minh City, Viet Nam during years 2009 and 2010. For sequencing, HPIV-positive samples were further amplified in a hemi-nested PCR approach with newly designed species-specific primers targeting overlapping regions of the viral genome (Table S2) . In this study, the median age and gender distribution of infected children and frequency of clinical presentation (fever, cough, sore throat, runny nose and nasal congestion) as well as vital signs (pulse and respiratory rate) and duration of illness at presentation were similar between HPIV species (p > 0.05). abstract: HPIVs are serologically and genetically grouped into four species that account for up to 10% of all hospitalizations due to acute respiratory infection in children under the age of five. Genetic and epidemiological data for the four HPIVs derived from two pediatric cohorts in Viet Nam are presented. Respiratory samples were screened for HPIV1–4 by real-time PCR. Demographic and clinical data of patients infected with different HPIV were compared. We used a hemi-nested PCR approach to generate viral genome sequences from HPIV-positive samples and conducted a comprehensive phylogenetic analysis. In total, 170 samples tested positive for HPIV. HPIV3 was most commonly detected in our cohort and 80 co-detections of HPIV with other respiratory viruses were found. Phylogenetic analyses suggest local endemic circulation as well as punctuated introductions of new HPIV lineages. Viral gene flow analysis revealed that Viet Nam is a net importer of viral genetic diversity. Epidemiological analyses imply similar disease severity for all HPIV species. HPIV sequences from Viet Nam formed local clusters and were interspersed with sequences from diverse geographic regions. Combined, this new knowledge will help to investigate global HPIV circulation patterns in more detail and ultimately define more suitable vaccine strains. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5931535/ doi: 10.1038/s41598-018-24767-4 id: cord-017959-g0nf1iwm author: Lipkin, W. Ian title: Diagnosis, Discovery and Dissection of Viral Diseases date: 2014-02-27 words: 5016.0 sentences: 216.0 pages: flesch: 37.0 cache: ./cache/cord-017959-g0nf1iwm.txt txt: ./txt/cord-017959-g0nf1iwm.txt summary: Nested PCR tests that can employ consensus or specifi c primers in two sequential amplifi cation reactions with either one (hemi-nested) or two (fully nested) primers located 3′ with respect to the fi rst primer set may both accommodate sequence variation and be more sensitive than fl uorescent or beacon-based singleplex assays. Whereas multiplex PCR systems support rapid highthroughput diagnosis with highest sensitivity for a limited number of agents, microarray-based systems provide detection of all known pathogens for which sequence information is available, but at the expense of some degree of sensitivity. Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fl uid microbead-based assay MassTag polymerasechain-reaction detection of respiratory pathogens, including a new rhinovirus genotype, that caused infl uenza-like illness in New York State during abstract: Only a few years ago, viral diagnosis was largely an exercise for academic researchers and public health practitioners with focus on epidemiologic analyses and outbreak prevention, detection, and control. Opportunities for therapeutic intervention were limited to only a few applications such as herpesvirus infections, influenza, and HIV/AIDS; hence, once a bacterial or fungal infection was excluded, clinicians were limited to providing supportive care for what was presumed to be a viral syndrome. Public health organizations tracked the incidence of viral infections and the development of resistance to the few antiviral drugs in use and provided input to governments and the pharmaceutical industry regarding selection of vaccine targets. More recently, interest in viral diagnostics has burgeoned with the advent of new tools for detection and discovery, global recognition of pandemic risk, high-throughput drug screening, rational drug design, and immunotherapeutics. An additional impetus has been the implication of viruses in chronic illnesses not previously attributed to infection. The objective of this chapter is to review the factors responsible for the rise in awareness of viral infections, methods for diagnosis and monitoring viral infections, and future prospects for improvements in discovery, detection, and response to the challenges of clinical virology. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122662/ doi: 10.1007/978-1-4899-7448-8_2 id: cord-021116-rh0e4n2w author: Lippens, Ronnie title: Viral Contagion and Anti-Terrorism: Notes on Medical Emergency, Legality and Diplomacy date: 2004 words: 5100.0 sentences: 259.0 pages: flesch: 56.0 cache: ./cache/cord-021116-rh0e4n2w.txt txt: ./txt/cord-021116-rh0e4n2w.txt summary: This paper traces the main outlines of this emerging imaginary that has left notions of Empire as spheres of integrative production firmly behind, and is now geared towards imagining Empire as a complete, organic body of free-but-organic-and-therefore-orderly flows that however needs to be kept intact by means of epidemiological interventions aimed at excluding or neutralizing viral entities. Law and diplomacy were important technologies (however repressive at times) by which nation-states as well as Empires were held together, or indeed, by which they were produced or maintained, and by which they were made to be productive. There is no need for the productive negotiations of a ''cosmopolitan globalism'' either (to use Mikkel Rasmussen''s words 30 ), nor for reconciliatory efforts (one does not reconcile with viruses): the sanitary exclusion of viral contagion will suffice to keep the body of today''s imperial new world order healthy. abstract: The dominant imagery in current international relations seems to betray the emergence of an imperialist imaginary that differs markedly from an earlier one. This paper traces the main outlines of this emerging imaginary that has left notions of Empire as spheres of integrative production firmly behind, and is now geared towards imagining Empire as a complete, organic body of free-but-organic-and-therefore-orderly flows that however needs to be kept intact by means of epidemiological interventions aimed at excluding or neutralizing viral entities. Dealing with terrorism, or invading states that allegedly breed them, in this imaginary, is first and foremost a matter of medical necessity and urgency. The legal and diplomatic 'logic' of UN resolutions (Resolution 1441 for example), in this imaginary space, can only be imagined as being of secondary importance. Cooperation and `cosmopolitan' negotiation, as alternatives, disappear in this imaginary that projects an imperialist globalism of epidemiological purity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149041/ doi: 10.1023/b:sela.0000033617.97749.13 id: cord-000708-iuo2cw23 author: Lippé, Roger title: Deciphering Novel Host–Herpesvirus Interactions by Virion Proteomics date: 2012-05-28 words: 5052.0 sentences: 261.0 pages: flesch: 43.0 cache: ./cache/cord-000708-iuo2cw23.txt txt: ./txt/cord-000708-iuo2cw23.txt summary: These studies include the alphaherpesvirinae herpes simplex virus type 1 (HSV-1) and pseudorabies virus (PRV; Loret et al., 2008; Kramer et al., 2011) , the betaherpesvirinae human and murine cytomegaloviruses (HCMV and MCMV, respectively; Kattenhorn et al., 2004; Varnum et al., 2004) and the gammaherpesvirinae Kaposi sarcoma herpesvirus (KSHV), gamma herpesvirus 68 (γHV68), Epstein-Barr virus (EBV), and Alcelaphine (Bortz et al., 2003; Johannsen et al., 2004; Bechtel et al., 2005; Zhu et al., 2005; Dry et al., 2008) . Cellular stress rather than stage of the cell cycle enhances the replication and plating efficiencies of herpes simplex virus type 1 ICP0-viruses Perturbation of cell cycle progression and cellular gene expression as a function of herpes simplex virus ICP0 Herpes simplex virus 1 alpha regulatory protein ICP0 interacts with and stabilizes the cell cycle regulator cyclin D3 Identification and functional evaluation of cellular and viral factors involved in the alteration of nuclear architecture during herpes simplex virus 1 infection abstract: Over the years, a vast array of information concerning the interactions of viruses with their hosts has been collected. However, recent advances in proteomics and other system biology techniques suggest these interactions are far more complex than anticipated. One particularly interesting and novel aspect is the analysis of cellular proteins incorporated into mature virions. Though sometimes considered purification contaminants in the past, their repeated detection by different laboratories suggests that a number of these proteins are bona fide viral components, some of which likely contribute to the viral life cycles. The present mini review focuses on cellular proteins detected in herpesviruses. It highlights the common cellular functions of these proteins, their potential implications for host–pathogen interactions, discusses technical limitations, the need for complementing methods and probes potential future research avenues. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390586/ doi: 10.3389/fmicb.2012.00181 id: cord-002337-8v907g24 author: Lipsitch, Marc title: Viral factors in influenza pandemic risk assessment date: 2016-11-11 words: 18953.0 sentences: 845.0 pages: flesch: 40.0 cache: ./cache/cord-002337-8v907g24.txt txt: ./txt/cord-002337-8v907g24.txt summary: Preference for a2,6-linked mammalian sialic acid receptors over a2,3-linked avian ones HA pH of activation HA avoids extracellular inactivation and undergoes conformational changes leading to membrane fusion at appropriate pH for human cells (5.0-5.4 or perhaps 5.5) (Russell, 2014) Polymerase complex efficiency Efficient replication in human cells (Cauldwell et al., 2014; Naffakh et al., 2008) Virus morphology Filamentous morphology associated with several adaptations to mammals (Seladi-Schulman et al., 2014; Seladi-Schulman et al., 2013; Campbell et al., 2014; Beale et al., 2014) Length of NA stalk Longer stalk of NA required to penetrate human mucus and deaggregate virions (Blumenkrantz et al., 2013) Antagonism of interferon production Species-specific binding of the NS1 protein to host factors (Rajsbaum et al., 2012) HA-NA "balance" Substrate selectivity and catalytic rate of NA are calibrated to "balance" avidity of HA for the cell-surface glycan receptor (Zanin et al., 2015; Baum and Paulson, 1991; Yen et al., 2011; Handel et al., 2014) DOI: 10.7554/eLife.18491.006 Glaser et al., 2005) ; most human H2 and H3 seasonal isolates (Connor et al., 1994; Matrosovich et al., 2000) *These anomalous results are speculated by the authors to be possibly, or even probably the result of laboratory adaptation to egg passage and may not reflect the properties of the primary isolate. abstract: The threat of an influenza A virus pandemic stems from continual virus spillovers from reservoir species, a tiny fraction of which spark sustained transmission in humans. To date, no pandemic emergence of a new influenza strain has been preceded by detection of a closely related precursor in an animal or human. Nonetheless, influenza surveillance efforts are expanding, prompting a need for tools to assess the pandemic risk posed by a detected virus. The goal would be to use genetic sequence and/or biological assays of viral traits to identify those non-human influenza viruses with the greatest risk of evolving into pandemic threats, and/or to understand drivers of such evolution, to prioritize pandemic prevention or response measures. We describe such efforts, identify progress and ongoing challenges, and discuss three specific traits of influenza viruses (hemagglutinin receptor binding specificity, hemagglutinin pH of activation, and polymerase complex efficiency) that contribute to pandemic risk. DOI: http://dx.doi.org/10.7554/eLife.18491.001 url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5156527/ doi: 10.7554/elife.18491 id: cord-273372-69rlh9or author: Litterman, Nadia title: Small molecules with antiviral activity against the Ebola virus date: 2015-02-09 words: 3257.0 sentences: 157.0 pages: flesch: 48.0 cache: ./cache/cord-273372-69rlh9or.txt txt: ./txt/cord-273372-69rlh9or.txt summary: In addition we propose that a collaborative database for sharing such published and novel information on small molecules is needed for the research community studying the Ebola virus. We have found that indeed there is much prior knowledge regarding small molecules that have been shown to be active against the Ebola virus in vitro or in animal models 10-13 , including a number of FDA-approved drugs 14-16 . Medicinal chemistry analysis of small molecules active against the Ebola virus We have recently described an expert''s medicinal chemistry 26 analysis of the over 320 NIH probe compounds using public and commercial sources of chemical structures and the issues related to doing this type of analysis 27 . By organizing the data on small molecules tested against the Ebola virus similarly in a central database and using machine learning models based on public data may help identify additional compounds for testing. abstract: The recent outbreak of the Ebola virus in West Africa has highlighted the clear shortage of broad-spectrum antiviral drugs for emerging viruses. There are numerous FDA approved drugs and other small molecules described in the literature that could be further evaluated for their potential as antiviral compounds. These molecules are in addition to the few new antivirals that have been tested in Ebola patients but were not originally developed against the Ebola virus, and may play an important role as we await an effective vaccine. The balance between using FDA approved drugs versus novel antivirals with minimal safety and no efficacy data in humans should be considered. We have evaluated 55 molecules from the perspective of an experienced medicinal chemist as well as using simple molecular properties and have highlighted 16 compounds that have desirable qualities as well as those that may be less desirable. In addition we propose that a collaborative database for sharing such published and novel information on small molecules is needed for the research community studying the Ebola virus. url: https://doi.org/10.12688/f1000research.6120.1 doi: 10.12688/f1000research.6120.1 id: cord-343350-04e6wvov author: Liu, Haipeng title: Antiviral immunity in crustaceans date: 2009-02-15 words: 8002.0 sentences: 441.0 pages: flesch: 43.0 cache: ./cache/cord-343350-04e6wvov.txt txt: ./txt/cord-343350-04e6wvov.txt summary: White spot syndrome virus (WSSV) infects specific hemocytes of the shrimp Penaeus merguiensis Preliminary study on haemocyte response to white spot syndrome virus infection in black tiger shrimp Penaeus monodon Time-course and levels of apoptosis in various tissues of black tiger shrimp Penaeus monodon infected with white-spot syndrome virus Protein expression profiling of the shrimp cellular response to white spot syndrome virus infection Cloning and characterization of a caspase gene from black tiger shrimp (Penaeus monodon)-infected with white spot syndrome virus (WSSV) Immunological responses of Penaeus monodon to DNA vaccine and its efficacy to protect shrimp against white spot syndrome virus (WSSV) Multiple envelope proteins are involved in white spot syndrome virus (WSSV) infection in crayfish Identification of white spot syndrome virus (WSSV) envelope proteins involved in shrimp infection DNA fragmentation, an indicator of apoptosis, in cultured black tiger shrimp Penaeus monodon infected with white spot syndrome virus (WSSV) abstract: Viral diseases of shrimp have caused negative effects on the economy in several countries in Asia, South America and America, where they have numerous shrimp culture industries. The studies on the immunity of shrimp and other crustaceans have mainly focused on general aspects of immunity and as a consequence little is known about the antiviral responses in crustaceans. The aim of this review is to update recent knowledge of innate immunity against viral infections in crustaceans. Several antiviral molecules have been isolated and characterized recently from decapods. Characterization and identification of these molecules might provide a promising strategy for protection and treatment of these viral diseases. In addition dsRNA-induced antiviral immunity is also included. url: https://www.ncbi.nlm.nih.gov/pubmed/19223016/ doi: 10.1016/j.fsi.2009.02.009 id: cord-264308-y6xuxj16 author: Liu, Rui title: Mouse lung slices: An ex vivo model for the evaluation of antiviral and anti-inflammatory agents against influenza viruses date: 2015-05-26 words: 7663.0 sentences: 403.0 pages: flesch: 55.0 cache: ./cache/cord-264308-y6xuxj16.txt txt: ./txt/cord-264308-y6xuxj16.txt summary: In this study, we established an ex vivo model using mouse lung slices to evaluate both antiviral and anti-inflammatory agents against influenza virus infection. Our results suggested that mouse lung slices provide a robust, convenient and cost-efficient model for the assessment of both antiviral and anti-inflammatory agents against influenza virus infection in one assay. Our results showed that the lung slice model provides a robust, convenient and cost-economical method for the screening and evaluation of both antiviral and anti-inflammatory agents against influenza virus infection in one assay. To meet the goal of this study in the establishment of an ex vivo mouse slice model for the screening and evaluation of both antiviral and anti-inflammatory drugs against influenza infection in one assay, ensuring that the ex vivo model has similar patterns in influenza-induced cytokine and chemokine responses is critical. abstract: The influenza A virus is notoriously known for its ability to cause recurrent epidemics and global pandemics. Antiviral therapy is effective when treatment is initiated within 48 h of symptom onset, and delaying treatment beyond this time frame is associated with decreased efficacy. Research on anti-inflammatory therapy to ameliorate influenza-induced inflammation is currently underway and seems important to the impact on the clinical outcome. Both antiviral and anti-inflammatory drugs with novel mechanisms of action are urgently needed. Current methods for evaluating the efficacy of anti-influenza drugs rely mostly on transformed cells and animals. Transformed cell models are distantly related to physiological and pathological conditions. Although animals are the best choices for preclinical drug testing, they are not time- or cost-efficient. In this study, we established an ex vivo model using mouse lung slices to evaluate both antiviral and anti-inflammatory agents against influenza virus infection. Both influenza virus PR8 (H1N1) and A/Human/Hubei/3/2005 (H3N2) can replicate efficiently in mouse lung slices and trigger significant cytokine and chemokine responses. The induction of selected cytokines and chemokines were found to have a positive correlation between ex vivo and in vivo experiments, suggesting that the ex vivo cultured lung slices may closely resemble the lung functionally in an in vivo configuration when challenged by influenza virus. Furthermore, a set of agents with known antiviral and/or anti-inflammatory activities were tested to validate the ex vivo model. Our results suggested that mouse lung slices provide a robust, convenient and cost-efficient model for the assessment of both antiviral and anti-inflammatory agents against influenza virus infection in one assay. This ex vivo model may predict the efficacy of drug candidates’ antiviral and anti-inflammatory activities in vivo. url: https://www.sciencedirect.com/science/article/pii/S016635421500128X doi: 10.1016/j.antiviral.2015.05.008 id: cord-257665-12gyrmh2 author: Liu, Shan-Lu title: Emerging Viruses without Borders: The Wuhan Coronavirus date: 2020-01-22 words: 790.0 sentences: 48.0 pages: flesch: 56.0 cache: ./cache/cord-257665-12gyrmh2.txt txt: ./txt/cord-257665-12gyrmh2.txt summary: We applaud the rapid release to the public of the genome sequence of the new virus by Chinese virologists, but we also believe that increased transparency on disease reporting and data sharing with international colleagues are crucial for curbing the spread of this newly emerging virus to other parts of the world. We applaud the rapid release to the public of the genome sequence of the new virus by Chinese virologists, but we also believe that increased transparency on disease reporting and data sharing with international colleagues are crucial for curbing the spread of this newly emerging virus to other parts of the world. We applaud the rapid release to the public of the genome sequence of the new virus by Chinese virologists [3] , as this represents an important first step in curbing the spread of the new virus to other parts of the world. abstract: The recently emerged coronavirus in Wuhan, China has claimed at least six lives as of January 22 and infected hundreds if not thousands of individuals. The situation has drawn international attention, including from the virology community. We applaud the rapid release to the public of the genome sequence of the new virus by Chinese virologists, but we also believe that increased transparency on disease reporting and data sharing with international colleagues are crucial for curbing the spread of this newly emerging virus to other parts of the world. url: https://doi.org/10.3390/v12020130 doi: 10.3390/v12020130 id: cord-005258-gps8rzb5 author: Liu, William J. title: The triphibious warfare against viruses date: 2017-12-01 words: 1616.0 sentences: 78.0 pages: flesch: 45.0 cache: ./cache/cord-005258-gps8rzb5.txt txt: ./txt/cord-005258-gps8rzb5.txt summary: Different elements may drive the current trends in emerging and re-emerging infectious diseases, which are as follows: (i) the contact patterns between human beings, their commensal organisms, and wildlife reservoirs are changing due to human behaviors, (ii) the interaction between viruses and their potential hosts and vectors, such as bats and mosquitoes, may cause changes in *Corresponding author (William J. The Chinese Academy of Sciences (CAS) has been one of the backbone forces during this process and has been playing essential roles in the fight against infectious diseases since 2005, when the H5N1 sub-type, a highly pathogenic avian influenza virus (HPAI), was identified among wild birds in Qinghai Lake (Liu et al., 2005) . The majority of emerging infectious diseases in human beings are zoonotic, which indicates the fundamental role of wildlife, especially rodents and bats, as the reservoirs of emerging viruses (Olival et The surveillance of viruses among natural vectors is also an important work, considering the recent global spread of arthropod-borne viruses such as Zika virus and dengue virus. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7089299/ doi: 10.1007/s11427-017-9252-y id: cord-321562-hk4hzl13 author: Liu, Xuan title: Cell membrane-derived biomimetic nanodecoys for viruses date: 2020-05-12 words: 1412.0 sentences: 78.0 pages: flesch: 38.0 cache: ./cache/cord-321562-hk4hzl13.txt txt: ./txt/cord-321562-hk4hzl13.txt summary: Such pathogenic binding and entry mechanisms offer opportunities for developing broadly applicable anti-viral strategy, which subvert the interaction of specific membrane proteins and viruses. For viral infection inhibition, MVs mimicking cell-surface receptors could compete with native cellular receptors to bind to the specific ligands. To divert Zika virus (ZIKV) away from its intended targets, an anti-ZIKV host-mimicking nanodecoy (ND) constructed by wrapping a polymeric core with mosquito medium host cell membranes was developed (Rao et al., 2019) . What is perhaps most convenient about these cell membrane-based viral decoys is the natural binding ability of host cells that makes the exogenous engineering of receptor moieties unnecessary. Membrane vesicles derived from the modified cells, named hNTCP-MVs, were conferred important surface properties to play a specific biological function. abstract: nan url: https://doi.org/10.1007/s11427-020-1669-x doi: 10.1007/s11427-020-1669-x id: cord-284156-btb4oodz author: Liu, Yiliu title: Host and Viral Modulation of RIG-I-Mediated Antiviral Immunity date: 2017-01-03 words: 7021.0 sentences: 397.0 pages: flesch: 38.0 cache: ./cache/cord-284156-btb4oodz.txt txt: ./txt/cord-284156-btb4oodz.txt summary: Retinoic acid-inducible gene-I (RIG-I) is critical in triggering antiviral and inflammatory responses for the control of viral replication in response to cytoplasmic virus-specific RNA structures. They function as cytoplasmic sensors for the recognition of a variety of RNA viruses and subsequent activation of downstream signaling to drive type I IFN production and antiviral gene expressions. (c) Interactions between RIG-I-TRIM25 complex and 14-3-3ϵ promote RIG-I translocation to mitochondrial mitochondrial antiviral signaling protein (MAVS) for downstream signaling, leading to interferon production. Protein purification and mass spectrometry analysis identified that phosphorylation of Thr170 in the CARDs antagonizes RIG-I signaling by inhibiting TRIM25-mediated Lys172 ubiquitination and MAVS binding (68) . Ebola virus VP35 protein binds double-stranded RNA and inhibits alpha/beta interferon production induced by RIG-I signaling Inhibition of dengue and chikungunya virus infections by RIG-I-mediated type I interferon-independent stimulation of the innate antiviral response abstract: Innate immunity is the first line of defense against invading pathogens. Rapid and efficient detection of pathogen-associated molecular patterns via pattern-recognition receptors is essential for the host to mount defensive and protective responses. Retinoic acid-inducible gene-I (RIG-I) is critical in triggering antiviral and inflammatory responses for the control of viral replication in response to cytoplasmic virus-specific RNA structures. Upon viral RNA recognition, RIG-I recruits the mitochondrial adaptor protein mitochondrial antiviral signaling protein, which leads to a signaling cascade that coordinates the induction of type I interferons (IFNs), as well as a large variety of antiviral interferon-stimulated genes. The RIG-I activation is tightly regulated via various posttranslational modifications for the prevention of aberrant innate immune signaling. By contrast, viruses have evolved mechanisms of evasion, such as sequestrating viral structures from RIG-I detections and targeting receptor or signaling molecules for degradation. These virus–host interactions have broadened our understanding of viral pathogenesis and provided insights into the function of the RIG-I pathway. In this review, we summarize the recent advances regarding RIG-I pathogen recognition and signaling transduction, cell-intrinsic control of RIG-I activation, and the viral antagonism of RIG-I signaling. url: https://www.ncbi.nlm.nih.gov/pubmed/28096803/ doi: 10.3389/fimmu.2016.00662 id: cord-281593-bq12grqo author: Liu, Zheng title: Transmission Electron Microscopy Studies of Cellular Responses to Entry of Virions: One Kind of Natural Nanobiomaterial date: 2012-04-11 words: 2043.0 sentences: 112.0 pages: flesch: 49.0 cache: ./cache/cord-281593-bq12grqo.txt txt: ./txt/cord-281593-bq12grqo.txt summary: For this paper, we chose Bombyx mori cypovirus 1 (BmCPV-1) interactions with midgut cells from silkworm, and severe acute respiratory syndrome (SARS) associated coronavirus interactions with Vero E6 cells, as examples to demonstrate the response of eukaryotic cells to two different types of virus from our previous studies. In this paper, we discuss our previous studies on Bombyx mori cypovirus 1 (BmCPV-1) interactions with midgut cells from silkworm, and severe acute respiratory syndrome (SARS) associated coronavirus interactions with Vero E6 cells as examples to demonstrate the response of eukaryotic cells to two different types of viruses [11, 12] . It could be seen with ultrathin sectioning and electron microscopy that the virions first attached themselves to the surface of host cell, then their envelopes fused with the cell membrane, and the whole nucleocapsids entered the cell. abstract: Virions are one kind of nanoscale pathogen and are able to infect living cells of animals, plants, and bacteria. The infection is an intrinsic property of the virions, and the biological process provides a good model for studying how these nanoparticles enter into cells. During the infection, the viruses employ different strategies to which the cells have developed respective responses. For this paper, we chose Bombyx mori cypovirus 1 (BmCPV-1) interactions with midgut cells from silkworm, and severe acute respiratory syndrome (SARS) associated coronavirus interactions with Vero E6 cells, as examples to demonstrate the response of eukaryotic cells to two different types of virus from our previous studies. The bacteriophage-bacteria interactions are also introduced to elucidate how the bacteriophage conquers the barrier of cell walls in the prokaryotic cells to transport genome into the host. url: https://doi.org/10.1155/2012/596589 doi: 10.1155/2012/596589 id: cord-161674-nk0wie0w author: Liu, Zhi title: Implications of the virus-encoded miRNA and host miRNA in the pathogenicity of SARS-CoV-2 date: 2020-04-10 words: 5137.0 sentences: 304.0 pages: flesch: 54.0 cache: ./cache/cord-161674-nk0wie0w.txt txt: ./txt/cord-161674-nk0wie0w.txt summary: Our results implicated that the immune response and cytoskeleton organization are two of the most notable biological processes regulated by the infection-modulated miRNAs. Impressively, we found hsa-miR-4661-3p was predicted to target the S gene of SARS-CoV-2, and a virus-encoded miRNA MR147-3p could enhance the expression of TMPRSS2 with the function of strengthening SARS-CoV-2 infection in the gut. In the gut, 54 genes were predicted to be enhanced by 34 miRNAs. The most notable target of the virus miRNA is TMPRSS2, which is reported to enhance SARS-CoV-2 infection together with ACE2 48 In the liver, the virus miRNA mainly regulates genes involved in the function of actin filament severing and regulation of cellular protein metabolic process ( Figure 3E ). There were more than human 800 genes were predicted to be regulated by these miRNA (Figure 4A) , and a notable enrichment at the immune system process was observed There were 27 SARS-CoV-2 encoded miRNA that can target the virus genome ( Figure 5A ). abstract: The outbreak of COVID-19 caused by SARS-CoV-2 has rapidly spread worldwide and has caused over 1,400,000 infections and 80,000 deaths. There are currently no drugs or vaccines with proven efficacy for its prevention and little knowledge was known about the pathogenicity mechanism of SARS-CoV-2 infection. Previous studies showed both virus and host-derived MicroRNAs (miRNAs) played crucial roles in the pathology of virus infection. In this study, we use computational approaches to scan the SARS-CoV-2 genome for putative miRNAs and predict the virus miRNA targets on virus and human genome as well as the host miRNAs targets on virus genome. Furthermore, we explore miRNAs involved dysregulation caused by the virus infection. Our results implicated that the immune response and cytoskeleton organization are two of the most notable biological processes regulated by the infection-modulated miRNAs. Impressively, we found hsa-miR-4661-3p was predicted to target the S gene of SARS-CoV-2, and a virus-encoded miRNA MR147-3p could enhance the expression of TMPRSS2 with the function of strengthening SARS-CoV-2 infection in the gut. The study may provide important clues for the mechisms of pathogenesis of SARS-CoV-2. url: https://arxiv.org/pdf/2004.04874v1.pdf doi: nan id: cord-309048-emmtplv3 author: Lomonossoff, George P. title: TMV Particles: The Journey From Fundamental Studies to Bionanotechnology Applications date: 2018-07-26 words: 9017.0 sentences: 407.0 pages: flesch: 46.0 cache: ./cache/cord-309048-emmtplv3.txt txt: ./txt/cord-309048-emmtplv3.txt summary: (1999) displayed peptides of either 10 or 15 amino acids from the spike protein of the coronavirus murine hepatitis virus on the surface of assembled particles. coli-produced protein with a minimum of 20% of plant-made TMV CP, an approach that enabled efficient RNA-guided assembly of TMV-CP His6 into particles of the expected length (Eiben et al., 2014) . Assembly of the particle of tobacco mosaic virus from RNA and disks of protein β-Structure of the coat protein subunits in spherical particles generated by tobacco mosaic virus thermal denaturation Expression of tobacco mosaic virus coat protein and assembly of pseudovirus particles in Escherichia coli In vitro assembly of tobacco mosaic virus coat protein variants derived from fission yeast expression clones or plants Modified tobacco mosaic virus particles as scaffolds for display of protein antigens for vaccine applications Display of peptides on the surface of tobacco mosaic virus particles Assembly of hybrid RNAs with tobacco mosaic virus coat protein. abstract: Ever since its initial characterization in the 19th century, tobacco mosaic virus (TMV) has played a prominent role in the development of modern virology and molecular biology. In particular, research on the three-dimensional structure of the virus particles and the mechanism by which these assemble from their constituent protein and RNA components has made TMV a paradigm for our current view of the morphogenesis of self-assembling structures, including viral particles. More recently, this knowledge has been applied to the development of novel reagents and structures for applications in biomedicine and bionanotechnology. In this article, we review how fundamental science has led to TMV being at the vanguard of these new technologies. url: https://doi.org/10.1016/bs.aivir.2018.06.003 doi: 10.1016/bs.aivir.2018.06.003 id: cord-322234-1zyy536y author: Lorusso, Alessio title: One-step real-time RT-PCR for pandemic influenza A virus (H1N1) 2009 matrix gene detection in swine samples date: 2009-12-17 words: 4162.0 sentences: 195.0 pages: flesch: 51.0 cache: ./cache/cord-322234-1zyy536y.txt txt: ./txt/cord-322234-1zyy536y.txt summary: To evaluate the applicability of the test as a diagnostic tool in the screening of field specimens from swine, 64 field isolates of North American swine, 5 equine and 48 avian influenza viruses collected during diagnostic investigations were analyzed retrospectively as well as samples collected during an experimental in vivo infection with two novel H1N1 isolates, A/California/04/2009 (H1N1)v virus and A/Mexico/4108/2009 (H1N1)v. Swine and equine influenza virus isolates and the clinical samples from pigs infected experimentally with 2009 (H1N1)v were subjected to the USDA-validated qRT-PCR procedure for the general detection of type A influenza virus RNA (matrix screening assay), following procedures described previously (Spackman and Suarez, 2008) . All endemic North American swine influenza virus isolates were negative for (H1N1) 2009 specific matrix gene RNA using the present qRT-PCR assay, whereas the (H1N1) 2009 strains used as positive control were positive. abstract: In the spring of 2009, a novel (H1N1) influenza A virus began to spread among humans worldwide. Although the 2009 H1N1 is related genetically to swine influenza viruses, human infection has not been connected to pig exposure. Because the virus is now circulating widely in the human population, swine herds are at increased risk of becoming infected. In order to investigate potential outbreaks of the 2009 pandemic virus in pigs, a quantitative real-time reverse transcriptase-polymerase chain reaction (qRT-PCR) for the detection of the (H1N1) 2009 RNA in clinical specimens was developed. To evaluate the applicability of the test as a diagnostic tool in the screening of field specimens from swine, 64 field isolates of North American swine, 5 equine and 48 avian influenza viruses collected during diagnostic investigations were analyzed retrospectively as well as samples collected during an experimental in vivo infection with two novel H1N1 isolates, A/California/04/2009 (H1N1)v virus and A/Mexico/4108/2009 (H1N1)v. The sensitivity of the qRT-PCR was shown to be higher with respect to standard techniques such as virus isolation and the reproducibility was satisfactory. The present unique and highly sensitive assay is able to detect as little as 1 × 10(1) copies of RNA per μl of template and it represents a rapid and useful approach for the screening and quantitation of (H1N1) 2009 RNA in porcine specimens. url: https://www.sciencedirect.com/science/article/pii/S0166093409005205 doi: 10.1016/j.jviromet.2009.12.002 id: cord-307817-2vy28i4m author: Lou, Zhiyong title: Current progress in antiviral strategies date: 2014-01-14 words: 7555.0 sentences: 343.0 pages: flesch: 36.0 cache: ./cache/cord-307817-2vy28i4m.txt txt: ./txt/cord-307817-2vy28i4m.txt summary: The prevalence of chronic viral infectious diseases, such as human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus; the emergence and re-emergence of new viral infections, such as picornaviruses and coronaviruses; and, particularly, resistance to currently used antiviral drugs have led to increased demand for new antiviral strategies and reagents. Based on the complex structure of the PA C-terminal domain (PA C ) and the first 25 amino acids of PB1 [99] , a subset of modifications on N-terminal peptide of PB1 was shown to diminish the binding affinity of PA and PB1, inhibit polymerase activity, and attenuate the replication of influenza virus [100] [101] [102] . Because both the polymerase complex and NP show significant conservation between different influenza viruses, these results demonstrated that targeting the formation of viral RNP is a valid approach to the development of small molecule therapies against serious antiviral resistance to currently available drugs, such as adamantanes or neuraminidase inhibitors. abstract: The prevalence of chronic viral infectious diseases, such as human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus; the emergence and re-emergence of new viral infections, such as picornaviruses and coronaviruses; and, particularly, resistance to currently used antiviral drugs have led to increased demand for new antiviral strategies and reagents. Increased understanding of the molecular mechanisms of viral infection has provided great potential for the discovery of new antiviral agents that target viral proteins or host factors. Virus-targeting antivirals can function directly or indirectly to inhibit the biological functions of viral proteins, mostly enzymatic activities, or to block viral replication machinery. Host-targeting antivirals target the host proteins that are involved in the viral life cycle, regulating the function of the immune system or other cellular processes in host cells. Here we review key targets and considerations for the development of both antiviral strategies. url: https://www.sciencedirect.com/science/article/pii/S0165614713002265 doi: 10.1016/j.tips.2013.11.006 id: cord-298051-ej8qxkce author: Louten, Jennifer title: Detection and Diagnosis of Viral Infections date: 2016-05-06 words: 11204.0 sentences: 602.0 pages: flesch: 57.0 cache: ./cache/cord-298051-ej8qxkce.txt txt: ./txt/cord-298051-ej8qxkce.txt summary: Cell lines can be infected with patient samples to allow viral replication within the cells; observable cytopathic effects can help to identify the identity of the virus. Infected cells can also be used for immunofluorescence assays, which use fluorescently labeled virus-specific antibodies to identify viruses in fixed cells or tissues. In the process of PCR, DNA (including any viral DNA present) is isolated from the clinical specimen, generally blood cells or tissue, and added to a tube containing primers, DNA polymerase, and nucleotides ( Fig. 7.14) . The diagnostic techniques described in this chapter identify the presence of a virus in a sample, or even the amount of viral nucleic acid, but these assays cannot determine the amount of virus present that is capable of productively infecting cells. Fluorescently labeled antibodies bind to viral antigens present in infected cells. abstract: Diagnostic tests are paramount in determining the etiology of viral infections. Direct diagnostic methods assay for the presence of the virus, while indirect methods test for effects of the virus. Cell culture is the process of growing cells or tissues in the laboratory. Cell lines can be infected with patient samples to allow viral replication within the cells; observable cytopathic effects can help to identify the identity of the virus. Infected cells can also be used for immunofluorescence assays, which use fluorescently labeled virus-specific antibodies to identify viruses in fixed cells or tissues. A variety of diagnostic immunoassays exist, including enzyme-linked immunosorbent assays/enzyme immunoassays, western blots, lateral flow immunoassays, and agglutination reactions. Assays that detect viral nucleic acids are based upon the principles of PCR or nucleic acid hybridization, are extremely sensitive, and are specific for a particular virus. url: https://api.elsevier.com/content/article/pii/B9780128009475000077 doi: 10.1016/b978-0-12-800947-5.00007-7 id: cord-255181-du6rqc6i author: Louz, Derrick title: Cross‐species transfer of viruses: implications for the use of viral vectors in biomedical research, gene therapy and as live‐virus vaccines date: 2005-06-29 words: 8017.0 sentences: 425.0 pages: flesch: 42.0 cache: ./cache/cord-255181-du6rqc6i.txt txt: ./txt/cord-255181-du6rqc6i.txt summary: This review addresses a number of potential risk factors and their implications for activities with viral vectors from the perspective of cross‐species transfer of viruses in nature, with emphasis on the occurrence of host‐range mutants resulting from either cell culture or tropism engineering. The HIV virus and contemporary human influenza viruses are prominent examples of viruses that have crossed the species barrier and established themselves permanently in the human population without further dependence on the presence of the original animal host reservoir. The emergence of HIV exemplifies how multiple independent cross-species transmissions of simian viruses that are not associated with disease in their natural hosts eventually resulted in the establishment of two types of HIV in the human population. The following examples demonstrate that upon persistent infection and passage in cell culture, cross-species transmissibility may be promoted by selection of virus variants with an altered host range. Adaptation in cell culture may result in changes in receptor specificity and tropism, and leads to the emergence of host-range mutant viruses. abstract: Summary All living organisms are continuously exposed to a plethora of viruses. In general, viruses tend to be restricted to the natural host species which they infect. From time to time viruses cross the host‐range barrier expanding their host range. However, in very rare cases cross‐species transfer is followed by the establishment and persistence of a virus in the new host species, which may result in disease. Recent examples of viruses that have crossed the species barrier from animal reservoirs to humans are hantavirus, haemorrhagic fever viruses, arboviruses, Nipah and Hendra viruses, avian influenza virus (AI), monkeypox virus, and the SARS‐associated coronavirus (SARS‐CoV). The opportunities for cross‐species transfer of mammalian viruses have increased in recent years due to increased contact between humans and animal reservoirs. However, it is difficult to predict when such events will take place since the viral adaptation that is needed to accomplish this is multifactorial and stochastic. Against this background the intensified use of viruses and their genetically modified variants as viral gene transfer vectors for biomedical research, experimental gene therapy and for live‐vector vaccines is a cause for concern. This review addresses a number of potential risk factors and their implications for activities with viral vectors from the perspective of cross‐species transfer of viruses in nature, with emphasis on the occurrence of host‐range mutants resulting from either cell culture or tropism engineering. The issues are raised with the intention to assist in risk assessments for activities with vector viruses. Copyright © 2005 John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/15986492/ doi: 10.1002/jgm.794 id: cord-007717-7x1mqqmf author: Lowen, Anice C. title: Transmission in the Guinea Pig Model date: 2014-07-08 words: 8045.0 sentences: 414.0 pages: flesch: 46.0 cache: ./cache/cord-007717-7x1mqqmf.txt txt: ./txt/cord-007717-7x1mqqmf.txt summary: This chapter describes influenza virus infection, growth, and transmission in guinea pigs; highlights how these properties differ among influenza viruses adapted to human, swine, and avian hosts; and provides an overview of knowledge gained through the study of influenza virus transmission in the guinea pig model. By virus histochemistry, the H3N2 subtype human influenza viruses studied (Pan/99 and A/Netherlands/213/03) attached mainly to the guinea pig upper respiratory tract and the trachea, with little to no binding detected on bronchiolar and alveolar epithelia. Seasonal H3N2 viruses and 2009 H1N1 pandemic strains show similar and high efficiency of transmission in both contact and respiratory droplet models (Lowen et al. Reverse genetics-derived Pan/99 viruses with and without the NA-E119V mutation were found to transmit with equal efficiency in the guinea pig contact transmission model, as had been seen with similar isolates in the ferret model (Herlocher et al. abstract: The ability of an influenza virus to transmit efficiently from human-to-human is a major factor in determining the epidemiological impact of that strain. The use of a relevant animal model to identify viral determinants of transmission, as well as host and environmental factors affecting transmission efficiency, is therefore critical for public health. The characterization of newly emerging influenza viruses in terms of their potential to transmit in a mammalian host is furthermore an important part of pandemic risk assessment. For these reasons, a guinea pig model of influenza virus transmission was developed in 2006. The guinea pig provides an important alternative to preexisting models for influenza. Most influenza viruses do not readily transmit among mice. Ferrets, while highly relevant, are expensive and can be difficult to obtain in high numbers. Moreover, it is generally accepted that efforts to accurately model human disease are strengthened by the use of multiple animal species. Herein, we provide an overview of influenza virus infectivity, growth, and transmission in the guinea pig and highlight knowledge gained on the topic of influenza virus transmission using the guinea pig model. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121145/ doi: 10.1007/82_2014_390 id: cord-031840-k9l91unc author: Lu, Li title: Forum: COVID-19 Dispatches date: 2020-09-11 words: 15686.0 sentences: 686.0 pages: flesch: 53.0 cache: ./cache/cord-031840-k9l91unc.txt txt: ./txt/cord-031840-k9l91unc.txt summary: With death count worldwide reaching 586,000 merely 7 months after its first outbreak in China in late December 2019 and 13.6 million cases reported in 188 countries and territories as of July 2020, this ongoing pandemic has spread far beyond domain of world health problem to become an unprecedented challenge facing humanity at every level. On one hand, the eagerness to build solidarity with East Asian countries represented by Japan and South Korea might be a strategy to react to the racialization of COVID-19 as a "Chinese virus" and the demonization of China as a "public enemy" and "trouble maker" in the Euro-American political and media agenda (Viala-Gaudefroy & Lindaman, 2020). On the other hand, the rise of this East Asian imaginary centering around China''s historical and cultural bonds with Japan and South Korea has far-reaching implications for China''s geopolitical strategies beyond the COVID-19 pandemic and the realm of public health. abstract: COVID-19 pandemic is the first truly global crisis in the digital age. With death count worldwide reaching 586,000 merely 7 months after its first outbreak in China in late December 2019 and 13.6 million cases reported in 188 countries and territories as of July 2020, this ongoing pandemic has spread far beyond domain of world health problem to become an unprecedented challenge facing humanity at every level. In addition to causing social and economic disruptions on a scale unseen before, it has turned the world into a site of biopolitical agon where science and reason are forced to betray their impotence against cultish thinking in the planetary endgame depicted in so many dystopian science fictions. It is in this context that this forum offers a set of modest reflections on the current impacts incurred by the COVID-19 virus. Blending ethnographic observations with theory-driven reflections, the five authors address issues made manifest by the crisis across different regions, while keeping their sight on the sociopolitical problems plaguing our life both individually and collectively. Taken together, they provide a grounded documentary for the archive that the COVID-19 virus is making us to construct. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7488168/ doi: 10.1177/1532708620953190 id: cord-007575-5ekgabx5 author: Luby, James P. title: Southwestern Internal Medicine Conference: Pneumonias in Adults Due to Mycoplasma, Chlamydiae, and Viruses date: 2016-01-14 words: 11991.0 sentences: 735.0 pages: flesch: 39.0 cache: ./cache/cord-007575-5ekgabx5.txt txt: ./txt/cord-007575-5ekgabx5.txt summary: Important trends and developments in the field include (1) the emergence of a Chlamydia psittaci strain (TWAR) that is passaged from human to human, causes a mycoplasma-like illness, and that is relatively resistant to erythromycin, (2) the recognition of respiratory syncytial virus as a pathogen in nursing home outbreaks and in immunosuppressed adults, (3) the continuing high lethality of fully developed influenza pneumonia, (4) the efficacy of acyclovir and adenine arabinoside in limiting the complications of varicella-zoster virus infections, and (5) the increasing frequency of pneumonia caused by cytomegalovirus and the severity of this disorder in highly immunosuppressed patients. Important trends and developments in the field include (1) the emergence of a Chlamydia psittaci strain (TWAR) that is passaged from human to human, causes a mycoplasma-like illness, and that is relatively resistant to erythromycin, (2) the recognition of respiratory syncytial virus as a pathogen in nursing home outbreaks and in immunosuppressed adults, (3) the continuing high lethality of fully developed influenza pneumonia, (4) the efficacy of acyclovir and adenine arabinoside in limiting the complications of varicella-zoster virus infections, and (5) the increasing frequency of pneumonia caused by cytomegalovirus and the severity of this disorder in highly immunosuppressed patients. abstract: Pneumonias in adults due to mycoplasma, chlamydiae, and viruses are a common clinical problem. These microorganisms contribute to the etiologies in 6–35% of all cases of pneumonia and are the sole pathogens in 1–17% of hospitalized cases. Important trends and developments in the field include (1) the emergence of a Chlamydia psittaci strain (TWAR) that is passaged from human to human, causes a mycoplasma-like illness, and that is relatively resistant to erythromycin, (2) the recognition of respiratory syncytial virus as a pathogen in nursing home outbreaks and in immunosuppressed adults, the continuing high lethality of fully developed influenza pneumonia, (4) the efficacy of acyclovir and adenine arabinoside in limiting the complications of varicella-zoster virus infections, and (5) the increasing frequency of pneumonia caused by cytomegalovirus and the severity of this disorder in highly immunosuppressed patients. Developments in the rapid diagnosis and therapy of respiratory syncytial virus infections with an aerosolized antiviral drug in children may pave the way for comparable advances in difficult pneumonias in adult patients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119385/ doi: 10.1097/00000441-198707000-00007 id: cord-287337-2ljbsia2 author: Ludwig, Christine title: Virus-like particles—universal molecular toolboxes date: 2008-01-04 words: 5065.0 sentences: 205.0 pages: flesch: 33.0 cache: ./cache/cord-287337-2ljbsia2.txt txt: ./txt/cord-287337-2ljbsia2.txt summary: It is noteworthy that VLPs assembled from HPV major capsid protein L1 in yeast were capable of inducing protective immune responses against HPV subtypes 16 and 18 causing cervical cancer in humans, thus resulting in a safe, well tolerated and highly immunogenic vaccine that received approval for marketing in 2006 [13] . Since particulate antigens had been demonstrated to induce better cellular and humoral immune responses than soluble antigens, the detection that HIV-1 Pr55Gag polyprotein self-assembles into particulate spheres provided a new rationale for generating a Gag-based VLP vaccine [15, 16] . The authors demonstrated efficient expression of murine leukemia virus (MLV) Gag-Env VLPs from plasmid DNA in vitro and used these plasmo-retroVLPs to induce strong specific CTL responses towards displayed T cell epitopes, protecting mice from lethal virus challenge. [52] have formerly shown that virosome-mediated targeting of mumps virus DNA to APCs induces specific CTL responses suggesting efficient expression and presentation of the encoded mumps antigens. DNA vaccines encoding retrovirusbased virus-like particles induce efficient immune responses without adjuvant abstract: Virus-like particles (VLPs) are highly organised spheres that self-assemble from virus-derived structural antigens. These stable and versatile subviral particles possess excellent adjuvant properties capable of inducing innate and cognate immune responses. Commercialised VLP-based vaccines have been successful in protecting humans from hepatitis B virus (HBV) and human papillomavirus (HPV) infection and are currently explored for their potential to combat other infectious diseases and cancer. Much insight into VLP-mediated immune stimulation and optimised VLP design has been gained from human immunodeficiency virus (HIV)-derived VLPs presenting promising components of current AIDS vaccine approaches. Owing to their unique features, VLPs and virosomes, the in vitro-reconstituted VLP counterparts, have recently gained ground in the field of nanobiotechnology as organic templates for the development of new biomaterials. url: https://api.elsevier.com/content/article/pii/S0958166907001462 doi: 10.1016/j.copbio.2007.10.013 id: cord-005246-cskb0njm author: Ludwig, George V. title: Insect-transmitted vertebrate viruses: Flaviviridae date: 1993 words: 8060.0 sentences: 416.0 pages: flesch: 41.0 cache: ./cache/cord-005246-cskb0njm.txt txt: ./txt/cord-005246-cskb0njm.txt summary: Additionally, these culture systems permit the study of flavivirus attachment, penetration, replication, and release from cells and have been instrumental in the production and characterization of live-attenuated vaccines. Cell culture is essential for the study of flaviviruses, and will continue to play a pivotal role in the isolation, characterization, and development of new vaccines against current and future flavivirus health threats. More recent research has shown that fusion of dengue, yellow fever, and Japanese encephalitis viruses may in fact involve fusion of virus directly to the cell''s plasma membrane (52, 108) . The observation that persistent dengue virus infections can be established in a non-vector mosquito cell line associated with changes in several of the important biological characteristics, such as temperature sensitivity and antigenic structure (64) , presents the possibility that genetic selection of attenuated virus strains may be possible with insect cell lines. abstract: The Flaviviridae include almost 70 viruses, nearly half of which have been associated with human disease. These viruses are among the most important arthropod-borne viruses worldwide and include dengue, yellow fever, and Japanese encephalitis viruses. Morbidity and mortality caused by these viruses vary, but collectively they account for millions of encephalitis, hemorrhagic fever, arthralgia, rash, and fever cases per year. Most of the members of this family are transmitted between vertebrate hosts by arthropod vectors, most commonly mosquitoes or ticks. Transmission cycles can be simple or complex depending on the hosts, vectors, the virus, and the environmental factors affecting both hosts and viruses. Replication of virus in invertebrate hosts does not seem to result in any significant pathology, which suggests a close evolutionary relationship between virus and vector. Another example of this relationship is the ability of these viruses to grow in invertebrate cell culture, where replication usually results in a steady state, persistent infection, often without cytopathic effect. Yields of virus from insect cell culture vary but are generally similar to yields in vertebrate cells. Replication kinetics are comparable between insect and vertebrate cell lines, despite differences in incubation temperature. Both vertebrate and insect cell culture systems continue to play a significant role in flavivirus isolation and the diagnosis of disease caused by these agents. Additionally, these culture systems permit the study of flavivirus attachment, penetration, replication, and release from cells and have been instrumental in the production and characterization of live-attenuated vaccines. Both vertebrate and insect cell culture systems will continue to play a significant role in basic and applied flavivirus research in the future. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7089231/ doi: 10.1007/bf02633958 id: cord-304481-yqc8r3ll author: Luis, Angela D. title: Network analysis of host–virus communities in bats and rodents reveals determinants of cross‐species transmission date: 2015-08-24 words: 5992.0 sentences: 307.0 pages: flesch: 52.0 cache: ./cache/cord-304481-yqc8r3ll.txt txt: ./txt/cord-304481-yqc8r3ll.txt summary: Here, we use a network approach to identify ecological and biological correlates of cross‐species virus transmission in bats and rodents, another important host group. We identify multiple communities of viral sharing within bats and rodents and highlight potential species traits that can help guide studies of novel pathogen emergence. Rodents are a suitable group for comparison because they also host many important zoonotic viruses and share many of the characteristics hypothesised to make bats suitable as viral reservoirs. Host traits that correlated with the highest degree within the bat network (the most connections or viruses shared), in order of importance, were gregariousness and sympatry; diet was marginally important (Fig. 2b, Table S6 and S7). For rodents, sympatry was the most important host trait; species whose distributions overlapped with a greater number of other rodent species had more viruses and higher degree and betweenness (Fig. 2d-f and Table S11-S19). abstract: Bats are natural reservoirs of several important emerging viruses. Cross‐species transmission appears to be quite common among bats, which may contribute to their unique reservoir potential. Therefore, understanding the importance of bats as reservoirs requires examining them in a community context rather than concentrating on individual species. Here, we use a network approach to identify ecological and biological correlates of cross‐species virus transmission in bats and rodents, another important host group. We show that given our current knowledge the bat viral sharing network is more connected than the rodent network, suggesting viruses may pass more easily between bat species. We identify host traits associated with important reservoir species: gregarious bats are more likely to share more viruses and bats which migrate regionally are important for spreading viruses through the network. We identify multiple communities of viral sharing within bats and rodents and highlight potential species traits that can help guide studies of novel pathogen emergence. url: https://www.ncbi.nlm.nih.gov/pubmed/26299267/ doi: 10.1111/ele.12491 id: cord-264794-bgygebgx author: Lundgren, A.-L. title: Feline non-suppurative meningoencephalomyelitis. A clinical and pathological study date: 1992-11-30 words: 4861.0 sentences: 288.0 pages: flesch: 48.0 cache: ./cache/cord-264794-bgygebgx.txt txt: ./txt/cord-264794-bgygebgx.txt summary: It has been argued that the syndrome may include several aetiologically unrelated conditions affecting the central nervous system of cats, e.g. toxoplasmosis (Hirth and Nielsen, 1969) and the cerebral form of feline infectious peritonitis (Slauson and Finn, 1972; Kornegay, 1978) . Histopathological examination revealed throughout the central nervous system a non-suppurative inflammation characterized by perivascular mononuclear cuffing, presence of inflammatory nodules and neuronal degeneration in all cats. Neuropathological examination of the cats of the present study showed a marked inflammatory reaction in the cerebral leptomeninges as well as in the grey matter of the brain and spinal cord. Neither the serological results nor the clinical and histopathological findings in the cats with staggering disease indicate a FeLV infection. Feline immunodeficiency virus (FIV) has emerged as an important cause of neurological disease in cats (Dow, Poss and Hoover, 1990; Sparger, 1991) , often in association with clinical syndromes typical of an immunodeficient state (chronic stomatitis, enteritis, dermatitis, etc). abstract: Abstract A spontaneous neurological disease in cats characterized by behavioural and motor disturbances was investigated by clinical, morphological and immunological methods. Neuropathological examination showed a marked inflammatory reaction in the cerebral leptomeninges and the grey matter of the brain. In the white matter, the reaction was moderate. The changes consisted of perivascular cuffing by mononuclear cells and neuronal damage. The brain stem (thalamus, mesencephalon, caudal colliculus) was most severely affected. The spinal cord and its leptomeninges were involved to a lesser degree. The histopathological picture as well as the laboratory findings suggests a viral cause of the disease. The morphology of the disease and serological as well as immunohistochemical results indicate that this disorder is different from previously known feline viral encephalitides. url: https://www.sciencedirect.com/science/article/pii/002199759290015M doi: 10.1016/0021-9975(92)90015-m id: cord-007792-596jxrm5 author: Luo, Ming title: Influenza Virus Entry date: 2011-08-26 words: 12446.0 sentences: 635.0 pages: flesch: 56.0 cache: ./cache/cord-007792-596jxrm5.txt txt: ./txt/cord-007792-596jxrm5.txt summary: The key player in virus entry is the surface glycoprotein HA that contains the host receptor binding site to allow the virus particle to attach to specifi c host cells, the fusion peptide that is inserted into the target cellular membrane during membrane fusion, and other structural elements that may refold during the membrane fusion process. When the HA amino acid substitutions are accumulated in the repertoire of infl uenza virus strains, they are mostly on the exposed surface of the HA glycoprotein except for the receptor binding site, the fusion peptide, and the amino acids that accommodate the fusion peptide before HA structural changes for membrane fusion (Wilson et al. The next 18 amino acids form part of the pocket that accommodates the hydrophobic fusion peptide in the metastable HA structure on the infl uenza virion prior to virus entry. abstract: As all the enveloped viruses, the entry of influenza viruses includes a number of steps in host cell infection. This chapter summarizes the current knowledge of the entry pathway and the role of the fusion protein of influenza virus, hemagglutinin, in this process. Hemagglutinin (HA) is a trimeric glycoprotein that is present in multiple copies in the membrane envelope of influenza virus. HA contains a fusion peptide, a receptor binding site, a metastable structural motif, and the transmembrane domain. The first step of influenza virus entry is the recognition of the host cell receptor molecule, terminal α-sialic acid, by HA. This multivalent attachment by multiple copies of trimetric HA triggers endocytosis of influenza virus that is contained in the endosome. The endosome-trapped virus traffics via a unidirectional pathway to near the nucleus. At this location, the interior pH of the endosome becomes acidic that induces a dramatic conformational change in HA to insert the fusion peptide into the host membrane, induce juxtaposition of the two membranes, and form a fusion pore that allows the release of the genome segments of influenza virus. HA plays a key role in the entire entry pathway. Inhibitors of virus entry are potentially effective antiviral drugs of influenza viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123407/ doi: 10.1007/978-1-4614-0980-9_9 id: cord-332632-u2ud0vmq author: Lussi, Carmela title: What can pestiviral endonucleases teach us about innate immunotolerance? date: 2016-03-17 words: 8703.0 sentences: 394.0 pages: flesch: 44.0 cache: ./cache/cord-332632-u2ud0vmq.txt txt: ./txt/cord-332632-u2ud0vmq.txt summary: In particular, the unique extension of ''self'' to include the viral genome by degrading immunostimulatory viral RNA by E(rns) is reminiscent of various host nucleases that are important to prevent inappropriate IFN activation by the host''s own nucleic acids in autoimmune diseases such as Aicardi-Goutières syndrome or systemic lupus erythematosus. Thus, the survival strategy of BVDV consists of being non-cytopathogenic and producing less dsRNA than its cp counterpart, and expressing the IFN antagonists N pro as the first protein in order to reduce or even avoid IFN production in infected cells and E rns to degrade immunostimulatory viral RNA before they might activate the host''s PRRs. Notably, both pestiviral IFN antagonists are not only required to constantly maintain innate immunotolerance during persistent infections, but they also play an important role in acute infections [25] . abstract: Pestiviruses including bovine viral diarrhea virus (BVDV), border disease virus (BDV) and classical swine fever virus (CSFV), occur worldwide and are important pathogens of livestock. A large part of their success can be attributed to the induction of central immunotolerance including B- and T-cells upon fetal infection leading to the generation of persistently infected (PI) animals. In the past few years, it became evident that evasion of innate immunity is a central element to induce and maintain persistent infection. Hence, the viral non-structural protease N(pro) heads the transcription factor IRF-3 for proteasomal degradation, whereas an extracellularly secreted, soluble form of the envelope glycoprotein E(rns) degrades immunostimulatory viral single- and double-stranded RNA, which makes this RNase unique among viral endoribonucleases. We propose that these pestiviral interferon (IFN) antagonists maintain a state of innate immunotolerance mainly pertaining its viral nucleic acids, in contrast to the well-established immunotolerance of the adaptive immune system, which is mainly targeted at proteins. In particular, the unique extension of ‘self’ to include the viral genome by degrading immunostimulatory viral RNA by E(rns) is reminiscent of various host nucleases that are important to prevent inappropriate IFN activation by the host’s own nucleic acids in autoimmune diseases such as Aicardi-Goutières syndrome or systemic lupus erythematosus. This mechanism of “innate tolerance” might thus provide a new facet to the role of extracellular RNases in the sustained prevention of the body’s own immunostimulatory RNA to act as a danger-associated molecular pattern that is relevant across various species. url: https://www.ncbi.nlm.nih.gov/pubmed/27021825/ doi: 10.1016/j.cytogfr.2016.03.003 id: cord-331714-2qj2rrgd author: Lvov, Dimitry Konstantinovich title: Single-Stranded RNA Viruses date: 2015-05-29 words: 64283.0 sentences: 4009.0 pages: flesch: 55.0 cache: ./cache/cord-331714-2qj2rrgd.txt txt: ./txt/cord-331714-2qj2rrgd.txt summary: Among them are viruses associated with sporadic cases or outbreaks of human disease, such as hemorrhagic fever with renal syndrome (viruses of the genus Hantavirus), Crimean–Congo hemorrhagic fever (CCHFV, Nairovirus), California encephalitis (INKV, TAHV, and KHATV; Orthobunyavirus), sandfly fever (SFCV and SFNV, Phlebovirus), Tick-borne encephalitis (TBEV, Flavivirus), Omsk hemorrhagic fever (OHFV, Flavivirus), West Nile fever (WNV, Flavivirus), Sindbis fever (SINV, Alphavirus) Chikungunya fever (CHIKV, Alphavirus) and others. Artashat virus (ARTSV, strain LEIV-2236Ar) was originally isolated from Ornithodoros alactagalis ticks (family Argasidae) collected in the burrows of a small five-toed jerboa (Allactaga elater) near Arevashat village (40 02 absence of antigenic relationships with any known viruses, it was referred to as an "unclassified bunyavirus." 1À3 Taxonomy. abstract: In this chapter, we describe 73 zoonotic viruses that were isolated in Northern Eurasia and that belong to the different families of viruses with a single-stranded RNA (ssRNA) genome. The family includes viruses with a segmented negative-sense ssRNA genome (families Bunyaviridae and Orthomyxoviridae) and viruses with a positive-sense ssRNA genome (families Togaviridae and Flaviviridae). Among them are viruses associated with sporadic cases or outbreaks of human disease, such as hemorrhagic fever with renal syndrome (viruses of the genus Hantavirus), Crimean–Congo hemorrhagic fever (CCHFV, Nairovirus), California encephalitis (INKV, TAHV, and KHATV; Orthobunyavirus), sandfly fever (SFCV and SFNV, Phlebovirus), Tick-borne encephalitis (TBEV, Flavivirus), Omsk hemorrhagic fever (OHFV, Flavivirus), West Nile fever (WNV, Flavivirus), Sindbis fever (SINV, Alphavirus) Chikungunya fever (CHIKV, Alphavirus) and others. Other viruses described in the chapter can cause epizootics in wild or domestic animals: Geta virus (GETV, Alphavirus), Influenza A virus (Influenzavirus A), Bhanja virus (BHAV, Phlebovirus) and more. The chapter also discusses both ecological peculiarities that promote the circulation of these viruses in natural foci and factors influencing the occurrence of epidemic and epizootic outbreaks url: https://api.elsevier.com/content/article/pii/B9780128017425000088 doi: 10.1016/b978-0-12-801742-5.00008-8 id: cord-018804-wj35q88f author: Lázaro, Ester title: Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity date: 2007 words: 8510.0 sentences: 398.0 pages: flesch: 44.0 cache: ./cache/cord-018804-wj35q88f.txt txt: ./txt/cord-018804-wj35q88f.txt summary: High error prone replication, together with the short replication times and large population sizes typical of RNA viruses, instead of being a handicap for survival provides an extraordinary evolutionary advantage by permitting the generation of a wide reservoir of mutants with different phenotypic properties [7] . However, the fact that DNA organisms, which usually live in constant environments, have evolved corrector activities, whereas RNA viruses have not, suggests that replication with high error rates is a selected character that strongly favours viral adaptation to fast changing conditions. Quasi-species replicating during a long time in a near-constant environment in the absence of large population size fluctuations can present a low rate of fixation of mutations in the consensus sequence, despite the continuous occurrence of mutants that is characteristic of the underlying dynamics of the population. The infection of a new host constitutes a sudden change in the environment in which viral replication takes place, usually with the consequence of a drastic decrease in the average fitness of the virus population, which prevents further transmission. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123777/ doi: 10.1007/978-3-540-35306-5_15 id: cord-309346-4mdxe6ri author: López-Medrano, Francisco title: Virus respiratorios: los más frecuentes, los más olvidados date: 2008-02-29 words: 1440.0 sentences: 149.0 pages: flesch: 53.0 cache: ./cache/cord-309346-4mdxe6ri.txt txt: ./txt/cord-309346-4mdxe6ri.txt summary: Los estudios de descripción epidemiológica, como el de Reina et al 10 son el primer paso para el desarrollo de nuevas posibilidades terapéuticas (antivirales) y profilácticas (vacunas) frente a metapneumovirus y VRS, que a buen seguro tendrían una importante repercusión sobre el control de la patología respiratoria de la población pediátrica. También en este número de ENFERMEDADES INFECCIOSAS Y MICROBIOLOGÍA CLÍNICA se publica un artículo de Perelló et al 12 sobre la implicación de los virus respiratorios en la neumonía adquirida en la comunidad (NAC) en sujetos infectados por el virus de la inmunodeficiencia humana (VIH). Sin embargo, es importante recordar que las infecciones por virus respiratorios pueden complicarse con infección de vías respiratorias bajas y neumonía en sujetos inmunodeprimidos, con una morbimortalidad no despreciable, como se ha demostrado recientemente en cohortes de pacientes con enfermedades hematológicas 5,6 y en portadores de trasplante de órgano sólido 7 . abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0213005X08726594 doi: 10.1157/13115538 id: cord-336948-8yqdhcnz author: Löhner, Rainald title: Detailed simulation of viral propagation in the built environment date: 2020-08-05 words: 5698.0 sentences: 314.0 pages: flesch: 55.0 cache: ./cache/cord-336948-8yqdhcnz.txt txt: ./txt/cord-336948-8yqdhcnz.txt summary: If, for the sake of argument, we consider Stoke''s law for the drag of spherical particles, valid below Reynolds numbers of Re = 1, the terminal sink velocity (also known as the settling velocity) of particles will be given by [26] : where ρ p , ρ g , g, μ, d denote the density of the particles (essentially water in the present case), density of the gas (air), gravity, dynamic viscosity of the gas and diameter of the particle respectively. -Spatial discretization using unstructured grids (in order to allow for arbitrary geometries and adaptive refinement); -Spatial approximation of unknowns with simple linear finite elements (in order to have a simple input/output and code structure); -Edge-based data structures (for reduced access to memory and indirect addressing); -Temporal approximation using implicit integration of viscous terms and pressure (the interesting scales are the ones associated with advection); -Temporal approximation using explicit, high-order integration of advective terms; -Low-storage, iterative solvers for the resulting systems of equations (in order to solve large 3-D problems); and -Steady results that are independent from the timestep chosen (in order to have confidence in convergence studies). abstract: A summary is given of the mechanical characteristics of virus contaminants and the transmission via droplets and aerosols. The ordinary and partial differential equations describing the physics of these processes with high fidelity are presented, as well as appropriate numerical schemes to solve them. Several examples taken from recent evaluations of the built environment are shown, as well as the optimal placement of sensors. url: https://doi.org/10.1007/s00466-020-01881-7 doi: 10.1007/s00466-020-01881-7 id: cord-331020-lyxje82u author: M. Najimudeen, Shahnas title: Infectious Bronchitis Coronavirus Infection in Chickens: Multiple System Disease with Immune Suppression date: 2020-09-24 words: 6966.0 sentences: 349.0 pages: flesch: 37.0 cache: ./cache/cord-331020-lyxje82u.txt txt: ./txt/cord-331020-lyxje82u.txt summary: The evolution of new strains of IBV during the last nine decades against vaccine-induced immune response and changing clinical and pathological manifestations emphasize the necessity of the rational development of intervention strategies based on a thorough understanding of IBV interaction with the host. For example, chickens infected with certain strains of IBV such as Mass, QX-like strain or Aust T at ages of 1-14 days develop cystic oviducts without impaired ovarian functions, which leads to false layer syndrome with no egg production [15, [63] [64] [65] . One of the immune cell types that bridges innate and adaptive host responses is the macrophages, and the available data show that certain IBV serotypes (i.e., Mass and Conn) target respiratory tract macrophages and replicate within them, thus leading to a productive infection [59, 88] . abstract: In the early 1930s, infectious bronchitis (IB) was first characterized as a respiratory disease in young chickens; later, the disease was also described in older chickens. The etiology of IB was confirmed later as being due to a coronavirus: the infectious bronchitis virus (IBV). Being a coronavirus, IBV is subject to constant genome change due to mutation and recombination, with the consequence of changing clinical and pathological manifestations. The potential use of live attenuated vaccines for the control of IBV infection was demonstrated in the early 1950s, but vaccine breaks occurred due to the emergence of new IBV serotypes. Over the years, various IBV genotypes associated with reproductive, renal, gastrointestinal, muscular and immunosuppressive manifestations have emerged. IBV causes considerable economic impacts on global poultry production due to its pathogenesis involving multiple body systems and immune suppression; hence, there is a need to better understand the pathogenesis of infection and the immune response in order to help developing better management strategies. The evolution of new strains of IBV during the last nine decades against vaccine-induced immune response and changing clinical and pathological manifestations emphasize the necessity of the rational development of intervention strategies based on a thorough understanding of IBV interaction with the host. url: https://doi.org/10.3390/pathogens9100779 doi: 10.3390/pathogens9100779 id: cord-290855-6umgvt28 author: Ma, Li title: Antiviral Effects of Plant-Derived Essential Oils and Their Components: An Updated Review date: 2020-06-05 words: 5620.0 sentences: 303.0 pages: flesch: 42.0 cache: ./cache/cord-290855-6umgvt28.txt txt: ./txt/cord-290855-6umgvt28.txt summary: Previous studies have demonstrated essential oils to be excellent candidates to treat antiviral-resistant infection associated with their chemical complexity which confers broad-spectrum mechanisms of action and non-specific antiviral properties. This review provides an up-to-date overview of the antiviral efficacy of essential oils from a wide range of plant species and their characteristic components, as well as their overall mechanisms of action, focusing on the last decade. Virucidal effects of EOs extracted from numerous aromatic and herbal plants are also well documented on a variety of viruses, such as IFV, HSV, HIV, yellow fever virus, and avian influenza, etc. Essential oils from Star Anise, Australian tea tree, oregano, Eucalyptus caesia, to name a few, have been demonstrated to exhibit high anti-HSV-1 activities in vitro (Table 1 ). abstract: The presence of resistance to available antivirals calls for the development of novel therapeutic agents. Plant-derived essential oils may serve as alternative sources of virus-induced disease therapy. Previous studies have demonstrated essential oils to be excellent candidates to treat antiviral-resistant infection associated with their chemical complexity which confers broad-spectrum mechanisms of action and non-specific antiviral properties. However, almost no comprehensive reviews are updated to generalize knowledge in this regard and disclose the interplay between the components and their antiviral activities. This review provides an up-to-date overview of the antiviral efficacy of essential oils from a wide range of plant species and their characteristic components, as well as their overall mechanisms of action, focusing on the last decade. The roles of individual components relative to the overall antiviral efficacy of essential oils, together with the antiviral activity of essential oils in comparison with commercial drugs are also discussed. Lastly, the inadequacies in current research and future research are put forward. This review will provide references in the design of new drug prototypes and improve our understanding of the proper applications of essential oils in the future. url: https://www.ncbi.nlm.nih.gov/pubmed/32516954/ doi: 10.3390/molecules25112627 id: cord-354582-fniymnmf author: Ma, Zhiqian title: Reverse genetic systems: Rational design of coronavirus live attenuated vaccines with immune sequelae date: 2020-06-30 words: 8373.0 sentences: 423.0 pages: flesch: 44.0 cache: ./cache/cord-354582-fniymnmf.txt txt: ./txt/cord-354582-fniymnmf.txt summary: In this review, we systematically describe the role of reverse genetics technology in studying the effects of coronavirus proteins on viral virulence and innate immunity, cell and tissue tropism and antiviral drug screening. Recently, reverse genetics techniques, including targeted RNA recombination, in vitro ligation and bacterial artificial chromosome systems, vaccinia virus vectors and transformation associated recombination (TAR) cloning, have been successfully used to manipulate the genome of coronaviruses (Fig. 2 ). Using a recombinant SARS-CoV strain with reduced nsp3 de-ADP-ribosylation activity showed that this mutant strain led to virus attenuation in mice but protected them from an otherwise lethal SARS-CoV infection and significantly enhanced the innate immune response, indicating that it is an important virulence factor for SARS-CoV . The N protein plays an important role in viral pathogenesis since BALB/c mice immunized with recombinant virus MVA-MERS-N exhibit stronger T cell responses and anti-N monoclonal antibodies protect mice from lethal infection by MHV (Nakanaga et al., 1986; Veit et al., 2018) . abstract: Since the end of 2019, the global COVID-19 outbreak has once again made coronaviruses a hot topic. Vaccines are hoped to be an effective way to stop the spread of the virus. However, there are no clinically approved vaccines available for coronavirus infections. Reverse genetics technology can realize the operation of RNA virus genomes at the DNA level and provide new ideas and strategies for the development of new vaccines. In this review, we systematically describe the role of reverse genetics technology in studying the effects of coronavirus proteins on viral virulence and innate immunity, cell and tissue tropism and antiviral drug screening. An efficient reverse genetics platform is useful for obtaining the ideal attenuated strain to prepare an attenuated live vaccine. url: https://doi.org/10.1016/bs.aivir.2020.06.003 doi: 10.1016/bs.aivir.2020.06.003 id: cord-000180-howix091 author: MacLeod, Iain J. title: Binding of Herpes Simplex Virus Type-1 Virions Leads to the Induction of Intracellular Signalling in the Absence of Virus Entry date: 2010-03-05 words: 6788.0 sentences: 316.0 pages: flesch: 49.0 cache: ./cache/cord-000180-howix091.txt txt: ./txt/cord-000180-howix091.txt summary: By taking advantage of the entry-defective phenotype of glycoprotein-deficient HSV-1 virus particles, the results presented here show that binding of virions to cellular receptors on the plasma membrane is sufficient to stimulate a change in cellular gene expression. As induction of the NF-kB reporter construct occurred within one hour of inoculation with DgH virions and peaked at around two-and-a-half hours post-inoculation, then the transcripts previHFFs were stimulated with 1000 particles/cell of DgB, DgD or DgH HSV-1 for six hours and a cDNA microarray corresponding to targets of 19 signalling pathways was used to detect changes in cellular gene expression when compared to mock-infected. Real-time PCR confirmed that changes in transcription associated with the NF-kB, JAK/STAT, JAK/Src and PI3K pathways were modulated as a result of virion binding, all of which required gD on the envelope surface To demonstrate that signalling occurred at physiologically relevant multiplicities of infection, HFFs were inoculated with either 1000, 100, 10 or 1 particles per cell of entry-defective HSV-1. abstract: The envelope of HSV-1 contains a number of glycoproteins, four of which are essential for virus entry. Virus particles lacking gB, gD, gH or gL are entry-defective, although these viruses retain the ability to bind to the plasma membrane via the remaining glycoproteins. Soluble forms of gD have been shown to trigger the nuclear translocation of the NF-κB transcriptional complex in addition to stimulating the production of Type I interferon. By taking advantage of the entry-defective phenotype of glycoprotein-deficient HSV-1 virus particles, the results presented here show that binding of virions to cellular receptors on the plasma membrane is sufficient to stimulate a change in cellular gene expression. Preliminary microarray studies, validated by quantitative real-time PCR, identified the differential expression of cellular genes associated with the NF-κB, PI3K/Akt, Jak/Stat and related Jak/Src pathways by virions lacking gB or gH but not gD. Gene induction occurred at a few particles per cell, corresponding to physiological conditions during primary infection. Reporter assay studies determined that NF-κB transcriptional activity is stimulated within an hour of HSV-1 binding, peaks between two and three hours post-binding and declines to background levels by five hours after induction. The immediate, transient nature of these signalling events suggests that HSV-1 glycoproteins, particularly gD, may alter the cellular environment pre-entry so as to condition the cell for viral replication. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832691/ doi: 10.1371/journal.pone.0009560 id: cord-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-351571-gwtkrt5u author: Mackay, Ian M. title: Community-Wide, Contemporaneous Circulation of a Broad Spectrum of Human Rhinoviruses in Healthy Australian Preschool-Aged Children During a 12-Month Period date: 2013-05-01 words: 3374.0 sentences: 160.0 pages: flesch: 43.0 cache: ./cache/cord-351571-gwtkrt5u.txt txt: ./txt/cord-351571-gwtkrt5u.txt summary: Human rhinovirus (HRV) infections trigger exacerbations of asthma and chronic obstructive pulmonary disease and the majority of acute respiratory illnesses (ARIs), some of which meet criteria for influenza-like illness. Nevertheless, each available majority sequence of an HRV-C type has to date represented a genetically unique, phylogenetically distinct, and globally distributed virus detected in patients with ARIs. There are specific seasonal and annual variations in respiratory virus circulation and interactions [11] [12] [13] . We sought to quantify the genetic diversity, epidemiology, and impact of HRV and enterovirus species, conjointly referred to hereafter as picornaviruses, circulating among a community cohort of preschool-aged children who provided respiratory samples over a 1-year period. 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 abstract: Human rhinovirus (HRV) replication triggers exacerbation of asthma and causes most acute respiratory illnesses (ARIs), which may manifest as influenza-like illness. The recent assignment of 60 previously unknown HRV types to a third HRV species, Human rhinovirus C, raised questions about the prevalence of these picornavirus types in the community, the extent of HRV diversity at a single site, and whether the HRVs have an equally diverse clinical impact on their hosts. We quantified HRV diversity, and there was no clinical impact attributable to HRV species and genotypes among a community population of preschool-aged children with ARI who provided respiratory samples during 2003. All HRV species were represented among 138 children with ARI, and 74 distinct HRV types were cocirculating. Fever accompanied 32.8% of HRV-positive ARI cases. HRVs were less likely than DNA viruses to be codetected with another virus, suggesting virus interference at the community level, demonstrated by the inverse correlation between influenza virus detection and HRV detection. url: https://doi.org/10.1093/infdis/jis476 doi: 10.1093/infdis/jis476 id: cord-317244-4su5on6s author: Maganga, Gael D. title: Identification of an Unclassified Paramyxovirus in Coleura afra: A Potential Case of Host Specificity date: 2014-12-31 words: 3476.0 sentences: 191.0 pages: flesch: 50.0 cache: ./cache/cord-317244-4su5on6s.txt txt: ./txt/cord-317244-4su5on6s.txt summary: In the present study, among 985 bats belonging to 6 species sampled in the Belinga caves of Gabon, RNA of an unclassified paramyxovirus (Belinga bat virus, BelPV) was discovered in 14 African sheath-tailed bats (Coleura afra), one of which exhibited several hemorrhagic lesions at necropsy, and viral sequence was obtained in two animals. To further investigate the presence of the virus in bat populations, a strain-specific real-time RT-PCR assay (primers: GB09-478-F, 59-GGCGGCTCTTAAAAGT-GAATG-39; GB09-478-R, 59-GCGGGGTCAAATTGGTCAT-39; probe: GB09-478-P, 59-TCCAGCACAAACATATCCGAGAAGGCTAG-39) was designed within the initial PCR fragment and was used to test total RNA extracted from mixed liver and spleen samples from each of all the other bat species. In order to determine the organ distribution of this virus in infected bats, total RNA was extracted from heart, liver, spleen, kidney, lung, intestine and brain samples from all 14 real-time RT-PCR-positive bats, as described previously, and screened, using the same strain-specific real-time RT-PCR assay shown above. abstract: Bats are known to harbor multiple paramyxoviruses. Despite the creation of two new genera, Aquaparamyxovirus and Ferlavirus, to accommodate this increasing diversity, several recently isolated or characterized viruses remain unclassified beyond the subfamily level. In the present study, among 985 bats belonging to 6 species sampled in the Belinga caves of Gabon, RNA of an unclassified paramyxovirus (Belinga bat virus, BelPV) was discovered in 14 African sheath-tailed bats (Coleura afra), one of which exhibited several hemorrhagic lesions at necropsy, and viral sequence was obtained in two animals. Phylogenetically, BelPV is related to J virus and Beilong virus (BeiPV), two other unclassified paramyxoviruses isolated from rodents. In the diseased BelPV-infected C. afra individual, high viral load was detected in the heart, and the lesions were consistent with those reported in wild rodents and mice experimentally infected by J virus. BelPV was not detected in other tested bat species sharing the same roosting sites and living in very close proximity with C. afra in the two caves sampled, suggesting that this virus may be host-specific for C. afra. The mode of transmission of this paramyxovirus in bat populations remains to be discovered. url: https://doi.org/10.1371/journal.pone.0115588 doi: 10.1371/journal.pone.0115588 id: cord-002581-r7mskri0 author: Magnani, Diogo M. title: A human inferred germline antibody binds to an immunodominant epitope and neutralizes Zika virus date: 2017-06-12 words: 5291.0 sentences: 313.0 pages: flesch: 55.0 cache: ./cache/cord-002581-r7mskri0.txt txt: ./txt/cord-002581-r7mskri0.txt summary: title: A human inferred germline antibody binds to an immunodominant epitope and neutralizes Zika virus The isolation of neutralizing monoclonal antibodies (nmAbs) against the Zika virus (ZIKV) might lead to novel preventative strategies for infections in at-risk individuals, primarily pregnant women. Here we describe the isolation of 18 plasmablast-derived human mAbs, sorted 12 days post onset of symptoms from a ZIKV-patient in São Paulo, Brazil. Interestingly, one of these mAbs (P1F12) exhibited no nucleotide mutations when compared to its corresponding germline sequences, but still recognized a ZIKV immunodominant epitope and neutralized the virus. Virus capture assay and recombinant E protein ELISA P1F12 binding was determined by both virus capture assay (VCA) and recombinant (r)E ELISAs. The VCA plates were coated overnight with the mouse-anti-Flavivirus monoclonal antibody 4G2 (clone D1-4G2-4-15, EMD Millipore) followed by incubation with viral stocks (ZIKV or DENV). Molecular determinants of human neutralizing antibodies isolated from a patient infected with Zika virus abstract: The isolation of neutralizing monoclonal antibodies (nmAbs) against the Zika virus (ZIKV) might lead to novel preventative strategies for infections in at-risk individuals, primarily pregnant women. Here we describe the characterization of human mAbs from the plasmablasts of an acutely infected patient. One of the 18 mAbs had the unusual feature of binding to and neutralizing ZIKV despite not appearing to have been diversified by affinity maturation. This mAb neutralized ZIKV (Neut(50) ~ 2 μg/ml) but did not react with any of the four dengue virus serotypes. Except for the expected junctional diversity created by the joining of the V-(D)-J genes, there was no deviation from immunoglobulin germline genes. This is a rare example of a human mAb with neutralizing activity in the absence of detectable somatic hypermutation. Importantly, binding of this mAb to ZIKV was specifically inhibited by human plasma from ZIKV-exposed individuals, suggesting that it may be of value in a diagnostic setting. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5481143/ doi: 10.1371/journal.pntd.0005655 id: cord-007094-ur9sz21s author: Mahabir, Esther title: Rodent and Germplasm Trafficking: Risks of Microbial Contamination in a High-Tech Biomedical World date: 2008-01-01 words: 6254.0 sentences: 268.0 pages: flesch: 39.0 cache: ./cache/cord-007094-ur9sz21s.txt txt: ./txt/cord-007094-ur9sz21s.txt summary: Preservation of mouse germ-plasm is achieved by cryopreservation of spermatozoa, embryos, or ovaries, and embryonic stem cells are used for the production of genetically engineered mice. In this article, we discuss regulations and practical issues in the shipping of live mice and mouse tissues, including spermatozoa, embryos, ovaries, and embryonic stem cells, and review work on microbial contamination of these biological materials. The importation paperwork for cryopreserved laboratory mouse tissues and cell lines is similar to that required for live animal importation to the United States (i.e., a pro forma invoice and declaration statements). Embryo transfer recipients in rederivation programs should be held in individually ventilated cages (IVCs 1 ) until testing shows that they are free of all unwanted microorganisms, including those listed in Appendix 3 of the Federation of Laboratory Animal Science Associations (FELASA) recommendations (Nicklas et al. Risk assessment of mouse hepatitis virus infection via in vitro fertilization and embryo transfer by the use of zona-intact and laser-microdissected oocytes abstract: High-tech biomedical advances have led to increases both in the number of mice used for research and in exchanges of mice and/or their tissues between institutions. The latter are associated with the risk of dissemination of infectious agents. Because of the lack of international standardization of health surveillance programs, health certificates for imported rodents may be informative but may not address the needs of the importing facility. Preservation of mouse germ-plasm is achieved by cryopreservation of spermatozoa, embryos, or ovaries, and embryonic stem cells are used for the production of genetically engineered mice. After embryo transfer, recipients and rederived pups that test negative in microbiological screening for relevant microorganisms are released into full barrier holding areas. However, current research shows that embryos may also transmit microorganisms, especially viruses, to the recipient mice. In this article, we discuss regulations and practical issues in the shipping of live mice and mouse tissues, including spermatozoa, embryos, ovaries, and embryonic stem cells, and review work on microbial contamination of these biological materials. In addition, we present ways to reduce the risk of transmission of pathogens to mice under routine conditions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108542/ doi: 10.1093/ilar.49.3.347 id: cord-314201-6njwigco author: Maher-Sturgess, Sheryl L title: Universal primers that amplify RNA from all three flavivirus subgroups date: 2008-01-24 words: 4625.0 sentences: 253.0 pages: flesch: 54.0 cache: ./cache/cord-314201-6njwigco.txt txt: ./txt/cord-314201-6njwigco.txt summary: Tanaka [3] published the first universal primer pair specific for mosquito borne flaviviruses in 1993; the YF1 and YF3 primers targeted the NS5/3''UTR of the genome and were based upon the six flavivirus sequences available at the time. In 2005 Gaunt and Gould designed a universal nested PCR, using six primers targeting the E gene, capable of amplifying cDNA from 60 flavivirus strains. In the present study, we identified conserved sites and developed a universal, non-nested primer pair that amplifies cDNA from each of the major subgroups of flaviviruses, and also TABV, under standard reaction conditions. Since the amplified products represent 8% of the genome, this is sufficient sequence to determine the species of the virus and thus potentially to identify unrecognised flaviviruses. Rapid subgroup identification of the flaviviruses using degenerate primer E-gene RT-PCR and site specific restriction enzyme analysis abstract: BACKGROUND: Species within the Flavivirus genus pose public health problems around the world. Increasing cases of Dengue and Japanese encephalitis virus in Asia, frequent outbreaks of Yellow fever virus in Africa and South America, and the ongoing spread of West Nile virus throughout the Americas, show the geographical burden of flavivirus diseases. Flavivirus infections are often indistinct from and confused with other febrile illnesses. Here we review the specificity of published primers, and describe a new universal primer pair that can detect a wide range of flaviviruses, including viruses from each of the recognised subgroups. RESULTS: Bioinformatic analysis of 257 published full-length Flavivirus genomes revealed conserved regions not previously targeted by primers. Two degenerate primers, Flav100F and Flav200R were designed from these regions and used to generate an 800 base pair cDNA product. The region amplified encoded part of the methyltransferase and most of the RNA-dependent-RNA-polymerase (NS5) coding sequence. One-step RT-PCR testing was successful using standard conditions with RNA from over 60 different flavivirus strains representing about 50 species. The cDNA from each virus isolate was sequenced then used in phylogenetic analyses and database searches to confirm the identity of the template RNA. CONCLUSION: Comprehensive testing has revealed the broad specificity of these primers. We briefly discuss the advantages and uses of these universal primers. url: https://doi.org/10.1186/1743-422x-5-16 doi: 10.1186/1743-422x-5-16 id: cord-021034-hnw7a3a1 author: Mahony, James B. title: Negative staining in the detection of viruses in clinical specimens date: 2002-10-09 words: 4164.0 sentences: 297.0 pages: flesch: 46.0 cache: ./cache/cord-021034-hnw7a3a1.txt txt: ./txt/cord-021034-hnw7a3a1.txt summary: In our experience the serum-in-agar (SIA) method is the most sensitive of the PAG IEM techniques for detection of rotavirus particles in clinical specimens. SPEIMDAGT employing colloidal gold-labeled secondary antibody has increased sensitivity and offers the advantage of detecting viral antigen when whole virus particles are not visible. Prior to the development of immunoassay techniques for detecting viral antigens, direct electron microscopy (DEM) with negative staining was the only method of providing a definitive diagnosis of several viral infections. We have used this method to detect rotavirus in fecal specimens (Wu et a!., 1989) (Fig. 2) Solid phase JEM Although IEM is considerably more sensitive than DEM, it is dependent upon the optimal concentrations of antibody and antigen and is susceptible to a prozone phenomenon. Development of a sensitive protein A-gold immunoelectron microscopy method for detecting viral antigens in fluid specimens abstract: Viruses have unique morphology and are therefore good candidates for negative staining. Negative staining with phosphotungstic acid (PTA) or uranyl acetate has facilitated the detection of many viruses in clinical specimens. Enhancement procedures have included the use of centrifugation and agar diffusion for concentrating virus particles, the use of solid phase capture reagents to trap virus particles and the use of secondary antibodies and electron dense markers to help visualize them. Techniques currently in use and employing negative staining include direct EM, immune electron microscopy (IEM), solid phase immune electron microscopy (SPIEM), colloidal gold-labeled protein A (PAG), solid phase IEM employing a second decorator antibody (SPIEMDAT), and solid phase IEM using colloided gold-labeled secondary antibodies (SPEIMDAGT). IEM methods assist with the detection of small viruses or viruses present in low numbers while PAG offers increased sensitivity over direct EM and IEM. In our experience the serum-in-agar (SIA) method is the most sensitive of the PAG IEM techniques for detection of rotavirus particles in clinical specimens. SPIEMDAT enhances the detection of small viruses which are often missed by other techniques due to background staining in specimens. SPEIMDAGT employing colloidal gold-labeled secondary antibody has increased sensitivity and offers the advantage of detecting viral antigen when whole virus particles are not visible. IEM techniques have recently been used for typing viruses using either monospecific antisera or monoclonal antibodies and colloidal gold-labeled secondary antibody. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148852/ doi: 10.1016/0739-6260(91)90062-5 id: cord-279694-25rblhwb author: Mahy, B.W.J title: Emerging and Reemerging Virus Diseases of Vertebrates date: 2014-11-28 words: 4322.0 sentences: 177.0 pages: flesch: 50.0 cache: ./cache/cord-279694-25rblhwb.txt txt: ./txt/cord-279694-25rblhwb.txt summary: Although it is still important to isolate viruses in cell culture for their complete characterization, it is now possible directly to detect viruses in diseased tissues by PCR, then, by sequencing the amplicon, to determine whether a new virus has emerged to cause the disease. For example, when hantavirus pulmonary syndrome, caused by a bunyavirus of rodents, Sin Nombre virus, was initially detected in 1993 in the Four Corners region of Western USA, it was found that rodents inside a house where people had been infected carried a virus identical in sequence to virus isolated from human cases. Then, in 1993, a new hantavirus emerged in the Four Corners region of Southwestern USA as the cause of a severe acute respiratory disease syndrome, with a fatality rate close to 40%, and named Sin Nombre virus. It will be important in the future to detect new viruses before they can emerge to cause disease in the population. abstract: In the last two decades, a large number of new viruses have been discovered, many of which are pathogenic in humans or other vertebrates. Among the more important causes of virus emergence have been changes in human behavior, population, and increases in travel to distant countries. In addition, the application of new molecular technologies has led to the recognition of many viruses that hitherto went undetected. Many of the new, emerging viruses have an RNA genome, and many are zoonoses. The spread of human immunodeficiency virus, causing acquired immune deficiency syndrome, and the use of immunosuppressive drugs following transplant surgery, have increased the numbers of people in the population that are highly susceptible to emerging virus infections. The threat of a new pandemic of influenza virus in the human population stresses the need for development of better methods for detection, surveillance, and control of emerging virus diseases. url: https://api.elsevier.com/content/article/pii/B9780128012383025642 doi: 10.1016/b978-0-12-801238-3.02564-2 id: cord-331584-z43ifmr3 author: Mahy, B.W.J. title: Emerging and Reemerging Virus Diseases of Vertebrates date: 2008-07-30 words: 3984.0 sentences: 160.0 pages: flesch: 49.0 cache: ./cache/cord-331584-z43ifmr3.txt txt: ./txt/cord-331584-z43ifmr3.txt summary: The threat of a new pandemic of influenza virus in the human population stresses the need for development of better methods for detection, surveillance, and control of emerging virus diseases. Although it is still important to isolate viruses in cell culture for their complete characterization, it is now possible directly to detect viruses in diseased tissues by PCR, then, by sequencing the amplicon, to determine whether a new virus has emerged to cause the disease. For example, when hantavirus pulmonary syndrome, caused by a bunyavirus of rodents, Sin Nombre virus, was initially detected in 1993 in the Four Corners region of Western USA, it was found that rodents inside a house where people had been infected carried a virus identical in sequence to virus isolated from human cases. Then, in 1993, a new hantavirus emerged in the Four Corners region of Southwestern USA as the cause of a severe acute respiratory disease syndrome, with a fatality rate close to 40%, and named Sin Nombre virus. abstract: In the last two decades, a large number of new viruses have been discovered, many of which are pathogenic in humans or other vertebrates. Among the more important causes of virus emergence have been changes in human behavior, population, and increases in travel to distant countries. In addition, the application of new molecular technologies has led to the recognition of many viruses that hitherto went undetected. Many of the new, emerging viruses have an RNA genome, and many are zoonoses. The spread of human immunodeficiency virus, causing acquired immune deficiency syndrome, and the use of immunosuppressive drugs following transplant surgery, have increased the numbers of people in the population that are highly susceptible to emerging virus infections. The threat of a new pandemic of influenza virus in the human population stresses the need for development of better methods for detection, surveillance, and control of emerging virus diseases. url: https://api.elsevier.com/content/article/pii/B9780123744104003836 doi: 10.1016/b978-012374410-4.00383-6 id: cord-280986-i27mge10 author: Mallia, Patrick title: How Viral Infections Cause Exacerbation of Airway Diseases date: 2017-01-25 words: 4238.0 sentences: 199.0 pages: flesch: 34.0 cache: ./cache/cord-280986-i27mge10.txt txt: ./txt/cord-280986-i27mge10.txt summary: Exacerbations are associated with increased airway inflammation in patients with both asthma and COPD, but many questions remain unanswered regarding the key inflammatory cells and mediators involved. 24, 25 In the lower respiratory tract, increases in Il-6, IL-8, and the chemokine regulated on activation, normal T-cell expressed and secreted (RANTES) have been documented in the sputum of asthmatic patients after experimental rhinovirus infection, 10, 26 and IL-8 has been detected in the sputum of children with naturally occurring exacerbations. A recent study 10 in patients with naturally occurring virusassociated asthma exacerbations found increased levels of IL-10 messenger RNA in the sputum of asthmatic patients compared to virus-infected healthy subjects, but no differences in the level of RANTES or IL-8 between the two groups. Studies 38 of airway inflammation in stable patients with COPD have shown that the disease is characterized by pulmonary infiltration of macrophages, neutrophils, and CD8ϩ T lymphocytes, together with increased expression of cytokines, chemokines, and adhesion molecules. abstract: Exacerbations of asthma and COPD are major causes of morbidity, mortality, and health-care costs. Over the last decade, studies using new molecular diagnostic techniques have established that respiratory viruses are a major cause of exacerbations of both asthma and COPD. The most prevalent viruses detected during exacerbations are the rhinoviruses. Despite the burden of disease associated with exacerbations, little is known about the mechanisms of virus-induced exacerbations of airway diseases. Exacerbations are associated with increased airway inflammation in patients with both asthma and COPD, but many questions remain unanswered regarding the key inflammatory cells and mediators involved. Identifying the key inflammatory mediators involved in exacerbations holds the promise of developing diagnostic and prognostic markers of exacerbation. In addition, such studies can identify new therapeutic targets for the development of novel drugs for the prevention and treatment of exacerbations. url: https://www.sciencedirect.com/science/article/pii/S0012369215511598 doi: 10.1378/chest.130.4.1203 id: cord-003482-f1uvohf0 author: Malmlov, Ashley title: Experimental Zika virus infection of Jamaican fruit bats (Artibeus jamaicensis) and possible entry of virus into brain via activated microglial cells date: 2019-02-04 words: 7503.0 sentences: 400.0 pages: flesch: 53.0 cache: ./cache/cord-003482-f1uvohf0.txt txt: ./txt/cord-003482-f1uvohf0.txt summary: Quantitative probe-based reverse transcription PCR (qRT-PCR) was performed on seruminoculated Vero cell supernatants, serum, brain, lung, liver, spleen, kidney, urinary bladder, prostate and testes from bats from both studies. Brain and testicular tissues stained with both goat polyclonal goat anti-Iba1 (green) and monoclonal 4G-2 flavivirus E specific antibodies (red) showed co-localization (yellow) of ZIKV antigen in cytoplasm of activated microglial cells with their characteristic morphology in the cerebral cortex of infected bats 10 dpi in the time course study and 28 day dpi in the pilot study (Fig 9) . Two bat infection experiments were conducted in this investigation; 1) a pilot study to determine susceptibility of Jamaican fruit bats to ZIKV infection, and 2) a time course study to better understand pathophysiology and chronology of events pertaining to the dynamics of viremia, viral tropism, replication and shedding of the virus in a New World bat species. abstract: The emergence of Zika virus (ZIKV) in the New World has led to more than 200,000 human infections. Perinatal infection can cause severe neurological complications, including fetal and neonatal microcephaly, and in adults there is an association with Guillain-Barré syndrome (GBS). ZIKV is transmitted to humans by Aedes sp. mosquitoes, yet little is known about its enzootic cycle in which transmission is thought to occur between arboreal Aedes sp. mosquitos and non-human primates. In the 1950s and ‘60s, several bat species were shown to be naturally and experimentally susceptible to ZIKV with acute viremia and seroconversion, and some developed neurological disease with viral antigen detected in the brain. Because of ZIKV emergence in the Americas, we sought to determine susceptibility of Jamaican fruit bats (Artibeus jamaicensis), one of the most common bats in the New World. Bats were inoculated with ZIKV PRVABC59 but did not show signs of disease. Bats held to 28 days post-inoculation (PI) had detectable antibody by ELISA and viral RNA was detected by qRT-PCR in the brain, saliva and urine in some of the bats. Immunoreactivity using polyclonal anti-ZIKV antibody was detected in testes, brain, lung and salivary glands plus scrotal skin. Tropism for mononuclear cells, including macrophages/microglia and fibroblasts, was seen in the aforementioned organs in addition to testicular Leydig cells. The virus likely localized to the brain via infection of Iba1(+) macrophage/microglial cells. Jamaican fruit bats, therefore, may be a useful animal model for the study of ZIKV infection. This work also raises the possibility that bats may have a role in Zika virus ecology in endemic regions, and that ZIKV may pose a wildlife disease threat to bat populations. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6382173/ doi: 10.1371/journal.pntd.0007071 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-268417-6eyetb5i author: Mandel, Benjamin title: Neutralization of Animal Viruses date: 1978-12-31 words: 23012.0 sentences: 1239.0 pages: flesch: 43.0 cache: ./cache/cord-268417-6eyetb5i.txt txt: ./txt/cord-268417-6eyetb5i.txt summary: Somewhat earlier, Morgan (1945''1 had reported that discrepancies in the quantitative aspects of the neutralization of WEE virus by immune rabbit sera were related to the use of fresh or heated serum, and that the addition of complement to the latter tended to eliminate the discrepancies. Further studies (Radwan et al., 1973) showed that the addition of complement to virus complexed with dependent antibody eventually resulted in lysis of the viral membrane. It was also shown (Yoshino and Taniguchi, 1966 ) that antibodies induced in guinea pigs by immunization, and in humans following herpes infection, were initially dependent and later independent of complement for neutralizing activity. A relevant observation has been made in several studies; neutralization of infectious virus-antibody complexes by antiglobulin also shows a single-hit mechanism, and at a rate that exceeds the rate of the homotypic reaction. abstract: Publisher Summary Various aspects of the interaction of bacterial viruses and antibody were studied by Andrewes and Elford in England. Similar studies, as well as studies on animal viruses, were carried out in Australia by Burnet and his colleagues. One result of their extensive studies, which were summarized in great detail, was the conclusion that, with respect to their interaction with antibody, bacterial and animal viruses were basically different. Specifically, the difference resided in the stability of the union of virus and antibody, whereas bacterial viruses formed stable complexes, animal viruses formed complexes that tended to dissociate readily. The introduction of animal cell cultures as host systems greatly aided in the study of animal viruses, with respect to fewer and more readily controlled variables, and by the use of the plaque assay in enhanced quantitative reliability. In 1956, Dulbecco et al. described the interaction of two animal viruses with their respective antibodies. The results of these studies led these investigators to conclude, among other things, that animal viruses, at least the two they studied, reacted with antibodies to form complexes that did not dissociate spontaneously. This interpretation was challenged by Fazekas de St. Groth and Reid. As more animal virus-antibody systems were studied by many investigators, there seemed to be a greater accord for irreversible, rather than reversible, interaction. For this reason, in this chapter it is assumed that there are no differences between bacterial viruses, as one category, and animal viruses, as a separate category, concerning their interaction with antibodies. Rather, differences, when they exist, are considered to be related to the viruses per se. Although this chapter is intended to survey the neutralization of animal viruses, occasional reference is made to the studies on bacterial viruses when these studies are pertinent and illuminating to the topic at hand. url: https://www.ncbi.nlm.nih.gov/pubmed/107731/ doi: 10.1016/s0065-3527(08)60101-3 id: cord-297790-tpjxt0w5 author: Mandl, Judith N. title: Going to Bat(s) for Studies of Disease Tolerance date: 2018-09-20 words: 9486.0 sentences: 393.0 pages: flesch: 40.0 cache: ./cache/cord-297790-tpjxt0w5.txt txt: ./txt/cord-297790-tpjxt0w5.txt summary: Among them are filoviruses (e.g., Marburg, Ebola), coronaviruses (e.g., SARS, MERS), henipaviruses (e.g., Hendra, Nipah) which share the common features that they are all RNA viruses, and that a dysregulated immune response is an important contributor to the tissue damage and hence pathogenicity that results from infection in humans. It is likely that differences in evolutionary history of pathogen exposure between bats and humans have led to distinct adaptations in anti-viral immune responses and the ability to tolerate certain infections without disease while being susceptible to others. We summarize this work below, but comparisons of observations made across species suggest that although a number of species appear to be capable of avoiding the pathological effects of RNA virus infection, each bat species may have achieved this through distinct pathways, possibly involving changes to both increase pathogen replication control and to mitigate any immunopathology through decreased inflammatory responses and hence increased disease tolerance. abstract: A majority of viruses that have caused recent epidemics with high lethality rates in people, are zoonoses originating from wildlife. Among them are filoviruses (e.g., Marburg, Ebola), coronaviruses (e.g., SARS, MERS), henipaviruses (e.g., Hendra, Nipah) which share the common features that they are all RNA viruses, and that a dysregulated immune response is an important contributor to the tissue damage and hence pathogenicity that results from infection in humans. Intriguingly, these viruses also all originate from bat reservoirs. Bats have been shown to have a greater mean viral richness than predicted by their phylogenetic distance from humans, their geographic range, or their presence in urban areas, suggesting other traits must explain why bats harbor a greater number of zoonotic viruses than other mammals. Bats are highly unusual among mammals in other ways as well. Not only are they the only mammals capable of powered flight, they have extraordinarily long life spans, with little detectable increases in mortality or senescence until high ages. Their physiology likely impacted their history of pathogen exposure and necessitated adaptations that may have also affected immune signaling pathways. Do our life history traits make us susceptible to generating damaging immune responses to RNA viruses or does the physiology of bats make them particularly tolerant or resistant? Understanding what immune mechanisms enable bats to coexist with RNA viruses may provide critical fundamental insights into how to achieve greater resilience in humans. url: https://doi.org/10.3389/fimmu.2018.02112 doi: 10.3389/fimmu.2018.02112 id: cord-293732-rxd1lyi7 author: Manoj, M.G. title: Potential link between compromised air quality and transmission of the novel corona virus (SARS-CoV-2) in affected areas date: 2020-08-01 words: 4180.0 sentences: 210.0 pages: flesch: 49.0 cache: ./cache/cord-293732-rxd1lyi7.txt txt: ./txt/cord-293732-rxd1lyi7.txt summary: Through a critical review of the current literature and a preliminary analysis of the link between SARS-CoV-2 transmission and air pollution in the affected regions, we offer a perspective that polluted environment could enhance the transmission rate of such deadly viruses under moderate-to-high humidity conditions. The aqueous atmospheric aerosols offer a conducive surface for adsorption/absorption of organic molecules and viruses onto them, facilitating a pathway for higher rate of transmission under favourable environmental conditions. Analysis of the air quality index (AQI, Fig. S1 , acquired on 16 th March 2020) reveals that the effected countries or regions had witnessed enhanced level of pollution ( frequently AQI > 100) which are qualified as "unhealthy" and even "hazardous", in the cold winter period. (2020) reports that air pollutants measured over Italy (PM 10 and PM 2.5 ) have a substantial influence on the COVID-19 transmission and infection rate there. abstract: The emergence of a novel human corona virus disease (COVID-19) has been declared as a pandemic by the World Health Organization. One of the mechanisms of airborne transmission of the severe acute respiratory syndrome - corona virus (SARS-CoV-2) amid humans is through direct ejection of droplets via sneezing, coughing and vocalizing. Nevertheless, there are ample evidences of the persistence of infectious viruses on inanimate surfaces for several hours to a few days. Through a critical review of the current literature and a preliminary analysis of the link between SARS-CoV-2 transmission and air pollution in the affected regions, we offer a perspective that polluted environment could enhance the transmission rate of such deadly viruses under moderate-to-high humidity conditions. The aqueous atmospheric aerosols offer a conducive surface for adsorption/absorption of organic molecules and viruses onto them, facilitating a pathway for higher rate of transmission under favourable environmental conditions. This mechanism partially explains the role of polluted air besides the exacerbation of chronic respiratory diseases in the rapid transmission of the virus amongst the public. Hence, it is stressed that more ambitious policies towards a cleaner environment are required globally to nip in the bud what could be the seeds of a fatal outbreak such as COVID-19. url: https://doi.org/10.1016/j.envres.2020.110001 doi: 10.1016/j.envres.2020.110001 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-000729-iq30z094 author: Marsh, Glenn A. title: Cedar Virus: A Novel Henipavirus Isolated from Australian Bats date: 2012-08-02 words: 6101.0 sentences: 277.0 pages: flesch: 49.0 cache: ./cache/cord-000729-iq30z094.txt txt: ./txt/cord-000729-iq30z094.txt summary: The genome size (18,162 nt) and organization of CedPV is very similar to that of HeV and NiV; its nucleocapsid protein displays antigenic cross-reactivity with henipaviruses; and it uses the same receptor molecule (ephrinB2) for entry during infection. Preliminary challenge studies with CedPV in ferrets and guinea pigs, both susceptible to infection and disease with known henipaviruses, confirmed virus replication and production of neutralizing antibodies although clinical disease was not observed. As part of our on-going field studies on HeV genetic diversity and infection dynamics in the Queensland flying fox populations, urine samples were collected on a regular basis for PCR and virus isolation. CedPV is more closely related to HeV and NiV than henipavirus-like sequences detected in African bats [26, 32] as shown in a phylogenetic tree based on the only sequences available of a 550-nt L gene fragment (Fig. S5) . abstract: The genus Henipavirus in the family Paramyxoviridae contains two viruses, Hendra virus (HeV) and Nipah virus (NiV) for which pteropid bats act as the main natural reservoir. Each virus also causes serious and commonly lethal infection of people as well as various species of domestic animals, however little is known about the associated mechanisms of pathogenesis. Here, we report the isolation and characterization of a new paramyxovirus from pteropid bats, Cedar virus (CedPV), which shares significant features with the known henipaviruses. The genome size (18,162 nt) and organization of CedPV is very similar to that of HeV and NiV; its nucleocapsid protein displays antigenic cross-reactivity with henipaviruses; and it uses the same receptor molecule (ephrin- B2) for entry during infection. Preliminary challenge studies with CedPV in ferrets and guinea pigs, both susceptible to infection and disease with known henipaviruses, confirmed virus replication and production of neutralizing antibodies although clinical disease was not observed. In this context, it is interesting to note that the major genetic difference between CedPV and HeV or NiV lies within the coding strategy of the P gene, which is known to play an important role in evading the host innate immune system. Unlike HeV, NiV, and almost all known paramyxoviruses, the CedPV P gene lacks both RNA editing and also the coding capacity for the highly conserved V protein. Preliminary study indicated that CedPV infection of human cells induces a more robust IFN-β response than HeV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3410871/ doi: 10.1371/journal.ppat.1002836 id: cord-295062-8rl4kswe author: Marsh, Mark title: Virus Entry: Open Sesame date: 2006-02-24 words: 8504.0 sentences: 401.0 pages: flesch: 42.0 cache: ./cache/cord-295062-8rl4kswe.txt txt: ./txt/cord-295062-8rl4kswe.txt summary: Virus Particles as Devices for Targeted Gene Transfer A viral particle is composed of nucleic acids (RNA or DNA), protein, and, in the case of enveloped viruses, membrane lipids. Viruses use signaling activities to induce changes in the cell that promote viral entry and early cytoplasmic events, as well as to optimize later processes in the replication cycle. Like cholera toxin, these viruses bind to the sugar moiety of gangliosides and enter cells via caveolar/raft pathways that are dependent on cholesterol ( Figures 2D and 2E ) and the activation of tyrosine-kinase signaling cascades (Anderson et al., 1996; Pelkmans et al., 2001; Smith et al., 2003a; Stang et al., 1997; Tsai et al., 2003) . Nevertheless, in the majority of cases, the transfer of viral genomes from cell to cell appears to occur through the formation of virus particles that are released from infected cells and use the mechanisms described above to enter new uninfected hosts. abstract: Detailed information about the replication cycle of viruses and their interactions with host organisms is required to develop strategies to stop them. Cell biology studies, live-cell imaging, and systems biology have started to illuminate the multiple and subtly different pathways that animal viruses use to enter host cells. These insights are revolutionizing our understanding of endocytosis and the movement of vesicles within cells. In addition, such insights reveal new targets for attacking viruses before they can usurp the host-cell machinery for replication. url: https://www.sciencedirect.com/science/article/pii/S0092867406001826 doi: 10.1016/j.cell.2006.02.007 id: cord-312688-12san3m7 author: Martin, Baptiste title: Filovirus proteins for antiviral drug discovery: A structure/function analysis of surface glycoproteins and virus entry date: 2016-09-14 words: 10226.0 sentences: 530.0 pages: flesch: 50.0 cache: ./cache/cord-312688-12san3m7.txt txt: ./txt/cord-312688-12san3m7.txt summary: title: Filovirus proteins for antiviral drug discovery: A structure/function analysis of surface glycoproteins and virus entry After replication of the viral genome and RNA transcription, nascent viral particles are assembled in a process mediated by the matrix protein VP40, and virus budding occurs at the cell surface membrane in a process that involves hijacking the host ESCRT machinery (Hartlieb and Weissenhorn, 2006; Noda et al., 2006) . However, no direct interaction between both molecules has been demonstrated yet, and recent studies suggest that a 5 b 1 -integrin is not required for GP-mediated binding of internalization, but rather is a positive regulator of cathepsins, which play an important role in processing GP 1 into its fusion-competent form within the endosomes of infected cells (Schornberg et al., 2009) . After attachment mediated by interaction between the filovirus surface protein GP 1,2 (PDB: 3CSY) and various attachment factors, the complex is internalized and routed to the endosome, where GP 1,2 is processed to trigger fusion of viral and host membranes. abstract: This review focuses on the recent progress in our understanding of filovirus protein structure/function and its impact on antiviral research. Here we focus on the surface glycoprotein GP(1,2) and its different roles in filovirus entry. We first describe the latest advances on the characterization of GP gene-overlapping proteins sGP, ssGP and Δ-peptide. Then, we compare filovirus surface GP(1,2) proteins in terms of structure, synthesis and function. As they bear potential in drug-design, the discovery of small organic compounds inhibiting filovirus entry is a currently very active field. Although it is at an early stage, the development of antiviral drugs against Ebola and Marburg virus entry might prove essential to reduce outbreak-associated fatality rates through post-exposure treatment of both suspected and confirmed cases. url: https://api.elsevier.com/content/article/pii/S0166354216304077 doi: 10.1016/j.antiviral.2016.09.001 id: cord-310439-z0bxsjug author: Martin, R. R. title: Pathogen-Tested Planting Material date: 2014-12-31 words: 7703.0 sentences: 349.0 pages: flesch: 50.0 cache: ./cache/cord-310439-z0bxsjug.txt txt: ./txt/cord-310439-z0bxsjug.txt summary: Buffer zone An area surrounding or adjacent to an area for production of plants in a certification scheme designed to minimize the probability of spread of the target pathogens, pollen, or seed into or out of the block, to meet phytosanitary or other control measures as defined in a certification standard. Many certification programs are based on a published standard that defines site selection and preparation, isolation distances from plants of the same species and other vegetation, number of inspections, record keeping on plant traceability so that tracebacks or traceforwards can be done if a problem should arise, a pest and disease management plan, records of all pest management activities, the conditions and protocols to be followed during plant or seed production, and types and amount of testing that needs to be done at each level in the propagation cycle. abstract: Abstract Certification programs have been developed to provide plant material that meets a predetermined level of plant health. The primary objectives of these programs are to limit pathogen incidence in plant material in order to minimize losses by growers and prevent movement of harmful pests and pathogens that may harm the environment. For many fruit and nut crops, orchards are expected to remain productive for years or decades; thus, starting with plants of high health status is essential. The components of certification programs in terms of plant health will be outlined, along with the benefits of harmonizing these programs where possible to facilitate plant movement without increasing trade in plant pathogens. url: https://api.elsevier.com/content/article/pii/B978044452512300173X doi: 10.1016/b978-0-444-52512-3.00173-x id: cord-287348-00yaxpkp author: Martinez, Maria Jose Abad title: Antiviral Activities of Polysaccharides from Natural Sources date: 2005-12-31 words: 7003.0 sentences: 323.0 pages: flesch: 41.0 cache: ./cache/cord-287348-00yaxpkp.txt txt: ./txt/cord-287348-00yaxpkp.txt summary: Although many compounds with potent antiviral activity in cell cultures and in experimental animals have been detected, at present only several molecules and a-interferon have been approved by the health authorities for therapy of viral infections in humans. Furthermore, several soluble derivatized dextrans with different percentages of carbomethyl, benzylamide and sulphonate/sulphate groups were also evaluated for possible inhibitory effects on HIV-1 infection, and from the results obtained, their use as anti-HIV therapeutic agents can be proposed [56] . Carrageenans and fucoidan are sulphated PS extracted from red seaweed and brown algae, which have shown potent inhibitory activity against different viruses including HIV. These compounds act as potent inhibitors of different enveloped viruses, including members of Herpesviridae, and their activity is linked to the anionic features of the molecule which hinder the attachment of viral particles to host cells. abstract: Abstract The ever increasing resistance of human pathogens to current anti-infective agents is a serious medical problem, leading to the need to develop novel antibiotic prototype molecules. In the case of viruses, the search for antiviral agents involves additional difficulties, particularly due to the nature of the infectious viral agents. Thus, many compounds that may cause the death of viruses are also very likely to injure the host cell that harbours them. Natural products are increasingly appreciated as leads for drug discovery and development. Screening studies have been carried out in order to find antiviral agents from natural sources, and the occurrence of antiviral activity in extracts of plants, marine organisms and fungi is frequent. The evidence indicates that there may be numerous potentially useful antiviral phytochemicals in nature, waiting to be evaluated and exploited. In addition, other plants, not previously utilized medicinally, may also reveal antivirals. Among natural antiviral agents, recent investigations have reconsidered the interest of phyto-polysaccharides, which act as potent inhibitors of different viruses. This chapter will illustrate a variety of antiviral polysaccharides from natural sources since 1990, with the aim of making this matter more accessible to drug development url: https://www.sciencedirect.com/science/article/pii/S1572599505800389 doi: 10.1016/s1572-5995(05)80038-9 id: cord-263315-g7os15m1 author: Martins-da-Silva, Andrea title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response date: 2018-01-18 words: 6975.0 sentences: 460.0 pages: flesch: 48.0 cache: ./cache/cord-263315-g7os15m1.txt txt: ./txt/cord-263315-g7os15m1.txt summary: title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response The two most abundant secreted peptides at 24 h in the dsRNA-transfected group were phospholipid scramblase, an interferon-inducible protein that mediates antiviral activity, and forskolin-binding protein (FKBP), a member of the immunophilin family, which mediates the effect of immunosuppressive drugs. In human and mouse plasmacytoid dendritic cells (pDCs), which are professional interferon-producing cells specialized in recognizing viral RNA and DNA through the endosomal Toll-like receptors (TLRs) TLR7 and TLR9, respectively, PLSCR1 was described as a TLR9-binding protein that plays a significant role in type-1 interferon responses in pDCs by regulating TLR9 expression and trafficking [57] . Binding of FKBP51 to TRAF proteins facilitates the type-I interferon response induced by dsRNA transfection or Newcastle disease virus (NDV) infection in murine fibroblasts. Binding of FKBP51 to TRAF proteins facilitates the type-I interferon response induced by dsRNA transfection or Newcastle disease virus (NDV) infection in murine fibroblasts. abstract: Hematophagous insects transmit infectious diseases. Sand flies are vectors of leishmaniasis, but can also transmit viruses. We have been studying immune responses of Lutzomyia longipalpis, the main vector of visceral leishmaniasis in the Americas. We identified a non-specific antiviral response in L. longipalpis LL5 embryonic cells when treated with non-specific double-stranded RNAs (dsRNAs). This response is reminiscent of interferon response in mammals. We are investigating putative effectors for this antiviral response. Secreted molecules have been implicated in immune responses, including interferon-related responses. We conducted a mass spectrometry analysis of conditioned medium from LL5 cells 24 and 48 h after dsRNA or mock treatment. We identified 304 proteins. At 24 h, 19 proteins had an abundance equal or greater than 2-fold change, while the levels of 17 proteins were reduced when compared to control cells. At the 48 h time point, these numbers were 33 and 71, respectively. The two most abundant secreted peptides at 24 h in the dsRNA-transfected group were phospholipid scramblase, an interferon-inducible protein that mediates antiviral activity, and forskolin-binding protein (FKBP), a member of the immunophilin family, which mediates the effect of immunosuppressive drugs. The transcription profile of most candidates did not follow the pattern of secreted protein abundance. url: https://www.ncbi.nlm.nih.gov/pubmed/29346269/ doi: 10.3390/v10010043 id: cord-263157-8jin6oru author: Martínez, Miguel Angel title: Progress in the Therapeutic Applications of siRNAs Against HIV-1 date: 2008-10-13 words: 9234.0 sentences: 466.0 pages: flesch: 45.0 cache: ./cache/cord-263157-8jin6oru.txt txt: ./txt/cord-263157-8jin6oru.txt summary: Recent advances regarding the utility of RNA-mediated interference (RNAi) to specifically inhibit HIV-1 replication have opened new possibilities for the development of gene-based therapies against HIV-1 infection. Importantly, this study made the extraordinary demonstration that cell transfection of synthetic 21 base pairs (bp) short interfering RNA (siRNA) duplexes can mediate RNAi in a sequence-specific manner; this finding enabled the specific regulation of gene expression in a variety of biological systems, including diseased cells. Soon after the demonstration that synthetic siRNAs were able to induce the RNAi mechanism in mammalian cells (15) , several studies reported that HIV-1 gene expression and replication ex vivo could be inhibited by virus-specific synthetic siR-NAs (16 22) or expressed siRNAs (16, 18) that were targeted to early or late phases of virus replication. To counteract this strategic weakness, co-expression of multiple siRNAs or shRNAs that target conserved RNA sequences could reduce the emergence of single siRNA-resistant virus with a comparable effect to that achieved by the multiple anti-HIV drug combination approach employed by HAART. abstract: Therapeutic options against the human immunodeficiency virus type 1 (HIV-1) continue to expand with the development of new drugs and new therapeutic strategies. Nevertheless, management of HIV-1 infected individuals has become increasingly complex. The emergence of drug-resistant variants, the growing recognition of the long-term toxicity of antiretroviral therapies and the persistence of viral reservoirs justify the continued efforts to develop new anti-HIV-1 strategies. Recent advances regarding the utility of RNA-mediated interference (RNAi) to specifically inhibit HIV-1 replication have opened new possibilities for the development of gene-based therapies against HIV-1 infection. Here, the recent advances in siRNA-based therapies are reviewed. url: https://www.ncbi.nlm.nih.gov/pubmed/19301656/ doi: 10.1007/978-1-60327-547-7_17 id: cord-300133-yc2wxgid author: Martínez, Miguel J. title: Ebola Virus Infection: Overview and Update on Prevention and Treatment date: 2015-09-12 words: 4302.0 sentences: 243.0 pages: flesch: 50.0 cache: ./cache/cord-300133-yc2wxgid.txt txt: ./txt/cord-300133-yc2wxgid.txt summary: In 2014 and 2015, the largest Ebola virus disease (EVD) outbreak in history affected large populations across West Africa. Relevant information was identified through a comprehensive literature search using Medline, PubMed and CINAHL Complete and using the search terms Ebola, Ebola virus disease, Ebola hemorrhagic fever, West Africa outbreak, Ebola transmission, Ebola symptoms and signs, Ebola diagnosis, Ebola treatment, vaccines for Ebola and clinical trials on Ebola. Over the past 17 months, the West Africa EVD outbreak has provided an important opportunity to consider use of and evaluate several therapeutic and prophylactic agents (e.g., vaccines) to determine their safety and efficacy [5, 6] . FGI-103, FGI-104, and FGI-106 are a group of broad-spectrum antiviral agents that inhibit viral replication in a dose-dependent manner among multiple and genetically distinct viruses including EBOV, bunyaviruses, dengue virus, Use of convalescent whole blood or plasma collected from patients recovered from Ebola virus disease for transfusion, as an emprical treatment during outbreaks abstract: In 2014 and 2015, the largest Ebola virus disease (EVD) outbreak in history affected large populations across West Africa. The goal of this report is to provide an update on the epidemic and review current progress in the development, evaluation and deployment of prevention and treatment strategies for EVD. Relevant information was identified through a comprehensive literature search using Medline, PubMed and CINAHL Complete and using the search terms Ebola, Ebola virus disease, Ebola hemorrhagic fever, West Africa outbreak, Ebola transmission, Ebola symptoms and signs, Ebola diagnosis, Ebola treatment, vaccines for Ebola and clinical trials on Ebola. Through 22 July 2015, a total of 27,741 EVD cases and 11,284 deaths were reported from all affected countries. Several therapeutic agents and novel vaccines for EVD have been developed and are now undergoing evaluation. Concurrent with active case investigation, contact tracing, surveillance and supportive care to patients and communities, there has been rapid progress in the development of new therapies and vaccines against EVD. Continued focus on strengthening clinical and public health infrastructure will have direct benefits in controlling the spread of EVD and will provide a strong foundation for deployment of new drugs and vaccines to affected countries when they become available. The unprecedented West Africa Ebola outbreak, response measures, and ensuing drug and vaccine development suggest that new tools for Ebola control may be available in the near future. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s40121-015-0079-5) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s40121-015-0079-5 doi: 10.1007/s40121-015-0079-5 id: cord-003926-ycdaw2vh author: Maslow, Joel N. title: Zika Vaccine Development—Current Progress and Challenges for the Future date: 2019-07-14 words: 3766.0 sentences: 189.0 pages: flesch: 43.0 cache: ./cache/cord-003926-ycdaw2vh.txt txt: ./txt/cord-003926-ycdaw2vh.txt summary: Of note, the first demonstration of immunoprotection was as part of a 1953 study to define the ultrastructural characteristics of Zika virus, that found intramuscular vaccination of mice with infectious viral filtrates protected against cerebral infection [36] . In pre-clinical studies, vaccinated mice and non-human primates were shown to develop B and T-cell immune responses against the Zika virus envelope and protected against development of neurologic disease and death in immunosuppressed, interferon α, β receptor deficient (IFNAR) mice [43] . A subsequent study in non-human primates vaccinated twice at four-week intervals with alum generated binding and microneutralization antibody titers of 3.54 and 3.55 log10, respectively, and complete protection against viremia and viruria following challenge with either Brazilian or Puerto Rican strains of Zika virus [47] . Guillain-Barre Syndrome outbreak associated with Zika virus infection in French Polynesia: A case-control study abstract: Zika virus is an emergent pathogen that gained significant importance during the epidemic in South and Central America as unusual and alarming complications of infection were recognized. Although initially considered a self-limited benign infection, a panoply of neurologic complications were recognized including a Guillain–Barré-like syndrome and in-utero fetal infection causing microcephaly, blindness, and other congenital neurologic complications. Numerous Zika virus vaccines were developed, with nine different vaccines representing five different platforms entered into clinical trials, one progressing to Phase II. Here we review the current landscape and challenges confronting Zika virus vaccine development. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6789600/ doi: 10.3390/tropicalmed4030104 id: cord-331343-qzvwwca9 author: Mason, Andrew L. title: Metagenomics and the case of the deadly hamster date: 2008-06-09 words: 2836.0 sentences: 172.0 pages: flesch: 49.0 cache: ./cache/cord-331343-qzvwwca9.txt txt: ./txt/cord-331343-qzvwwca9.txt summary: 1 The authors then tried panmicrobial microarray analysis with 29,455 oligonucleotide probes reactive to known vertebrate viruses, bacteria, fungi, and parasites, 5 and after drawing a blank with all these studies, they resorted to brute sequencing of all RNA in the infected tissue to discover the new virus. 8 In humans, metagenomic analysis has been used to study viral communities in blood and respiratory secretions, 6 to differentiate bacterial species in gut flora, 9 and to catalog the collective DNA and RNA viral species in stool samples of healthy subjects 10, 11 and patients with diarrhea. 16 They would have saved a considerable amount of time and effort if they could have sequenced RNA from a few "non-A non-B virus" infected livers (assuming that they could have had access to human genome data that were not available at the time). abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/18666226/ doi: 10.1002/hep.22452 id: cord-029419-b0w9nomq author: Matthews, Adam title: Review of Mark Honigsbaum (2020). The Pandemic Century—A History of Global Contagion from the Spanish Flu to Covid-19: Cambridge, MA: Penguin. 321 pp. ISBN 9780753558287 date: 2020-07-20 words: 3955.0 sentences: 186.0 pages: flesch: 54.0 cache: ./cache/cord-029419-b0w9nomq.txt txt: ./txt/cord-029419-b0w9nomq.txt summary: Honigsbaum surveys with biological detail the genealogy and history of influenza, the plague, Parrot Fever, Legionnaires Disease, Aids, SARS, Ebola, Zika and Covid-19. Honigsbaum describes ecological disruption amplifying the mutation and spread of a virus which had existed in its natural environment for centuries. From a postdigital perspective, the ten cases detailed by Honigsbaum in The Pandemic Century (2020) show how digital and wider technologies are not separate from the natural and social world. The questions then, which The Pandemic Century (Honigsbaum 2020) illustrates is whether to take a posthuman perspective and pull back from technological and human development and reduce ecological disruption and work with the natural environment as equals or to push on unabated with technological developments to go beyond what has been done already to ''fix'' ourselves and the planet, including new viral outbreaks. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7369538/ doi: 10.1007/s42438-020-00170-z id: cord-016652-x8t3lf1x author: Matthews, David title: Viruses and the Nucleolus date: 2011-05-23 words: 6630.0 sentences: 348.0 pages: flesch: 33.0 cache: ./cache/cord-016652-x8t3lf1x.txt txt: ./txt/cord-016652-x8t3lf1x.txt summary: This process is crucial for virus biology because if the viral proteins that are required for cytoplasmic functions such as RNA synthesis and encapsidation are sequestered in the nucleolus or nucleus, then progeny virus production will be affected as has been revealed by inhibitor and genetic studies (Lee et al. Viruses may interact with the nucleolus to usurp host cell functions and recruit nucleolar proteins to facilitate virus replication. Initial studies utilising the prototype g-2 herpesvirus, herpes virus saimiri (HVS), demonstrated that the HVS nucleolar trafficking ORF57 protein induces nucleolar redistribution of the host cell human TREX proteins, which are involved in mRNA nuclear export (Boyne and Whitehouse 2006) . The localisation of porcine reproductive and respiratory syndrome virus nucleocapsid protein to the nucleolus of infected cells and identification of a potential nucleolar localization signal sequence Sequence requirements for nucleolar localization of human T cell leukemia virus type I pX protein, which regulates viral RNA processing abstract: The nucleolus is a dynamic sub-nuclear structure integral to the function of a eukaryotic cell. Some of its major roles involve ribosome subunit biogenesis, RNA processing, cell cycle control and responding to cellular stress, such as infection. Our understanding of the relationship between viruses and the nucleolus has moved from a phenomenological approach describing protein localisation to functional studies involving genetic analysis and proteomic approaches. These advances have provided fundamental insights as to how and why the nucleolus is targeted by many different viruses both to usurp normal functioning and to recruit nucleolar proteins to facilitate virus replication. This knowledge has been exploited for therapeutic strategies involving targeted inhibition of virus replication and live-attenuated recombinant vaccines. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121007/ doi: 10.1007/978-1-4614-0514-6_14 id: cord-318786-qd0k8174 author: Mauriz, Elba title: Recent Progress in Plasmonic Biosensing Schemes for Virus Detection date: 2020-08-22 words: 9868.0 sentences: 516.0 pages: flesch: 35.0 cache: ./cache/cord-318786-qd0k8174.txt txt: ./txt/cord-318786-qd0k8174.txt summary: Technological advancements in plasmonic biosensing including colorimetric and fluorescence enhancement as well as the utilization of nanomaterials and optical aperture nanostructures for achieving highly sensitive virus detection are described in this section. Technological advancements in plasmonic biosensing including colorimetric and fluorescence enhancement as well as the utilization of nanomaterials and optical aperture nanostructures for achieving highly sensitive virus detection are described in this section. Typically, most of quantum dots'' applications have been exploited in LSPR-based biosensors because the distance and dimensions of the adjacent gold nanoparticles can affect the fluorescence signal and, therefore, be quenched depending on the analyte concentration. Typically, most of quantum dots'' applications have been exploited in LSPR-based biosensors because the distance and dimensions of the adjacent gold nanoparticles can affect the fluorescence signal and, therefore, be quenched depending on the analyte concentration. abstract: The global burden of coronavirus disease 2019 (COVID-19) to public health and global economy has stressed the need for rapid and simple diagnostic methods. From this perspective, plasmonic-based biosensing can manage the threat of infectious diseases by providing timely virus monitoring. In recent years, many plasmonics’ platforms have embraced the challenge of offering on-site strategies to complement traditional diagnostic methods relying on the polymerase chain reaction (PCR) and enzyme-linked immunosorbent assays (ELISA). This review compiled recent progress on the development of novel plasmonic sensing schemes for the effective control of virus-related diseases. A special focus was set on the utilization of plasmonic nanostructures in combination with other detection formats involving colorimetric, fluorescence, luminescence, or Raman scattering enhancement. The quantification of different viruses (e.g., hepatitis virus, influenza virus, norovirus, dengue virus, Ebola virus, Zika virus) with particular attention to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was reviewed from the perspective of the biomarker and the biological receptor immobilized on the sensor chip. Technological limitations including selectivity, stability, and monitoring in biological matrices were also reviewed for different plasmonic-sensing approaches. url: https://www.ncbi.nlm.nih.gov/pubmed/32842601/ doi: 10.3390/s20174745 id: cord-290993-bsnja161 author: McAuliffe, Josephine title: Replication of SARS coronavirus administered into the respiratory tract of African Green, rhesus and cynomolgus monkeys date: 2004-12-05 words: 4548.0 sentences: 203.0 pages: flesch: 52.0 cache: ./cache/cord-290993-bsnja161.txt txt: ./txt/cord-290993-bsnja161.txt summary: Serologic evidence of infection, defined as a four-fold rise in Nt Ab titer, was observed in 4 of 4 rhesus, 3 of 4 cynomolgus, and 4 of 4 AGMs. Although the study described above indicated that all three species of monkeys were infected with SARS-CoV, there were significant discrepancies between our findings and published reports of cynomolgus macaques infected with SARS-CoV; Kuiken et al. Mean titers of virus (expressed as log 10 TCID 50 /ml of sample; y axis) detected on indicated days (x axis) in the upper respiratory tract (left panels, A, C, and E, closed symbols) and lower respiratory tract (right panels, B, D, and F, open symbols) of rhesus (panels A and B, x, w), cynomolgus (panels C and D, E, 4), and African Green (panels E and F, n, 5) monkeys following intranasal and intratracheal administration of 10 6 TCID 50 of SARS-CoV. abstract: SARS coronavirus (SARS-CoV) administered intranasally and intratracheally to rhesus, cynomolgus and African Green monkeys (AGM) replicated in the respiratory tract but did not induce illness. The titer of serum neutralizing antibodies correlated with the level of virus replication in the respiratory tract (AGM>cynomolgus>rhesus). Moderate to high titers of SARS-CoV with associated interstitial pneumonitis were detected in the lungs of AGMs on day 2 and were resolving by day 4 post-infection. Following challenge of AGMs 2 months later, virus replication was highly restricted and there was no evidence of enhanced disease. These species will be useful for the evaluation of the immunogenicity of candidate vaccines, but the lack of apparent clinical illness in all three species, variability from animal to animal in level of viral replication, and rapid clearance of virus and pneumonitis in AGMs must be taken into account by investigators considering the use of these species in efficacy and challenge studies. url: https://www.ncbi.nlm.nih.gov/pubmed/15527829/ doi: 10.1016/j.virol.2004.09.030 id: cord-273343-als886fe author: McClenahan, Shasta D. title: Discovery of a Bovine Enterovirus in Alpaca date: 2013-08-12 words: 4596.0 sentences: 214.0 pages: flesch: 51.0 cache: ./cache/cord-273343-als886fe.txt txt: ./txt/cord-273343-als886fe.txt summary: A cytopathic virus was isolated using Madin-Darby bovine kidney (MDBK) cells from lung tissue of alpaca that died of a severe respiratory infection. To identify the virus, the infected cell culture supernatant was enriched for virus particles and a generic, PCR-based method was used to amplify potential viral sequences. The new alpaca virus sequence was most similar to recently designated Enterovirus species F, previously bovine enterovirus (BEVs), viruses that are globally prevalent in cattle, although they appear not to cause significant disease. Analysis of the full polyprotein and the individual capsid, 2A protease, 3C protease, and polymerase proteins of the alpaca-infecting virus relative to sequences of other representative enteroviruses from bovine EV-E (BEV-A serotypes 1-4) and EV-F (BEV-B serotypes 1-4), and sequences from three unclassified EV-F viruses [16] , two from bovine sources (AY724744 and AY724745) [20] , and one from a capped langur (JX538037) [21] , possum, porcine (PEV), and human (HEV) hosts. abstract: A cytopathic virus was isolated using Madin-Darby bovine kidney (MDBK) cells from lung tissue of alpaca that died of a severe respiratory infection. To identify the virus, the infected cell culture supernatant was enriched for virus particles and a generic, PCR-based method was used to amplify potential viral sequences. Genomic sequence data of the alpaca isolate was obtained and compared with sequences of known viruses. The new alpaca virus sequence was most similar to recently designated Enterovirus species F, previously bovine enterovirus (BEVs), viruses that are globally prevalent in cattle, although they appear not to cause significant disease. Because bovine enteroviruses have not been previously reported in U.S. alpaca, we suspect that this type of infection is fairly rare, and in this case appeared not to spread beyond the original outbreak. The capsid sequence of the detected virus had greatest homology to Enterovirus F type 1 (indicating that the virus should be considered a member of serotype 1), but the virus had greater homology in 2A protease sequence to type 3, suggesting that it may have been a recombinant. Identifying pathogens that infect a new host species for the first time can be challenging. As the disease in a new host species may be quite different from that in the original or natural host, the pathogen may not be suspected based on the clinical presentation, delaying diagnosis. Although this virus replicated in MDBK cells, existing standard culture and molecular methods could not identify it. In this case, a highly sensitive generic PCR-based pathogen-detection method was used to identify this pathogen. url: https://doi.org/10.1371/journal.pone.0068777 doi: 10.1371/journal.pone.0068777 id: cord-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-341303-1iayp8oa author: McINTOSH, KENNETH title: Immunofluorescence in Diagnostic Virology date: 2006-12-16 words: 2850.0 sentences: 126.0 pages: flesch: 47.0 cache: ./cache/cord-341303-1iayp8oa.txt txt: ./txt/cord-341303-1iayp8oa.txt summary: In the 1930s Parker and Muckenfuss first developed the complement fixation reaction using lymph mixed with antibody and a fresh source of complement.s I n fact, this became the procedure of choice for the laboratory diagnosis of smallpox before and even after the general use of tissue culture for viral isolation. Immunofluorescence (IF) was also recognized early as a potentially valuable tool for detection of viral antigen^,''.^.^ but its use as a procedure that could supplement and, at times, replace tissue culture in diagnostic laboratories has been only gradually gaining acceptance. IF has, of course, been used at several stages in the diagnosis of viral diseases: the measurement of antibody, particularly when there is some highly specific antigen in question, as with Epstein-Barr virus or cytomegalovirus; the identification of viruses in tissue culture; and the direct detection of viruses in body fluids. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/6372604/ doi: 10.1111/j.1749-6632.1983.tb22226.x 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-252048-ftbjsoup author: McKinley, Enid T. title: Attenuated live vaccine usage affects accurate measures of virus diversity and mutation rates in avian coronavirus infectious bronchitis virus date: 2011-04-22 words: 6380.0 sentences: 309.0 pages: flesch: 55.0 cache: ./cache/cord-252048-ftbjsoup.txt txt: ./txt/cord-252048-ftbjsoup.txt summary: The full-length genomes of 11 infectious bronchitis virus (IBV) field isolates from three different types of the virus; Massachusetts (Mass), Connecticut (Conn) and California (CAL) isolated over a 41, 25 and 8 year period respectively, were sequenced and analyzed to determine the mutation rates and level of polymorphisms across the genome. The genetic data also identified a recombinant IBV isolate with 7 breakpoints distributed across the entire genome suggesting that viruses within the same serotype can have a high degree of genetic variability outside of the spike gene. The objective of this study was to determine the levels of polymorphism across the entire genome of IBV isolates with similar spike genes and to examine the mutation rates for viruses with and without vaccine selection pressure. abstract: The full-length genomes of 11 infectious bronchitis virus (IBV) field isolates from three different types of the virus; Massachusetts (Mass), Connecticut (Conn) and California (CAL) isolated over a 41, 25 and 8 year period respectively, were sequenced and analyzed to determine the mutation rates and level of polymorphisms across the genome. Positive selection was not detected and mutation rates ranged from 10(−4) to 10(−6) substitutions/site/year for Mass and Conn IBV types where attenuated live vaccines are routinely used to control the disease. In contrast, for CAL type viruses, for which no vaccine exists, positive selection was detected and mutation rates were 10 fold higher ranging from 10(−2) to 10(−3) substitutions/site/year. Lower levels of genetic diversity among the Mass and Conn viruses as well as sequence similarities with vaccine virus genomes suggest that the origin of the Mass and all but one of the Conn viruses was likely vaccine virus that had been circulating in the field for an unknown but apparently short period of time. The genetic data also identified a recombinant IBV isolate with 7 breakpoints distributed across the entire genome suggesting that viruses within the same serotype can have a high degree of genetic variability outside of the spike gene. These data are important because inaccurate measures of genetic diversity and mutation rates could lead to underestimates of the ability of IBV to change and potentially emerge to cause disease. url: https://doi.org/10.1016/j.virusres.2011.04.006 doi: 10.1016/j.virusres.2011.04.006 id: cord-017764-h1w9gbxk author: Meanwell, Nicholas A. title: The Discovery and Development of Daclatasvir: An Inhibitor of the Hepatitis C Virus NS5A Replication Complex date: 2018-06-08 words: 9250.0 sentences: 389.0 pages: flesch: 39.0 cache: ./cache/cord-017764-h1w9gbxk.txt txt: ./txt/cord-017764-h1w9gbxk.txt summary: A groundbreaking clinical trial that combined daclatasvir (1) with the protease inhibitor asunaprevir (52) established that a chronic HCV infection could be cured with small molecule therapy in the absence of immune stimulation, setting the stage for approval of this regimen for the treatment of GT-1b-infected subjects by the Japanese health authorities on July 4, 2014. The discovery of the hepatitis C virus (HCV) nonstructural 5A (NS5A) replication complex inhibitor daclatasvir (1) began with the development of a genotype 1b (GT-1b) replicon that was implemented as a phenotypic screen using a design that conferred a stringent triaging of hit molecules [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] . A screen of compounds selected from the library of HCV NS5A inhibitors assessed in the presence of 1 using the Tyr93Asn GT-1aresistant replicon, followed by SAR optimization, identified Syn-395 (52) as a molecule capable of restoring the sensitivity of resistant virus to the inhibitory effects of 1. Discovery of daclatasvir, a pan-genotypic hepatitis C virus NS5A replication complex inhibitor with potent clinical effect abstract: The discovery of the hepatitis C virus (HCV) NS5A replication inhibitor daclatasvir (1) had its origins in a phenotypic screening lead. However, during the optimization campaign, it was observed that some members of the chemotype underwent a radical dimerization under the assay conditions. This redirected the effort to focus on palindromic molecules, a species subsequently shown to complement the dimeric nature of the NS5A protein. The most challenging aspect of the discovery program was extending antiviral activity to encompass GT-1a virus which was accomplished only after the development of extensive structure-activity relationships. In clinical trials, oral administration of daclatasvir (1) produced a profound effect on viral load with onset that was more rapid than had been seen previously with either NS3 protease or NS5B polymerase inhibitors. A groundbreaking clinical trial that combined daclatasvir (1) with the protease inhibitor asunaprevir (52) established that a chronic HCV infection could be cured with small molecule therapy in the absence of immune stimulation, setting the stage for approval of this regimen for the treatment of GT-1b-infected subjects by the Japanese health authorities on July 4, 2014. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122418/ doi: 10.1007/7355_2018_47 id: cord-280429-4fota9rl author: Medvedev, Kirill E. title: Functional and evolutionary analysis of viral proteins containing a Rossmann‐like fold date: 2018-06-13 words: 7468.0 sentences: 465.0 pages: flesch: 49.0 cache: ./cache/cord-280429-4fota9rl.txt txt: ./txt/cord-280429-4fota9rl.txt summary: 10 However, structural analyses of virion architecture and coat protein topology have revealed unexpected similarities, not visible in sequence comparisons, suggesting a common origin for viruses that infect hosts residing in different domains of life. In this current work, we provide functional and evolutionary analysis of viral proteins containing a Rossmann-like fold that can be found in the Evolutionary Classification of protein Domains (ECOD) database developed in our lab. The structures represented gene products from 21 viral taxonomical families with host ranges from all kingdoms of life (http://prodata.swmed.edu/rossmann_fold/viruses/). Our analysis detected 14 different bacterial virus structure topology types defined by ECOD T-groups that contain a Rossmann-like fold (Fig. 2, 12 topology groups shown). Like the bacterial and eukaryotic branches in the tree of life, the Archea are host to a multitude of Functional and Evolutionary Analysis of Viral Proteins viruses. 61 Among viral protein structures containing the minimal Rossmann fold, 14 protein families are known helicases (http://prodata.swmed.edu/ross-mann_fold/viruses/). abstract: Viruses are the most abundant life form and infect practically all organisms. Consequently, these obligate parasites are a major cause of human suffering and economic loss. Rossmann‐like fold is the most populated fold among α/β‐folds in the Protein Data Bank and proteins containing Rossmann‐like fold constitute 22% of all known proteins 3D structures. Thus, analysis of viral proteins containing Rossmann‐like domains could provide an understanding of viral biology and evolution as well as could propose possible targets for antiviral therapy. We provide functional and evolutionary analysis of viral proteins containing a Rossmann‐like fold found in the evolutionary classification of protein domains (ECOD) database developed in our lab. We identified 81 protein families of bacterial, archeal, and eukaryotic viruses in light of their evolution‐based ECOD classification and Pfam taxonomy. We defined their functional significance using enzymatic EC number assignments as well as domain‐level family annotations. url: https://www.ncbi.nlm.nih.gov/pubmed/29722076/ doi: 10.1002/pro.3438 id: cord-023721-e0zp2gux author: Meissner, H. Cody title: Bronchiolitis date: 2013-02-10 words: 5111.0 sentences: 278.0 pages: flesch: 34.0 cache: ./cache/cord-023721-e0zp2gux.txt txt: ./txt/cord-023721-e0zp2gux.txt summary: Bronchiolitis may be defined as an episode of obstructive lower airway disease precipitated by a viral infection in infants younger than 24 months of age. Monthly administration of monoclonal antiF anti body (palivizumab) throughout the RSV season reduces the inci dence of hospitalization due to RSV infection in infants with bronchopulmonary dysplasia, congenital heart disease, and pre maturity by about 50% (see Chapter 225, Respiratory Syncytial Virus). Early trials indicated that ribavirin therapy was associated with modest improvement in clinical scores, oxygenation, and duration of mechanical ventilation for infants with severe bron chiolitis due to RSV infection. Duration of hospitalization in previously well infants with respiratory syncytial virus infection Ribavirin aerosol treatment of bronchiolitis associated with respiratory syncytial virus infection in infants Intravenous immunoglobulin treatment of respiratory syncytial virus infections in infants and young children Respiratory syncytial virus immune globulin treatment of RSV lower respiratory tract infection in previously healthy children abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173523/ doi: 10.1016/b978-1-4377-2702-9.00033-7 id: cord-252769-fe50u028 author: Mendes, J. Pinto title: Infecção na modulaçâo da asma 1 1 Trabalho apresentado no XXIII Congresso de Pneumologia da SPP – Guarda, Novembro 2007 / Paper presented at the XXIII Congresso de Pneumologia da SPP / PSP Pulmonology Congress, Guarda, November 2007 date: 2008-10-31 words: 14003.0 sentences: 964.0 pages: flesch: 56.0 cache: ./cache/cord-252769-fe50u028.txt txt: ./txt/cord-252769-fe50u028.txt summary: Animal research is difficult to extrapolate to man but suggests RSV can induce allergic sensitisation 28 , increase bronchial and interleukin (IL)-13 hyperresponsiveness, and rão, na maioria dos casos, consequências remotas, embora algumas vezes descrevam sibilâncias que irão desaparecer aos 3 -5 anos e só raramente se prolongam, instalando -se ou não uma asma. This phenomenon has been put to the test in inhalatory challenge tests which could bring on asthma episodes or exacerbations in children and adults 82, 102 , but, to test this seeming paradox, it is not necessary to resort to these arguments as in a German study 82 , the degree of early life exposure to domestic endotoxins was in direct correla-Infecção na modulaçâo da asma J Pinto Mendes fende um efeito daquelas células na supressão simultânea das respostas Th 1 e Th 2 . abstract: Abstract This paper reviews the impact of infections on the onset and clinical course of bronchial asthma. A just emphasis is given to the role viral infections, particularly rhinovirus infections, play in exacerbations, and that played by respiratory syncytial virus, suspected of triggering the asthmatic syndrome. The mechanisms of the immune response to virus attacks are explained, highlighting the asthmatic and allergic patient’s weakened response, particularly in the perinatal period. Further stressed is a potentiating effect of viral aggression on the allergic response. The hygiene hypothesis and its lack of scientific consistency is detailed, at least as far as the role it seeks to confer on an unproven antagonism of the Th1 and Th2 lymphocyte responses. The current importance of research not into bacteria, but into bacterial products, including endotoxins, on the modulation of asthma and allergy is noted. Studies which, along these lines, show an environmental impact on genetic secretion in the phenotype are underlined. Also discussed in passing are several mechanisms which go towards explaining neutrophilic asthma – for many a contradiction, given eosinophilia’s stranglehold on asthmatic inflammation. Rev Port Pneumol 2008; XIV (5): 647-675 url: https://api.elsevier.com/content/article/pii/S0873215915302750 doi: 10.1016/s0873-2159(15)30275-0 id: cord-355489-tkvfneje author: Mendez, Jairo A title: Phylogenetic history demonstrates two different lineages of dengue type 1 virus in Colombia date: 2010-09-14 words: 4615.0 sentences: 235.0 pages: flesch: 48.0 cache: ./cache/cord-355489-tkvfneje.txt txt: ./txt/cord-355489-tkvfneje.txt summary: Yet, the phylogenetic relationships between strains isolated along the covered period of time suggests that viral strains detected in some years, although belonging to the same genotype V, have different recent origins corresponding to multiple re-introduction events of viral strains that were circulating in neighbor countries. Due to the importance of DENV in public health, the particular goals of this research were to reconstruct the phylogenetic history of DENV-1 and to date the phylogenetic tree using isolation time as calibration points to establish date of introduction of virus and rate evolution patterns of virus in Colombia. Previously reported genotypes were represented in the tree and placed most of the Colombian isolates nesting in the genotype V clade (America, Africa) and were closely related to Argentina, Brazil and Paraguay virus strains. abstract: BACKGROUND: Dengue Fever is one of the most important viral re-emergent diseases affecting about 50 million people around the world especially in tropical and sub-tropical countries. In Colombia, the virus was first detected in the earliest 70's when the disease became a major public health concern. Since then, all four serotypes of the virus have been reported. Although most of the huge outbreaks reported in this country have involved dengue virus serotype 1 (DENV-1), there are not studies about its origin, genetic diversity and distribution. RESULTS: We used 224 bp corresponding to the carboxyl terminus of envelope (E) gene from 74 Colombian isolates in order to reconstruct phylogenetic relationships and to estimate time divergences. Analyzed DENV-1 Colombian isolates belonged to the formerly defined genotype V. Only one virus isolate was clasified in the genotype I, likely representing a sole introduction that did not spread. The oldest strains were closely related to those detected for the first time in America in 1977 from the Caribbean and were detected for two years until their disappearance about six years later. Around 1987, a split up generated 2 lineages that have been evolving separately, although not major aminoacid changes in the analyzed region were found. CONCLUSION: DENV-1 has been circulating since 1978 in Colombia. Yet, the phylogenetic relationships between strains isolated along the covered period of time suggests that viral strains detected in some years, although belonging to the same genotype V, have different recent origins corresponding to multiple re-introduction events of viral strains that were circulating in neighbor countries. Viral strains used in the present study did not form a monophyletic group, which is evidence of a polyphyletic origin. We report the rapid spread patterns and high evolution rate of the different DENV-1 lineages. url: https://doi.org/10.1186/1743-422x-7-226 doi: 10.1186/1743-422x-7-226 id: cord-102908-sr7j8z9c author: Mersmann, Sophia F. title: Learning to count: determining the stoichiometry of bio-molecular complexes using fluorescence microscopy and statistical modelling date: 2020-07-24 words: 5244.0 sentences: 260.0 pages: flesch: 42.0 cache: ./cache/cord-102908-sr7j8z9c.txt txt: ./txt/cord-102908-sr7j8z9c.txt summary: We used differential binary labelling and statistical modelling to extract estimates of stoichiometry, our strategy is outlined in Figure 1 ; note that this approach can be generalised to apply to many other multi-component systems (i.e. how many protein x are found in assembly y?). As described above, our experimental design utilizes antibody labelled with spectrally distinct dyes allowing binary scoring of individual virus particles as positive if they interact with at least one Ab B molecule ( Figure 1 ). We have demonstrated quantitative analysis of 9C12 interaction with individual Adv particles ( Figure 3) ; we have confirmed that differential labelling of antibody does not bias binding ( Figure 4A & B) ; and that we could detect single molecules of 9C12 Biotin allowing discrimination of positive and negative AdV-9C12 complexes ( Figure 4C & D). However, using stoichiometric estimates to calibrate fluorescent data revealed population heterogeneity with a small proportion of virus particles binding ∼200 antibody molecules. abstract: Cellular biology occurs through myriad interactions between diverse molecular components, many of which assemble in to specific complexes. Various techniques can provide a qualitative survey of which components are found in a given complex. However, quantitative analysis of the absolute number of molecules within a complex (known as stoichiometry) remains challenging. Here we provide a novel method that combines fluorescence microscopy and statistical modelling to derive accurate molecular counts. We have devised a system in which a given biomolecule is differentially labelled with spectrally distinct fluorescent dyes (label A or B), which are then mixed such that B-labelled molecules are vastly outnumbered by those with label A. Complexes, containing this component, are then simply scored as either being positive or negative for label B. The frequency of positive complexes is directly related to the stoichiometry of interaction and molecular counts can be inferred by statistical modelling. We demonstrate this method using complexes of Adenovirus particles and monoclonal antibodies, achieving counts that are in excellent agreement with previous estimates. Beyond virology, this approach is readily transferable to other experimental systems and, therefore, provides a powerful tool for quantitative molecular biology. The statistical models used in our analysis are available here: https://github.com/sophiamersmann/molecular-counting, the raw data used for molecular counting can be found here: 10.5281/zenodo.3955142. url: https://doi.org/10.1101/2020.07.23.217745 doi: 10.1101/2020.07.23.217745 id: cord-000777-7cty5s6o author: Merten, O.-W. title: Virus contaminations of cell cultures – A biotechnological view date: 2002-01-01 words: 14936.0 sentences: 650.0 pages: flesch: 48.0 cache: ./cache/cord-000777-7cty5s6o.txt txt: ./txt/cord-000777-7cty5s6o.txt summary: These may include the use of production media devoid of animal derived substances, validation of viral clearance in downstream processing or analytics for detecting adventitious viruses in cell culture and final biological product. However, the best means to increase the biological safety of the produced viral vaccines is the use of diploid or continuous cell lines, because it can be determined that such cells are free of animal derived viruses: This can be achieved by establishing master (seed stock) and working (distribution and user stocks) cell banks which have been rigorously tested and validated for the absence of microbial as well as viral contaminants (see chapter by Freshney and the section on ''Testing-virus screening in cell banks'' of this article). As animal derived substances such as serum can be contaminated by adventitious viruses, γ irradition is, after routine quality control for virus detection, the best method to increase the safety of using serum in the production of animal cell culture derived biologicals. abstract: In contrast to contamination by microbes and mycoplasma, which can be relatively easily detected, viral contamination present a serious threat because of the difficulty in detecting some viruses and the lack of effective methods of treating infected cell cultures. While some viruses are capable of causing morphological changes to infected cells (e.g. cytopathic effect)which are detectable by microscopy some viral contaminations result in the integration of the viral genome as provirus, this causes no visual evidence, by means of modification of the cellular morphology. Virus production from such cell lines, are potentially dangerous for other cell cultures (in research labs)by cross contaminations, or for operators and patients (in the case of the production of injectable biologicals) because of potential infection. The only way to keep cell cultures for research, development, and the biotech industry virus-free is the prevention of such contaminations. Cell cultures can become contaminated by the following means: firstly, they may already be contaminated as primary cultures (because the source of the cells was already infected), secondly, they were contaminated due to the use of contaminated raw materials, or thirdly, they were contaminated via an animal passage. This overview describes the problems and risks associated with viral contaminations in animal cell culture, describes the origins of these contaminations as well as the most important virsuses associated with viral contaminations in cell culture. In addition, ways to prevent viral contaminations as well as measures undertaken to avoid and assess risks for viral contaminations as performed in the biotech industry are briefly described. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463984/ doi: 10.1023/a:1022969101804 id: cord-001958-2gt3fwpy author: Meseda, Clement A. title: Percutaneous Vaccination as an Effective Method of Delivery of MVA and MVA-Vectored Vaccines date: 2016-02-19 words: 8161.0 sentences: 361.0 pages: flesch: 43.0 cache: ./cache/cord-001958-2gt3fwpy.txt txt: ./txt/cord-001958-2gt3fwpy.txt summary: Our data suggest that MVA administered by percutaneous inoculation, elicited vaccinia-specific antibody responses, and protected mice from lethal vaccinia virus challenge, at levels comparable to or better than subcutaneous or intramuscular inoculation. In the work described here, we demonstrate in mouse models that percutaneous inoculation of MVA elicited protective immune responses against lethal intranasal challenge with the Western Reserve (WR) strain of vaccinia virus, and at low doses of MVA, lower morbidity was recorded in mice that were vaccinated via the percutaneous route than in those immunized via the intramuscular or subcutaneous routes. In a preliminary experiment to investigate the utility of the percutaneous route for the delivery of MVA, we observed that MVA delivered by tail scarification, while statistically insignificant (p = 0.298), elicited a higher vaccinia-specific IgG response and protection in mice than the same dose (10 6 pfu) delivered by the intramuscular route (S1 Fig) . abstract: The robustness of immune responses to an antigen could be dictated by the route of vaccine inoculation. Traditional smallpox vaccines, essentially vaccinia virus strains, that were used in the eradication of smallpox were administered by percutaneous inoculation (skin scarification). The modified vaccinia virus Ankara is licensed as a smallpox vaccine in Europe and Canada and currently undergoing clinical development in the United States. MVA is also being investigated as a vector for the delivery of heterologous genes for prophylactic or therapeutic immunization. Since MVA is replication-deficient, MVA and MVA-vectored vaccines are often inoculated through the intramuscular, intradermal or subcutaneous routes. Vaccine inoculation via the intramuscular, intradermal or subcutaneous routes requires the use of injection needles, and an estimated 10 to 20% of the population of the United States has needle phobia. Following an observation in our laboratory that a replication-deficient recombinant vaccinia virus derived from the New York City Board of Health strain elicited protective immune responses in a mouse model upon inoculation by tail scarification, we investigated whether MVA and MVA recombinants can elicit protective responses following percutaneous administration in mouse models. Our data suggest that MVA administered by percutaneous inoculation, elicited vaccinia-specific antibody responses, and protected mice from lethal vaccinia virus challenge, at levels comparable to or better than subcutaneous or intramuscular inoculation. High titers of specific neutralizing antibodies were elicited in mice inoculated with a recombinant MVA expressing the herpes simplex type 2 glycoprotein D after scarification. Similarly, a recombinant MVA expressing the hemagglutinin of attenuated influenza virus rgA/Viet Nam/1203/2004 (H5N1) elicited protective immune responses when administered at low doses by scarification. Taken together, our data suggest that MVA and MVA-vectored vaccines inoculated by scarification can elicit protective immune responses that are comparable to subcutaneous vaccination, and may allow for antigen sparing when vaccine supply is limited. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4760941/ doi: 10.1371/journal.pone.0149364 id: cord-353297-jizitnfl author: Meyer, R.F. title: Viruses and Bioterrorism date: 2008-07-30 words: 3817.0 sentences: 184.0 pages: flesch: 43.0 cache: ./cache/cord-353297-jizitnfl.txt txt: ./txt/cord-353297-jizitnfl.txt summary: The requirements for an ideal biological warfare agent include availability, ease of production, stability after production, a susceptible population, absence of specific treatment, ability to incapacitate or kill the host, appropriate particle size in aerosol so that the virus can be carried long distances by prevailing winds and inhaled deeply into the lungs of unsuspecting victims, ability to be disseminated via food or water, and the availability of a vaccine to protect certain groups. Instead, the ectromelia virus vector expressing IL-4 altered the host''s immune response to this virus resulting in lethal infections in normally genetically Classification of viral agents that are considered to be of concern for bioterrorism and biowarfare and those that have been weaponized or studied for offensive or defensive purposes as part of former or current national biological weapons programs resistant mice (e.g., C57BL/6). abstract: The use of viral agents for biological warfare has a long history, which predates their recognition and isolation by culture. Advances in viral culture and virus stabilization made during the second half of the twentieth century raised the level of concern by facilitating the large-scale production of viral agents for aerosol dissemination. Furthermore, the nucleic acid of many viruses, including some that are currently not threats, can be manipulated in the laboratory. Thus, the potential for genetic engineering and misuse of biotechnology is a serious threat. An effective defense against viral agents requires a comprehensive approach including restricting access to viral stocks, detecting deliberately induced disease outbreaks, rapid laboratory identification of viral agents in clinical specimens, preventing person-to-person transmission, using reliable decontamination procedures, and developing effective vaccines and antiviral drugs. url: https://api.elsevier.com/content/article/pii/B9780123744104005495 doi: 10.1016/b978-012374410-4.00549-5 id: cord-311012-wyglrpqh author: Meyers, Craig title: Ethanol and Isopropanol Inactivation of Human Coronavirus on Hard Surfaces date: 2020-09-28 words: 3271.0 sentences: 171.0 pages: flesch: 54.0 cache: ./cache/cord-311012-wyglrpqh.txt txt: ./txt/cord-311012-wyglrpqh.txt summary: AIM: There are few data showing the efficacy of multiple concentrations of EtOH, IPA, and SH on a human coronavirus (HCoV) dried on surfaces using short contact times. FINDINGS: Concentrations of EtOH and IPA from 62% to 80% were very efficient at inactivating high numbers of HCoV dried on tile surfaces even with a 15 sec contact time. CONCLUSIONS: EtOH, IPA, and SH at multiple concentrations efficiently inactivated infectious virus on hard surfaces, typical of those found in public places. Interestingly, at the highest concentrations tested, 95% EtOH and 95% IPA, we observed significant reductions in inactivating, with some contact times producing less than a 2 log 10 reduction of infectious virus. Our studies demonstrate that EtOH and IPA at concentrations ranging from 62% to 80% are highly effective at inactivating HCoV on tile surfaces even with contact times as low as 15 sec. abstract: BACKGROUND: The COVID-19 pandemic has greatly increased the frequency of disinfecting surfaces in public places causing a strain on the ability to obtain disinfectant solutions. An alternative is to supply plain alcohols (EtOH and IPA) or sodium hypochlorite (SH). AIM: There are few data showing the efficacy of multiple concentrations of EtOH, IPA, and SH on a human coronavirus (HCoV) dried on surfaces using short contact times. METHODS: Multiple concentrations of EtOH, IPA, and SH to inactivate high numbers of HCoV under real-life conditions were tested. High concentrations of infectious HCoV were dried on porcelain and ceramic tiles, then treated with multiple concentrations of the alcohols for contact times of 15 sec, 30 sec, and 1 min. Center for Disease Control (CDC) recommended three concentrations of SH were also tested. Reductions in titres were measured by using the tissue culture infectious dose 50 (TCID(50)) assay. FINDINGS: Concentrations of EtOH and IPA from 62% to 80% were very efficient at inactivating high numbers of HCoV dried on tile surfaces even with a 15 sec contact time. Concentrations of 95% dehydrated the virus, allowing infectious virus to survive. The CDC recommended 1/10 and 1/50 dilutions of SH were efficient at inactivating high numbers of HCoV dried on tile surfaces, whereas, a 1/100 dilution had substantially lower activity. CONCLUSIONS: EtOH, IPA, and SH at multiple concentrations efficiently inactivated infectious virus on hard surfaces, typical of those found in public places. Often no remaining infectious HCoV could be detected. url: https://api.elsevier.com/content/article/pii/S0195670120304515 doi: 10.1016/j.jhin.2020.09.026 id: cord-102704-wfuzk2dp author: Meza, Diana K. title: Predicting the presence and titer of rabies virus neutralizing antibodies from low-volume serum samples in low-containment facilities date: 2020-04-30 words: 3183.0 sentences: 192.0 pages: flesch: 43.0 cache: ./cache/cord-102704-wfuzk2dp.txt txt: ./txt/cord-102704-wfuzk2dp.txt summary: Despite small conflicts, titer predictions were correlated across tests repeated on different dates both for dog samples (r = 0.93), and for a second dataset of sera from wild common vampire bats (r = 0.72, N = 41), indicating repeatability. The pmRFFIT enables high-throughput detection of rabies virus neutralizing antibodies in low-biocontainment settings and is suited to studies in wild or captive animals where large serum volumes cannot be obtained. The binomial and log-normal models fit to 193 this data subset included only the fixed effect of the virus-infected N2A cell counts, but the random 194 effects were identical to those explained above (i.e. test date and field). A final distinction is that 316 instead of scoring microscope field or wells as virus positive or negative, the pmRFFIT predicts 317 serological status and RVNA titer from infected cell counts in a single serum dilution using statistical 318 abstract: Serology is a core component of the surveillance and management of viral zoonoses. Virus neutralization tests are a gold standard serological diagnostic, but requirements for large volumes of serum and high biosafety containment can limit widespread use. Here, focusing on Rabies lyssavirus, a globally important zoonosis, we developed a pseudotype micro-neutralization rapid fluorescent focus inhibition test (pmRFFIT) that overcomes these limitations. Specifically, we adapted an existing micro-neutralization test to use a green fluorescent protein–tagged murine leukemia virus pseudotype in lieu of pathogenic rabies virus, reducing the need for specialized reagents for antigen detection and enabling use in low-containment laboratories. We further used statistical analysis to generate rapid, quantitative predictions of the probability and titer of rabies virus neutralizing antibodies from microscopic imaging of neutralization outcomes. Using 47 serum samples from domestic dogs with neutralizing antibody titers estimated using the fluorescent antibody virus neutralization test (FAVN), pmRFFIT showed moderate sensitivity (78.79%) and high specificity (84.62%). Despite small conflicts, titer predictions were correlated across tests repeated on different dates both for dog samples (r = 0.93), and for a second dataset of sera from wild common vampire bats (r = 0.72, N = 41), indicating repeatability. Our test uses a starting volume of 3.5 μL of serum, estimates titers from a single dilution of serum rather than requiring multiple dilutions and end point titration, and may be adapted to target neutralizing antibodies against alternative lyssavirus species. The pmRFFIT enables high-throughput detection of rabies virus neutralizing antibodies in low-biocontainment settings and is suited to studies in wild or captive animals where large serum volumes cannot be obtained. url: https://doi.org/10.1101/2020.04.24.060095 doi: 10.1101/2020.04.24.060095 id: cord-290556-x7t7zqjd author: Middleton, Peter J title: Viruses that multiply in the gut and cause endemic and epidemic gastroenteritis date: 1996-08-31 words: 3932.0 sentences: 261.0 pages: flesch: 47.0 cache: ./cache/cord-290556-x7t7zqjd.txt txt: ./txt/cord-290556-x7t7zqjd.txt summary: Objective: To nominate the various viral agents that cause enteritis, discuss the pathogenesis, clinical features, epidemiology and diagnostic procedures employed. Results: The viruses causing gastroenteritis include: Rotaviruses; Adenoviruses-especially Ad 31, Ad 40 and Ad 41; members of the Caliciviridae, e.g. Norwalk virus, Hawaii virus, Snow Mountain virus, Taunton virus, Southampton virus, Toronto virus (formerly mini-reovirus) and others; Astrovirus; Coronavirus; Torovirus; Cytomegalovirus (CMV) and possibly Picobirnavirus. Rotavirus eventually became established as the leading worldwide cause of serious viral enteritis in infants and young children. Antigens or virions that form the basis of these serological tests may be obtained by purification procedures on infected stools; by cell culture cultivation, e.g. adenovirus, rotavirus and, in the case of Norwalk virus (NV), by self-assembled recombinant NV (rNV) particles expressed in a baculovirus system (Jiang et al., 1990 (Jiang et al., , 1993 . Enteric viruses and diarrhea in HIV-infected patients abstract: Abstract Background: Acute infectious diarrhea in young children is a leading cause of morbidity and mortality in developing countries. Even in developed countries, infectious enteritis is second only to respiratory infections as a cause of morbidity in early childhood. Objective: To nominate the various viral agents that cause enteritis, discuss the pathogenesis, clinical features, epidemiology and diagnostic procedures employed. Study design: Pertinent literature was reviewed and the findings of investigations carried out on viral enteritis by various colleagues recalled. Results: The viruses causing gastroenteritis include: Rotaviruses; Adenoviruses-especially Ad 31, Ad 40 and Ad 41; members of the Caliciviridae, e.g. Norwalk virus, Hawaii virus, Snow Mountain virus, Taunton virus, Southampton virus, Toronto virus (formerly mini-reovirus) and others; Astrovirus; Coronavirus; Torovirus; Cytomegalovirus (CMV) and possibly Picobirnavirus. Enteritis-producing viruses replicate in columar epithelial cells in the distal parts of villi of the small intestine. Two mechanisms are addressed to explain why diarrhea occurs. Clinically, the main expression of illness is a watery diarrhea that lasts 24 h to about 7 days. Vomiting is of shorter duration and may not always accompany the diarrhea. Fever is generally ⩽ 38.5°C. Virus is shed in the stool for about 3–7 days. Diagnostic procedures employ electron microscopy (EM), immune electron microscopy (IEM), enzyme-linked immunosorbent assay (ELISA), time-resolved fluoroimmunoassay (TR-FIA), latex agglutination, polyacrylamide gel electrophoresis (PAGE) and the polymerase chain reaction (PCR). Conclusion: In developed countries viral enteritis among young children may be up to three times more common than bacterial gut disease. With the exception of CMV enteric involvement, the stool is characteristically not bloody and white blood cells are not found. Patient management may involve the employment of IV replacement therapy to counter dehydration and electrolyte imbalance. Milder cases may be managed with oral rehydration. url: https://api.elsevier.com/content/article/pii/0928019796002310 doi: 10.1016/0928-0197(96)00231-0 id: cord-319761-bu5pzbnv author: Miller, Craig S. title: Pleiotropic mechanisms of virus survival and persistence date: 2005-07-16 words: 5655.0 sentences: 308.0 pages: flesch: 38.0 cache: ./cache/cord-319761-bu5pzbnv.txt txt: ./txt/cord-319761-bu5pzbnv.txt summary: Accordingly, this review focuses on specific viral cell interactions that allow the virus to survive the cellular attack and evade the immune system, establish persistent infections, and cause chronic disease. 13, 14 Viruses regulate apoptosis by several mechanisms including the targeting of the tumor suppressor gene product p53, the Fas death receptor, and by producing caspase inhibitors and viral Bcl-2 homologs. 24, 25 The alpha herpesvirus HSV-1 encodes several antiapoptotic gene products (ie, ICP4, ICP27, c34.5, U s 3, gJ) [26] [27] [28] [29] [30] that modulate apoptosis at several levels, including antagonism of double-stranded RNA-activated protein kinase (PKR), a downstream induction molecule of the interferon signaling pathway 31, 32 Of note, all c-herpesviruses express viral homologues of cellular antiapoptotic genes, including 1 or 2 Bcl-2 homologues. In the majority of infections, viruses encode products that antagonize either the IFN signal transduction pathway or cellular proteins induced by IFN that are responsible for inhibiting virus replication (Fig 2) . abstract: Viruses are enormously efficient infectious agents that have been implicated in causing human disease for centuries. Transmission of these pathogens continues to be from one life form to another in the form of isolated cases, epidemics, and pandemics. Each infection requires entry into a susceptible host, replication, and evasion of the immune system. Viruses are successful pathogens because they target specific cells for their attack, exploit the cellular machinery, and are efficient in circumventing and/or inhibiting key cellular events required of survival. This article reviews some of the advances that have taken place in human virology in the past 50 years, emphasizing mechanisms that contribute to, and are involved with, virus survival and persistence. url: https://api.elsevier.com/content/article/pii/S1079210405002374 doi: 10.1016/j.tripleo.2005.03.017 id: cord-022252-9yiuuye3 author: Mims, Cedric A. title: Mechanisms of Cell and Tissue Damage date: 2013-11-17 words: 28864.0 sentences: 1432.0 pages: flesch: 48.0 cache: ./cache/cord-022252-9yiuuye3.txt txt: ./txt/cord-022252-9yiuuye3.txt summary: A few viruses are remarkable because they cause no pathological changes at all in the cell, even during a productive infection in which infectious virus particles are produced. Primary consideration will be given to those substances which are produced under ecologically significant conditions (i.e. in the natural host or relevant animal model) and cause (also in biologically relevant systems) damage to cells or tissues thereby contributing to disease. Here we consider toxins which act on extracellular substances and are responsible for many of the main features of the diseases caused by the infecting organism. Circulating immune complexes are also deposited in the walls of small blood vessels in the skin and elsewhere, where they may induce inflammatory changes.* The prodromal rashes seen in exanthematous virus infections and in hepatitis B are probably caused in this way. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155491/ doi: 10.1016/b978-0-12-498262-8.50015-1 id: cord-002482-2t09zqqi author: Miras, Manuel title: Non-canonical Translation in Plant RNA Viruses date: 2017-04-06 words: 13890.0 sentences: 732.0 pages: flesch: 51.0 cache: ./cache/cord-002482-2t09zqqi.txt txt: ./txt/cord-002482-2t09zqqi.txt summary: Here, we review the tools utilized by positive-sense single-stranded (+ss) RNA plant viruses to initiate non-canonical translation, focusing on cis-acting sequences present in viral mRNAs. We highlight how these elements may interact with host translation factors and speculate on their contribution for achieving translational control. In this review, we describe current knowledge on the mechanisms used by positive-sense single-stranded (+ss) RNA plant viruses to initiate translation, focusing on cis-acting sequences present in viral mRNAs. We also describe other protein translation strategies used by plant viruses to optimize the usage of the coding capacity of their very compact genomes, including leaky scanning initiation, ribosomal frameshifting and stop-codon readthrough. abstract: Viral protein synthesis is completely dependent upon the host cell's translational machinery. Canonical translation of host mRNAs depends on structural elements such as the 5′ cap structure and/or the 3′ poly(A) tail of the mRNAs. Although many viral mRNAs are devoid of one or both of these structures, they can still translate efficiently using non-canonical mechanisms. Here, we review the tools utilized by positive-sense single-stranded (+ss) RNA plant viruses to initiate non-canonical translation, focusing on cis-acting sequences present in viral mRNAs. We highlight how these elements may interact with host translation factors and speculate on their contribution for achieving translational control. We also describe other translation strategies used by plant viruses to optimize the usage of the coding capacity of their very compact genomes, including leaky scanning initiation, ribosomal frameshifting and stop-codon readthrough. Finally, future research perspectives on the unusual translational strategies of +ssRNA viruses are discussed, including parallelisms between viral and host mRNAs mechanisms of translation, particularly for host mRNAs which are translated under stress conditions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5382211/ doi: 10.3389/fpls.2017.00494 id: cord-264406-s5c0grz0 author: Miró-Cañís, Sílvia title: Multiplex PCR reveals that viruses are more frequent than bacteria in children with cystic fibrosis date: 2016-11-13 words: 2084.0 sentences: 128.0 pages: flesch: 47.0 cache: ./cache/cord-264406-s5c0grz0.txt txt: ./txt/cord-264406-s5c0grz0.txt summary: Bacterial infections are very frequent in children with cystic fibrosis, but because rapid Methods: for screening for the wide variety of potentially involved viruses were unavailable until recently, the frequency of viral presence is unknown. Bacterial infections are very frequent in children with cystic fibrosis, but because rapid Methods: for screening for the wide variety of potentially involved viruses were unavailable until recently, the frequency of viral presence is unknown. Study design: In this 2-year prospective study, we obtained paired nasopharyngeal-swab and sputum specimens from children with cystic fibrosis during clinical respiratory examinations separated by at least 14 days. Study design: In this 2-year prospective study, we obtained paired nasopharyngeal-swab and sputum specimens from children with cystic fibrosis during clinical respiratory examinations separated by at least 14 days. This study aimed to evaluate the frequency viruses and bacteria in respiratory specimens and to clarify the incidence and characteristics (seasonality and age of patients) of different viruses in children with cystic fibrosis. abstract: BACKGROUND: Cystic fibrosis is a degenerative disease characterized by progressive epithelial secretory gland dysfunction associated with repeated respiratory infections. Bacterial infections are very frequent in children with cystic fibrosis, but because rapid METHODS: for screening for the wide variety of potentially involved viruses were unavailable until recently, the frequency of viral presence is unknown. Multiplex PCR enables screening for many viruses involved in respiratory infections. OBJECTIVES: This study aimed to evaluate the frequency of viruses and bacteria in respiratory specimens from children with cystic fibrosis and to clarify the incidence and characteristics (seasonality and age of patients) of different viruses detected in children with cystic fibrosis. STUDY DESIGN: In this 2-year prospective study, we obtained paired nasopharyngeal-swab and sputum specimens from children with cystic fibrosis during clinical respiratory examinations separated by at least 14 days. We analyzed viruses in nasopharyngeal-swab specimens with multiplex PCR and bacteria in sputum with standard methods. RESULTS: We analyzed 368 paired specimens from 33 children. We detected viruses in 154 (41.8%) and bacteria in 132 (35.9%). Bacteria were commoner in spring and summer; viruses were commoner in autumn and winter. In every season, Staphylococcus aureus was the commonest bacteria and rhinovirus was the commonest virus. Nearly all infections with Haemophilus influenzae occurred in autumn and winter. Viruses were more prevalent in children <5 years old, and bacteria were more prevalent in children ≥12 years old. CONCLUSIONS: Multiplex PCR screening for respiratory viruses is feasible in children with cystic fibrosis; the clinical implications of screening warrant further study. url: https://api.elsevier.com/content/article/pii/S1386653216305893 doi: 10.1016/j.jcv.2016.11.004 id: cord-302055-s155i4e9 author: Mitchell, Edith P. title: Corona Virus: Global Pandemic Causing World-Wide Shutdown date: 2020-04-03 words: 898.0 sentences: 70.0 pages: flesch: 59.0 cache: ./cache/cord-302055-s155i4e9.txt txt: ./txt/cord-302055-s155i4e9.txt summary: Human coronaviruses constitute a large family of viruses that usually cause mild to moderate upper respiratory illnesses in people such as the common cold. 1 Initial characterization of the coronavirus occurred in the 1960''s when Tyrell and Bynoe described passage of a virus named B814 at the time, as a group of viruses causing a large proportion of respiratory tract infections in humans. Strategies to prevent infection with the new coronavirus from World Health Organization (WHO) and the Center for Disease Control (CDC) recommend following these precautions for avoiding COVID-19: The Publisher of Journal of the National Medical Association, Elsevier, has compiled an extensive list of publications that may also be useful to physicians and other clinicians and can be found at: Elsevier''s Novel Coronavirus Information Center. A previously undescribed coronavirus associated with respiratory disease in humans abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0027968420300675 doi: 10.1016/j.jnma.2020.03.015 id: cord-018437-yjvwa1ot author: Mitchell, Michael title: Taxonomy date: 2013-08-26 words: 9283.0 sentences: 561.0 pages: flesch: 48.0 cache: ./cache/cord-018437-yjvwa1ot.txt txt: ./txt/cord-018437-yjvwa1ot.txt summary: Classifi cation is based on the genomic nucleic acid used by the virus (DNA or RNA), strandedness (single or double stranded), and method of replication. The nucleocapsids of some viruses are surrounded by envelopes composed of lipid bilayers and host-or viral-encoded proteins. The sequence of negative-sense ssRNA is complementary to the coding sequence for translation, so mRNA must be synthesized by RNA polymerase, typically carried within the virion, before translation into viral proteins. Among the families of viruses able to infect humans and other vertebrate hosts, there are many species that target and cause disease in the lung. The nucleocapsid is surrounded by an envelope derived from host-cell membrane and viral envelope proteins, including hepatitis B surface antigen. The genome of human parainfl uenza viruses is ~15 kb in length with an organization and six reading frames (N, P, M, F, HN, L) typical of the Paramyxoviridae (Karron and Collins 2007 ) . abstract: This chapter addresses the classification and taxonomy of viruses with special attention to viruses that show pneumotropic properties. Information provided in this chapter supplements that provided in other chapters in Parts II–V of this volume that discuss individual viral pathogens. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123310/ doi: 10.1007/978-3-642-40605-8_3 id: cord-329429-ur8g68vp author: Miłek, Justyna title: Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds date: 2018-12-10 words: 3809.0 sentences: 187.0 pages: flesch: 50.0 cache: ./cache/cord-329429-ur8g68vp.txt txt: ./txt/cord-329429-ur8g68vp.txt summary: Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3''UTR or 5''UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution. This taxonomic name includes IBV which causes a highly contagious disease of chickens, and genetically similar viruses isolated from other domestic galliformes: turkey coronavirus (TCoV), responsible for turkey enteritis, and the more recently detected guinea fowl coronavirus (GfCoV), the aetiological factor of fulminating disease in this species (2, 6, 27) . abstract: Coronaviruses (CoVs) are a large group of enveloped viruses with a single-strand RNA genome, which continuously circulate in mammals and birds and pose a threat to livestock, companion animals, and humans. CoVs harboured by avian species are classified to the genera gamma- and deltacoronaviruses. Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. Additionally, IBVs have been detected in healthy wild birds, demonstrating that they may act as the vector between domestic and free-living birds. Moreover, CoVs other than IBVs, are identified in wild birds, which suggests that wild birds play a key role in the epidemiology of other gammaCoVs and deltaCoVs. Development of molecular techniques has significantly improved knowledge of the prevalence of CoVs in avian species. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3’UTR or 5’UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution. url: https://www.ncbi.nlm.nih.gov/pubmed/30584600/ doi: 10.2478/jvetres-2018-0035 id: cord-001397-nrq4ncdf author: Mlera, Luwanika title: The role of viral persistence in flavivirus biology date: 2014-05-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In nature, vector-borne flaviviruses are persistently cycled between either the tick or mosquito vector and small mammals such as rodents, skunks, and swine. These viruses account for considerable human morbidity and mortality worldwide. Increasing and substantial evidence of viral persistence in humans, which includes the isolation of RNA by RT-PCR and infectious virus by culture, continues to be reported. Viral persistence can also be established in vitro in various human, animal, arachnid and insect cell lines in culture. Although some research has focused on the potential roles of defective virus particles, evasion of the immune response through the manipulation of autophagy and/or apoptosis, the precise mechanism of flavivirus persistence is still not well understood. We propose additional research for further understanding of how viral persistence is established in different systems. Avenues for additional studies include determining if the multifunctional flavivirus protein NS5 has a role in viral persistence, the development of relevant animal models of viral persistence as well as investigating the host responses that allow vector borne flavivirus replication without detrimental effects on infected cells. Such studies might shed more light on the viral-host relationships, and could be used to unravel the mechanisms for establishment of persistence. url: https://academic.oup.com/femspd/article-pdf/71/2/137/17943040/71-2-137.pdf doi: 10.1111/2049-632x.12178 id: cord-018058-n3majqes author: Modrow, Susanne title: Historical Overview date: 2013-08-12 words: 5376.0 sentences: 262.0 pages: flesch: 46.0 cache: ./cache/cord-018058-n3majqes.txt txt: ./txt/cord-018058-n3majqes.txt summary: Many of the steps that characterize a viral infection were first discovered in experiments with bacterial viruses: such processes include attachment and penetration, the reproduction-cycledependent regulation of gene expression that results in early and late synthesized proteins, and lysogeny, which is associated with the existence of prophages. Besides the importance for tumour virus research, these observations aroused interest in the question concerning the basis of the high susceptibility of newborn animals to viral infections, and suggested investigations on the innate resistance of an organism to infections as well as the time and the causes of its formation. Between 1918 and 1920, a pandemic emerging viral disease, Spanish flu, claimed more than 20 million lives, i.e., more than in the First World War. After cultivation of the virus responsible in embryonated chicken eggs in 1933, their haemagglutinating properties were discovered in 1941 (i.e., their ability to agglutinate red blood cells), thereby laying the basis for the development of haemagglutination tests to detect viruses. abstract: “Poisons” were originally considered as the causative agents of illnesses that we know as viral diseases today. At that time, there were no standard methods to detect pathogenic (disease-causing) organisms such as bacteria and protozoa in the supposed “poisonous materials”. Only animal experiments performed by Louis Pasteur at the end of the nineteenth century, in which no dilution of the poisonous properties was achieved even after several passages, suggested that the disease-causing agent was able to multiply in the organism. Therefore, there was talk of a reproducible “virus” (Latin for “poison” or “slime”) in living organisms, and later also in cells. In St. Petersburg in 1892, Dimitri I. Ivanovski demonstrated that tobacco mosaic disease is caused by an “ultrafilterable” agent, whose size is significantly smaller than that of bacteria: tobacco mosaic virus (bacteria filters have a pore size of approximately 0.2 μm, however, most viruses are smaller than 0.1 μm). Soon afterwards, Martinus Willem Beijerinck came to the same conclusion: he developed, for the first time, the notion of a self-replicating, “liquid” agent (contagium vivum fluidum). The discovery of foot-and-mouth disease virus by Friedrich Loeffler and Paul Frosch in Greifswald in 1898 was the first evidence of an animal pathogenic virus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122844/ doi: 10.1007/978-3-642-20718-1_1 id: cord-018165-afzjx2ci author: Modrow, Susanne title: Vaccines date: 2013-08-12 words: 4013.0 sentences: 213.0 pages: flesch: 43.0 cache: ./cache/cord-018165-afzjx2ci.txt txt: ./txt/cord-018165-afzjx2ci.txt summary: Live vaccines contain attenuated, replication-competent pathogens that can replicate in the vaccinated person, i.e. they are able to infect certain cells and initiate the synthesis of viral proteins and particles, but without triggering the respective clinical picture. Therefore, the immune response that is triggered by attenuated viruses is suitable to induce a long-lasting, effective protection against infections with the respective pathogen. Similarly, vaccinia viruses that were originally used to produce a protective immune response against smallpox virus induced local infections in humans, which in very rare cases had a generalized or fatal course. It is being attempted to modify well-explored, less pathogenic viruses (e.g. adenoviruses) and vaccine viruses that were used successfully in the past (usually vaccinia viruses) by using genetic engineering methods in such a way that they encode proteins of other viral species, in addition to their own gene products necessary for infection and replication (▶ Sects. abstract: Vaccines are predominantly used for prevention; that means they should establish a protection in immunized people or animals which will protect them from a possible infection and the subsequent illness when they come into contact with the respective pathogens. Fundamentally, there are two kinds of immunization: active and passive. The latter is based on the administration of immunoglobulin preparations that can neutralize a specific virus. Therefore, passive vaccination is applied only in special cases, such as when the person to be protected recently had verifiable contact with a specific virus (postexposure prophylaxis), or if the risk of exposure to pathogens cannot be ruled out in the following weeks and an active vaccination is not possible, as in short-term planned trips to Third World countries (exposure prophylaxis). An example is the administration of antibodies specific for hepatitis B virus in cases of contamination with blood from people who have an acute or chronically persistent infection with this virus, and thus have high concentrations of infectious particles in the blood. Such accidents occur primarily in medical personnel by needlestick injury (10.1007/978-3-642-20718-1_19). In certain cases, the administration is performed in combination with an active vaccination (active–passive immunization). Specific immunoglobulin preparations are also administered when people have been bitten by animals that may be infected with the rabies virus (10.1007/978-3-642-20718-1_15). In the case of early application (together with an active vaccination), the antibodies can neutralize the virus, and impede its spread in the body. Since the time between contact with the virus and its spread in the organism is often very short, passive immunization is limited to a period shortly before or after exposure to the infective agent (usually within 4 days). Therefore, it is reserved for cases in which the contact with the potential pathogen is well documented and the type of infection is known, and when an appropriate immunoglobulin preparation is available. The protection afforded by antibody preparations lasts just a few weeks, as immunoglobulins are rapidly degraded in the organism. Therefore, postexposure administration of active vaccines is increasingly preferred, e.g. in the context of outbreak-control vaccination. In veterinary medicine, passive immunization is employed occasionally in young animals which were born in a flock with high infection pressure. This approach is applied, for example, in kennels when infections occur with canine parvovirus (10.1007/978-3-642-20718-1_20). However, its value is controversial, as the immunoglobulins administered hinder the more advantageous active immunization. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122972/ doi: 10.1007/978-3-642-20718-1_10 id: cord-018477-hgvqd1ej author: Modrow, Susanne title: Pathogenesis date: 2013-08-12 words: 3661.0 sentences: 210.0 pages: flesch: 51.0 cache: ./cache/cord-018477-hgvqd1ej.txt txt: ./txt/cord-018477-hgvqd1ej.txt summary: These cells are loaded with the virus particles and proteins and migrate to the immunologically active centres of the nearest lymph nodes, encountering there other immune cells such as CD4 + and CD8 + T lymphocytes, B lymphocytes and macrophages, which start to proliferate by contact with the pathogen proteins or with MHC-peptide complexes and by the influence of cytokines secreted by activated immune cells (▶ Chaps. During herpes simplex virus infections of the conjunctiva and the cornea, reactivated pathogens migrate from the ganglia of the nerve fibres into the eye, where they may spread in the epithelium of the cornea and cause inflammations. In pregnant women, haematogenously disseminated viruses such as rubella virus, cytomegalovirus and parvovirus B19 are transported via the bloodstream into the placenta and infect the endothelial cells of this organ. Other viruses, such poliovirus and tick-borne encephalitis virus, overcome the barriers probably by infection of endothelial cells, as occurs by infecting other organs (▶ Sects. abstract: Pathogenesis describes the spread of a virus in the organism and the mutual relationship between the pathogen and its host during infection. These processes can be analysed in several ways by using different histological, virological and immunological methods. Viral infections can be with or without symptoms (also called apparent or inapparent infection courses). In both cases, the host organism responds with immunological defence responses, which usually lead to overcoming the primary disease symptoms and to the elimination of the virus. The immune response may also contribute in the context of immunopathogenesis to specific disease symptoms and either temporary or permanent damage to the host. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123358/ doi: 10.1007/978-3-642-20718-1_4 id: cord-291063-de7v4e5s author: Moens, Ugo title: Silencing Viral MicroRNA as a Novel Antiviral Therapy? date: 2009-05-28 words: 9122.0 sentences: 526.0 pages: flesch: 49.0 cache: ./cache/cord-291063-de7v4e5s.txt txt: ./txt/cord-291063-de7v4e5s.txt summary: The expressions of EBV-encoded miRNAs in clinical samples and computational analysis to predict putative targets were applied to unravel the biological functions of EBV miRNAs. These approaches showed that the miR-BARTs are abundantly expressed in latently infected epithelial cells, nasopharyngeal carcinomas, EBV-associated gastric carcinoma cell lines and tissues, Burkitt''s lymphomas latency type I, EBV positive primary effusion lymphomas, and diffuse large B-cell lymphomas, but at a significantly lower level in B cells. However, computational alignment of the potential HIV-1 miRNAs with specific human T-cell mRNAs identified potential cellular targets including genes encoding CD4, CD28 and interleukin-2, IL-3, and IL-12 [119] . The idea of targeting viral transcripts is not new, and RNA interference has been demonstrated to efficiently mediate inhibition of replication of human pathogenic viruses such as HIV-1, HCV, dengue virus, severe acute respiratory syndrome (SARS) coronavirus, poliovirus, human rhinovirus, influenza A virus, hepatitis D virus, HBV, HSV-1, HPV, JCV, EBV, and CMV in cell culture (reviewed in [12] ). abstract: Viruses are intracellular parasites that ensure their existence by converting host cells into viral particle producing entities or into hiding places rendering the virus invisible to the host immune system. Some viruses may also survive by transforming the infected cell into an immortal tumour cell. MicroRNAs are small non-coding transcripts that function as posttranscriptional regulators of gene expression. Viruses encode miRNAs that regulate expression of both cellular and viral genes, and contribute to the pathogenic properties of viruses. Hence, neutralizing the action of viral miRNAs expression by complementary single-stranded oligonucleotides or so-called anti-miRNAs may represent a strategy to combat viral infections and viral-induced pathogenesis. This review describes the miRNAs encoded by human viruses, and discusses the possible therapeutic applications of anti-miRNAs against viral diseases. url: https://doi.org/10.1155/2009/419539 doi: 10.1155/2009/419539 id: cord-327199-ggomuomb author: Moerdyk-Schauwecker, Megan title: Cellular Proteins Associated with the Interior and Exterior of Vesicular Stomatitis Virus Virions date: 2014-08-08 words: 6425.0 sentences: 288.0 pages: flesch: 43.0 cache: ./cache/cord-327199-ggomuomb.txt txt: ./txt/cord-327199-ggomuomb.txt summary: In another example, the presence of host complement control proteins such as CD46, CD55 and CD59 in the viral envelope has been shown to protect against antibody dependent complement mediated virus lysis in several viruses including human T cell leukemia/ lymphoma virus type I [16] , human cytomegalovirus [16] , hepatitis C virus [17] , HIV-1 [18, 19] , extracellular enveloped vaccinia virus [20] , simian virus 5 [21] and mumps virus [21] . As discussed in the previous section, proteins not associated with the interior of the virion, including proteins embedded in the host derived viral envelope, can be identified by their absence in ProK treated samples or by a size shift upon ProK treatment. While many of the proteins identified in VSV virions appear to be associated with viral assembly, budding or the host-derived viral envelope, they may also have additional functions that affect virus replication. abstract: Virus particles (virions) often contain not only virus-encoded but also host-encoded proteins. Some of these host proteins are enclosed within the virion structure, while others, in the case of enveloped viruses, are embedded in the host-derived membrane. While many of these host protein incorporations are likely accidental, some may play a role in virus infectivity, replication and/or immunoreactivity in the next host. Host protein incorporations may be especially important in therapeutic applications where large numbers of virus particles are administered. Vesicular stomatitis virus (VSV) is the prototypic rhabdovirus and a candidate vaccine, gene therapy and oncolytic vector. Using mass spectrometry, we previously examined cell type dependent host protein content of VSV virions using intact (“whole”) virions purified from three cell lines originating from different species. Here we aimed to determine the localization of host proteins within the VSV virions by analyzing: i) whole VSV virions; and ii) whole VSV virions treated with Proteinase K to remove all proteins outside the viral envelope. A total of 257 proteins were identified, with 181 identified in whole virions and 183 identified in Proteinase K treated virions. Most of these proteins have not been previously shown to be associated with VSV. Functional enrichment analysis indicated the most overrepresented categories were proteins associated with vesicles, vesicle-mediated transport and protein localization. Using western blotting, the presence of several host proteins, including some not previously shown in association with VSV (such as Yes1, Prl1 and Ddx3y), was confirmed and their relative quantities in various virion fractions determined. Our study provides a valuable inventory of virion-associated host proteins for further investigation of their roles in the replication cycle, pathogenesis and immunoreactivity of VSV. url: https://www.ncbi.nlm.nih.gov/pubmed/25105980/ doi: 10.1371/journal.pone.0104688 id: cord-285330-td4vr0zv author: Mohammadi, Ali title: Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus date: 2015-11-12 words: 3157.0 sentences: 180.0 pages: flesch: 56.0 cache: ./cache/cord-285330-td4vr0zv.txt txt: ./txt/cord-285330-td4vr0zv.txt summary: title: Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus An Iranian isolate of avian infectious bronchitis virus IRFIBV32 was quantified in experimentally infected broilers using real-time reverse transcriptase polymerase chain reaction and histopathological changes was investigated. In this study, we identified IBV load in different tissues of experimentally infected broilers to clarify the replication strength of IRFIBV32 Isolate at intervals post challenge. Gross lesions were recorded and their trachea, lungs, kidneys, caecal tonsils, testes and ovaries were aseptically collected separately for the virus detection, titration and histopathological evaluations. We detected the viral RNA in the caecal tonsils of infected chicken from 1 to 20 dpi and the maximal loads of the virus were on 5 dpi. Pathogenesis and tissue distribution of avian infectious bronchitis virus isolate IRFIBV32 (793/b serotype) in experimentally infected broiler chickens Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens abstract: An Iranian isolate of avian infectious bronchitis virus IRFIBV32 was quantified in experimentally infected broilers using real-time reverse transcriptase polymerase chain reaction and histopathological changes was investigated. Thirty-six 3-week-old commercial broilers were inoculated by 10(5) ELD50/0.1 ml of the virus. On the various days post inoculation (dpi) different tissues were collected. The virus strongly started the replication in trachea at 1 dpi and reached to the maximum titer at 3 dpi. The highest IBV RNA level was shown in this organ. In lung, the virus was replicated with the titer lower than that of the trachea, but it rose up more at 5 dpi. The kidneys were the tissues with the least viral genome copy number, although the duration of the virus presence was considerable. The virus replicated in testes sooner than ovaries also disappeared sooner but the maximum viral yield in the ovaries was more. The virus titer in the studied tissues had an interesting fluctuation especially in caecal tonsils. Testes and ovaries were the organs that the virus could reactivate without using any chemical. The most severe lesions were observed in tracheae but they appeared in the lungs later. Lymphocyte infiltration in the kidneys was noted from 5 dpi even sooner than the lungs. There were no lesions in the caecal tonsils, testes and ovaries in spite of the virus replication in a high titer. url: https://www.ncbi.nlm.nih.gov/pubmed/26645044/ doi: 10.1007/s13337-015-0286-4 id: cord-313312-h607itv2 author: Mok, Darren Z. L. title: The Effects of Pre-Existing Antibodies on Live-Attenuated Viral Vaccines date: 2020-05-08 words: 7417.0 sentences: 349.0 pages: flesch: 34.0 cache: ./cache/cord-313312-h607itv2.txt txt: ./txt/cord-313312-h607itv2.txt summary: Pre-existing antibodies, derived from either from maternal–fetal transmission, or by previous infection or vaccination, have been demonstrated to interfere with vaccine immunogenicity of measles, adenovirus, and influenza LAVs. Immune interference of LAVs can be caused by the formation of virus–antibody complexes that neutralize virus infection in antigen-presenting cells, or by the cross-linking of the B-cell receptor with the inhibitory receptor, FcγRIIB. The clinical trial finding that subjects with a limited range of cross-reactive antibodies from a prior Japanese Encephalitis vaccine were able to enhance yellow fever vaccination, by prolonging vaccine viremia duration that leads to higher antibody titers, thus hints at the possibility that whether pre-existing antibodies inhibit or augment flavivirus infection will depend on both antibody titers and the type/specificity of antibodies produced [85] . By contrast, at sub-neutralizing titers, pre-existing antibodies can enable viruses to better infect cells and increase innate immune responses that augment LAV immunogenicity. By contrast, at sub-neutralizing titers, pre-existing antibodies can enable viruses to better infect cells and increase innate immune responses that augment LAV immunogenicity. abstract: Live-attenuated vaccines (LAVs) have achieved remarkable successes in controlling virus spread, as well as for other applications such as cancer immunotherapy. However, with rapid increases in international travel, globalization, geographic spread of viral vectors, and widespread use of vaccines, there is an increasing need to consider how pre-exposure to viruses which share similar antigenic regions can impact vaccine efficacy. Pre-existing antibodies, derived from either from maternal–fetal transmission, or by previous infection or vaccination, have been demonstrated to interfere with vaccine immunogenicity of measles, adenovirus, and influenza LAVs. Immune interference of LAVs can be caused by the formation of virus–antibody complexes that neutralize virus infection in antigen-presenting cells, or by the cross-linking of the B-cell receptor with the inhibitory receptor, FcγRIIB. On the other hand, pre-existing antibodies can augment flaviviral LAV efficacy such as that of dengue and yellow fever virus, especially when pre-existing antibodies are present at sub-neutralizing levels. The increased vaccine immunogenicity can be facilitated by antibody-dependent enhancement of virus infection, enhancing virus uptake in antigen-presenting cells, and robust induction of innate immune responses that promote vaccine immunogenicity. This review examines the literature on this topic and examines the circumstances where pre-existing antibodies can inhibit or enhance LAV efficacy. A better knowledge of the underlying mechanisms involved could allow us to better manage immunization in seropositive individuals and even identify possibilities that could allow us to exploit pre-existing antibodies to boost vaccine-induced responses for improved vaccine efficacy. url: https://www.ncbi.nlm.nih.gov/pubmed/32397218/ doi: 10.3390/v12050520 id: cord-340503-zwdewiu1 author: Mokhtarzadeh, Ahad title: Nanomaterial-based biosensors for detection of pathogenic virus date: 2017-10-13 words: 7710.0 sentences: 401.0 pages: flesch: 42.0 cache: ./cache/cord-340503-zwdewiu1.txt txt: ./txt/cord-340503-zwdewiu1.txt summary: Electron microscopy Viral particle Hours Broad spectrum; rapid method Necessity for presence of around 10 6 virus particles/mL for detection; similarity of morphologies [11] Hemagglutination assay Viral protein Hours Easy; inexpensive Poor sensitivity; necessity for fresh reagents [12] ELISA Viral protein Hours Only one incubation step; no hook effect at high analyte concentrations Limited concentration range in which the analyte can be quantified without sample dilution; and that the antigen or antibody produce the same response and not distinguishable in a one step [13] PCR Viral nucleic acid Hours Extremely high sensitivity; Easy to set up Extremely liable to contamination; Not easy to quantitate results; High degree of operator skill required [14] As an example for HIV, a type of virus that gradually attacks the immune system and makes it harder to fight off infections and diseases in infected body, a QDs-based rapid capture and imaging system was developed by Kim et al. abstract: Viruses are real menace to human safety that cause devastating viral disease. The high prevalence of these diseases is due to improper detecting tools. Therefore, there is a remarkable demand to identify viruses in a fast, selective and accurate way. Several biosensors have been designed and commercialized for detection of pathogenic viruses. However, they present many challenges. Nanotechnology overcomes these challenges and performs direct detection of molecular targets in real time. In this overview, studies concerning nanotechnology-based biosensors for pathogenic virus detection have been summarized, paying special attention to biosensors based on graphene oxide, silica, carbon nanotubes, gold, silver, zinc oxide and magnetic nanoparticles, which could pave the way to detect viral diseases and provide healthy life for infected patients. url: https://doi.org/10.1016/j.trac.2017.10.005 doi: 10.1016/j.trac.2017.10.005 id: cord-325750-x7jpsnxg author: Mokili, John L title: Metagenomics and future perspectives in virus discovery date: 2012-01-20 words: 8742.0 sentences: 463.0 pages: flesch: 40.0 cache: ./cache/cord-325750-x7jpsnxg.txt txt: ./txt/cord-325750-x7jpsnxg.txt summary: In this article, we review virus discovery techniques with a focus on metagenomic approaches that employ high-throughput sequencing technologies to characterize novel viruses. This method lacks sufficient sensitivity to detect viruses when the viral burden is low or when the DNA sequence of the suspected etiological agent is not clearly distinguishable from the control sample [31] . The following items should be included in any report on viral metagenomic studies: firstly, the sequencing platform and its version number; secondly, raw sequence data accession numbers in a public database; thirdly, details about the bioinformatic analysis, including the homology search tool and the database being used to assign the taxonomy, and their versions; fourthly, a list of known and previously unknown viruses found, clearly showing if the ''novel'' viruses are new strains of a previously described species or completely different viruses; and fifthly, causality evidence if any. abstract: Monitoring the emergence and re-emergence of viral diseases with the goal of containing the spread of viral agents requires both adequate preparedness and quick response. Identifying the causative agent of a new epidemic is one of the most important steps for effective response to disease outbreaks. Traditionally, virus discovery required propagation of the virus in cell culture, a proven technique responsible for the identification of the vast majority of viruses known to date. However, many viruses cannot be easily propagated in cell culture, thus limiting our knowledge of viruses. Viral metagenomic analyses of environmental samples suggest that the field of virology has explored less than 1% of the extant viral diversity. In the last decade, the culture-independent and sequence-independent metagenomic approach has permitted the discovery of many viruses in a wide range of samples. Phylogenetically, some of these viruses are distantly related to previously discovered viruses. In addition, 60–99% of the sequences generated in different viral metagenomic studies are not homologous to known viruses. In this review, we discuss the advances in the area of viral metagenomics during the last decade and their relevance to virus discovery, clinical microbiology and public health. We discuss the potential of metagenomics for characterization of the normal viral population in a healthy community and identification of viruses that could pose a threat to humans through zoonosis. In addition, we propose a new model of the Koch's postulates named the ‘Metagenomic Koch's Postulates’. Unlike the original Koch's postulates and the Molecular Koch's postulates as formulated by Falkow, the metagenomic Koch's postulates focus on the identification of metagenomic traits in disease cases. The metagenomic traits that can be traced after healthy individuals have been exposed to the source of the suspected pathogen. url: https://doi.org/10.1016/j.coviro.2011.12.004 doi: 10.1016/j.coviro.2011.12.004 id: cord-260496-s2ba7uy3 author: Moncany, Maurice L.J. title: Identification of conserved lentiviral sequences as landmarks of genomic flexibility date: 2006-08-08 words: 5991.0 sentences: 296.0 pages: flesch: 51.0 cache: ./cache/cord-260496-s2ba7uy3.txt txt: ./txt/cord-260496-s2ba7uy3.txt summary: Comparison of entire genomes, including 237 human, simian and non-primate mammal lentiviruses and 103 negative control viruses, led to identify 28 Conserved Lentiviral Sequences (CLSs). Immunodeficiency lentiviral genomes correspond to 171 human viruses (155 HIV-1s and 16 HIV-2s), 33 simian viruses (3 CPZ, 9 AGM, 8 Macaque, 2 Mandrill, 10 Sooty Mangabey, 1 Sykes'' monkey viruses) and 33 non-primate mammal viruses (2 bovine, 2 caprine, 11 equine, 9 feline, 3 ovine and 6 ovine/caprine viruses). From the particular organization of the HIV-1 and HIV-2 ( Fig. 1) , AGM and macaque (Fig. 2) , CPZ, feline, equine and D-particle-forming viruses (Fig. 3) and that of sooty mangabey, mandrill and other non-primate lentiviruses (supplementary data), it appears that a given CLS occupied on the viral genome a specific position that was roughly conserved in the different viral families. abstract: Considering that recombinations produce quasispecies in lentivirus spreading, we identified and localized highly conserved sequences that may play an important role in viral ontology. Comparison of entire genomes, including 237 human, simian and non-primate mammal lentiviruses and 103 negative control viruses, led to identify 28 Conserved Lentiviral Sequences (CLSs). They were located mainly in the structural genes forming hot spots particularly in the gag and pol genes and to a lesser extent in LTRs and regulatory genes. The CLS pattern was the same throughout the different HIV-1 subtypes, except for some HIV-1-O strains. Only CLS 3 and 4 were detected in both negative control HTLV-1 oncornaviruses and D-particle-forming simian viruses, which are not immunodeficiency inducers and display a genetic stability. CLSs divided the virus genomes into domains allowing us to distinguish sequence families leading to the notion of ‘species self’ besides that of ‘lentiviral self’. Most of acutely localized CLSs in HIV-1s (82%) corresponded to wide recombination segments being currently reported. To cite this article: M.L.J. Moncany et al., C. R. Biologies 329 (2006). url: https://www.sciencedirect.com/science/article/pii/S1631069106001661 doi: 10.1016/j.crvi.2006.07.001 id: cord-275795-ee7qyw5h author: Monette, Anne title: T Lymphocytes as Measurable Targets of Protection and Vaccination Against Viral Disorders date: 2018-10-24 words: 28265.0 sentences: 1205.0 pages: flesch: 38.0 cache: ./cache/cord-275795-ee7qyw5h.txt txt: ./txt/cord-275795-ee7qyw5h.txt summary: We focus on immunity generated against both natural infection and vaccination, where a steady shift in conferred vaccination immunogenicity is observed from quantifying activated and proliferating, long-lived effector memory T cell subsets, as the prominent biomarkers of long-term immunity against viruses and their associated disorders causing high morbidity and mortality rates. Since that time, the occurrence of epidemics and outbreaks are now at lower risk, following the introduction of massive vaccination programs able to induce immune system targeting of viruses causing severe disorders affecting distinct geographical locations, and with many epidemiological reports demonstrating long-term efficacy of viral control of non-naïve populations. This approach is being developed to use virus-infected cell-killing antibodies that produce an antiviral environment; these termed antibody-dependent cellular cytotoxicity (ADCC)-mediating antibodies, which are predicted to link innate and adaptive immune responses, and is becoming possible due to new technologies for rapid isolation and characterization of monoclonal antibodies targeting conserved regions of influenza virus, reviewed in Jegaskanda et al. abstract: Continuous epidemiological surveillance of existing and emerging viruses and their associated disorders is gaining importance in light of their abilities to cause unpredictable outbreaks as a result of increased travel and vaccination choices by steadily growing and aging populations. Close surveillance of outbreaks and herd immunity are also at the forefront, even in industrialized countries, where previously eradicated viruses are now at risk of re-emergence due to instances of strain recombination, contractions in viral vector geographies, and from their potential use as agents of bioterrorism. There is a great need for the rational design of current and future vaccines targeting viruses, with a strong focus on vaccine targeting of adaptive immune effector memory T cells as the gold standard of immunity conferring long-lived protection against a wide variety of pathogens and malignancies. Here, we review viruses that have historically caused large outbreaks and severe lethal disorders, including respiratory, gastric, skin, hepatic, neurologic, and hemorrhagic fevers. To observe trends in vaccinology against these viral disorders, we describe viral genetic, replication, transmission, and tropism, host-immune evasion strategies, and the epidemiology and health risks of their associated syndromes. We focus on immunity generated against both natural infection and vaccination, where a steady shift in conferred vaccination immunogenicity is observed from quantifying activated and proliferating, long-lived effector memory T cell subsets, as the prominent biomarkers of long-term immunity against viruses and their associated disorders causing high morbidity and mortality rates. url: https://www.sciencedirect.com/science/article/pii/S1937644818300844 doi: 10.1016/bs.ircmb.2018.07.006 id: cord-214795-8jweuq50 author: Mongia, Aanchal title: DeepVir -- Graphical Deep Matrix Factorization for"In Silico"Antiviral Repositioning: Application to COVID-19 date: 2020-09-22 words: 6420.0 sentences: 369.0 pages: flesch: 47.0 cache: ./cache/cord-214795-8jweuq50.txt txt: ./txt/cord-214795-8jweuq50.txt summary: Results on our curated RNA drug virus association (DVA) dataset shows that the proposed approach excels over state-of-the-art graph regularized matrix completion techniques. It shows how the matrix completion framework can be used to computationally predict the drugs that could be effective against SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the virus responsible for the ongoing pandemic, COVID-19 (COrona VIrus Disease-2019). In this present work, we propose to solve the problem of drug-virus association prediction via graph regularized deep matrix factorization. Among all the methodologies compared in [52] , graph regularized matrix factorization based technique (GRMF) provided the best results for the validation setting where drugs are predicted for novel viruses. In our proposed technique, multi-graph regularization is incorporated in the deep matrix factorization formulation with the aim to incorporate the metadata associated with the drugs and viruses in the form of similarity information as shown below: abstract: This work formulates antiviral repositioning as a matrix completion problem where the antiviral drugs are along the rows and the viruses along the columns. The input matrix is partially filled, with ones in positions where the antiviral has been known to be effective against a virus. The curated metadata for antivirals (chemical structure and pathways) and viruses (genomic structure and symptoms) is encoded into our matrix completion framework as graph Laplacian regularization. We then frame the resulting multiple graph regularized matrix completion problem as deep matrix factorization. This is solved by using a novel optimization method called HyPALM (Hybrid Proximal Alternating Linearized Minimization). Results on our curated RNA drug virus association (DVA) dataset shows that the proposed approach excels over state-of-the-art graph regularized matrix completion techniques. When applied to"in silico"prediction of antivirals for COVID-19, our approach returns antivirals that are either used for treating patients or are under for trials for the same. url: https://arxiv.org/pdf/2009.10333v1.pdf doi: nan id: cord-232446-vvb2ffhv author: Mongia, Aanchal title: A computational approach to aid clinicians in selecting anti-viral drugs for COVID-19 trials date: 2020-07-03 words: 7123.0 sentences: 382.0 pages: flesch: 47.0 cache: ./cache/cord-232446-vvb2ffhv.txt txt: ./txt/cord-232446-vvb2ffhv.txt summary: In view to assist acceleration of this process (by pruning down the search space), we create and share a publicly available DVA database, along with a number of matrix completion techniques (mentioned above) for drug-virus association prediction. Such a computational approach requires the chemical structure of the drugs and, in case of graph-regularized matrix completion techniques, the genome of the viruses, or existing associations otherwise. A clear observation from the experiments is that the graph regularized-based matrix completion algorithms that incorporate the similarity information associated with the drugs and viruses, perform fairly well giving an AUC greater or equal than 0.83 in CV1. It can be noted that the standard matrix completion methods, which do not take into account the metadata, fail to learn from the association data giving a near-random performance as far as the prediction on novel viruses is concerned, depicting how very important the similarity information is. abstract: COVID-19 has fast-paced drug re-positioning for its treatment. This work builds computational models for the same. The aim is to assist clinicians with a tool for selecting prospective antiviral treatments. Since the virus is known to mutate fast, the tool is likely to help clinicians in selecting the right set of antivirals for the mutated isolate. The main contribution of this work is a manually curated database publicly shared, comprising of existing associations between viruses and their corresponding antivirals. The database gathers similarity information using the chemical structure of drugs and the genomic structure of viruses. Along with this database, we make available a set of state-of-the-art computational drug re-positioning tools based on matrix completion. The tools are first analysed on a standard set of experimental protocols for drug target interactions. The best performing ones are applied for the task of re-positioning antivirals for COVID-19. These tools select six drugs out of which four are currently under various stages of trial, namely Remdesivir (as a cure), Ribavarin (in combination with others for cure), Umifenovir (as a prophylactic and cure) and Sofosbuvir (as a cure). Another unanimous prediction is Tenofovir alafenamide, which is a novel tenofovir prodrug developed in order to improve renal safety when compared to the counterpart tenofovir disoproxil. Both are under trail, the former as a cure and the latter as a prophylactic. These results establish that the computational methods are in sync with the state-of-practice. We also demonstrate how the selected drugs change as the SARS-Cov-2 mutates over time, suggesting the importance of such a tool in drug prediction. The dataset and software is available publicly at https://github.com/aanchalMongia/DVA and the prediction tool with a user-friendly interface is available at http://dva.salsa.iiitd.edu.in. url: https://arxiv.org/pdf/2007.01902v2.pdf doi: nan 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-320030-ojtp90na author: Montero, Antonio title: Fiebre chikungunya - Una nueva amenaza global date: 2015-08-07 words: 3949.0 sentences: 372.0 pages: flesch: 60.0 cache: ./cache/cord-320030-ojtp90na.txt txt: ./txt/cord-320030-ojtp90na.txt summary: Resumen Las epidemias causadas, entre otros, por los virus Ébola, Marburgo, Nipah, Lassa, coronavirus, virus del Nilo Occidental, virus de Saint Louis, virus de la inmunodeficiencia humana, dengue, fiebre amarilla y fiebre hemorrágica venezolana han puesto sobre el tapete el riesgo que estos agentes representan para la salud pública global. El riesgo de epidemias y endemicidad en las Amé ricas parece muy elevado debido a la existencia de una població n sensible a la enfermedad, la ubicuidad de los mosquitos vectores y la introducció n cada vez má s frecuente de casos importados. Debido a la amplia distribució n de los Aedes en las Amé ricas, toda la regió n es susceptible a la invasió n y la diseminació n de este virus, y la aparició n reciente de epidemias urbanas de dengue en Sudamé rica destaca el peligro potencial de fiebre chikungunya. abstract: Resumen Las epidemias causadas, entre otros, por los virus Ébola, Marburgo, Nipah, Lassa, coronavirus, virus del Nilo Occidental, virus de Saint Louis, virus de la inmunodeficiencia humana, dengue, fiebre amarilla y fiebre hemorrágica venezolana han puesto sobre el tapete el riesgo que estos agentes representan para la salud pública global. Entre las nuevas amenazas destaca el virus chikungunya, que ha extendido rápidamente su área endémica desde regiones remotas de África hacia la cuenca del océano Índico y el Pacífico Oriental, causando importantes epidemias en África, Asia, islas del Índico y Europa Occidental, llegando a establecerse recientemente en islas del Caribe. Debido a su comportamiento dual endémico y epidémico, a sus propiedades virológicas y a la presencia global de sus vectores, este virus entraña el riesgo de causar grandes epidemias e instalarse en el territorio continental de las Américas a partir de la introducción de casos importados y a la circulación local vista en la región caribeña. Se revisan las principales características epidemiológicas y clínicas de la fiebre chikungunya y el riesgo de introducción de esta enfermedad en las Américas, enfatizando el rol de la vigilancia y la lucha contra los mosquitos en su prevención. Abstract The recent onset of epidemics caused by viruses such as Ebola, Marburg, Nipah, Lassa, coronavirus, West-Nile encephalitis, Saint Louis encephalitis, human immunodeficiency virus, dengue, yellow fever and Venezuelan hemorrhagic fever alerts about the risk these agents represent for the global health. Chikungunya virus represents a new threat. Surged from remote African regions, this virus has become endemic in the Indic ocean basin, the Indian subcontinent and the southeast of Asia, causing serious epidemics in Africa, Indic Ocean Islands, Asia and Europe. Due to their epidemiological and biological features and the global presence of their vectors, chikungunya represents a serious menace and could become endemic in the Americas. Although chikungunya infection has a low mortality rate, its high attack ratio may collapse the health system during epidemics affecting a sensitive population. In this paper, we review the clinical and epidemiological features of chikungunya fever as well as the risk of its introduction into the Americas. We remark the importance of the epidemiological control and mosquitoes fighting in order to prevent this disease from being introduced into the Americas. url: https://doi.org/10.1016/j.medcli.2014.05.031 doi: 10.1016/j.medcli.2014.05.031 id: cord-322082-80ym2rsq author: Monto, Arnold S title: Lessons From Influenza Pandemics of the Last 100 Years date: 2020-03-01 words: 4089.0 sentences: 229.0 pages: flesch: 46.0 cache: ./cache/cord-322082-80ym2rsq.txt txt: ./txt/cord-322082-80ym2rsq.txt summary: Since this was the first true pandemic since 1918, there was immediate concern about its potential impact and great relief when it was found to resemble seasonal influenza with morbidity highest in children and mortality at the extremes of age [26, 27] (Figure 3 ). However, the new A(H3N2) virus completely replaced the previous subtype, and its variants, more than 50 years later, have been responsible for the greatest proportion of mortality from influenza viruses. In the United States, there was particular attention directed to nonpharmaceutical interventions, a result of the recognition that pandemic-specific vaccines would be available relatively late and that influenza-specific antiviral drugs, while important, would be limited in quantity. " The latter issue has been made worse by the repeated recognition of the pandemic potential of different avian influenza virus variants that have infected humans [63] [64] [65] . abstract: Seasonal influenza is an annual occurrence, but it is the threat of pandemics that produces universal concern. Recurring reports of avian influenza viruses severely affecting humans have served as constant reminders of the potential for another pandemic. Review of features of the 1918 influenza pandemic and subsequent ones helps in identifying areas where attention in planning is critical. Key among such issues are likely risk groups and which interventions to employ. Past pandemics have repeatedly underscored, for example, the vulnerability of groups such as pregnant women and taught other lessons valuable for future preparedness. While a fundamental difficulty in planning for the next pandemic remains their unpredictability and infrequency, this uncertainty can be mitigated, in part, by optimizing the handling of the much more predictable occurrence of seasonal influenza. Improvements in antivirals and novel vaccine formulations are critical in lessening the impact of both pandemic and seasonal influenza. url: https://www.ncbi.nlm.nih.gov/pubmed/31420670/ doi: 10.1093/cid/ciz803 id: cord-007149-m4xsx9ev author: Morahan, Pages S title: VIRUSES AND THE VERSATILE MACROPHAGE date: 1985-01-17 words: 6129.0 sentences: 375.0 pages: flesch: 43.0 cache: ./cache/cord-007149-m4xsx9ev.txt txt: ./txt/cord-007149-m4xsx9ev.txt summary: 5S~63 Enhanced infection requires monocytes, peritoneal MuJ>or M(J>-like cell lines with Fc receptors, and non-cytophilic IgG antibody that exhibits virus serotype or cross-reactive specificity. Monocytes or M4> infected with CMV, influenza, Sendai or poliovirus have been shown to be suppressive Functions of mononuclear phagocytes that may be affected by virus infection Chemotaxis Attachment and phagocytosis of particles through nonspecific, Fc or complement receptors Intracallular oxidatrve response Lysosome-phegosome fusion Intracellular microbicidaJ activity Synthesis and/or secretion of txologicalry active molecules, e.g. prostaglandini, neutral proteases, interferon and complement Antigen presentation Regulation of immune responses, i e accessory and suppressor activity M$ activation procees for microbicidai and tumoncidal activity Antibody dependent cytotoxicrty (ADCC) by M$ Wound healing ONA synthesis and M$ proliferation in response to macrophage growth factor Mi) differentiation for certain lymphocyte responses. Antibody-mediated enhancement of dengue virus infection in mouse macrophage cell lines, Mkl and Mini (41802) abstract: Mononuclear phagocytes, including circulating monocytes and tissue macrophages, play a central role in resistance to viruses. This resitance can be expressed both non-specifically, and specifically in indiction, regulation and amplification of humoral and cell mediated immune responses to viruses. These lead to the extrinsic effect of macrophages on other virus-infected cells or free virus, and the intrinsic effect on viruses within macrophages. While these interactions usually appear to be protective, immunopathologic consequences as well as macrophage dysfunctions have also been noted. The outcome of any given interaction (viral elimination, peristance, latency or transformation) varies markedly with the type of macrophage. The molecular mechanisms involved in these very diverse macrophage-virus interactions are currently under study. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109651/ doi: 10.1093/oxfordjournals.bmb.a072017 id: cord-325925-010xj69x author: Mordecai, Gideon J title: Endangered wild salmon infected by newly discovered viruses date: 2019-09-03 words: 5549.0 sentences: 259.0 pages: flesch: 48.0 cache: ./cache/cord-325925-010xj69x.txt txt: ./txt/cord-325925-010xj69x.txt summary: Population surveys of >6000 wild juvenile Chinook and sockeye salmon showed divergent distributions of viruses, implying different epidemiological processes. The discovery in dead and dying farmed salmon of previously unrecognised viruses that are also widely distributed in wild salmon, emphasizes the potential role that viral disease may play in the population dynamics of wild fish stocks, and the threat that these viruses may pose to aquaculture. Together, sequencing of dead or moribund aquaculture salmon and live-sampled wild salmon, in-situ hybridization, and epidemiological surveys revealed that previously unknown viruses, some of which are associated with disease, infect wild salmon from different populations. High-throughput RT-PCR screening of >6000 wild juvenile Chinook and sockeye salmon showed dissimilar geographical distributions of infected fish, reflecting differences in epidemiological patterns of transmission and infection dynamics for each of the viruses ( Figure 2) . abstract: The collapse of iconic, keystone populations of sockeye (Oncorhynchus nerka) and Chinook (Oncorhynchus tshawytscha) salmon in the Northeast Pacific is of great concern. It is thought that infectious disease may contribute to declines, but little is known about viruses endemic to Pacific salmon. Metatranscriptomic sequencing and surveillance of dead and moribund cultured Chinook salmon revealed a novel arenavirus, reovirus and nidovirus. Sequencing revealed two different arenavirus variants which each infect wild Chinook and sockeye salmon. In situ hybridisation localised arenavirus mostly to blood cells. Population surveys of >6000 wild juvenile Chinook and sockeye salmon showed divergent distributions of viruses, implying different epidemiological processes. The discovery in dead and dying farmed salmon of previously unrecognised viruses that are also widely distributed in wild salmon, emphasizes the potential role that viral disease may play in the population dynamics of wild fish stocks, and the threat that these viruses may pose to aquaculture. url: https://doi.org/10.7554/elife.47615 doi: 10.7554/elife.47615 id: cord-002921-i5jxn1vj author: Morens, David M title: Pandemic Zika: A Formidable Challenge to Medicine and Public Health date: 2017-12-15 words: 1978.0 sentences: 104.0 pages: flesch: 42.0 cache: ./cache/cord-002921-i5jxn1vj.txt txt: ./txt/cord-002921-i5jxn1vj.txt summary: Because of the pandemic''s uniqueness and the insidious ability of Zika virus to harm unborn children, the pandemic has captured the attention of infectious disease researchers and practitioners of clinical and public health medicine around the world, as well as the attention of allied colleagues working in entomology, vector control, informatics, teratology, immunology, and a host of other disciplines [3] [4] [5] . Furthermore, some studies have suggested that preexisting flavivirus immunity (eg, from prior dengue virus infection) might potentiate Zika [16] via antibody-dependent infection enhancement in some circumstances [17] , while other research has countered this view [18] . As with most flaviviruses, small-animal models of Zika virus infection and disease have been problematic, but considerable progress has nonetheless been made, including important new information bearing on teratogenicity and vaccine design strategy [20] . Evolutionary enhancement of Zika virus infectivity in Aedes aegypti mosquitoes abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5853239/ doi: 10.1093/infdis/jix383 id: cord-316063-9bg2dm8e author: Morgan, Marcus title: Why meaning-making matters: the case of the UK Government’s COVID-19 response date: 2020-10-15 words: 25744.0 sentences: 1020.0 pages: flesch: 52.0 cache: ./cache/cord-316063-9bg2dm8e.txt txt: ./txt/cord-316063-9bg2dm8e.txt summary: The paper also offers more specific contributions to cultural sociology by showing why social performance theory needs to consider the effects of casting non-human actors in social dramas, how metaphor forms a powerful tool of political action through simplifying and shaping complex realities, and how casting can shift responsibility and redefine the meaning of emotionally charged events such as human death. On 28th February, the first death of a British national occurred on the quarantined Diamond Princess cruise ship, and the Sunday Times reported that around the same time Dominic Cummings (Johnson''s Chief Advisor, and former director of the successful Vote Leave campaign) had ''outlined the government''s strategy'' for the UK''s national response to the virus ''at a private engagement'', quoting those present as claiming that it was ''herd immunity, protect the economy, and if that means some pensioners die, too bad'' (Shipman and Wheeler 2020) . abstract: Through analysis of the UK government’s management of the COVID-19 outbreak, this paper offers an empirical demonstration of the principle of culture’s relative autonomy. It does so by showing how the outcome of meaning-making struggles had impacts on political legitimacy, public behaviour, and control over the spread of the virus. Ultimately, these impacts contributed to the avoidable deaths of tens of thousands of UK citizens. Dividing the crisis into phases within a secular ritual passage or ‘social drama’, it shows how each phase was defined by struggles between the government and other actors to code the unfolding events in an appropriate moral way, to cast actors in their proper roles, and to plot them together in a storied fashion under a suitable narrative genre. Taken together, these processes constituted a conflictual effort to define the meaning of what was occurring. The paper also offers more specific contributions to cultural sociology by showing why social performance theory needs to consider the effects of casting non-human actors in social dramas, how metaphor forms a powerful tool of political action through simplifying and shaping complex realities, and how casting can shift responsibility and redefine the meaning of emotionally charged events such as human death. url: https://www.ncbi.nlm.nih.gov/pubmed/33078075/ doi: 10.1057/s41290-020-00121-y id: cord-295873-kykyubdq author: Morikawa, Saeko title: Seasonal variations of respiratory viruses and etiology of human rhinovirus infection in children date: 2015-10-22 words: 2888.0 sentences: 171.0 pages: flesch: 49.0 cache: ./cache/cord-295873-kykyubdq.txt txt: ./txt/cord-295873-kykyubdq.txt summary: authors: Morikawa, Saeko; Kohdera, Urara; Hosaka, Taisuke; Ishii, Kousuke; Akagawa, Shohei; Hiroi, Satoshi; Kase, Tetsuo STUDY DESIGN: Nasal aspirate samples were obtained from outpatients and inpatients of a children''s hospital and these samples were subjected to real-time PCR to detect 16 respiratory viruses. Seasonal variations of the 16 viruses and the clinical outcomes such as wheezing, the need for oxygenation and prolonged hospitalization of patients with single viral infections and multiple infections were determined for the 5 most often detected viruses. PCR makes it possible to detect uncultivable viruses such as human bocavirus and rhinovirus C and discover concurrent viral infections. Though there was no significant difference in the number of hospitalization days of patients with single infections by rhinoviruses or other respiratory viruses, our data suggested the importance of rhinoviruses as a potential cause of pediatric pneumonia. abstract: BACKGROUND: Using the polymerase chain reaction (PCR) method it is possible to detect uncultivable viruses and discover multiple viral infections. However, the clinical importance of these findings in relation to symptoms is not known. OBJECTIVES: The seasonal fluctuations of respiratory viruses and the clinical outcomes of single infections and dual infections were investigated. STUDY DESIGN: Nasal aspirate samples were obtained from outpatients and inpatients of a children’s hospital and these samples were subjected to real-time PCR to detect 16 respiratory viruses. Seasonal variations of the 16 viruses and the clinical outcomes such as wheezing, the need for oxygenation and prolonged hospitalization of patients with single viral infections and multiple infections were determined for the 5 most often detected viruses. RESULTS: Among 512 specimens analyzed, one or more viruses were detected in 424 (83%) specimens. Two or more viruses were detected in 160 samples (31% of all samples). The epidemic peaks of the viruses did not coincide with each other. Rhinoviruses were the most frequently detected viruses and their coinfection rates were also higher. However, the disease severity in the lower respiratory tract did not differ in most respiratory viral infections regardless of whether there was single infection or dual infection with a rhinovirus and other respiratory virus. CONCLUSIONS: Seasonal distribution was seen for each virus. There were no significant differences in clinical symptoms in the children studied. Because the infection of rhinoviruses is the common occurrence in children, it is hypothesized that the factors related to disease severity are mainly the underlying conditions of the children. url: https://www.ncbi.nlm.nih.gov/pubmed/26521224/ doi: 10.1016/j.jcv.2015.10.001 id: cord-017158-w2tlq6ho author: Moriones, Enrique title: Recombination in the TYLCV Complex: a Mechanism to Increase Genetic Diversity. Implications for Plant Resistance Development date: 2007 words: 6282.0 sentences: 290.0 pages: flesch: 39.0 cache: ./cache/cord-017158-w2tlq6ho.txt txt: ./txt/cord-017158-w2tlq6ho.txt summary: The potential of begomoviruses to generate genetic diversity through recombination can be relevant for their ecological fitness, because greater sequence heterogeneity provides a reservoir of virus variants in the population that enables rapid adaptation to changing environmental conditions. Thus, begomoviruses like those in the Tomato yellow leaf curl virus (TYLCV) complex exploit gene flow provided by recombination as a mechanism to increase their evolutionary potential and local adaptation. Also, when region I was analyzed, phylogenetic analyses revealed that all TYLCV isolates grouped in a single clade related to Tomato yellow leaf curl Sardinia virus (TYLCSV), another species of the TYLCV complex causing the TYLCD. Tomato yellow leaf curl Sardinia virus (TYLCSV) is another monopartite begomovirus species of the TYLCV complex that comprises isolates infecting tomato in the Mediterranean Basin, both in southern Europe and northern Africa (Noris et al., 1994; . abstract: Mutation, reassortment, and recombination are the major sources of genetic variation of plant viruses (García-Arenal et al., 2001; Worobey & Holmes, 1999). During mixed infections, viruses can exchange genetic material through recombination or reassortment of segments (when the parental genomes are fragmented) if present in the same cell context of the host plant. Hybrid progeny viruses might then arise, some of them with novel pathogenic characteristics and well adapted in the population that can cause new emerging diseases. Genetic exchange provides organisms with a tool to combine sequences from different origins which might help them to quickly evolve (Crameri et al., 1998). In many DNA and RNA viruses, genetic exchange is achieved through recombination (Froissart et al., 2005; Martin et al., 2005). As increasing numbers of viral sequences become available, recombinant viruses are recognized to be frequent in nature and clear evidence is found for recombination to play a key role in virus evolution (Awadalla, 2003; Chenault & Melcher, 1994; Moonan et al., 2000; Padidam et al., 1999; Revers et al., 1996; García-Arenal et al., 2001; Moreno et al., 2004). Understanding the role of recombination in generating and eliminating variation in viral sequences is thus essential to understand virus evolution and adaptation to changing environments Knowledge about the existence and frequency of recombination in a virus population might help understanding the extent at which genes are exchanged and new virus variants arise. This information is essential, for example, to predict durability of genetic resistance because new recombinant variants might be formed with increased fitness in host-resistant genotypes. Determination of the extent and rate at which genetic rearrangement through recombination does occur in natural populations is also crucial if we use genome and genetic-mapping information to locate genes responsible of important phenotypes such as genes associated with virulence, transmission, or breakdown of resistance. Therefore, better estimates of the rate of recombination will facilitate the development of more robust strategies for virus control (Awadalla, 2003). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121651/ doi: 10.1007/978-1-4020-4769-5_7 id: cord-021069-v9f9874x author: Morrison, Lynda A. title: Viral pathogenesis and central nervous system infection date: 2004-11-23 words: 3816.0 sentences: 201.0 pages: flesch: 37.0 cache: ./cache/cord-021069-v9f9874x.txt txt: ./txt/cord-021069-v9f9874x.txt summary: Stages in viral pathogenesis defined as (1) virus entry, (2) spread, (3) tropism, (4) virulence and injury to the host, and (5) the outcome of infection are discussed for viral infections in general and those aspects unique to infections of the central nervous system . Stages in viral pathogenesis defined as (1) virus entry, (2) spread, (3) tropism, (4) virulence and injury to the host, and (5) the outcome of infection are discussed for viral infections in general and those aspects unique to infections of the central nervous system . Genetic determinants of disease susceptibility have been found for infection of mice with strains of most neurotropic viruses, in at least one case of coronavirus reflecting lack of a gene encoding a virus receptor protein . abstract: Both host defense and viral genetic factors influence the development of viral infection and disease. Due to the presence of the blood-brain barrier, infection of the central nervous system creates additional complexities in interactions between a virus and its host. Stages in viral pathogenesis defined as (1) virus entry, (2) spread, (3) tropism, (4) virulence and injury to the host, and (5) the outcome of infection are discussed for viral infections in general and those aspects unique to infections of the central nervous system. Information about neuronal physiology and function has also been revealed through studying virus infection. An increased understanding of viral pathogenetic mechanisms and host response to infection raises interesting possibilities for vaccine development and for basic studies in neurology and neurobiology. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148964/ doi: 10.1016/1044-5765(91)90002-6 id: cord-341298-mqpovrms author: Morse, S.A. title: Viruses and Bioterrorism date: 2016-10-31 words: 4787.0 sentences: 224.0 pages: flesch: 44.0 cache: ./cache/cord-341298-mqpovrms.txt txt: ./txt/cord-341298-mqpovrms.txt summary: Requirements for an ideal biological warfare agent may include: availability; ease of production; stability after production; a susceptible population (human or animal); absence of specific treatment; ability to incapacitate or kill the host; appropriate particle size in aerosols so that the virus can be carried long distances by prevailing winds and inhaled deeply into the lungs of unsuspecting victims; ability to be disseminated via food or water; and, the availability of a vaccine to protect certain groups. Classification of viral agents that are considered to be of concern for bioterrorism and biowarfare and those that have been weaponized or studied for offensive or defensive purposes as part of former or current national biological weapons programs incapacitating (eg, VEE) or lethal infections (EEE case fatality rates range from 50 to 75%) (Sidwell and Smee, 2003) . An Australian research group (Jackson et al., 2001) was investigating virally vectored immunocontraceptive vaccines based on ectromelia virus, the causative agent of the disease termed mousepox. abstract: The target for a terrorist attack with a viral agent can range from humans to animals and plants. However, the use of a viral agent may pose a challenge due to problems associated with acquisition, cultivation, and dissemination. Agricultural targets are of concern as they would require relatively little specialized expertise and technology and can have large economic consequences. Viral agents are prone to genetic variation and mutation, and can be manipulated or created in the laboratory. Unlike bacterial diseases, many of which are treatable with antimicrobials, there are fewer medical countermeasures to employ when dealing with viral infections. url: https://www.sciencedirect.com/science/article/pii/B9780128096338110076 doi: 10.1016/b978-0-12-809633-8.11007-6 id: cord-308686-tbwecf7o author: Mortamet, G. title: Étude prospective de l’écologie virale hivernale dans un service de réanimation pédiatrique date: 2015-04-30 words: 2233.0 sentences: 193.0 pages: flesch: 58.0 cache: ./cache/cord-308686-tbwecf7o.txt txt: ./txt/cord-308686-tbwecf7o.txt summary: Résumé Le but de cette étude prospective était d''évaluer l''épidémiologie des virus respiratoires chez les enfants hospitalisés dans une unité de réanimation et de soins continus pédiatriques pendant 3 mois d''hiver, en 2012–2013. Ont été inclus tous les enfants admis en réanimation pédiatrique du centre hospitalier universitaire (CHU) de Caen et ayant bénéficié d''une recherche d''infection par un virus respiratoire à partir d''un prélèvement nasal analysé par amplification génique (PCR) multiplex. Cette étude révèle cependant un taux élevé d''infections respiratoires causées par des virus chez les enfants qui ne présentent pas de symptômes respiratoires à leur admission en unité de réanimation et soins continus. Le but de cette étude prospective était d''évaluer l''épidémiologie des virus respiratoires chez les enfants hospitalisés dans une unité de réanimation et de soins continus pédiatrique pendant 3 mois d''hiver. abstract: Résumé Le but de cette étude prospective était d’évaluer l’épidémiologie des virus respiratoires chez les enfants hospitalisés dans une unité de réanimation et de soins continus pédiatriques pendant 3 mois d’hiver, en 2012–2013. Ont été inclus tous les enfants admis en réanimation pédiatrique du centre hospitalier universitaire (CHU) de Caen et ayant bénéficié d’une recherche d’infection par un virus respiratoire à partir d’un prélèvement nasal analysé par amplification génique (PCR) multiplex. Sur 105 enfants admis, 84 répondaient aux critères d’inclusion. Trente-sept enfants présentaient un ou plusieurs symptômes respiratoires à l’admission. Cinquante-quatre échantillons étaient positifs (64,3 %) avec 70 virus détectés. Le virus dont la prévalence était la plus élevée était le virus respiratoire syncytial (VRS) (n =28 ; 40,0 %), suivi par le rhinovirus (n =24 ; 34,3 %). Parmi les enfants sans symptômes respiratoires, 42,6 % étaient infectés par un ou plusieurs virus. Aucune différence de durée d’hospitalisation, de durée de ventilation mécanique n’a été mise en évidence en fonction du virus détecté. La principale limite de cette étude est l’analyse par PCR, beaucoup plus sensible que d’autres méthodes de détection, notamment chez des sujets asymptomatiques sur le plan respiratoire. Cette étude révèle cependant un taux élevé d’infections respiratoires causées par des virus chez les enfants qui ne présentent pas de symptômes respiratoires à leur admission en unité de réanimation et soins continus. Elle suggère un intérêt du dépistage de ces infections virales à l’admission des enfants et un bénéfice à l’extension des mesures d’isolement pour tous les enfants en réanimation pédiatrique. Summary Introduction Viral respiratory infections are common in children, most of which are due to a virus. They can lead to serious infections, and these children may require treatment in a pediatric intensive care unit (PICU). This prospective study evaluated the epidemiology of respiratory viruses and associated illnesses among children hospitalized in a PICU during the three winter months of 2012–2013. Methods All the children admitted to the PICU, University Hospital of Caen, France, were included. Nasal swabs were collected and specimens were tested using a single real-time PCR (polymerase chain reaction). Results Of the 105 patients admitted to the PICU during the study period, 84 fulfilled the inclusion criteria. The “respiratory group” included 37 patients with respiratory symptoms at admission while the “nonrespiratory group” included 47 patients with no respiratory symptoms. The 84 nasal swabs collected included 54 that were considered positive (64.3%) and 70 viruses were detected. The most commonly detected virus was RSV (n =28; 40.0% positive samples), followed by HRV (n =24; 34.3%). Viruses were more frequently detected in the respiratory (86.5%) than in the nonrespiratory (42.6%) group (P <0.001). Statistical analysis by subgroups revealed that RSV infections were significantly more frequent in the respiratory group (54.1%) than in the nonrespiratory group (6.4%) (P <0.001). There was no difference for HRV (32.4% and 27.7%) or for the other viruses. No difference in duration of hospitalization or duration of mechanical ventilation was demonstrated depending on the virus detected. Discussion The use of the very sensitive multiplex PCR technique increased virus detection rates in both symptomatic and asymptomatic subjects. Conclusion We have confirmed the frequency of RSV infections in a PICU and found that many patients without respiratory symptoms have respiratory infections caused by viruses. The impact of these infections on patient outcome should now be analyzed in order to demonstrate the role played by respiratory viruses. url: https://api.elsevier.com/content/article/pii/S0929693X14005181 doi: 10.1016/j.arcped.2014.10.025 id: cord-260705-huyyw5z6 author: Moshe, Adi title: Virus-Induced Aggregates in Infected Cells date: 2012-10-17 words: 5063.0 sentences: 265.0 pages: flesch: 39.0 cache: ./cache/cord-260705-huyyw5z6.txt txt: ./txt/cord-260705-huyyw5z6.txt summary: During infection, many viruses induce cellular remodeling, resulting in the formation of insoluble aggregates/inclusions, usually containing viral structural proteins. The aggregates are utilized by viruses to house a large complex of proteins of both viral and host origin to promote virus replication, translation, intraand intercellular transportation. In plant cells, both RNA and DNA viruses are associated with large inclusions detected in the cytoplasm and nucleus, however, their role in virus propagation or oppositely in virus restraint is less investigated than in infected mammalian cells. In general, mammalian and plant viruses make use of aggregates as scaffolds for anchoring the replication complex, increasing the local concentration of viral and host components required for replication and assembly, and shielding the process of replication from host defense. abstract: During infection, many viruses induce cellular remodeling, resulting in the formation of insoluble aggregates/inclusions, usually containing viral structural proteins. Identification of aggregates has become a useful diagnostic tool for certain viral infections. There is wide variety of viral aggregates, which differ by their location, size, content and putative function. The role of aggregation in the context of a specific virus is often poorly understood, especially in the case of plant viruses. The aggregates are utilized by viruses to house a large complex of proteins of both viral and host origin to promote virus replication, translation, intra- and intercellular transportation. Aggregated structures may protect viral functional complexes from the cellular degradation machinery. Alternatively, the activation of host defense mechanisms may involve sequestration of virus components in aggregates, followed by their neutralization as toxic for the host cell. The diversity of virus-induced aggregates in mammalian and plant cells is the subject of this review. url: https://www.ncbi.nlm.nih.gov/pubmed/23202461/ doi: 10.3390/v4102218 id: cord-263619-p17oomzn author: Moss, William J. title: Measles date: 2009-01-30 words: 9541.0 sentences: 457.0 pages: flesch: 41.0 cache: ./cache/cord-263619-p17oomzn.txt txt: ./txt/cord-263619-p17oomzn.txt summary: Although providing passive immunity to young infants, maternally acquired antibodies can interfere with the immune responses to the attenuated measles vaccine by inhibiting replication of vaccine virus. Women with vaccine-induced immunity tend to have lower antimeasles virus antibody titers than women with naturally acquired immunity, and their children may be susceptible to measles at an earlier age. The cumulative distribution can reach 50% by 1 year of age, with a significant proportion of children acquiring measles virus infection before 9 months, the age of routine vaccination. Infants and younger children, although susceptible if not protected by immunization, are not exposed to measles virus at a rate sufficient to cause a large disease burden in this age group. The only documented case of disease induced by vaccine virus in an HIV-infected person was in a 20-year-old man who died 15 months after receiving his second dose of measles vaccine ( Angel et al., 1998 ) . abstract: Abstract Measles is a highly contagious disease characterized by a prodromal illness of fever, cough, coryza, and conjunctivitis followed by the appearance of a generalized maculopapular rash. Measles virus is a nonsegmented, single-stranded, negative-sense RNA virus and a member of the Morbillivirus genus in the family of Paramyxoviridae. Although RNA viruses have high mutation rates, measles virus is an antigenically monotypic virus and the surface proteins responsible for inducing protective immunity have retained their antigenic structure. The public health significance is that measles vaccines developed decades ago from a single measles virus strain remain protective worldwide. Prior to the development and widespread use of measles vaccine, 30 million cases of measles were estimated to occur each year, resulting in more than 1 million deaths. Several live, attenuated measles vaccines are available, either as single-antigen vaccines or in combination with rubella and mumps vaccines (MR and MMR vaccines). Most of the currently used measles vaccines were derived from the Edmonston strain of measles virus that was isolated by Enders and Peebles in 1954. Measles vaccines are recommended for all susceptible children and adults for whom the vaccine is not contraindicated. Despite progress in reducing measles mortality, measles remains a major cause of vaccine-preventable death and an important cause of morbidity and mortality in children, particularly sub-Saharan Africa and in Asia. The ideal measles vaccine would be inexpensive, safe, heat-stable, immunogenic in neonates or very young infants, and administered as a single dose without needle or syringe. A number of vaccine candidates with some of these characteristics are undergoing preclinical studies, including DNA vaccines and various viral and bacterial vectored vaccines. The high infectivity of measles virus is a characteristic suitable to a biothreat agent. However, increasingly high levels of measles vaccination coverage throughout the world as part of accelerated measles control efforts would protect many from the deliberate use of measles virus as a biothreat agent. Genetic engineering of a measles virus strain that was not neutralized by antibodies induced by the current attenuated measles vaccines would likely have reduced infectivity, as suggested by the fact that wild-type measles viruses have not mutated to alter their neutralizing epitopes. Measles virus meets many of the biological criteria for disease eradication. Measles virus has no nonhuman reservoir, can be accurately diagnosed, and measles vaccination is a highly effective intervention. Where measles virus differs from smallpox and polio viruses is that it is more highly infectious, necessitating higher levels of population immunity to interrupt transmission. It remains unclear whether the threat from bioterrorism precludes stopping measles vaccination after eradication, but provision of a second opportunity for measles vaccination likely could be stopped following eradication. url: https://www.sciencedirect.com/science/article/pii/B9780123694089000305 doi: 10.1016/b978-0-12-369408-9.00030-5 id: cord-004751-4vl0cvyq author: Mostow, S. R. title: The behaviour in vitro of attenuated recombinant influenza viruses date: 1973 words: 2245.0 sentences: 132.0 pages: flesch: 60.0 cache: ./cache/cord-004751-4vl0cvyq.txt txt: ./txt/cord-004751-4vl0cvyq.txt summary: Influenza strains produced by recombination and tested as possible live vaccine candidates were studied in organ cultures of trachea. Two strains which proved to be too virulent in human volunteers regularly caused damage to the ciliated epithelium and viruses grew to high titre. Attenuated influenza viruses have been produced recently by genetic recombination of avirulent laboratory-adapted strains and virulent parents (BEARE and HALL, 1971; McCAHo~ and SCHILD, 1972) . This method, which is the most rapid means of producing attenuated influenza strains to date, results in a spectrum of both attenuated and virulent clones as judged by their effects in human volunteers. The use of L-15 medium and rolling the screw-topped tubes prolonged the survival of the ciliated epithelium beyond that obtained using other standard media, and, in the conditions finally used, the human embryo trachea regularly survived for periods of 30--50 and occasionally 90 days. The recombinant viruses did not cause ciliary damage, but at 5 days the growth in ferret epithelium was similar to that in human tissue. abstract: Influenza strains produced by recombination and tested as possible live vaccine candidates were studied in organ cultures of trachea. Two strains which proved to be too virulent in human volunteers regularly caused damage to the ciliated epithelium and viruses grew to high titre. Two strains which proved to be attenuated for volunteers did not cause appreciable damage, although they replicated to low titre in the epithelium. Similar results were obtained with influenza A virus attenuated by passage in the presence of horse sera. The method may be of value for detecting virulent live influenza vaccine candidates without risking severe illness in volunteers. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086870/ doi: 10.1007/bf01556156 id: cord-018089-m94q75xn author: Mubareka, Samira title: Influenza Virus: The Biology of a Changing Virus date: 2010-06-18 words: 7034.0 sentences: 392.0 pages: flesch: 39.0 cache: ./cache/cord-018089-m94q75xn.txt txt: ./txt/cord-018089-m94q75xn.txt summary: The genetic diversity of influenza A viruses and their capability to successfully infect an array of hosts, including avian and mammalian species, are highlighted in a discussion about host range and evolution. In contrast, avian hosts including waterfowl and domestic poultry harbor sialic acid with a2,3 linkage (SAa2,3Gal) which is distributed in the gastrointestinal tract, reflecting the fecal-oral mode of transmission of avian influenza strains in these species [23] . Specifically, changes at amino acid position 225 impart the ability of A/New York/1/18 to bind both avian and human host influenza virus receptors [26] . Since 1997, several avian influenza viruses, including H5N1, H7N2, H7N3, H7N7, H9N2, and H10N7 subtypes, have infected humans [76], though limited evidence for person to person spread exists [77, 78] . Pathology of fatal human infection associated with avian influenza A H5N1 virus abstract: Influenza viruses are members of the family Orthomyxoviridae and include influenza virus types A, B, and C. This introduction provides an overview of influenza virus classification, structure, and life cycle. We also include a brief review of the clinical manifestations of influenza and the molecular determinants for virulence. The genetic diversity of influenza A viruses and their capability to successfully infect an array of hosts, including avian and mammalian species, are highlighted in a discussion about host range and evolution. The importance of viral receptor-binding hemagglutinins and host sialic acid distribution in species-restricted binding of viruses is underscored. Finally, recent advances in our understanding of the seasonality and transmission of influenza viruses are described, and their importance for the control of the spread of these viruses is discussed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122879/ doi: 10.1007/978-3-0346-0279-2_1 id: cord-260420-4s7akmdp author: Mubareka, Samira title: Bioaerosols and Transmission, a Diverse and Growing Community of Practice date: 2019-02-21 words: 4020.0 sentences: 206.0 pages: flesch: 29.0 cache: ./cache/cord-260420-4s7akmdp.txt txt: ./txt/cord-260420-4s7akmdp.txt summary: There is a need to enhance the knowledge translation for researchers, stakeholders, and private partners to support a growing network of individuals and agencies to achieve common goals to mitigate interand intra-species pathogen transmission via bioaerosols. New developments have enabled progress in this domain, and one of the major turning points has been the recognition that cross-disciplinary collaborations across spheres of human and animal health, microbiology, biophysics, engineering, aerobiology, infection control, public health, occupational health, and industrial hygiene are essential. There is a need to enhance the knowledge translation for researchers, stakeholders, and private partners to support a growing network of individuals and agencies to achieve common goals to mitigate inter-and intra-species pathogen transmission via bioaerosols. A network approach has proven successful in other cross-disciplinary fields, including One Health and eco-health whereby wildlife, computational and evolutionary biologists, microbiologists, virologists, epidemiologists, ecologists, environmental scientists, climatologists, and human, animal, and public health practitioners are collaborating to address challenges in zoonotic diseases research and control (17, 18) . abstract: The transmission of infectious microbes via bioaerosols is of significant concern for both human and animal health. However, gaps in our understanding of respiratory pathogen transmission and methodological heterogeneity persist. New developments have enabled progress in this domain, and one of the major turning points has been the recognition that cross-disciplinary collaborations across spheres of human and animal health, microbiology, biophysics, engineering, aerobiology, infection control, public health, occupational health, and industrial hygiene are essential. Collaborative initiatives support advances in topics such as bioaerosol behavior, dispersion models, risk assessment, risk/exposure effects, and mitigation strategies in clinical, experimental, agricultural, and other field settings. There is a need to enhance the knowledge translation for researchers, stakeholders, and private partners to support a growing network of individuals and agencies to achieve common goals to mitigate inter- and intra-species pathogen transmission via bioaerosols. url: https://www.ncbi.nlm.nih.gov/pubmed/30847337/ doi: 10.3389/fpubh.2019.00023 id: cord-269324-zh1a3gwh author: Mubareka, Samira title: Human Genes and Influenza date: 2008-01-01 words: 1822.0 sentences: 93.0 pages: flesch: 36.0 cache: ./cache/cord-269324-zh1a3gwh.txt txt: ./txt/cord-269324-zh1a3gwh.txt summary: Specific genes responsible for the host immune response have been invoked as major determinants of the clinical course of HIV-associated disease and hepatitis B and C virus infections [2, 3] . Clinical and animal studies indicate that cytokine dysregulation is associated with acute respiratory distress syndrome and death among hosts infected with avian influenza virus (H5N1) [4 -6] . TLR4 has been implicated in the innate immune response to respiratory syncytial virus (RSV) infection, and polymorphisms in the TLR4 gene have been associated with severe bronchiolitis in RSV-infected infants, although the significance of the Asp299Gly polymorphism appears to be a matter of ongoing debate [9 -12] . All of these genes would be excellent candidates for an analysis to iden-tify determinants of severity of disease after influenza virus infection. Association between common Toll-like receptor 4 mutations and severe respiratory syncytial virus disease Association between mannose-binding lectin gene polymorphisms and susceptibility to severe acute respiratory syndrome coronavirus infection abstract: nan url: https://doi.org/10.1086/524067 doi: 10.1086/524067 id: cord-315918-12rbbe8c author: Mukherjee, Pulok K. title: Antiviral Evaluation of Herbal Drugs date: 2019-06-21 words: 12776.0 sentences: 660.0 pages: flesch: 49.0 cache: ./cache/cord-315918-12rbbe8c.txt txt: ./txt/cord-315918-12rbbe8c.txt summary: To test the inhibitory activity of a new antiviral agent, it is first necessary to select the host cell system(s) in which the virus replication can be measured. (d) Assay systems based on the measurement of specialized functions and viral products; a number of viruses do not produce plaques nor do they cause CPE readily, but they may be quantified by certain specialized functions based on their unique properties, for example, hemagglutination and hemadsorption tests used to study the antiviral activity against myxoviruses and ELISA, used to determine the extent of virus replication and, thus, obtain a measure of the inhibitory effect of various antiviral agents on virus replication, etc. On the other hand, the antiviral activity is determined by comparing the virus titers of infected cells, which have been cultured with a maintenance medium containing plant extracts or test substances and a maintenance medium without test material (Colegate and Molyneux, 1993) . abstract: The viral infection and resistance to the existing antiviral drugs are alarming, which is a serious public health concern. Medicinal plants are valuable resources for treatment of viral infections and can be used for the management of infections like herpes simplex virus (HSV), human immunodeficiency virus (HIV), influenza, etc. The antiviral screening of plant extracts should be highly selective, specific, and sensitive for bioactivity guided isolation of the active compounds from the plant extracts. The antiviral screening system should be validated for accuracy, reproducibility, simplicity, and cost effectiveness. This chapter highlights on various aspects for screening and evaluation of antiviral natural components including factors affecting antiviral in vivo studies, host cells, organisms, and culture media followed by different virus-specific assays for antiviral screening of natural products. url: https://api.elsevier.com/content/article/pii/B9780128133743000168 doi: 10.1016/b978-0-12-813374-3.00016-8 id: cord-335774-15fhg8o9 author: Mull, Nathaniel title: Ecology of Neglected Rodent-Borne American Orthohantaviruses date: 2020-04-26 words: 6842.0 sentences: 333.0 pages: flesch: 38.0 cache: ./cache/cord-335774-15fhg8o9.txt txt: ./txt/cord-335774-15fhg8o9.txt summary: Information regarding the presence and genetic diversity of many orthohantaviruses throughout the distributional range of their hosts is minimal and would significantly benefit from virus isolations to indicate a reservoir role. However, mammals, particularly rodents, are still the most common natural hosts of hantaviruses, encompassing viruses in the largest subfamily (Mammantavirinae) and genus (Orthohantavirus) [9] , and only rodent-borne orthohantaviruses have been linked to human disease [10] . For example, range expansion of a North American grassland rodent species, Baiomys taylori, was recently found in New Mexico, United States, likely due to an increase in grassland areas, particularly along roadsides, due to climate change and habitat disturbance [61] . In the absence of empirical data, we shed light on the diversity, transmission, and risk of spillover for neglected American orthohantaviruses and viral genotypes using the ecology of their hosts and information on ANDV and SNV. Since multiple rodent species are commonly found RT-PCR positive for particular American orthohantavirus strains (Table A1) , virus-host relationships are unclear. abstract: The number of documented American orthohantaviruses has increased significantly over recent decades, but most fundamental research has remained focused on just two of them: Andes virus (ANDV) and Sin Nombre virus (SNV). The majority of American orthohantaviruses are known to cause disease in humans, and most of these pathogenic strains were not described prior to human cases, indicating the importance of understanding all members of the virus clade. In this review, we summarize information on the ecology of under-studied rodent-borne American orthohantaviruses to form general conclusions and highlight important gaps in knowledge. Information regarding the presence and genetic diversity of many orthohantaviruses throughout the distributional range of their hosts is minimal and would significantly benefit from virus isolations to indicate a reservoir role. Additionally, few studies have investigated the mechanisms underlying transmission routes and factors affecting the environmental persistence of orthohantaviruses, limiting our understanding of factors driving prevalence fluctuations. As landscapes continue to change, host ranges and human exposure to orthohantaviruses likely will as well. Research on the ecology of neglected orthohantaviruses is necessary for understanding both current and future threats to human health. url: https://www.ncbi.nlm.nih.gov/pubmed/32357540/ doi: 10.3390/pathogens9050325 id: cord-314325-nquov2i0 author: Murphy, F.A. title: Epidemiology of Human and Animal Viral Diseases date: 2008-07-30 words: 5495.0 sentences: 245.0 pages: flesch: 38.0 cache: ./cache/cord-314325-nquov2i0.txt txt: ./txt/cord-314325-nquov2i0.txt summary: Viral disease epidemiology has come to have a major role in clarifying the etiologic role of particular viruses and viral variants as the cause of specific diseases, in improving our understanding of the overall nature of specific viral diseases, and in determining factors affecting host susceptibility and immunity, in unraveling modes of transmission, in clarifying the interaction of viruses with environmental determinants of disease, in determining the safety, efficacy, and utility of vaccines and antiviral drugs, and especially in alerting and directing disease prevention and control actions. Epidemiology is also effective in (1) clarifying the role of particular viruses and viral variants as the cause of disease, (2) clarifying the interaction of viruses with environmental determinants of disease, (3) determining factors affecting host susceptibility, (4) unraveling modes of transmission, and (5) field testing of vaccines and antiviral drugs. abstract: Viral disease epidemiology is the study of the determinants, dynamics, and distribution of viral diseases in populations. The risk of infection or disease in a population is determined by characteristics of the virus, the host, and the host population, as well as behavioral, environmental, and ecological factors that affect virus transmission from one host to another. Viral disease epidemiology has come to have a major role in clarifying the etiologic role of particular viruses and viral variants as the cause of specific diseases, in improving our understanding of the overall nature of specific viral diseases, and in determining factors affecting host susceptibility and immunity, in unraveling modes of transmission, in clarifying the interaction of viruses with environmental determinants of disease, in determining the safety, efficacy, and utility of vaccines and antiviral drugs, and especially in alerting and directing disease prevention and control actions. Information on incidence, prevalence, and morbidity and mortality rates contributes directly to the establishment of priorities for prevention and control programs, whether this involves vaccine or drug development and delivery, environmental and hygienic improvements, enhancement of nutritional status, personal or community behavior, agricultural and food processing enhancements, reservoir host and vector control, and international cooperation and communication. url: https://api.elsevier.com/content/article/pii/B9780123744104003903 doi: 10.1016/b978-012374410-4.00390-3 id: cord-331217-uup16bhm author: Murphy, Frederick A. title: Adventitious Agents and Smallpox Vaccine in Strategic National Stockpile date: 2005-07-17 words: 2282.0 sentences: 105.0 pages: flesch: 42.0 cache: ./cache/cord-331217-uup16bhm.txt txt: ./txt/cord-331217-uup16bhm.txt summary: In keeping with current standards, we urge that old smallpox vaccines that were made in animal skin and are still a key part of our strategic national stockpile be tested for adventitious infectious agents. However, if these old vaccines are to be considered valid parts of our national stockpile we should expect not only continuing testing of potency and sterility but also testing for adventitious agents with methods that reflect the standards of today. We were unable to find a comprehensive list of possible adventitious agents when ovine materials are used, as is the case for the Lister strain smallpox vaccine produced in Europe and old vaccine stocks held by some European countries for biologic defense. Concerns about the possible presence of adventitious agents in old smallpox vaccine stocks are amplified further by current concerns about prions and the zoonotic potential of prion diseases. abstract: In keeping with current standards, we urge that old smallpox vaccines that were made in animal skin and are still a key part of our strategic national stockpile be tested for adventitious infectious agents. The advisory especially applies to viruses that have the potential for zoonotic transmission to human vaccine recipients. url: https://www.ncbi.nlm.nih.gov/pubmed/16022785/ doi: 10.3201/eid1107.050277 id: cord-329078-gnnis7pl author: Musella, Simona title: Identification of an indol-based derivative as potent and selective varicella zoster virus (VZV) inhibitor date: 2016-11-29 words: 3935.0 sentences: 215.0 pages: flesch: 48.0 cache: ./cache/cord-329078-gnnis7pl.txt txt: ./txt/cord-329078-gnnis7pl.txt summary: title: Identification of an indol-based derivative as potent and selective varicella zoster virus (VZV) inhibitor Tryptamine derivative 17a was found to have a selective inhibitory activity against human varicella zoster virus (VZV) replication in vitro, being inactive against a variety of other DNA and RNA viruses. Arbidol [34] and delavirdine [35] , are examples of marketed indole-containing antiviral drugs, whereas Panobinostat (LBH589) [36] , being a HDAC (histone deacetylase) inhibitor, is actively undergoing clinical evaluation against human immunodeficiency virus (HIV) type 1 (See Fig. 1 ). The antiviral activity was expressed as EC50, being the compound concentration required to reduce virus-plaque formation (VZV) by 50%. The mixture was stirred for 3 h at room temperature, then was washed with water (3 Â 50 mL), dried over anhydrous Na2SO4, filtered, concentrated and purified by column chromatography using DCM/MeOH (9:1 v/v) as mobile phase. 4-Benzyloxy-gamma-sultone derivatives: discovery of a novel family of non-nucleoside inhibitors of human cytomegalovirus and varicella zoster virus abstract: We report the synthesis and antiviral activity of a new family of non-nucleoside antivirals, derived from the indole nucleus. Modifications of this template through Mannich and Friedel-Crafts reactions, coupled with nucleophilic displacement and reductive aminations led to 23 final derivatives, which were pharmacologically tested. Tryptamine derivative 17a was found to have a selective inhibitory activity against human varicella zoster virus (VZV) replication in vitro, being inactive against a variety of other DNA and RNA viruses. A structure-activity relationship (SAR) study showed that the presence of a biphenyl ethyl moiety and the acetylation at the amino group of tryptamine are a prerequisite for anti-VZV activity. The novel compound shows the same activity against thymidine kinase (TK)-competent (TK(+)) and TK-deficient (TK(−)) VZV strains, pointing to a novel mechanism of antiviral action. url: https://api.elsevier.com/content/article/pii/S0223523416307401 doi: 10.1016/j.ejmech.2016.09.014 id: cord-004719-3stcx0dd author: Mushegian, A. R. title: Cell-to-cell movement of plant viruses: Insights from amino acid sequence comparisons of movement proteins and from analogies with cellular transport systems date: 1993 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Cell-to-cell movement is a crucial step in plant virus infection. In many viruses, the movement function is secured by specific virus-encoded proteins. Amino acid sequence comparisons of these proteins revealed a vast superfamily containing a conserved sequence motif that may comprise a hydrophobic interaction domain. This superfamily combines proteins of viruses belonging to all principal groups of positive-strand RNA viruses, as well as single-stranded DNA containing geminiviruses, double-stranded DNA-containing pararetroviruses (caulimoviruses and badnaviruses), and tospoviruses that have negative-strand RNA genomes with two ambisense segments. In several groups of positive-strand RNA viruses, the movement function is provided by the proteins encoded by the so-called triple gene block including two putative small membrane-associated proteins and a putative RNA helicase. A distinct type of movement proteins with very high content of proline is found in tymoviruses. It is concluded that classification of movement proteins based on comparison of their amino acid sequences does not correlate with the type of genome nucleic acid or with grouping of viruses based on phylogenetic analysis of replicative proteins or with the virus host range. Recombination between unrelated or distantly related viruses could have played a major role in the evolution of the movement function. Limited sequence similarities were observed between i) movement proteins of dianthoviruses and the MIP family of cellular integral membrane proteins, and ii) between movement proteins of bromoviruses and cucumoviruses and M1 protein of influenza viruses which is involved in nuclear export of viral ribonucleoproteins. It is hypothesized that all movement proteins of plant viruses may mediate hydrophobic interactions between viral and cellular macromolecules. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086723/ doi: 10.1007/bf01313766 id: cord-288734-xinkqs6u author: Muñoz-Fontela, César title: Ebola Virus Disease in Humans: Pathophysiology and Immunity date: 2017-03-30 words: 9957.0 sentences: 451.0 pages: flesch: 44.0 cache: ./cache/cord-288734-xinkqs6u.txt txt: ./txt/cord-288734-xinkqs6u.txt summary: Discovered in 1976 during the first documented outbreak of Ebola virus disease (EVD) in the town of Yambuku in northern Zaire (today Democratic Republic of the Congo), EBOV has since caused sporadic human disease outbreaks of varying magnitude in Equatorial African countries (Sanchez et al. Antigen-presenting cells are a putative initial target of EBOV infection and previous research in animal models of disease has indicated that dendritic cells (DCs) and macrophages are early and preferred targets of EBOV and support virus replication (Geisbert et al. Clinical presentation, biochemical, and haematological parameters and their association with outcome in patients with Ebola virus disease: an observational cohort study Sequence-based human leukocyte antigen-B typing of patients infected with Ebola virus in Uganda in 2000: identification of alleles associated with fatal and nonfatal disease outcomes abstract: Viruses of the Ebolavirus genus cause sporadic epidemics of severe and systemic febrile disease that are fueled by human-to-human transmission. Despite the notoriety of ebolaviruses, particularly Ebola virus (EBOV), as prominent viral hemorrhagic fever agents, and the international concern regarding Ebola virus disease (EVD) outbreaks, very little is known about the pathophysiology of EVD in humans and, in particular, about the human immune correlates of survival and immune memory. This lack of basic knowledge about physiological characteristics of EVD is probably attributable to the dearth of clinical and laboratory data gathered from past outbreaks. The unprecedented magnitude of the EVD epidemic that occurred in West Africa from 2013 to 2016 has allowed, for the first time, evaluation of clinical, epidemiological, and immunological parameters in a significant number of patients using state-of-the-art laboratory equipment. This review will summarize the data from the literature regarding human pathophysiologic and immunologic responses to filoviral infection. url: https://doi.org/10.1007/82_2017_11 doi: 10.1007/82_2017_11 id: cord-017008-c7skxte0 author: Méthot, Pierre-Olivier title: Emerging Disease and the Evolution of Virulence: The Case of the 1918–1919 Influenza Pandemic date: 2014-08-22 words: 17589.0 sentences: 788.0 pages: flesch: 49.0 cache: ./cache/cord-017008-c7skxte0.txt txt: ./txt/cord-017008-c7skxte0.txt summary: Next, we describe the biology of infl uenza viruses with a focus on the 1918-19 pandemics and we move on to the ecological-evolutionary explanations of its exceptional virulence, paying attention to the trade-off model, before turning to molecular 4 On the history, epistemology, and social aspects of the concept of emerging disease see Grmek ( 1993 ); Farmer ( 1996 ) , King ( 2004 ) ; and Weir and Mykhalovski ( 2010 ) . 6 Whereas the ecological (or exogenous) style focuses on processes (e.g. selective pressures, population density, within and between host competition, and so on) acting on the hosts and the pathogen, the molecular (or endogenous) style traces the evolutionary pathway, or patterns, of the infl uenza virus from animal(s) to man, and, by constructing molecular phylogenies, identifi es particular genes for pathogenesis and mutation sites within lineages. abstract: “Why do parasites harm their host?” is a recurrent question in evolutionary biology and ecology, and has several implications for the biomedical sciences, particularly public health and epidemiology. Contrasting the meaning(s) of the concept of “virulence” in molecular pathology and evolutionary ecology, we review different explanations proposed as to why, and under what conditions, parasites cause harm to their host: whereas the former uses molecular techniques and concepts to explain changes and the nature of virulence seen as a categorical trait, the latter conceptualizes virulence as a phenotypic quantitative trait (usually related to a reduction in the host’s fitness). After describing the biology of emerging influenza viruses we illustrate how the ecological and the molecular approaches provide distinct (but incomplete) explanations of the 1918–19 influenza pandemic. We suggest that an evolutionary approach is necessary to understand the dynamics of disease transmission but that a broader understanding of virulence will ultimately benefit from articulating and integrating the ecological dynamics with cellular mechanisms of virulence. Both ecological and functional perspectives on host-pathogens’ interactions are required to answer the opening question but also to devise appropriate health-care measures in order to prevent (and predict?) future influenza pandemics and other emerging threats. Finally, the difficult co-existence of distinct explanatory frameworks reflects the fact that scientists can work on a same problem using various methodologies but it also highlights the enduring tension between two scientific styles of practice in biomedicine. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121464/ doi: 10.1007/978-94-017-8887-8_5 id: cord-263165-bv4dh9eu author: Möstl, Karin title: Coronaviridae, pathogenetic and clinical aspects: An update date: 1990-12-31 words: 4906.0 sentences: 331.0 pages: flesch: 45.0 cache: ./cache/cord-263165-bv4dh9eu.txt txt: ./txt/cord-263165-bv4dh9eu.txt summary: The recent detection of previously unknown coronaviruses or mutants, like the "Porcine Epidemic Diarrhea"-virus (PEDV) and the TGE-like "Porcine Respiratory Coronavirus" (PRCV) on one hand and new knowledge about pathogenetic mechanisms, for example in FIPV-infections, on the other hand are the basis for this review article. For diagnosis TGEV antigen can be detected by immunofluorescence in the small intestine of piglets at an early stage of disease, by virus isolation in tissue culture or by ELISA. As it causes a respiratory infection and does not replicate in the enteric tract, it was named "Respiratory Variant" of TGEV [16] and recently "Porcine respiratory coronavirus". Pedersen [51] assumed that not only the properties of the infecting virus strain were responsible for the outcome of the disease, but that also the immunologic situation of the host and the type and degree of developing immunity may be of great importance. Natural infection with the Porcine Respiratory Coronavirus induces protective lactogenic immunity against Transmissible Gastroenteritis abstract: Abstract A review is given about pathogenetic and clinical aspects of the well-known as well as of recently detected members of the family Coronaviridae. Special attention is paid to coronavirus infections of domestic cattle and pets, whereas avian, murine, rat and human coronaviruses are summarized briefly. url: https://www.ncbi.nlm.nih.gov/pubmed/1963836/ doi: 10.1016/0147-9571(90)90085-8 id: cord-323710-cmbg0ty8 author: Mühlebach, Michael D. title: Development of Recombinant Measles Virus-Based Vaccines date: 2016-11-26 words: 4306.0 sentences: 258.0 pages: flesch: 48.0 cache: ./cache/cord-323710-cmbg0ty8.txt txt: ./txt/cord-323710-cmbg0ty8.txt summary: For this purpose, the foreign antigen-encoding genes are cloned into additional transcription units of plasmid based full-length MV vaccine strain genomes, which in turn are used to rescue recombinant MV by providing both full-length viral RNA genomes respective anti-genomes together with all protein components of the viral ribonucleoprotein complex after transient transfection of the so-called rescue cells. After demonstrating efficacy in appropriate mouse and primate animal models [8] , this recombinant vaccine delivered proof of Triggered antigen-specific immune responses after immunization determined by measuring total antibodies (ELISA), neutralizing antibodies (nAbs), or reactive T cells determined by ELISpot or intracellular cytokine staining (ICS) c Protective capacity of vaccine-induced immune responses after challenge of the appropriate animal model determined by reduction of pathogen load or attenuation of etiopathology principle for safety and immunogenicity in human patients, irrespective of preformed anti-measles immunity [9] . abstract: This chapter describes the development of recombinant measles virus (MV)-based vaccines starting from plasmid DNA. Live-attenuated measles vaccines are very efficient and safe. Since the availability of a reverse genetic system to manipulate MV genomes and to generate respective recombinant viruses, a considerable number of recombinant viruses has been generated that present antigens of foreign pathogens during MV replication. Thereby, robust humoral and cellular immune responses can be induced, which have shown protective capacity in a substantial number of experiments. For this purpose, the foreign antigen-encoding genes are cloned into additional transcription units of plasmid based full-length MV vaccine strain genomes, which in turn are used to rescue recombinant MV by providing both full-length viral RNA genomes respective anti-genomes together with all protein components of the viral ribonucleoprotein complex after transient transfection of the so-called rescue cells. Infectious centers form among these transfected cells, which allow clonal isolation of single recombinant viruses that are subsequently amplified, characterized in vitro, and then evaluated for their immunogenicity in appropriate preclinical animal models. url: https://doi.org/10.1007/978-1-4939-6869-5_9 doi: 10.1007/978-1-4939-6869-5_9 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-027654-k0uby99n author: Nabel, Gary J. title: The development of gene-based vectors for immunization date: 2020-06-22 words: 6550.0 sentences: 321.0 pages: flesch: 37.0 cache: ./cache/cord-027654-k0uby99n.txt txt: ./txt/cord-027654-k0uby99n.txt summary: The advantages of their ability to induce cellular immunity, immunogenicity, safety, mode of antigen presentation, and other attractive features are countered by limitations in knowledge about clinical effi cacy, production methodologies, DNA vaccination as the initial vaccine constituent and replication-defective viral vectors, including modifi ed vaccinia Ankara virus (MVA), 21,28 rAd 22,23,27,29 or proteins to boost the initial response. 31, 32 In addition, the development of improved enhancer/ promoter regions can allow for even higher expression 5 and these vaccines have advanced into multiple human Phase I studies, alone or in combination with other gene-based vectors. Depending on their ability to target antigen presenting cells, ability to develop packaging lines, inherent immunogenicity of both the vector and insert, and other factors (Table 62 -2), these viral vectors are helping to improve vaccine effi cacy in a variety of infectious disease models. Comparative immunogenicity in rhesus monkeys of DNA plasmid, recombinant vaccinia virus, and replication-defective adenovirus vectors expressing a human immunodefi ciency virus type 1 gag gene abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310921/ doi: 10.1016/b978-1-4160-3611-1.50066-0 id: cord-329050-vzsy6xw1 author: Nabi, Ghulam title: Bats and birds as viral reservoirs: A physiological and ecological perspective date: 2020-09-22 words: 5059.0 sentences: 296.0 pages: flesch: 54.0 cache: ./cache/cord-329050-vzsy6xw1.txt txt: ./txt/cord-329050-vzsy6xw1.txt summary: These convergent traits in birds and bats and their ecological interactions with domestic animals and humans increase the potential risk of viral spillover transmission and facilitate the emergence of novel viruses that most likely sources of zoonoses with the potential to cause global pandemics. This paper reviews convergent traits in the physiology, immunology and flight-related ecology of birds and bats with the aim of a better understanding of why these species are such important reservoirs of viral zoonoses, and the potential risk of bat and bird viruses infecting humans. The convergent traits of miniaturized body size, enhanced metabolic rate and antioxidant capacity, prolonged lifespan, a short but efficient digestive tract, and possessing some specific immunological features relative to non-flying mammals are thought to be the result of functional constraints on evolution imposed by the demands of powered flight (Thomas and Suthers, 1972; Norberg, 1990; Caviedes-Vidal et al., 2007; Costantini, 2008; Munshi-South and Wilkinson, 2010; Song et al., 2020; ) . abstract: The birds (class Aves) and bats (order Chiroptera, class Mammalia) are well known natural reservoirs of a diverse range of viruses, including some zoonoses. The only extant volant vertebrates, bats and birds have undergone dramatic adaptive radiations that have allowed them to occupy diverse ecological niches and colonize most of the planet. However, few studies have compared the physiology and ecology of these ecologically, and medically, important taxa. Here, we review convergent traits in the physiology, immunology, flight-related ecology of birds and bats that might enable these taxa to act as viral reservoirs and asymptomatic carriers. Many species of birds and bats are well adapted to urban environments and may host more zoonotic pathogens than species that do not colonize anthropogenic habitats. These convergent traits in birds and bats and their ecological interactions with domestic animals and humans increase the potential risk of viral spillover transmission and facilitate the emergence of novel viruses that most likely sources of zoonoses with the potential to cause global pandemics. url: https://api.elsevier.com/content/article/pii/S0048969720359015 doi: 10.1016/j.scitotenv.2020.142372 id: cord-285856-0sw3wt1i author: Naesens, Lieve title: Anti-influenza virus activity and structure–activity relationship of aglycoristocetin derivatives with cyclobutenedione carrying hydrophobic chains date: 2009-02-05 words: 2963.0 sentences: 149.0 pages: flesch: 38.0 cache: ./cache/cord-285856-0sw3wt1i.txt txt: ./txt/cord-285856-0sw3wt1i.txt summary: We here report on the chemical synthesis, anti-influenza virus activity and structure-activity relationship of novel glycopeptide compounds carrying a hydrophobic side chain on an aglycoristocetin backbone ( Fig. 1) . b HPLC conditions: instrument: Waters 600 with UV230nm detection; column: Lichrospher RP-8 (4 mm × 250 mm; 10 m); injection volume: 20 l (corresponding to 2 g compound); solvents: Table 2 , several asymmetric squaric diamides derived from aglycoristocetin exerted marked activity against influenza virus, the most potent compounds being the phenylbenzyl derivative 8e [average antiviral EC 50 : 0.4 M; selectivity index (SI), defined as the ratio of MCC to EC 50 : 50]; the hexanol deriva-tive 8a (EC 50 : 1 M; SI: 14) and the naphthyl derivative 8f (EC 50 : 1.4 M; SI: 10). With regard to the antiviral mode of action, time-of-addition studies suggested that 8e blocks the viral entry process, since optimal anti-influenza virus activity was obtained when the compound was added to MDCK cells 30 min prior to or simultaneously with virus infection. abstract: Previous studies have demonstrated that glycopeptide compounds carrying hydrophobic substituents can have favorable pharmacological (i.e. antibacterial and antiviral) properties. We here report on the in vitro anti-influenza virus activity of aglycoristocetin derivatives containing hydrophobic side chain-substituted cyclobutenedione. The lead compound 8e displayed an antivirally effective concentration of 0.4 μM, which was consistent amongst influenza A/H1N1, A/H3N2 and B viruses, and a selectivity index ≥50. Structural analogues derived from aglycovancomycin were found to be inactive. The hydrophobic side chain was shown to be an important determinant of activity. The narrow structure–activity relationship and broad activity against several human influenza viruses suggest a highly conserved interaction site, which is presumably related to the influenza virus entry process. Compound 8e proved to be inactive against several unrelated RNA and DNA viruses, except for varicella-zoster virus, against which a favorable activity was noted. url: https://doi.org/10.1016/j.antiviral.2009.01.003 doi: 10.1016/j.antiviral.2009.01.003 id: cord-004743-ido065mh author: Nagy, Éva title: Polypeptide patterns of infectious bronchitis virus serotypes fall into two categories date: 1979 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Molecular weights of six major polypeptides of infectious bronchitis virus (IBV) are: 1. 75,000; 2. 50,000; 3. 45,000; 4. 35,000; 5. 28,000 or 24,000, and 6. 22,000 dalton. According to the mobility of protein 5 the polypeptide patterns of IBV serotypes fall into two main categories. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086840/ doi: 10.1007/bf01315022 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-298032-3zlu8g8y author: Nan, Yuchen title: Antisense Phosphorodiamidate Morpholino Oligomers as Novel Antiviral Compounds date: 2018-04-20 words: 10577.0 sentences: 524.0 pages: flesch: 46.0 cache: ./cache/cord-298032-3zlu8g8y.txt txt: ./txt/cord-298032-3zlu8g8y.txt summary: An earlier study showed that a 22mer PPMO targeting the translation start site region of EBOV VP35 positive-sense RNA exhibited sequence-specific, time-and dose-dependent inhibition of EBOV replication in cultured cells (Enterlein et al., 2006) . However, PPMO targeting conserved internal ribosome entry site (IRES) sequences have been shown to be highly effective in protecting cultured cells against infection by human rhinovirus type 14, coxsackievirus type B2, and poliovirus type 1 (PV1) (Stone et al., 2008) , with reduction of PV1 titers by up to 6 log10. In this study, virus replication in MDCK cells was significantly inhibited by three PPMO targeting either the translation start site region of PB1 or NP mRNA or the 3 -terminal region of NP viral RNA (vRNA). Inhibition of influenza virus infection in human airway cell cultures by an antisense peptide-conjugated morpholino oligomer targeting the hemagglutinin-activating protease TMPRSS2 abstract: Phosphorodiamidate morpholino oligomers (PMO) are short single-stranded DNA analogs that are built upon a backbone of morpholine rings connected by phosphorodiamidate linkages. As uncharged nucleic acid analogs, PMO bind to complementary sequences of target mRNA by Watson–Crick base pairing to block protein translation through steric blockade. PMO interference of viral protein translation operates independently of RNase H. Meanwhile, PMO are resistant to a variety of enzymes present in biologic fluids, a characteristic that makes them highly suitable for in vivo applications. Notably, PMO-based therapy for Duchenne muscular dystrophy (DMD) has been approved by the United States Food and Drug Administration which is now a hallmark for PMO-based antisense therapy. In this review, the development history of PMO, delivery methods for improving cellular uptake of neutrally charged PMO molecules, past studies of PMO antagonism against RNA and DNA viruses, PMO target selection, and remaining questions of PMO antiviral strategies are discussed in detail and new insights are provided. url: https://doi.org/10.3389/fmicb.2018.00750 doi: 10.3389/fmicb.2018.00750 id: cord-252871-qfrpuy3t author: Nasir, Arshan title: Investigating the Concept and Origin of Viruses date: 2020-11-03 words: 5153.0 sentences: 298.0 pages: flesch: 46.0 cache: ./cache/cord-252871-qfrpuy3t.txt txt: ./txt/cord-252871-qfrpuy3t.txt summary: We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution. We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution. In turn, the origin of archaeoviruses from Archaea, bacterioviruses from Bacteria, and eukaryoviruses from Eukarya also seems less likely as these viruses share several conserved protein folds involved in virion synthesis and other functions, indicating that they may have evolved prior to the diversification of LUCA into modern cells. abstract: The ongoing COVID-19 pandemic has piqued public interest in the properties, evolution, and emergence of viruses. Here, we discuss how these basic questions have surprisingly remained disputed despite being increasingly within the reach of scientific analysis. We review recent data-driven efforts that shed light into the origin and evolution of viruses and explain factors that resist the widespread acceptance of new views and insights. We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution. We note that the philosophical aspects of virus evolution also impact the way we might prepare for future outbreaks. url: https://api.elsevier.com/content/article/pii/S0966842X20302304 doi: 10.1016/j.tim.2020.08.003 id: cord-277400-w7mvk3x4 author: Nasir, Arshan title: Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification date: 2017-03-10 words: 7527.0 sentences: 398.0 pages: flesch: 47.0 cache: ./cache/cord-277400-w7mvk3x4.txt txt: ./txt/cord-277400-w7mvk3x4.txt summary: While the member viruses within a lineage exhibit strong 3D structural similarities in capsid/coat fold architectures (or principles in constructing a functional virion) regardless of the viral replicon (i.e., DNA or RNA) and/or infected host type, the lineages however are believed to be unrelated to each other indicating the polyphyletic origin of viruses (Bamford, 2003) . The b.121 fold in the SCOP hierarchy includes 7 children FSFs (that are not necessarily related in evolution according to SCOP definitions): (i) "PHM/PNGase F" FSF (b.121.1) involved in oxidation-reduction metabolic processes (not detected in any of our sampled viral proteomes), (ii) "Group II dsDNA viruses VP" FSF (b.121.2), which is the "double β-barrel" fold signature of the PRD1/Adenovirus-like lineage (read below), (iii) "Nucleoplasmin-like core domain" FSF (b.121.3) involved in the assembly of nucleosomes in cells, and (iv-vii) FSFs b.121.4, b.121.5, b.121.6, and b.121.7 (Figure 1 ) that define the picornavirus-like lineage and are individually described below. abstract: The viral supergroup includes the entire collection of known and unknown viruses that roam our planet and infect life forms. The supergroup is remarkably diverse both in its genetics and morphology and has historically remained difficult to study and classify. The accumulation of protein structure data in the past few years now provides an excellent opportunity to re-examine the classification and evolution of viruses. Here we scan completely sequenced viral proteomes from all genome types and identify protein folds involved in the formation of viral capsids and virion architectures. Viruses encoding similar capsid/coat related folds were pooled into lineages, after benchmarking against published literature. Remarkably, the in silico exercise reproduced all previously described members of known structure-based viral lineages, along with several proposals for new additions, suggesting it could be a useful supplement to experimental approaches and to aid qualitative assessment of viral diversity in metagenome samples. url: https://doi.org/10.3389/fmicb.2017.00380 doi: 10.3389/fmicb.2017.00380 id: cord-341029-49360l2a author: Nasir, Arshan title: A phylogenomic data-driven exploration of viral origins and evolution date: 2015-09-25 words: 14410.0 sentences: 794.0 pages: flesch: 49.0 cache: ./cache/cord-341029-49360l2a.txt txt: ./txt/cord-341029-49360l2a.txt summary: Viruses harboring different replicon types and infecting distantly related hosts shared many metabolic and informational protein structural domains of ancient origin that were also widespread in cellular proteomes. Here, we analyzed a total of 5080 completely sequenced proteomes from cells and viruses and assigned FSF domains to their proteins using structure-based hidden Markov models (HMMs) defined by the SUPER-FAMILY database (version 1.75) (20) . Viral supergroup behaves similarly to cellular superkingdoms in terms of FSF sharing patterns A total of 1995 significant FSF domains (E < 0.0001) were detected iñ 11 million proteins of 5080 proteomes sampled from cells and viruses. It also suggests that viruses are very ancient and most likely infected the last common ancestor of each superkingdom because viral FSFs were present in a diverse array of cellular organisms ranging from small microbes to large eukaryotes. abstract: The origin of viruses remains mysterious because of their diverse and patchy molecular and functional makeup. Although numerous hypotheses have attempted to explain viral origins, none is backed by substantive data. We take full advantage of the wealth of available protein structural and functional data to explore the evolution of the proteomic makeup of thousands of cells and viruses. Despite the extremely reduced nature of viral proteomes, we established an ancient origin of the “viral supergroup” and the existence of widespread episodes of horizontal transfer of genetic information. Viruses harboring different replicon types and infecting distantly related hosts shared many metabolic and informational protein structural domains of ancient origin that were also widespread in cellular proteomes. Phylogenomic analysis uncovered a universal tree of life and revealed that modern viruses reduced from multiple ancient cells that harbored segmented RNA genomes and coexisted with the ancestors of modern cells. The model for the origin and evolution of viruses and cells is backed by strong genomic and structural evidence and can be reconciled with existing models of viral evolution if one considers viruses to have originated from ancient cells and not from modern counterparts. url: https://www.ncbi.nlm.nih.gov/pubmed/26601271/ doi: 10.1126/sciadv.1500527 id: cord-325712-9kbnyqt3 author: Nathan, Lakshmi title: Single Virion Tracking Microscopy for the Study of Virus Entry Processes in Live Cells and Biomimetic Platforms date: 2019-07-18 words: 10235.0 sentences: 489.0 pages: flesch: 41.0 cache: ./cache/cord-325712-9kbnyqt3.txt txt: ./txt/cord-325712-9kbnyqt3.txt summary: title: Single Virion Tracking Microscopy for the Study of Virus Entry Processes in Live Cells and Biomimetic Platforms In addition, for HIV [9] , influenza [10] , and Ebola virus [11] , most virions that encounter a cell are not involved in productive entry so the ability of single virion techniques to distinguish entry-competent particles from non-competent ones and characterize their individual behavior provides valuable data on heterogeneity in viral populations and its ultimate impact on infection. The remaining part of the chapter will focus on single particle tracking microscopy techniques compatible with dynamic/temporal data acquisition, their salient features, and how the data generated complement ensemble methods for studying viral entry processes and their intermediate steps and mechanisms. Here, binding and fusion is studied by monitoring liposomes decorated with host cell receptors interacting with the planar virus-like bilayer containing embedded viral proteins [59] [60] [61] . abstract: The most widely-used assays for studying viral entry, including infectivity, cofloatation, and cell-cell fusion assays, yield functional information but provide low resolution of individual entry steps. Structural characterization provides high-resolution conformational information, but on its own is unable to address the functional significance of these conformations. Single virion tracking microscopy techniques provide more detail on the intermediate entry steps than infection assays and more functional information than structural methods, bridging the gap between these methods. In addition, single virion approaches also provide dynamic information about the kinetics of entry processes. This chapter reviews single virion tracking techniques and describes how they can be applied to study specific virus entry steps. These techniques provide information complementary to traditional ensemble approaches. Single virion techniques may either probe virion behavior in live cells or in biomimetic platforms. Synthesizing information from ensemble, structural, and single virion techniques ultimately yields a more complete understanding of the viral entry process than can be achieved by any single method alone. url: https://www.ncbi.nlm.nih.gov/pubmed/31317494/ doi: 10.1007/978-3-030-14741-9_2 id: cord-344009-hm36pepp author: Nathanson, N. title: Virus perpetuation in populations: biological variables that determine persistence or eradication date: 2005 words: 3463.0 sentences: 180.0 pages: flesch: 46.0 cache: ./cache/cord-344009-hm36pepp.txt txt: ./txt/cord-344009-hm36pepp.txt summary: However, small animal populations can turnover significantly each year, permitting the perpetuation of some viruses that cause acute infections. Measles has several attributes that -in the aggregate -are not seen for other common viral diseases: (i) There are longterm records of measles incidence, collected by many health departments in the United States and other countries; (ii) 95% of all measles infections manifest as illness (in contrast to 1% for poliomyelitis for example); (iii) the symptoms of measles are sufficiently pathognomonic so that it can be distinguished from other viral infections by clinical observers; and (iv) population-wide reports can be corrected for under-reporting (about 15% of measles cases were reported in most cities in the United States prior to the introduction of measles vaccine in 1963). Vaccine-induced reduction of susceptible individuals in such a population can be guesstimated to reduce the number of new infections per trough generation period below the threshold for virus perpetuation. abstract: In this review, I use the term “perpetuation” for persistence of a virus in a population, since this is a different phenomenon from persistence of a virus in an infected host. Important variables that influence perpetuation differ in small (<1,000 individuals) and large (>10,000) populations: in small populations, two important variables are persistence in individuals, and turnover of the population, while in large populations important variables are transmissibility, generation time, and seasonality. In small populations, viruses such as poliovirus that cause acute infections cannot readily be perpetuated, in contrast to viruses such as hepatitis B virus, that cause persistent infections. However, small animal populations can turnover significantly each year, permitting the perpetuation of some viruses that cause acute infections. Large populations of humans are necessary for the perpetuation of acute viruses; for instance, measles required a population of 500,000 for perpetuation in the pre-measles vaccine era. Furthermore, if an acute virus, such as poliovirus, exhibits marked seasonality in large populations, then it may disappear during the seasonal trough, even in the presence of a large number of susceptible persons. Eradication is the converse of perpetuation and can be used as a definitive approach to the control of a viral disease, as in the instance of smallpox. Therefore, the requirements for perpetuation have significant implications for practical public health goals. url: https://www.ncbi.nlm.nih.gov/pubmed/16355865/ doi: 10.1007/3-211-29981-5_2 id: cord-022254-8y5sq72c author: Nathanson, Neal title: IMMUNOSUPPRESSION AND VIRUS INFECTION OF RODENTS date: 2012-12-02 words: 3210.0 sentences: 172.0 pages: flesch: 35.0 cache: ./cache/cord-022254-8y5sq72c.txt txt: ./txt/cord-022254-8y5sq72c.txt summary: One example of specific deletion is the use of anti-mu antiserum to delete IgM bearing B cells from neonatal animals, thus blocking the B cell arm of the immune response (43-46). Complement plays an important ancillary role as a host defense, since in conjunction with specific antiviral antibody, it can lyse either virions or virus-infected cells (60). The recent development of methods for the cloning of T cells and the culture of T cell lines (88) (89) (90) (91) (92) , has made it possible to study the effect of specific T cell subsets upon virus infection (93) (94) (95) (96) . I. Comparative effectiveness of antibody and reconstitution of immune spleen cells on immunosuppressed mice Protection of mice from fatal herpes simplex virus type 1 infection by adoptive transfer of cloned virusspecific and H-2-restricted cytotoxic T lymphocytes Dual role of the immune response in street rabies virus infection of mice abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155493/ doi: 10.1016/b978-0-12-095785-9.50036-6 id: cord-355906-yeaw9nr8 author: Nedjadi, Taoufik title: Tackling dengue fever: Current status and challenges date: 2015-12-09 words: 6821.0 sentences: 355.0 pages: flesch: 46.0 cache: ./cache/cord-355906-yeaw9nr8.txt txt: ./txt/cord-355906-yeaw9nr8.txt summary: Recent advances in molecular biology have revealed that the genetic makeup of the three elements of dengue infection (the virus, the vector, and the host) plays a primordial role in the pathogenesis of the disease and could potentially contribute to the DHF progression [19, 24, 35] . Dengue virus serotype-1 antigen was expressed in a vector based on pediatric live-attenuated Schwarz measles vaccine (MV) by using the envelope domain III (EDIII) fused with the ectodomain of the membrane protein (ectoM). The Centers for Disease Control and Prevention (USA) have also developed a live-attenuated vaccine named DENVax, which was found to be highly immunogenic in both children and adults and has currently entered phase I clinical trial in the United States [96, 97] . abstract: According to recent statistics, 96 million apparent dengue infections were estimated worldwide in 2010. This figure is by far greater than the WHO prediction which indicates the rapid spread of this disease posing a growing threat to the economy and a major challenge to clinicians and health care services across the globe particularly in the affected areas. This article aims at bringing to light the current epidemiological and clinical status of the dengue fever. The relationship between genetic mutations, single nucleotide polymorphism (SNP) and the pathophysiology of disease progression will be put into perspective. It will also highlight the recent advances in dengue vaccine development. Thus far, a significant progress has been made in unraveling the risk factors and understanding the molecular pathogenesis associated with the disease. However, further insights in molecular features of the disease and the development of animal models will enormously help improving the therapeutic interventions and potentially contribute to finding new preventive measures for population at risk. url: https://www.ncbi.nlm.nih.gov/pubmed/26645066/ doi: 10.1186/s12985-015-0444-8 id: cord-326225-crtpzad7 author: Neill, John D. title: Simultaneous rapid sequencing of multiple RNA virus genomes date: 2014-06-01 words: 3804.0 sentences: 204.0 pages: flesch: 55.0 cache: ./cache/cord-326225-crtpzad7.txt txt: ./txt/cord-326225-crtpzad7.txt summary: This procedure utilized primers composed of 20 bases of known sequence with 8 random bases at the 3′-end that also served as an identifying barcode that allowed the differentiation each viral library following pooling and sequencing. There is a wealth of information in these isolates, but up till now, it has been time consuming and expensive to sequence these viral genomes, often requiring sets of strain-specific primers for PCR amplification and sequencing. These primers were developed so that the 20 base known sequence was used for PCR amplification of the library as well as served as a barcode for identifying each viral library following pooling and sequencing. This virus, a BVDV 1b strain isolated from alpaca (GenBank accession JX297520.1; Table 2 , library 3, barcode 10), was assembled from Ion Torrent data and was found to have only 1 base difference from the sequence determined earlier (data not shown). One virus, library 1, barcode 9, had only 658 viral sequence reads but 94.4% of the genome was assembled. abstract: Comparing sequences of archived viruses collected over many years to the present allows the study of viral evolution and contributes to the design of new vaccines. However, the difficulty, time and expense of generating full-length sequences individually from each archived sample have hampered these studies. Next generation sequencing technologies have been utilized for analysis of clinical and environmental samples to identify viral pathogens that may be present. This has led to the discovery of many new, uncharacterized viruses from a number of viral families. Use of these sequencing technologies would be advantageous in examining viral evolution. In this study, a sequencing procedure was used to sequence simultaneously and rapidly multiple archived samples using a single standard protocol. This procedure utilized primers composed of 20 bases of known sequence with 8 random bases at the 3′-end that also served as an identifying barcode that allowed the differentiation each viral library following pooling and sequencing. This conferred sequence independence by random priming both first and second strand cDNA synthesis. Viral stocks were treated with a nuclease cocktail to reduce the presence of host nucleic acids. Viral RNA was extracted, followed by single tube random-primed double-stranded cDNA synthesis. The resultant cDNAs were amplified by primer-specific PCR, pooled, size fractionated and sequenced on the Ion Torrent PGM platform. The individual virus genomes were readily assembled by both de novo and template-assisted assembly methods. This procedure consistently resulted in near full length, if not full-length, genomic sequences and was used to sequence multiple bovine pestivirus and coronavirus isolates simultaneously. url: https://doi.org/10.1016/j.jviromet.2014.02.016 doi: 10.1016/j.jviromet.2014.02.016 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-253466-7gpije5d author: Netherton, Christopher title: A Guide to Viral Inclusions, Membrane Rearrangements, Factories, and Viroplasm Produced During Virus Replication date: 2007-08-31 words: 26372.0 sentences: 1363.0 pages: flesch: 45.0 cache: ./cache/cord-253466-7gpije5d.txt txt: ./txt/cord-253466-7gpije5d.txt summary: Significantly, Poliovirus infection causes enrichment of GEFs in membranes containing replicase proteins, and this would provide a mechanism for increasing levels of Arf1-GTP at sites of virus replication. There is evidence that Tobacco mosaic virus also uses the ER as a site of replication because the replicase enzyme and viral RNA are located on the ER of infected cells, and infection causes major changes in ER morphology (Reichel and Beachy, 1998) , including ER aggregation and formation of lamella structures. Even though these viruses infect a diverse range of hosts from different phyla, including vertebrates [poxviruses, African swine fever virus (ASFV)], arthropods (entomopox, ASFV, chloriridoviruses), amphibians and fish (Ranavirus, Megalocytivirus, and Lymphocystivirus genera of the Iridoviridae family), marine algae (phycodnaviruses), and protozoa (mimivirus), they all generate cytoplasmic factories as major sites of virus assembly and replication (illustrated in Fig. 4 ). Formation of DNA replication structures in herpes virus-infected cells requires a viral DNA binding protein abstract: Virus replication can cause extensive rearrangement of host cell cytoskeletal and membrane compartments leading to the “cytopathic effect” that has been the hallmark of virus infection in tissue culture for many years. Recent studies are beginning to redefine these signs of viral infection in terms of specific effects of viruses on cellular processes. In this chapter, these concepts have been illustrated by describing the replication sites produced by many different viruses. In many cases, the cellular rearrangements caused during virus infection lead to the construction of sophisticated platforms in the cell that concentrate replicase proteins, virus genomes, and host proteins required for replication, and thereby increase the efficiency of replication. Interestingly, these same structures, called virus factories, virus inclusions, or virosomes, can recruit host components that are associated with cellular defences against infection and cell stress. It is possible that cellular defence pathways can be subverted by viruses to generate sites of replication. The recruitment of cellular membranes and cytoskeleton to generate virus replication sites can also benefit viruses in other ways. Disruption of cellular membranes can, for example, slow the transport of immunomodulatory proteins to the surface of infected cells and protect against innate and acquired immune responses, and rearrangements to cytoskeleton can facilitate virus release. url: https://www.sciencedirect.com/science/article/pii/S0065352707700040 doi: 10.1016/s0065-3527(07)70004-0 id: cord-322904-9mta0aem author: Neu, Ursula title: The Polyomaviridae: Contributions of virus structure to our understanding of virus receptors and infectious entry date: 2009-02-01 words: 9629.0 sentences: 493.0 pages: flesch: 53.0 cache: ./cache/cord-322904-9mta0aem.txt txt: ./txt/cord-322904-9mta0aem.txt summary: The mPyV and the two human polyomaviruses, JCV and BKV are known to require sialic acid for binding to host cells as "receptor destroying enzyme" or neuraminidase inhibits the viruses'' ability to agglutinate red blood cells and to infect cells (Table 1) . High-resolution structural information on the interaction of viral attachment proteins with sialylated carbohydrates is available for the following systems: Influenza virus A haemagglutinin (HA) in complex with oligosaccharides containing α2,3-linked and α2,6linked NeuNAc (Eisen et al., 1997; Gamblin et al., 2004; Ha et al., 2001; Ha et al., 2003; Russell et al., 2006; Sauter et al., 1992; Stevens et al., 2006; Stevens et al., 2004; Weis et al., 1988) , mPyV VP1 with a fragment of ganglioside GD1a (Stehle and Harrison, 1997) , rhesus, swine and human rotavirus VP8⁎ with methyl-α2,3-sialoside (Blanchard et al., 2007; Dormitzer et al., 2002a) , adenovirus Ad37 fiber knob (Ad37) with α2,3and α2,6-sialyllactose (Burmeister et al., 2004) and SV40 VP1 with ganglioside GM1 (Neu et al., 2008) . abstract: This review summarizes the fields major findings related to the characterization of polyomavirus structures and to the characterization of virus receptors and mechanisms of host cell invasion. Four members of the family that have received the most attention in this regard are the mouse polyomavirus (mPyV), the monkey polyomavirus SV40, and the two human polyomaviruses, JCV and BKV. The structures of both the mPyV and SV40 alone and in complex with receptor fragments have been solved to high resolution. The majority of polyomaviruses recognize terminal sialic acid in either an α 2,3 linkage or an α 2,6 linkage to the underlying galactose. Studies on virus structure, receptor utilization and mechanisms of entry have led to new insights into how these viruses interact in an active way with cells to ensure the nuclear delivery and expression of their genomes. Critical work on virus entry has led to the discovery of a pH neutral endocytic compartment that accepts cargo from caveolae and to novel roles for endoplasmic reticulum (ER) associated factors in virus uncoating and penetration of ER membranes. This review will summarize the major findings and compare and contrast the mechanisms used by these viruses to infect cells. url: https://doi.org/10.1016/j.virol.2008.12.021 doi: 10.1016/j.virol.2008.12.021 id: cord-303533-6s01qplg author: Neuman, Benjamin W. title: Does form meet function in the coronavirus replicative organelle? date: 2014-07-15 words: 3642.0 sentences: 177.0 pages: flesch: 39.0 cache: ./cache/cord-303533-6s01qplg.txt txt: ./txt/cord-303533-6s01qplg.txt summary: This review takes a virus-centric look at the coronavirus replication transcription complex organelle in the context of the wider world of positive sense RNA viruses, examining how the mechanisms of protein expression and function act to produce the factories that power the viral replication cycle. This review takes a virus-centric look at the coronavirus replication transcription complex organelle in the context of the wider world of positive sense RNA viruses, examining how the mechanisms of protein expression and function act to produce the factories that power the viral replication cycle. Whatever their purpose, it is clear that the coronavirus organelle is dynamic [9] , closely tied to vesicular transport in the host cell [5, 10] , and consists mainly of paired membranes that form a variety of complex shapes including convoluted membranes and double-membrane vesicles (DMVs) [2, 11] . Formation of plant RNA virus replication complexes on membranes: role of an endoplasmic reticulum-targeted viral protein abstract: If we use the analogy of a virus as a living entity, then the replicative organelle is the part of the body where its metabolic and reproductive activities are concentrated. Recent studies have illuminated the intricately complex replicative organelles of coronaviruses, a group that includes the largest known RNA virus genomes. This review takes a virus-centric look at the coronavirus replication transcription complex organelle in the context of the wider world of positive sense RNA viruses, examining how the mechanisms of protein expression and function act to produce the factories that power the viral replication cycle. url: https://www.sciencedirect.com/science/article/pii/S0966842X14001322 doi: 10.1016/j.tim.2014.06.003 id: cord-279418-3r1ijafm author: Nevers, Quentin title: Negri bodies and other virus membrane-less replication compartments() date: 2020-08-21 words: 6437.0 sentences: 406.0 pages: flesch: 44.0 cache: ./cache/cord-279418-3r1ijafm.txt txt: ./txt/cord-279418-3r1ijafm.txt summary: We particularly examine the interplay between viral factories and the cellular innate immune response, of which several components also form membrane-less condensates in infected cells. With the rapid identification of cellular membraneless compartments and proteins that undergo LLPS in vitro, a major challenge in the field is to demonstrate unambiguously that a specific structure is indeed a phase-separated liquid body in the cellular context. Until now, only a few specific cellular factors, which directly interact with viral proteins such as the nucleoproteins and phosphoproteins of MNV, have been shown to concentrate in these structures. Upon Infection, Cellular WD Repeat-Containing Protein 5 (WDR5) Localizes to Cytoplasmic Inclusion Bodies and Enhances Measles Virus Replication The Ebola Virus Nucleoprotein Recruits the Nuclear RNA Export Factor NXF1 into Inclusion Bodies to Facilitate Viral Protein Expression The Cellular Protein CAD is Recruited into Ebola Virus Inclusion Bodies by the Nucleoprotein NP to Facilitate Genome Replication and Transcription abstract: Viruses reshape the organization of the cell interior to achieve different steps of their cellular cycle. Particularly, viral replication and assembly often take place in viral factories where specific viral and cellular proteins as well as nucleic acids concentrate. Viral factories can be either membrane-delimited or devoid of any cellular membranes. In the latter case, they are referred as membrane-less replication compartments. The most emblematic ones are the Negri bodies, which are inclusion bodies that constitute the hallmark of rabies virus infection. Interestingly, Negri bodies and several other viral replication compartments have been shown to arise from a liquid-liquid phase separation process and, thus, constitute a new class of liquid organelles. This is a paradigm shift in the field of virus replication. Here, we review the different aspects of membrane-less virus replication compartments with a focus on the Mononegavirales order and discuss their interactions with the host cell machineries and the cytoskeleton. We particularly examine the interplay between viral factories and the cellular innate immune response, of which several components also form membrane-less condensates in infected cells. url: https://doi.org/10.1016/j.bbamcr.2020.118831 doi: 10.1016/j.bbamcr.2020.118831 id: cord-304569-o39kl5k4 author: Nguyen-Van-Tam, Jonathan S title: From the Editor''s desk date: 2015-04-23 words: 1210.0 sentences: 66.0 pages: flesch: 50.0 cache: ./cache/cord-304569-o39kl5k4.txt txt: ./txt/cord-304569-o39kl5k4.txt summary: If one shifts the focus away from influenza, the ongoing MERS-CoV outbreak in the Middle East, is also of substantial concern, because despite its likely introduction into humans via close contact with dromedary camels, 9 nosocomial transmission appears to be a central concern, 10,11 case-fatality is high, household transmission is also described, 12 and there are currently no vaccines or specific therapies available. Papers considered for rapid peer-review will need to be of immediate relevance, interest, or importance to scientists, clinicians, public health practitioners or policy makers, usually in relation to a current or evolving event related to respiratory virus activity. Accepted Articles are published online a few days after final acceptance, appear in PDF format only, are given a Digital Object Identifier (DOI), which allows them to be cited and tracked, and are indexed by PubMed. Effectiveness of neuraminidase inhibitors in reducing mortality in patients admitted to hospital with influenza A H1N1pdm09 virus infection: a meta-analysis of individual participant data abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/25824028/ doi: 10.1111/irv.12311 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-316996-8yimrpaz author: Nicholls, John M. title: The use of sialidase therapy for respiratory viral infections date: 2013-04-17 words: 7337.0 sentences: 340.0 pages: flesch: 43.0 cache: ./cache/cord-316996-8yimrpaz.txt txt: ./txt/cord-316996-8yimrpaz.txt summary: DAS181 is an inhaled bacterial sialidase which functions by removing sialic acid (Sia) from the surface of epithelial cells, preventing attachment and subsequent infection by respiratory viruses that utilize Sia as a receptor. DAS181 is the first antiviral compound in Phase II development that functions by blocking this pathogen-host interaction, by destroying the influenza host-cell receptor, sialic acid (Sia), on the surface of respiratory epithelial cells. In this paper, we provide background information on Sia and sialidases; discuss the potential role of bacterial sialidases as antiviral agents; review the in vitro and Phase II evaluation of DAS181 for the treatment of influenza; and note evidence that the drug would also be useful against parainfluenza virus infections. Even though influenza virus has been the most well characterized of the pathogens studied, it must be noted that other viruses, including cytomegalovirus (Taylor and Cooper, 1989) , rhinovirus 87 (Blomqvist et al., 2002) , mumps Urabe AM9 (ReyesLeyva et al., 2007) and the paramyxoviruses all utilize Sia (Suzuki et al., 2001) (Paulson et al., 1979) , suggesting that sialidase treatment may potentially be useful for these infections. abstract: DAS181 is an inhaled bacterial sialidase which functions by removing sialic acid (Sia) from the surface of epithelial cells, preventing attachment and subsequent infection by respiratory viruses that utilize Sia as a receptor. DAS181 is typical of bacterial sialidases in cleaving Sia α2-3 and Sia α2-6 linkages, and it also has a demonstrated effect against acetylated and hydroxylated forms of Sia. The potency of the compound has been enhanced by coupling the active sialidase with an amphiregulin tag, allowing a longer duration of action and minimizing spread to the systemic circulation. DAS181 is now in Phase II development for the treatment of influenza, and it has also demonstrated activity in individual cases of parainfluenza in immunosuppressed patients. Continued evaluation of the roles and activities of bacterial sialidases is required to expand the range of successful antiviral therapies targeting Sia or its derivatives. url: https://doi.org/10.1016/j.antiviral.2013.04.012 doi: 10.1016/j.antiviral.2013.04.012 id: cord-269623-9pxdeva3 author: Nicholson, Karl G title: Influenza date: 2003-11-22 words: 9797.0 sentences: 506.0 pages: flesch: 43.0 cache: ./cache/cord-269623-9pxdeva3.txt txt: ./txt/cord-269623-9pxdeva3.txt summary: The contrast between recent cases of H5N1 infection, associated with high mortality, and the typically mild, self-limiting nature of human infections with avian H7N7 and H9N2 influenza shows the gaps in our understanding of molecular correlates of pathogenicity and underlines the need for continuing international research into pandemic influenza. We gave priority to randomised controlled trials when available, to larger studies, articles published in high-impact journals that have a wide readership, and the systematic review and economic decision modelling, for the prevention and treatment of influenza, commissioned by the Health Technology Assessment Programme on behalf of the National Institute of Clinical Excellence. A meta-analysis of reports published before 2001 showed that vaccination reduces numbers of cases of influenza-like illness by 35%, hospital admissions for pneumonia and influenza by 47%, and all-cause mortality by 50%. abstract: Although most influenza infections are self-limited, few other diseases exert such a huge toll of suffering and economic loss. Despite the importance of influenza, there had been, until recently, little advance in its control since amantadine was licensed almost 40 years ago. During the past decade, evidence has accrued on the protection afforded by inactivated vaccines and the safety and efficacy in children of live influenza-virus vaccines. There have been many new developments in vaccine technology. Moreover, work on viral neuraminidase has led to the licensing of potent selective antiviral drugs, and economic decision modelling provides further justification for annual vaccination and a framework for the use of neuraminidase inhibitors. Progress has also been made on developing near-patient testing for influenza that may assist individual diagnosis or the recognition of widespread virus circulation, and so optimise clinical management. Despite these advances, the occurrence of avian H5N1, H9N2, and H7N7 influenza in human beings and the rapid global spread of severe acute respiratory syndrome are reminders of our vulnerability to an emerging pandemic. The contrast between recent cases of H5N1 infection, associated with high mortality, and the typically mild, self-limiting nature of human infections with avian H7N7 and H9N2 influenza shows the gaps in our understanding of molecular correlates of pathogenicity and underlines the need for continuing international research into pandemic influenza. Improvements in animal and human surveillance, new approaches to vaccination, and increasing use of vaccines and antiviral drugs to combat annual influenza outbreaks are essential to reduce the global toll of pandemic and interpandemic influenza. url: https://api.elsevier.com/content/article/pii/S0140673603148544 doi: 10.1016/s0140-6736(03)14854-4 id: cord-353190-7qcoxl81 author: Nicklas, Werner title: Viral Infections of Laboratory Mice date: 2012-05-17 words: 27775.0 sentences: 1482.0 pages: flesch: 39.0 cache: ./cache/cord-353190-7qcoxl81.txt txt: ./txt/cord-353190-7qcoxl81.txt summary: This chapter covers infections of mice with the following viruses: herpesviruses, mousepox virus, murine adenoviruses, polyomaviruses, parvoviruses, lactate dehydrogenase-elevating virus, lymphocytic choriomeningitis virus, mammalian orthoreovirus serotype 3, murine hepatitis virus, murine norovirus, murine pneumonia virus, murine rotavirus, Sendai virus, and Theiler''s murine encephalomyelitis virus. These results are very difficult to summarize because the outcome of experimental infection in laboratory mice depends on various factors such as mouse strain and age, virus strain and passage history [26] , virus dose and route of inoculation [24] . Experimental infection of laboratory mice with MHV-68 is a frequently used model system for the study of human gammaherpesvirus pathogenesis, e.g. of Kaposi''s sarcoma-associated herpesvirus or Epstein-Barr virus (EBV) [62, 63] which are members of the same subfamily. Early descriptions of naturally occurring disease may have been complicated by concurrent infections such as MHV (murine hepatitis virus) or murine rotavirus A (MuRV-A)/epizootic diarrhoea of infant mice (EDIM) virus that contributed to the severity of the lesions especially in liver, pancreas, CNS and intestine. abstract: Viral infections of laboratory mice have considerable impact on research results, and prevention of such infections is therefore of crucial importance. This chapter covers infections of mice with the following viruses: herpesviruses, mousepox virus, murine adenoviruses, polyomaviruses, parvoviruses, lactate dehydrogenase-elevating virus, lymphocytic choriomeningitis virus, mammalian orthoreovirus serotype 3, murine hepatitis virus, murine norovirus, murine pneumonia virus, murine rotavirus, Sendai virus, and Theiler’s murine encephalomyelitis virus. For each virus, there is a description of the agent, epizootiology, clinical symptoms, pathology, methods of diagnosis and control, and its impact on research. url: https://api.elsevier.com/content/article/pii/B9780123820082000192 doi: 10.1016/b978-0-12-382008-2.00019-2 id: cord-003466-599x0euj author: Nickol, Michaela E. title: A year of terror and a century of reflection: perspectives on the great influenza pandemic of 1918–1919 date: 2019-02-06 words: 5772.0 sentences: 283.0 pages: flesch: 45.0 cache: ./cache/cord-003466-599x0euj.txt txt: ./txt/cord-003466-599x0euj.txt summary: MAIN TEXT: The 1918 H1N1 pandemic virus spread across Europe, North America, and Asia over a 12-month period resulting in an estimated 500 million infections and 50–100 million deaths worldwide, of which ~ 50% of these occurred within the fall of 1918 (Emerg Infect Dis 12:15-22, 2006, Bull Hist Med 76:105-115, 2002). Influenza viruses have posed a continual threat to global public health since at least as early as the Middle Ages, resulting in an estimated 3-5 million cases of severe illness and 291,243-645,832 deaths annually worldwide, according to a recent estimate [1] . To be considered a pandemic, an influenza virus must: i) spread globally from a distinct location with high rates of infectivity resulting in increased mortality; and ii) the hemagglutinin (HA) cannot be related to influenza strains circulating prior to the outbreak nor have resulted from mutation [14, 15] . abstract: BACKGROUND: In the spring of 1918, the “War to End All Wars”, which would ultimately claim more than 37 million lives, had entered into its final year and would change the global political and economic landscape forever. At the same time, a new global threat was emerging and would become one of the most devastating global health crises in recorded history. MAIN TEXT: The 1918 H1N1 pandemic virus spread across Europe, North America, and Asia over a 12-month period resulting in an estimated 500 million infections and 50–100 million deaths worldwide, of which ~ 50% of these occurred within the fall of 1918 (Emerg Infect Dis 12:15-22, 2006, Bull Hist Med 76:105-115, 2002). However, the molecular factors that contributed to the emergence of, and subsequent public health catastrophe associated with, the 1918 pandemic virus remained largely unknown until 2005, when the characterization of the reconstructed pandemic virus was announced heralding a new era of advanced molecular investigations (Science 310:77-80, 2005). In the century following the emergence of the 1918 pandemic virus we have landed on the Moon, developed the electronic computer (and a global internet), and have eradicated smallpox. In contrast, we have a largely remedial knowledge and understanding of one of the greatest scourges in recorded history. CONCLUSION: Here, we reflect on the 1918 influenza pandemic, including its emergence and subsequent rapid global spread. In addition, we discuss the pathophysiology associated with the 1918 virus and its predilection for the young and healthy, the rise of influenza therapeutic research following the pandemic, and, finally, our level of preparedness for future pandemics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364422/ doi: 10.1186/s12879-019-3750-8 id: cord-300020-edolh7ww author: Nielsen, Anne Ahlmann title: Persistence of Low-Pathogenic Avian Influenza H5N7 and H7N1 Subtypes in House Flies (Diptera: Muscidae) date: 2011-05-01 words: 4313.0 sentences: 259.0 pages: flesch: 56.0 cache: ./cache/cord-300020-edolh7ww.txt txt: ./txt/cord-300020-edolh7ww.txt summary: The objective of the present work was to investigate the potential transmission of LPAIV by persistence of the virus in the alimentary tract of house flies, Musca domestica L. The persistence of HPAIV H5N1 in house ßies and blow ßies as well as Newcastle disease virus (family Paramyxoviridae, genus avulavirus, NDV), turkey coronavirus (family Coronaviridae, genus Coronavirus, TCV), and reticuloendotheliosis virus (family Retroviridae, genus Gammaretrovirus, REV) has been studied in the laboratory (Calibeo-Hayes et al. The current study investigated the persistence of LPAIV in the alimentary tract of house ßies that were fed various concentrations of subtypes H5N7 and H7N1 viruses and incubated at different temperatures for up to 24 h. Our study demonstrated that infective low-pathogenic avian inßuenza virus of the H7N1 and H5N7 subtypes can be isolated from the alimentary tract of house ßies for at least 24 h postfeeding and that factors such as temperature, incubation period postfeeding, and load of ingested virus play an important role in the persistence of infective virus. abstract: Avian influenza caused by avian influenza virus (AIV) has a negative impact on poultry production. Low-pathogenic AIV (LPAIV) is naturally present in wild birds, and the introduction of the virus into domestic poultry is assumed to occur through contact with wild birds and by human activity, including the movement of live and dead poultry, and fomites such as clothing and vehicles. At present, the possible role of insects in the spread of AIV is dubious. The objective of the present work was to investigate the potential transmission of LPAIV by persistence of the virus in the alimentary tract of house flies, Musca domestica L. (Diptera: Muscidae). Flies were fed three virus concentrations of two AIV strains and then incubated at different temperatures for up to 24 h. The persistence of the two virus strains in the flies declined with increasing incubation temperatures and incubation periods. Similarly, increased virus uptake by the flies increased the persistence of virus. Persistence of infective AIV in flies differed significantly between the two virus strains. The laboratory experiments of the present study indicate that the house fly can be a potential carrier of AIV. url: https://www.ncbi.nlm.nih.gov/pubmed/21661322/ doi: 10.1603/me11017 id: cord-342124-jdv17u86 author: Nieto‐Rabiela, Fabiola title: Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis date: 2019-06-20 words: 4447.0 sentences: 264.0 pages: flesch: 51.0 cache: ./cache/cord-342124-jdv17u86.txt txt: ./txt/cord-342124-jdv17u86.txt summary: title: Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis To address this gap in knowledge, we compared the associative capacity of the host–virus networks in rodents and bats with the identification of those viruses with zoonotic potential. (2015) analyse viral networks between rodents and bats at global scale identifying several ecology factors to explain virus-host associations. The parameter "betweenness" can be used to Impacts • The analysis of virus and host networks (rodents and bats) allows us to measure the potential risk of zoonotic diseases. • Measuring network connectivity can be a useful tool for identifying hosts and viruses of potential importance in the transmission dynamic of zoonotic diseases. Therefore, in this study we aimed to compare and recognize the differences in the associative capacity of the host-virus networks in rodents and bats worldwide, as well as to identify the viruses that may shift across species, including humans, suggesting zoonotic potential. abstract: Bats and rodents are recognized to host a great diversity of viruses and several important viral zoonoses, but how this viral diversity is structured and how viruses are connected, shared and distributed among host networks is not well understood. To address this gap in knowledge, we compared the associative capacity of the host–virus networks in rodents and bats with the identification of those viruses with zoonotic potential. A virus database, detected by molecular methods, was constructed in the two taxonomic groups. We compiled 5,484 records: 825 in rodents and 4,659 in bats. We identified a total of 173 and 166 viruses, of which 53 and 40 are zoonotic viruses, in rodents and bats, respectively. Based on a network theory, a non‐directed bipartite host–virus network was built for each group. Subsequently, the networks were collapsed to represent the connections among hosts and viruses. We identified both discrete and connected communities. We observed a greater degree of connectivity in bat viruses and more discrete communities in rodents. The Coronaviridae recorded in bats have the highest values of degree, betweenness and closeness centralities. In rodents, higher degree positions were distributed homogeneously between viruses and hosts. At least in our database, a higher proportion of rodent viruses were zoonotic. Rodents should thus not be underestimated as important reservoirs of zoonotic disease. We found that viruses were more frequently shared among bats than in rodents. Network theory can reveal some macroecological patterns and identify risks that were previously unrecognized. For example, we found that parvovirus in megabats and Gbagroube virus in rodents may represent a zoonotic risk due to the proximity to humans and other zoonotic viruses. We propose that epidemiological surveillance programmes should consider the connectivity of network actors as a measure of the risks of dispersion and transmission. url: https://doi.org/10.1111/zph.12618 doi: 10.1111/zph.12618 id: cord-013176-6ckuya1w author: Ninfali, Paolino title: Antiviral Properties of Flavonoids and Delivery Strategies date: 2020-08-21 words: 8102.0 sentences: 372.0 pages: flesch: 35.0 cache: ./cache/cord-013176-6ckuya1w.txt txt: ./txt/cord-013176-6ckuya1w.txt summary: Quercetin, extracted from Embelia ribes (Mirsinaceae), exhibited antiviral effects against HCV, exerted through activity inhibition of the viral protease Non-Structural protein 3 (NS3), leading to a decrease in HCV replication [36] . The natural extract of Tetrastigma hemsleyanum (Vitaceae) contains many flavonoids, including vitexin, vitexin-2-O-rhamnoside, isorhamnetin, rutin, kaempferol, astragalin, quercitrin, quercetin and iso-quercetin, which were shown to be able to exert anti-influenza virus activity, with different efficiency, through the reduction of the number of plaques induced by the influenza virus in infected Madin-Darby Canine Kidney (MDCK) cells [21] . In future perspective, this approach could be considered in order to possibly improve the antiviral activity of some flavonoids, like baicalin, that was able, like fludarabine [65] , to act against HIV-1 chronic infection of human monocytes and macrophages, inhibiting the fusion of HIV virus envelope proteins with these cells [73] . abstract: This review summarizes the latest advancements in phytochemicals as functional antiviral agents. We focused on flavonoids, like apigenin, vitexin, quercetin, rutin and naringenin, which have shown a wide range of biological effects including antiviral activities. The molecular mechanisms of their antiviral effects mainly consist in the inhibition of viral neuraminidase, proteases and DNA/RNA polymerases, as well as in the modification of various viral proteins. Mixtures of different flavonoids or combination of flavonoids with antiviral synthetic drugs provide an enhancement of their antiviral effects. Recent strategies in drug delivery significantly contribute to overcoming the low bioavailability of flavonoids. Frequent viral infections worldwide have led to the need for new effective antiviral agents, which can be identified among the various phytochemicals. In this light, screening the antiviral activities of a cocktail of flavonoids would be advantageous in order to prevent viral infections and improve current antiviral therapies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7551920/ doi: 10.3390/nu12092534 id: cord-024188-d7tnku8z author: Nissen, Michael D. title: Respiratory Infections date: 2010-03-27 words: 5267.0 sentences: 249.0 pages: flesch: 39.0 cache: ./cache/cord-024188-d7tnku8z.txt txt: ./txt/cord-024188-d7tnku8z.txt summary: For example, recent findings from the New Vaccine Surveillance Network in the United States show that despite respiratory syncytial virus (RSV), parainfluenza viruses (PIVs), and human coronaviruses (HCoVs) all being common in early childhood; RSV and PIVs are more common causes of hospital admission with acute febrile and respiratory illness than HCoVs [33, 41] . A review of healthy adult human volunteer studies showed that viral shedding increased sharply between 0.5 and 1 day after influenza virus challenge, peaking on day two; shedding can be detected 24 to 28 h before clinical onset, and has a mean duration of 4.8 days; two-thirds of subjects had symptomatic infection, and total symptom scores peaked on day three [11] . Infections due to common viruses that result in disease severe enough to warrant laboratory testing, notification, or hospitalisation occur in the young, the very old, or both, such as with RSV and influenza [9, 14] . 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-001748-7e8px4vx author: Nobach, Daniel title: Shedding of Infectious Borna Disease Virus-1 in Living Bicolored White-Toothed Shrews date: 2015-08-27 words: 4873.0 sentences: 249.0 pages: flesch: 47.0 cache: ./cache/cord-001748-7e8px4vx.txt txt: ./txt/cord-001748-7e8px4vx.txt summary: The bicolored white-toothed shrew (Crocidura leucodon) has recently been identified as reservoir of the neurotropic Borna disease virus 1 (BoDV-1). In animals caught in 2013 (group 1: female #2, male #5, female #6), after an adaption phase of one month, samples of saliva, lacrimal fluid, skin surface, urine and excrements from the BoDV-1-infected shrews were taken weekly over a period of 4 weeks as necessary veterinary care. The five other shrews did not exhibit any evidence for BoDV-1-infection, neither infectious virus nor viral RNA was detected at any time point investigated. Current data from living shrews provide reliable evidence that natural BoDV-1-infection in these animals is indeed clinically inconspicuous over a long time period as already previously assumed [15, 18] despite persistent infection with shedding of infectious virus via various sites. Distribution of Borna Disease Virus Antigen and RNA in Tissues of naturally infected Bicolored White-Toothed Shrews, Crocidura leucodon, supporting their role as Reservoir Host Species abstract: BACKGROUND: Many RNA viruses arise from animal reservoirs, namely bats, rodents and insectivores but mechanisms of virus maintenance and transmission still need to be addressed. The bicolored white-toothed shrew (Crocidura leucodon) has recently been identified as reservoir of the neurotropic Borna disease virus 1 (BoDV-1). PRINCIPAL FINDINGS: Six out of eleven wild living bicoloured white-toothed shrews were trapped and revealed to be naturally infected with BoDV-1. All shrews were monitored in captivity in a long-term study over a time period up to 600 days that differed between the individual shrews. Interestingly, all six animals showed an asymptomatic course of infection despite virus shedding via various routes indicating a highly adapted host-pathogen interaction. Infectious virus and viral RNA were demonstrated in saliva, urine, skin swabs, lacrimal fluid and faeces, both during the first 8 weeks of the investigation period and for long time shedding after more than 250 days in captivity. CONCLUSIONS: The various ways of shedding ensure successful virus maintenance in the reservoir population but also transmission to accidental hosts such as horses and sheep. Naturally BoDV-1-infected living shrews serve as excellent tool to unravel host and pathogen factors responsible for persistent viral co-existence in reservoir species while maintaining their physiological integrity despite high viral load in many organ systems. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4552160/ doi: 10.1371/journal.pone.0137018 id: cord-002407-25cawzi0 author: Nogales, Aitor title: Reverse Genetics Approaches for the Development of Influenza Vaccines date: 2016-12-22 words: 11127.0 sentences: 598.0 pages: flesch: 41.0 cache: ./cache/cord-002407-25cawzi0.txt txt: ./txt/cord-002407-25cawzi0.txt summary: To date, three types of influenza virus vaccines are approved by the Food and Drug Administration (FDA) for human use: recombinant viral HA, inactivated virus and live-attenuated viruses [65] [66] [67] [68] [69] . Plasmid-based reverse genetics for influenza virus allows for the simultaneous expression of the viral components involved in viral genome replication and gene transcription (PB2, PB1, PA and NP) and the eight negative-stranded vRNAs in transfected susceptible cells, which together generate de novo, recombinant IAVs or IBVs (Figure 3 ) [48] . Plasmid-based reverse genetic technologies have allowed the engineering of recombinant influenza viruses that contain single or multiple mutations in the viral genome, which can be potentially implemented as novel or improved vaccine approaches. Importantly, influenza viruses generated by codon deoptimization showed similar viral replication kinetics to WT virus in MDCK cells, which is important for their effective use for vaccine production. abstract: Influenza viruses cause annual seasonal epidemics and occasional pandemics of human respiratory disease. Influenza virus infections represent a serious public health and economic problem, which are most effectively prevented through vaccination. However, influenza viruses undergo continual antigenic variation, which requires either the annual reformulation of seasonal influenza vaccines or the rapid generation of vaccines against potential pandemic virus strains. The segmented nature of influenza virus allows for the reassortment between two or more viruses within a co-infected cell, and this characteristic has also been harnessed in the laboratory to generate reassortant viruses for their use as either inactivated or live-attenuated influenza vaccines. With the implementation of plasmid-based reverse genetics techniques, it is now possible to engineer recombinant influenza viruses entirely from full-length complementary DNA copies of the viral genome by transfection of susceptible cells. These reverse genetics systems have provided investigators with novel and powerful approaches to answer important questions about the biology of influenza viruses, including the function of viral proteins, their interaction with cellular host factors and the mechanisms of influenza virus transmission and pathogenesis. In addition, reverse genetics techniques have allowed the generation of recombinant influenza viruses, providing a powerful technology to develop both inactivated and live-attenuated influenza vaccines. In this review, we will summarize the current knowledge of state-of-the-art, plasmid-based, influenza reverse genetics approaches and their implementation to provide rapid, convenient, safe and more effective influenza inactivated or live-attenuated vaccines. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5297655/ doi: 10.3390/ijms18010020 id: cord-309381-cb80ntxs author: Nogales, Aitor title: Host Single Nucleotide Polymorphisms Modulating Influenza A Virus Disease in Humans date: 2019-09-30 words: 10222.0 sentences: 590.0 pages: flesch: 45.0 cache: ./cache/cord-309381-cb80ntxs.txt txt: ./txt/cord-309381-cb80ntxs.txt summary: IAV RNAs are mainly recognized by the endosomal, membrane-associated PRR Toll-like receptors (TLRs) 3 (double-stranded RNAs, dsRNAs) or 7/8 (ssRNAs), respectively [50, 51] , by the cytoplasmic PRR retinoic acid-inducible gene I (RIG-I), which detects dsRNA and 5 -triphosphates of the negative ssRNA viral genome [50, 52] , generated during replication of multiple viruses, by the NOD-like receptor family member NOD-, LRR-and pyrin domain-containing 3 (NLRP3), which recognizes various stimuli (see below) [53] and by the absent in melanoma 2 (AIM2) protein, recognizing not well-characterized influenza stimuli [54] . Another important SNP (rs34481144) associated with risk of severe influenza in humans from the United States (US) infected with seasonal IAVs is located in the 5 -UTR of the IFITM3 gene [123, 124] . abstract: A large number of human genes associated with viral infections contain single nucleotide polymorphisms (SNPs), which represent a genetic variation caused by the change of a single nucleotide in the DNA sequence. SNPs are located in coding or non-coding genomic regions and can affect gene expression or protein function by different mechanisms. Furthermore, they have been linked to multiple human diseases, highlighting their medical relevance. Therefore, the identification and analysis of this kind of polymorphisms in the human genome has gained high importance in the research community, and an increasing number of studies have been published during the last years. As a consequence of this exhaustive exploration, an association between the presence of some specific SNPs and the susceptibility or severity of many infectious diseases in some risk population groups has been found. In this review, we discuss the relevance of SNPs that are important to understand the pathology derived from influenza A virus (IAV) infections in humans and the susceptibility of some individuals to suffer more severe symptoms. We also discuss the importance of SNPs for IAV vaccine effectiveness. url: https://doi.org/10.3390/pathogens8040168 doi: 10.3390/pathogens8040168 id: cord-003166-k3jxvzfi author: Noh, Ji Yeong title: Isolation and characterization of novel bat paramyxovirus B16-40 potentially belonging to the proposed genus Shaanvirus date: 2018-08-22 words: 4670.0 sentences: 244.0 pages: flesch: 51.0 cache: ./cache/cord-003166-k3jxvzfi.txt txt: ./txt/cord-003166-k3jxvzfi.txt summary: Even though the HN amino acids sequences were similar to those from viruses in the proposed genera Shaanvirus, it was also related to that of Sendai virus and human parainfluenza virus 1, which belong to a different genus, Respirovirus showing (Table 1) . In addition, among three pooled sera (two mouse sera each) against human parainfluenza virus 1 (KBPV-VR-44), one pooled serum was cross-reactive to the bat paramyxovirus B16-40 with 40 as the end-point titer for the fluorescent signal ( Table 2 , Fig. 4 ). Notably, even though the HN amino acids sequences were similar to those from viruses in the proposed genera Shaanvirus, it was also related to that of Sendai virus and human parainfluenza virus 1, which belong to a different genus, Respirovirus (Table 1) . In fact, in this study, when mouse antisera were made and tested against bat paramyxovirus B16-40 and human parainfluenza virus 1 (KBPV-VR-44), the two viruses were partially cross-reactive to each other in an indirect immunofluorescence assay. abstract: The bat paramyxovirus B16-40 was first isolated in Korea in this study. Using the isolated virus, we could obtain not only genomic information, but also several biological characteristics of the virus. In the phylogenetic analysis, the virus was found to belong to the recently proposed genus Shaanvirus. Through sequence analyses and in vitro testing, the isolated virus was also found to have haemagglutinin-neuraminidase (HN) protein as one of the structural proteins. When mouse antiserum was generated against the isolated virus and tested, it was cross-reactive to human parainfluenza virus 1 in an indirect immunofluorescence assay but could not cross-neutralize human parainfluenza virus 1. In addition, the bat paramyxovirus B16-40 was not infectious in the mouse model. Collectively, this study provided basic information on further classification of the bat paramyxovirus B16-40 and related viruses in the proposed genus Shaanvirus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6105681/ doi: 10.1038/s41598-018-30319-7 id: cord-285547-7m3dh8hu author: Nomura, Naoki title: Characterization of avian influenza viruses isolated from domestic ducks in Vietnam in 2009 and 2010 date: 2011-11-09 words: 3271.0 sentences: 154.0 pages: flesch: 51.0 cache: ./cache/cord-285547-7m3dh8hu.txt txt: ./txt/cord-285547-7m3dh8hu.txt summary: In the present study, a surveillance of avian influenza was carried out in Vietnam in domestic ducks and wild birds in 2009 and 2010, and the isolates were antigenically and phylogenetically analyzed and their pathogenicity in birds and mammals was assessed. One hundred tracheal and cloacal swab samples that were viral gene positive from 600 domestic ducks and 207 wild birds (night heron, Nycticorax nycticorax; grey heron, Ardea cinerea; purple heron, Ardea purpurea; chinese pond heron, Ardeola bacchus; chinese egret, Egretta eulophotes; little egret, Egretta garzetta; intermediate egret, Egretta intermedia; cormorant, Phalacrocorax carbo; little cormorant, Microcarbo niger; Japanese bush warbler, Cettia diphone; black-browed reed warbler, Acrocephalus bistrigiceps; olive bulbul, Iole virescens; black capped kingfisher, Halcyon pileata; collared kingfisher, Halcyon chloris; racket tailed treepie, Crypsirina temia; oriental magpie robin, Copsychus saularis; tiger shrike, Lanius tigrinus; yellow bittern, Ixobrychus sinensis; indian cuckoo, Cuculus micropterus; common koel, Eudynamys scolopacea; and black collared starling, Sturnus nigricollis) in April 2009 and March 2010 in southern Vietnam were inoculated into the allantoic cavities of 10-day-old embryonated chicken eggs. abstract: In the surveillance of avian influenza in Vietnam, 26 H9N2, 1 H3N2, 1 H3N8, 7 H4N6, 3 H11N3, and 1 H11N9 viruses were isolated from tracheal and cloacal swab samples of 300 domestic ducks in April 2009, and 1 H9N6 virus from 300 bird samples in March 2010. Out of the 27 H9 virus isolates, the hemagglutinins of 18 strains were genetically classified as belonging to the sublineage G1, and the other nine belonged to the Korean sublineage. Phylogenetic analysis revealed that one of the 27 H9 viruses was a reassortant in which the PB2 gene belonged to the Korean sublineage and the other seven genes belonged to the G1 sublineage. Three representative H9N2 viruses were intranasally inoculated into ducks, chickens, pigs, and mice. On the basis of experimental infection studies, it was found that each of the three viruses readily infected pigs and replicated in their upper respiratory tracts, and they infected chickens with slight replication. Viruses were recovered from the lungs of mice inoculated with two of the three isolates. The present results reveal that H9 avian influenza viruses are prevailing and genetic reassortment occurs among domestic ducks in Vietnam. It is recommended that careful surveillance of swine influenza with H9 viruses should be performed to prepare for pandemic influenza. url: https://www.ncbi.nlm.nih.gov/pubmed/22068881/ doi: 10.1007/s00705-011-1152-3 id: cord-030279-pv770doe author: Novossiolova, Tatyana title: Twenty-first Century Governance Challenges in the Life Sciences date: 2016-11-29 words: 15222.0 sentences: 743.0 pages: flesch: 42.0 cache: ./cache/cord-030279-pv770doe.txt txt: ./txt/cord-030279-pv770doe.txt summary: From ''dual-use life science research of concern'' through the rise of amateur biology to the advent of personalised medicine, the chapter exposes the limitations of the existing governance mechanisms in accommodating the multifaceted ethical, social, security, and legal concerns arising from cutting-edge scientific and technological developments. Indeed, rapid advances in the field have produced a knowledge base and set of tools and techniques that enable biological processes to be understood, manipulated and controlled to an extent never possible before 5 ; they have found various applications in numerous spheres of life, generating enormous benefits and offering bright prospects for human betterment; and they have come to be regarded as a key driver of economic development with potential to close the gap between resource-rich and resource-poor countries. abstract: The chapter explores the rapid advancement of biotechnology over the past few decades, outlining an array of factors that drive innovation and, at the same time, raise concerns about the extent to which the scope and pace of novel life science developments can be adequately governed. From ‘dual-use life science research of concern’ through the rise of amateur biology to the advent of personalised medicine, the chapter exposes the limitations of the existing governance mechanisms in accommodating the multifaceted ethical, social, security, and legal concerns arising from cutting-edge scientific and technological developments. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7416832/ doi: 10.1007/978-3-319-51004-0_4 id: cord-353509-yfkiaq80 author: Nugraha, Rhea Veda title: Traditional Herbal Medicine Candidates as Complementary Treatments for COVID-19: A Review of Their Mechanisms, Pros and Cons date: 2020-10-10 words: 7433.0 sentences: 413.0 pages: flesch: 48.0 cache: ./cache/cord-353509-yfkiaq80.txt txt: ./txt/cord-353509-yfkiaq80.txt summary: This review discusses some herbal agents extracted from various plants, including Echinacea, Cinchona, Curcuma longa, and Curcuma xanthorrhiza, which are considered for the treatment of COVID-19. e single cause of this highly communicable disease is a novel coronavirus, called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the seventh known virus of the Coronaviridae family capable of infecting humans [2] . Studies that describe the relation of some herbal drugs with the molecular mechanisms of COVID-19 infection, treatment, and prevention remain to be explained. in their systematic review about convalescent plasma transfusion (CPT) for the treatment of COVID-19 suggested that CPT could be an effective therapeutic option with promising evidence on safety, improvement of clinical symptoms, and reduced mortality, in addition to antiviral/antimicrobial drugs. A clinical trial study is needed to confirm the effect of using curcumin as a preventive agent against COVID-19. abstract: Coronavirus disease 2019 (COVID-19) is a new infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that belongs to the coronavirus family. The first case was reported in December 2019, and the disease has become a pandemic. Impaired immune regulation is one of the factors that play a role in its pathogenesis and results in poor outcomes of COVID-19 patients. There have been many studies with drug candidates used as antivirals or immunomodulators. However, the results of these investigations showed that the drug candidates were not significantly effective against the disease. Meanwhile, people believe that consuming herbal immunomodulators can prevent or even cure COVID-19. Unfortunately, specific preclinical and clinical trials to evaluate the effects of herbal immunoregulators have not been conducted. Certain natural compounds might be effective for the treatment of COVID-19 based on general concepts from previous experiments. This review discusses some herbal agents extracted from various plants, including Echinacea, Cinchona, Curcuma longa, and Curcuma xanthorrhiza, which are considered for the treatment of COVID-19. In addition, we discuss the pros and cons of utilising herbal medicine during the COVID-19 pandemic, draw some conclusions, and make recommendations at the end of the session. url: https://doi.org/10.1155/2020/2560645 doi: 10.1155/2020/2560645 id: cord-002136-mkl89qkt author: Nunes, Sandro F. title: An ex vivo swine tracheal organ culture for the study of influenza infection date: 2009-12-09 words: 4719.0 sentences: 241.0 pages: flesch: 45.0 cache: ./cache/cord-002136-mkl89qkt.txt txt: ./txt/cord-002136-mkl89qkt.txt summary: Objectives We aimed to develop an air interface EVOC using pig tracheas in the study of influenza infection demonstrating that tracheal explants can be effectively maintained in organ culture and support productive influenza infection. 1, 3 Influenza infection in humans and pigs is primarily restricted to the upper and lower respiratory tract with viral replication occurring in the epithelial cells present on the surface of the respiratory mucosa. Ex vivo organ cultures (EVOC) of tracheal explants with an air interface system have been successfully developed and used in the study of both human and animal respiratory pathogens. To determine if the swine tracheal explants supported productive viral replication, explants were infected with 2AE5 · 10 2 pfu of swine influenza virus and maintained in organ culture for 5 days. Cultures of equine respiratory epithelial cells and organ explants as tools for the study of equine influenza virus infection abstract: Background The threat posed by swine influenza viruses with potential to transmit from pig populations to other hosts, including humans, requires the development of new experimental systems to study different aspects of influenza infection. Ex vivo organ culture (EVOC) systems have been successfully used in the study of both human and animal respiratory pathogens. Objectives We aimed to develop an air interface EVOC using pig tracheas in the study of influenza infection demonstrating that tracheal explants can be effectively maintained in organ culture and support productive influenza infection. Methods Tracheal explants were maintained in the air interface EVOC system for 7 days. Histological characteristics were analysed with different staining protocols and co‐ordinated ciliary movement on the epithelial surface was evaluated through a bead clearance assay. Explants were infected with a swine H1N1 influenza virus. Influenza infection of epithelial cells was confirmed by immunohistochemistry and viral replication was quantified by plaque assays and real‐time RT‐PCR. Results Histological analysis and bead clearance assay showed that the tissue architecture of the explants was maintained for up to 7 days, while ciliary movement exhibited a gradual decrease after 4 days. Challenge with swine H1N1 influenza virus showed that the EVOC tracheal system shows histological changes consistent with in vivo influenza infection and supported productive viral replication over multiple cycles of infection. Conclusion The air interface EVOC system using pig trachea described here constitutes a useful biological tool with a wide range of applications in the study of influenza infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941949/ doi: 10.1111/j.1750-2659.2009.00119.x id: cord-035015-slgywe0c author: Nunn, Alistair V. W. title: SARS-CoV-2 and mitochondrial health: implications of lifestyle and ageing date: 2020-11-09 words: 14660.0 sentences: 715.0 pages: flesch: 36.0 cache: ./cache/cord-035015-slgywe0c.txt txt: ./txt/cord-035015-slgywe0c.txt summary: Data is now showing that COVID-19 patients do have populations of T-cells displaying mitochondrial dysfunction, as well as altered mitochondrial markers in monocyteshinting that immune-metabolic phenotyping could be used to understand disease pathogenesis and possible treatments; this could include targeting mitochondria [32] . The underlying aetiology for "inflammaging" has long thought to be associated with mitochondrial dysfunction as suggested by Nick Lane in 2003 in his "double agent" theory [5] , and is now receiving renewed interest, for instance, in how decreasing mitochondrial function can reduce T-cell function and enhance immune senescence, as mitochondria are pivotal in metabolic reprogramming towards the Warburg effect [40] . Furthermore, as evidence indicates that many viruses, which most likely include SARs-CoV-2, modulate bioenergetics and redox in both the immune system and other cells they infect to enhance their own replication, they could potentially induce excessive stress in these systems if their mitochondria are already sub-optimally functional. abstract: Infection with SARs-COV-2 displays increasing fatality with age and underlying co-morbidity, in particular, with markers of the metabolic syndrome and diabetes, which seems to be associated with a “cytokine storm” and an altered immune response. This suggests that a key contributory factor could be immunosenescence that is both age-related and lifestyle-induced. As the immune system itself is heavily reliant on mitochondrial function, then maintaining a healthy mitochondrial system may play a key role in resisting the virus, both directly, and indirectly by ensuring a good vaccine response. Furthermore, as viruses in general, and quite possibly this new virus, have also evolved to modulate immunometabolism and thus mitochondrial function to ensure their replication, this could further stress cellular bioenergetics. Unlike most sedentary modern humans, one of the natural hosts for the virus, the bat, has to “exercise” regularly to find food, which continually provides a powerful adaptive stimulus to maintain functional muscle and mitochondria. In effect the bat is exposed to regular hormetic stimuli, which could provide clues on how to resist this virus. In this paper we review the data that might support the idea that mitochondrial health, induced by a healthy lifestyle, could be a key factor in resisting the virus, and for those people who are perhaps not in optimal health, treatments that could support mitochondrial function might be pivotal to their long-term recovery. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7649575/ doi: 10.1186/s12979-020-00204-x 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-290149-eed4v2jl author: ODEND''HAL, STEWART title: Porcine Hemagglutinating Encephalomyelitis Virus date: 2012-12-02 words: 221.0 sentences: 24.0 pages: flesch: 32.0 cache: ./cache/cord-290149-eed4v2jl.txt txt: ./txt/cord-290149-eed4v2jl.txt summary: key: cord-290149-eed4v2jl title: Porcine Hemagglutinating Encephalomyelitis Virus This chapter provides an overview of the classification, description, hosts, key developments, diagnostic techniques, and diagnostic reagents for porcine hemagglutinating encephalomyelitis virus. Porcine hemagglutinating encephalomyelitis virus causes two distinct syndromes; one is known as vomiting and wasting disease, and the other involves encephalomyelitis. The hosts of porcine hemagglutinating encephalomyelitis virus are pigs. Vomiting and wasting disease and encephalomyelitis were initially reported as two separate diseases in Canada in the late 1950s. Porcine hemagglutinating encephalomyelitis virus was isolated in 1962, and the common etiology of the two syndromes was shown in 1969. The diagnostic techniques for porcine hemagglutinating encephalomyelitis virus are virus neutralisation (VN) and agar gel immunodiffusion (AGID). To day in Canada the virus is endemic and antibodies can be demonstrated, but the disease syndrome is no longer evident (5). abstract: This chapter provides an overview of the classification, description, hosts, key developments, diagnostic techniques, and diagnostic reagents for porcine hemagglutinating encephalomyelitis virus. Porcine hemagglutinating encephalomyelitis virus belongs to the family Coronaviridae; genus Coronavirus; and species Porcine hemagglutinating encephalomyelitis virus (HEV). Porcine hemagglutinating encephalomyelitis virus causes two distinct syndromes; one is known as vomiting and wasting disease, and the other involves encephalomyelitis. The hosts of porcine hemagglutinating encephalomyelitis virus are pigs. Vomiting and wasting disease and encephalomyelitis were initially reported as two separate diseases in Canada in the late 1950s. Porcine hemagglutinating encephalomyelitis virus was isolated in 1962, and the common etiology of the two syndromes was shown in 1969. The diagnostic techniques for porcine hemagglutinating encephalomyelitis virus are virus neutralisation (VN) and agar gel immunodiffusion (AGID). url: https://www.sciencedirect.com/science/article/pii/B978012524180950087X doi: 10.1016/b978-0-12-524180-9.50087-x id: cord-303297-fiievwy7 author: Oberemok, Volodymyr V. title: SARS-CoV-2 will continue to circulate in the human population: an opinion from the point of view of the virus-host relationship date: 2020-04-30 words: 4082.0 sentences: 174.0 pages: flesch: 49.0 cache: ./cache/cord-303297-fiievwy7.txt txt: ./txt/cord-303297-fiievwy7.txt summary: In this article, we will concentrate on the facts currently available about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has caused COVID-19 (coronavirus disease 2019) pandemic and try to predict its development and consequences based on the virus-host relationship. In addition, it seems that the virus is also more likely to affect the heart than any other similar viruses, so although pneumonia is often the main cause of death, cardiologists and infectionists, for example in Russia, are seeing infected patients whose worst symptoms are not respiratory, but cardiac and many people infected with COVID-19 are dying from heart attacks, as a possible complication of SARS-CoV-2 infection. Despite the initial reports stating that most of the laboratory-confirmed infected patients (27 of 41 cases) had links to the Wuhan seafood market where different animals, including bats, snakes, birds, pangolins, and other small mammals are normally traded within the market [6] , it is now obvious that the newly identified coronavirus SARS-CoV-2 is transmitted with enormous efficacy from human to human via respiratory droplets or close contact. abstract: At the population level, the virus-host relationship is not set up to end with the complete elimination of either or both. Pathogen-resistant individuals will always remain in the host population. In turn, the virus can never completely eliminate the host population, because evolutionarily such an event is a dead end for the virus as an obligate intracellular parasite. A certain existential balance exists in the virus-host relationship. Against this backdrop, viral epidemics and pandemics only become manifest and egregious to human beings when tens and hundreds of thousands of people die and the question emerges what caused the high mortality peaks on the death chart. The answer seems clear; the emerging strain of the virus is new to the host population, and new mutations of the virus and natural selection will lead to a survival of only genetically resistant individuals in a host population. The dangers inherent to a novel virus are due to new features generally inthe molecular structure of proteins, which enable the virus to infect the cells of the host organism more intensively, dramatically challenging host immunity, and thus be transmitted more readily in the host population. In this article, we will concentrate on the facts currently available about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has caused COVID-19 (coronavirus disease 2019) pandemic and try to predict its development and consequences based on the virus-host relationship. In fact, only two scenarios will occur simultaneously in the very near future: people who are genetically resistant to the virus will get sick, recover, and develop immunity, while people who are sensitive to the virus will need drugs and vaccines, which will have to be researched and developed if they are to recover. If the pandemic does not stop, in a few decades it is anticipated that SARS-CoV-2 will become as safe as the four non-severe acute respiratory syndrome human coronaviruses (HCoV-NL63, HCoV-HKU1, HCoV-OC43, and HCoV-229E) currently circulating but causing low mortality in the human population. url: https://www.ncbi.nlm.nih.gov/pubmed/32350571/ doi: 10.1007/s00011-020-01352-y id: cord-000238-om92cx5q author: Ogbunugafor, C. Brandon title: On the possible role of robustness in the evolution of infectious diseases date: 2010-06-30 words: 6717.0 sentences: 347.0 pages: flesch: 39.0 cache: ./cache/cord-000238-om92cx5q.txt txt: ./txt/cord-000238-om92cx5q.txt summary: We also draw attention to other infectious disease systems where robustness theory may prove useful for bridging evolutionary biology and biomedicine, especially the evolution of antibiotic resistance in bacteria, immune evasion by influenza, and malaria parasite infections. [14] [15] [16] In reviewing these results, we hope to highlight the importance of empirical work in RNA viruses for testing theory pertaining to robustness, as well as for better understanding the evolutionary biology and evolvability of infectious organisms in general. 1 However, theory and artificial-life data 9 support the idea that genetic robustness should be strongly favored when populations experience elevated mutation rates, suggesting that RNA viruses would be fruitful systems to explore how genetic robustness evolves. [33] [34] [35] Regardless, preliminary experiments showed that UVC exposure for periods up to 30 min greatly increased mortality in wild type phage 6 ͑Fig. 2͒, indicating that this environmental effect should produce strong selection for UVC resistance in populations of the virus. abstract: Robustness describes the capacity for a biological system to remain canalized despite perturbation. Genetic robustness affords maintenance of phenotype despite mutational input, necessarily involving the role of epistasis. Environmental robustness is phenotypic constancy in the face of environmental variation, where epistasis may be uninvolved. Here we discuss genetic and environmental robustness, from the standpoint of infectious disease evolution, and suggest that robustness may be a unifying principle for understanding how different disease agents evolve. We focus especially on viruses with RNA genomes due to their importance in the evolution of emerging diseases and as model systems to test robustness theory. We present new data on adaptive constraints for a model RNA virus challenged to evolve in response to UV radiation. We also draw attention to other infectious disease systems where robustness theory may prove useful for bridging evolutionary biology and biomedicine, especially the evolution of antibiotic resistance in bacteria, immune evasion by influenza, and malaria parasite infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909313/ doi: 10.1063/1.3455189 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: 4788.0 sentences: 282.0 pages: flesch: 44.0 cache: ./cache/cord-276348-vr5fit8r.txt txt: ./txt/cord-276348-vr5fit8r.txt summary: 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. 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. Children at increased risk from RSV infection include young infants with prematurity, bronchopulmonary dysplasia, congenital heart disease, congenital or acquired immunodeficiency, subjects with hematologic malignancies, patients with bone-marrow or organ transplants, and cystic fibrosis. 6 It is important to recognise that virtually all children who get infected with RSV develop virus-specific IgE homocytotropic antibody in the respiratory tract. 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-020712-l9cn0n99 author: Ohnishi, Shun-Ichi title: Chapter 9 Fusion of Viral Envelopes with Cellular Membranes date: 2008-05-30 words: 11708.0 sentences: 735.0 pages: flesch: 56.0 cache: ./cache/cord-020712-l9cn0n99.txt txt: ./txt/cord-020712-l9cn0n99.txt summary: Residues 80-100 in El and residues 100-131 in G, which have sequence homology among the strains, may be such stretches though not strongly hydrophobic (Table 262 SHUN-ICHI OHNlSHl and the putative fusogenic segment should be able to interact with the target membrane, inducing some disturbance eventually leading to fusion (Fig. Ib) . Presence of receptors for the amino-terminal segments in target membranes has been suggested from studies on inhibition of virus replication by small peptides with amino acid sequences similar to that of the viral amino terminus (Richardson et al., 1980; Richardson and Choppin, 1983) . Why is a specific amino acid sequence of F glycoprotein required for the membrane fusion reaction between envelope of HVJ (Sendai virus) and target cell membranes? pH-Dependent membrane fusion activity of a synthetic twenty amino acid peptide with the same sequence as that of the hydrophobic segment in influenza virus hemagglutinin abstract: This chapter reviews some characteristic features of membrane fusion activity for each virus and discusses the mechanisms of membrane fusion, especially low pH-induced membrane fusion. It concentrates on the interaction of the hydrophobic segment with the target cell membrane lipid bilayer and suggests the entrance of the segment into the lipid bilayer hydrophobic core as a key step in fusion. The envelope is a lipid bilayer membrane with the virus specific glycoproteins spanning it. The bilayer originates from the host cell membrane and has a lipid composition and transbilayer distribution quite similar to the host's. The viral glycoproteins have the functions of binding to the target cell surface and fusion with the cell membranes. The two functions are carried by a single glycoprotein in influenza virus (HA), vesicular stomatitis virus (VSV) G glycoprotein, and Semliki Forest virus SFV E glycoprotein. In Sendai virus (HVJ), the functions are carried by separate glycoproteins, hemagglutinin-neuraminidase (HN) for binding and fusion glycoprotein (F) for fusion. When viruses encounter target cells, they first bind to the cell surface through an interaction of the viral glycoprotein with receptors. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7146812/ doi: 10.1016/s0070-2161(08)60137-9 id: cord-345359-okmkgsbr author: Ohno, Marumi title: Influenza virus infection affects insulin signaling, fatty acid-metabolizing enzyme expressions, and the tricarboxylic acid cycle in mice date: 2020-07-02 words: 6474.0 sentences: 314.0 pages: flesch: 45.0 cache: ./cache/cord-345359-okmkgsbr.txt txt: ./txt/cord-345359-okmkgsbr.txt summary: After infecting mice with intranasal applications of 500 plaque-forming units of A/Puerto Rico/8/34 (H1N1; PR8) virus, the serum levels of most intermediates in the tricarboxylic acid (TCA) cycle and related metabolic pathways were significantly reduced. www.nature.com/scientificreports/ investigated metabolic changes by determining the serum levels of metabolites, insulin sensitivity in the liver, glucose availability, and hepatic gene expressions in the early stages of symptom onset as well as the lethal phase of influenza in a mouse model. The results of this study indicate that influenza virus infection dysregulates glucose and fatty acid metabolism and decreases tricarboxylic acid (TCA) cycle activity, leading to enhanced degradation of adenosine triphosphate (ATP) and guanosine triphosphate (GTP). Metabolites that were present at reduced levels in the sera of PR8 virus-infected mice were mainly related to the TCA cycle, urea cycle, and amino acid metabolism, as indicated by the serum levels of metabolite in these pathways at 1, 3, and 6 dpi (Fig. 2) . abstract: Although the severity of influenza virus infections has been associated with host energy metabolism, the related mechanisms have not yet been clarified. Here we examined the effects of influenza virus infection on host energy metabolism in mice. After infecting mice with intranasal applications of 500 plaque-forming units of A/Puerto Rico/8/34 (H1N1; PR8) virus, the serum levels of most intermediates in the tricarboxylic acid (TCA) cycle and related metabolic pathways were significantly reduced. These data suggest that substrate supply to the TCA cycle is reduced under these conditions, rather than specific metabolic reactions being inhibited. Then, we focused on glucose and fatty acid metabolism that supply substrates to the TCA cycle. Akt phosphorylation following insulin injections was attenuated in the livers of PR8 virus-infected mice. Furthermore, glucose tolerance tests revealed that the PR8 virus-infected mice showed higher blood glucose levels than the vehicle-inoculated control mice. These results suggest that influenza virus infection impairs insulin signaling, which regulates glucose uptake. However, increases in the hepatic expressions of fatty acid-metabolizing enzymes suggest that fatty acids accumulate in liver cells of infected mice. Collectively, our data indicate that influenza virus infection dysregulates host energy metabolism. This line of investigation provides novel insights into the pathogenesis of influenza. url: https://doi.org/10.1038/s41598-020-67879-6 doi: 10.1038/s41598-020-67879-6 id: cord-355771-pxkkd3s1 author: Olagnier, David title: Oncolytic Viral Immunotherapy in the Time of COVID-19 date: 2020-11-04 words: 1793.0 sentences: 81.0 pages: flesch: 38.0 cache: ./cache/cord-355771-pxkkd3s1.txt txt: ./txt/cord-355771-pxkkd3s1.txt summary: The 2020 global pandemic of Covid-19 has refocused the entire scientific community towards understanding the SARS coronavirus-2 (SARS-CoV-2) and developing urgently needed therapies and vaccines to halt the spread of this newly emerging virus. In this special issue of Cytokines and Growth Factor Reviews -Oncolytic Viral Immunotherapy 2020, international experts discuss the innovative approaches developed for OV-based immunotherapies. Interferons (IFNs) are the most potent anti-viral cytokines induced by virus-infected cells and can reduce the efficacy of OVs. However, many types of cancer cells have been shown to be compromised in terms of generating a potent IFN antiviral state, thus making these tumours a particularly sensitive niche population for oncolytic virus replication. Four reviews in this issue describe our current understanding of the factors that can contribute to a successful super-spreading oncolytic and immune stimulating event within tumours. abstract: nan url: https://doi.org/10.1016/j.cytogfr.2020.10.009 doi: 10.1016/j.cytogfr.2020.10.009 id: cord-317508-03u2vtzk author: Oldstone, M.B.A. title: History of Virology date: 2019-08-28 words: 1347.0 sentences: 73.0 pages: flesch: 53.0 cache: ./cache/cord-317508-03u2vtzk.txt txt: ./txt/cord-317508-03u2vtzk.txt summary: were clinically evident in early human history, the initial isolation of individual viruses and their assignment to specific diseases did not occur until about 1898, 120 years ago, a proverbial drop in the bucket of time. Although the majority of life-threatening and debilitating acute virus infections are now controlled through vaccination, it is worthwhile considering the consequences of acute infections like smallpox, measles, and yellow fever in the prevaccine era. This devastating depopulation came primarily from smallpox and measles infections, since these viruses had never before existed in the New World (Oldstone, 2010) . However, measles virus infection was and remains a serious disease today with approximately one per thousand infected persons developing severe destruction of the central nervous system requiring institutionalization. Now these and many other acute virus infections are controlled by vaccination or antivirals and public health policies when and where they are instituted. abstract: The history of virology can be traced as the personalities involved have described their concepts and published their experimental results. Although infections we now know as, e.g., rabies, yellow fever, smallpox, etc. were clinically evident in early human history, the initial isolation of individual viruses and their assignment to specific diseases did not occur until about 1898, 120 years ago, a proverbial drop in the bucket of time. Just one lifetime ago, Peter Medawar, awarded the Nobel Prize in Medicine and Physiology in 1960, defined viruses as a piece of nucleic acid surrounded by bad news. url: https://www.sciencedirect.com/science/article/pii/B9780128012383000787 doi: 10.1016/b978-0-12-801238-3.00078-7 id: cord-010222-5oxie0zc author: Oldstone, Michael B.A. title: Virus-induced autoimmunity: Molecular mimicry as a route to autoimmune disease date: 2004-04-11 words: 2752.0 sentences: 125.0 pages: flesch: 39.0 cache: ./cache/cord-010222-5oxie0zc.txt txt: ./txt/cord-010222-5oxie0zc.txt summary: Because the studies described above indicate that many viruses share antigenic determinants (linear or conformation) with normal host proteins, the next step was to determine experimentally whether molecular mimicry could elicit autoimmune diseases. The most likely explanation for how molecular mimicry causes disease is that an immune response against the determinant shared by host and virus takes the form of a tissue-specific attack, presumably capable of destroying cells and eventually the tissue. In any case, molecular mimicry would occur only when the virus and host determinants are sufficiently similar to induce a cross-reactive response yet different enough to break B or T-cell immunologic tolerance. Thus, the human AChR a-chain 160-167 peptide specifically cross-reacts with a shared homologous domain on herpes simplex virus glycoprotein D, residues 286-293, by binding and inhibition studies, and elicits antibodies in myasthenic patients that bind to the native AChR protein; these antibodies are capable of causing a biologic effect. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172880/ doi: 10.1016/0896-8411(89)90130-3 id: cord-023740-g84fa45m author: Oldstone, Michael B.A. title: Mimicry by Virus of Host Molecules: Implications for Autoimmune Disease date: 2014-06-27 words: 2498.0 sentences: 117.0 pages: flesch: 41.0 cache: ./cache/cord-023740-g84fa45m.txt txt: ./txt/cord-023740-g84fa45m.txt summary: Monoclonal antibodies against 11 different viruses including DNA and RNA viruses known to cause human infection from the herpes virus group, vaccinia virus, myxoviruses, paramyxoviruses, arenaviruses, flaviviruses, alphaviruses, rhabdovirus, and coronaviruses cross-react with host cell determinants expressed on uninfected tissues. other examples (reviewed in Oldstone and Notkins, 1986 ) suggest a mechanism whereby immune reactants directed against a viral or microbial component may cross-react with a host component and generate autoimmune disease. Since, on the basis of antibody cross-reactivity, many viruses share antigenic sites with normal host cell components, the next step was to look for crossreactive capability in eliciting autoimmunity and related disease. The most likely mechanism by which molecular mimicry would cause disease is by eliciting an immune response against a determinant shared between the host and the virus to bring forth a tissue-specific immune response, presumably capable of destroying cells and eventually the tissue. abstract: Molecular mimicry defines the shared identity of molecules from disparate genes or proteins. Thus, although their origins are as separate as a virus and the self-determinant of a human or lower animal, two molecules' linear amino acid sequences or their conformational fits may be shared. Such molecular homologies between proteins occur frequently and likely play roles in the processing of viral proteins inside cells. The homologies shared between viruses and host cytoskeletal proteins likely indicate that shared determinants on cell linker proteins guided viral proteins along highways and stop points inside cells. Most importantly, these unexpected cross-reactivities have broad and major implications for understanding autoimmune disease. Molecular mimicry is detected either by using humoral or cellular immune components, that cross-react with two presumably unrelated protein structures, or by computer searches to match descriptions of proteins in storage banks. The use of both these approaches to define molecular mimicry and establish its potential role in autoimmune disease is the topic of this chapter. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173565/ doi: 10.1016/b978-0-12-174685-8.50079-2 id: cord-307918-8y89p11a author: Onyango, Clayton O. title: Influenza Surveillance Among Children With Pneumonia Admitted to a District Hospital in Coastal Kenya, 2007–2010 date: 2012-12-15 words: 3678.0 sentences: 155.0 pages: flesch: 42.0 cache: ./cache/cord-307918-8y89p11a.txt txt: ./txt/cord-307918-8y89p11a.txt summary: Nasopharyngeal samples from children aged <12 years who were admitted to Kilifi District Hospital during 2007–2010 with severe or very severe pneumonia and resided in the local demographic surveillance system were screened for influenza A, B, and C viruses by molecular methods. The following clinical and laboratory features obtained on admission or that relate to discharge outcome were compared between influenza-positive and influenza-negative children: duration of hospitalization >14 days, very severe pneumonia, wheezing, hypoxia (oxygen saturation level <90%, by fingertip pulse oximetry), circulatory shock (capillary refill time ≥3 seconds), severe anemia (hemoglobin level <5 g/dL), prematurity, congenital heart disease, positivity for HIV antibody (by 2 rapid tests), severe underweight (weight for age Z score ≤3), slide positivity for Plasmodium species, bacteremia, concurrent viral infection diagnosis, and death before discharge [2] . Our study identified all 3 influenza viruses in circulation in this rural coastal Kenya location among patients hospitalized with severe or very severe pneumonia and among outpatients with URTI. abstract: Background. Influenza data gaps in sub-Saharan Africa include incidence, case fatality, seasonal patterns, and associations with prevalent disorders. Methods. Nasopharyngeal samples from children aged <12 years who were admitted to Kilifi District Hospital during 2007–2010 with severe or very severe pneumonia and resided in the local demographic surveillance system were screened for influenza A, B, and C viruses by molecular methods. Outpatient children provided comparative data. Results. Of 2002 admissions, influenza A virus infection was diagnosed in 3.5% (71), influenza B virus infection, in 0.9% (19); and influenza C virus infection, in 0.8% (11 of 1404 tested). Four patients with influenza died. Among outpatients, 13 of 331 (3.9%) with acute respiratory infection and 1 of 196 without acute respiratory infection were influenza positive. The annual incidence of severe or very severe pneumonia, of influenza (any type), and of influenza A, was 1321, 60, and 43 cases per 100 000 <5 years of age, respectively. Peak occurrence was in quarters 3–4 each year, and approximately 50% of cases involved infants: temporal association with bacteremia was absent. Hypoxia was more frequent among pneumonia cases involving influenza (odds ratio, 1.78; 95% confidence interval, 1.04–1.96). Influenza A virus subtypes were seasonal H3N2 (57%), seasonal H1N1 (12%), and 2009 pandemic H1N1 (7%). Conclusions. The burden of influenza was small during 2007–2010 in this pediatric hospital in Kenya. Influenza A virus subtype H3N2 predominated, and 2009 pandemic influenza A virus subtype H1N1 had little impact. url: https://doi.org/10.1093/infdis/jis536 doi: 10.1093/infdis/jis536 id: cord-317971-kuwargnp author: Opatz, Till title: Thoughts on What Chemists Can Contribute to Fighting SARS‐CoV‐2 – A Short Note on Hand Sanitizers, Drug Candidates and Outreach date: 2020-05-08 words: 2881.0 sentences: 176.0 pages: flesch: 53.0 cache: ./cache/cord-317971-kuwargnp.txt txt: ./txt/cord-317971-kuwargnp.txt summary: [11] Exposure to concentrations of just 30 % of either ethanol or isopropanol for 30 seconds fully suppressed viral infectivity.Likewise,the virucidal activity of the hand rub solutions known as WHO formulation 1, with 85 % ethanol, and WHO formulation 2, with 75 %i sopropanol, against SARS-CoV-2 was found to be excellent, with full inactivation of the coronavirus at 40 %or30%concentration, respectively.W hile the alcohol component is the main virucide,0 .125 % v/v H 2 O 2 is added to kill bacterial spores that may be present in the raw materials or the container.The addition of 1.45 % v/v glycerol as ah umectant improves the dermatological properties and thus the acceptance of the product. abstract: The SARS‐CoV‐2 outbreak causing the respiratory disease COVID‐19 has left many chemists in academia without an obvious option to contribute to fighting the pandemic. Some of our recent experiences indicate that there are ways to overcome this dilemma. A three‐pronged approach is proposed. url: https://www.ncbi.nlm.nih.gov/pubmed/32329159/ doi: 10.1002/anie.202004721 id: cord-290282-oxyzndsj author: Ortego, Javier title: Transmissible gastroenteritis coronavirus gene 7 is not essential but influences in vivo virus replication and virulence date: 2003-03-30 words: 4287.0 sentences: 215.0 pages: flesch: 53.0 cache: ./cache/cord-290282-oxyzndsj.txt txt: ./txt/cord-290282-oxyzndsj.txt summary: Transmissible gastroenteritis coronavirus (TGEV) contains eight overlapping genes that are expressed from a 3′-coterminal nested set of leader-containing mRNAs. To facilitate the genetic manipulation of the viral genome, genes were separated by duplication of transcription regulating sequences (TRSs) and introduction of unique restriction endonuclease sites at the 5′ end of each gene using an infectious cDNA clone. All the rTGEV viruses conserved the modifications engineered in the cDNAs (data not shown), indicating that the ORF separation and the insertion of unique endonuclease restriction sites between genes were stably maintained in the rTGEV genomes. Interestingly, analysis of viral growth in the gut of infected piglets showed a 100-to 5000-fold reduction of recombinant viruses containing one or more restriction sites in relation to the rTGEV-wt virus ( Fig. 5D and E) . abstract: Transmissible gastroenteritis coronavirus (TGEV) contains eight overlapping genes that are expressed from a 3′-coterminal nested set of leader-containing mRNAs. To facilitate the genetic manipulation of the viral genome, genes were separated by duplication of transcription regulating sequences (TRSs) and introduction of unique restriction endonuclease sites at the 5′ end of each gene using an infectious cDNA clone. The recombinant TGEV (rTGEV) replicated in cell culture with similar efficiency to the wild-type virus and stably maintained the modifications introduced into the genome. In contrast, the rTGEV replication level in the lungs and gut of infected piglets and virulence were significantly reduced. rTGEV in which gene 7 expression was abrogated (rTGEV-Δ7) were recovered from cDNA constructs, indicating that TGEV gene 7 was a nonessential gene for virus replication. Interestingly, in vivo infections with rTGEV-Δ7 showed an additional reduction in virus replication in the lung and gut, and in virulence, indicating that TGEV gene 7 influences virus pathogenesis. url: https://www.ncbi.nlm.nih.gov/pubmed/12706086/ doi: 10.1016/s0042-6822(02)00096-x id: cord-356188-rwf78stz author: Oshansky, Christine M. title: The human side of influenza date: 2012-07-01 words: 9515.0 sentences: 486.0 pages: flesch: 36.0 cache: ./cache/cord-356188-rwf78stz.txt txt: ./txt/cord-356188-rwf78stz.txt summary: Few studies have examined the role of monocytes during influenza infection in humans, particularly regarding the specific subsets mentioned above, but comparison of IFN-␥ production from T cells cocultured with CD64 ϩ CD16 Ϫ and CD64 Ϫ CD16 ϩ monocytes [119, 120] Cellular immunity Class I HLA presents peptides from internal and external viral proteins. As influenza primarily infects epithelial cells lining the respiratory tract, lung-resident DCs and macrophages are particularly important for efficient development of an adaptive immune response. [189] ), and in vitro studies suggest that activated human V␥9V␦2 T cells may have a role in the antiviral response by killing influenza-infected, monocyte-derived macrophages and producing high levels of IFN-␥ [190, 191] . Broadly cross-reactive antibodies dominate the human B cell response against 2009 pandemic H1N1 influenza virus infection Characterization of the human CD8ϩ T cell response following infection with 2009 pandemic influenza H1N1 virus abstract: A clear understanding of immunity in individuals infected with influenza virus is critical for the design of effective vaccination and treatment strategies. Whereas myriad studies have teased apart innate and adaptive immune responses to influenza infection in murine models, much less is known about human immunity as a result of the ethical and technical constraints of human research. Still, these murine studies have provided important insights into the critical correlates of protection and pathogenicity in human infection and helped direct the human studies that have been conducted. Here, we examine and review the current literature on immunity in humans infected with influenza virus, noting evidence offered by select murine studies and suggesting directions in which future research is most warranted. url: https://www.ncbi.nlm.nih.gov/pubmed/22362872/ doi: 10.1189/jlb.1011506 id: cord-009791-k09vcq96 author: Osterhaus, A. title: Antiviral Antibodies in Dogs in the Netherlands date: 2010-05-13 words: 3041.0 sentences: 214.0 pages: flesch: 57.0 cache: ./cache/cord-009791-k09vcq96.txt txt: ./txt/cord-009791-k09vcq96.txt summary: SUMMARY: Antiviral antibodies in dogs in the Netherlands A collection of more than 700 canine sera, coming from open and closed populations and from kennels with frequent neonatal mortality, were screened for the prevalence of antibodies to canine adenoviruses, canine herpesvirus, polyoma virus, REOviruses, parainfluenza viruses, equine influenza viruses and vomiting and wasting disease virus of pigs. Sera from six animal attendants from a CP kennel, cornprizing a total of at least 170 dogs, were tested for the prevalence of HA1 antibodies to CAV,, CAV, , REOvirus types 1, 2 and 3, parainfluenzavirus types 1, 2 and 3 and VW virus. Summary Antiviral antibodies in dogs in the Netherlands A collection of more than 700 canine sera, coming from open and closed populations and from kennels with frequent neonatal mortality, were screened for the prevalence of antibodies to canine adenoviruses, canine herpesvirus, polyoma virus, REOviruses,. abstract: SUMMARY: Antiviral antibodies in dogs in the Netherlands A collection of more than 700 canine sera, coming from open and closed populations and from kennels with frequent neonatal mortality, were screened for the prevalence of antibodies to canine adenoviruses, canine herpesvirus, polyoma virus, REOviruses, parainfluenza viruses, equine influenza viruses and vomiting and wasting disease virus of pigs. The data from the different groups were compared and related to the results of similar studies carried out in other countries. ZUSAMMENFASSUNG: Virus‐Antikörper bei Hunden in den Niederlanden Antivirale Antikörper in Hunden in den Niederlanden. Über 700 Sera von Hunden aus der offenen Population, isolierten Kollektiven sowie aus Zwingern mit hoher Welpensterblichkeit wurden auf Antikörper gegen die folgenden Viren untersucht: canine Adeno‐ und Herpesviren, Polyomavirus, REOviren, Parainfluenzaviren, Pferdeinfluenzaviren und das porcine „vomiting and wasting disease”‐Virus. Die aus den verschiedenen Kollektiven erhaltenen Werte wurden untereinander verglichen wie auch mit den Ergebnissen ähnlicher Erhebungen im Ausland. RÉSUMÉ: Anticorps antiviraux chez des chiens aux Pays‐Bas On a recherché des anticorps contre les virus suivants sur plus que 700 sérums de chiens pris dans la population ouverte, dans des collectivités isolées et dans des chenils avec forte mortalité des chiots: Adeno‐ et Herpesvirus canins, Polyomavirus, REOvirus, Parainfluenzavirus, Influenzavirus du cheval et le virus du «vomiting ans wasting disease» du porc. Les valeurs obtenues dans les différentes collectives ont été comparées entre elles et également avec les résultats de recherches semblables faites à l'éranger. RESUMEN: Anticuerpos antivirales en perros de los Países Bajos Se examinaron más de 700 sueros sanguíneos de perros de la población abierta, colectivos aislados y perreras con mortalidad elevada de cachorros en cuanto a la presencia de anticuerpos contra los virus siguientes: adeno y herpes caninos, polioma, REO, parainfluenza, influenza equina y de la enfermedad del vómito y extenuación en porcinos. Se compararon entre sí los valores obtenidos en los diversos colectivos, así como también con los resultados de pesquisas semejantes Ilevadas a cabo en el extranjero. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165579/ doi: 10.1111/j.1439-0450.1977.tb00982.x id: cord-023034-j8zwcfys author: Osterhaus, Albert D. M. E. title: Feline Infectious Peritonitis Virus: II. Propagation in Suckling Mouse Brain date: 2010-05-13 words: 2273.0 sentences: 157.0 pages: flesch: 45.0 cache: ./cache/cord-023034-j8zwcfys.txt txt: ./txt/cord-023034-j8zwcfys.txt summary: SUMMARY: Feline infectious peritonitis (FIP) virus multiplication was demonstrated in the brains of one‐day‐old laboratory mice using direct immunofluorescence tests. In order to determine the specificity of the observed fluorescence for FIP virus, indirect IFT were carried out in parallel on poslitive mouse brain sections (homologous reaction) and on porcine kidney cells infected with TGE virus (heterologous reaction). The conclusive experiment for establishing the FIP virus specificity of the immunofluorescence in mouse brain was performed by inoculating SPF kittens with fluorescence-positive material of the 6th mouse passage (isolation series A, Table 1 ). Feline infectious peritonitis (FIP) virus multiplication was demonstrated in the brains of one-day-old laboratory mice using direct immunofluorescence tests. Specificity was assessed by virus reisolation, indirect immunofluorescence and reproduction of FIP after inoculation of SPF kittens using brain material from the 6th mouse passage. Specificity was assessed by virus reisolation, indirect immunofluorescence and reproduction of FIP after inoculation of SPF kittens using brain material from the 6th mouse passage. abstract: SUMMARY: Feline infectious peritonitis (FIP) virus multiplication was demonstrated in the brains of one‐day‐old laboratory mice using direct immunofluorescence tests. Specificity was assessed by virus reisolation, indirect immunofluorescence and reproduction of FIP after inoculation of SPF kittens using brain material from the 6th mouse passage. ZUSAMMENFASSUNG: Virus der felinen infektiösen Peritonitis II. Vermehrung im Gehirn von Säuglingsmäusen Mit Hilfe der direkten Immunofluoreszenz wurde die Vermehrung des Virus der Felinen Infektiösen Peritonitis (FIP) im Gehirn eintägiger Laboratoriumsmäuse nachgewiesen. Die Spezifität wurde durch Reisolierung des Virus und indirekte Immunofluoreszenz belegt, sowie durch die Auslösung der FIP nach Inokulation von Gehirnmaterial der sechsten Mäusepassage in SPF Katzenwelpen. RÉSUMÉ: Virus de la péritonite infectieuse du chat II. Multiplication dans le cerveau de la souris nouveau‐née A l'aide de l'immunofluorescence directe la multiplication du virus de la péritonite infectieuze féline a été démontrée dans le cerveau de la souris nouveau‐née. Epreuves de spécificité étaient le réisolement du virus, l'immunofluorescence indirecte et la reproduction de la maladie par inoculation de chats SPF utilisant du material cerveau provenant du 6ième passage en souris. RESUMEN: Virus de la peritonitis infecciosa del gato II. Multiplicación en cerebro de ratoncitos recién‐nacidos Utilizando la inmunofluorescencia directa se mostró la multiplicación en cerebro de ratoncitos recién‐nacidos del virus de la peritonitis infecciosa del gato. Se pudo evidenciar la especificidad por medio de re‐aislamiento del virus y de la inmunofluorescencia indirecta; además, se logró reproducir la enfermedad en gatos SPF, inoculándoles material del 6° pasaje en cerebros de ratoncitos. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165968/ doi: 10.1111/j.1439-0450.1978.tb01683.x id: cord-339854-scb7pz87 author: Overend, Christopher title: The synthetic futures of vesicular stomatitis virus date: 2012-07-11 words: 1089.0 sentences: 77.0 pages: flesch: 42.0 cache: ./cache/cord-339854-scb7pz87.txt txt: ./txt/cord-339854-scb7pz87.txt summary: Vesicular stomatitis virus (VSV) is one of the most promising viruses for engineering vaccines and oncolytic therapies [2] . Of particular interest is a study in which VSV expressing the H5 antigen from highly pathogenic avian influenza induced sterilizing immunity against heterologous challenge in mice [4] . This demonstrates the safety and efficacy potential of VSV when live virus vaccination would otherwise be contraindicated. Even more promising, recombinant VSV expressing a secreted form of a virulence factor protein for Yersinia pestis, LcrV, induced high levels of LcrV-specific antibodies, protecting 90% of the mice challenged with 10 LD 50 [6] . Vesicular stomatitis virus-based Ebola vaccine is well-tolerated and protects immunocompromised nonhuman primates Potent vesicular stomatitis virus-based avian influenza vaccines provide long-term sterilizing immunity against heterologous challenge Heterologous boosting of recombinant adenoviral prime immunization with a novel vesicular stomatitis virus-vectored tuberculosis vaccine SARS vaccine based on a replicationdefective recombinant vesicular stomatitis virus is more potent than one based on a replication-competent vector abstract: nan url: https://doi.org/10.1016/j.tibtech.2012.06.002 doi: 10.1016/j.tibtech.2012.06.002 id: cord-018555-3lta1tbp author: Overstreet, Robin M. title: Host–Symbiont Relationships: Understanding the Change from Guest to Pest date: 2016-01-06 words: 15626.0 sentences: 706.0 pages: flesch: 47.0 cache: ./cache/cord-018555-3lta1tbp.txt txt: ./txt/cord-018555-3lta1tbp.txt summary: We provide examples involving multiple triggers for organisms associated with termites, for an endemic virus being affected by multiple factors and having multiple effects on its commercial penaeid shrimp hosts, and for contrasting variables associated with two exotic viruses in wild and cultured commercial penaeid shrimps with an emphasis on hypothesizing how the pathogenicity developed in these two viruses. Atypical temperatures, such as warm water associated with power plants, can cause infections of a specific parasite during periods when the hosts are more likely to be consumed by predators, more susceptible to disease, or more susceptible to interactions among parasites that can occur and result in unusual pathogenic conditions. The transformation triggers phenotypic and behavioral changes specifically attracting infective specimens to predatory birds in which the trematode matures considerable detail the host-symbiont relationships affecting the outcome of pathogenic viruses in populations of commercial penaeid shrimp. abstract: The several meanings for the term “symbiosis” create confusion, which can be avoided when the author provides details of the interrelationships between the symbiotic organism and the “host” so that a reader can clearly understand what definition is implied in each case. For example, we, as opposed to many other mentioned readers, consider a symbiont as an organism living in an association with another regardless of whether it causes a pathologic response or not, but from our title, the reader may incorrectly infer that we consider a parasite to be different from a symbiont. A symbiont is an organism that uses another organism as a habitat. This chapter discusses the primary associations and associated conflicts involving the terminology. It also provides both differentiation between and conflicting views regarding the interpretation of the terms “infect” and “infest,” “infection” and “disease,” and other terms. Many seemingly harmless symbionts of a wide array of taxonomic groups are triggered to become pathogenic or virulent, and we provide several examples of the provoking (stimulating) triggers, with the understanding that in most cases, the conditions for the triggered activities are much more complex and complicated than presented. Examples of triggers follow: environmental ones like temperature, toxic chemicals (dose), chemotherapeutics, dietary changes, and geographic habits; internal ones like host site, host resistance or susceptibility, and host modifications; and combinations of these and other conditions. We provide examples involving multiple triggers for organisms associated with termites, for an endemic virus being affected by multiple factors and having multiple effects on its commercial penaeid shrimp hosts, and for contrasting variables associated with two exotic viruses in wild and cultured commercial penaeid shrimps with an emphasis on hypothesizing how the pathogenicity developed in these two viruses. The chapter ends by trying to answer the question of why would a symbiont become pathogenic in some hosts and not in others from an evolutionary perspective. It uses two hypotheses to explain the increased virulence. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123458/ doi: 10.1007/978-3-319-28170-4_2 id: cord-018811-zhwr3h07 author: Oxford, John title: Influenza Vaccines Have a Short but Illustrious History of Dedicated Science Enabling the Rapid Global Production of A/Swine (H1N1) Vaccine in the Current Pandemic date: 2010-06-18 words: 13247.0 sentences: 618.0 pages: flesch: 48.0 cache: ./cache/cord-018811-zhwr3h07.txt txt: ./txt/cord-018811-zhwr3h07.txt summary: The international investment into public health measures for a global human outbreak of avian H5N1 influenza together with a focus of swine influenza H1N1 is leading to enhanced production of conventional vaccine and to a new research searchlight on T-cell epitope vaccines, viral live-attenuated carriers of influenza proteins, and even more innovative substrates to cultivate virus, including plant cells. This was particularly well demonstrated by studies during the swine influenza campaign in the USA in 1976, when many observers reported results, which ultimately led to the recommended use in children of two doses of split-type rather than whole-virus vaccines. It has been known for many years that the serological response to inactivated vaccine depends on the previous experience of the recipient to infection by viruses of the same subtype of influenza A virus as that present in the vaccine. Comparison of inactivated vaccine A/HongKong/68 (H3N2) given intranasally or subcutaneously showed that following challenge with live virus only those who had developed a serum antibody response after vaccine by either route resisted infection. abstract: Vaccines for the swine flu pandemic of 2009 have been produced in an exquisitely short time frame. This speed of production comes because of 50 years of hard work by virologists worldwide in pharma groups, research laboratories, and government licensing units. The present chapter presents the background framework of influenza vaccine production and its evolution over 50 years. Isolation of the causative virus of influenza in 1933, followed by the discovery of embryonated hen eggs as a substrate, quickly led to the formulation of vaccines. Virus-containing allantoic fluid was inactivated with formalin. The phenomenon of antigenic drift of the virus HA was soon recognized and as WHO began to coordinate the world influenza surveillance, it became easier for manufacturers to select an up-to-date virus. Influenza vaccines remain unique in that the virus strain composition is reviewed yearly, but modern attempts are being made to free manufacturers from this yolk by investigating internal virus proteins including M2e and NP as “universal” vaccines covering all virus subtypes. Recent technical innovations have been the use of Vero and MDCK cells as the virus cell substrate, the testing of two new adjuvants, and the exploration of new presentations to the nose or epidermal layers as DNA or antigen mixtures. The international investment into public health measures for a global human outbreak of avian H5N1 influenza together with a focus of swine influenza H1N1 is leading to enhanced production of conventional vaccine and to a new research searchlight on T-cell epitope vaccines, viral live-attenuated carriers of influenza proteins, and even more innovative substrates to cultivate virus, including plant cells. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123788/ doi: 10.1007/978-3-0346-0279-2_6 id: cord-334082-fyxn0g3v author: O’Carroll, I.P. title: Viral Nucleic Acids date: 2015-08-20 words: 5495.0 sentences: 271.0 pages: flesch: 54.0 cache: ./cache/cord-334082-fyxn0g3v.txt txt: ./txt/cord-334082-fyxn0g3v.txt summary: This scheme in turn places two requirements on the nucleic acid: it must be replicated in the virus-producing cell, to provide the genetic material encased in the progeny virus particles; and it must encode the proteins needed for the production of the progeny particles, including at a minimum the structural proteins from which the particles will be assembled. The DNAs of ssDNA viruses are replicated by a mechanism similar to ''rolling circle'' replication, involving synthesis of dsDNA intermediates containing multiple tandem copies of the viral genome. These viruses are unique in that their genomic RNA is translated immediately upon infection; that is, the virus particle is simply a package that introduces an mRNA molecule into the cell. When the particle infects a new host cell, the RNA-dependent DNA polymerase or ''reverse transcriptase'' in the virus copies this RNA into dsDNA. abstract: Viral genomes exhibit extraordinary diversity with respect to nucleic acid type, size, complexity, and the information transfer pathways they follow. Thus, viral nucleic acids can be DNA or RNA, double-stranded or single-stranded, monopartite or multipartite, linear or circular, as short as 2 kb or up to 2500 kb long. The goal of a virus is to replicate itself. To do so, viruses have evolved various strategies to replicate their genomes and produce the structural and catalytic proteins needed for the formation of new viruses. This article is a brief introduction to viral genomes and viral replication. url: https://www.sciencedirect.com/science/article/pii/B9780123944474100616 doi: 10.1016/b978-0-12-394447-4.10061-6 id: cord-290432-4dli5emd author: O’Grady, Kerry-Ann F. title: Upper airway viruses and bacteria in urban Aboriginal and Torres Strait Islander children in Brisbane, Australia: a cross-sectional study date: 2017-04-04 words: 3764.0 sentences: 184.0 pages: flesch: 44.0 cache: ./cache/cord-290432-4dli5emd.txt txt: ./txt/cord-290432-4dli5emd.txt summary: We aimed to describe the prevalence of upper airway viruses and bacteria in symptomatic and asymptomatic urban-based Australian Indigenous children aged less than 5 years. METHODS: A cross-sectional analysis of data collected at baseline in an ongoing prospective cohort study of urban Aboriginal and Torres Strait Islander children registered with a primary health care service in the northern suburbs of Brisbane, Australia. Thus, in 164 urban-based Indigenous children presenting to an urban primary health care service, we described the prevalence of upper airway respiratory viruses and bacteria. We analysed data from a cohort of urban Aboriginal and Torres Strait Islander children aged less than 5 years collected at time of enrolment into a prospective study of ARIwC. In a study of upper airway viruses and bacteria in Central Australian Aboriginal children hospitalised for pneumonia [8] , a population with high rates of hospitalised lower ARI [15] and nasal colonisation [16] , the [8] . abstract: BACKGROUND: Respiratory morbidity in Australian Indigenous children is higher than their non-Indigenous counterparts, irrespective of urban or remote residence. There are limited studies addressing acute respiratory illness (ARI) in urban Indigenous children, particularly those that address the upper airway microbiome and its relationship to disease. We aimed to describe the prevalence of upper airway viruses and bacteria in symptomatic and asymptomatic urban-based Australian Indigenous children aged less than 5 years. METHODS: A cross-sectional analysis of data collected at baseline in an ongoing prospective cohort study of urban Aboriginal and Torres Strait Islander children registered with a primary health care service in the northern suburbs of Brisbane, Australia. Clinical, demographic and epidemiological data and bilateral anterior nasal swabs were collected on enrolment. Polymerase chain reaction was performed on nasal swabs to detect 17 respiratory viruses and 7 bacteria. The primary outcome was the prevalence of these microbes at enrolment. Logistic regression was performed to investigate differences in microbe prevalence between children with and without acute respiratory illness with cough as a symptom (ARIwC) at time of specimen collection. RESULTS: Between February 2013 and October 2015, 164 children were enrolled. The median age at enrolment was 18.0 months (IQR 7.2–34.3), 49.4% were boys and 56 children (34.2%) had ARIwC. Overall, 133/164 (81%) nasal swabs were positive for at least one organism; 131 (79.9%) for any bacteria, 59 (36.2%) for any virus and 57 (34.8%) for both viruses and bacteria. Co-detection of viruses and bacteria was more common in females than males (61.4% vs 38.6%, p = 0.044). No microbes, alone or in combination, were significantly associated with the presence of ARIwC. CONCLUSIONS: The prevalence of upper airways microbes in asymptomatic children is similar to non-Indigenous children with ARIwC from the same region. Determining the aetiology of ARIwC in this community is complicated by the high prevalence of multiple respiratory pathogens in the upper airways. STUDY REGISTRATION: Australia New Zealand Clinical Trial Registry Registration Number: 12,614,001,214,628. Retrospectively registered. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-017-2349-1) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/28376882/ doi: 10.1186/s12879-017-2349-1 id: cord-259458-o2yts5pq author: O’Grady, Kerry‐Ann F. title: Successful application of a simple specimen transport method for the conduct of respiratory virus surveillance in remote Indigenous communities in Australia date: 2011-03-21 words: 3636.0 sentences: 176.0 pages: flesch: 49.0 cache: ./cache/cord-259458-o2yts5pq.txt txt: ./txt/cord-259458-o2yts5pq.txt summary: This study assessed the sensitivity of a simple method for transporting respiratory samples from a remote setting for viral PCR compared with frozen specimens. To inform the design of surveillance and intervention studies addressing respiratory infections in remote communities, we compared the sensitivity of a simple, cost-efficient method for transporting respiratory samples from a remote setting for viral real-time PCR with transport using frozen specimens. Given the sensitivity and specificity of real-time PCR diagnosis, we considered a specimen from either nostril positive for any virus to represent a true-positive, similar to previous studies (Lambert et al. Determining the aetiology and burden of viral respiratory infections in remote communities has to date been limited by the inability to store and transport clinical specimens requiring freezing ⁄ refrigeration to urban laboratories. We propose that this method, combining standard clinic refrigeration and weekly surface mailing of specimens combined with real-time PCR, can be used for viral respiratory research in remote locations. abstract: Objective Surveillance programs and research for acute respiratory infections in remote Aboriginal communities are complicated by difficulties in the storage and transport of frozen samples to urban laboratories for testing. This study assessed the sensitivity of a simple method for transporting respiratory samples from a remote setting for viral PCR compared with frozen specimens. Methods We sampled every individual who presented to a remote Aboriginal community clinic in a non‐epidemic respiratory season. Two anterior nasal swabs were collected from each participant. The left nare specimen was mailed to the laboratory via routine postal services. The right nare specimen was transported frozen. Testing for 16 viruses was undertaken using real‐time multiplex PCR. Results A total of 140 participants were enrolled who contributed 150 study visits. Respiratory illnesses accounted for 10% of the reasons for presentation. Sixty‐one viruses were identified in 50 (33.3%) presentations for 40 (28.6%) individuals; bocavirus and rhinovirus were the most common viruses identified (14.0% and 12.6% of episodes respectively). The sensitivity for any virus detected in mailed specimens was 67.2% (95%CI 55.4, 78.9) compared to 65.6% (95%CI 53.7, 77.5) for frozen specimens. Conclusion The mailing of unfrozen nasal specimens from remote communities does not compromise the viability of the specimen for viral studies. url: https://www.ncbi.nlm.nih.gov/pubmed/21418445/ doi: 10.1111/j.1365-3156.2011.02757.x id: cord-340629-1fle5fpz author: O’Shea, Helen title: Viruses Associated With Foodborne Infections date: 2019-05-21 words: 9409.0 sentences: 500.0 pages: flesch: 46.0 cache: ./cache/cord-340629-1fle5fpz.txt txt: ./txt/cord-340629-1fle5fpz.txt summary: In infants, prior to the introduction of rotavirus vaccines, RVAs could be detected in up to 50%-60% of all childhood hospitalisations due to acute gastroenteritis each year, were estimated to cause 138 million cases of gastroenteritis annually, and 527,000 deaths in children o5 years of age living in developing countries. Recent emerging epidemic and pandemic virus infections that cause severe disease in humans and that are associated with food production, preparation and food contamination include the coronavirus, severe acute respiratory syndrome (SARS-CoV), Nipah virus, Ebola virus and some of the highly pathogenic influenza virus strains, such as the H5N1 subtype. Infections by Severe Acute Respiratory Syndrome (SARS) virus, Nipah virus (NiV), H5N1 virus, Hepatitis A virus (HAV), Hepatitis E virus (HEV), Adenovirus, Astrovirus, Norovirus (NoV) and Rotavirus (RVA) in humans and animals are detected by nucleic acid amplification tests and serologic tests. abstract: Foodborne pathogens cause acute and chronic health outcomes of very different durations, severity and mortality, resulting in high costs and burdens to society. The issues of food safety and food poisoning are being increasingly emphasised, particularly in developed countries. Infection/contamination with many agents i.e., bacterial, parasitic and viral entities can result in foodborne illness. This article will focus mainly on viral agents of infection. A range of different viruses can cause food poisoning/foodborne infection, and infection can result in a myriad of symptoms, ranging from mild, acute disease to chronic, debilitating disease and even death. Due to the inherent differences between bacteria and viruses, namely the fact that viruses do not replicate in food, while bacteria do, viruses are frequently difficult to detect. This is compounded by the fact that many of the viruses associated with enteric disease do not replicate in cell culture. These factors can lead to a lag between reporting, detection and analysis of foodborne viruses versus bacterial agents. Despite these constraints, it is now evident that there are both well-established and emerging viruses implicated in foodborne infections, and the role of molecular detection and characterisation is becoming increasingly important. url: https://www.sciencedirect.com/science/article/pii/B9780128096338902735 doi: 10.1016/b978-0-12-809633-8.90273-5 id: cord-021465-2pj26fmv author: PERDUE, MICHAEL L. title: Impact of Avian Viruses date: 2007-05-09 words: 14076.0 sentences: 696.0 pages: flesch: 46.0 cache: ./cache/cord-021465-2pj26fmv.txt txt: ./txt/cord-021465-2pj26fmv.txt summary: Although there is variation in the economic or ecological impact of various viral groups from year to year and among geographic sites, the "Top Ten" list of virus groups exhibiting routine significant impact on commercial poultry worldwide (not necessarily in order of impact) are paramyxoviruses (Newcastle disease); coronaviruses (infectious bronchitis); herpesviruses (infectious laryngotracheitis; Marek''s disease; duck enteritis); reoviruses (viral arthritis); picornaviruses (avian encephalomyelitis); adenoviruses (egg drop syndrome); retroviruses (lymphoid leukosis); orthomyxoviruses (avian influenza); poxviruses (fowlpox); and birnaviruses (infectious bursal disease). With the recent documented transmission of a lethal avian influenza virus from commercial poultry to humans, these ecological relationships take on new significance. Lymphomas caused by MDV and retroviruses are still the most common viral neoplastic diseases of poultry, and a recent increase in mortality and evolution of more virulent MDV strains indicates that the impact of these viruses will continue to be felt (Witter, 1996) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149826/ doi: 10.1016/b978-012362675-2/50016-1 id: cord-335279-cfv18qn0 author: Paillot, Romain title: Special Issue “Equine Viruses”: Old “Friends” and New Foes? date: 2020-01-29 words: 2070.0 sentences: 112.0 pages: flesch: 49.0 cache: ./cache/cord-335279-cfv18qn0.txt txt: ./txt/cord-335279-cfv18qn0.txt summary: With this Special Issue, which assembles a collection of communications, research articles, and reviews, we intend to explore our understanding of a panel of equine viruses, looking at their pathogenicity, their importance in terms of welfare and potential association with diseases, their economic importance and impact on performance, and how their identification can be helped by new technologies and methods. The authors highlight the potential protective role of eqMx1, which primarily targets the virus nucleoprotein (NP), against the transmission of new IAVs in horses (i.e., eqMx1 could only inhibit the polymerase activity of IAVs of avian and human origin but remained inactive against the equine IAVs tested). To date, equine influenza virus remains one of the most important respiratory pathogens of horses worldwide, with a potential damaging impact on the equine industry, as clearly illustrated in 2007 in Australia and in 2019 in Europe [20, 21] . abstract: The Food and Agriculture Organization of the United Nations has recently estimated that the world equid population exceeds 110 million (FAOSTAT 2017).[...]. url: https://www.ncbi.nlm.nih.gov/pubmed/32013127/ doi: 10.3390/v12020153 id: cord-268501-z4oztgi0 author: Palatnik-de-Sousa, Clarisa B. title: What Would Jenner and Pasteur Have Done About COVID-19 Coronavirus? The Urges of a Vaccinologist date: 2020-08-26 words: 6331.0 sentences: 280.0 pages: flesch: 46.0 cache: ./cache/cord-268501-z4oztgi0.txt txt: ./txt/cord-268501-z4oztgi0.txt summary: In fact, by May 11th, 2020 seven vaccines had already entered Phase I clinical trials: (1) encapsulated mRNA encoding protein S (Moderna and NIAID, USA); (2) Adenovirus expressing protein S (Cansino Biologics, China); (3) DCs modified with lentivirus expressing several proteins and CTLs (Shenzen Geno-Immune Medical, China); (4) an APC modified with lentivirus expressing several viral proteins (35); (5) Inno 4800, SARS CoV2 DNA Injection (Innovio, USA); (6) ChAdOx1 vaccine from the Jenner Institute, Oxford University, (UK) which is a genetically modified Adenovirus expressing Coronavirus proteins (39) , and is also being tested in a Phase II trial; and finally (7) the whole inactivated coronavirus with Alum by Sinovac, China (40) . Furthermore, in vaccinated monkeys, seven days after infection, the Sinovac inactivated vaccine at 6 µg/dose induced high titers of IgG antibodies directed against the S, RBD and lower levels of anti-N protein antibodies, high titers of virus neutralizing antibodies with no detected antibodydependent enhancement of disease (ADE) (40) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32983183/ doi: 10.3389/fimmu.2020.02173 id: cord-323793-c69joaqs author: Palmieri, V. title: Can graphene take part in the fight against COVID-19? date: 2020-05-07 words: 2813.0 sentences: 155.0 pages: flesch: 41.0 cache: ./cache/cord-323793-c69joaqs.txt txt: ./txt/cord-323793-c69joaqs.txt summary: In response to this global outbreak, we summarized the current state of knowledge of graphene and virus interaction as well as possible successful applications to fight COVID-19. Antibody-conjugated graphene sheets can rapidly detect targeted virus proteins and can be useful for large population screening, but also for the development of environmental sensors and filters, given the low cost of graphene materials. While government bodies are struggling in preventing further spread of COVID-19, researchers immediately started tests on vaccines and a clinical trial is currently underway with potential treatments for severe acute respiratory syndrome coronavirus -2 (SARS-CoV-2) [1] . Ziem and colleagues synthesized thermal rGO sulfate derivatives and demonstrated their antiviral activity against African swine fever virus, orthopoxvirus and herpesvirus strains [14, 15] . Synergistic antiviral effect of curcumin functionalized graphene oxide against respiratory syncytial virus infection abstract: The pneumonia outbreak of coronavirus disease 2019 (COVID-19) represents a global issue. The bidimensional material graphene has captured much attention due to promising antimicrobial applications and has also demonstrated antiviral efficacy. In response to this global outbreak, we summarized the current state of knowledge of graphene and virus interaction as well as possible successful applications to fight COVID-19. Antibody-conjugated graphene sheets can rapidly detect targeted virus proteins and can be useful for large population screening, but also for the development of environmental sensors and filters, given the low cost of graphene materials. The functionalized graphene has demonstrated a good viral capture capacity that, combined with heat or light-mediated inactivation, could be used as a disinfectant. Graphene sensors arrays can be implemented on standard utility textiles and drug efficacy screening. Thanks to its high versatility, we foresee that graphene may have a leading role in the fight against COVID-19. url: https://www.sciencedirect.com/science/article/pii/S1748013220300529?v=s5 doi: 10.1016/j.nantod.2020.100883 id: cord-254932-b447w202 author: Panda, Aruna title: Role of fusion protein cleavage site in the virulence of Newcastle disease virus date: 2003-11-18 words: 5550.0 sentences: 259.0 pages: flesch: 53.0 cache: ./cache/cord-254932-b447w202.txt txt: ./txt/cord-254932-b447w202.txt summary: The genetic stability of the mutations introduced into the genome of LaSota V.F. virus was determined by sequence analysis of the RT-PCR fragment that covered the region of the F protein cleavage site of the mutant virus that was passed five times in 9-day-old chicken embryos, and also from the mutant virus that was passaged once in chicken brains. These results demonstrated that the efficiency of cleavage of the F protein plays an important role if the NDV is delivered directly into the brains of chicks, but there could be other viral factors that probably affect peripheral replication, viremia, or entry into the central nervous system. These results demonstrated that the efficiency of cleavage of the F protein plays an important role if the NDV is delivered directly into the brains of chicks, but there could be other viral factors that probably affect peripheral replication, viremia, or entry into the central nervous system. abstract: Newcastle disease virus (NDV) causes a highly contagious and economically important disease in poultry. Viral determinants of NDV virulence are not completely understood. The amino acid sequence at the protease cleavage site of the fusion (F) protein has been postulated as a major determinant of NDV virulence. In this study, we have examined the role of F protein cleavage site sequence in NDV virulence using reverse genetics technology. The sequence G-R-Q-G-R present at the cleavage site of the F protein of avirulent strain LaSota was mutated to R-R-Q-K-R, which is present in the F cleavage site of neurovirulent strain Beaudette C (BC). The resultant mutated LaSota V.F. virus did not require exogenous protease for infectivity in cell culture, indicating that the F protein was cleaved by intracellular proteases. The virulence of the mutant and parental viruses was evaluated in vivo by intracerebral pathogenicity index (ICPI) and intravenous pathogenicity index (IVPI) tests in chickens. Our results showed that the modification of the F protein cleavage site resulted in a dramatic increase in virulence from an ICPI value of 0.00 for LaSota to a value of 1.12 for LaSota V.F. However, the ICPI value of LaSota V.F. was lower than that of BC, which had a value of 1.58. Interestingly, the IVPI tests showed values of 0.00 for both LaSota and LaSota V.F. viruses, compared to the IVPI value of 1.45 of BC. In vitro characteristics of the viruses were also studied. Our results demonstrate that the efficiency of cleavage of the F protein plays an important role if the NDV is delivered directly into the brains of chicks, but there could be other viral factors that probably affect peripheral replication, viremia, or entry into the central nervous system. url: https://www.sciencedirect.com/science/article/pii/S0882401003001669 doi: 10.1016/j.micpath.2003.07.003 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: 7342.0 sentences: 400.0 pages: flesch: 34.0 cache: ./cache/cord-259927-xh9cw9ao.txt txt: ./txt/cord-259927-xh9cw9ao.txt summary: 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. Here we provide an overview of the options and highlight some of the most promising approaches in vRTI treatment, including symptomatic medication, immunomodulatory drugs, antiviral agents, and natural products, as well as in vRTI prevention, ranging from vaccines to immunostimulators and public health policies. Early in vivo evidence suggested that azithromycin has anti-inflammatory and antiviral effects through induction of interferon-stimulated gene mRNA expression and reduced viral replication and release in patients with asthma and chronic obstructive lung disease. mAb therapies to viral infections, such as EBV (rituximab) or RSV (palivizumab), provide passive immunization and are licensed, whereas similar agents targeting influenza and other viruses are in preclinical development. 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-286741-h3oix9zc author: Park, Mee Sook title: Animal models for the risk assessment of viral pandemic potential date: 2020-04-22 words: 9619.0 sentences: 484.0 pages: flesch: 46.0 cache: ./cache/cord-286741-h3oix9zc.txt txt: ./txt/cord-286741-h3oix9zc.txt summary: Focusing on the pandemic potential of viral infectious diseases, we suggest what should be assessed to prevent global catastrophes from influenza virus, Middle East respiratory syndrome coronavirus, dengue and Zika viruses. When a virus with a nonhuman origin HA and an efficient human transmissibility gets transmitted from the adaptation host swine to human (4), a pandemic might ensue (5) of IAVs, avian and swine species should be considered the natural reservoir animals, and in case of MERS-CoVs, bats and dromedary camels [32, 87, 90] . In addition to NHP and hDPP4-mouse models, rabbits might be a good candidate for MERS-CoV transmission experiments due to its camel-like receptor distribution in the upper respiratory tract (Table 2 ) [142, 150] . Human-like symptoms of MERS-CoV infection have not been reproduced in other animals than hDPP4-mice and NHPs. Starting from the distinct receptor specificities of the HA proteins between avian and human IAVs, host restriction determinants of IAVs have been documented [56] . abstract: Pandemics affect human lives severely and globally. Experience predicts that there will be a pandemic for sure although the time is unknown. When a viral epidemic breaks out, assessing its pandemic risk is an important part of the process that characterizes genomic property, viral pathogenicity, transmission in animal model, and so forth. In this review, we intend to figure out how a pandemic may occur by looking into the past influenza pandemic events. We discuss interpretations of the experimental evidences resulted from animal model studies and extend implications of viral pandemic potentials and ingredients to emerging viral epidemics. Focusing on the pandemic potential of viral infectious diseases, we suggest what should be assessed to prevent global catastrophes from influenza virus, Middle East respiratory syndrome coronavirus, dengue and Zika viruses. url: https://doi.org/10.1186/s42826-020-00040-6 doi: 10.1186/s42826-020-00040-6 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-268540-wrjzr3ws author: Park, You Jeong title: Fighting the War Against COVID-19 via Cell-Based Regenerative Medicine: Lessons Learned from 1918 Spanish Flu and Other Previous Pandemics date: 2020-08-13 words: 16363.0 sentences: 868.0 pages: flesch: 45.0 cache: ./cache/cord-268540-wrjzr3ws.txt txt: ./txt/cord-268540-wrjzr3ws.txt summary: A potential target for drug development for COVID-19 also involves inhibition of ACE2, the host cell receptor for the S protein of SARS-CoV-2 that is primed by TMPRSS2 protease and may prevent the entry of the virus. As previously described, the intermolecular interaction between the viral SP and human ACE2 Phase II CAStem cells will be intravenously injected into patients with or without acute respiratory distress syndrome (ARDS) induced by COVID-19. Phase II Patients with acute respiratory distress syndrome caused by COVID-19 will be treated with intravenous UC-MSCs at a dose 1 million xKg. Patient improvement will be evaluated over three weeks, along with the assessment of the immune profile, investigating the stem cells'' effect on the cytokine storm. The similarities in systemic multi-organ complications between H7N9 and Sars-Cov-2 infections, along with direct evidence of the benefits of MSCs transplantation for COVID-19, further supports the potential of stem cells as an effective treatment [138] . abstract: The human population is in the midst of battling a rapidly-spreading virus— Severe Acute Respiratory Syndrome Coronavirus 2, responsible for Coronavirus disease 2019 or COVID-19. Despite the resurgences in positive cases after reopening businesses in May, the country is seeing a shift in mindset surrounding the pandemic as people have been eagerly trickling out from federally-mandated quarantine into restaurants, bars, and gyms across America. History can teach us about the past, and today’s pandemic is no exception. Without a vaccine available, three lessons from the 1918 Spanish flu pandemic may arm us in our fight against COVID-19. First, those who survived the first wave developed immunity to the second wave, highlighting the potential of passive immunity-based treatments like convalescent plasma and cell-based therapy. Second, the long-term consequences of COVID-19 are unknown. Slow-progressive cases of the Spanish flu have been linked to bacterial pneumonia and neurological disorders later in life, emphasizing the need to reduce COVID-19 transmission. Third, the Spanish flu killed approximately 17 to 50 million people, and the lack of human response, overcrowding, and poor hygiene were key in promoting the spread and high mortality. Human behavior is the most important strategy for preventing the virus spread and we must adhere to proper precautions. This review will cover our current understanding of the pathology and treatment for COVID-19 and highlight similarities between past pandemics. By revisiting history, we hope to emphasize the importance of human behavior and innovative therapies as we wait for the development of a vaccine. [Figure: see text] url: https://www.ncbi.nlm.nih.gov/pubmed/32789802/ doi: 10.1007/s12015-020-10026-5 id: cord-104317-t30dg6oj author: Parker, Michael T. title: An Ecological Framework of the Human Virome Provides Classification of Current Knowledge and Identifies Areas of Forthcoming Discovery date: 2016-09-30 words: 7986.0 sentences: 408.0 pages: flesch: 40.0 cache: ./cache/cord-104317-t30dg6oj.txt txt: ./txt/cord-104317-t30dg6oj.txt summary: However, the obvious importance of viruses in the composition of all biomes has not (yet) been met with an appropriate fervor for the characterization of the viral REVIEW Recent advances in sequencing technologies have opened the door for the classification of the human virome. The discovery of intimate interactions of viruses with humans, like the role of endogenous retrovirus (ERV †) syncytins in placentation [27] , are categorically dissimilar to the classical view of viruses only as parasites and brings to issue how scientists are approaching the study of the virome. The application of this scaffold will not only deepen the understanding of known virus-host interactions in the ecological context of the virome, but will also identify logical next steps and gaps in current knowledge that are tantalizing areas for future exploration. Additionally, further characterization of the human virome is likely to uncover more viruses that persistently infect humans [31] , and such discoveries could pave the way for the treatment of diseases of currently unknown etiology. abstract: Recent advances in sequencing technologies have opened the door for the classification of the human virome. While taxonomic classification can be applied to the viruses identified in such studies, this gives no information as to the type of interaction the virus has with the host. As follow-up studies are performed to address these questions, the description of these virus-host interactions would be greatly enriched by applying a standard set of definitions that typify them. This paper describes a framework with which all members of the human virome can be classified based on principles of ecology. The scaffold not only enables categorization of the human virome, but can also inform research aimed at identifying novel virus-host interactions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045143/ doi: nan id: cord-008551-yu71iewp author: Parrish, Colin R. title: Emergence, Natural History, and Variation of Canine, Mink, and Feline Parvoviruses date: 2008-04-11 words: 11842.0 sentences: 635.0 pages: flesch: 52.0 cache: ./cache/cord-008551-yu71iewp.txt txt: ./txt/cord-008551-yu71iewp.txt summary: This chapter discusses the emergence of canine parvovirus (CPV), the evidence concerning the previous emergence of mink enteritis virus (MEV) as the cause of a new disease in minks in the 1940s, and the mechanisms that determine the host ranges and other specific properties of the viruses of cats, minks, and dogs. Feline panleukopenia virus (FPV), MEV, and CPV are classified as "host range variants." In addition to the viruses of cats, minks, and dogs, similar viruses naturally infect many species within the families Felidae, Canidae, Procyonidae, Mustelidae, and possibly the Viverridae. Feline panleukopenia virus (FPV), MEV, and CPV are classified as "host range variants." In addition to the viruses of cats, minks, and dogs, similar viruses naturally infect many species within the families Felidae, Canidae, Procyonidae, Mustelidae, and possibly the Viverridae. abstract: This chapter discusses the emergence of canine parvovirus (CPV), the evidence concerning the previous emergence of mink enteritis virus (MEV) as the cause of a new disease in minks in the 1940s, and the mechanisms that determine the host ranges and other specific properties of the viruses of cats, minks, and dogs. The viruses are classified as the feline parvovirus subgroup of the genus Parvovirus, within the family Parvoviridae. Feline panleukopenia virus (FPV), MEV, and CPV are classified as “host range variants.” In addition to the viruses of cats, minks, and dogs, similar viruses naturally infect many species within the families Felidae, Canidae, Procyonidae, Mustelidae, and possibly the Viverridae. The differences in virulence for minks observed after inoculation of MEV or FPV suggests that there are subtle differences between FPV and MEV that have yet to be defined. Genetic mapping studies indicate that only three or four sequence differences between the FPV and CPV-2 isolates within the VP-1 lVP-2 gene determine all of the specific properties of CPV that have been defined: the pH dependence of hemagglutination, the CPV-specific epitope, and the host range for canine cells and dogs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7131698/ doi: 10.1016/s0065-3527(08)60867-2 id: cord-272405-jmwn8pdn author: Parvez, Mohammad K. title: Evolution and Emergence of Pathogenic Viruses: Past, Present, and Future date: 2017-08-04 words: 4192.0 sentences: 210.0 pages: flesch: 43.0 cache: ./cache/cord-272405-jmwn8pdn.txt txt: ./txt/cord-272405-jmwn8pdn.txt summary: Despite substantial advancements in the understanding of the biology of pathogens, the breakthroughs in prevention, and their effects on public health and the global economy, the emergence of novel pandemic viruses remains an enduring puzzle. This review presents an update on the knowledge of important emerging/re-emerging viral infections worldwide, discussing their possible origin, evolution, natural reservoirs, human adaptations, and risk factors ( Fig. 1 ). To understand this further, a recently isolated HEV genotype 3 from a chronic hepatitis E patient containing a recombinant virus-host RNA genome was shown to infect cultured human, pig, and deer hepatocytes [39] . The field of phylodynamics, combining a modeling framework for host, epidemiological, and molecular data, especially for RNA viruses, shows particular promise for Parvez understanding the patterns of viral evolution during epidemics [40, 41] . Despite landmark advances in understanding the nature and biology of many pathogenic viruses, there is limited knowledge on emerging novel viruses, their potential reservoirs, and their modes of transmission. abstract: Incidences of emerging/re-emerging deadly viral infections have significantly affected human health despite extraordinary progress in the area of biomedical knowledge. The best examples are the recurring outbreaks of dengue and chikungunya fever in tropical and sub-tropical regions, the recent epidemic of Zika in the Americas and the Caribbean, and the SARS, MERS, and influenza A outbreaks across the globe. The established natural reservoirs of human viruses are mainly farm animals, and, to a lesser extent, wild animals and arthropods. The intricate “host-pathogen-environment” relationship remains the key to understanding the emergence/re-emergence of pathogenic viruses. High population density, rampant constructions, poor sanitation, changing climate, and the introduction of anthropophilic vectors create selective pressure on host-pathogen reservoirs. Nevertheless, the knowledge and understanding of such zoonoses and pathogen diversity in their known non-human reservoirs are very limited. Prevention of arboviral infections using vector control methods has not been very successful. Currently, new approaches to protect against food-borne infections, such as consuming only properly cooked meats and animal products, are the most effective control measures. Though significant progress in controlling human immunodeficiency virus and hepatitis viruses has been achieved, the unpredictable nature of evolving viruses and the rare occasions of outbreaks severely hamper control and preventive modalities. url: https://doi.org/10.1159/000478729 doi: 10.1159/000478729 id: cord-317496-6o2upns3 author: Pascual-Iglesias, Alejandro title: Recombinant Chimeric Transmissible Gastroenteritis Virus (TGEV)—Porcine Epidemic Diarrhea Virus (PEDV) Virus Provides Protection against Virulent PEDV date: 2019-07-25 words: 7100.0 sentences: 404.0 pages: flesch: 48.0 cache: ./cache/cord-317496-6o2upns3.txt txt: ./txt/cord-317496-6o2upns3.txt summary: In this line, we engineered an attenuated virus based on the transmissible gastroenteritis virus (TGEV) genome, expressing a chimeric spike protein from a virulent United States (US) PEDV strain. The rTGEV-RS-SPEDV vaccine candidate was also attenuated in three-week-old animals that were used to evaluate the protection conferred by this virus, compared with the protection induced by infection with a virulent PEDV US strain (PEDV-NVSL). Interestingly, Viruses 2019, 11, 682 9 of 18 when viral RNA was isolated from feces of 21-day-old piglets at seven days post-vaccination (see below) and rTGEV-RS-SPEDV virus was sequenced, the same modifications were observed. An attenuated chimeric rTGEV virus expressing the ectodomain of a virulent US PEDV S protein (rTGEV-RS-SPEDV) was engineered as vaccine candidate for PEDV and evaluated in a young piglet model system. An attenuated chimeric rTGEV virus expressing the ectodomain of a virulent US PEDV S protein (rTGEV-RS-SPEDV) was engineered as vaccine candidate for PEDV and evaluated in a young piglet model system. abstract: Porcine epidemic diarrhea virus (PEDV) is an enteric coronavirus causing high morbidity and mortality in porcine herds worldwide. Although both inactivated and live attenuated vaccines have been extensively used, the emergence of highly virulent strains and the recurrent outbreaks even in vaccinated farms highlight the need of effective vaccines. Engineering of genetically defined live attenuated vaccines is a rational approach for novel vaccine development. In this line, we engineered an attenuated virus based on the transmissible gastroenteritis virus (TGEV) genome, expressing a chimeric spike protein from a virulent United States (US) PEDV strain. This virus (rTGEV-RS-SPEDV) was attenuated in highly-sensitive five-day-old piglets, as infected animals did not lose weight and none of them died. In addition, the virus caused very minor tissue damage compared with a virulent virus. The rTGEV-RS-SPEDV vaccine candidate was also attenuated in three-week-old animals that were used to evaluate the protection conferred by this virus, compared with the protection induced by infection with a virulent PEDV US strain (PEDV-NVSL). The rTGEV-RS-SPEDV virus protected against challenge with a virulent PEDV strain, reducing challenge virus titers in jejunum and leading to undetectable challenge virus RNA levels in feces. The rTGEV-RS-SPEDV virus induced a humoral immune response specific for PEDV, including neutralizing antibodies. Altogether, the data indicated that rTGEV-RS-SPEDV is a promising vaccine candidate against virulent PEDV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/31349683/ doi: 10.3390/v11080682 id: cord-254963-cnvxlv6h author: Paskey, Adrian C. title: Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples date: 2019-02-26 words: 6201.0 sentences: 267.0 pages: flesch: 45.0 cache: ./cache/cord-254963-cnvxlv6h.txt txt: ./txt/cord-254963-cnvxlv6h.txt summary: In order to test this newly expanded probe panel and to specifically assess the effect of hybridization-based viral enrichment on the sensitivity of HTS for detection of a single virus within a complex environmental sample, commercial bat guano was spiked with increasing concentrations of Influenza virus (IFV). As expected, a dose-dependent effect in the proportion of sequencing reads derived from IFV was observed as the number of spiked genome copies increased ( Fig. 1a and Additional file 1: Table S1 ), in both the unbiased shotgun sequence data as well as the virus enriched sequence data. Such limitations have been of particular concern for U.S. Department of Defense (DoD) laboratories tasked with biosurveillance and biodefense activities in regions with limited material resources and human We demonstrate here that hybridization-based viral target enrichment yields robust coverage of small genomes from clinical samples, even yielding full-length, deeply covered genomes at concentrations whereby Fig. 3 Detection of close relative viruses irrespective of extensive multiplexing. abstract: BACKGROUND: Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and contribution of host or environmental nucleic acids. Hybridization-based target enrichment is one potential method for increasing the sensitivity of viral detection via high-throughput sequencing. RESULTS: This study expands upon two previously developed panels of virus enrichment probes (for filoviruses and for respiratory viruses) to include other viruses of biodefense and/or biosurveillance concern to the U.S. Department of Defense and various international public health agencies. The newly expanded and combined panel is tested using carefully constructed synthetic metagenomic samples that contain clinically relevant amounts of viral genetic material. Target enrichment results in a dramatic increase in sensitivity for virus detection as compared to shotgun sequencing, yielding full, deeply covered viral genomes from materials with Ct values suggesting that amplicon sequencing would be likely to fail. Increased pooling to improve cost- and time-effectiveness does not negatively affect the ability to obtain full-length viral genomes, even in the case of co-infections, although as expected, it does decrease depth of coverage. CONCLUSIONS: Hybridization-based target enrichment is an effective solution to obtain full-length viral genomes for samples from which virus detection would fail via unbiased, shotgun sequencing or even via amplicon sequencing. As the development and testing of probe sets for viral target enrichment expands and continues, the application of this technique, in conjunction with deeper pooling strategies, could make high-throughput sequencing more economical for routine use in biosurveillance, biodefense and outbreak investigations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5543-2) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12864-019-5543-2 doi: 10.1186/s12864-019-5543-2 id: cord-319379-qe56u93a author: Patil, Vaishali M. title: A systematic review on use of aminoquinolines for the therapeutic management of COVID-19: Efficacy, safety and clinical trials date: 2020-05-11 words: 2813.0 sentences: 186.0 pages: flesch: 34.0 cache: ./cache/cord-319379-qe56u93a.txt txt: ./txt/cord-319379-qe56u93a.txt summary: The well reported and clinically used anti-malarial aminoquinoline drugs (chloroquine and hydroxychloroquine) have shown potential to be repurposed to control the present pandemic by inhibition of COVID-19. The review elaborates the mechanism of action, safety (side effects, adverse effects, toxicity) and worldwide clinical trials for chloroquine and hydroxychloroquine to benefit the clinicians, medicinal chemist, pharmacologist actively involved in the management of COVID-19 infection. In vitro inhibition of human influenza A virus replication by chloroquine Anti-malaria drug chloroquine is highly effective in treating avian influenza A H5N1 virus infection in an animal model Inhibition of human immunodeficiency virus type 1 replication by hydroxychloroquine in T cells and monocytes Inhibition of A/Human/Hubei/3/2005 (H3N2) influenza virus infection by silver nanoparticles in vitro and in vivo Mycophenolic acid inhibits dengue virus infection by preventing replication of viral RNA Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro abstract: Recent global outbreak of the pandemic caused by coronavirus (COVID-19) emphasizes the urgent need for novel antiviral therapeutics. It can be supplemented by utilization of efficient and validated drug discovery approaches such as drug repurposing/repositioning. The well reported and clinically used anti-malarial aminoquinoline drugs (chloroquine and hydroxychloroquine) have shown potential to be repurposed to control the present pandemic by inhibition of COVID-19. The review elaborates the mechanism of action, safety (side effects, adverse effects, toxicity) and worldwide clinical trials for chloroquine and hydroxychloroquine to benefit the clinicians, medicinal chemist, pharmacologist actively involved in the management of COVID-19 infection. url: https://www.sciencedirect.com/science/article/pii/S0024320520305233?v=s5 doi: 10.1016/j.lfs.2020.117775 id: cord-271076-436nxsua author: Paul-Pierre, Pastoret title: Emerging diseases, zoonoses and vaccines to control them date: 2009-10-30 words: 3723.0 sentences: 173.0 pages: flesch: 43.0 cache: ./cache/cord-271076-436nxsua.txt txt: ./txt/cord-271076-436nxsua.txt summary: In Northern America, the spectacular spread of West Nile virus infection, another vector transmitted disease, in humans and horses, was rapidly followed by the development of several vaccines, including a DNA-based vaccine for horses. To prevent Nipah virus (Henipavirus) infection in pigs a vaccine has recently been developed but, unfortunately, in countries like Bangladesh, humans are directly infected by the reservoir, a fruit bat species. The changes following globalisation, climatic change [6, 7] , and the opening of previously closed ecosystems, have considerably modified the pattern of endemic (or enzootic) infections/diseases, and contributed to the emergence of new agents that are pathogenic for humans and domestic animals. It is even more true when facing a really emerging disease that moreover is zoonotic such as Nipah virus infection [27] for which no vaccine was available yet, because the causative agent was previously unknown; the only solution is once again to kill and destroy the infected and in-contact animals. abstract: Abstract Vaccination, when available, is undoubtedly the most cost-effective means of preventing and controlling, and even eradicating, infectious diseases. In recent years vaccination has also been used for other purposes in animal health, production and welfare, e.g. immunocastration. Vaccination of animals serves many different purposes, such as controlling animal infections and infestations, thus improving animal health and welfare; controlling anthropozoonoses and food poisoning in humans, thereby protecting public health; solving problems associated with antibiotic and anthelmintic resistance; helping to leave food-producing animals free of chemical residues; protecting the environment and biodiversity and ensuring animal farming sustainability. The problem is nevertheless more complex when facing emerging or re-emerging infections particularly zoonotic ones. url: https://api.elsevier.com/content/article/pii/S0264410X0900872X doi: 10.1016/j.vaccine.2009.06.021 id: cord-025704-icedihm2 author: Pawestri, Hana A. title: Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008–2015 date: 2020-06-01 words: 6529.0 sentences: 323.0 pages: flesch: 43.0 cache: ./cache/cord-025704-icedihm2.txt txt: ./txt/cord-025704-icedihm2.txt summary: Since the initial detection in 2003, Indonesia has reported 200 human cases of highly pathogenic avian influenza H5N1 (HPAI H5N1), associated with an exceptionally high case fatality rate (84%) compared to other geographical regions affected by other genetic clades of the virus. Sequencing data contain valuable information about viral genetic characteristics, including presence of known human adaptive markers, resistance against available antiviral drugs or other changes that can explain the high and rising mortality, while antigenic characterization will help assess the potential protection of pre-pandemic vaccines. Amino acid sequences were analyzed to identify substitutions potentially linked to human adaptation, virulence, antiviral resistance and antigenic properties as listed in the CDC H5N1 Genetic Change Inventory [37] . Although some genetic diversity was observed in the polymerase genes, well-known substitutions such as PB2-E627K and PB2-D701N, which are often selected upon infection of humans and affects the virulence of avian influenza viruses such as H5N1 [12, 66, 67, 79] , were not commonly found in the new samples. abstract: Since the initial detection in 2003, Indonesia has reported 200 human cases of highly pathogenic avian influenza H5N1 (HPAI H5N1), associated with an exceptionally high case fatality rate (84%) compared to other geographical regions affected by other genetic clades of the virus. However, there is limited information on the genetic diversity of HPAI H5N1 viruses, especially those isolated from humans in Indonesia. In this study, the genetic and antigenic characteristics of 35 HPAI H5N1 viruses isolated from humans were analyzed. Full genome sequences were analyzed for the presence of substitutions in the receptor binding site, and polymerase complex, as markers for virulence or human adaptation, as well as antiviral drug resistance substitutions. Only a few substitutions associated with human adaptation were observed, a remarkably low prevalence of the human adaptive substitution PB2-E627K, which is common during human infection with other H5N1 clades and a known virulence marker for avian influenza viruses during human infections. In addition, the antigenic profile of these Indonesian HPAI H5N1 viruses was determined using serological analysis and antigenic cartography. Antigenic characterization showed two distinct antigenic clusters, as observed previously for avian isolates. These two antigenic clusters were not clearly associated with time of virus isolation. This study provides better insight in genetic diversity of H5N1 viruses during human infection and the presence of human adaptive markers. These findings highlight the importance of evaluating virus genetics for HPAI H5N1 viruses to estimate the risk to human health and the need for increased efforts to monitor the evolution of H5N1 viruses across Indonesia. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11262-020-01765-1) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7262163/ doi: 10.1007/s11262-020-01765-1 id: cord-352619-s2x53grh author: Payne, Natalie title: Novel Circoviruses Detected in Feces of Sonoran Felids date: 2020-09-15 words: 3263.0 sentences: 177.0 pages: flesch: 45.0 cache: ./cache/cord-352619-s2x53grh.txt txt: ./txt/cord-352619-s2x53grh.txt summary: Genomes from several families of circular Rep-encoding single-stranded DNA viruses (CRESS-DNA viruses) are part of the phylum Cressdnaviricota [22] and have been identified in fecal samples of other mammals, including domestic cats [23, 24] , bobcats, African lions [25] , capybaras [26] , and Tasmanian devils [27] . Here we used a metagenomic approach to identify novel circoviruses in the feces of two species of Sonoran felids, the puma and bobcat; although not endangered, knowledge of viral threats facing these species could help prevent future population decline, as well as indicate potential threats to the endangered ocelot and jaguar. Based on the species-demarcation threshold for circoviruses which is 80% genome-wide identity [28] , both of these belong to a new species which we refer to as Sonfela (derived from Sonoran felid associated) circovirus 1. As the viral genomes were derived from scat samples, the circoviruses could have infected the bobcat prey species or the felids themselves or be environmentally derived. abstract: Sonoran felids are threatened by drought and habitat fragmentation. Vector range expansion and anthropogenic factors such as habitat encroachment and climate change are altering viral evolutionary dynamics and exposure. However, little is known about the diversity of viruses present in these populations. Small felid populations with lower genetic diversity are likely to be most threatened with extinction by emerging diseases, as with other selective pressures, due to having less adaptive potential. We used a metagenomic approach to identify novel circoviruses, which may have a negative impact on the population viability, from confirmed bobcat (Lynx rufus) and puma (Puma concolor) scats collected in Sonora, Mexico. Given some circoviruses are known to cause disease in their hosts, such as porcine and avian circoviruses, we took a non-invasive approach using scat to identify circoviruses in free-roaming bobcats and puma. Three circovirus genomes were determined, and, based on the current species demarcation, they represent two novel species. Phylogenetic analyses reveal that one circovirus species is more closely related to rodent associated circoviruses and the other to bat associated circoviruses, sharing highest genome-wide pairwise identity of approximately 70% and 63%, respectively. At this time, it is unknown whether these scat-derived circoviruses infect felids, their prey, or another organism that might have had contact with the scat in the environment. Further studies should be conducted to elucidate the host of these viruses and assess health impacts in felids. url: https://doi.org/10.3390/v12091027 doi: 10.3390/v12091027 id: cord-352475-cmmpy5u7 author: Pemmada, Rakesh title: Science-Based Strategies of Antiviral Coatings with Viricidal Properties for the COVID-19 Like Pandemics date: 2020-09-11 words: 7770.0 sentences: 402.0 pages: flesch: 37.0 cache: ./cache/cord-352475-cmmpy5u7.txt txt: ./txt/cord-352475-cmmpy5u7.txt summary: The worldwide, extraordinary outbreak of coronavirus pandemic (i.e., COVID-19) and other emerging viral expansions have drawn particular interest to the design and development of novel antiviral, and viricidal, agents, with a broad-spectrum of antiviral activity. Hence, it is highly desirable to search for potential antiviral and viricidal elements (materials and coatings) to design personal protective equipment (PPE), hygienic implements, and other devices to fight against the rise of viral pandemics and virus-associated fatal risks [22] . In addition, a large number of studies have reported coating materials containing metal ions (i.e., silver, copper, zinc), which have demonstrated an excellent antiviral ability with long-term, persistent effects [30] [31] [32] [33] [51] [52] [53] [54] [55] . Various strategies involved in the development of antiviral and viricidal coatings, like modifying the surface of a substrate via antiviral polymers, incorporation of metal ions/oxides, and functional nanoparticles were discussed. abstract: The worldwide, extraordinary outbreak of coronavirus pandemic (i.e., COVID-19) and other emerging viral expansions have drawn particular interest to the design and development of novel antiviral, and viricidal, agents, with a broad-spectrum of antiviral activity. The current indispensable challenge lies in the development of universal virus repudiation systems that are reusable, and capable of inactivating pathogens, thus reducing risk of infection and transmission. In this review, science-based methods, mechanisms, and procedures, which are implemented in obtaining resultant antiviral coated substrates, used in the destruction of the strains of the different viruses, are reviewed. The constituent antiviral members are classified into a few broad groups, such as polymeric materials, metal ions/metal oxides, and functional nanomaterials, based on the type of materials used at the virus contamination sites. The action mode against enveloped viruses was depicted to vindicate the antiviral mechanism. We also disclose hypothesized strategies for development of a universal and reusable virus deactivation system against the emerging COVID-19. In the surge of the current, alarming scenario of SARS-CoV-2 infections, there is a great necessity for developing highly-innovative antiviral agents to work against the viruses. We hypothesize that some of the antiviral coatings discussed here could exert an inhibitive effect on COVID-19, indicated by the results that the coatings succeeded in obtaining against other enveloped viruses. Consequently, the coatings need to be tested and authenticated, to fabricate a wide range of coated antiviral products such as masks, gowns, surgical drapes, textiles, high-touch surfaces, and other personal protective equipment, aimed at extrication from the COVID-19 pandemic. url: https://doi.org/10.3390/ma13184041 doi: 10.3390/ma13184041 id: cord-351482-hzh5tyoo author: Peng, Xinxia title: Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection date: 2011-11-15 words: 7697.0 sentences: 348.0 pages: flesch: 49.0 cache: ./cache/cord-351482-hzh5tyoo.txt txt: ./txt/cord-351482-hzh5tyoo.txt summary: The small RNAs identified also included many non-miRNA small RNAs, such as small nucleolar RNAs (snoRNAs), in addition to nonannotated small RNAs. An integrative sequencing analysis of both small RNAs and long transcripts from the same samples showed that the results revealing differential expression of miRNAs during infection were largely due to transcriptional regulation and that the predicted miRNA-mRNA network could modulate global host responses to virus infection in a combinatorial fashion. In total, of 4,473,273 start positions in the genome with at least one uniquely mapped read, we found that about 5% (233,236) gave at least 4 reads of the same length in a sample, resulting in 16,054 nonredundant candidate loci for putative small RNAs. About 1.7% (276/16,054) of the candidate loci (median length, 39 nt) were differentially expressed during SARS-CoV and/or influenza virus infection (see Table S2 and Fig. S4a in the supplemental material); 46 of those candidate loci overlapped with annotated miRNA precursors (miRBase version 16). abstract: We previously reported widespread differential expression of long non-protein-coding RNAs (ncRNAs) in response to virus infection. Here, we expanded the study through small RNA transcriptome sequencing analysis of the host response to both severe acute respiratory syndrome coronavirus (SARS-CoV) and influenza virus infections across four founder mouse strains of the Collaborative Cross, a recombinant inbred mouse resource for mapping complex traits. We observed differential expression of over 200 small RNAs of diverse classes during infection. A majority of identified microRNAs (miRNAs) showed divergent changes in expression across mouse strains with respect to SARS-CoV and influenza virus infections and responded differently to a highly pathogenic reconstructed 1918 virus compared to a minimally pathogenic seasonal influenza virus isolate. Novel insights into miRNA expression changes, including the association with pathogenic outcomes and large differences between in vivo and in vitro experimental systems, were further elucidated by a survey of selected miRNAs across diverse virus infections. The small RNAs identified also included many non-miRNA small RNAs, such as small nucleolar RNAs (snoRNAs), in addition to nonannotated small RNAs. An integrative sequencing analysis of both small RNAs and long transcripts from the same samples showed that the results revealing differential expression of miRNAs during infection were largely due to transcriptional regulation and that the predicted miRNA-mRNA network could modulate global host responses to virus infection in a combinatorial fashion. These findings represent the first integrated sequencing analysis of the response of host small RNAs to virus infection and show that small RNAs are an integrated component of complex networks involved in regulating the host response to infection. url: https://www.ncbi.nlm.nih.gov/pubmed/22086488/ doi: 10.1128/mbio.00198-11 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-278093-0twnkv93 author: Perveen, Shagufta title: Coronavirus nCOVID-19: A Pandemic Disease and the Saudi precautions date: 2020-06-18 words: 3149.0 sentences: 162.0 pages: flesch: 56.0 cache: ./cache/cord-278093-0twnkv93.txt txt: ./txt/cord-278093-0twnkv93.txt summary: Recently a novel coronavirus (nCOVID-19) has first emerged in China, causing multiple symptoms in humans and closely related to those caused by SARS (Severe Acute Respiratory Syndrome) and MERS (Middle East Respiratory Syndrome). In these circumstances, rapid reviews which recommended by WHO (World Health Organization), and these recommendations are very significant, helpful and cover current data with different preventive measures developed by the Saudi CDC (Saudi Centre for Disease Prevention and Control). Taking into consideration the preventive measures by pharmacists as part of health care professions, however, the number of infected people, especially those with close contact with nCOVID-19 patients, are rise day by day and currently seems unstoppable. In comparison to other members of coronaviruses ,which cause humans respiratory infections, SARS-CoV (first then it has spread to 216 different countries and territories all over the world, and it seems more deadly. abstract: Now nCOVID-19 has a foothold in many countries, and the threat of a pandemic situation has risen. Recently a novel coronavirus (nCOVID-19) has first emerged in China, causing multiple symptoms in humans and closely related to those caused by SARS (Severe Acute Respiratory Syndrome) and MERS (Middle East Respiratory Syndrome). The nCOVID-19 has reported in Wuhan city of China has recently infected over six million people and at least 0.4 million confirmed deaths all over the world, while 2.8 million people has recovered from this deadly virus. Many instances of this respiratory syndrome coronavirus infection have already reported in more than 216 countries and territories. In contrast, the majority of cases reported in the USA, Brazil, Russia, Spain, UK, Italy, France and many more countries. In today's context, the coronavirus is one of the significant issues faced by the world with plenty of cases. In these circumstances, rapid reviews which recommended by WHO (World Health Organization), and these recommendations are very significant, helpful and cover current data with different preventive measures developed by the Saudi CDC (Saudi Centre for Disease Prevention and Control). This review article describes the possible modes of transmission so that proper preventive actions should be taking. Importantly, this work mentioned the animal reservoir through which may infect humans, and it must be identified to break the transmission chain. In additions, this review paper briefly discussed the spread of the coronavirus in the Arabian Peninsula and what precaution measures are in place by each country to limit the spreading of this virus. Taking into consideration the preventive measures by pharmacists as part of health care professions, however, the number of infected people, especially those with close contact with nCOVID-19 patients, are rise day by day and currently seems unstoppable. url: https://doi.org/10.1016/j.jsps.2020.06.006 doi: 10.1016/j.jsps.2020.06.006 id: cord-344093-3bniy5b5 author: Peteranderl, Christin title: The Impact of the Interferon/TNF-Related Apoptosis-Inducing Ligand Signaling Axis on Disease Progression in Respiratory Viral Infection and Beyond date: 2017-03-22 words: 12546.0 sentences: 578.0 pages: flesch: 34.0 cache: ./cache/cord-344093-3bniy5b5.txt txt: ./txt/cord-344093-3bniy5b5.txt summary: A prominent regulator of disease outcome, especially in-but not limited to-respiratory viral infection, is the IFN-dependent mediator TRAIL (TNF-related apoptosis-inducing ligand) produced by several cell types including immune cells such as macrophages or T cells. (73) Cell death induction, e.g., Bcl-2-associated X protein, caspase-8, Fas-associated protein with death domain, Fas ligand, and TNF-related apoptosis-inducing ligand (TRAIL) dsRNA, polyI:C (4, 110) IAV (4, 5, 10, 115) Sendai virus (110) TRAIL Virus control by apoptosis induction in infected cells IAV (6, 170, 171) Tissue injury by apoptosis of both infected and non-infected alveolar epithelial cells, lung macrophages IAV (5, 7, 10) RSV (137) Necrosis of fibroblasts, dendritic cells, and epithelial cells IAV (146, 147, 168) Increased cellular infiltration CoV (175) Decreased expression of Na,K-ATPase, impaired epithelial fluid reabsorption IAV (11) iNTRODUCTiON In 1957, Isaacs and Lindenmann (1) first recognized the potential of a soluble and probably cell-derived factor to combat influenza virus infection and named this factor interferon [(IFN) from latin interferre, to interfere]. abstract: Interferons (IFNs) are well described to be rapidly induced upon pathogen-associated pattern recognition. After binding to their respective IFN receptors and activation of the cellular JAK/signal transducer and activator of transcription signaling cascade, they stimulate the transcription of a plethora of IFN-stimulated genes (ISGs) in infected as well as bystander cells such as the non-infected epithelium and cells of the immune system. ISGs may directly act on the invading pathogen or can either positively or negatively regulate the innate and adaptive immune response. However, IFNs and ISGs do not only play a key role in the limitation of pathogen spread but have also been recently found to provoke an unbalanced, overshooting inflammatory response causing tissue injury and hampering repair processes. A prominent regulator of disease outcome, especially in—but not limited to—respiratory viral infection, is the IFN-dependent mediator TRAIL (TNF-related apoptosis-inducing ligand) produced by several cell types including immune cells such as macrophages or T cells. First described as an apoptosis-inducing agent in transformed cells, it is now also well established to rapidly evoke cellular stress pathways in epithelial cells, finally leading to caspase-dependent or -independent cell death. Hereby, pathogen spread is limited; however in some cases, also the surrounding tissue is severely harmed, thus augmenting disease severity. Interestingly, the lack of a strictly controlled and well balanced IFN/TRAIL signaling response has not only been implicated in viral infection but might furthermore be an important determinant of disease progression in bacterial superinfections and in chronic respiratory illness. Conclusively, the IFN/TRAIL signaling axis is subjected to a complex modulation and might be exploited for the evaluation of new therapeutic concepts aiming at attenuation of tissue injury. url: https://doi.org/10.3389/fimmu.2017.00313 doi: 10.3389/fimmu.2017.00313 id: cord-348161-757c51xw author: Petrosova, A. title: Development of a highly sensitive, field operable biosensor for serological studies of Ebola virus in central Africa date: 2007-03-26 words: 5428.0 sentences: 264.0 pages: flesch: 48.0 cache: ./cache/cord-348161-757c51xw.txt txt: ./txt/cord-348161-757c51xw.txt summary: We employed a photo immobilization methodology based on a photoactivatable electrogenerated poly(pyrrole-benzophenone) film deposited upon an indium tin oxide (ITO) modified conductive surface fiber-optic. The photochemically modified optical fibers were tested as an immunosensor for detection of antibodies against Ebola virus, in animal and human sera, by use of a coupled chemiluminescent reaction. In this study we present a newly developed optical immunosensor for detection of antibodies to Ebola virus strains Zaire and Sudan, by using a photoimmobilization methodology based on a photoactivable electrogenerated polymer film. The optical fibers coated with poly(pyrrole-benzophenone) were soaked in diluted solution containing inactivated Ebola virus antigen (approximately 7.5 g/ml, the concentration was determined by Micro BCA Protein assay kit, PIERCE) and irradiated with UV light. The calibration curve obtained from the optical fiber immunosensor and ELISA for the detection of anti-Ebola subtype Zaire antibodies. abstract: We describe herein a newly developed optical immunosensor for detection of antibodies directed against antigens of the Ebola virus strains Zaire and Sudan. We employed a photo immobilization methodology based on a photoactivatable electrogenerated poly(pyrrole-benzophenone) film deposited upon an indium tin oxide (ITO) modified conductive surface fiber-optic. It was then linked to a biological receptor, Ebola virus antigen in this case, on the fiber tip through a light driven reaction. The photochemically modified optical fibers were tested as an immunosensor for detection of antibodies against Ebola virus, in animal and human sera, by use of a coupled chemiluminescent reaction. The immunosensor was tested for sensitivity, specificity, and compared to standard chemiluminescent ELISA under the same conditions. The analyte, anti-Ebola IgG, was detected at a low titer of 1:960,000 and 1:1,000,000 for subtypes Zaire and Sudan, respectively. While the same serum tested by ELISA was one order (24 times) less sensitive. url: https://doi.org/10.1016/j.snb.2006.07.005 doi: 10.1016/j.snb.2006.07.005 id: cord-298678-hjxph9jm author: Petrović, T. title: Viral Contamination of Food date: 2016-02-05 words: 10126.0 sentences: 479.0 pages: flesch: 52.0 cache: ./cache/cord-298678-hjxph9jm.txt txt: ./txt/cord-298678-hjxph9jm.txt summary: Results of surveys on the presence of viruses in different kind of foods commodities (fresh produces and shellfish) and in some cases connections to caused outbreaks are presented. Human Norovirus followed by hepatitis A virus are the most common foodborne viruses, which are transmitted by food consumed raw, such as shellfish, fresh vegetables, and berry fruit. These viruses have been identified in a variety of environmental samples, including wastewater, sludge, in marine, surface, and drinking waters, and shellfish, but no foodborne or waterborne outbreaks associated with the enteric HAdV have been reported (Greening, 2006) . The presented data suggest a high prevalence of different human enteric viruses, but mostly NoV, HAV, EV, HAdV, and HRV were found in shellfish samples collected from growing areas, as well as from the market in different countries. abstract: A review of the relevant foodborne viruses is presented. Published data from scientific journals as well as the data presented in official reports and published on the Internet were used for this review. In the review, information is given for the main foodborne viruses, implicated virus species, and food matrices involved, some history data are given, as well as modes of transmission, and sources of the virus presence in food. Results of surveys on the presence of viruses in different kind of foods commodities (fresh produces and shellfish) and in some cases connections to caused outbreaks are presented. Also, possible zoonotic infection and implicated viruses that could be transmitted through food are given. Human Norovirus followed by hepatitis A virus are the most common foodborne viruses, which are transmitted by food consumed raw, such as shellfish, fresh vegetables, and berry fruit. In developed countries, hepatitis E virus is increasingly being recognized as an emerging viral foodborne pathogen that includes zoonotic transmission via pork products. The existing knowledge gaps and the major future expectations in the detection and surveillance of foodborne viruses are mentioned. url: https://api.elsevier.com/content/article/pii/B978012800723500005X doi: 10.1016/b978-0-12-800723-5.00005-x id: cord-314254-9ye8tfvz author: Pfaender, Stephanie title: Natural reservoirs for homologs of hepatitis C virus date: 2014-03-26 words: 6841.0 sentences: 322.0 pages: flesch: 47.0 cache: ./cache/cord-314254-9ye8tfvz.txt txt: ./txt/cord-314254-9ye8tfvz.txt summary: To date, there is no evidence for an animal reservoir of viruses closely related to hepatitis C virus which may have crossed the species barrier to cause disease in humans and resulted in the current pandemic. Recently, several studies discovered new viruses related to hepatitis C virus, belonging to the hepaciand pegivirus genera, in small wild mammals (rodents and bats) and domesticated animals which live in close contact with humans (dogs and horses). Non-primate hepaciviruses (NPHV) were initially discovered in domestic dogs and subsequently in horses 12, 13 and other diverse and widespread HCV-like viruses have been reported in wild populations of rodents and bats. Furthermore, liver function analyses revealed no indication for hepatic inflammation as c-glutamyl transferase and glutamate dehydrogenase values were within reference range, with the exception of a mildly elevated c-glutamyl transferase New HCV-like viruses in different mammalian hosts Pfaender et al 4 level in one horse. abstract: Hepatitis C virus is considered a major public health problem, infecting 2%–3% of the human population. Hepatitis C virus infection causes acute and chronic liver disease, including chronic hepatitis, cirrhosis and hepatocellular carcinoma. In fact, hepatitis C virus infection is the most frequent indication for liver transplantation and a vaccine is not available. Hepatitis C virus displays a narrow host species tropism, naturally infecting only humans, although chimpanzees are also susceptible to experimental infection. To date, there is no evidence for an animal reservoir of viruses closely related to hepatitis C virus which may have crossed the species barrier to cause disease in humans and resulted in the current pandemic. In fact, due to this restricted host range, a robust immunocompetent small animal model is still lacking, hampering mechanistic analysis of virus pathogenesis, immune control and prophylactic vaccine development. Recently, several studies discovered new viruses related to hepatitis C virus, belonging to the hepaci- and pegivirus genera, in small wild mammals (rodents and bats) and domesticated animals which live in close contact with humans (dogs and horses). Genetic and biological characterization of these newly discovered hepatitis C virus-like viruses infecting different mammals will contribute to our understanding of the origins of hepatitis C virus in humans and enhance our ability to study pathogenesis and immune responses using tractable animal models. In this review article, we start with an introduction on the genetic diversity of hepatitis C virus and then focus on the newly discovered viruses closely related to hepatitis C virus. Finally, we discuss possible theories about the origin of this important viral human pathogen. url: https://doi.org/10.1038/emi.2014.19 doi: 10.1038/emi.2014.19 id: cord-013073-siy7dvlo author: Pfäfflin, Albrecht title: Influenza virus-flow from insects to humans as causative for influenza seasonality date: 2020-10-09 words: 1845.0 sentences: 130.0 pages: flesch: 42.0 cache: ./cache/cord-013073-siy7dvlo.txt txt: ./txt/cord-013073-siy7dvlo.txt summary: title: Influenza virus-flow from insects to humans as causative for influenza seasonality A model of viral flow is described and specified to explain influenza virus seasonality, which, in temperate climate, usually evolves when insects have mostly disappeared. The incidence of influenza under different circumstances e.g. temperature, humidity, or tropical conditions and different aspects like synchronicity of infections or in respect to evolutionary conditions do sustain this hypothesis if the behaviour of insects is considered. When influenza virus has reached humans and persists there, it disappears during off-season but re-emerges regularly. Seasonality of influenza is explainable using this insect-compartment model in temperate climate conditions. Associations of global weather conditions to the dynamics of seasonal influenza are found regularly, but the biological mechanism between climate variations and influenza epidemics is dubious [27] . Here, an viral-flow model contributory to explain seasonality of influenza is applied to elucidate questions and circumstances concerning influenza infections like synchronicity, environmental factors. abstract: Virus biomass outweighs human biomass, and insects biomass outweighs human biomass. Insects are regularly habited by viruses as well as humans, humans are further inhabited via insects. A model of viral flow is described and specified to explain influenza virus seasonality, which, in temperate climate, usually evolves when insects have mostly disappeared. With this hypothesis a coherent description of regular seasonal influenza and other seasonal respiratory virus infections in temperate climates is possible. The incidence of influenza under different circumstances e.g. temperature, humidity, or tropical conditions and different aspects like synchronicity of infections or in respect to evolutionary conditions do sustain this hypothesis if the behaviour of insects is considered. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7545380/ doi: 10.1186/s13062-020-00272-5 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: 2708.0 sentences: 161.0 pages: flesch: 44.0 cache: ./cache/cord-255623-qdpdsye9.txt txt: ./txt/cord-255623-qdpdsye9.txt summary: 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. e clinical presentation depends on the specific causative agent but typically includes fever and lower respiratory tract symptoms, such as tachypnoea, nonproductive cough, wheeze, and increased breath sound [7, 8] . In the present study, we used the xTAG RVP FAST assay to identify the viruses causing RI in children and the relationship between specific viruses and clinical outcome. We enrolled 194 pediatric infants (2-24 months old) who had lower respiratory tract infections and were treated at the Vietnam National Children''s Hospital. Bronchiolitis was the most common clinical characteristic of lower respiratory tract infection at the Vietnam National Children''s Hospital. 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-022960-u4s23x1r author: Pihlstrom, Bruce Lee title: Selections from the current literature date: 2020-04-17 words: 1107.0 sentences: 63.0 pages: flesch: 54.0 cache: ./cache/cord-022960-u4s23x1r.txt txt: ./txt/cord-022960-u4s23x1r.txt summary: In the context of the novel coronavirus pandemic, the authors reviewed relevant literature about the virus and made recommendations for controlling its transmission in dental offices. 2 In light of these reports, the authors noted that dental patients and personnel can be exposed to this virus because of face-to-face communication with patients, frequent exposure to saliva, blood, and aerosols, and by handling sharp instruments. They also noted that the virus could be spread by direct or indirect contact with human fluids, patient materials, contaminated dental instruments, and environmental surfaces. [3] [4] Because of the likelihood of 2019-nCoV transmission in the dental office, the authors made several recommendations to help mitigate the spread of the virus in this setting. This is an important study because as the authors noted, it may explain why this virus appears to persist in the environment and is more transmissible than other coronaviruses. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164843/ doi: 10.1016/j.aime.2020.04.020 id: cord-271790-3s8o774l author: Pinto Mendes, J. title: The role of infection in asthma date: 2008-10-31 words: 13929.0 sentences: 956.0 pages: flesch: 56.0 cache: ./cache/cord-271790-3s8o774l.txt txt: ./txt/cord-271790-3s8o774l.txt summary: Animal research is difficult to extrapolate to man but suggests RSV can induce allergic sensitisation 28 , increase bronchial and interleukin (IL)-13 hyperresponsiveness, and rão, na maioria dos casos, consequências remotas, embora algumas vezes descrevam sibilâncias que irão desaparecer aos 3 -5 anos e só raramente se prolongam, instalando -se ou não uma asma. If viral infection in acute asthma, particularly RV -the most studied -is associated with neutrophilic inflammation, cellular lysis and production of interferons (IFNs) 46 and if the environment is rich in IL-4, the production of IL-5, RANTES (Regulated upon Activated T cell Expressed and Selected), eotaxin, eosinophilic infiltration and IgE production 47 generally occur. While children at risk at allergic asthma have long been told to avoid contact with these animals, it is concluded that prolonged early life exposure to Feld-1 induces a form of immune tolerance specific to that allergen 89 . abstract: Abstract This paper reviews the impact of infections on the onset and clinical course of bronchial asthma. A just emphasis is given to the role viral infections, particularly rhinovirus infections, play in exacerbations, and that played by respiratory syncytial virus, suspected of triggering the asthmatic syndrome. The mechanisms of the immune response to virus attacks are explained, highlighting the asthmatic and allergic patient's weakened response, particularly in the perinatal period. Further stressed is a potentiating effect of viral aggression on the allergic response. The hygiene hypothesis and its lack of scientific consistency is detailed, at least as far as the role it seeks to confer on an unproven antagonism of the Th1 and Th2 lymphocyte responses. The current importance of research not into bacteria, but into bacterial products, including endotoxins, on the modulation of asthma and allergy is noted. Studies which, along these lines, show an environmental impact on genetic secretion in the phenotype are underlined. Also discussed in passing are several mechanisms which go towards explaining neutrophilic asthma – for many a contradiction, given eosinophilia's stranglehold on asthmatic inflammation. url: https://api.elsevier.com/content/article/pii/S2173511508702975 doi: 10.1016/s2173-5115(08)70297-5 id: cord-336447-hpnkou41 author: Pitlik, Silvio Daniel title: COVID-19 Compared to Other Pandemic Diseases date: 2020-07-31 words: 6148.0 sentences: 396.0 pages: flesch: 49.0 cache: ./cache/cord-336447-hpnkou41.txt txt: ./txt/cord-336447-hpnkou41.txt summary: Despite multiple publications and increasing knowledge regarding the biological secrets of SARS-CoV-2, as of the writing of this paper, there is neither an approved vaccine nor medication to prevent infection or cure for this highly infectious disease. 7, 8 This paper reviews the microbiological, clinical, and epidemiological characteristics of the coronavirus disease 2019 (COVID-19) pandemic, as well as its socio-economic impact. In the early days of the pandemic great effort was invested into understanding the life cycle of SARS-CoV-2, 9 so as to provide a basis for discovery of an effective vaccine to prevent COVID-19 and/or a safe and efficacious drug to cure it, or at the least, to ameliorate its symptoms, shorten its duration, and/ or block its mechanism of transmission. 59 Unfortunately, to date, no human genetic markers predisposing to SARS-CoV-2 infection, nor the severity of COVID-19, have been found-although recent isolated exceptions to this statement can be found. abstract: In December 2019, the first cases of a new contagious disease were diagnosed in the city of Wuhan, the capital of Hubei province in China. Within a short period of time the outbreak developed exponentially into a pandemic that infected millions of people, with a global death toll of more than 500,000 during its first 6 months. Eventually, the novel disease was named coronavirus disease 2019 (COVID-19), and the new virus was identified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Similar to all known pandemics throughout history, COVID-19 has been accompanied by a large degree of fear, anxiety, uncertainty, and economic disaster worldwide. Despite multiple publications and increasing knowledge regarding the biological secrets of SARS-CoV-2, as of the writing of this paper, there is neither an approved vaccine nor medication to prevent infection or cure for this highly infectious disease. Past pandemics were caused by a wide range of microbes, primarily viruses, but also bacteria. Characteristically, a significant proportion of them originated in different animal species (zoonoses). Since an understanding of the microbial cause of these diseases was unveiled relatively late in human history, past pandemics were often attributed to strange causes including punishment from God, demonic activity, or volatile unspecified substances. Although a high case fatality ratio was common to all pandemic diseases, some striking clinical characteristics of each disease allowed contemporaneous people to clinically diagnose the infection despite null microbiological information. In comparison to past pandemics, SARS-CoV-2 has tricky and complex mechanisms that have facilitated its rapid and catastrophic spread worldwide. url: https://doi.org/10.5041/rmmj.10418 doi: 10.5041/rmmj.10418 id: cord-016475-7ldxvbpz author: Pleschka, Stephan title: Anti-viral approaches against influenza viruses date: 2006 words: 17084.0 sentences: 860.0 pages: flesch: 44.0 cache: ./cache/cord-016475-7ldxvbpz.txt txt: ./txt/cord-016475-7ldxvbpz.txt summary: After influenza virus infection antibodies directed against all major viral proteins can be detected in humans and the level of serum antibodies correlate with resistance to disease (Couch, 2003; Couch and Kasel, 1983; Coulter et al., 2003; Nichol et al., 1998; Potter and Oxford, 1979) . Nevertheless, IKK and NFκB might not only have anti-viral functions as two recent studies demonstrate that influenza viruses replicate much better in cells where NFκB is pre-activated (Nimmerjahn et al., 2004; Wurzer et al., 2004) . Apoptosis is mainly regarded to be a host cell defense against virus viruses (reviewed in: Julkunen et al., 2000; Ludwig et al., 2003; infections since many viruses express anti-apoptotic proteins to prevent this cellular response. Influenza virus-induced NF-kappaB-dependent gene expression is mediated by overexpression of viral proteins and involves oxidative radicals and activation of IkappaB kinase abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120762/ doi: 10.1007/978-0-387-31047-3_5 id: cord-355181-affuyn8z author: Poggio, Claudio title: Copper-Alloy Surfaces and Cleaning Regimens against the Spread of SARS-CoV-2 in Dentistry and Orthopedics. From Fomites to Anti-Infective Nanocoatings date: 2020-07-22 words: 5793.0 sentences: 304.0 pages: flesch: 43.0 cache: ./cache/cord-355181-affuyn8z.txt txt: ./txt/cord-355181-affuyn8z.txt summary: SARS-CoV-2 (acronym for severe acute respiratory syndrome coronavirus 2), responsible for the current outbreak that causes COVID-19 (acronym for "corona virus disease 2019"), is reported to be able of surviving on inanimate surfaces for days. An interesting 2008 article that dealt with environmental hygiene focused on the importance of the transmission of respiratory tract infections Genetic material of SARS-CoV-2 has recently been demonstrated in the plasma of patients with COVID-19, thus feeding concerns for virus shedding during surgical procedures [16] . Incorporation of copper alloy surfaces in conjunction with effective cleaning regimens and good clinical practice could help to control transmission of respiratory coronaviruses, including MERS and SARS [52, 53] . Incorporation of copper alloy surfaces in conjunction with effective cleaning regimens and good clinical practice could help to control transmission of respiratory coronaviruses, including MERS and SARS [52, 53] . abstract: The latest diffusion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the coronavirus disease (COVID-19), has involved the whole world population. Even if huge efforts to control the pandemic have been done, the viral spread is still continuing. COVID-19 is reported as a zoonosis jumped from bats and pangolins to humans. After infection in humans, SARS-CoV-2 is found in the nasopharyngeal and salivary secretions. The virus has also been detected in the blood plasma of infected patients. The viral spread occurs through droplets exhaled from the nose and mouth of the infected people when they breath or talk, or through droplets propelled as a dense cloud by chough or sneeze. The virus can also be delivered as an aerosol from blood plasma, through surgical procedures. Following these ways, the virus can disperse in the air, then reaching and settling on the exposed surfaces. How long the virus will survive on a surface depends on the material the surface is made from. Infection via high-touch surfaces should be prevented. Copper alloy coatings, combined with efficient hygienic/disinfectant procedures and careful surgical practice, could be helpful to health protection in dental practice and can also be adopted in orthopedic traumatology. url: https://www.ncbi.nlm.nih.gov/pubmed/32707757/ doi: 10.3390/ma13153244 id: cord-015764-ly68q5z0 author: Poissy, J. title: La modulation de la signature transcriptomique de l’hôte infecté : une nouvelle stratégie thérapeutique dans les viroses graves ? Exemple de la grippe date: 2016-04-07 words: 3985.0 sentences: 344.0 pages: flesch: 53.0 cache: ./cache/cord-015764-ly68q5z0.txt txt: ./txt/cord-015764-ly68q5z0.txt summary: Une des approches possibles pour le développement de nouveaux antiviraux à plus large spectre d''action est de cibler non pas le virus, mais la cellule de l''hôte infecté, en utilisant la signature transcriptomique cellulaire de l''infection pour sélectionner et repositionner des molécules déjà sur le marché qui vont moduler ce profil transcriptomique, supposé comme étant favorable à l''infection. Les admissions en réanimation pour détresse respiratoire associée à une infection par influenza de type A sont estimées à 12/100 000 personnes.an chez l''adulte [13] . Par ailleurs, plusieurs méthodes de criblage à haut débit (petits ARN interférents [siRNA], interaction protéine-protéine) ont été menées ces dernières années et ont identifié plusieurs centaines de facteurs cellulaires impliqués dans la réplication des virus influenza et/ou la pathogenèse associée à l''infection, proposant ainsi autant de cibles thérapeutiques potentielles [43, 44] . Global host immune response: pathogenesis and transcriptional profiling of type A influenza viruses expressing the hemagglutinin and neuraminidase genes from the 1918 pandemic virus abstract: During the last decades, emergence and reemergence of viruses were responsible for epidemic and pandemic infectious diseases, with variable degrees of severity. Current preventive strategies are not sufficient at all, and available therapeutic drugs are very limited. Indeed, genetic variations of viruses can impair the efficacy of antiviral compounds by the apparition of resistance. Moreover, current delay needed for de novo development of drugs does not allow a rapid response in case of important epidemic or pandemic events. In this context, new therapeutic approaches are necessary. An innovative concept is to repurpose already marketed compounds that can reverse the host cellular transcriptomic response to the infection. By targeting the host, these molecules exhibit a broad-spectrum activity and are potentially effective even against new emergent strains. This strategy implements the characterization of specific host gene expression profiles, the in silico screening of drugs, and their validation in in vitro and in vivo models, until their evaluation in clinical trials. Here, we will present this approach, with the example of the flu. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7117810/ doi: 10.1007/s13546-016-1188-1 id: cord-267567-w39f584z author: Pombo, Joao Palma title: Perturbation of Intracellular Cholesterol and Fatty Acid Homeostasis During Flavivirus Infections date: 2018-06-04 words: 4034.0 sentences: 217.0 pages: flesch: 32.0 cache: ./cache/cord-267567-w39f584z.txt txt: ./txt/cord-267567-w39f584z.txt summary: Upon flavivirus infections, these are significantly altered: on the one hand, these viruses can co-opt lipid metabolic pathways to generate ATP to facilitate replication, or to synthesize membrane components to generate replication sites; on the other hand, more recent evidence suggests counter strategies employed by host cells, which actively modulate several of these networks in response to infection, enhancing interferon signaling by doing so, and thus creating an antiviral environment. In this review, we discuss recent data on mechanisms of alteration of lipid metabolic pathways during infection by flaviviruses, with a focus on cholesterol and fatty acid biosynthesis, which can be manipulated by the invading viruses to support replication, but can also be modulated by the host immune system itself, as a means to fight infection. abstract: Cellular lipid homeostasis is maintained through an intricately linked array of anabolic and catabolic pathways. Upon flavivirus infections, these are significantly altered: on the one hand, these viruses can co-opt lipid metabolic pathways to generate ATP to facilitate replication, or to synthesize membrane components to generate replication sites; on the other hand, more recent evidence suggests counter strategies employed by host cells, which actively modulate several of these networks in response to infection, enhancing interferon signaling by doing so, and thus creating an antiviral environment. In this review, we discuss recent data on mechanisms of alteration of lipid metabolic pathways during infection by flaviviruses, with a focus on cholesterol and fatty acid biosynthesis, which can be manipulated by the invading viruses to support replication, but can also be modulated by the host immune system itself, as a means to fight infection. url: https://doi.org/10.3389/fimmu.2018.01276 doi: 10.3389/fimmu.2018.01276 id: cord-302716-wfla3l20 author: Popov, Vsevolod L. title: Electron Microscopy in Discovery of Novel and Emerging Viruses from the Collection of the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA) date: 2019-05-25 words: 5445.0 sentences: 318.0 pages: flesch: 45.0 cache: ./cache/cord-302716-wfla3l20.txt txt: ./txt/cord-302716-wfla3l20.txt summary: Viruses can be differentiated by their specific morphology (ultrastructure): shape, size, intracellular location, or from the ultrastructural cytopathic effects and specific structures forming in the host cell Upolu, Aransas Bay [22] , Sinu [23] , and Trinity [24] orthobunyaviruses [25] [26] [27] , nyamiviruses [28] , a new reovirus from Cameroon (Fako virus) [29] and Colombia [30] , a new paramyxovirus [31] , an insect-specific (capable of replication in insects but not in vertebrates) alphavirus [32] , a new flavivirus genus [33] and other novel flaviviruses [34] [35] [36] [37] and rhabdoviruses [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] . Insect-specific viruses isolated recently from mosquitoes and phlebotomine sandflies have been characterized and proposed to represent a new genus (Negevirus) related to genera of mite-infecting plant viruses (Blunervirus, Cilevirus, and Higrevirus) in the new family Kitaviridae [49, 73] , or novel members of Entomobirnavirus, family Birnaviridae ( Figure 10D ). abstract: Since the beginning of modern virology in the 1950s, transmission electron microscopy (TEM) has been an important and widely used technique for discovery, identification and characterization of new viruses. Using TEM, viruses can be differentiated by their ultrastructure: shape, size, intracellular location and for some viruses, by the ultrastructural cytopathic effects and/or specific structures forming in the host cell during their replication. Ultrastructural characteristics are usually sufficient for the identification of a virus to the family level. In this review, we summarize 25 years of experience in identification of novel viruses from the collection of the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA). url: https://doi.org/10.3390/v11050477 doi: 10.3390/v11050477 id: cord-309642-wwaa6ls0 author: Potgieter, Leon N.D. title: Pathogenesis of Viral Infections date: 1986-11-30 words: 10859.0 sentences: 770.0 pages: flesch: 40.0 cache: ./cache/cord-309642-wwaa6ls0.txt txt: ./txt/cord-309642-wwaa6ls0.txt summary: 7 · 18 · 84 · 133 Such restrictions function at the cellular level either as the presence or absence of appropriate cell surface receptors (in some instances, they have been shown to be inherited as dominant alleles in a Mendelian manner) 9 · 18 · 26 · 46 · 68 · 97 ·u 9 · 120 or the intracellular hospitality of the cell (several genetic host restrictions on virus replication have been identified).18·32·59·80·82·108·109·120·126 Restricted growth of several DNA viruses in some cells results in transformation without production of progeny viruses. 112 The phenomenon appears to be mediated by virus-induced receptors on the surface membrane of cells and may be one mechanism of the often-encountered secondary bacterial infections associated with viral diseases. 51 · 52 · 104 Viral respiratory tract disease is a consequence of mechanical and biochemical injury to epithelial cells and alveolar macrophages, which can, in the most severe instances, result in secondary bacterial infection, pneumonia, and death. abstract: The article considers factors that influence pathogenesis, initiation of infection, dissemination of virus within a host, lytic viral infections, viral immunosuppression, viral immunopathology, and viral oncogenesis. url: https://api.elsevier.com/content/article/pii/S0195561686501297 doi: 10.1016/s0195-5616(86)50129-7 id: cord-271172-y48dovux author: Potter, Christopher William title: Chapter 25 Respiratory tract viruses date: 1998-12-31 words: 8618.0 sentences: 346.0 pages: flesch: 37.0 cache: ./cache/cord-271172-y48dovux.txt txt: ./txt/cord-271172-y48dovux.txt summary: Adenoviruses, spread by droplet infection, impinge on epithelial cells in the pharynx or in the lower respiratory tract to enter and kill cells by a combination of inhibition of cellular metabolism, virus replication and the toxic effects of the penton: the results are extensive desquamation of affected areas, causing sore throat, necrotizing bronchitis, bronchiolitis and interstitial pneumonia. 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. 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. 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-290617-45be6gxe author: Poulain, Florian title: Footprint of the host restriction factors APOBEC3 on the genome of human viruses date: 2020-08-14 words: 10515.0 sentences: 610.0 pages: flesch: 56.0 cache: ./cache/cord-290617-45be6gxe.txt txt: ./txt/cord-290617-45be6gxe.txt summary: Certain viruses actively encode viral proteins antagonizing the APOBEC3s, others passively face the APOBEC3 selection pressure thanks to a depleted genome for APOBEC3-targeted motifs. By breaking down the human viruses into their respective Baltimore''s group (S3 Fig), we observed that NTC depletion is not present in reverse transcribing nor in negative sense single strand RNA viruses. We also observed a mild general NCC depletion in single strand DNA and double strand RNA viruses, justifying further investigation for a possible A3G-induced footprint (S1 Fig). In order to identify A3-footprinted viruses, we detailed the NTC and NNGANN ratios for 870 human viral species (Fig 4A) . B. The observed/expected ratios of TC dinucleotide at various codon positions and on both strands (i.e. NNTCNN, TCN, NTC, GAN, NGA and NNGANN) were calculated for the putative A3-footprinted viral species and depicted by a heatmap. abstract: APOBEC3 enzymes are innate immune effectors that introduce mutations into viral genomes. These enzymes are cytidine deaminases which transform cytosine into uracil. They preferentially mutate cytidine preceded by thymidine making the 5’TC motif their favored target. Viruses have evolved different strategies to evade APOBEC3 restriction. Certain viruses actively encode viral proteins antagonizing the APOBEC3s, others passively face the APOBEC3 selection pressure thanks to a depleted genome for APOBEC3-targeted motifs. Hence, the APOBEC3s left on the genome of certain viruses an evolutionary footprint. The aim of our study is the identification of these viruses having a genome shaped by the APOBEC3s. We analyzed the genome of 33,400 human viruses for the depletion of APOBEC3-favored motifs. We demonstrate that the APOBEC3 selection pressure impacts at least 22% of all currently annotated human viral species. The papillomaviridae and polyomaviridae are the most intensively footprinted families; evidencing a selection pressure acting genome-wide and on both strands. Members of the parvoviridae family are differentially targeted in term of both magnitude and localization of the footprint. Interestingly, a massive APOBEC3 footprint is present on both strands of the B19 erythroparvovirus; making this viral genome one of the most cleaned sequences for APOBEC3-favored motifs. We also identified the endemic coronaviridae as significantly footprinted. Interestingly, no such footprint has been detected on the zoonotic MERS-CoV, SARS-CoV-1 and SARS-CoV-2 coronaviruses. In addition to viruses that are footprinted genome-wide, certain viruses are footprinted only on very short sections of their genome. That is the case for the gamma-herpesviridae and adenoviridae where the footprint is localized on the lytic origins of replication. A mild footprint can also be detected on the negative strand of the reverse transcribing HIV-1, HIV-2, HTLV-1 and HBV viruses. Together, our data illustrate the extent of the APOBEC3 selection pressure on the human viruses and identify new putatively APOBEC3-targeted viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32797103/ doi: 10.1371/journal.ppat.1008718 id: cord-007530-eyk015n3 author: Powell, H.C. title: Electron-microscopic appearance of the DA virus, a demyelinating murine virus() date: 2003-03-06 words: 2105.0 sentences: 100.0 pages: flesch: 48.0 cache: ./cache/cord-007530-eyk015n3.txt txt: ./txt/cord-007530-eyk015n3.txt summary: abstract: The DA virus is a neurotropic murine virus which can induce acute encephalomyelitis in suckling mice and a chronic myelopathy in weanlings. The agent has been attenuated by serial passage in baby hamster kidney (BHK-21) cells. When attenuated virus is inoculated in 8-week-old C(3)HeJ mice a myelopathy of delayed onset with prominent demyelination of lateral and anterior columns occurs. The DA virus is believed to be related to the Theiler murine encephalomyelitis (TME) viruses because of the similar clinical and pathological conditions which it causes, and because neutralization tests indicate shared antigens between it and GD7, a TME virus. This paper reports electron-microscopic studies of BHK-21 cells infected with DA virus. The cells were prepared 24 and 48 hr after inoculation. Cytopathic effects were observed and infected cells contained plaques consisting of numerous 25 nm virus particles in crystalline array. The virions were exclusively intracytoplasmic and were morphologically indistinguishable from human poliomyelitis virus. These observations appear to establish DA as a picorna virus, related to the TME virus group. The chronic myelopathy caused by DA may prove relevant to chronic demyelinative myelopathies in man, such as multiple sclerosis, and also to amyotrophic lateral sclerosis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118415/ doi: 10.1016/0022-510x(77)90087-9 id: cord-340481-i3qrxnpr author: Pozo, Francisco title: Aplicación de los métodos moleculares al diagnóstico y el estudio epidemiológico de las infecciones respiratorias causadas por virus date: 2008-07-31 words: 9085.0 sentences: 740.0 pages: flesch: 48.0 cache: ./cache/cord-340481-i3qrxnpr.txt txt: ./txt/cord-340481-i3qrxnpr.txt summary: En comparación con las técnicas de diagnóstico clásicas, como son el cultivo de virus en líneas celulares (CC) o la detección de antígenos mediante ensayos de inmunofluorescencia (IF) u otros métodos, la reacción en cadena de la polimerasa (PCR), en sus múltiples variantes, ha permitido incre-mentar de manera considerable el número de muestras respiratorias en las que se detecta la presencia de alguno de los virus asociados con IRA. La elevada sensibilidad de los ensayos de PCR también comporta algunos inconvenientes para el diagnóstico etiológico de la IRA, como son la detección de virus que se encuentran colonizando la mucosa respiratoria de personas asintomáticas o la detección, a consecuencia de excreción prolongada, del virus en secreciones de pacientes que ya se han recuperado de una infección. abstract: Hasta la fecha se han identificado más de 200 virus pertenecientes a 6 familias taxonómicas diferentes asociados con la infección del tracto respiratorio humano. La utilización generalizada de métodos moleculares en los laboratorios de microbiología clínica no sólo ha aportado grandes ventajas al diagnóstico de estas infecciones, sino también está permitiendo profundizar en el conocimiento de la enfermedad y el comportamiento epidemiológico de los virus causantes. Esta tecnología incrementa de manera notable el rendimiento de detección de virus en las muestras respiratorias, debido a su elevada sensibilidad en comparación con las técnicas clásicas y a la posibilidad de identificar virus no cultivables o de crecimiento fastidioso en las líneas celulares habituales, lo que permite realizar el diagnóstico etiológico con mayor rapidez. Sin embargo, también comporta algunos inconvenientes, como son detectar virus que se encuentran colonizando la mucosa respiratoria de personas asintomáticas, o en secreciones de pacientes que ya se han recuperado de una infección pasada, a consecuencia de excreción prolongada de éstos. La secuenciación de los productos obtenidos en la reacción de amplificación genómica permite caracterizar de forma adicional los virus detectados mediante su genotipado, realizar estudios de epidemiología molecular e identificar resistencias a determinados antivirales, por citar sólo algunos ejemplos. To date, more than two hundred viruses, belonging to six different taxonomic families, have been associated with human respiratory tract infection. The widespread incorporation of molecular methods into clinical microbiology laboratories has not only led to notable advances in the etiological diagnosis of viral respiratory infections but has also increased insight into the pathology and epidemiological profiles of the causative viruses. Because of their high sensitivity, molecular techniques markedly increase the efficiency of viral detection in respiratory specimens, particularly those that fail to propagate successfully in common cell cultures, thus allowing more rapid etiologic diagnosis. However, there are also some disadvantages in the use of these new technologies such as detection of viruses that merely colonize the respiratory tract of healthy people, or those found in the nasopharyngeal secretions of patients who have recovered from respiratory infections, due to longterm viral shedding, when the viruses are unlikely to act as pathogens. Additionally, sequencing of the amplification products allows further characterization of detected viruses, including molecular epidemiology, genotyping, or detection of antiviral resistance, to cite only a few examples. url: https://www.sciencedirect.com/science/article/pii/S0213005X08765376 doi: 10.1016/s0213-005x(08)76537-6 id: cord-345020-ai5tib7h author: Price, O. H. title: Using routine testing data to understand circulation patterns of influenza A, respiratory syncytial virus and other respiratory viruses in Victoria, Australia date: 2019-06-17 words: 4186.0 sentences: 211.0 pages: flesch: 40.0 cache: ./cache/cord-345020-ai5tib7h.txt txt: ./txt/cord-345020-ai5tib7h.txt summary: Studies investigating viral interference since the pandemic are sparser, though two studies reported that the timing and magnitude of respiratory virus epidemics were affected by the timing of the seasonal influenza A peak [15, 16] . We used routine diagnostic testing data of specimens from both the community and hospitals at the Victorian Infectious Diseases Reference Laboratory (VIDRL) between 2002 and 2017 to describe relationships between respiratory viruses, with a focus on influenza A and RSV. Seasonality of viruses was assessed visually by time series analysis and for further investigation each virus was compared with influenza A and RSV using cross-correlations that estimated the association between peaks in epidemic curves at a lag or lead of up to 15 weeks. Results of further investigation by logistic regression adjusted for covariates that are predictors of codetection (sex, age and season) were compatible with influenza A, RSV and picornavirus conferring temporary immunity against infection by another respiratory virus. abstract: Several studies have reported evidence of interference between respiratory viruses: respiratory viruses rarely reach their epidemic peak concurrently and there appears to be a negative association between infection with one respiratory virus and co-infection with another. We used results spanning 16 years (2002–2017) of a routine diagnostic multiplex panel that tests for nine respiratory viruses to further investigate these interactions in Victoria, Australia. Time series analyses were used to plot the proportion positive for each virus. The seasonality of all viruses included was compared with respiratory syncytial virus (RSV) and influenza A virus using cross-correlations. Logistic regression was used to explore the likelihood of co-infection with one virus given infection with another. Seasonal peaks were observed each year for influenza A and RSV and less frequently for influenza B, coronavirus and parainfluenza virus. RSV circulated an average of 6 weeks before influenza A. Co-infection with another respiratory virus was less common with picornavirus, RSV or influenza A infection. Our findings provide further evidence of a temporal relationship in the circulation of respiratory viruses. A greater understanding of the interaction between respiratory viruses may enable better prediction of the timing and magnitude of respiratory virus epidemics. url: https://doi.org/10.1017/s0950268819001055 doi: 10.1017/s0950268819001055 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-276585-m1dkkbq7 author: Pulliam, Juliet R. C. title: Viral Host Jumps: Moving toward a Predictive Framework date: 2008-02-13 words: 6920.0 sentences: 349.0 pages: flesch: 41.0 cache: ./cache/cord-276585-m1dkkbq7.txt txt: ./txt/cord-276585-m1dkkbq7.txt summary: Focusing on the appearance of viral pathogens in new host species, I outline a framework that uses specific molecular characteristics to rank virus families by their expected a priori ability to complete each of three steps in the emergence process (encounter, infection, and propagation). This approach yields predictions consistent with empirical observations regarding the ability of specific viral families to infect novel host species but highlights the need for consideration of other factors, such as the ecology of host interactions and the determinants of cellular susceptibility and permissivity to specific virus groups, when trying to predict the frequency with which a virus will encounter a novel host species or the probability of propagation within a novel host species once infection has occurred. Although he makes no attempt to quantitatively determine the relative frequency of emergence for different types of pathogens, Burke claims that recent pandemics in humans and wildlife have mostly been caused by RNA viruses, citing multiple examples (influenza A, HIV-1, enteroviruses 70 and 71, human T-cell lymphoma virus, three paramyxoviruses, porcine respiratory coronavirus, and a calicivirus that causes hemorrhagic disease in rabbits). abstract: In order to predict pathogen emergence, we must distinguish between emergence phenomena that occur via different processes. Focusing on the appearance of viral pathogens in new host species, I outline a framework that uses specific molecular characteristics to rank virus families by their expected a priori ability to complete each of three steps in the emergence process (encounter, infection, and propagation). I then discuss the degree to which the patterns expected, based solely on molecular-level structural characteristics, agree with observations regarding the ability of animal viruses to infect humans. This approach yields predictions consistent with empirical observations regarding the ability of specific viral families to infect novel host species but highlights the need for consideration of other factors, such as the ecology of host interactions and the determinants of cellular susceptibility and permissivity to specific virus groups, when trying to predict the frequency with which a virus will encounter a novel host species or the probability of propagation within a novel host species once infection has occurred. url: https://doi.org/10.1007/s10393-007-0149-6 doi: 10.1007/s10393-007-0149-6 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-345157-fhmhpobi author: Qi, Dan title: Virus infection-induced host mRNA degradation and potential application of live cell imaging date: 2018-12-12 words: 2619.0 sentences: 158.0 pages: flesch: 49.0 cache: ./cache/cord-345157-fhmhpobi.txt txt: ./txt/cord-345157-fhmhpobi.txt summary: Herein, we focus on several possible mechanisms of infection-induced host RNA turnover, which seems to be a common strategy for both prokaryotic and eukaryotic viruses during the very early stage of infection and a potential application of live cell imaging on its visualization. Many viruses also impair the translation of cellular mRNA [1e3], one of the mechanisms during the shift of gene expression from host to virus, a process termed "host shutoff", in order to prevent the production of anti-viral, host protecting proteins [4] . Moreover, Gaglia et al.''s work showed that viral encoded proteins trigger host mRNA degradation by a primary endonucleolytic cleavage causing shutoff of host gene expression and a host exonuclease such as Xrn1, an important 5 0 to 3 0 exonuclease in human cells, were required in subsequent completion of host mRNA turnover [5] . abstract: Viruses exist wherever there is life. They can cause allergy, immune response, inflammation, and even fatal diseases directly or indirectly. Accumulating evidence shows that host RNA undergoes rapid degradation during virus infection. Herein, we focus on several possible mechanisms of infection-induced host RNA turnover, which seems to be a common strategy for both prokaryotic and eukaryotic viruses during the very early stage of infection and a potential application of live cell imaging on its visualization. url: https://doi.org/10.1016/j.jrid.2018.12.002 doi: 10.1016/j.jrid.2018.12.002 id: cord-278456-gsv6dh36 author: Qureshi, Abid title: AVCpred: an integrated web server for prediction and design of antiviral compounds date: 2016-09-09 words: 3465.0 sentences: 211.0 pages: flesch: 49.0 cache: ./cache/cord-278456-gsv6dh36.txt txt: ./txt/cord-278456-gsv6dh36.txt summary: In this study, we have developed quantitative structure–activity relationship (QSAR)‐based models for predicting antiviral compounds (AVCs) against deadly viruses like human immunodeficiency virus (HIV), hepatitis C virus (HCV), hepatitis B virus (HBV), human herpesvirus (HHV) and 26 others using publicly available experimental data from the ChEMBL bioactivity database. We have integrated these models in the AVCpred web server, which will be helpful for virtual screening of AVCs and designing new compounds to target the viruses. The QSAR models have been integrated into a freely available and easy to use web server, ''AVCpred'', where users can predict the antiviral potential of their query molecules against the different viruses in terms of percent inhibition value. In this study, we developed virus specific as well as general prediction models to identify the likelihood of a compound being antiviral using selected chemical attributes of experimentally validated AVCs. PaDEL, an open-source software, was used to calculate molecular descriptors and fingerprints. abstract: Viral infections constantly jeopardize the global public health due to lack of effective antiviral therapeutics. Therefore, there is an imperative need to speed up the drug discovery process to identify novel and efficient drug candidates. In this study, we have developed quantitative structure–activity relationship (QSAR)‐based models for predicting antiviral compounds (AVCs) against deadly viruses like human immunodeficiency virus (HIV), hepatitis C virus (HCV), hepatitis B virus (HBV), human herpesvirus (HHV) and 26 others using publicly available experimental data from the ChEMBL bioactivity database. Support vector machine (SVM) models achieved a maximum Pearson correlation coefficient of 0.72, 0.74, 0.66, 0.68, and 0.71 in regression mode and a maximum Matthew's correlation coefficient 0.91, 0.93, 0.70, 0.89, and 0.71, respectively, in classification mode during 10‐fold cross‐validation. Furthermore, similar performance was observed on the independent validation sets. We have integrated these models in the AVCpred web server, freely available at http://crdd.osdd.net/servers/avcpred. In addition, the datasets are provided in a searchable format. We hope this web server will assist researchers in the identification of potential antiviral agents. It would also save time and cost by prioritizing new drugs against viruses before their synthesis and experimental testing. url: https://doi.org/10.1111/cbdd.12834 doi: 10.1111/cbdd.12834 id: cord-310141-2jofy8fo author: Qureshi, Abid title: A review on current status of antiviral siRNA date: 2018-04-15 words: 3380.0 sentences: 254.0 pages: flesch: 42.0 cache: ./cache/cord-310141-2jofy8fo.txt txt: ./txt/cord-310141-2jofy8fo.txt summary: Short interfering RNA technology affords a potential tractable strategy to combat viral pathogenesis because siRNAs are specific, easy to design, and can be directed against multiple strains of a virus by targeting their conserved gene regions. For example, siRNAs directed against different genes of deadly viruses like human immunodeficiency virus (HIV), 9, 10 influenza virus (INFV), 11, 12 hepatitis B virus (HBV), 13 SARS coronavirus (SARS-CoV), 14, 15 human papillomavirus (HPV), 16 and West Nile virus (WNV) 17 in infected cells displayed encouraging results in inhibiting viral replication. 18, 19 Short interfering RNAs for various human viruses like respiratory syncytial virus (RSV), hepatitis C virus (HCV), HBV, and HIV are also appearing in clinical trials, which further elucidate their importance in inhibiting viral infections. Effective small interfering RNAs targeting matrix and nucleocapsid protein gene inhibit influenza A virus replication in cells and mice abstract: Viral diseases like influenza, AIDS, hepatitis, and Ebola cause severe epidemics worldwide. Along with their resistant strains, new pathogenic viruses continue to be discovered so creating an ongoing need for new antiviral treatments. RNA interference is a cellular gene‐silencing phenomenon in which sequence‐specific degradation of target mRNA is achieved by means of complementary short interfering RNA (siRNA) molecules. Short interfering RNA technology affords a potential tractable strategy to combat viral pathogenesis because siRNAs are specific, easy to design, and can be directed against multiple strains of a virus by targeting their conserved gene regions. In this review, we briefly summarize the current status of siRNA therapy for representative examples from different virus families. In addition, other aspects like their design, delivery, medical significance, bioinformatics resources, and limitations are also discussed. url: https://doi.org/10.1002/rmv.1976 doi: 10.1002/rmv.1976 id: cord-276715-d1nh2dvb author: Raha, Syamal title: Is Copper beneficial for COVID-19 patients? date: 2020-05-05 words: 1610.0 sentences: 103.0 pages: flesch: 50.0 cache: ./cache/cord-276715-d1nh2dvb.txt txt: ./txt/cord-276715-d1nh2dvb.txt summary: Besides, Cu can kill several infectious viruses such as bronchitis virus, poliovirus, human immunodeficiency virus type 1(HIV-1), other enveloped or nonenveloped, singleor double-stranded DNA and RNA viruses. Based on available data, we hypothesize that enrichment of plasma copper levels will boost both the innate and adaptive immunity in people. Copper exposure to human coronavirus 229E destroyed the viral genomes and irreversibly affected virus morphology, including disintegration of envelope and dispersal of surface spikes [16] . Copper deficiency could lead a decreased number of circulatory blood cells with a greater susceptibility towards infection in older people In a study of 11 men on a low-Cu diet (0.66 mg Cu/day for 24 days and 0.38 mg/day for another 40 days) showed a decreased proliferation response of their white blood cells when presented with an immune challenge in cell culture [33] . Thujaplicin-copper chelates inhibit replication of human influenza viruses Effects of low-copper diets on human immune response abstract: Copper (Cu) is an essential micronutrient for both pathogens and the hosts during viral infection. Cu is involved in the functions of critical immune cells such as T helper cells, B cells, neutrophils natural killer (NK) cells, and macrophages. These blood cells are involved in the killing of infectious microbes, in cell-mediated immunity and the production of specific antibodies against the pathogens. Cu-deficient humans show an exceptional susceptibility to infections due to the decreased number and function of these blood cells. Besides, Cu can kill several infectious viruses such as bronchitis virus, poliovirus, human immunodeficiency virus type 1(HIV-1), other enveloped or nonenveloped, single- or double-stranded DNA and RNA viruses. Moreover, Cu has the potent capacity of contact killing of several viruses, including SARS‐CoV‐2. Since the current outbreak of the COVID-19 continues to develop, and there is no vaccine or drugs are currently available, the critical option is now to make the immune system competent to fight against the SARS‐CoV‐2. Based on available data, we hypothesize that enrichment of plasma copper levels will boost both the innate and adaptive immunity in people. Moreover, owing to its potent antiviral activities, Cu may also act as a preventive and therapeutic regime against COVID-19. url: https://doi.org/10.1016/j.mehy.2020.109814 doi: 10.1016/j.mehy.2020.109814 id: cord-304278-0qy1nngs author: Raj, G. Dhinakar title: Infectious bronchitis virus: immunopathogenesis of infection in the chicken date: 2007-11-12 words: 12530.0 sentences: 665.0 pages: flesch: 45.0 cache: ./cache/cord-304278-0qy1nngs.txt txt: ./txt/cord-304278-0qy1nngs.txt summary: While infectious bronchitis (IB) is considered primarily a disease of the respiratory system, different IBV strains may show variable tissue tropisms and also affect the oviduct and the kidneys, with serious consequences. Nevertheless, the lack of correlation between antibodies and resistance, discrepancies between in vitro strain differentiation by VN tests and in vivo cross-protection results (Darbyshire, 1985) and re-excretion of virus in the presence of high titres of circulating antibodies (Jones & Ambali, 1987) all suggest that while humoral antibodies play a role in recovery from IBV infection, other immunological mechanisms are involved. Comparison of the susceptibility of chicks of different ages to infection with nephrosis-nephritis causing strain of infectious bronchitis virus Challenge experiments to evaluate cross-protection induced at the trachea and kidney level by vaccine strains and Belgian nephropathogenic isolates of avian infectious bronchitis virus Effects of avian infectious bronchitis virus (Arkansas strain) on vaccinated laying chickens abstract: The immunopathogenesis of infectious bronchitis virus (IBV) infection in the chicken is reviewed. While infectious bronchitis (IB) is considered primarily a disease of the respiratory system, different IBV strains may show variable tissue tropisms and also affect the oviduct and the kidneys, with serious consequences. Some strains replicate in the intestine but apparently without pathological changes. Pectoral myopathy has been associated with an important recent variant. Several factors can influence the course of infection with IBV, including the age, breed and nutrition of the chicken, the environment and intercurrent infection with other infectious agents. Immunogenic components of the virus include the S (spike) proteins and the N nucleoprotein. The humoral, local and cellular responses of the chicken to IBV are reviewed, together with genetic resistance of the chicken. In long-term persistence of IBV, the caecal tonsil or kidney have been proposed as the sites of persistence. Antigenic variation among IBV strains is related to relatively small differences in amino acid sequences in the S1 spike protein. However, antigenic studies alone do not adequately define immunological relationships between strains and cross-immunisation studies have been used to classify IBV isolates into ‘protectotypes’. It has been speculated that changes in the S1 protein may be related to differences in tissue tropisms shown by different strains. Perhaps in the future, new strains of IBV may arise which affect organs or systems not normally associated with IB. url: https://www.ncbi.nlm.nih.gov/pubmed/18483939/ doi: 10.1080/03079459708419246 id: cord-334771-uy3s6443 author: Rao, BL title: A large outbreak of acute encephalitis with high fatality rate in children in Andhra Pradesh, India, in 2003, associated with Chandipura virus date: 2004-09-09 words: 3672.0 sentences: 187.0 pages: flesch: 49.0 cache: ./cache/cord-334771-uy3s6443.txt txt: ./txt/cord-334771-uy3s6443.txt summary: Samples obtained were: 54 blood samples, 22 throat swabs, ten CSF samples, and one brain aspirate from 55 patients with encephalitis; five blood samples and nine throat swabs from 13 fever cases; and ten blood samples and one throat swab from ten family contacts (including specimens from the brother and mother of a patient who Methods Cell lines and peripheral blood lymphocyte co-cultures were used to isolate the causative agent from clinical samples. The confirmed Chandipura virus encephalitis group consisted of individuals from whose samples we isolated the virus, viral RNA, or reactive IgM antibodies. The viruses isolated in different cell lines from clinical samples from patients with encephalitis were confirmed as Chandipura virus with various techniques including complement fixation, neutralisation test, and immunofluorescence assay. Moreover, the presence of Chandipura virus RNA in nine patients with encephalitis, all from samples obtained before day 4 after onset of illness, suggests an early viraemic phase of the infection process. abstract: BACKGROUND: An outbreak of acute encephalitis of unknown origin with high case fatality (183 of 329 cases) was reported in children from Andhra Pradesh state in southern India during 2003. We investigated the causative agent. METHODS: Cell lines and peripheral blood lymphocyte co-cultures were used to isolate the causative agent from clinical samples. Identity of the agent was established by electron microscopy and serological and molecular assays. FINDINGS: Clinical samples tested negative for IgM antibodies to Japanese encephalitis, West Nile, dengue, and measles viruses, and for RNA of coronavirus, paramyxovirus, enterovirus, and influenza viruses. Virus was isolated from six patients with encephalitis and was identified as Chandipura virus by electron microscopy, complement fixation, and neutralisation tests. Chandipura virus RNA was detected in clinical samples from nine patients. Sequencing of five of these RNA samples showed 96·7–97·5% identity with the reference strain of 1965. Chandipura viral antigen and RNA were detected in brain tissue of a deceased child by immunofluorescent antibody test and PCR. Neutralising, IgG, and IgM antibodies to Chandipura virus were present in some patients' serum samples. Serum samples obtained after 4 days of illness were more frequently positive for IgM to Chandipura virus than were those obtained earlier (p<0·001). A similar trend was noted for neutralising antibodies. INTERPRETATION: Our findings suggest that this outbreak of acute encephalitis in Andhra Pradesh was associated with Chandipura virus, adding to the evidence suggesting that this virus should be considered as an important emerging pathogen. url: https://www.sciencedirect.com/science/article/pii/S0140673604169821 doi: 10.1016/s0140-6736(04)16982-1 id: cord-000050-tfcerilc author: Rao, Srinivas title: Multivalent HA DNA Vaccination Protects against Highly Pathogenic H5N1 Avian Influenza Infection in Chickens and Mice date: 2008-06-18 words: 5605.0 sentences: 256.0 pages: flesch: 44.0 cache: ./cache/cord-000050-tfcerilc.txt txt: ./txt/cord-000050-tfcerilc.txt summary: METHODOLOGY / PRINCIPAL FINDINGS: The ability of DNA vaccines encoding hemagglutinin (HA) proteins from different HPAI H5N1 serotypes was evaluated for its ability to elicit neutralizing antibodies and to protect against homologous and heterologous HPAI H5N1 strain challenge in mice and chickens after DNA immunization by needle and syringe or with a pressure injection device. After optimization of injection conditions, alternative multivalent DNA vaccine regimens were analyzed and compared for magnitude and breadth of neutralizing antibodies, as well as protective efficacy after challenge in mouse and chicken models of HPAI H5N1 infection. The ability of chickens to generate specific antibodies was assessed with three strains that showed broad cross protection in mouse studies (A/Vietnam/1203/2004, A/Anhui/ 1/2005 and A/Indonesia/05/2005), administered individually or in combination, by different injection methods. abstract: BACKGROUND: Sustained outbreaks of highly pathogenic avian influenza (HPAI) H5N1 in avian species increase the risk of reassortment and adaptation to humans. The ability to contain its spread in chickens would reduce this threat and help maintain the capacity for egg-based vaccine production. While vaccines offer the potential to control avian disease, a major concern of current vaccines is their potency and inability to protect against evolving avian influenza viruses. METHODOLOGY / PRINCIPAL FINDINGS: The ability of DNA vaccines encoding hemagglutinin (HA) proteins from different HPAI H5N1 serotypes was evaluated for its ability to elicit neutralizing antibodies and to protect against homologous and heterologous HPAI H5N1 strain challenge in mice and chickens after DNA immunization by needle and syringe or with a pressure injection device. These vaccines elicited antibodies that neutralized multiple strains of HPAI H5N1 when given in combinations containing up to 10 HAs. The response was dose-dependent, and breadth was determined by the choice of the influenza virus HA in the vaccine. Monovalent and trivalent HA vaccines were tested first in mice and conferred protection against lethal H5N1 A/Vietnam/1203/2004 challenge 68 weeks after vaccination. In chickens, protection was observed against heterologous strains of HPAI H5N1 after vaccination with a trivalent H5 serotype DNA vaccine with doses as low as 5 µg DNA given twice either by intramuscular needle injection or with a needle-free device. CONCLUSIONS/SIGNIFICANCE: DNA vaccines offer a generic approach to influenza virus immunization applicable to multiple animal species. In addition, the ability to substitute plasmids encoding different strains enables rapid adaptation of the vaccine to newly evolving field isolates. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657001/ doi: 10.1371/journal.pone.0002432 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-348860-zaimorg0 author: Ratra, Ruchi title: Functional genomics as a tool in virus research date: 2008-06-01 words: 3379.0 sentences: 171.0 pages: flesch: 39.0 cache: ./cache/cord-348860-zaimorg0.txt txt: ./txt/cord-348860-zaimorg0.txt summary: The genomics era has revolutionized the biological sciences and has heralded the emergence of new ''omics'' methodologies such as transcriptomics (study of the gene expression and expression levels of mRNAs at a given time and condition), proteomics (study of the entire protein content of a cell/tissue under various conditions, their structure and functions), metabolomics (study of the metabolite profi le of different cellular processes), phosphoproteomics (a branch of proteomics that characterizes proteins that are phosphorylated), interactomics/system biology (a science that unifi es transcriptomics, proteomics and metabolomics to look at the organism as a whole) and so on. DNA microarrays, proteomics and bioinformatic analysis are routinely used to analyze changes in host and viral gene and protein expression that occur in a virus infected cell [25] . abstract: Genomics is the study of an organism’s entire genome. It started out as a great scientific endeavor in the 1990s which aimed to sequence the complete genomes of certain biological species. However viruses are not new to this field as complete viral genomes have routinely been sequenced since the past thirty years. The ‘genomic era’ has been said to have revolutionized biology. This knowledge of full genomes has created the field of functional genomics in today’s post-genomic era, which, is in most part concerned with the studies on the expression of the organism’s genome under different conditions. This article is an attempt to introduce its readers to the application of functional genomics to address and answer several complex biological issues in virus research. url: https://www.ncbi.nlm.nih.gov/pubmed/23100713/ doi: 10.1007/s12088-008-0032-3 id: cord-004781-ajf9zig0 author: Ray, N. B. title: Rabies viruses infect primary cultures of murine, feline, and human microglia and astrocytes date: 2014-03-07 words: 2337.0 sentences: 125.0 pages: flesch: 43.0 cache: ./cache/cord-004781-ajf9zig0.txt txt: ./txt/cord-004781-ajf9zig0.txt summary: Primary cultures of murine, feline, and human microglia and astrocytes were infected with several different rabies viruses: two unpassaged street virus isolates, a cell culture-adapted strain, and a mouse brain-passaged strain. Primary cultures of murine, feline, and human microglia and astrocytes were infected with several different rabies viruses: two unpassaged street virus isolates, a cell culture-adapted strain, and a mouse brain-passaged strain. In addition, a number of studies have reported rabies viral antigens and virions in human [1, 13, 29] and murine astrocytes [10, 18, 23] , and in murine rami®ed microglial cells [27] , begging the question of the role of these cells in viral replication and persistence, as well as pathogenesis. In the present study, as an initial step toward evaluation of the potential involvement of these glial cells in rabies virus infections, we have directly examined the ability of different rabies virus strains and isolates to infect and replicate in primary cultures of microglia and astrocytes. abstract: Recent studies have reported the detection of rabies viral antigens and virions in astrocytes and microglia of rabies-infected animals. As a first step toward understanding whether these glial cells may be involved in rabies virus replication, persistence, and/or pathogenesis, we explored their potential to be infected in vitro. Primary cultures of murine, feline, and human microglia and astrocytes were infected with several different rabies viruses: two unpassaged street virus isolates, a cell culture-adapted strain, and a mouse brain-passaged strain. Infection, as determined by immunofluorescence, was detected in 15 of the 16 (94%) virus-glial cell combinations. Replication of infectious virus, determined by infectivity assay, was detected in 7 of the 8 (88%) virus-cell combinations. These results show that astrocytes and microglia can be infected by rabies viruses, suggesting that they may have a potential role in disease, perhaps contributing to viral spread, persistence and/or neuronal dysfunction. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086959/ doi: 10.1007/s007050050136 id: cord-003216-5qioku84 author: Rehman, Zaib Ur. title: Pathobiology of Avian avulavirus 1: special focus on waterfowl date: 2018-09-19 words: 5614.0 sentences: 277.0 pages: flesch: 41.0 cache: ./cache/cord-003216-5qioku84.txt txt: ./txt/cord-003216-5qioku84.txt summary: Besides the strong innate immune responses, waterfowl are generally considered long-term carrier of APMV-1 and disease outbreaks have been reported since 1997 [12] [13] [14] , and were confirmed by follow up experimental studies. Host innate immune responses of ducks infected with Newcastle disease viruses of different pathogenicities Pathotypical and genotypical characterization of strains of Newcastle disease virus isolated from outbreaks in chicken and goose flocks in some regions of China during Histopathological alterations in immune organs of chickens and ducks after experimental infection with virulent 9a5b newcastle disease virus Experimental co-infections of domestic ducks with a virulent Newcastle disease virus and low or highly pathogenic avian influenza viruses Phylogenetic diversity among low-virulence newcastle disease viruses from waterfowl and shorebirds and comparison of genotype distributions to those of poultry-origin isolates Genomic characterizations of a Newcastle disease virus isolated from ducks in live bird markets in China abstract: Avian avulaviruses serotype 1 (abbreviated as APMV-1 for the historical name avian paramyxovirus 1) are capable of infecting a wide spectrum of avian species with variable clinical symptoms and outcomes. Ease of transmission has allowed the virus to spread worldwide with varying degrees of virulence depending upon the virus strain and host species. The emergence of new virulent genotypes from global epizootics, and the year-to-year genomic changes in low and high virulence APMV-1 imply that distinct genotypes of APMV-1 are simultaneously evolving at different geographic locations across the globe. This vast genomic diversity may be favoured by large variety of avian species susceptibility to APMV-1 infection, and by the availability of highly mobile wild birds. It has long been considered that waterfowls are not sensitive to APMV-1 and are unable to show any clinical signs, however, outbreaks from the 90′s contradict these concepts. The APMV-1 isolates are increasingly reported from the waterfowl. Waterfowl have strong innate immune responses, which minimize the impact of virus infection, however, are unable to prevent the viral shedding. Numerous APMV-1 are carried by domestic waterfowl intermingling with terrestrial poultry. Therefore, commercial ducks and geese should be vaccinated against APMV-1 to minimize the virus shedding and for the prevention the transmission. Genetic diversity within APMV-1 demonstrates the need for continual monitoring of viral evolution and periodic updates of vaccine seed-strains to achieve efficient control and eradication of APMV-1 in waterfowls. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13567-018-0587-x) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6148804/ doi: 10.1186/s13567-018-0587-x id: cord-270161-vaejyy4i author: Reicks, Darwin L. title: Effective biosecurity to protect North American studs and clients from emerging infectious disease date: 2019-10-01 words: 5263.0 sentences: 253.0 pages: flesch: 53.0 cache: ./cache/cord-270161-vaejyy4i.txt txt: ./txt/cord-270161-vaejyy4i.txt summary: Circumstances in North America in the period of 1999–2004 resulted in numerous PRRS virus (Porcine Reproductive and Respiratory Syndrome) negative boar studs becoming infected and disseminating virus to sow farms. Cleary defined physical barriers for people and animal entry and exit, sanitization and/or down time on incoming supplies, risk mitigation and testing of feed ingredients, and filtration have been keys to changing the incidence of emerging infectious disease introduction into boar studs. Biosecurity measures to prevent PRRS (Porcine Reproductive and Respiratory Syndrome) virus transfer among farms has largely influenced the biosecurity practices of boar studs in North America and worldwide. The purpose of this paper is to review practical effective biosecurity procedures that have made an impact in reducing the risk of emerging infectious disease entering boar studs and infecting sow farms through semen. Air filtration can be an effective way to prevent aerosol transmission of important swine viral diseases that can spread from the boars through the semen and infect sow farms. abstract: Protecting boar studs and their clients from emerging infectious disease first involves effective biosecurity measures to keep a disease out that was not present, and second, early identification and ceasing semen distribution prior to disseminating infectious disease. Experiences in the field can best guide us as to what has been effective. Circumstances in North America in the period of 1999–2004 resulted in numerous PRRS virus (Porcine Reproductive and Respiratory Syndrome) negative boar studs becoming infected and disseminating virus to sow farms. Earlier detection methods were needed, and withholding of semen pending negative test results became standard. To accomplish this, diagnostic labs complied with industry requests for same day testing. At the same time, research efforts helped clarify the major routes of PRRS virus introduction into the farms. The risk of fomites and aerosol spread became viewed as major risks. Addressing issues with people and supply entry alone did not eliminate new virus entry. The implementation of air filtration during 2005–2008 had a major impact on the rate of new virus introductions into boar studs after other measures alone were unsuccessful. Risks exposed with the introduction of PED virus (Porcine Epidemic Diarrhea) into North America further highlighted other risk factors such as feed ingredients, trailer sanitation, and the presence of clear physical barriers. The successful adaptation of testing procedures, combined with biosecurity procedures including air filtration, has made the incidence of infectious disease introduction extremely rare in North American boar studs over the last decade. While survivability of infectious disease agents can vary in different materials or in the air, successful protocols should be applied and adjusted as needed to accommodate new information or risks. Cleary defined physical barriers for people and animal entry and exit, sanitization and/or down time on incoming supplies, risk mitigation and testing of feed ingredients, and filtration have been keys to changing the incidence of emerging infectious disease introduction into boar studs. url: https://doi.org/10.1016/j.theriogenology.2019.05.041 doi: 10.1016/j.theriogenology.2019.05.041 id: cord-331673-xv1tcugl author: Reina, Giacomo title: Hard Nanomaterials in Time of Viral Pandemics date: 2020-07-15 words: 15712.0 sentences: 976.0 pages: flesch: 44.0 cache: ./cache/cord-331673-xv1tcugl.txt txt: ./txt/cord-331673-xv1tcugl.txt summary: For instance, in the case of Herpesviridae and Paramyxoviridae viruses (both enveloped viruses with embedded viral-encoded glycoproteins), AgNPs can effectively reduce their infectivity, by blocking the interaction between the viral particles and the host cells with an antiviral activity strictly dependent on the size and ζ potential of the AgNPs. As a general observation, it was reported that smaller nanoparticles have better antiviral effect. cAgNPs could reduce cytopathic effects induced by RSV and showed efficient antiviral activity against infection by directly inactivating the virus prior to entry into the host cells. have reported that porous AuNPs are able to inhibit influenza A infection more efficiently than nonporous AuNPs. 39 This effect has been associated with the higher surface area of the porous material that favors their interaction with capsids and thus increases their antiviral activity ( Figure 4 ). abstract: [Image: see text] The SARS-Cov-2 pandemic has spread worldwide during 2020, setting up an uncertain start of this decade. The measures to contain infection taken by many governments have been extremely severe by imposing home lockdown and industrial production shutdown, making this the biggest crisis since the second world war. Additionally, the continuous colonization of wild natural lands may touch unknown virus reservoirs, causing the spread of epidemics. Apart from SARS-Cov-2, the recent history has seen the spread of several viral pandemics such as H2N2 and H3N3 flu, HIV, and SARS, while MERS and Ebola viruses are considered still in a prepandemic phase. Hard nanomaterials (HNMs) have been recently used as antimicrobial agents, potentially being next-generation drugs to fight viral infections. HNMs can block infection at early (disinfection, entrance inhibition) and middle (inside the host cells) stages and are also able to mitigate the immune response. This review is focused on the application of HNMs as antiviral agents. In particular, mechanisms of actions, biological outputs, and limitations for each HNM will be systematically presented and analyzed from a material chemistry point-of-view. The antiviral activity will be discussed in the context of the different pandemic viruses. We acknowledge that HNM antiviral research is still at its early stage, however, we believe that this field will rapidly blossom in the next period. url: https://doi.org/10.1021/acsnano.0c04117 doi: 10.1021/acsnano.0c04117 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-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-017489-ftz9190a author: Richards, Guy A. title: Viruses in the Intensive Care Unit (ICU) date: 2005 words: 5792.0 sentences: 330.0 pages: flesch: 44.0 cache: ./cache/cord-017489-ftz9190a.txt txt: ./txt/cord-017489-ftz9190a.txt summary: Pneumonia is the most common complication, which occurs in high-risk patients including those with comorbid illness such as cardiovascular or pulmonary disease, diabetes, renal failure, immunosuppression, the elderly, or residents of nursing homes. A study performed in our ICU indicates that corticosteroids may dramatically alter the course of the most severe disease and should be considered in addition to antiviral therapy along with appropriate supportive care in any previously well patient with life threatening varicella pneumonia (42). Patients with HIV or AIDS (acquired immunodeficiency syndrome) who are hospitalized with chickenpox appear to be at high risk for developing varicella pneumonia, which manifests in a similar clinical fashion to that in immunocompetent individuals. In another study of 68 adult patients admitted with measles diagnosed on clinical and serological grounds, 9 required intensive care, six mechanical ventilation for approximately 15 days, and two deaths occurred. abstract: Whereas viruses are not usually considered to be important causes of ICU admission this review has demonstrated this perception to be incorrect. Viruses and their manifestations differ from continent to continent and hemisphere to hemisphere and it is essential that the intensivist be familiar with diagnosis and management of these ubiquitous organisms. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122063/ doi: 10.1007/0-387-23380-6_3 id: cord-007170-svsfu7fj author: Richt, J. A. title: Infection with Borna Disease Virus: Molecular and Immunobiological Characterization of the Agent date: 1992-06-17 words: 6125.0 sentences: 325.0 pages: flesch: 42.0 cache: ./cache/cord-007170-svsfu7fj.txt txt: ./txt/cord-007170-svsfu7fj.txt summary: Studies on BDV may help to illuminate several important areas of neurobiology, including the mechanisms regulating the replication of a new type of RNA virus in the nuclei of neural cells, the neuroinvasiveness and neurotropism of such viruses, their T cell-mediated immunopathology, tolerance in newborn animals to persistent viral infection of the central nervous system, and behavioral diseases and eating disorders induced by such agents. Persistently infected MDCK (Madin-Darby canine kidney) cells are widely used in indirect immunofluorescence assays for the detection of BDV-specific antibodies in serum and CSF of affected animals and humans [18, 20] . The pathological changes in the brain and retina of BDVinfected animals resemble certain types of encephalitis and Most studies on the pathogenesis of BDV infection have involved experimentally inoculated Lewis rats. Although infection of newborn rats resulted in persistent viral replication in the CNS as well as in visceral organs, these animals developed no inflammatory response or signs of Borna disease. abstract: Borna disease virus (BDV), which seems to be distinct from all other known viruses, exhibits a unique mechanism of pathogenesis. This review highlights several aspects of the biology of infection with this virus and summarizes the preliminary characterization of the agent. Studies on BDV may help to illuminate several important areas of neurobiology, including the mechanisms regulating the replication of a new type of RNA virus in the nuclei of neural cells, the neuroinvasiveness and neurotropism of such viruses, their T cell-mediated immunopathology, tolerance in newborn animals to persistent viral infection of the central nervous system, and behavioral diseases and eating disorders induced by such agents. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109702/ doi: 10.1093/clinids/14.6.1240 id: cord-102898-eyyd7ent author: Rizvi, Vaseef A. title: Translation regulation of Japanese encephalitis virus revealed by ribosome profiling date: 2020-07-17 words: 3048.0 sentences: 159.0 pages: flesch: 44.0 cache: ./cache/cord-102898-eyyd7ent.txt txt: ./txt/cord-102898-eyyd7ent.txt summary: Using ribosome profiling, we identify multiple mechanisms including frameshifting, tRNA dysregulation and alternate translation initiation sites that regulate viral protein synthesis. downstream polyprotein, 2) Significant modulation in levels of a distinct subset of ribosome-bound tRNAs 48 that cannot be explained by virtue of codon usage and 3) Translation from an upstream ORF (uORF) using 49 a non-canonical initiation codon in the 5 UTR region of JEV. However, these sites do not represent commonly associated Studies on RNA viruses have suggested adaptations in codon usage of viral genes to the host translation [30] . Interestingly, JEV infection appears to stimulate 251 expression from UUG start site by almost 67% suggesting viral or virus-induced host trans-regulatory factors 252 promoting uORF translation (Fig.4D) . We also identify a subset of ribosome associated 286 tRNAs whose levels are modulated globally upon JEV infection (Fig.3) . abstract: Japanese encephalitis virus (JEV), a neurotropic flavivirus, is the leading cause of viral encephalitis in endemic regions of Asia. Although the mechanisms modulating JEV virulence and neuroinvasiveness are poorly understood, several acquired mutations in the live attenuated vaccine strain (SA14-14-2) point towards translation regulation as a key strategy. Using ribosome profiling, we identify multiple mechanisms including frameshifting, tRNA dysregulation and alternate translation initiation sites that regulate viral protein synthesis. A significant fraction (~ 40%) of ribosomes undergo frameshifting on NS1 coding sequence leading to early termination, translation of NS1′ protein and modulation of viral protein stoichiometry. Separately, a tRNA subset (glutamate, serine, leucine and histidine) was found to be associated in high levels with the ribosomes upon JEV infection. We also report a previously uncharacterised translational initiation event from an upstream UUG initiation codon in JEV 5′ UTR. A silent mutation at this start site in the vaccine strain has been shown to abrogate neuroinvasiveness suggesting the potential role of translation from this region. Together, our study sheds light on distinct mechanisms that modulate JEV translation with likely consequences for viral pathogenesis. url: https://doi.org/10.1101/2020.07.16.206920 doi: 10.1101/2020.07.16.206920 id: cord-003403-ypefqm71 author: Roberts, Christine C. title: Assay Challenges for Emerging Infectious Diseases: The Zika Experience date: 2018-10-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: From the perspective of vaccine development, it is imperative to accurately diagnose target infections in order to exclude subjects with prior exposure from evaluations of vaccine effectiveness, to track incident infection during the course of a clinical trial and to differentiate immune reactions due to natural infections from responses that are vaccine related. When vaccine development is accelerated to a rapid pace in response to emerging infectious disease threats, the challenges to develop such diagnostic tools is even greater. This was observed through the recent expansion of Zika virus infections into the Western Hemisphere in 2014–2017. When initial Zika vaccine clinical trials were being designed and launched in response to the outbreak, there were no standardized sets of viral and immunological assays, and no approved diagnostic tests for Zika virus infection. The diagnosis of Zika virus infection is still an area of active research and development on many fronts. Here we review emerging infectious disease vaccine clinical assay development and trial execution with a special focus on the state of Zika virus clinical assays and diagnostics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6313918/ doi: 10.3390/vaccines6040070 id: cord-320713-b37c8aye author: Roberts, Lisa O. title: Chapter 9 Viral Strategies to Subvert the Mammalian Translation Machinery date: 2009-10-27 words: 20205.0 sentences: 1067.0 pages: flesch: 48.0 cache: ./cache/cord-320713-b37c8aye.txt txt: ./txt/cord-320713-b37c8aye.txt summary: 6 The rate of translation initiation in mammalian cells is also controlled by sequence elements within the 5 0 -and 3 0 -UTRs of mRNAs which regulate this process by providing sites for interaction of regulatory proteins and RNAs. These include upstream open reading frames (uORFs), microRNA (miRNA) target sites, and polyadenylation elements. 5 It was suggested that alternative eIF4F complexes lacking PABP could selectively promote the synthesis of viral, but not host, proteins, so that KSHV-encoded mRNAs would compete more effectively for host translation machinery in infected cells. Picornavirus translation is directed by internal ribosome entry sites (IRESs) within the 5 0 -UTRs of the viral RNAs. The central one-third of eIF4G, containing the eIF3 and one eIF4A-binding domain, is sufficient to support translation initiation from these IRESs. 43 This allows picornavirus RNAs to compete effectively for the host translation machinery following infection, although the situation appears to be more complicated than this (see Section III). abstract: Viruses do not carry their own protein biosynthesis machinery and the translation of viral proteins therefore requires that the virus usurps the machinery of the host cell. To allow optimal translation of viral proteins at the expense of cellular proteins, virus families have evolved a variety of methods to repress the host translation machinery, while allowing effective viral protein synthesis. Many viruses use noncanonical mechanisms that permit translation of their own RNAs under these conditions. Viruses have also developed mechanisms to evade host innate immune responses that would repress translation under conditions of viral infection, in particular PKR activation in response to double-stranded RNA (dsRNA). Importantly, the study of viral translation mechanisms has enormously enhanced our understanding of many aspects of the cellular protein biosynthesis pathway and its components. A number of unusual mechanisms of translation initiation that were first discovered in viruses have since been observed in cellular mRNAs, and it has become apparent that a diverse range of translation mechanisms operates in eukaryotes, allowing subtle regulation of this essential process. url: https://api.elsevier.com/content/article/pii/S1877117309900096 doi: 10.1016/s1877-1173(09)90009-6 id: cord-333262-xvfl7ycj author: Robson, B. title: COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles’ heel conserved region to minimize probability of escape mutations and drug resistance date: 2020-04-11 words: 21671.0 sentences: 953.0 pages: flesch: 50.0 cache: ./cache/cord-333262-xvfl7ycj.txt txt: ./txt/cord-333262-xvfl7ycj.txt summary: The Wuhan and related isolates revealed a coronavirus that resides in the subgenus Sarbecovirus of the genus Betacoronavirus [2] , and although genetically distinct from its predecessor SARS-CoV it appeared to have similar external binding proteins, meaning here the spike glycoprotein discussed extensively in the present paper. In brief summary, the justifications for the ensemble pharmacophore in the coronavirus case, i.e. the contributions to "fuzziness", include parsimony, that proteins and parts of proteins sometimes have more than one function [12] encouraged by limited numbers of accessible sites (due to e.g. glycosylation) and exemplified by parallel alternative mechanisms of cell entry, multiple methods of drug action, escape from scientific defense measures by virus mutation, polymorphism of human proteins involved, different expression levels of human proteins involved, and the potential problem of the "specter of vaccine development" (concerns about missing the appropriate region of the virus that allows common cold viruses to escape the appropriate immune response). abstract: Abstract This paper continues a recent study of the spike protein sequence of the COVID-19 virus (SARS-CoV-2). It is also in part an introductory review to relevant computational techniques for tackling viral threats, using COVID-19 as an example. Q-UEL tools for facilitating access to knowledge and bioinformatics tools were again used for efficiency, but the focus in this paper is even more on the virus. Subsequence KRSFIEDLLFNKV of the S2′ spike glycoprotein proteolytic cleavage site continues to appear important. Here it is shown to be recognizable in the common cold coronaviruses, avian coronaviruses and possibly as traces in the nidoviruses of reptiles and fish. Its function or functions thus seem important to the coronaviruses. It might represent SARS-CoV-2 Achilles’ Heel, less likely to acquire resistance by mutation, as has happened in some early SARS vaccine studies discussed in the previous paper. Preliminary conformational analysis of the receptor (ACE2) binding site of the spike protein is carried suggesting that while it is somewhat conserved, it appears to be more variable than KRSFIEDLLFNKV. However compounds like emodin that inhibit SARS entry, apparently by binding ACE2, might also have functions at several different human protein binding studies. The enzyme 11β-hydroxysteroid dehydrogenase type 1 is again argued to be a convenient model pharmacophore perhaps representing an ensemble of targets, and it is noted that it occurs both in lung and alimentary tract. Perhaps it benefits the virus to block an inflammatory response by inhibiting the dehydrogenase, but a fairly complex web involves several possible targets. url: https://doi.org/10.1016/j.compbiomed.2020.103749 doi: 10.1016/j.compbiomed.2020.103749 id: cord-333351-homxj9uz author: Rodhain, F. title: Bats and Viruses: complex relationships date: 2015-10-10 words: 10167.0 sentences: 794.0 pages: flesch: 63.0 cache: ./cache/cord-333351-homxj9uz.txt txt: ./txt/cord-333351-homxj9uz.txt summary: Plus d''une soixantaine de virus a été isolée ou détectée chez des chauves-souris qui, selon différentes modalités, se trouvent ainsi impliquées dans la circulation de beaucoup d''entre eux ; c''est le cas, notamment, de Rhabdoviridae du genre Lyssavirus, de Paramyxoviridae comme les virus Nipah et Hendra, de Filoviridae (virus Ebola et Marburg) ou de Coronaviridae comme les agents du syndrome respiratoire aigu sévère (SRAS) et du syndrome respiratoire du Moyen-Orient (MERS). Cependant, même si les contacts entre les Hommes et les chauves-souris sont faibles, la rareté des infections humaines par des Lyssavirus n''appartenant pas au génotype 1 n''est pas clairement expliquée car certains au moins de ces virus sont très largement répandus depuis longtemps ; sans doute leur véritable pathogénicité pour l''Homme est-elle faible (l''observation de cas non mortels et de sujets en bonne santé apparente porteurs d''anticorps semble en témoigner), mais les déterminants de cette pathogénicité demeurent inconnus. abstract: With more than 1 200 species, bats and flying foxes (Order Chiroptera) constitute the most important and diverse order of Mammals after Rodents. Many species of bats are insectivorous while others are frugivorous and few of them are hematophagous. Some of these animals fly during the night, others are crepuscular or diurnal. Some fly long distances during seasonal migrations. Many species are colonial cave-dwelling, living in a rather small home range while others are relatively solitary. However, in spite of the importance of bats for terrestrial biotic communities and ecosystem ecology, the diversity in their biology and lifestyles remain poorly known and underappreciated. More than sixty viruses have been detected or isolated in bats; these animals are therefore involved in the natural cycles of many of them. This is the case, for instance, of rabies virus and other Lyssavirus (Family Rhabdoviridae), Nipah and Hendra viruses (Paramyxoviridae), Ebola and Marburg viruses (Filoviridae), SARS-CoV and MERS-CoV (Coronaviridae). For these zoonotic viruses, a number of bat species are considered as important reservoir hosts, efficient disseminators or even directly responsible of the transmission. Some of these bat-borne viruses cause highly pathogenic diseases while others are of potential significance for humans and domestic or wild animals; so, bats are an important risk in human and animal public health. Moreover, some groups of viruses developed through different phylogenetic mechanisms of coevolution between viruses and bats. The fact that most of these viral infections are asymptomatic in bats has been observed since a long time but the mechanisms of the viral persistence are not clearly understood. The various bioecology of the different bat populations allows exchange of virus between migrating and non-migrating conspecific species. For a better understanding of the role of bats in the circulation of these viral zoonoses, epidemiologists must pay attention to some of their biologic properties which are not fully documented, like their extreme longevity, their diet, the population size and the particular densities observed in species with crowded roosting behavior, the population structure and migrations, the hibernation permitting overwintering of viruses, their particular innate and acquired immune response, probably related at least partially to their ability to fly, allowing persistent virus infections and preventing immunopathological consequences, etc. It is also necessary to get a better knowledge of the interactions between bats and ecologic changes induced by man and to attentively follow bat populations and their viruses through surveillance networks involving human and veterinary physicians, specialists of wild fauna, ecologists, etc. in order to understand the mechanisms of disease emergence, to try to foresee and, perhaps, to prevent viral emergences beforehand. Finally, a more fundamental research about immune mechanisms developed in viral infections is essential to reveal the reasons why Chiroptera are so efficient reservoir hosts. Clearly, a great deal of additional work is needed to document the roles of bats in the natural history of viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/26330152/ doi: 10.1007/s13149-015-0448-z id: cord-008700-knbf8m4x author: Rodrigues, Merlyn R. title: Methods for Rapid Detection of Human Ocular Viral Infections date: 2013-10-30 words: 3011.0 sentences: 171.0 pages: flesch: 38.0 cache: ./cache/cord-008700-knbf8m4x.txt txt: ./txt/cord-008700-knbf8m4x.txt summary: Simple techniques of immunofluorescence and negative stain electron microscopy are used for the rapid detection of viruses in human adenoviral, herpetic, rubella, molluscum contagiosum, and vaccinial infections. Lens aspirate from a 2-year-old patient with clinical ocular rubella was examined by immunofluorescence and negative stain electron microscopy. 10 In a recent epidemic of EKC at a Vietnamese refugee camp in Florida, adenovirus type 8 was recovered in 81% of cases cultured within two weeks of onset of infection.U Dawson et aP 2 described adenovirus-like particles in the conjunctiva of one patient and in the corneal epithelium of another by transmission electron microscopy of tissue culture preparations. In the present study, the typical virions of herpes simplex keratitis were readily identified both by immunofluorescence and by negative stain transmission electron microscopy. Herpes simplex hominis type 1 was recovered in culture and demonstrated by direct immunofluorescence and negative stain electron microscopy in three patients with herpetic dendritic keratitis. abstract: Recent methods for detection of viruses in clinical specimens include immunofluorescence, immunoperoxidase, immune adherence hemagglutination, radioimmunoassay, enzyme-linked immunosorbent assay (ELISA), and immunoelectron microscopy. Some are useful for the detection of traces of viral antigens but are more complicated and timeconsuming than others. Simple techniques of immunofluorescence and negative stain electron microscopy are used for the rapid detection of viruses in human adenoviral, herpetic, rubella, molluscum contagiosum, and vaccinial infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133697/ doi: 10.1016/s0161-6420(79)35507-5 id: cord-293421-0ksn0fc7 author: Rodriguez, J. M. title: Detection of animal pathogens by using the polymerasechain reaction (PCR) date: 1997-05-31 words: 9106.0 sentences: 559.0 pages: flesch: 49.0 cache: ./cache/cord-293421-0ksn0fc7.txt txt: ./txt/cord-293421-0ksn0fc7.txt summary: Summary The polymerase chain reaction (PCR) is a nucleic acid-based technique that enables the rapid and sensitive detection of specific micro-organisms. Althougla PCR has some shortcomings, such as the problems caused by contaminants and inhibitors or the lack of suitable sequences for designing specific primers, the outstanding research effort focused on tiffs technique, together with the remarkable development of molecular biology have minimized the deficiencies and allowed its increased general use as a diagnostic tool. Sensitive studies using reference strains of BVDV fi-om persistently infected carriers have shown that reverse transo-iption (RT)-PCR has greater sensitivity than other tests, including enzyme-linked immunosorbent assay (ELISA) (Horner el aL, 1995) ; unfortunately, cost currently makes this technique unsuitahle for large-scale testing but it should be valuahle as a coniirmatm T test in cases where ELISA resuhs are in the ''suspicious range'' or where the viral titre is low, such as in batches of foetal bovine serum. Comparison of polymerase chain reaction and virus isolation for detection of epizootic hemorrhagic disease in clinical samples from naturally infected deer abstract: Summary The polymerase chain reaction (PCR) is a nucleic acid-based technique that enables the rapid and sensitive detection of specific micro-organisms. Although this technique is widely used in veterinary research, it has not yet found applications in routine microbiological analysis of veterinary clinical samples. However, advances in sample preparation together with the increasing availability of specific gene sequences will probably lead to the more widespread diagnostic use of PCR in the future. PCR is likely to have a strong impact in the epidemiology, treatment and prevention of animal infectious diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/9232118/ doi: 10.1016/s1090-0233(97)80063-9 id: cord-294312-ju6vuywm author: Rohde, Rodney E. title: Common Myths and Legends of Rabies date: 2019-04-19 words: 4488.0 sentences: 281.0 pages: flesch: 60.0 cache: ./cache/cord-294312-ju6vuywm.txt txt: ./txt/cord-294312-ju6vuywm.txt summary: While in fact, today''s treatment regimen is typically only four vaccinations (five for immunocompromised individuals) in the arm, plus a dose of humane rabies immune globulin (HRIG). A viral disease of the central nervous system, rabies transmits between animals, including humans, when saliva containing the virus enters an opening in the skin. Usually, the rabies virus enters through the bite of a rabid animal, but transmission can also occur when infected saliva enters through mucous membranes or a break in the skin. According to the Centers for Disease Control and Prevention (CDC), the first clinical signs and symptoms of rabies may be very similar to those of the flu including general weakness or discomfort, fever, or headache. For the rabies virus to get to the salivary glands, it has to travel first from the site of entry (usually a bite wound) through the animal''s nervous system, then to the brain. abstract: Humankind has somewhat of a dark, yet almost fascinating, supernatural relationship with rabies. Even after Pasteur's rabies vaccine discovery, globally people continue to be stricken with it today. History has carried along the myths and legends that surround this diabolical virus. Some still believe that rabies treatment requires 20 or more shots to the stomach by some monstrously long needle. However, today's treatment regimen is typically only four vaccinations (five for immunocompromised) in the arm, plus human rabies immune globulin. This chapter explores the misunderstood concepts of rabies prevalence, signs and symptoms, exposures, and treatment protocols. url: https://www.sciencedirect.com/science/article/pii/B9780323639798000052 doi: 10.1016/b978-0-323-63979-8.00005-2 id: cord-261171-iknoqb4d author: Roingeard, Philippe title: Viral detection by electron microscopy: past, present and future date: 2012-01-09 words: 4446.0 sentences: 227.0 pages: flesch: 44.0 cache: ./cache/cord-261171-iknoqb4d.txt txt: ./txt/cord-261171-iknoqb4d.txt summary: In research, new imaging techniques for fluorescence light microscopy have supplanted TEM, making it possible to study live cells and dynamic interactions between viruses and the cellular machinery. This large diversity of viruses potentially involved in human gastroenteritis contributed to the use of TEM on negatively stained samples for routine diagnosis by this rapid ''catch-all'' method in clinical virology ( Figures 2C and 2D ). The new techniques, which can be used on living cells, make it possible to follow the fate of individual viral particles and to monitor dynamic interactions between viruses and cellular structures, making it possible to study steps in infection that could previously not be observed. HIV morphogenesis also provides a remarkable example of intensive research into virus-host cell interactions, for which the debate concerning the Figure 6 Budding of HCV Ultrastructural analysis of cells producing the HCV core protein shows that this protein self-assembles into HCV-like particles (arrows) at convoluted and electron-dense ER membranes surrounding the lipid droplets (LD) present in the perinuclear area. abstract: Viruses are very small and most of them can be seen only by TEM (transmission electron microscopy). TEM has therefore made a major contribution to virology, including the discovery of many viruses, the diagnosis of various viral infections and fundamental investigations of virus—host cell interactions. However, TEM has gradually been replaced by more sensitive methods, such as the PCR. In research, new imaging techniques for fluorescence light microscopy have supplanted TEM, making it possible to study live cells and dynamic interactions between viruses and the cellular machinery. Nevertheless, TEM remains essential for certain aspects of virology. It is very useful for the initial identification of unknown viral agents in particular outbreaks, and is recommended by regulatory agencies for investigation of the viral safety of biological products and/or the cells used to produce them. In research, only TEM has a resolution sufficiently high for discrimination between aggregated viral proteins and structured viral particles. Recent examples of different viral assembly models illustrate the value of TEM for improving our understanding of virus—cell interactions. url: https://www.ncbi.nlm.nih.gov/pubmed/18627353/ doi: 10.1042/bc20070173 id: cord-275719-ru33ubss author: Roingeard, Philippe title: Virus detection by transmission electron microscopy: Still useful for diagnosis and a plus for biosafety date: 2018-11-09 words: 2555.0 sentences: 146.0 pages: flesch: 44.0 cache: ./cache/cord-275719-ru33ubss.txt txt: ./txt/cord-275719-ru33ubss.txt summary: Despite the lack of established methods of biological sample preparation for transmission electron microscopy (TEM) at this time, Helmut Ruska was able to characterize the morphology of several viruses and he developed a rough viral classification based on the size and shape of the viral particles. 4 TEM was rapidly adopted for its first major use in clinical virology: the differential diagnosis of smallpox, caused by the variola virus Abbreviations: ELISA, enzyme-linked immunosorbent assay; EM, electron microscopy; EMEA, European Medicines Agency; FDA, Food and Drug Administration; FPERT, fluorescent product-enhanced reverse transcription; LCMV, lymphocytic choriomeningitis virus; PCR, polymerase chain reaction; SARS, severe acute respiratory syndrome; SFTS, severe fever with thrombocytopenia syndrome; TEM, transmission electron microscopy from the poxvirus family, and chickenpox, caused by the varicellazoster virus of the herpes family, based on investigations of fluid samples from the vesicles on the patients'' skin. Detection of retrovirus-like particles by transmission electron microscopy (TEM) with negative staining in bulk harvests of rodent cells used for the production of biological products. abstract: Transmission electron microscopy (TEM) is the only imaging technique allowing the direct visualization of viruses, due to its nanometer‐scale resolution. Between the 1960s and 1990s, TEM contributed to the discovery of many types of viruses and served as a diagnostic tool for identifying viruses directly in biological samples, either in suspension or in sections of tissues or mammalian cells grown in vitro in contact with clinical samples. The diagnosis of viral infections improved considerably during the 1990s, with the advent of highly sensitive techniques, such as enzyme‐linked immunosorbent assay (ELISA) and PCR, rendering TEM obsolete for this purpose. However, the last 20 years have demonstrated the utility of this technique in particular situations, due to its “catch‐all” nature, making diagnosis possible through visualization of the virus, without the need of prior assumptions about the infectious agent sought. Thus, in several major outbreaks in which molecular techniques failed to identify the infectious agent, TEM provided the answer. TEM is also still occasionally used in routine diagnosis to characterize infections not diagnosed by molecular assays. It is also used to check the microbiological safety of biological products. Many biopharmaceuticals are produced in animal cells that might contain little‐known, difficult‐to‐detect viruses. In this context, the “catch‐all” properties of TEM make it possible to document the presence of viruses or virus‐like particles in these products. url: https://doi.org/10.1002/rmv.2019 doi: 10.1002/rmv.2019 id: cord-341324-f9g9gitn author: Rojas, José M. title: Viral pathogen-induced mechanisms to antagonize mammalian interferon (IFN) signaling pathway date: 2020-10-21 words: 10837.0 sentences: 595.0 pages: flesch: 42.0 cache: ./cache/cord-341324-f9g9gitn.txt txt: ./txt/cord-341324-f9g9gitn.txt summary: This includes for instance cooperating in PRR recognition of viral PAMPs, stabilizing signaling complexes to improve their resistance to degradation, stopping virus entry, blocking viral capsid formation, impairing trafficking and budding of virions from the infected cells, but also modulating the IFN response to avoid the toxicity of these potent immune mediators. The phosphorylated STAT1/STAT2 heterodimer associates with interferon regulatory factor 9 (IRF9) to form the transcriptional factor complex ISGF3, which translocate to the nucleus and binds the IFN-response elements (ISRE) in ISG promoters leading to the expression of ISG products [36] (Fig. 2 The oligoadenylate synthetase (OAS)-latent RNase (RNase L) pathway is another IFN-inducible pathway that provides the cell with an effector mechanism upon recognition of viral dsRNA (reviewed in [44] ). abstract: Antiviral responses of interferons (IFNs) are crucial in the host immune response, playing a relevant role in controlling viralw infections. Three types of IFNs, type I (IFN-α, IFN-β), II (IFN-γ) and III (IFN-λ), are classified according to their receptor usage, mode of induction, biological activity and amino acid sequence. Here, we provide a comprehensive review of type I IFN responses and different mechanisms that viruses employ to circumvent this response. In the first part, we will give an overview of the different induction and signaling cascades induced in the cell by IFN-I after virus encounter. Next, highlights of some of the mechanisms used by viruses to counteract the IFN induction will be described. And finally, we will address different mechanism used by viruses to interference with the IFN signaling cascade and the blockade of IFN induced antiviral activities. url: https://www.ncbi.nlm.nih.gov/pubmed/33084946/ doi: 10.1007/s00018-020-03671-z id: cord-255690-xc4bxin4 author: Rolain, Jean-Marc title: Recycling of chloroquine and its hydroxyl analogue to face bacterial, fungal and viral infections in the 21st century date: 2007-07-16 words: 7020.0 sentences: 351.0 pages: flesch: 39.0 cache: ./cache/cord-255690-xc4bxin4.txt txt: ./txt/cord-255690-xc4bxin4.txt summary: Here we review available in vitro and in vivo data on the effects of CQ/HCQ on bacterial, fungal and viral infections, with the concept that manipulation of the intracellular pH in cells and modification of glycosylation of proteins by lysosomotropic agents instead of antimicrobial compounds is a powerful approach as new therapeutic strategies for the prevention and therapeutic management of several infectious diseases, including some of great public health concern worldwide. Coxiella burnetii [5, 13] Histoplasma capsulatum [24] HIV [2, [29] [30] [31] [32] ] Tropheryma whipplei [7, 8] Cryptococcus neoformans [15, 25] SARS-CoV [33, 34] Legionella pneumophila [11] Paracoccidioides brasiliensis [26] Influenza viruses [35] [36] [37] [38] Francisella tularensis [12] Penicillium marneffei [15, 27] Flavivirus, including yellow fever virus [39] Mycobacterium tuberculosis [14] Aspergillus fumigatus [28] Rubella virus [ tetracycline and quinolone regimen for at least 4 years, with a high percentage of relapses [6] . abstract: Chloroquine (CQ) and its hydroxyl analogue hydroxychloroquine (HCQ) are weak bases with a half-century long use as antimalarial agents. Apart from this antimalarial activity, CQ and HCQ have gained interest in the field of other infectious diseases. One of the most interesting mechanisms of action is that CQ leads to alkalinisation of acid vesicles that inhibit the growth of several intracellular bacteria and fungi. The proof of concept of this effect was first used to restore intracellular pH allowing antibiotic efficacy for Coxiella burnetii, the agent of Q fever, and doxycycline plus HCQ is now the reference treatment for chronic Q fever. There is also strong evidence of a similar effect in vitro against Tropheryma whipplei, the agent of Whipple's disease, and a clinical trial is in progress. Other bacteria and fungi multiply in an acidic environment and encouraging in vitro data suggest that this concept may be generalised for all intracellular organisms that multiply in an acidic environment. For viruses, CQ led to inhibition of uncoating and/or alteration of post-translational modifications of newly synthesised proteins, especially inhibition of glycosylation. These effects have been well described in vitro for many viruses, with human immunodeficiency virus (HIV) being the most studied. Preliminary in vivo clinical trials suggest that CQ alone or in combination with antiretroviral drugs might represent an interesting way to treat HIV infection. In conclusion, our review re-emphasises the paradigm that activities mediated by lysosomotropic agents may offer an interesting weapon to face present and future infectious diseases worldwide. url: https://api.elsevier.com/content/article/pii/S0924857907002580 doi: 10.1016/j.ijantimicag.2007.05.015 id: cord-102383-m5ahicqb author: Romano, Alessandra title: Energy dynamics for systemic configurations of virus-host co-evolution date: 2020-05-15 words: 3776.0 sentences: 190.0 pages: flesch: 43.0 cache: ./cache/cord-102383-m5ahicqb.txt txt: ./txt/cord-102383-m5ahicqb.txt summary: A systems-thinking representation, based on stock-flow diagramming of virus-host interaction at the cellular level, is used here for the first time to simulate the system energy dynamics. A systems-thinking representation, based on stock-flow diagramming of virus-host interaction at the cellular level, is used here for the first time to simulate the system energy dynamics. A systems-thinking representation, based on stock-flow diagramming of virus-host interaction at the cellular level, is used here for the first time to simulate the system energy dynamics. Viral load and early addressing (in the first two days from infection) of leverage points are the most effective strategies on stock dynamics to minimize virion assembly and preserve host-cell bioenergetics. Viral load and early addressing (in the first two days from infection) of leverage points are the most effective strategies on stock dynamics to minimize virion assembly and preserve host-cell bioenergetics. abstract: Virus cause multiple outbreaks, for which comprehensive tailored therapeutic strategies are still missing. Virus and host cell dynamics are strictly connected, and convey in virion assembly to ensure virus spread in the body. Study of the systemic behavior of virus-host interaction at the single-cell level is a scientific challenge, considering the difficulties of using experimental approaches and the limited knowledge of the behavior of emerging novel virus as a collectivity. This work focuses on positive-sense, single-stranded RNA viruses, like human coronaviruses, in their virus-individual host interaction, studying the changes induced in the host cell bioenergetics. A systems-thinking representation, based on stock-flow diagramming of virus-host interaction at the cellular level, is used here for the first time to simulate the system energy dynamics. We found that reducing the energy flow which fuels virion assembly is the most affordable strategy to limit the virus spread, but its efficacy is mitigated by the contemporary inhibition of other flows relevant for the system. Summary Positive-single-strand ribonucleic acid ((+)ssRNA) viruses can cause multiple outbreaks, for which comprehensive tailored therapeutic strategies are still missing. Virus and host cell dynamics are strictly connected, generating a complex dynamics that conveys in virion assembly to ensure virus spread in the body. This work focuses on (+)ssRNA viruses in their virus-individual host interaction, studying the changes induced in the host cell bioenergetics. A systems-thinking representation, based on stock-flow diagramming of virus-host interaction at the cellular level, is used here for the first time to simulate the energy dynamics of the system. By means of a computational simulator based on the systemic diagramming, we identifid host protein recycling and folded-protein synthesis as possible new leverage points. These also address different strategies depending on time setting of the therapeutic procedures. Reducing the energy flow which fuels virion assembly is addressed as the most affordable strategy to limit the virus spread, but its efficacy is mitigated by the contemporary inhibition of other flows relevant for the system. Counterintuitively, targeting RNA replication or virion budding does not give rise to relevant systemic effects, and can possibly contribute to further virus spread. The tested combinations of multiple systemic targets are less efficient in minimizing the stock of virions than targeting only the virion assembly process, due to the systemic configuration and its evolution overtime. Viral load and early addressing (in the first two days from infection) of leverage points are the most effective strategies on stock dynamics to minimize virion assembly and preserve host-cell bioenergetics. As a whole, our work points out the need for a systemic approach to design effective therapeutic strategies that should take in account the dynamic evolution of the system. url: https://doi.org/10.1101/2020.05.13.092866 doi: 10.1101/2020.05.13.092866 id: cord-294842-aesiff1f author: Romero-Brey, Inés title: Membranous Replication Factories Induced by Plus-Strand RNA Viruses date: 2014-07-22 words: 11038.0 sentences: 520.0 pages: flesch: 40.0 cache: ./cache/cord-294842-aesiff1f.txt txt: ./txt/cord-294842-aesiff1f.txt summary: Three-dimensional reconstructions of the WNV KUN replication sites revealed an intimate association of the rough ER (rER) with the bounding membrane of the VPs [20] (Figure 2B ), resembling the vesicles observed in DENV-infected cells. In cells infected with TBEV, one of the most important tick-transmitted viruses in Europe and Asia, virus particles and membrane-connected vesicles were also observed inside the ER [25] , similar to what was described for DENV and WNV KUN . Importantly, pulse-radiolabeling experiments localized sites of active RNA replication to the outer surface of single-membrane tubules [71] and isolation of the membranous replication factories and their subsequent visualization by EM revealed that they form rosette-like structures composed of virus-induced cytoplasmic vesicles [124] . Formation of plant RNA virus replication complexes on membranes: Role of an endoplasmic reticulum-targeted viral protein abstract: In this review, we summarize the current knowledge about the membranous replication factories of members of plus-strand (+) RNA viruses. We discuss primarily the architecture of these complex membrane rearrangements, because this topic emerged in the last few years as electron tomography has become more widely available. A general denominator is that two “morphotypes” of membrane alterations can be found that are exemplified by flaviviruses and hepaciviruses: membrane invaginations towards the lumen of the endoplasmatic reticulum (ER) and double membrane vesicles, representing extrusions also originating from the ER, respectively. We hypothesize that either morphotype might reflect common pathways and principles that are used by these viruses to form their membranous replication compartments. url: https://doi.org/10.3390/v6072826 doi: 10.3390/v6072826 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-330296-706hf4qw author: Romette, J. L. title: The European Virus Archive goes global: A growing resource for research date: 2018-10-31 words: 6297.0 sentences: 252.0 pages: flesch: 37.0 cache: ./cache/cord-330296-706hf4qw.txt txt: ./txt/cord-330296-706hf4qw.txt summary: Abstract The European Virus Archive (EVA) was created in 2008 with funding from the FP7-EU Infrastructure Programme, in response to the need for a coordinated and readily accessible collection of viruses that could be made available to academia, public health organisations and industry. The European Virus Archive (EVA) was created in 2008 with funding from the FP7-EU Infrastructure Programme, in response to the need for a coordinated and readily accessible collection of viruses that could be made available to academia, public health organisations and industry (Gould et al., 2012) . In fact, besides the EVAg, we are unaware of any non-profit organization that is concerned with facilitating reliable access globally to viruses and associated reagents from individual virus collections for research and/or diagnostic laboratories, teaching centres or industries involved in the production of diagnostic reagents, pharmaceuticals and vaccines solely for the benefit of science, in a safe and carefully regulated manner. abstract: Abstract The European Virus Archive (EVA) was created in 2008 with funding from the FP7-EU Infrastructure Programme, in response to the need for a coordinated and readily accessible collection of viruses that could be made available to academia, public health organisations and industry. Within three years, it developed from a consortium of nine European laboratories to encompass associated partners in Africa, Russia, China, Turkey, Germany and Italy. In 2014, the H2020 Research and Innovation Framework Programme (INFRAS projects) provided support for the transformation of the EVA from a European to a global organization (EVAg). The EVAg now operates as a non-profit consortium, with 26 partners and 20 associated partners from 21 EU and non-EU countries. In this paper, we outline the structure, management and goals of the EVAg, to bring to the attention of researchers the wealth of products it can provide and to illustrate how end-users can gain access to these resources. Organisations or individuals who would like to be considered as contributors are invited to contact the EVAg coordinator, Jean-Louis Romette, at jean-louis.romette@univmed.fr. url: https://www.ncbi.nlm.nih.gov/pubmed/30059721/ doi: 10.1016/j.antiviral.2018.07.017 id: cord-027473-8zerjwa0 author: Roos, Yrjö H. title: Water and Pathogenic Viruses Inactivation—Food Engineering Perspectives date: 2020-06-20 words: 9805.0 sentences: 515.0 pages: flesch: 43.0 cache: ./cache/cord-027473-8zerjwa0.txt txt: ./txt/cord-027473-8zerjwa0.txt summary: The large number of virus species, differences in spreading, likelihood of foodborne infections, unknown infective doses, and difficulties of infective virus quantification are often limiting experimental approaches to establish accurate data required for detailed understanding of virions'' stability and inactivation kinetics in various foods. The stability of enteric viruses, human norovirus (HuNoV), and hepatitis A (HAV) virions in food materials and their resistance against inactivation in traditional food processing and preservation is well recognized. The small size, concentration, and a tiny infective dose of virions besides the need of host cells for reproduction of viral material result in challenges in studies analyzing virus survival and infectiousness in food, water, and the environment [60] . Here, we summarize studies reporting on virus survival and degradation kinetics with critical evaluation of the importance of known data to understanding losses of virus infectivity in normal circumstances, and particularly as affected by water from a food engineering and safety perspective. abstract: Water is an essential component of food structures and biological materials. The importance of water as a parameter affecting virion stability and inactivation has been recognized across disciplinary areas. The large number of virus species, differences in spreading, likelihood of foodborne infections, unknown infective doses, and difficulties of infective virus quantification are often limiting experimental approaches to establish accurate data required for detailed understanding of virions’ stability and inactivation kinetics in various foods. Furthermore, non-foodborne viruses, as shown by the SARS-CoV-2 (Covid-19) pandemic, may spread within the food chain. Traditional food engineering benefits from kinetic data on effects of relative humidity (RH) and temperature on virion inactivation. The stability of enteric viruses, human norovirus (HuNoV), and hepatitis A (HAV) virions in food materials and their resistance against inactivation in traditional food processing and preservation is well recognized. It appears that temperature-dependence of virus inactivation is less affected by virus strains than differences in temperature and RH sensitivity of individual virus species. Pathogenic viruses are stable at low temperatures typical of food storage conditions. A significant change in activation energy above typical protein denaturation temperatures suggests a rapid inactivation of virions. Furthermore, virus inactivation mechanisms seem to vary according to temperature. Although little is known on the effects of water on virions’ resistance during food processing and storage, dehydration, low RH conditions, and freezing stabilize virions. Enveloped virions tend to have a high stability at low RH, but low temperature and high RH may also stabilize such virions on metal and other surfaces for several days. Food engineering has contributed to significant developments in stabilization of nutrients, flavors, and sensitive components in food materials which provides a knowledge base for development of technologies to inactivate virions in foods and environment. Novel food processing, particularly high pressure processing (HPP) and cold plasma technologies, seem to provide efficient means for virion inactivation and food quality retention prior to packaging or food preservation by traditional technologies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7305474/ doi: 10.1007/s12393-020-09234-z id: cord-306733-df36w6l7 author: Rosales-Mendoza, Sergio title: What Does Plant-Based Vaccine Technology Offer to the Fight against COVID-19? date: 2020-04-14 words: 8591.0 sentences: 420.0 pages: flesch: 39.0 cache: ./cache/cord-306733-df36w6l7.txt txt: ./txt/cord-306733-df36w6l7.txt summary: Transient nuclear genome transformation Rapid production; high productivity; implemented at the industrial level Seed bank cannot be generated; requires purification of the antigen to eliminate toxic compounds from the host and ag-robacteria residues S protein; multiepitope vaccines A chimeric protein of GFP and amino acids 1-658 of the SARS-CoV-1 S protein (S1:GFP) was transiently expressed in tobacco leaves and stably transformed in tobacco and lettuce. No immunization assays were performed The SARS-CoV-1 N protein was transiently expressed in Nicotiana benthamiana, which induced in mice high levels of IgG1 and IgG2a and up regulation of IFN-γ and IL-10 in splenocytes. The precedents of SARS-CoV-1 and MERS antigens expressed in recombinant systems leading to the formation of VLPs constitute important guides for the topic of COVID-19 vaccine development. Thus, VLPs based on the main SARS-CoV-2 structural proteins is an attractive approach for vaccine development against coronavirus infections. abstract: The emergence of new pathogenic viral strains is a constant threat to global health, with the new coronavirus strain COVID-19 as the latest example. COVID-19, caused by the SARS-CoV-2 virus has quickly spread around the globe. This pandemic demands rapid development of drugs and vaccines. Plant-based vaccines are a technology with proven viability, which have led to promising results for candidates evaluated at the clinical level, meaning this technology could contribute towards the fight against COVID-19. Herein, a perspective in how plant-based vaccines can be developed against COVID-19 is presented. Injectable vaccines could be generated by using transient expression systems, which offer the highest protein yields and are already adopted at the industrial level to produce VLPs-vaccines and other biopharmaceuticals under GMPC-processes. Stably-transformed plants are another option, but this approach requires more time for the development of antigen-producing lines. Nonetheless, this approach offers the possibility of developing oral vaccines in which the plant cell could act as the antigen delivery agent. Therefore, this is the most attractive approach in terms of cost, easy delivery, and mucosal immunity induction. The development of multiepitope, rationally-designed vaccines is also discussed regarding the experience gained in expression of chimeric immunogenic proteins in plant systems. url: https://www.ncbi.nlm.nih.gov/pubmed/32295153/ doi: 10.3390/vaccines8020183 id: cord-023831-93xqrblk author: Rosenberg, Helene F. title: Pneumonia Virus of Mice (PVM): Exploring Novel Therapeutic Options In a Severe Respiratory Disease Model date: 2010-03-30 words: 3599.0 sentences: 160.0 pages: flesch: 35.0 cache: ./cache/cord-023831-93xqrblk.txt txt: ./txt/cord-023831-93xqrblk.txt summary: Our laboratories have pioneered the use of the PVM model for the study of human clinical disease, which has provided important insights into the role of the inflammatory response in the pathogenesis of severe respiratory virus infection. Our laboratories have pioneered the use of the PVM model for the study of human clinical disease, which has provided important insights into the role of the inflammatory response in the pathogenesis of severe respiratory virus infection. With these factors in mind, around 1997, we began our collaborative exploration of the pneumonia virus of mice (PVM) pathogen for the study of respiratory virus replication and the ensuing inflammatory response within a natural, evolutionarily relevant host-pathogen relationship. In a study performed using young adult (eight-12 weeks) through aged (up to 78 weeks), but otherwise immunologically naïve mice, we observed no change in the kinetics of PVM replication, but diminished local production of several proinflammatory mediators, including MIP-1a, MCP-1, and IFN-g, along with diminished recruitment of granulocytes to the lung tissue [35] . abstract: Respiratory syncytial virus (RSV) is the most important respiratory pathogen among infants and toddlers, with infections prevalent and nearly universal in this age group. Severe infections are more common among premature infants, those with cardiac and pulmonary anomalies, and the immunosupressed. Effective prophylactic monoclonal antibody treatment is available for high-risk infants, but there is no effective vaccine. Mouse challenge models have been used for the study of the human RSV pathogen, but the most severe forms of RSV disease are not replicated by this approach. Pneumonia virus of mice (PVM; family Paramyxoviridae, genus Pneumovirus) is a mouse pathogen of the same family as human respiratory syncytial virus. PVM replicates efficiently in mouse-lung epithelial cells in vivo in response to a minimal virus inoculum, and replication is accompanied by local production of proinflammatory cytokines (MIP-1α, MIP-2, MCP-1, and IFN-γ) and granulocyte recruitment to the lung. PVM infection and the ensuing inflammatory response can lead to pulmonary edema and respiratory compromise. Our laboratories have pioneered the use of the PVM model for the study of human clinical disease, which has provided important insights into the role of the inflammatory response in the pathogenesis of severe respiratory virus infection. As part of this work, we have presented several immunomodulatory strategies that clearly reduce morbidity and mortality when administered to PVM infected, symptomatic mice, and thus hold promise as realistic therapeutic strategies for severe RSV infection in human subjects. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176177/ doi: 10.1007/978-1-60761-512-5_35 id: cord-256615-gvq8uyfk author: Rosenberg, Ronald title: Detecting the emergence of novel, zoonotic viruses pathogenic to humans date: 2014-11-22 words: 6688.0 sentences: 306.0 pages: flesch: 45.0 cache: ./cache/cord-256615-gvq8uyfk.txt txt: ./txt/cord-256615-gvq8uyfk.txt summary: RNA viruses, with their high potential for mutation and epidemic spread, are the most common class of pathogens found as new causes of human illness. An analysis of virus discovery indicates that the small number of novel viruses discovered annually is an artifact of inadequate surveillance in tropical and subtropical countries, where even established endemic pathogens are often misdiagnosed. Many of the emerging viruses of the future are already infecting humans but remain to be uncovered by a strategy of disease surveillance in selected populations. Despite the differences in clinical presentation and geographical location, these three pathogens share three characteristics: all were unknown before found infecting humans, all are RNA viruses, and all have proven or putative non-human, animal sources. A single subtropical bat species hardly represents all mammal species and indeed many viruses are known to infect more than one species; they tested for only 9 of the 25 virus families pathogenic to humans. abstract: RNA viruses, with their high potential for mutation and epidemic spread, are the most common class of pathogens found as new causes of human illness. Despite great advances made in diagnostic technology since the 1950s, the annual rate at which novel virulent viruses have been found has remained at 2–3. Most emerging viruses are zoonoses; they have jumped from mammal or bird hosts to humans. An analysis of virus discovery indicates that the small number of novel viruses discovered annually is an artifact of inadequate surveillance in tropical and subtropical countries, where even established endemic pathogens are often misdiagnosed. Many of the emerging viruses of the future are already infecting humans but remain to be uncovered by a strategy of disease surveillance in selected populations. url: https://doi.org/10.1007/s00018-014-1785-y doi: 10.1007/s00018-014-1785-y id: cord-316295-x636ux34 author: Roth, Bernhard title: Isolation of influenza viruses in MDCK 33016PF cells and clearance of contaminating respiratory viruses date: 2012-01-11 words: 4140.0 sentences: 190.0 pages: flesch: 44.0 cache: ./cache/cord-316295-x636ux34.txt txt: ./txt/cord-316295-x636ux34.txt summary: Abstract This paper summarizes results obtained by multiplex PCR screening of human clinical samples for respiratory viruses and corresponding data obtained after passaging of virus-positive samples in MDCK 33016PF cells. Using lower inoculum dilutions than those normally applied for preparations containing influenza virus (total dilution of the original sample of ∼104), the positive results for the different viruses turned negative already after 2 or 3 passages in MDCK 33016PF cells. In a similar way, samples with positive and questionable multiplex PCR results only for viruses other than influenza virus were also cultivated for 2 or 3 passages in MDCK 33016PF cells. Considering the selection of specimens, the high percentage of influenza-positive results is not surprising, but a significant number of samples (66/370 or 17.8%) also tested positive for other viruses, such as adenovirus, bocavirus, coronavirus, enterovirus, metapneumovirus (HMPV), parainfluenza virus (PIV), rhinovirus, and respiratory syncytial virus (RSV). abstract: Abstract This paper summarizes results obtained by multiplex PCR screening of human clinical samples for respiratory viruses and corresponding data obtained after passaging of virus-positive samples in MDCK 33016PF cells. Using the ResPlexII v2.0 (Qiagen) multiplex PCR, 393 positive results were obtained in 468 clinical samples collected during an influenza season in Germany. The overall distribution of positive results was influenza A 42.0%, influenza B 38.7%, adenovirus 1.5%, bocavirus 0.5%, coronavirus 3.3%, enterovirus 5.6%, metapneumovirus 1.0%, parainfluenza virus 0.8%, rhinovirus 4.1%, and respiratory syncytial virus (RSV) 2.5%. Double infections of influenza virus together with another virus were found for adenovirus B and E, bocavirus, coronavirus, enterovirus and for rhinovirus. These other viruses were rapidly lost upon passages in MDCK 33016PF cells and under conditions as applied to influenza virus passaging. Clinical samples, in which no influenza virus but other viruses were found, were also subject to passages in MDCK 33016PF cells. Using lower inoculum dilutions than those normally applied for preparations containing influenza virus (total dilution of the original sample of ∼104), the positive results for the different viruses turned negative already after 2 or 3 passages in MDCK 33016PF cells. These results demonstrate that, under practical conditions as applied to grow influenza viruses, contaminating viruses can be effectively removed by passages in MDCK cells. In combination with their superior isolation efficiency, MDCK cells appear highly suitable to be used as an alternative to embryonated eggs to isolate and propagate influenza vaccine candidate viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/22119922/ doi: 10.1016/j.vaccine.2011.11.063 id: cord-290540-r0d6oaez author: Rottier, Peter J.M. title: The molecular dynamics of feline coronaviruses date: 1999-09-01 words: 3820.0 sentences: 200.0 pages: flesch: 56.0 cache: ./cache/cord-290540-r0d6oaez.txt txt: ./txt/cord-290540-r0d6oaez.txt summary: Special attention is given to the genetic dynamics of the viruses as these now allow us to begin to understand the origin of the different phenotypes, in particular the genesis of virulence during persistent infection. The conclusion from these experiments is that feline coronaviruses may persist in the lower intestinal tract where the virus continues to replicate at low levels. Conceivably, the persisting virus confers to its host resistance against superinfection by the closely related feline coronaviruses, which were infecting the other cats. The idea was that''feline enteric coronaviruses'' are indeed restricted in tropism, while''FIP viruses'' would cross the epithelium, infect macrophages and go systemically. The result of all these studies is that generally there is no protection when an antibody response to the spike protein is induced there is rather an enhancement of the infection, with an''early death'' phenomenon. Detection of feline coronavirus RNA in feces, tissues and body fluids of naturally infected cats by reverse transcriptase PCR abstract: Feline coronaviruses are widespread and come in different flavors. There are two main serotypes both of which occur in two pathotypes, the avirulent enteric viruses and the virulent, usually fatal peritonitis viruses, the latter in turn occurring either in a ‘wet’ or exudative form or in a ‘dry’ or proliferative form. In this paper a concise overview is given of the molecular features of these viruses. Special attention is given to the genetic dynamics of the viruses as these now allow us to begin to understand the origin of the different phenotypes, in particular the genesis of virulence during persistent infection. As discussed, the surprising new insights obtained over the last few years call for a critical reevaluation of strategies for protection. url: https://www.sciencedirect.com/science/article/pii/S0378113599000991 doi: 10.1016/s0378-1135(99)00099-1 id: cord-266762-z08rn959 author: Rouse, Barry T. title: 25 Host Defenses to Viruses date: 2019-12-31 words: 7272.0 sentences: 388.0 pages: flesch: 45.0 cache: ./cache/cord-266762-z08rn959.txt txt: ./txt/cord-266762-z08rn959.txt summary: authors: Rouse, Barry T.; Mueller, Scott N. However, broadly neutralizing antiviral antibodies have the potential to be effective therapies against many different human infections, including HIV, influenza viruses, and Ebola virus. Initiation of adaptive immunity is closely dependent on early innate mechanisms that activate antigen-presenting cells (APCs), principally subsets of DCs. APCs and lymphocytes are drawn into lymphoid tissues by chemokine and cytokine signals and are retained there for a few days to facilitate effective intercellular interactions. 19 T-cell immunity against a particular virus involves both CD4 + and CD8 + T-cell subsets that recognize peptides derived from viral antigens bound to surface MHC proteins (class II and class I, respectively) (Chapters 5, 6). Immune responses against virus-infected cells often result in tissue damage, especially if cell killing is involved or if there is extensive recruitment and activation of inflammatory cell types, such as macrophages and sometimes neutrophils. abstract: Abstract Virus infections continue to pose a substantial threat to human health. Unravelling the intricacies of immune defenses against viruses should lead to improved control of infections through the design of new vaccines and therapies. Our understanding of the fundamental cellular and molecular mechanisms involved in the immune systems response to virus infection has improved substantially in recent years. This wealth of new information and the promise of new insight from systems biology approaches continue to drive research in this field. Such knowledge has revealed why viruses sometimes induce immune dysfunction or trigger disastrous pathology and has paved the way for new therapies being tested against chronic and emerging infections. In this chapter, we briefly summarize the general concepts in immunity to virus infections and highlight some of the key challenges remaining for the future. Virus infections continue to pose a substantial threat to human health. url: https://api.elsevier.com/content/article/pii/B9780702068966000259 doi: 10.1016/b978-0-7020-6896-6.00025-9 id: cord-275683-1qj9ri18 author: Roux, Simon title: Metagenomics in Virology date: 2019-06-12 words: 5891.0 sentences: 225.0 pages: flesch: 37.0 cache: ./cache/cord-275683-1qj9ri18.txt txt: ./txt/cord-275683-1qj9ri18.txt summary: Against the background of an extensive viral diversity revealed by metagenomics across many environments, new sequence assembly approaches that reconstruct complete genome sequences from metagenomes have recently revealed surprisingly cosmopolitan viruses in specific ecological niches. However, these techniques can only detect previously known viruses, and often require Box 1 Use of complementary methods to target different types of viruses A number of approaches have been developed to specifically select and survey the genetic material contained by virus particles in a given sample. Virus sequences obtained from "bulk" metagenomes will typically reflect viruses infecting their host cell at the time of sampling, either actively replicating or not, while viromes enables a deeper and more focused exploration of the virus diversity in a specific site or sample. With viral metagenomics being applied to a larger set of samples and environments, and with bioinformatic analyses including genome assembly and interpretation constantly improving, novel groups of dominant and widespread viruses may thus be progressively revealed across many environments. abstract: Metagenomics, i.e., the sequencing and analysis of genomic information extracted directly from clinical or environmental samples, has become a fundamental tool to explore the viral world. Against the background of an extensive viral diversity revealed by metagenomics across many environments, new sequence assembly approaches that reconstruct complete genome sequences from metagenomes have recently revealed surprisingly cosmopolitan viruses in specific ecological niches. Metagenomics is also applied to clinical samples as a non-targeted diagnostic and surveillance tool. By enabling the study of these uncultivated viruses, metagenomics provides invaluable insights into the virus-host interactions, epidemiology, ecology, and evolution of viruses across all ecosystems. url: https://api.elsevier.com/content/article/pii/B9780128096338209576 doi: 10.1016/b978-0-12-809633-8.20957-6 id: cord-006997-sghhdjyi author: Rowland, M.G.M. title: Viruses and diarrhoea in West Africa and London: a collaborative study date: 1978-01-17 words: 1758.0 sentences: 96.0 pages: flesch: 58.0 cache: ./cache/cord-006997-sghhdjyi.txt txt: ./txt/cord-006997-sghhdjyi.txt summary: Rotaviruses and, in some cases, adenoviruses are found on electron microscopy of faeces of a substantial proportion of children with acute diarrhoea in various parts of the world and there is evidence that these organisms can cause the disease (BISHOP et al., 1974; BRYDEN et al., 1975; MIDDLETON et al., 1974; SEXTON et al., 1974; FLEWETT et al., 1975; SCHOUB et al., 1975) . This study was undertaken to look systematically and by comparable techniques for the viral causes of childhood diarrhoea in a typical village in rural Africa and a comparison group of children and adults in north-west London. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107246/ doi: 10.1016/0035-9203(78)90308-5 id: cord-261160-g92zhv19 author: Rowland, Raymond R.R title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero date: 2003-10-30 words: 6383.0 sentences: 322.0 pages: flesch: 48.0 cache: ./cache/cord-261160-g92zhv19.txt txt: ./txt/cord-261160-g92zhv19.txt summary: title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero Even though PRRSV-specific antibody appears as early as 5 days post-infection and is followed by serum neutralizing activity and cell-mediated immunity Molitor, 1997, 1999; Rowland et al., 1999 Rowland et al., , 2001 persistently infected pigs can continue to shed virus. The purpose of this study was to further understand persistent infection in congenitally infected pigs by characterizing the course of clinical disease, sites of virus replication and the capacity to transmit virus in a group of pigs exposed to PRRSV in utero. Analysis of virus and antibody in blood and/or umbilical cords from the 28 live neonates showed that at least 20 or 74% were virus isolation (VI) or RT-PCR positive for PRRSV at the time of farrowing indicating that in utero infection was successful. abstract: The ability of porcine reproductive and respiratory syndrome virus (PRRSV) to establish a persistent infection is the principal contributing factor to the world-wide spread of the disease. Several studies have documented the course of viral infection in postnatally infected pigs; however, very little is known regarding sites of virus replication during persistent infection of pigs exposed to PRRSV in utero. In this study, virus replication and PRRSV-specific antibody were followed for several hundred days in a group of pigs derived from three sows infected at 90 days of gestation with PRRSV isolate VR-2332. Eighty-four percent of pigs were born viremic with a mortality of 54% within 21 days after birth. At approximately 60 days sera from pigs were negative for virus by virus isolation. Analysis of virus replication in the tissues of pigs randomly sacrificed between 63 and 132 days showed no evidence of virus in lung and other non-lymphoid organs. However, virus was easily recovered from tonsil and lymph nodes and in situ hybridization identified these tissues as sites of virus replication. Even though replication was at a low level, virus was easily transmitted to sentinel pigs. By 260 days pigs became seronegative and did not transmit virus to sentinel pigs. Sacrifice of remaining pigs after 300 days showed no evidence of virus in blood and tissues. This study shows that congenital PRRSV-infected pigs can support virus replication for an extended period during which virus replication is primarily restricted to tonsil and lymph nodes. url: https://www.ncbi.nlm.nih.gov/pubmed/14559170/ doi: 10.1016/j.vetmic.2003.07.006 id: cord-001831-3aonqyub author: Royle, Jamie title: Emerging Roles of Viroporins Encoded by DNA Viruses: Novel Targets for Antivirals? date: 2015-10-16 words: 6390.0 sentences: 311.0 pages: flesch: 42.0 cache: ./cache/cord-001831-3aonqyub.txt txt: ./txt/cord-001831-3aonqyub.txt summary: Studies have highlighted the essential nature of a group of small, highly hydrophobic, membrane embedded, channel-forming proteins in the life cycles of a growing number of RNA viruses. This review article summarizes the recent developments in our understanding of these novel viroporins; describes their roles in the virus life cycles and in pathogenesis and speculates on their potential as targets for anti-viral therapeutic intervention. Research over recent decades has identified a group of virus-encoded proteins able to mediate the passage of ions and solutes across cellular membranes, termed viroporins [1, 2] . Due to these broad perturbations to host cell physiology, it is not surprising that viroporin function has been shown to assist in all stages of the virus life cycle including entry, membrane penetration, genome replication and virus egress [1, 2] . This review will summarize our understanding of these putative viroporins, describe their known functions and attempt to highlight how possible ion channel activity may aid the life cycles of these small DNA tumor viruses. abstract: Studies have highlighted the essential nature of a group of small, highly hydrophobic, membrane embedded, channel-forming proteins in the life cycles of a growing number of RNA viruses. These viroporins mediate the flow of ions and a range of solutes across cellular membranes and are necessary for manipulating a myriad of host processes. As such they contribute to all stages of the virus life cycle. Recent discoveries have identified proteins encoded by the small DNA tumor viruses that display a number of viroporin like properties. This review article summarizes the recent developments in our understanding of these novel viroporins; describes their roles in the virus life cycles and in pathogenesis and speculates on their potential as targets for anti-viral therapeutic intervention. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632388/ doi: 10.3390/v7102880 id: cord-334947-pa0p5dif author: Rozen-Gagnon, Kathryn title: Alphavirus Mutator Variants Present Host-Specific Defects and Attenuation in Mammalian and Insect Models date: 2014-01-16 words: 8887.0 sentences: 415.0 pages: flesch: 44.0 cache: ./cache/cord-334947-pa0p5dif.txt txt: ./txt/cord-334947-pa0p5dif.txt summary: Since residue 483 is conserved among alphaviruses, we examined the analogous mutations in Sindbis virus (SINV), which also reduced polymerase fidelity and generated replication defects in mosquito cells. To estimate the population diversity of variants by deep sequencing, cDNA libraries were prepared by Superscript III from RNA extracted from virus generated in BHK-21 or C6/36 cells, and the viral genome was amplified using a high fidelity polymerase (Phusion) to generate 5 overlapping amplicons 2-3 kb in length. To address the possibility that the fitness cost of defective replication, observed in mosquito cell culture, would favor the reversion of these mutant polymerases to wildtype, we deep sequenced virus from the body of an individual mosquito that presented the median titer from each group. abstract: Arboviruses cycle through both vertebrates and invertebrates, which requires them to adapt to disparate hosts while maintaining genetic integrity during genome replication. To study the genetic mechanisms and determinants of these processes, we use chikungunya virus (CHIKV), a re-emerging human pathogen transmitted by the Aedes mosquito. We previously isolated a high fidelity (or antimutator) polymerase variant, C483Y, which had decreased fitness in both mammalian and mosquito hosts, suggesting this residue may be a key molecular determinant. To further investigate effects of position 483 on RNA-dependent RNA-polymerase (RdRp) fidelity, we substituted every amino acid at this position. We isolated novel mutators with decreased replication fidelity and higher mutation frequencies, allowing us to examine the fitness of error-prone arbovirus variants. Although CHIKV mutators displayed no major replication defects in mammalian cell culture, they had reduced specific infectivity and were attenuated in vivo. Unexpectedly, mutator phenotypes were suppressed in mosquito cells and the variants exhibited significant defects in RNA synthesis. Consequently, these replication defects resulted in strong selection for reversion during infection of mosquitoes. Since residue 483 is conserved among alphaviruses, we examined the analogous mutations in Sindbis virus (SINV), which also reduced polymerase fidelity and generated replication defects in mosquito cells. However, replication defects were mosquito cell-specific and were not observed in Drosophila S2 cells, allowing us to evaluate the potential attenuation of mutators in insect models where pressure for reversion was absent. Indeed, the SINV mutator variant was attenuated in fruit flies. These findings confirm that residue 483 is a determinant regulating alphavirus polymerase fidelity and demonstrate proof of principle that arboviruses can be attenuated in mammalian and insect hosts by reducing fidelity. url: https://www.ncbi.nlm.nih.gov/pubmed/24453971/ doi: 10.1371/journal.ppat.1003877 id: cord-276039-nqqwnmwc author: Rua, Rejane title: Origin, evolution and innate immune control of simian foamy viruses in humans date: 2015-02-17 words: 4070.0 sentences: 229.0 pages: flesch: 52.0 cache: ./cache/cord-276039-nqqwnmwc.txt txt: ./txt/cord-276039-nqqwnmwc.txt summary: In this review, we present current data on the discovery, cross-species transmission, and molecular evolution of SFV in human populations initially infected and thus at risk for zoonotic emergence. In this brief review, we will present the current available data on the discovery, cross-species transmission and molecular evolution of the simian foamy viruses (SFV) present in different human populations at risk for zoonotic emergence. They were mostly hunters who reported direct contacts with blood and/or body fluids from wild NHPs. We extended such studies into different areas and populations of this Central African country and found the presence of SFV infection in at least 50 persons [12 ] . Origin, evolution and innate immune control of simian foamy viruses in humans Rua and Gessain 51 Table 1 SFV tropism and viral load in the blood of SFV-infected humans and NHPs. The proportion of SFV DNA positive samples among leukocyte populations in SFV-infected NHP and SFVinfected humans is indicated. abstract: Most viral pathogens that have emerged in humans have originated from various animal species. Emergence is a multistep process involving an initial spill-over of the infectious agent into single individuals and its subsequent dissemination into the human population. Similar to simian immunodeficiency viruses and simian T lymphotropic viruses, simian foamy viruses (SFV) are retroviruses that are widespread among non-human primates and can be transmitted to humans, giving rise to a persistent infection, which seems to be controlled in the case of SFV. In this review, we present current data on the discovery, cross-species transmission, and molecular evolution of SFV in human populations initially infected and thus at risk for zoonotic emergence. url: https://www.sciencedirect.com/science/article/pii/S1879625714002351 doi: 10.1016/j.coviro.2014.12.003 id: cord-030028-s6sxi8uj author: Rubio, Luis title: Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution date: 2020-07-17 words: 14687.0 sentences: 698.0 pages: flesch: 40.0 cache: ./cache/cord-030028-s6sxi8uj.txt txt: ./txt/cord-030028-s6sxi8uj.txt summary: This technique has been used to differentiate isolates of some plant viruses, such as prunus necrotic ringspot virus (PNRSV), TYLCV and CTV (Gillings et al., 1993; Hammond et al., 1998; Font et al., 2007) ; iii) Single-strand conformation polymorphism (SSCP) analysis is based on electrophoresis of denatured dsDNA in non-denaturing gels so migration of single-stranded DNA depends on its conformation determined by its nucleotide sequence and the electrophoretic conditions. This technique followed by sequencing of the different haplotypes detected has been used to evaluate the genetic variation of some plant viruses, such as cucumber mosaic virus (CMV), citrus psorosis virus (CPsV) and CTV (Rubio et al., 1996; Rubio et al., 1999; Vives et al., 2002; Lin et al., 2003; Martıń et al., 2006) . Procedures to detect and identify various viruses or virus strains in a single assay simultaneously reduce time and cost of the analysis (see Pallaś et al., 2018 for a comprehensive review), and are especially suitable for evaluating mixed infections in individual plants. abstract: Plant viruses cause considerable economic losses and are a threat for sustainable agriculture. The frequent emergence of new viral diseases is mainly due to international trade, climate change, and the ability of viruses for rapid evolution. Disease control is based on two strategies: i) immunization (genetic resistance obtained by plant breeding, plant transformation, cross-protection, or others), and ii) prophylaxis to restrain virus dispersion (using quarantine, certification, removal of infected plants, control of natural vectors, or other procedures). Disease management relies strongly on a fast and accurate identification of the causal agent. For known viruses, diagnosis consists in assigning a virus infecting a plant sample to a group of viruses sharing common characteristics, which is usually referred to as species. However, the specificity of diagnosis can also reach higher taxonomic levels, as genus or family, or lower levels, as strain or variant. Diagnostic procedures must be optimized for accuracy by detecting the maximum number of members within the group (sensitivity as the true positive rate) and distinguishing them from outgroup viruses (specificity as the true negative rate). This requires information on the genetic relationships within-group and with members of other groups. The influence of the genetic diversity of virus populations in diagnosis and disease management is well documented, but information on how to integrate the genetic diversity in the detection methods is still scarce. Here we review the techniques used for plant virus diagnosis and disease control, including characteristics such as accuracy, detection level, multiplexing, quantification, portability, and designability. The effect of genetic diversity and evolution of plant viruses in the design and performance of some detection and disease control techniques are also discussed. High-throughput or next-generation sequencing provides broad-spectrum and accurate identification of viruses enabling multiplex detection, quantification, and the discovery of new viruses. Likely, this technique will be the future standard in diagnostics as its cost will be dropping and becoming more affordable. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7380168/ doi: 10.3389/fpls.2020.01092 id: cord-264408-vk4lt83x author: Ruiz, Sara I. title: Animal Models of Human Viral Diseases date: 2017-06-23 words: 34464.0 sentences: 1865.0 pages: flesch: 47.0 cache: ./cache/cord-264408-vk4lt83x.txt txt: ./txt/cord-264408-vk4lt83x.txt summary: Well-developed animal models are necessary to understand disease progression, pathogenesis, and immunologic responses to viral infections in humans. NHPs including marmosets, cotton-top tamarins, and rhesus macaques infected with Norwalk virus are monitored for the extent of viral shedding; however, no clinical disease is observed in these models. Intracerebral and IN routes of infection resulted in a fatal disease that was highly dependent on dose while intradermal (ID) and subQ inoculations caused only 50% fatality in mice regardless of the amount of virus (liu et al., 1970) . Ferrets infected with Hendra or Nipah virus display the same clinical disease as seen in the hamster model and human cases (Bossart et al., 2009; Pallister et al., 2011) . Characterization studies with IFNAr −/− mice challenged with different routes (IP, IN, IM, and subQ) showed that CCHFV causes acute disease with high viral loads, pathology in liver and lymphoid tissues, increased proinflammatory response, severe thrombocytopenia, coagulopathy, and death, all of which are characteristics of human disease . abstract: As the threat of exposure to emerging and reemerging viruses within a naïve population increases, it is vital that the basic mechanisms of pathogenesis and immune response be thoroughly investigated. Recent outbreaks of Middle East respiratory syndrome corona virus, Ebola virus, Chikungunya virus, and Zika virus illustrate the emerging threats that are encountered. By utilizing animal models in this endeavor, the host response to viruses can be studied in a more complex and integrated context to identify novel drug targets, and assess the efficacy and safety of new products rapidly. This is especially true in the advent and implementation of the FDA animal rule. Although no one animal model is able to recapitulate all aspects of human disease, understanding the current limitations allows for a more targeted experimental design. Important facets to consider prior to an animal study are route of viral exposure, species of animal, biomarkers of disease, and a humane endpoint. This chapter covers the current animal models for medically important human viruses, and demonstrates where the gaps in knowledge exist. url: https://www.sciencedirect.com/science/article/pii/B9780128094686000334 doi: 10.1016/b978-0-12-809468-6.00033-4 id: cord-319933-yp9ofhi8 author: Ruiz, Sara I. title: Chapter 38 Animal Models of Human Viral Diseases date: 2013-12-31 words: 28834.0 sentences: 1797.0 pages: flesch: 46.0 cache: ./cache/cord-319933-yp9ofhi8.txt txt: ./txt/cord-319933-yp9ofhi8.txt summary: An experimental study with cell culture-adapted hepatitis Avirus in guinea pigs challenged by oral or intraperitoneal routes did not result in clinical disease, increase in liver enzymes, or seroconversion. 32 NHPs including marmosets, cotton-top tamarins, and rhesus macaques infected with Norwalk virus can be monitored for the extent of viral shedding; however, no clinical disease is observed in these models. 66, 67 Intracerebral and intranasal routes of infection resulted in a fatal disease that was highly dependent on dose, while intradermal and subcutaneous inoculations caused only 50% fatality in mice regardless of the amount of virus. A mouse-adapted (MA) strain of Dengue virus 2 introduced into AG129 mice developed vascular leak syndrome similar to the severe disease seen in humans. [138] [139] [140] [141] [142] [143] [144] Inoculation of WNV into NHPs intracerebrally resulted in the development of either encephalitis, febrile disease, or an asymptomatic infection, depending on the virus strain and dose. abstract: Abstract As the threat of exposure to emerging and reemerging viruses within a naive population increases, it is vital that the basic mechanisms of pathogenesis and immune response be thoroughly investigated. By using animal models in this endeavor, the response to viruses can be studied in a more natural context to identify novel drug targets, and assess the efficacy and safety of new products. This is especially true in the advent of the Food and Drug Administration's animal rule. Although no one animal model is able to recapitulate all the aspects of human disease, understanding the current limitations allows for a more targeted experimental design. Important facets to be considered before an animal study are the route of challenge, species of animals, biomarkers of disease, and a humane endpoint. This chapter covers the current animal models for medically important human viruses, and demonstrates where the gaps in knowledge exist. url: https://api.elsevier.com/content/article/pii/B9780124158948000385 doi: 10.1016/b978-0-12-415894-8.00038-5 id: cord-274080-884x48on author: Rumlová, Michaela title: In vitro methods for testing antiviral drugs date: 2018-06-30 words: 17989.0 sentences: 941.0 pages: flesch: 41.0 cache: ./cache/cord-274080-884x48on.txt txt: ./txt/cord-274080-884x48on.txt summary: For the majority of animal viruses, the activation of these fusion or penetration mechanisms occurs through conformational changes and structural rearrangements in viral surface proteins and/or the whole virion shell that may destabilize the capsid core. D: Three mechanisms (I.-III.) of DNA viruses replication are shown: (I): Following entry and uncoating, the DNA genome is transported to the nucleus; products of early genes (regulatory proteins, transcription factors) regulate the synthesis of viral enzymes (e.g. DNA polymerase) required for genome replication; expression of late genes encoding structural capsid proteins in the cytosol, they are then transported into nucleus where packaging and pre-assembly take place; preassembled procapsids exit the nucleus and leave the cell (e.g. Herpesviruses). Here, we provide an overview of in vitro methods, including cell-based assays, that may be suitable for screening of antivirotics that interfere with the key steps of viral life cycles and target either virus or cell-encoded proteins required for the infectivity. abstract: Abstract Despite successful vaccination programs and effective treatments for some viral infections, humans are still losing the battle with viruses. Persisting human pandemics, emerging and re-emerging viruses, and evolution of drug-resistant strains impose continuous search for new antiviral drugs. A combination of detailed information about the molecular organization of viruses and progress in molecular biology and computer technologies has enabled rational antivirals design. Initial step in establishing efficacy of new antivirals is based on simple methods assessing inhibition of the intended target. We provide here an overview of biochemical and cell-based assays evaluating the activity of inhibitors of clinically important viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/29292156/ doi: 10.1016/j.biotechadv.2017.12.016 id: cord-003707-fbe47bgi author: Russo, Alice G title: Novel insights into endogenous RNA viral elements in Ixodes scapularis and other arbovirus vector genomes date: 2019-06-18 words: 9010.0 sentences: 611.0 pages: flesch: 55.0 cache: ./cache/cord-003707-fbe47bgi.txt txt: ./txt/cord-003707-fbe47bgi.txt summary: I. scapularis NIRVS are enriched in bunyaand orthomyxo-like sequences, reflecting that ticks are a dominant host for these virus groups. NIRVS arise from the reverse transcription of viral RNA into cDNA and its integration into the genome of a host germ cell, followed by vertical transmission to offspring (Katzourakis and Gifford 2010) . Yet recent evidence has highlighted the abundance of NIRVS in some arthropod genomes-e.g., Ae. aegypti and Ae. albopictus contain >100 NIRVS from over eight RNA virus families encompassing þssRNA, ÀssRNA, and dsRNA viral groups (Palatini et al. Using the well-studied genomes of Aedes mosquitoes to validate our analysis, we employed a bioinformatic pipeline to characterise NIRVS in seven non-Aedes arbovirus vectors that have representative genomic sequences (Table 1 and Fig. 1 ). scapularis lacked NIRVS from positive-sense RNA viruses, which comprise about one tenth of NIRVS in Aedes mosquitoes ( Fig. 3; Supplementary Table S2 ). abstract: Many emerging arboviruses are not transmitted by traditional mosquito vectors, but by lesser-studied arthropods such as ticks, midges, and sand flies. Small RNA (sRNA) silencing pathways are the main antiviral defence mechanism for arthropods, which lack adaptive immunity. Non-retroviral integrated RNA virus sequences (NIRVS) are one potential source of sRNAs which comprise these pathways. NIRVS are remnants of past germline RNA viral infections, where viral cDNA integrates into the host genome and is vertically transmitted. In Aedes mosquitoes, NIRVS are widespread and produce PIWI-interacting RNAs (piRNAs). These are hypothesised to target incoming viral transcripts to modulate viral titre, perhaps rendering the organism a more efficient arbovirus vector. To explore the NIRVS landscape in alternative arbovirus vectors, we validated the NIRVS landscape in Aedes spp. and then identified novel NIRVS in six medically relevant arthropods and also in Drosophila melanogaster. We identified novel NIRVS in Phlebotomus papatasi, Culicoides sonorensis, Rhipicephalus microplus, Anopheles gambiae, Culex quinquefasciatus, and Ixodes scapularis. Due to their unexpected abundance, we further characterised NIRVS in the blacklegged tick I. scapularis (n = 143). Interestingly, NIRVS are not enriched in R. microplus, another hard tick, suggesting this is an Ixodes-specific adaptation. I. scapularis NIRVS are enriched in bunya- and orthomyxo-like sequences, reflecting that ticks are a dominant host for these virus groups. Unlike in mosquitoes, I. scapularis NIRVS are more commonly derived from the non-structural region (replicase) of negative-sense viruses, as opposed to structural regions (e.g. glycoprotein). Like other arthropods, I. scapularis NIRVS preferentially integrate into genomic piRNA clusters, and serve as a template for primary piRNA production in the commonly used embryonic I. scapularis ISE6 cell line. Interestingly, we identified a two-fold enrichment of non-long terminal repeat (non-LTR) retrotransposons, in genomic proximity to NIRVS, contrasting with studeis in Ae. aegypti, where LTR retrotransposons are instead associated with NIRVS formation. We characterised NIRVS phylogeny and integration patterns in the important vector, I. scapularis, revealing they are distinct from those in Aedes spp. Future studies will explore the possible antiviral mechanism conferred by NIRVS to I. scapularis,which may help the transmission of pathogenic arboviruses. Finally, this study explored NIRVS as an untapped wealth of viral diversity in arthropods. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6580184/ doi: 10.1093/ve/vez010 id: cord-332165-31tbc31x author: Rustmeier, Nils H. title: The Symmetry of Viral Sialic Acid Binding Sites—Implications for Antiviral Strategies date: 2019-10-14 words: 5820.0 sentences: 316.0 pages: flesch: 43.0 cache: ./cache/cord-332165-31tbc31x.txt txt: ./txt/cord-332165-31tbc31x.txt summary: In this review, we will evaluate the structures of non-enveloped virus capsid proteins bound to sialylated glycan receptors and discuss the potential of these structures for the development of potent antiviral attachment inhibitors. This concept of targeting multiple, symmetric receptor binding sites by multivalent inhibitors is also applicable for many viruses, since viral capsids are often icosahedral and, therefore, highly symmetric structures. Many members of the polyomavirus family bind sialic acid-based glycans using their VP1 proteins, so the binding sites on individual pentamers are always linked by local five-fold symmetry (Figure 4a , TSPyV). The glycooligopeptide-VP1 complex structures displayed a similar ligand binding mode that was reported for sialic acid in an earlier study [50] and showed, for the compounds, that the linker between the ligand and the scaffold occupies the space that is usually targeted by the natural glycan receptor moieties (Figure 5a,b, right) . abstract: Virus infections are initiated by the attachment of the viral particle to protein or carbohydrate receptors on the host cell. Sialic acid-bearing glycan structures are prominently displayed at the cell surface, and, consequently, these structures can function as receptors for a large number of diverse viruses. Structural biology research has helped to establish the molecular bases for many virus–sialic acid interactions. Due to the icosahedral 532 point group symmetry that underlies many viral capsids, the receptor binding sites are frequently arranged in a highly symmetric fashion and linked by five-fold, three-fold, or two-fold rotation axes. For the inhibition of viral attachment, one emerging strategy is based on developing multivalent sialic acid-based inhibitors that can simultaneously engage several of these binding sites, thus binding viral capsids with high avidity. In this review, we will evaluate the structures of non-enveloped virus capsid proteins bound to sialylated glycan receptors and discuss the potential of these structures for the development of potent antiviral attachment inhibitors. url: https://www.ncbi.nlm.nih.gov/pubmed/31615155/ doi: 10.3390/v11100947 id: cord-009702-02bo7pnl author: SCOTT, G. R. title: Guidelines for the Control of Equine Viral Infections date: 2010-04-23 words: 3364.0 sentences: 253.0 pages: flesch: 53.0 cache: ./cache/cord-009702-02bo7pnl.txt txt: ./txt/cord-009702-02bo7pnl.txt summary: At least twenty‐eight of the fifty‐eight viruses induce clinical disease but the range of syndromes is limited; eleven provoke respiratory symptoms and eleven cause encephalitis. There is possibly one Coronavirus infecting horses; Ditchfield (1969) isolated a virus from a Thoroughbred with undifferentiated respiratory disease and found that it possessed a morphology similar to that of infectious bronchitis virus of poultry, the type-virus of the Coronavirus group. Equine infectious anaemia virus probably belongs to the Oncornavirus group, i.e. the RNA tumour viruses. Eleven of the thirty-four known vector-transmitted viruses cause disease and vaccines have been developed against six of them (Table VII) . Seventeen of the twenty known viral contagions of horses cause disease and vaccines have been developed against five of them (Table VIII ). At least twenty-eight of the fifty-eight viruses induce clinical disease but the range of syndromes is limited; eleven provoke respiratory symptoms and eleven cause encephalitis. The vector-transmitted virus diseases are best controlled by prophylactic vaccination. abstract: SUMMARY: Twelve DNA viruses and forty‐three RNA viruses are known to infect horses. In addition, there are three unclassified viruses and, at least, three alleged viruses infecting horses. Differential diagnosis is difficult. At least twenty‐eight of the fifty‐eight viruses induce clinical disease but the range of syndromes is limited; eleven provoke respiratory symptoms and eleven cause encephalitis. Thirty‐four equine viruses with a limited geographical distribution are transmitted by arthropod vectors. Twenty viruses are spread by contact and their distribution, in general, is global. The vector‐transmitted virus diseases are best controlled by prophylactic vaccination. The viral contagions are not, in general, well controlled by vaccination and it is likely that prophylactic chemotherapy will become increasingly important in the future. RÉSUMÉ: On sait que douze virus ADN et quarante trois virus ARN sont responsables d'infections chez le cheval. En outre trois virus non classés et trois autres agents de type viral au moins sont également infectants pour cette espèce. Le diagnostic différentiel est difficile. Vingt huit au moins des cinquante trois virus provoquent des maladies cliniques mais la gamme des syndromes est restreinte: Onze virus engendrent des symptomes respiratoires, onze déterminent des encéphalites. Trente quatre virus dont la distribution géographique est limitée sont transmis par des arthropodes vecteurs. Vingt virus sont disséminés par contact et leur répartition est en général à l'échelle du globe. Les maladies provoquées par des virus à propagation vectorielle sont mieux controlées par une vaccination préventive. Les contagions virales ne sont pas, en général, efficacement controlées par la vaccination et l'on peut penser que la chimiothérapie préventive de ces affections connaitra une importance croissante à l'avenir. ZUSAMMENFASSUNG: Zwölf DNS‐Viren und 43 RNS‐Viren vermögen das Pferd zu infizieren. Dazu kommen drei unklassierte Viren und zum mindesten drei Erreger, die angeblich Viruscharakter haben. Die Differentialdiagnose ist schwierig. Mindestens 28 der 58 Viren verursachen klinisch manifeste Krankheiten, aber die Eigenart der Syndrome ist limitiert; elf davon provozieren respiratorische Symptome und elf rufen Encephalitis hervor. 34 equine Viren benötigen als Vektoren Arthropoden; ihre geographische Ausbreitung ist beschränkt. 20 Viren werden durch Kontakt übertragen; sie werden in der Regel auf der ganzen Welt angetroffen. Die durch Vektoren übertragenen Viruskrankheiten können am besten durch prophylaktische Impfungen kontrolliert werden. Die übrigen können im allgemeinen durch Impfungen nicht gut kontrolliert werden und es scheint wahrscheinlich, dass die prophylaktische Chemotherapie in Zukunft an Bedeutung gewinnen wird. SUMARIO: VIRUS EQUINOS Doce DNA virus y cuarenta y tres RNA virus son reconcodios como infectantes al caballo. En adicion hay tres no clasidicados virus y por lo menos tres tipos de virus muy se mejantes que afectan el caballo. El diagnostico diferencial es dificultoso. Aproximadamente 28 de los 28 virus inducen enfermedades clinicas con y espectro de sindromes limitado. 11 provocan sintomas respiratorios y 11 causan encefalitis. 34 virus equinos con limitacion en su distribucion geografica son transmitidos por vectores artropodos. Veinte virus son diseminados por contacto y su distribucion en general es global. Es controlada la enfermeead de estos vectiores per medio de vacunacion. Los contagio del virus no son bien controlados por lo general mediante vacunacion y solo una terapia profilactica que havenido tomando aunge en el futuro. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163504/ doi: 10.1111/j.2042-3306.1971.tb04431.x id: cord-020969-lh2ergpm author: STRAUSS, JAMES H. title: Gene Therapy date: 2012-07-27 words: 11793.0 sentences: 597.0 pages: flesch: 52.0 cache: ./cache/cord-020969-lh2ergpm.txt txt: ./txt/cord-020969-lh2ergpm.txt summary: Together with methods for cloning and manipulating viral genomes, this information has made possible the use of viruses as vectors to express foreign genes. The use of minus-strand RNA viruses as vectors was delayed because the virion RNA itself is not infectious, but recent developments has made it possible to rescue virus from cloned DNA by using coexpression of the appropriate viral proteins in a transfected cell. It is also possible to transfect cells with the E1 or E3 expression cassette together with DNA clones encoding the rest of the adenovirus genome, in which case homologous recombination results in the production of virus. Because the poliovirus replicon lacks a full complement of the structural genes (it is a suicide vector), packaging to produce particles requires infection of a cell that expresses the polioviral structural proteins by some mechanism. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148746/ doi: 10.1016/b978-0-12-373741-0.50014-3 id: cord-023726-2fduzqyb author: STRAUSS, JAMES H. title: The Structure of Viruses date: 2012-07-27 words: 10614.0 sentences: 633.0 pages: flesch: 57.0 cache: ./cache/cord-023726-2fduzqyb.txt txt: ./txt/cord-023726-2fduzqyb.txt summary: Also shown for each family is the presence or absence of an envelope in the virion, the triangulation number (defined later) if the virus is icosahedral, the morphology of the nucleocapsid or core, and figure numbers where the structures of members of a family are illustrated. Structural studies of viruses have shown that the capsid proteins that form the virions of many plant and animal icosahedral viruses have a common fold. The largest particle is the nucleocapsid of herpes simplex virus, which is 1250 Å in diameter and has T=16 symmetry (the virion is enveloped but only the nucleocapsid is regular FIGURE 2.5 Gallery of three-dimensional reconstructions of icosahedral viruses from cryoelectron micrographs. For most RNA viruses, nucleocapsids can be recognized as distinct structures within the infected cell and can be isolated from virions by treatment with detergents that dissolve the envelope. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173534/ doi: 10.1016/b978-0-12-373741-0.50005-2 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-001207-yjaiybwf author: Sachsenröder, Jana title: The General Composition of the Faecal Virome of Pigs Depends on Age, but Not on Feeding with a Probiotic Bacterium date: 2014-02-19 words: 5919.0 sentences: 302.0 pages: flesch: 49.0 cache: ./cache/cord-001207-yjaiybwf.txt txt: ./txt/cord-001207-yjaiybwf.txt summary: faecium) NCIMB 10415 on the pig faecal virome composition was analysed in a pig feeding trial with sows and their piglets, which received either the probiotic bacterium or not. RESULTS: From 8 pooled faecal samples derived from the feeding trial, DNA and RNA virus particles were prepared and subjected to process-controlled Next Generation Sequencing resulting in 390,650 sequence reads. However, it is not known so far, whether probiotic bacteria can also influence the general composition of the faecal virome, e.g. by changing the composition of the bacterial community, which represents the host population for bacteriophages, or by direct interactions with specific viruses. Faecal samples from sows and their piglets experimentally fed with or without the probiotic bacterium were analyzed using a process-controlled deep sequencing method. As the detection rate of the bacteriophages is -besides technical factors -also dependent on the amount of viruses initially present in the analyzed sample, improved deep sequencing methods enabling quantitative analyses should be developed in future for comparative virome investigations. abstract: BACKGROUND: The pig faecal virome, which comprises the community of viruses present in pig faeces, is complex and consists of pig viruses, bacteriophages, transiently passaged plant viruses and other minor virus species. Only little is known about factors influencing its general composition. Here, the effect of the probiotic bacterium Enterococcus faecium (E. faecium) NCIMB 10415 on the pig faecal virome composition was analysed in a pig feeding trial with sows and their piglets, which received either the probiotic bacterium or not. RESULTS: From 8 pooled faecal samples derived from the feeding trial, DNA and RNA virus particles were prepared and subjected to process-controlled Next Generation Sequencing resulting in 390,650 sequence reads. In average, 14% of the reads showed significant sequence identities to known viruses. The percentage of detected mammalian virus sequences was highest (55–77%) in the samples of the youngest piglets and lowest (8–10%) in the samples of the sows. In contrast, the percentage of bacteriophage sequences increased from 22–44% in the youngest piglets to approximately 90% in the sows. The dominating mammalian viruses differed remarkably among 12 day-old piglets (kobuvirus), 54 day-old piglets (boca-, dependo- and pig stool-associated small circular DNA virus [PigSCV]) and the sows (PigSCV, circovirus and “circovirus-like” viruses CB-A and RW-A). In addition, the Shannon index, which reflects the diversity of sequences present in a sample, was generally higher for the sows as compared to the piglets. No consistent differences in the virome composition could be identified between the viromes of the probiotic bacterium-treated group and the control group. CONCLUSION: The analysis indicates that the pig faecal virome shows a high variability and that its general composition is mainly dependent on the age of the pigs. Changes caused by feeding with the probiotic bacterium E. faecium could not be demonstrated using the applied metagenomics method. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929612/ doi: 10.1371/journal.pone.0088888 id: cord-273326-gmw8gl2r author: Saiz, Juan-Carlos title: Host-Directed Antivirals: A Realistic Alternative to Fight Zika Virus date: 2018-08-24 words: 7111.0 sentences: 293.0 pages: flesch: 34.0 cache: ./cache/cord-273326-gmw8gl2r.txt txt: ./txt/cord-273326-gmw8gl2r.txt summary: In this line, and contrary to above mentioned report [73] , CQ, an FDA-approved anti-inflammatory 4-aminoquinoline and an autophagy inhibitor widely used as an anti-malaria drug that is administered to pregnant women at risk of exposure to Plasmodium parasites, was shown to have anti-ZIKV activity in different cell types (Vero cells, human brain microvascular endothelial cells (hBMECs), and human neural stem cells (NSCs)), affecting early stages of the viral life cycle, possibly by raising the endosomal pH and inhibiting the fusion of the envelope protein to the endosomal membrane [74, 75] . Similarly, by using a drug repurposing screening of over 6000 molecules, it was found that emricasan, a pan-caspase inhibitor that restrains ZIKV-induced increases in caspase-3 activity and is currently in phase 2 clinical trials in chronic hepatitis C virus (HCV)-infected patients, protected human cortical neural progenitor cells (NPC) in both monolayer and three-dimensional organoid cultures, showing neuroprotective activity without suppression of viral replication [82] . abstract: Zika virus (ZIKV), a mosquito-borne flavivirus, was an almost neglected pathogen until its introduction in the Americas in 2015, where it has been responsible for a threat to global health, causing a great social and sanitary alarm due to its increased virulence, rapid spread, and an association with severe neurological and ophthalmological complications. Currently, no specific antiviral therapy against ZIKV is available, and treatments are palliative and mainly directed toward the relief of symptoms, such as fever and rash, by administering antipyretics, anti-histamines, and fluids for dehydration. Nevertheless, lately, search for antivirals has been a major aim in ZIKV investigations. To do so, screening of libraries from different sources, testing of natural compounds, and repurposing of drugs with known antiviral activity have allowed the identification of several antiviral candidates directed to both viral (structural proteins and enzymes) and cellular elements. Here, we present an updated review of current knowledge about anti-ZIKV strategies, focusing on host-directed antivirals as a realistic alternative to combat ZIKV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/30149598/ doi: 10.3390/v10090453 id: cord-267134-5gz2dotn author: Sallenave, Jean-Michel title: Innate Immune Signaling and Proteolytic Pathways in the Resolution or Exacerbation of SARS-CoV-2 in Covid-19: Key Therapeutic Targets? date: 2020-05-28 words: 5347.0 sentences: 239.0 pages: flesch: 39.0 cache: ./cache/cord-267134-5gz2dotn.txt txt: ./txt/cord-267134-5gz2dotn.txt summary: The first anatomical/histological reports from the lungs of severely SARS-CoV-2-affected patients experiencing acute respiratory disease syndrome (ARDS) revealed excessive inflammatory activation and destruction of the bronchial and alveolar epithelium, features already observed during the first SARS pandemics in 2003 (3, 4). The following sections will give an overview of the molecular and cellular mechanisms underpinning SARS-CoV virus infections and how lung and systemic host innate immune responses affect survival either positively, through downregulating the initial viral load, or negatively, by triggering uncontrolled inflammation. Regarding the lung, the differentiated Calu-3 cell line [when cultured at the air-liquid interface (ALI)] is the model of choice: in that set-up, SARS-CoV infection triggered an inflammatory response characterized by increased production of interleukin (IL)-6, IL-8, gamma interferon (IFN-γ), inducible protein 10 (IP-10), and activation of the transcription factor NF-κB (56) . Innate immune response of human alveolar type II cells infected with severe acute respiratory syndrome-coronavirus abstract: COVID-19 is caused by the Severe Acute Respiratory Syndrome (SARS) coronavirus (Cov)-2, an enveloped virus with a positive-polarity, single-stranded RNA genome. The initial outbreak of the pandemic began in December 2019, and it is affecting the human health of the global community. In common with previous pandemics (Influenza H1N1 and SARS-CoV) and the epidemics of Middle east respiratory syndrome (MERS)-CoV, CoVs target bronchial and alveolar epithelial cells. Virus protein ligands (e.g., haemagglutinin or trimeric spike glycoprotein for Influenza and CoV, respectively) interact with cellular receptors, such as (depending on the virus) either sialic acids, Dipeptidyl peptidase 4 (DPP4), or angiotensin-converting enzyme 2 (ACE2). Host proteases, e.g., cathepsins, furin, or members of the type II transmembrane serine proteases (TTSP) family, such as Transmembrane protease serine 2 (TMPRSS2), are involved in virus entry by proteolytically activating virus ligands. Also involved are Toll Like Receptor (TLR) family members, which upregulate anti-viral and pro-inflammatory mediators [interleukin (IL)-6 and IL-8 and type I and type III Interferons among others], through the activation of Nuclear Factor (NF)-kB. When these events (virus cellular entry and innate immune responses) are uncontrolled, a deleterious systemic response is sometimes encountered in infected patients, leading to the well-described “cytokine storm” and an ensuing multiple organ failure promoted by a downregulation of dendritic cell, macrophage, and T-cell function. We aim to describe how the lung and systemic host innate immune responses affect survival either positively, through downregulating initial viral load, or negatively, by triggering uncontrolled inflammation. An emphasis will be put on host cellular signaling pathways and proteases involved with a view on tackling these therapeutically. url: https://www.ncbi.nlm.nih.gov/pubmed/32574272/ doi: 10.3389/fimmu.2020.01229 id: cord-318853-mxyxwkhx author: Sallie, Richard title: Replicative homeostasis II: Influence of polymerase fidelity on RNA virus quasispecies biology: Implications for immune recognition, viral autoimmunity and other "virus receptor" diseases date: 2005-08-22 words: 10541.0 sentences: 396.0 pages: flesch: 25.0 cache: ./cache/cord-318853-mxyxwkhx.txt txt: ./txt/cord-318853-mxyxwkhx.txt summary: Perhaps more importantly, ineluctable generation of broad phenotypic diversity after viral RNA is translated to protein quasispecies suggests a mechanism of disease that specifically targets, and functionally disrupts, the host cell surface molecules – including hormone, lipid, cell signalling or neurotransmitter receptors – that viruses co-opt for cell entry. Hence, as relative concentrations of wild-type and variant viral proteins vary, alteration of both processivity and fidelity of RNA pol results, permitting viruses to adaptively respond to environmental changes, including immune recognition and reaction to evolving cell receptors. As clear evidence exists for viral disruption of leptin function [106] and virus-associated weight gain in humans [107] and monkeys [108] , is it possible the global epidemics of type II diabetes mellitus, insulin resistance, hyperlipidaemia and obesity now prevalent [109] [110] [111] [112] [113] [114] [115] [116] , are just that; epidemics fundamentally caused by viruses that co-opt insulin or leptin or other associated receptors for cell access and generate protein quasispecies that disrupt receptor function? abstract: Much of the worlds' population is in active or imminent danger from established infectious pathogens, while sporadic and pandemic infections by these and emerging agents threaten everyone. RNA polymerases (RNA(pol)) generate enormous genetic and consequent antigenic heterogeneity permitting both viruses and cellular pathogens to evade host defences. Thus, RNA(pol )causes more morbidity and premature mortality than any other molecule. The extraordinary genetic heterogeneity defining viral quasispecies results from RNA(pol )infidelity causing rapid cumulative genomic RNA mutation a process that, if uncontrolled, would cause catastrophic loss of sequence integrity and inexorable quasispecies extinction. Selective replication and replicative homeostasis, an epicyclical regulatory mechanism dynamically linking RNApol fidelity and processivity with quasispecies phenotypic diversity, modulating polymerase fidelity and, hence, controlling quasispecies behaviour, prevents this happening and also mediates immune escape. Perhaps more importantly, ineluctable generation of broad phenotypic diversity after viral RNA is translated to protein quasispecies suggests a mechanism of disease that specifically targets, and functionally disrupts, the host cell surface molecules – including hormone, lipid, cell signalling or neurotransmitter receptors – that viruses co-opt for cell entry. This mechanism – "Viral Receptor Disease (VRD)" – may explain so-called "viral autoimmunity", some classical autoimmune disorders and other diseases, including type II diabetes mellitus, and some forms of obesity. Viral receptor disease is a unifying hypothesis that may also explain some diseases with well-established, but multi-factorial and apparently unrelated aetiologies – like coronary artery and other vascular diseases – in addition to diseases like schizophrenia that are poorly understood and lack plausible, coherent, pathogenic explanations. url: https://www.ncbi.nlm.nih.gov/pubmed/16115320/ doi: 10.1186/1743-422x-2-70 id: cord-284941-wfn0pnev author: Samal, S.K. title: Paramyxoviruses of Animals date: 2008-07-30 words: 4948.0 sentences: 251.0 pages: flesch: 41.0 cache: ./cache/cord-284941-wfn0pnev.txt txt: ./txt/cord-284941-wfn0pnev.txt summary: The members of this virus family are enveloped and have genomes consisting of a single segment of negative-sense RNA that contains 6–10 genes encoding up to 12 proteins. The family Paramyxoviridae contains a large number of viruses of animals (Table 1) , including a number of major animal pathogens (such as Newcastle disease virus (NDV), canine distemper virus, and rinderpest virus), zoonotic pathogens (such as Hendra and Nipah viruses), and a number of somewhat obscure viruses whose natural histories are poorly understood. A number of animal paramyxoviruses have been recovered from cDNAs using reverse genetics, including simian virus 5, NDV, bovine parainfluenza virus 3, Sendai virus, canine distemper virus, rinderpest virus, bovine respiratory syncytial virus, and avian metapneumovirus. Infection occurs by several different routes, including aerosols (NDV, bovine respiratory syncytial virus, avian metapneumovirus) and contaminated feed and water (Newcastle disease, canine distemper, and rinderpest viruses). abstract: Paramyxoviruses (some of which are also called parainfluenza viruses) cause a wide variety of diseases in animals. Many paramyxoviruses cause primarily respiratory disease, while others cause serious systemic disease. Many diseases caused by animal paramyxoviruses also have a neurological component or a reproductive disease component. Several of the most devastating diseases of animals, such as rinderpest, Newcastle disease, and canine distemper, are caused by paramyxoviruses. Some of the animal paramyxoviruses, such as the Hendra and Nipah viruses, are emerging zoonotic pathogens of major public health concern. New paramyxoviruses are being isolated on a continuing basis from a wide variety of animals. All animal paramyxoviruses belong to the family Paramyxoviridae. The members of this virus family are enveloped and have genomes consisting of a single segment of negative-sense RNA that contains 6–10 genes encoding up to 12 proteins. Although there are many animal paramyxoviruses, only a few effective vaccines are currently available. In the last decade, methods of producing many animal paramyxoviruses entirely from cDNA clones (reverse genetics) have been developed. This has not only greatly improved our understanding of the molecular biology and pathogenesis of these viruses, but has also made it possible to engineer improved vaccines for them. url: https://api.elsevier.com/content/article/pii/B978012374410400460X doi: 10.1016/b978-012374410-4.00460-x id: cord-017331-ru7mvfc0 author: Samanta, Indranil title: Infectious Diseases date: 2017-02-25 words: 37735.0 sentences: 2273.0 pages: flesch: 45.0 cache: ./cache/cord-017331-ru7mvfc0.txt txt: ./txt/cord-017331-ru7mvfc0.txt summary: The chapter includes history, etiology, susceptible hosts, transmission, pathogenesis, clinical symptoms, lesion, diagnosis, zoonosis, Treatment and control strategy of Tuberculosis, Salmonellosis, Chlamydiosis, Campylobacteriosis, Lyme disease, other bacterial infection, Newcastle disease, Avian Influenza infection, West Nile Virus infection, Usutu virus infection, Avian Borna Virus infection, Beak and feather disease, other viral infection, Toxoplasmosis, Giardiasis, Cryptosporidiosis, other parasitic infection, Cryptococcosis, Aspergillosis, Other fungal infections. Clinical samples include faeces or cloacal swabs, blood/serum of live birds and affected tissues, such as liver, spleen, heart, intestine/caeca, lung, esophagus/crop, brain and kidney in 10% buffered formalin. Non-specific clinical symptoms such as neurological signs (head between legs), depression, ruffled feathers, and standing at the bottom of the cage are observed in pet birds with AIV infection (Fig. 2.13) . The virus is detected in brain, heart, liver, kidney, lungs, and intestinal tissues of laboratory mice and naturally infected birds. abstract: The chapter describes bacerial, viral, parasitic and fungal infections commonly detected in pet birds. The chapter includes history, etiology, susceptible hosts, transmission, pathogenesis, clinical symptoms, lesion, diagnosis, zoonosis, Treatment and control strategy of Tuberculosis, Salmonellosis, Chlamydiosis, Campylobacteriosis, Lyme disease, other bacterial infection, Newcastle disease, Avian Influenza infection, West Nile Virus infection, Usutu virus infection, Avian Borna Virus infection, Beak and feather disease, other viral infection, Toxoplasmosis, Giardiasis, Cryptosporidiosis, other parasitic infection, Cryptococcosis, Aspergillosis, Other fungal infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121861/ doi: 10.1007/978-981-10-3674-3_2 id: cord-296819-gztmidn2 author: Sambri, Vittorio title: Diagnosis of West Nile Virus Human Infections: Overview and Proposal of Diagnostic Protocols Considering the Results of External Quality Assessment Studies date: 2013-09-25 words: 6732.0 sentences: 304.0 pages: flesch: 42.0 cache: ./cache/cord-296819-gztmidn2.txt txt: ./txt/cord-296819-gztmidn2.txt summary: title: Diagnosis of West Nile Virus Human Infections: Overview and Proposal of Diagnostic Protocols Considering the Results of External Quality Assessment Studies This paper reviews the presently available methods to achieve the laboratory diagnosis of West Nile virus infections in humans, discussing the most prominent advantages and disadvantages of each in light of the results obtained during four different External Quality Assessment studies carried out by the European Network for ''Imported'' Viral Diseases (ENIVD). For the routine detection of WNV RNA using molecular techniques there are two distinct diagnostic settings: the first involves blood and organ donation screening from subjects living in an area where WNV circulation is known to be occurring, and the second involves the identification of viral genomes in serum, plasma and CSF samples from patients presenting with a clinical picture typical of WNV infection [21] . abstract: West Nile virus, genus Flavivirus, is transmitted between birds and occasionally other animals by ornithophilic mosquitoes. This virus also infects humans causing asymptomatic infections in about 85% of cases and <1% of clinical cases progress to severe neuroinvasive disease. The virus also presents a threat since most infections remain unapparent. However, the virus contained in blood and organs from asymptomatically infected donors can be transmitted to recipients of these infectious tissues. This paper reviews the presently available methods to achieve the laboratory diagnosis of West Nile virus infections in humans, discussing the most prominent advantages and disadvantages of each in light of the results obtained during four different External Quality Assessment studies carried out by the European Network for ‘Imported’ Viral Diseases (ENIVD). url: https://www.ncbi.nlm.nih.gov/pubmed/24072061/ doi: 10.3390/v5102329 id: cord-278479-vl296i1b author: Samuel, Arthur S title: Experimental infection of hamsters with avian paramyxovirus serotypes 1 to 9 date: 2011-02-23 words: 6316.0 sentences: 335.0 pages: flesch: 46.0 cache: ./cache/cord-278479-vl296i1b.txt txt: ./txt/cord-278479-vl296i1b.txt summary: In this study, groups of hamsters were infected with a prototype strain of each APMV serotype by the intranasal route and monitored for virus replication, clinical symptoms, histopathology, and seroconversion. Our results showed that each of the APMV serotypes replicated in hamsters without causing adverse clinical signs of illness, although histopathologic evidence of disease was observed in some cases, and also induced high neutralizing antibody titers. Necropsies were performed immediately postmortem and the following tissue samples were collected for immunohistochemistry (IHC), histopathology, and virus isolation: brain, nasal turbinates, lung, spleen, kidney and small intestine. Deparaffinized sections of the virus-infected and uninfected control tissue (brain, lungs, nasal turbinates, small intestine, kidney, and spleen) were immunostained using polyclonal antisera against the N protein of the homologous APMV serotypes. In animals infected with any of the other APMV serotypes, virus-specific antigens were detected on 3 dpi in the lungs and nasal turbinates (Figure 3 ). abstract: Avian paramyxoviruses (APMVs) are frequently isolated from domestic and wild birds throughout the world and are separated into nine serotypes (APMV-1 to -9). Only in the case of APMV-1, the infection of non-avian species has been investigated. The APMVs presently are being considered as human vaccine vectors. In this study, we evaluated the replication and pathogenicity of all nine APMV serotypes in hamsters. The hamsters were inoculated intranasally with each virus and monitored for clinical disease, pathology, histopathology, virus replication, and seroconversion. On the basis of one or more of these criteria, each of the APMV serotypes was found to replicate in hamsters. The APMVs produced mild or inapparent clinical signs in hamsters except for APMV-9, which produced moderate disease. Gross lesions were observed over the pulmonary surface of hamsters infected with APMV-2 & -3, which showed petechial and ecchymotic hemorrhages, respectively. Replication of all of the APMVs except APMV-5 was confirmed in the nasal turbinates and lungs, indicating a tropism for the respiratory tract. Histologically, the infection resulted in lung lesions consistent with bronchointerstitial pneumonia of varying severity and nasal turbinates with blunting or loss of cilia of the epithelium lining the nasal septa. The majority of APMV-infected hamsters exhibited transient histological lesions that self resolved by 14 days post infection (dpi). All of the hamsters infected with the APMVs produced serotype-specific HI or neutralizing antibodies, confirming virus replication. Taken together, these results demonstrate that all nine known APMV serotypes are capable of replicating in hamsters with minimal disease and pathology. url: https://www.ncbi.nlm.nih.gov/pubmed/21345199/ doi: 10.1186/1297-9716-42-38 id: cord-256036-gd53s4dv author: Sandmann, Lisa title: Barriers of hepatitis C virus interspecies transmission date: 2013-01-01 words: 7894.0 sentences: 373.0 pages: flesch: 40.0 cache: ./cache/cord-256036-gd53s4dv.txt txt: ./txt/cord-256036-gd53s4dv.txt summary: In contrast to human hepatocytes, murine cells do not support HCV entry thereby creating a first and important barrier for a broader host tropism of the virus. Utilizing blocking antibodies specific to CD81 or the viral envelope protein E2, expression of entry factor mutants and mice with a targeted disruption of the SCARB1 gene validated uptake of HCV into murine hepatocytes in an HCV glycoprotein-mediated fashion. Taking advantage of the high mutational plasticity of HCV, three adaptive mutations in the viral glycoproteins E1 and E2 were identified that allowed the virus to enter cells expressing human SCARB1, CLDN1, OCLN and mouse CD81. Recently, a genetically humanized mouse model was constructed utilizing cell culture produced recombinant hepatitis C virus to activate a cellular encoded reporter (Dorner et al., 2011, in press ). Human occludin is a hepatitis C virus entry factor required for infection of mouse cells A humanized mouse model to study Hepatitis C virus infection, immune response, and liver disease abstract: Hepatitis C virus (HCV) is a major causative agent of severe liver disease including fibrosis, cirrhosis and liver cancer. Therapy has improved over the years, but continues to be associated with adverse side effects and variable success rates. Furthermore, a vaccine protecting against HCV infection remains elusive. Development of more effective intervention measures has been delayed by the lack of a suitable animal model. Naturally, HCV infects only humans and chimpanzees. The determinants of this limited host range are poorly understood in part due to difficulties of studying HCV in cell culture. Some progress has been made elucidating the barriers for the HCV lifecycle in non-permissive species which will help in the future to construct animal models for HCV infection, immunity and pathogenesis. url: https://doi.org/10.1016/j.virol.2012.09.044 doi: 10.1016/j.virol.2012.09.044 id: cord-279798-b5tduubu author: Sano, Daisuke title: Risk management of viral infectious diseases in wastewater reclamation and reuse: Review date: 2016-03-14 words: 7986.0 sentences: 341.0 pages: flesch: 38.0 cache: ./cache/cord-279798-b5tduubu.txt txt: ./txt/cord-279798-b5tduubu.txt summary: The objectives of this review were to calculate representative values of virus removal efficiency in wastewater treatment units based on published datasets, and to identify research topics that should be further addressed for improving implementation of the multiple-barrier system. In this review article, current guidelines for designing wastewater reclamation and reuse systems from the viewpoint of virus risk management are overviewed, and the efficiency of virus removal from wastewater by currently employed wastewater treatment units are shown by the results of meta-analysis. The United States Environmental Protection Agency (USEPA) (2012) guideline explicitly notes that setting a tolerable virus concentration in reclaimed wastewater (virus limit) is not recommended for the following reasons: 1) viruses are well reduced by appropriate wastewater treatments, 2) identification and enumeration of viruses is time-and labor-consuming, 3) detection of infectious viruses in water is further labor-and time-consuming, 4) molecular-based virus detection does not always indicate the presence of infectious viruses, and 5) waterborne viral infections due to reclaimed water have not been documented. abstract: Inappropriate usage of reclaimed wastewater has caused outbreaks of viral infectious diseases worldwide. International and domestic guidelines for wastewater reuse stipulate that virus infection risks are to be regulated by the multiple-barrier system, in which a wastewater treatment process composed of sequential treatment units is designed based on the pre-determined virus removal efficiency of each unit. The objectives of this review were to calculate representative values of virus removal efficiency in wastewater treatment units based on published datasets, and to identify research topics that should be further addressed for improving implementation of the multiple-barrier system. The removal efficiencies of human noroviruses, rotaviruses and enteroviruses in membrane bioreactor (MBR) and conventional activated sludge (CAS) processes were obtained by a systematic review protocol and a meta-analysis approach. The log(10) reduction (LR) of norovirus GII and enterovirus in MBR were 3.35 (95% confidence interval: 2.39, 4.30) and 2.71 (1.52, 3.89), respectively. The LR values of rotavirus, norovirus GI and GII in CAS processes were 0.87 (0.20, 1.53), 1.48 (0.96, 2.00) and 1.35 (0.52, 2.18), respectively. The systematic review process eliminated a substantial number of articles about virus removal in wastewater treatment because of the lack of information required for the meta-analysis. It is recommended that future publications should explicitly describe their treatment of left-censored datasets. Indicators, surrogates and methodologies appropriate for validating virus removal performance during daily operation of wastewater reclamation systems also need to be identified. url: https://www.ncbi.nlm.nih.gov/pubmed/26985655/ doi: 10.1016/j.envint.2016.03.001 id: cord-300522-okbupw61 author: Sansone, Clementina title: Marine Algal Antioxidants as Potential Vectors for Controlling Viral Diseases date: 2020-05-07 words: 4774.0 sentences: 248.0 pages: flesch: 31.0 cache: ./cache/cord-300522-okbupw61.txt txt: ./txt/cord-300522-okbupw61.txt summary: Given the ability of various algal molecules—mainly sulfated polysaccharides—to inhibit viral infection at Stage I (adsorption and invasion of cells), we envisage a need to further investigate the antiviral ability of algae, and their mechanisms of action. Oxidative stress-a loss in the balance between the production of free radicals including reactive oxygen species (ROS) and antioxidant cell signaling pathways [2] -can be a key factor of the pathogenesis in many acute or chronical human diseases [3] . For that, we explore the relationship between oxidative stress and viral infections, looking for solutions through the deciphering of cell signaling pathways that can inhibit virus replication and infections, and the mechanisms of action of potential antiviral molecules. Three polysaccharides extracted from marine microalgae, naviculan from the diatom Navicula directa, and two others (named A1 and A2) from the dinoflagellate Cochlodinium polykrikoides also displayed antiviral activities against several enveloped viruses, such as HIV-1, HSV-1 or influenza virus type A (IFV-A) [71] . abstract: As the COVID-19 epidemic expands in the world, and with the previous SARS epidemic, avian flu, Ebola and AIDS serving as a warning, biomedical and biotechnological research has the task to find solutions to counteract viral entry and pathogenesis. A novel approach can come from marine chemodiversity, recognized as a relevant source for developing a future natural “antiviral pharmacy”. Activities of antioxidants against viruses can be exploited to cope with human viral infection, from single individual infections to protection of populations. There is a potentially rich and fruitful reservoir of such compounds thanks to the plethora of bioactive molecules and families present in marine microorganisms. The aim of this communication is to present the state-of-play of what is known on the antiviral activities recognized in (micro)algae, highlighting the different molecules from various algae and their mechanisms of actions, when known. Given the ability of various algal molecules—mainly sulfated polysaccharides—to inhibit viral infection at Stage I (adsorption and invasion of cells), we envisage a need to further investigate the antiviral ability of algae, and their mechanisms of action. Given the advantages of microalgal production compared to other organisms, the opportunity might become reality in a short period of time. url: https://doi.org/10.3390/antiox9050392 doi: 10.3390/antiox9050392 id: cord-350235-yoy3hj3j author: Sansonetti, Philippe J title: COVID‐19, chronicle of an expected pandemic date: 2020-05-04 words: 2988.0 sentences: 152.0 pages: flesch: 56.0 cache: ./cache/cord-350235-yoy3hj3j.txt txt: ./txt/cord-350235-yoy3hj3j.txt summary: Philippe Sansonetti, Infectious disease specialist and Chief Editor of EMBO Molecular Medicine, explains why the fate of the epidemic is in our hands.[Image: see text] Philippe Sansonetti, Infectious Disease Specialist and Chief Editor of EMBO Molecular Medicine, explains why the fate of the epidemic is in our hands. Beta-coronaviruses like SARS-CoV-2 (the official name of COVID-19 virus) on the other hand are well adapted to their reservoir, the bat, but not to humans, which explains why human infections are so damaging. Molecular diagnosis has revolutionized this field, and despite the initial delays in communicating about this epidemic, Chinese doctors and biologists quickly reported the first evidence for SARS-CoV-2, and provided the first sequences, clearing the way for the global scientific community to further develop diagnostic tools and engage in a race to discover dedicated drugs and vaccines. abstract: What is COVID‐19? What are the causes, parameters, and effects of this disease? What are the short‐ and long‐term prospects? Philippe Sansonetti, Infectious disease specialist and Chief Editor of EMBO Molecular Medicine, explains why the fate of the epidemic is in our hands.[Image: see text] url: https://www.ncbi.nlm.nih.gov/pubmed/32259394/ doi: 10.15252/emmm.202012463 id: cord-317404-jvtozj4v author: Santos, Marfran C.D. title: Spectroscopy with computational analysis in virological studies: A decade (2006–2016) date: 2017-09-21 words: 8440.0 sentences: 428.0 pages: flesch: 43.0 cache: ./cache/cord-317404-jvtozj4v.txt txt: ./txt/cord-317404-jvtozj4v.txt summary: The potential of spectroscopic techniques in the detection and identification of virus-infected cells has been studied using statistical methods as a sensitive, rapid and reliable methodology. First, we will discuss the most commonly used spectroscopic techniques, then we will discuss the computational processes used to extract useful information from the obtained spectra (spectral preprocessing, multivariate classification algorithms, performance evaluation), and finally we will discuss some works published in the period from 2006 to 2016 using spectroscopy and multivariate analysis in studies involving viruses. For example, the potential of Raman spectroscopy followed by statistical methods in detecting and identifying Herpes Simplex Virus type 1 (HSV-1) infections as a sensitive, rapid and reliable method has been evaluated by Salman et al. (2014) [25] evaluated the potential of Raman spectroscopy as a sensitive, reliable and rapid method for detecting and identifying viral infection by Herpes simplex virus type 1 (HSV-1) in cell culture. abstract: This review presents a retrospective of the studies carried out in the last 10 years (2006–2016) using spectroscopic methods as a research tool in the field of virology. Spectroscopic analyses are sensitive to variations in the biochemical composition of the sample, are non-destructive, fast and require the least sample preparation, making spectroscopic techniques tools of great interest in biological studies. Herein important chemometric algorithms that have been used in virological studies are also evidenced as a good alternative for analyzing the spectra, discrimination and classification of samples. Techniques that have not yet been used in the field of virology are also suggested. This methodology emerges as a new and promising field of research, and may be used in the near future as diagnosis tools for detecting diseases caused by viruses. url: https://doi.org/10.1016/j.trac.2017.09.015 doi: 10.1016/j.trac.2017.09.015 id: cord-257163-hodykbcb author: Sanz, Ivan title: Viral Etiology of Chronic Obstructive Pulmonary Disease Exacerbations during the A/H1N1pdm09 Pandemic and Postpandemic Period date: 2015-05-07 words: 3825.0 sentences: 176.0 pages: flesch: 44.0 cache: ./cache/cord-257163-hodykbcb.txt txt: ./txt/cord-257163-hodykbcb.txt summary: During the study period (2009–2012), respiratory viruses were identified in 48.7% of samples, and the proportion of viral detections in AE-COPD was higher in patients aged 30–64 years than ≥65 years. Studies conducted before emergence of the pandemic H1N1pdm09 strain showed that half of all AE-COPD cases were associated with viral infections and that picornaviruses (especially human rhinovirus and enterovirus (HREV)) were the dominant viral pathogens diagnosed in these patients [15, 16] . The aim of this study is to describe the etiological characteristics of respiratory viruses linked to COPD exacerbations after a singular pandemic period caused by a new influenza virus. We used the OR to analyze the probability of detection of viral categories (ORP, HREV, any influenza virus, and RSV) as well as viral coinfections in AE-COPD patients among different demographic and epidemiological characteristics such as gender, age groups, and the different periods analyzed. abstract: Viral infections are one of the main causes of acute exacerbations of chronic obstructive pulmonary disease (AE-COPD). Emergence of A/H1N1pdm influenza virus in the 2009 pandemic changed the viral etiology of exacerbations that were reported before the pandemic. The aim of this study was to describe the etiology of respiratory viruses in 195 Spanish patients affected by AE-COPD from the pandemic until the 2011-12 influenza epidemic. During the study period (2009–2012), respiratory viruses were identified in 48.7% of samples, and the proportion of viral detections in AE-COPD was higher in patients aged 30–64 years than ≥65 years. Influenza A viruses were the pathogens most often detected during the pandemic and the following two influenza epidemics in contradistinction to human rhino/enteroviruses that were the main viruses causing AE-COPD before the pandemic. The probability of influenza virus detection was 2.78-fold higher in patients who are 30–64 years old than those ≥65. Most respiratory samples were obtained during the pandemic, but the influenza detection rate was higher during the 2011-12 epidemic. There is a need for more accurate AE-COPD diagnosis, emphasizing the role of respiratory viruses. Furthermore, diagnosis requires increased attention to patient age and the characteristics of each influenza epidemic. url: https://www.ncbi.nlm.nih.gov/pubmed/26064118/ doi: 10.1155/2015/560679 id: cord-292416-3hhi4wps author: Sarid, Ronit title: Investigating an Emerging Virus During a Sudden Pandemic Outbreak date: 2020-07-31 words: 4869.0 sentences: 230.0 pages: flesch: 41.0 cache: ./cache/cord-292416-3hhi4wps.txt txt: ./txt/cord-292416-3hhi4wps.txt summary: Five years later, in 2020, when the World Health Organization declared the coronavirus disease 2019 (COVID-19)-caused by the newly emerging SARS-CoV-2 virus-to be a pandemic, this talk was widely acknowledged to be almost prophetic. 24, 25 All four reportedly mild pathogenic coronaviruses are associated with 10%-30% of cases of the common cold, 26 -28 yet they have the potential to cause severe lower respiratory tract infection in infants, in the elderly, and in patients with other underlying illness, 29 while hCoV-OC43, like SARS-CoV-2, has been associated with neurologic dysfunction as well. Development of animal models for SARS-CoV-2 infection is vital in providing comprehensive understanding of the pathogenic mechanisms involved but may also serve for screening anti-viral drugs and vaccines. Accordingly, transfusion of convalescent plasma is likely to be beneficial to SARS-CoV-2, 45 ,46 yet its effect on virus shedding and disease outcome must be evaluated when given to healthy individuals and patients at different stages and severity of the disease. abstract: At the time of writing, in July 2020, the recently emerging SARS-CoV-2 pandemic has attracted major attention to viral diseases, in particular coronaviruses. In spite of alarming molecular evidence, documentation of interspecies transmission in livestock, and the emergence of two new and relatively virulent human coronaviruses within a 10-year period, many gaps remain in the study and understanding of this family of viruses. This paper provides an overview of our knowledge regarding the coronavirus family, while highlighting their key biological properties in the context of our overall understanding of viral diseases. url: https://doi.org/10.5041/rmmj.10414 doi: 10.5041/rmmj.10414 id: cord-319746-6bccxgbd author: Saxena, Latika title: Production and Characterization of Human Monoclonal Antibodies from the Cells of A(H1N1)pdm2009 Influenza Virus Infected Indian Donors date: 2015-12-31 words: 3526.0 sentences: 174.0 pages: flesch: 48.0 cache: ./cache/cord-319746-6bccxgbd.txt txt: ./txt/cord-319746-6bccxgbd.txt summary: title: Production and Characterization of Human Monoclonal Antibodies from the Cells of A(H1N1)pdm2009 Influenza Virus Infected Indian Donors Abstract Analysis of human monoclonal antibodies (mAbs) developed from influenza infected donors have enormously contributed to the identification of neutralization sensitive epitopes of influenza virus. In this study, we generated strongly neutralizing novel human monoclonal antibodies that were selected from the immune repertoire of influenza infected seropositive patients. Monoclonal antibody 2D8 showed the maximum binding in the in vitro assays and neutralized the human isolate of the pandemic strain as well as the reference strain at lowest concentrations when compared to the 2F12 antibody. The antibodies however, showed comparative neutralization and HAI activity between the laboratory isolates of the pandemic virus and the reference strain A/Cal/07/2009(H1N1). To, the best of our knowledge, these antibodies are the first fully human monoclonal antibodies generated from the immune repertoire of Indian patients infected with A(H1N1)pdm09 virus. abstract: Abstract Analysis of human monoclonal antibodies (mAbs) developed from influenza infected donors have enormously contributed to the identification of neutralization sensitive epitopes of influenza virus. The HA protein is a crucial target of neutralizing antibodies and at monoclonal level only Abs binding to HA have been able to neutralize the virus. In this study, eight A (H1N1)pdm 2009 seropositive patients within the age range of 20-50 years (median=36 years) were recruited. Two anti-HA mAbs secreting stable clones, 2D8 and 2F12 were established under optimized conditions from the peripheral blood mononuclear cells (PBMCs) of the volunteers. These antibodies efficiently neutralized the homologous laboratory isolated strain of the pandemic virus as well as the reference strain. Our study suggests that the anti-HA antibodies derived from infected Indian patients display neutralization potential against the A(H1N1)pdm 2009 virus. This is the first ever study of generation of mAbs against the pandemic influenza virus involving the immune repertoire if Indian patients. Molecular characterization of the target regions will help in identifying potential immunogens in the Indian pandemic isolates and confer protective immunity against this virus. url: https://api.elsevier.com/content/article/pii/S1877282X15000107 doi: 10.1016/j.provac.2015.05.009 id: cord-352178-irjhmxsg author: Saxton-Shaw, Kali D. title: O''nyong nyong Virus Molecular Determinants of Unique Vector Specificity Reside in Non-Structural Protein 3 date: 2013-01-24 words: 5953.0 sentences: 299.0 pages: flesch: 49.0 cache: ./cache/cord-352178-irjhmxsg.txt txt: ./txt/cord-352178-irjhmxsg.txt summary: Fifteen distinct chimeric viruses were constructed to evaluate both structural and non-structural regions of the genome and infection patterns were determined through artificial infectious feeds in An. gambiae with each of these chimeras. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from CHIKV virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. Our study analyzed both structural and non-structural regions of the ONNV genome using chimeric viruses and artificially infected Anopheles gambiae mosquitoes. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from chikungunya virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. Six additional non-structural chimeric viruses were also constructed using a novel type II restriction enzyme cloning strategy to examine the broader genome with respect to ONNV''s unique vector specificity for An. gambiae mosquitoes (Figure 2) . abstract: O'nyong nyong virus (ONNV) and Chikungunya virus (CHIKV) are two closely related alphaviruses with very different infection patterns in the mosquito, Anopheles gambiae. ONNV is the only alphavirus transmitted by anopheline mosquitoes, but specific molecular determinants of infection of this unique vector specificity remain unidentified. Fifteen distinct chimeric viruses were constructed to evaluate both structural and non-structural regions of the genome and infection patterns were determined through artificial infectious feeds in An. gambiae with each of these chimeras. Only one region, non-structural protein 3 (nsP3), was sufficient to up-regulate infection to rates similar to those seen with parental ONNV. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from CHIKV virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. No other single gene or viral region addition was able to restore infection rates. Thus, we have shown that a non-structural genome element involved in viral replication is a major element involved in ONNV's unique vector specificity. url: https://www.ncbi.nlm.nih.gov/pubmed/23359824/ doi: 10.1371/journal.pntd.0001931 id: cord-354848-7aakik9a author: Sayres, Lauren title: Contemporary Understanding of Ebola and Zika Virus in Pregnancy date: 2020-10-16 words: 4375.0 sentences: 253.0 pages: flesch: 41.0 cache: ./cache/cord-354848-7aakik9a.txt txt: ./txt/cord-354848-7aakik9a.txt summary: In particular, Ebola virus is associated with high case fatality and pregnancy and neonatal loss rates, while Zika virus has been associated with multiple congenital anomalies; these features present critical clinical dilemmas for management of pregnant and reproductive aged women. The Monitored Emergency Use of Unregistered and Investigational Interventions ethical framework recommends that vulnerable Contemporary Understanding of Ebola and Zika Virus populations including pregnant women be offered similar treatments to the nonpregnant population when potential benefits can outweigh risks. 75 Attention must be paid to the successes and failures of the response to the Ebola and Zika outbreaks as physicians strive to provide excellent care for pregnant women who are affected by or at risk for emerging infectious diseases. Prevention of Ebola virus includes containment of infected substances and personal protection equipment use, and prevention of Zika virus entails protection against mosquito bites, avoidance of high-risk regions, and delay of childbearing. abstract: Understanding the pathophysiology, management, and prevention of emerging infectious diseases among pregnant women is imperative to achieve a successful response from the medical community. Ebola and Zika viruses represent infections with profound public health implications. In particular, Ebola virus is associated with high case fatality and pregnancy and neonatal loss rates, while Zika virus has been associated with multiple congenital anomalies; these features present critical clinical dilemmas for management of pregnant and reproductive aged women. The objective of this article is to summarize key background information and best practices for management of Ebola and Zika virus in pregnancy. url: https://www.ncbi.nlm.nih.gov/pubmed/33153665/ doi: 10.1016/j.clp.2020.08.005 id: cord-288879-rj03dsib author: Schein, Catherine H. title: Polyglutamine Repeats in Viruses date: 2018-09-04 words: 6195.0 sentences: 301.0 pages: flesch: 45.0 cache: ./cache/cord-288879-rj03dsib.txt txt: ./txt/cord-288879-rj03dsib.txt summary: While the mechanisms for the function and toxicity of extended polyQ segments (or the nucleic regions that encode them) in eukaryotic proteins continue to be actively studied [16] , there has been little exploration of their occurrence and possible roles, even in neurovirulent viruses. At the start of this work, the ViPR database [29] , which allows rapid access to the published sequences of over 75,000 viral genomes or genome segments, was used to determine which RNA and DNA viruses contain polyQ repeats. As discussed below, the longest repeats were found in DNA virus proteins that function in enhancing transmissibility (cowpox ATI) or contribute to viral latency (herpes viruses). Under growth conditions allowing the virus to resume lytic growth, where the enzyme activity is required to ensure efficient replication, the region Fig. 2 Soluble polyQ segments (of cell or viral origin) may prevent beclin-1-induced autophagy, which depends on the DNA binding ability of the polyQ segment of wt-ataxin-3 (based on [2, 67] ). abstract: This review explores the presence and functions of polyglutamine (polyQ) in viral proteins. In mammals, mutations in polyQ segments (and CAG repeats at the nucleotide level) have been linked to neural disorders and ataxias. PolyQ regions in normal human proteins have documented functional roles, in transcription factors and, more recently, in regulating autophagy. Despite the high frequency of polyQ repeats in eukaryotic genomes, little attention has been given to the presence or possible role of polyQ sequences in virus genomes. A survey described here revealed that polyQ repeats occur rarely in RNA viruses, suggesting that they have detrimental effects on virus replication at the nucleotide or protein level. However, there have been sporadic reports of polyQ segments in potyviruses and in reptilian nidoviruses (among the largest RNA viruses known). Conserved polyQ segments are found in the regulatory control proteins of many DNA viruses. Variable length polyQ tracts are found in proteins that contribute to transmissibility (cowpox A-type inclusion protein (ATI)) and control of latency (herpes viruses). New longer-read sequencing methods, using original biological samples, should reveal more details on the presence and functional role of polyQ in viruses, as well as the nucleotide regions that encode them. Given the known toxic effects of polyQ repeats, the role of these segments in neurovirulent and tumorigenic viruses should be further explored. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12035-018-1269-4) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/30182336/ doi: 10.1007/s12035-018-1269-4 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-323333-keshu99t author: Schleis, Thomas G. title: The Process: New Methods of Purification and Viral Safety date: 2013-01-16 words: 2212.0 sentences: 132.0 pages: flesch: 47.0 cache: ./cache/cord-323333-keshu99t.txt txt: ./txt/cord-323333-keshu99t.txt summary: From the transmission of hepatitis C virus by gammaglobulins in 1994 to the emergence of new viruses and concern over prions, intravenous immunoglobulin (IGIV) manufacturers have continued to address safety issues and respond to changing needs. Because the different techniques can affect the biologic function of the IgG molecule, the methods of viral inactivation may account for some of the differences among IGIV products in terms of side effects and efficacy (Table 1) . Because intravenous immunoglobulins are derived from human plasma, they are potentially susceptible to contamination by a variety of blood-borne pathogens; consequently, patients receiving and clinicians administering IGIV are concerned about disease transmission. From the transmission of HCV by gammaglobulins in 1994 to the emergence of new viruses or concern over prions, IGIV manufacturers have continued to address safety issues and respond to changing needs. abstract: From the transmission of hepatitis C virus by gammaglobulins in 1994 to the emergence of new viruses and concern over prions, intravenous immunoglobulin (IGIV) manufacturers have continued to address safety issues and respond to changing needs. New IGIV products not only provide superior antiviral safety, but also show advances in product purity and manufacturing processes. Several manufacturers have also addressed the concern over prion transmission. The sum of the processes used have collectively ensured continuous product safety. Newer products will be further differentiated by their tolerability and efficacy profiles. url: https://www.ncbi.nlm.nih.gov/pubmed/16229677/ doi: 10.1592/phco.2005.25.11part2.73s id: cord-010188-884d196k author: Schlesinger, Sondra title: Alphaviruses — vectors for the expression of heterologous genes date: 2004-08-26 words: 3049.0 sentences: 140.0 pages: flesch: 47.0 cache: ./cache/cord-010188-884d196k.txt txt: ./txt/cord-010188-884d196k.txt summary: Sindbis virus and Semliki Forest vires are best known as valuable models for molecular and cell biology, and it is these two viruses that are presently being developed as vectors for the expression of heterologous genes. The basic strategy for using alphaviruses as vectors for the expression of heterologous genes has been to construct cDNAs of the alphavirus genome, in which the heterologous gene is placed downstream from the promoter used to transcribe a subgenomic RNA 13 (Fig. 2a) . A second potential problem is recombination between the packaging helper virus RNA and vector RNAs. The two Sindbis RNAs can undergo recombination to produce a single molecule of RNA containing the genes that encode both the nonstructural and structural proteins m. The initial studies with Sindbis and Semliki Forest virus suggest that both viruses are promising as vectors for heterologous gene expression. abstract: DNA viruses and retroviruses are well established as vectors for the expression of heterologous genes, but there is increasing interest in the possibilities of using RNA viruses, which do not replicate through a DNA intermediate, for this purpose. This article summarizes some of the general properties of RNA viruses and concentrates on one class of RNA viruses — the alphaviruses — and their potential as expression vectors. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172487/ doi: 10.1016/0167-7799(93)90070-p id: cord-008716-38sqkh9m author: Schmidt, Alexander C title: Current research on respiratory viral infections: Third International Symposium date: 2001-06-01 words: 24743.0 sentences: 1086.0 pages: flesch: 43.0 cache: ./cache/cord-008716-38sqkh9m.txt txt: ./txt/cord-008716-38sqkh9m.txt summary: Renewed efforts in vaccine development against respiratory viruses began in the 1960s with the observation that infants and young children, after having recovered from respiratory tract infection with adenoviruses, shed virus from their gastrointestinal tract for an extended period of time without experiencing gastrointestinal symptoms. Earlier studies of viral pathogens in immunocompromised adults indicated that CMV, herpes simplex, influenza, parainfluenza, rhinovirus, adenovirus, enterovirus, and RSV cause lower respiratory infection (Connolly et al., 1994) . Children with RSV, adenovirus or influenza virus infections have a 30% risk of developing AOM within 2 weeks of the onset of the respiratory tract infection (Henderson et al., 1982) , and coinfection with bacteria and viruses also adversely influences the outcome of AOM. Populations at high risk for complications resulting from respiratory viral infections are now better defined and a more targeted prophylaxis is possible, be it passive prophylaxis against RSV disease with monoclonal antibody preparations or active prophylaxis with influenza-or adenovirus vaccines. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133842/ doi: 10.1016/s0166-3542(01)00136-x id: cord-297834-me1ajoyb author: Schountz, Tony title: Hantavirus Immunology of Rodent Reservoirs: Current Status and Future Directions date: 2014-03-14 words: 6425.0 sentences: 334.0 pages: flesch: 38.0 cache: ./cache/cord-297834-me1ajoyb.txt txt: ./txt/cord-297834-me1ajoyb.txt summary: The immune response is energetically expensive for wild animals, thus the findings of experimental studies will be critical for understanding the ecoimmunology of reservoir hosts of hantaviruses [6, 7] , and experiments using wild rodents in natural or semi-natural environments [8, 9] will be required to validate laboratory findings. Currently, three laboratory infection systems have been developed to study hantavirus infections of reservoir hosts: Seoul virus (SEOV) infection of the Norway rat (Rattus norvegicus), Puumala virus (PUUV) infection of the bank vole (Myodes glareolus), and Sin Nombre virus (SNV) infection of the deer mouse (Peromyscus maniculatus) [12, 14, 16] . Experimental data have also shown that patterns of the expression of genes related to the immune response are different in infected males and females [32] , and it is likely these differences have important roles in hantavirus ecology. abstract: Hantaviruses are hosted by rodents, insectivores and bats. Several rodent-borne hantaviruses cause two diseases that share many features in humans, hemorrhagic fever with renal syndrome in Eurasia or hantavirus cardiopulmonary syndrome in the Americas. It is thought that the immune response plays a significant contributory role in these diseases. However, in reservoir hosts that have been closely examined, little or no pathology occurs and infection is persistent despite evidence of adaptive immune responses. Because most hantavirus reservoirs are not model organisms, it is difficult to conduct meaningful experiments that might shed light on how the viruses evade sterilizing immune responses and why immunopathology does not occur. Despite these limitations, recent advances in instrumentation and bioinformatics will have a dramatic impact on understanding reservoir host responses to hantaviruses by employing a systems biology approach to identify important pathways that mediate virus/reservoir relationships. url: https://www.ncbi.nlm.nih.gov/pubmed/24638205/ doi: 10.3390/v6031317 id: cord-012418-6ralcn8p author: Schwanke, Hella title: Of Keeping and Tipping the Balance: Host Regulation and Viral Modulation of IRF3-Dependent IFNB1 Expression date: 2020-07-07 words: 15685.0 sentences: 761.0 pages: flesch: 38.0 cache: ./cache/cord-012418-6ralcn8p.txt txt: ./txt/cord-012418-6ralcn8p.txt summary: Due to its key role during the induction of the initial IFN response, the activity of the transcription factor interferon regulatory factor 3 (IRF3) is tightly regulated by the host and fiercely targeted by viral proteins at all conceivable levels. The crucial role of IRF3 and the posttranslational changes it undergoes upon viral infection were first reported more than 20 years ago: Upon stimulation, IRF3 gets phosphorylated and accumulates in the nucleus where it interacts with the coactivators CREB-binding protein (CBP)/p300 to specifically bind to virus-inducible enhancer elements and exerts transcriptional activation of the IFNB1 gene [21, [36] [37] [38] (Figure 2 ). The crucial role of IRF3 and the posttranslational changes it undergoes upon viral infection were first reported more than 20 years ago: Upon stimulation, IRF3 gets phosphorylated and accumulates in the nucleus where it interacts with the coactivators CREB-binding protein (CBP)/p300 to specifically bind to virus-inducible enhancer elements and exerts transcriptional activation of the IFNB1 gene [21, [36] [37] [38] (Figure 2 ). abstract: The type I interferon (IFN) response is a principal component of our immune system that allows to counter a viral attack immediately upon viral entry into host cells. Upon engagement of aberrantly localised nucleic acids, germline-encoded pattern recognition receptors convey their find via a signalling cascade to prompt kinase-mediated activation of a specific set of five transcription factors. Within the nucleus, the coordinated interaction of these dimeric transcription factors with coactivators and the basal RNA transcription machinery is required to access the gene encoding the type I IFN IFNβ (IFNB1). Virus-induced release of IFNβ then induces the antiviral state of the system and mediates further mechanisms for defence. Due to its key role during the induction of the initial IFN response, the activity of the transcription factor interferon regulatory factor 3 (IRF3) is tightly regulated by the host and fiercely targeted by viral proteins at all conceivable levels. In this review, we will revisit the steps enabling the trans-activating potential of IRF3 after its activation and the subsequent assembly of the multi-protein complex at the IFNβ enhancer that controls gene expression. Further, we will inspect the regulatory mechanisms of these steps imposed by the host cell and present the manifold strategies viruses have evolved to intervene with IFNβ transcription downstream of IRF3 activation in order to secure establishment of a productive infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7411613/ doi: 10.3390/v12070733 id: cord-304251-dohglrm1 author: Scully, C title: Emerging and changing viral diseases in the new millennium date: 2015-08-06 words: 6254.0 sentences: 322.0 pages: flesch: 47.0 cache: ./cache/cord-304251-dohglrm1.txt txt: ./txt/cord-304251-dohglrm1.txt summary: Thus recent decades have seen a most dramatic change with the emergence globally also of new viral infections – notably human immunodeficiency viruses (HIV) – and the appearance of some other dangerous and sometimes lethal infections formerly seen mainly in, and reported from, resource‐poor areas especially in parts of Asia, Latin America and Africa. Gradually, however, the unexpected consequences of some oral viral infections have emerged and been recognised, not without some surprise (Scully, 1983) especially the oncogenicity of some herpesviruses (Eglin et al, 1983) and human papillomaviruses (HPVs) which we (Eglin et al, 1983; Maitland et al, 1987; Cox et al, 1993 ) and many others (e.g. Lind et al, 1986) have explored, culminating in the appreciation of unanticipated transmission routes for some cancers, such as sexual (Scully, 2002) . The recent several decades have also seen a most dramatic change with the emergence globally of new viral infectionsnotably human immunodeficiency viruses (HIV)and the appearance also in resource-rich countries, of some other dangerous and sometimes lethal infections hitherto latent, unrecognised or unappreciated in resource-poor areas. abstract: Most viral infections encountered in resource‐rich countries are relatively trivial and transient with perhaps fever, malaise, myalgia, rash (exanthema) and sometimes mucosal manifestations (enanthema), including oral in some. However, the apparent benignity may be illusory as some viral infections have unexpected consequences – such as the oncogenicity of some herpesviruses and human papillomaviruses. Infections are transmitted from various human or animal vectors, especially by close proximity, and the increasing movements of peoples across the globe, mean that infections hitherto confined largely to the tropics now appear worldwide. Global warming also increases the range of movement of vectors such as mosquitoes. Thus recent decades have seen a most dramatic change with the emergence globally also of new viral infections – notably human immunodeficiency viruses (HIV) – and the appearance of some other dangerous and sometimes lethal infections formerly seen mainly in, and reported from, resource‐poor areas especially in parts of Asia, Latin America and Africa. This study offers a brief update of the most salient new aspects of the important viral infections, especially those with known orofacial manifestations or other implications for oral health care. url: https://doi.org/10.1111/odi.12356 doi: 10.1111/odi.12356 id: cord-306424-gf0bglm0 author: Scutigliani, Enzo Maxim title: Interaction of the innate immune system with positive-strand RNA virus replication organelles date: 2017-06-27 words: 8320.0 sentences: 382.0 pages: flesch: 36.0 cache: ./cache/cord-306424-gf0bglm0.txt txt: ./txt/cord-306424-gf0bglm0.txt summary: Thus, these data indicate that MAMs are critical locations for antiviral signaling and have an important role in expression of type I and III IFNs. Moreover, increasing evidence suggests that at least some +RNA viruses in fact occupy or hijack MAM-membranes during infection, as MAMs of HCV-infected cells were found to contain proteins involved in virus assembly and fully assembled virions [111] . At last, based on recent studies that demonstrated how IFN-g inducible GTPases are capable of disrupting PVs, we discussed the possibility of a general function of IFN-inducible GTPases in the targeting of viral ROs. In summary, upon infection, +RNA viruses hamper IFN and ISG induction at multiple levels to decelerate antiviral innate immune signaling. Antiviral innate immune response interferes with the formation of replication-associated membrane structures induced by a +RNA virus abstract: The potential health risks associated with (re-)emerging positive-strand RNA (+RNA) viruses emphasizes the need for understanding host-pathogen interactions for these viruses. The innate immune system forms the first line of defense against pathogenic organisms like these and is responsible for detecting pathogen-associated molecular patterns (PAMPs). Viral RNA is a potent inducer of antiviral innate immune signaling, provoking an antiviral state by directing expression of interferons (IFNs) and pro-inflammatory cytokines. However, +RNA viruses developed various methods to avoid detection and downstream signaling, including isolation of viral RNA replication in membranous viral replication organelles (ROs). These structures therefore play a central role in infection, and consequently, loss of RO integrity might simultaneously result in impaired viral replication and enhanced antiviral signaling. This review summarizes the first indications that the innate immune system indeed has tools to disrupt viral ROs and other non- or aberrant-self membrane structures, and may do this by marking these membranes with proteins such as microtubule-associated protein 1A/1B-light chain 3 (LC3) and ubiquitin, resulting in the recruitment of IFN-inducible GTPases. Further studies should evaluate whether this process forms a general effector mechanism in +RNA virus infection, thereby creating the opportunity for development of novel antiviral therapies. url: https://api.elsevier.com/content/article/pii/S1359610117300667 doi: 10.1016/j.cytogfr.2017.05.007 id: cord-017326-1caeui30 author: Seay, Montrell title: Digesting Oneself and Digesting Microbes: Autophagy as a Host Response to Viral Infection date: 2005 words: 11363.0 sentences: 489.0 pages: flesch: 34.0 cache: ./cache/cord-017326-1caeui30.txt txt: ./txt/cord-017326-1caeui30.txt summary: Genetic studies in yeast and mammalian cells have also shown that the eIF2 kinase signaling pathway is required for starvation and herpes simplex virus-induced autophagy 18 . The role of some of the Atg proteins, including ones that act in the lipid kinase signaling complex and in the ubiquitin-like conjugation pathways, has been studied in plant and mammalian viral infections (see Table 1 ). Together, the studies of Sindbis virus infection in neurons overexpressing beclin 1 or in cultured cells lacking beclin 1 or atg5 demonstrate a role for mammalian autophagy genes in both restricting viral replication and in protection against virus-induced cell death. The interferon-inducible, antiviral PKR signaling pathway positively regulates autophagy, and both mammalian and plant autophagy genes restrict viral replication and protect against virus-induced cell death. The interferon-inducible, antiviral PKR signaling pathway positively regulates autophagy, and both mammalian and plant autophagy genes restrict viral replication and protect against virus-induced cell death. abstract: Although research in this area is still in a stage of infancy, it seems likely that the lysosomal degradation pathway of autophagy plays an evolutionarily conserved role in antiviral immunity. The interferon-inducible, antiviral PKR signaling pathway positively regulates autophagy, and both mammalian and plant autophagy genes restrict viral replication and protect against virus-induced cell death. Given this role of autophagy in innate immunity, it is not surprising that viruses have evolved numerous strategies to inhibit host autophagy. Different viral gene products can either modulate autophagy regulatory signals or directly interact with components of the autophagy execution machinery. Moreover, certain RNA viruses have managed to “co-apt” the autophagy pathway, selectively utilizing certain components of the dynamic membrane rearrangement system to promote their own replication inside the host cytoplasm. In addition to this newly emerging role of autophagy in innate immunity, autophagy plays an important role in many other fundamental biological processes, including tissue homeostasis, differentiation and development, cell growth control, and the prevention of aging. Accordingly, the inhibition of host autophagy by viral gene products has important implications not only for understanding mechanisms of immune evasion, but also for understanding novel mechanisms of viral pathogenesis. It will be interesting to dissect the role of viral inhibition of autophagy in acute, persistent, and latent viral replication, as well as in the pathogenesis of cancer and other medical diseases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121853/ doi: 10.1007/1-4020-3242-0_11 id: cord-270335-8vqi9c68 author: Seifert, Stephanie N title: Rousettus aegyptiacus Bats Do Not Support Productive Nipah Virus Replication date: 2019-11-04 words: 3272.0 sentences: 155.0 pages: flesch: 47.0 cache: ./cache/cord-270335-8vqi9c68.txt txt: ./txt/cord-270335-8vqi9c68.txt summary: Nipah virus is capable of infecting a broad range of hosts including humans, pigs, ferrets, dogs, cats, hamsters, and at least 2 genera of bats. Studies of wild caught Pteropus spp suggest potential for viral recrudescence [16, 23] ; however, the hypothesis that NiV may persist in an individual bat and re-emerge under times of stress has yet to be confirmed experimentally. In contrast, the Egyptian fruit bat (EFB), Rousettus aegyptiacus, belongs to the same taxonomic family as Pteropus spp, Pteropodidae, and has been successfully used to model Marburg virus transmission [24, 25] and serological cross-reactivity after filovirus challenge [26] . Previous studies have demonstrated that EFB cells are permissive to Ebola virus, but experimentally challenged bats did not shed virus or support productive replication [38, 39] despite compatibility between the Ebola virus glycoprotein and the host receptor, NPC1 [40] . abstract: Nipah virus (NiV) is a bat-borne zoonotic pathogen that can cause severe respiratory distress and encephalitis upon spillover into humans. Nipah virus is capable of infecting a broad range of hosts including humans, pigs, ferrets, dogs, cats, hamsters, and at least 2 genera of bats. Little is known about the biology of NiV in the bat reservoir. In this study, we evaluate the potential for the Egyptian fruit bat (EFB), Rousettus aegyptiacus, to serve as a model organism for studying NiV in bats. Our data suggest that NiV does not efficiently replicate in EFBs in vivo. Furthermore, we show a lack of seroconversion against NiV glycoprotein and a lack of viral replication in primary and immortalized EFB-derived cell lines. Our data show that despite using a conserved target for viral entry, NiV replication is limited in some bat species. We conclude that EFBs are not an appropriate organism to model NiV infection or transmission in bats. url: https://doi.org/10.1093/infdis/jiz429 doi: 10.1093/infdis/jiz429 id: cord-334108-4ey725dv author: Seymour, I.J. title: Foodborne viruses and fresh produce date: 2008-07-07 words: 10241.0 sentences: 596.0 pages: flesch: 52.0 cache: ./cache/cord-334108-4ey725dv.txt txt: ./txt/cord-334108-4ey725dv.txt summary: The most frequently reported foodborne viral infections are viral gastroenteritis and hepatitis A: both have been associated with the consumption of fresh fruit or vegetables. There are many groups of viruses which could contaminate food items, but the major foodborne viral pathogens are those that infect via the gastrointestinal tract, such as the gastroenteritis viruses and hepatitis A virus. There is a need to develop more effective quantitative methods in order to assess the survival of viruses on fresh produce and to determine the decontamination ef®ciencies of current commercial washing systems for fruit and vegetables. Mounting evidence suggests that viruses can survive long enough and in high enough numbers to cause human diseases through direct contact with polluted water or contaminated foods (Nasser 1994; Bosch 1995) . When hepatitis A virus was detected in lettuce from Costa Rica, it was suggested that the possible source of contamination was the discharge of untreated sewage into river water used to irrigate crops, which is common practice in some less well-developed countries (Hernandez et al. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/11722652/ doi: 10.1046/j.1365-2672.2001.01427.x id: cord-007843-yqdqm4rh author: Shader, Richard I. title: Zoonotic Viruses: The Mysterious Leap From Animals to Man date: 2018-07-26 words: 980.0 sentences: 88.0 pages: flesch: 58.0 cache: ./cache/cord-007843-yqdqm4rh.txt txt: ./txt/cord-007843-yqdqm4rh.txt summary: Nipah and Hendra viruses are both members of the Paramyxoviridae family; neither virus is known to cause disease in their host bats. Similarly, although infrequent, the H1N1 influenza virus can be transmitted from infected pigs to humans, hence its common name of swine flu. 8 Even more uncommon is for a virus to be transmitted from an infected human to an animal. In theory, infected humans could transmit the rabies virus to animals; no cases have been documented. For this issue of Clinical Therapeutics, our Infectious Diseases Topic Editor Dr Ravi Jhaveri has assembled a collection of articles entitled "Hot Topics in Viral Diseases." The collection highlights recent controversies in vaccine licensure and recommendation, as well as advances in antiviral therapies for herpesvirus, hepatitis B and C, respiratory syncytial virus, and influenza, with an emphasis on pediatric patients. A review of therapeutics in clinical development for respiratory syncytial virus and influenza in children abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7124381/ doi: 10.1016/j.clinthera.2018.06.016 id: cord-265751-q1ecpfyg author: Shahani, Lokesh title: Antiviral therapy for respiratory viral infections in immunocompromised patients date: 2017-01-16 words: 10657.0 sentences: 523.0 pages: flesch: 34.0 cache: ./cache/cord-265751-q1ecpfyg.txt txt: ./txt/cord-265751-q1ecpfyg.txt summary: â�¢ High prevalence of M2 inhibitors resistance detected in influenza A (H3N2) and 2009 H1N1 virus strains preclude their use for prophylaxis or empiric treatment of seasonal influenza â�¢ Neuraminidase inhibitors are the first line agents for treatment of Influenza and treatment is most likely to provide the most benefit when initiated within the first 48 h of illness â�¢ Zanamivir is currently the therapy of choice for the treatment of oseltamivir-resistant influenza infection â�¢ An immunodeficiency scoring index for RSV, that accounts for the number of risk factors, can be used to identify HSCT recipients who are at high risk for progression to RSV LRTI and RSV associated mortality â�¢ Ribavirin-based therapy (alone or in combination with immunomodulators) can be effective in preventing progression from URTI to LRTI and may improve mortality in highly immunosuppressed adult HSCT recipients â�¢ The safety and efficacy of DAS181 in immunocompromised patients with PIV pneumonia, is currently being studied in an ongoing phase 2 double-blind, placebo-controlled trial. 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-324280-e8mj6ecl author: Shaman, Jeffrey title: Asymptomatic Summertime Shedding of Respiratory Viruses date: 2018-04-01 words: 2600.0 sentences: 128.0 pages: flesch: 41.0 cache: ./cache/cord-324280-e8mj6ecl.txt txt: ./txt/cord-324280-e8mj6ecl.txt summary: Here, we explore respiratory virus infection rates in a segment of this population through a convenience survey and sampling study of adult visitors to a New York City tourist attraction during spring and summer 2016. Among all participants there was a statistically significant positive association between reporting a greater tendency to get sick and total self-reported symptom score (P < .0001 by the Tukey test); however, there was no significant association between reporting a greater tendency to get sick and actual detection of respiratory virus shedding (P = .10 by χ 2 analysis). The best-fit logistic regression model supported an association between an increased likelihood of testing positive for respiratory virus infection and a higher total symptom score (P < .0001) and being Hispanic (P < .005). abstract: To determine rates of both symptomatic and asymptomatic infection among ambulatory adults, we collected nasopharyngeal swab specimens, demographic characteristics, and survey information from 1477 adult visitors to a New York City tourist attraction during April–July 2016. Multiplex polymerase chain reaction analysis was used to identify specimens positive for common respiratory viruses. A total of 7.2% of samples tested positive for respiratory viruses; among positive samples, 71.0% contained rhinovirus, and 21.5% contained coronavirus. Influenza virus, respiratory syncytial virus, and parainfluenza virus were also detected. Depending on symptomatologic definition, 57.7%–93.3% of positive samples were asymptomatic. These findings indicate that significant levels of asymptomatic respiratory viral shedding exist during summer among the ambulatory adult population. url: https://doi.org/10.1093/infdis/jix685 doi: 10.1093/infdis/jix685 id: cord-330827-gu2mt6zp author: Shanmugaraj, Balamurugan title: Emergence of Novel Coronavirus 2019-nCoV: Need for Rapid Vaccine and Biologics Development date: 2020-02-22 words: 3730.0 sentences: 175.0 pages: flesch: 40.0 cache: ./cache/cord-330827-gu2mt6zp.txt txt: ./txt/cord-330827-gu2mt6zp.txt summary: The emergence of the 2019 novel coronavirus (2019-nCoV) has recently added to the list of problematic emerging pathogens in the 21st century, which was suspected to originate from the persons exposed to a seafood or wet market in Wuhan, Hubei Province, China, suggesting animal-to-human transmission [2, 3] . Several reports in the last two decades have enough evidence to prove that the plant produced biopharmaceuticals are as effective as the mammalian cell-based proteins and also elicit potent neutralizing antibodies, or shown therapeutic effects against the particular pathogen or infection [17] [18] [19] . Many reports reviewed the importance of plant expression system for the rapid production of candidate vaccines and therapeutic antibodies against infectious diseases [22] [23] [24] [25] [26] [27] . As plant-made biopharmaceuticals provide efficacious and cost-effective strategies to protect against emerging infectious diseases, plant expression systems can be employed for the development of vaccines against nCoV. abstract: Novel Coronavirus (2019-nCoV) is an emerging pathogen that was first identified in Wuhan, China in late December 2019. This virus is responsible for the ongoing outbreak that causes severe respiratory illness and pneumonia-like infection in humans. Due to the increasing number of cases in China and outside China, the WHO declared coronavirus as a global health emergency. Nearly 35,000 cases were reported and at least 24 other countries or territories have reported coronavirus cases as early on as February. Inter-human transmission was reported in a few countries, including the United States. Neither an effective anti-viral nor a vaccine is currently available to treat this infection. As the virus is a newly emerging pathogen, many questions remain unanswered regarding the virus’s reservoirs, pathogenesis, transmissibility, and much more is unknown. The collaborative efforts of researchers are needed to fill the knowledge gaps about this new virus, to develop the proper diagnostic tools, and effective treatment to combat this infection. Recent advancements in plant biotechnology proved that plants have the ability to produce vaccines or biopharmaceuticals rapidly in a short time. In this review, the outbreak of 2019-nCoV in China, the need for rapid vaccine development, and the potential of a plant system for biopharmaceutical development are discussed. url: https://doi.org/10.3390/pathogens9020148 doi: 10.3390/pathogens9020148 id: cord-026130-ki7bn67o author: Sharma, Anand Kumar title: Novel Coronavirus Disease (COVID-19) date: 2020-06-05 words: 5073.0 sentences: 330.0 pages: flesch: 57.0 cache: ./cache/cord-026130-ki7bn67o.txt txt: ./txt/cord-026130-ki7bn67o.txt summary: In humans, coronaviruses cause respiratory tract infections that are typically mild, such as some cases of the common cold (among other possible causes, predominantly rhinoviruses), though rarer forms such as Middle East Respiratory Syndrome (MERS), Severe Acute Respiratory Syndrome (SARS), and COVID-19 can be lethal [4] . Based on currently available information and clinical expertise, older adults of over 60 years and people of any age who have serious underlying medical conditions (comorbidities) might be at higher risk of developing the severe disease with SARS-CoV-2, which may even lead to death. As of April 22, 2020, more than 2.5 million people all over the world have tested positive for COVID19 countries including India have evaluated the pandemic situation and have taken the "extraordinary measures" of complete lockdown to contain the virus. abstract: The present outbreak of the novel coronavirus initially called as “2019 novel coronavirus” or “2019-nCoV” by the World Health Organization (WHO), is also known as “Wuhan coronavirus” or “Wuhan pneumonia”, as it started in the Wuhan city of China in early December of 2019. This new coronavirus-associated acute respiratory deadly disease is now officially named as Corona Virus Disease-19 (COVID-19) by the WHO. From China, this epidemic has now spread to all over the world. On 11 March 2020, the WHO recognised COVID-19 as a pandemic. A pandemic refers to a disease that has spread to several countries, continents, if not worldwide. While the information available on this newly identified virus is limited and evolving, here is a quick run-down of what has been figured out so far. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7274062/ doi: 10.1007/s12045-020-0981-3 id: cord-257008-7q5s1vu1 author: Sharma, Virender K. title: Environmental chemistry is most relevant to study coronavirus pandemics date: 2020-05-20 words: 1326.0 sentences: 85.0 pages: flesch: 42.0 cache: ./cache/cord-257008-7q5s1vu1.txt txt: ./txt/cord-257008-7q5s1vu1.txt summary: In the environment, SARS-CoV-2 may survive in the air, on the surfaces, in water and wastewater (Qu et al. Systematically designed experiments will help us gain insight into the virus survival on various surfaces, thus minimizing the exposure of the novel coronavirus to the humans. During wastewater treatment, oxidants and disinfectants can inactivate enveloped viruses (Manoli et al. Research on enveloped-virus transmission and on the treatment of wastewater must include a wide range of enveloped viruses. The recommendation of using oxidants and disinfectants to inactivate SARS-CoV-2 must be experimentally based, which includes testing dose demand and contact time under the environmental conditions at which the virus would be presented. Overall, research in environmental chemistry is disclosing unique knowledge that may help to understand the behavior of viruses and other microbial pathogens in the environment. An imperative need for research on the role of environmental factors in transmission of novel coronavirus (COVID-19) abstract: nan url: https://doi.org/10.1007/s10311-020-01017-6 doi: 10.1007/s10311-020-01017-6 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-021966-5m21bsrw author: Shaw, Alan R. title: Vaccines date: 2009-05-15 words: 21170.0 sentences: 897.0 pages: flesch: 33.0 cache: ./cache/cord-021966-5m21bsrw.txt txt: ./txt/cord-021966-5m21bsrw.txt summary: Because a number of proteins produced in isolation by recombinant methods have been observed to elicit lower immune responses than do natural infections or live attenuated vaccines, the development and use of adjuvants to optimize recombinant vaccine immunogenicity represent an important parallel area for future exploration. Modern molecular biology and biochemistry have provided numerous options for vaccine immunogen presentation, including recombinant proteins (and recombinant virus-like particles (VLPs)), synthetic proteins, protein-polysaccharide conjugates, and gene delivery systems (recombinant viral vectors, or DNA vaccines) >> Is the antigen of interest sufficiently immunogenic on its own, or is augmentation of the desired immune response by conjugation to a specific carrier or addition of an adjuvant necessary to elicit a sufficient and sufficiently durable immune response in individuals in the target population for vaccination? abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152278/ doi: 10.1016/b978-0-323-04404-2.10092-2 id: cord-277641-nb1p1akx author: Shaw, D. M. title: Invisible Enemies: Coronavirus and Other Hidden Threats date: 2020-08-25 words: 2734.0 sentences: 117.0 pages: flesch: 62.0 cache: ./cache/cord-277641-nb1p1akx.txt txt: ./txt/cord-277641-nb1p1akx.txt summary: Fourth, I go on to explore the underlying structural weaknesses and disparities in society that have been exposed by the virus but previously remained unconsidered for so long that they too have become camouflaged, even if their effects are all too apparent; like the virus, neoliberal capitalism is an invisible enemy that has made prisoners of us all. Only by rendering the rest of humanity morally visible to ourselves can we overcome capitalism and stop treating other people as invisible enemies. Socio-economic inequalities existed for centuries before coronavirus came along, but the crisis exposes the invisible enemy that underlies all our lives. The essential flaw of capitalism is that it forces us to treat other people as invisible enemies against whom we are always competing, day in, day out, in a battle to the death. But despite the necessity of physical distancing, coronavirus has reduced our moral distance from the people we share our planet with, revealing them to be not invisible enemies but friends in need. abstract: To say that coronavirus is highly visible is a massive understatement in terms of its omnipresence in our lives and media coverage concerning it, yet also clearly untrue in terms of the virus itself. COVID-19 is our invisible enemy, changing our lives radically without ever revealing itself directly. In this paper I explore its invisibility and how it relates to and exposes other invisible enemies we are and have been fighting, in many cases without even realizing. First, I analyse the virus itself and how its stealthy nature has transformed our lives. Second, I describe how the invisible epidemic of social media sharing of fake news about the virus worsens the situation further. Third, I explore how the virus has revealed to us what really matters in our lives and has forced us to re-evaluate our priorities. Fourth, I go on to explore the underlying structural weaknesses and disparities in society that have been exposed by the virus but previously remained unconsidered for so long that they too have become camouflaged, even if their effects are all too apparent; like the virus, neoliberal capitalism is an invisible enemy that has made prisoners of us all. I conclude by suggesting that the coronavirus pandemic represents a hidden opportunity to overcome perhaps the biggest invisible enemy of all: the moral distance that separates us from others. Only by rendering the rest of humanity morally visible to ourselves can we overcome capitalism and stop treating other people as invisible enemies. url: https://doi.org/10.1007/s11673-020-10015-w doi: 10.1007/s11673-020-10015-w id: cord-003880-uuuzfyjm author: Shen, Meng-xin title: Antiviral Properties of R. tanguticum Nanoparticles on Herpes Simplex Virus Type I In Vitro and In Vivo date: 2019-09-04 words: 6674.0 sentences: 346.0 pages: flesch: 49.0 cache: ./cache/cord-003880-uuuzfyjm.txt txt: ./txt/cord-003880-uuuzfyjm.txt summary: We first conducted plaque reduction assays using HEp-2 cells to test the capacity of these nanoparticles to inactivate the HSV-1 virions and block the viral attachment and entry into cells, following the evaluation of inhibitory effect on viral replication using real-time quantitative PCR, Western blot, and immunofluorescence methods. tanguticum nanoparticles were added to HEp-2 cell monolayers at indicated time periods after HSV-1 infection (MOI = 0.01). tanguticum nanoparticles could suppress HSV-1 viral plaque formation in a dose-dependent manner ( Figure 3B ) and with the increase of drug concentrations, a noted increased antiviral activity was observed. Our previous study showed that the ethanol extracts of Rheum tanguticum, emodin inhibit the herpes simplex virus in vitro and in vivo, which the most effective dose orally administered to mice was 6.7 g/kg/day (Xiong et al., 2011) . abstract: Herpes simplex virus type 1 (HSV-1), an enveloped DNA virus, plays a key role in varieties of diseases including recurrent cold sores, keratoconjunctivitis, genital herpes and encephalitis in humans. Great efforts have been made in developing more effective and less side-effects anti-herpes simplex virus agents, including traditional Chinese herbal medicines. In the present study, we evaluated the antiviral efficacy of Rheum tanguticum nanoparticles against HSV-1 in vitro and in vivo. R. tanguticum nanoparticles could inactivate the HSV-1 virions and block the viral attachment and entry into cells. Time-of-addition assay indicated that R. tanguticum nanoparticles could interfere with the entire phase of viral replication. Besides, R. tanguticum nanoparticles showed the ability to inhibit the mRNA expression of HSV-1 immediate early gene ICP4 and early gene ICP8 as well as the expression of viral protein ICP4 and ICP8. Moreover, R. tanguticum nanoparticles have been proved to protect mice against HSV-1 induced lethality by decreasing the viral load and alleviated pathological changes in brain tissues. In conclusion, we demonstrated that R. tanguticum nanoparticles could inhibit HSV-1 infection through multiple mechanisms. These results suggest that R. tanguticum nanoparticles may have novel roles in the treatment of HSV-1 infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6737004/ doi: 10.3389/fphar.2019.00959 id: cord-009383-ozx5u0t3 author: Sheppard, Michael title: Viral Vectors for Veterinary Vaccines date: 2007-09-28 words: 4166.0 sentences: 203.0 pages: flesch: 43.0 cache: ./cache/cord-009383-ozx5u0t3.txt txt: ./txt/cord-009383-ozx5u0t3.txt summary: Second, genes from pathogens that encode proteins that will induce an appropriate protective immune response and can be stably integrated into the vector''s genome and expressed need to be identified. The vector only expresses the antigens from the pathogen that are required to elicit a protective immune response and therefore reduces or eliminates the chance of disease by being exposed to the whole pathogen as with a killed or modified live vaccine. One of the main disadvantages of using viral vectors for vaccine delivery is that like subunit vaccines each vector can only deliver one or a relatively small number of foreign antigens to the host animal and therefore rely on those being able to elicit a completely protective immune response. Construction of a defective adenovirus vector expressing the pseudorabies virus glycoprotein gp50 and its use as a live vaccine Expression in recombinant vaccinia virus of the equine herpesvirus 1 gene encoding glycoprotein 13 and protection of immunized animals abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149319/ doi: 10.1016/s0065-3519(99)80014-7 id: cord-302614-siyyve9e author: Shigeta, Shiro title: Anti-RNA virus activity of polyoxometalates date: 2006-05-24 words: 3511.0 sentences: 165.0 pages: flesch: 52.0 cache: ./cache/cord-302614-siyyve9e.txt txt: ./txt/cord-302614-siyyve9e.txt summary: Among these, HS-054 exhibited broad spectrum anti-myxovirus activity and its selectivity indices (SI) for FluV-A, RSV-A, MLSV and PfluV-2 were 333, 31, 167, and 111, respectively, which exceeded those of ribavirin for each virus. We examined anti-FluV A activity with several different ratio combination of PM-523 and ribavirin in vitro and compared this with the individual respective compounds in terms of the effective dose by several parameters of inhibition. We examined seven titanium or vanadium substituted polyoxotungstates (all have Keggin or Keggin All of the compounds exhibited broad spectrum anti-RNA virus activity except that PM-43, PM-518 and PM-523 did not have antiviral activities against PfluV 2, CDV and DFV, respectively. Although, as yet there are no reports of POMs in clinical use, most of the in vitro and some of the in vivo experiments have shown these compounds to be potent and broad spectrum in terms of their antiviral activities against acute respiratory disease viruses. abstract: The anti-RNA virus activity of polyoxometalates (POM) is reviewed, with a special emphasis on the anti-respiratory virus activities. There are many causative agents of acute viral respiratory infections; and it is rather difficult to identify the relevant agent in a given case by rapid clinical means. During acute progress of infection before the definitive diagnosis is obtained physicians need to prescribe certain broad spectrum anti-viral drugs. A titanium containing polyoxotungstate, PM-523 exhibited potent anti-influenza virus (FluV) A and anti-respiratory syncytial virus (RSV) activities in vitro. Therapeutic effect of FluV A infected mice with aerosol inhalation of PM-523 was proven. A vanadium substituted polyoxotungstate, PM-1001 has antiviral activity against FluV A, RSV, parainfluenza virus (PfluV) type 2, Dengue fiver virus, HIV-1 and SARS coronavirus in vitro. Thus, POMs have been proven to be broad spectrum and non-toxic anti-RNA virus agents in both in vitro and in vivo experiments and are promising candidates for first-line therapeutics in acute respiratory diseases. url: https://www.sciencedirect.com/science/article/pii/S0753332206000643 doi: 10.1016/j.biopha.2006.03.009 id: cord-272066-f6q6q3io author: Shim, Byoung-Shik title: Sublingual Delivery of Vaccines for the Induction of Mucosal Immunity date: 2013-06-30 words: 2763.0 sentences: 114.0 pages: flesch: 20.0 cache: ./cache/cord-272066-f6q6q3io.txt txt: ./txt/cord-272066-f6q6q3io.txt summary: These studies have successfully demonstrated the safety and efficacy of sublingual immunization in inducing antigen-specific systemic and mucosal immune responses and protection against pathogen challenges. Taken together, these studies recognized the sublingual mucosa as a potential route of vaccine delivery, which promotes the induction broadly distributed humoral and cell-mediated immune response in systemic lymphoid tissues as well as various mucosal compartments, to offer protection against pathogens that possess tropism for mucosal epithelia. In one study, a recombinant influenza virus M2 protein-based subunit vaccine containing three tandem copies of the M2e (3M2eC) was expressed in Escherichia coli, and the protective efficacy of parenteral and sublingual immunizations was compared (7) . Sublingual sHA1 immunization induced neutralizing antibody responses in the serum and in the respiratory mucosa and provided complete protection against a lethal challenge with pandemic H1N1 influenza A/CA/04/09 virus. In this report, sublingual administration of rADV-S in mice induced SARS virus-specific neutralizing antibody response in the serum and secretory IgA response in the respiratory mucosa. abstract: The mucosal surfaces are constantly exposed to incoming pathogens which can cause infections that result in severe morbidity and/or mortality. Studies have reported that mucosal immunity is important for providing protection against these pathogens and that mucosal vaccination is effective in preventing local infections. For many years, the sublingual mucosa has been targeted to deliver immunotherapy to treat allergic hypersensitivities. However, the potential of vaccine delivery via sublingual mucosal has received little attention until recently. Recent studies exploring such potential have documented the safety and effectiveness of sublingual immunization, demonstrating the ability of sublingual immunization to induce both systemic and mucosal immune responses against a variety of antigens, including soluble proteins, inter particulate antigens, and live-attenuated viruses. This review will summarize the recent findings that address the promising potential of sublingual immunization in proving protection against various mucosal pathogens. url: https://doi.org/10.4110/in.2013.13.3.81 doi: 10.4110/in.2013.13.3.81 id: cord-001676-68y733y3 author: Shoemaker, Jason E. title: An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation date: 2015-06-05 words: 10356.0 sentences: 460.0 pages: flesch: 43.0 cache: ./cache/cord-001676-68y733y3.txt txt: ./txt/cord-001676-68y733y3.txt summary: After filtering transcripts for minimally confident variation (we required at least one time-matched, infected condition compared with mock-infected absolute fold change 2 and a false discovery rate [FDR]-adjusted P-value < 0.01), the log 2 of the normalized intensity of the retained transcripts (16, 063) for all 167 samples were then clustered by using the Weighted Gene Co-expression Network Analysis (WGCNA) algorithm [18] . Data corresponding to macrophage signatures in different cellular states are colored red (see S3 Table for Within the inflammation-associated modules (N1 and N2), the H5N1 virus induced the earliest gene expression changes and the highest peak expression levels, corroborating previous observations that H5N1 viruses are strong inducers of inflammatory and IFN response signaling in vivo [10, 24, 25] . We infected mice with 10 3 PFU of the H5N1 virus (a 100-fold reduced dose compared with that used in the experiments to fit the model), determined lung virus titers at the same time points used for the initial experiment (S3 Fig), and then evaluated the segmented linear model''s ability to predict cytokine-associated gene expression. abstract: Influenza viruses present major challenges to public health, evident by the 2009 influenza pandemic. Highly pathogenic influenza virus infections generally coincide with early, high levels of inflammatory cytokines that some studies have suggested may be regulated in a strain-dependent manner. However, a comprehensive characterization of the complex dynamics of the inflammatory response induced by virulent influenza strains is lacking. Here, we applied gene co-expression and nonlinear regression analysis to time-course, microarray data developed from influenza-infected mouse lung to create mathematical models of the host inflammatory response. We found that the dynamics of inflammation-associated gene expression are regulated by an ultrasensitive-like mechanism in which low levels of virus induce minimal gene expression but expression is strongly induced once a threshold virus titer is exceeded. Cytokine assays confirmed that the production of several key inflammatory cytokines, such as interleukin 6 and monocyte chemotactic protein 1, exhibit ultrasensitive behavior. A systematic exploration of the pathways regulating the inflammatory-associated gene response suggests that the molecular origins of this ultrasensitive response mechanism lie within the branch of the Toll-like receptor pathway that regulates STAT1 phosphorylation. This study provides the first evidence of an ultrasensitive mechanism regulating influenza virus-induced inflammation in whole lungs and provides insight into how different virus strains can induce distinct temporal inflammation response profiles. The approach developed here should facilitate the construction of gene regulatory models of other infectious diseases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457877/ doi: 10.1371/journal.ppat.1004856 id: cord-310870-w8wu8vno author: Shorten, Robert J. title: The risk of transmission of a viral haemorrhagic fever infection in a United Kingdom laboratory date: 2017-05-18 words: 1636.0 sentences: 97.0 pages: flesch: 45.0 cache: ./cache/cord-310870-w8wu8vno.txt txt: ./txt/cord-310870-w8wu8vno.txt summary: [9] [10] [11] [12] In addition, over 9,000 cases of Crimean Congo Haemorrhagic Fever (CCHF) were reported in Turkey between 2002 and 2014, with an estimated minimum 180,000 blood samples processed in routine laboratories with no additional precautions. Although it is reassuring that large numbers of samples from patients with CCHF infection have been processed safely in routine laboratories in Turkey, it should be noted that this bunyavirus is rarely transmitted person to person, so the parallels between this and other VHF viruses need to be carefully considered. Manufacturers must validate their decontamination method against appropriate surrogate model enveloped viruses. Viral inactivation validation studies have successfully used surrogate model viruses with properties similar to wildtype viruses to provide evidence for the safety of human blood plasma products for over a decade. Once assessed by appropriately designed viral inactivation validation studies on relevant surrogate model enveloped viruses, the decontamination process has been shown to be effective against all known and future emerging enveloped viruses, which includes Ebola, CCHF, Lassa fever, and Marburg virus. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/28545142/ doi: 10.1371/journal.pntd.0005358 id: cord-004841-wf0o3whi author: Sibalin, M. title: Herpesvirus strigis, a new avian herpesvirus: II. Biochemical and biophysical properties date: 1974 words: 1900.0 sentences: 154.0 pages: flesch: 57.0 cache: ./cache/cord-004841-wf0o3whi.txt txt: ./txt/cord-004841-wf0o3whi.txt summary: Tissue cultured virus proved sensitive to ether, chloroform, 0.5 per cent trypsin, and to pH levels of 4.0 or lower. Biological properties described in a foregoing paper sustained such grouping, and indicated that the agent was a new avian herpesvirus for which the nameherpesvirus strigis was proposed. According to Table 1 , both herpesviruses tested, i.e. HSIS and IBI~, got completely inactivated by ether as well as chloroform indicating that their virions were sensitive to lipid solvents. Other authors had observed similar core structures with some of their herpesviruses (12, 20) , and also fringes on the viral envelope (3, 12, 20) , of the size recorded here for herpesvirus strigis. Based on its biological properties described in our first paper (7), which allowed to differentiate it from other herpesviruses, we proposed tISIS as a new avian virus species to be named herpesvirus strigis. abstract: A virus (HSIS) originating from dead owls was successfully cultivated in chicken embryo fibroblasts. Its replication was inhibited by IUDR. Tissue cultured virus proved sensitive to ether, chloroform, 0.5 per cent trypsin, and to pH levels of 4.0 or lower. Infectivity was rapidly destroyed at 56° C. Negatively stained naked virions of 100 nm average diameter were seen, and enveloped virions with 160–250 nm size. The capsid was built up of hollow cyclindrical capsomeres, arranged in equilateral triangles, carrying 5 capsomeres along each edge. Cubical symmetry and icosahedron structure yielded a total number of 162 capsomeres. All these biochemical and biophysical data lead to classification of HSIS virus into the genus herpesvirus. Biological properties described in a foregoing paper sustained such grouping, and indicated that the agent was a new avian herpesvirus for which the nameherpesvirus strigis was proposed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087248/ doi: 10.1007/bf01251017 id: cord-010374-z9ygudv6 author: Siddell, S.G. title: Coronaviridae1 date: 2008-07-24 words: 1541.0 sentences: 111.0 pages: flesch: 51.0 cache: ./cache/cord-010374-z9ygudv6.txt txt: ./txt/cord-010374-z9ygudv6.txt summary: The main characteristics of the member viruses are: (i) Morphological: Enveloped pleomorphic particles typically 100 nm in diameter (range 60-220 nm), bearing about 20 nm long club-shaped surface projections, (ii) Structural: A single-stranded infectious molecule of genomic RNA of about (5-7) × 10(6) molecular weight. (iv) Antigenic: 3 major antigens, each corresponding to one class of virion protein, (v) Biological: Predominantly restricted to infection of natural vertebrate hosts by horizontal transmission via the fecal/oral route. Recently, there have been reports of virus-specific RNA poly merases in coronavirus-infected cells, but the components of the enzyme have not been iden tified. UV inactivation studies in dicate that coronavirus mRNAs are not pro duced by the processing of a larger RNA, although extensive sequence homologies have been detected at the 5'' ends of ail murine hepatitis virus-specific subgenomic RNAs. For murine hepatitis virus, the mRNA function of each of the subgenomic viral RNAs has been demonstrated in vitro, and the mRNAs encod ing each of the virion proteins, or its precur sors, have been identified ( fig. abstract: The family Coronavirtdae comprises a monogeneric group of 11 viruses which infect vertebrates. The main characteristics of the member viruses are: (i) Morphological: Enveloped pleomorphic particles typically 100 nm in diameter (range 60-220 nm), bearing about 20 nm long club-shaped surface projections, (ii) Structural: A single-stranded infectious molecule of genomic RNA of about (5-7) × 10(6) molecular weight. A phosphorylated nucleocapsid protein [mol.wt. (50-60) × 10(3)] complexed with the genome as a helical ribonucleoprotein; a surface (peplomer) protein, associated with one or two glycosylated polypeptides [mol.wt. (90-180) × 10(3)]; a transmembrane (matrix) protein, associated with one polypeptide which may be glycosylated to different degrees [mol.wt. (20-35) × 10(3)]. (iii) Replicative: Production in infected cells of multiple 3′ coterminal sub genomic mRNAs extending for different lengths in the 5′ direction. Virions bud intracytoplasmically. (iv) Antigenic: 3 major antigens, each corresponding to one class of virion protein, (v) Biological: Predominantly restricted to infection of natural vertebrate hosts by horizontal transmission via the fecal/oral route. Responsible mainly for respiratory and gastrointestinal disorders. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7182641/ doi: 10.1159/000149390 id: cord-282204-j1slaefb author: Silva, José V.J. title: A scoping review of Chikungunya virus infection: epidemiology, clinical characteristics, viral co-circulation complications, and control date: 2018-12-31 words: 8010.0 sentences: 464.0 pages: flesch: 43.0 cache: ./cache/cord-282204-j1slaefb.txt txt: ./txt/cord-282204-j1slaefb.txt summary: de; Oliveira, Renato A.S.; Durães-Carvalho, Ricardo; Lopes, Thaísa R.R.; Silva, Daisy E.A.; Gil, Laura H.V.G. title: A scoping review of Chikungunya virus infection: epidemiology, clinical characteristics, viral co-circulation complications, and control Laboratory tests for specific diagnosis of CHIKV infection are based on virus isolation, viral RNA detection and serology (Johnson et al., 2016) . Anti-CHIKV candidates that have been already tested in humans and/or animals include inactivated-, attenuated-, virus like particle-(VLP), DNA-and chimeric vaccines (Eckels et al., 1970; Levitt et al., 1986; Muthumani et al., 2008; Wang et al., 2008; Tiwari et al., 2009; Sharma et al., 2012 Akahata et al., 2010 Plante et al., 2011; Wang et al., 2011; Gorchakov et al., 2012; Brandler et al., 2013; Chang et al., 2014; García-Arriaza et al., 2014; Tretyakova et al., 2014; van den Doel et al., 2014; Erasmus et al., 2017) . abstract: Abstract Chikungunya fever is a mosquito-borne viral illness characterized by a sudden onset of fever associated with joint pains. It was first described in the 1950s during a Chikungunya virus (CHIKV) outbreak in southern Tanzania and has since (re-) emerged and spread to several other geographical areas, reaching large populations and causing massive epidemics. In recent years, CHIKV has gained considerable attention due to its quick spread to the Caribbean and then in the Americas, with many cases reported between 2014 and 2017. CHIKV has further garnered attention due to the clinical diagnostic difficulties when Zika (ZIKV) and dengue (DENV) viruses are simultaneously present. In this review, topical CHIKV-related issues, such as epidemiology and transmission, are examined. The different manifestations of infection (acute, chronic and atypical) are described and a particular focus is placed upon the diagnostic handling in the case of ZIKV and DENV co-circulating. Natural and synthetic compounds under evaluation for treatment of chikungunya disease, including drugs already licensed for other purposes, are also discussed. Finally, previous and current vaccine strategies, as well as the control of the CHIKV transmission through an integrated vector management, are reviewed in some detail. url: https://doi.org/10.1016/j.actatropica.2018.09.003 doi: 10.1016/j.actatropica.2018.09.003 id: cord-010273-0c56x9f5 author: Simmonds, Peter title: Virology of hepatitis C virus date: 2001-10-10 words: 7897.0 sentences: 337.0 pages: flesch: 41.0 cache: ./cache/cord-010273-0c56x9f5.txt txt: ./txt/cord-010273-0c56x9f5.txt summary: 1,2 The identification of HCV led to the development of diagnostic assays for infection, based either on detection of antibody to recombinant polypeptides expressed from cloned HCV sequences or direct detection of virus ribonucleic acid (RNA) sequences by polymerase chain reaction (PCR) using primers complimentary to the HCV genome. 6 ''13 Remarkably, a series of plant viruses that are structurally distinct from each of the mammalian virus groups, and with different genome organizations, have RNA-dependent RNA polymerase amino acid sequences that are perhaps more similar to those of HCV than are the flaviviruses. In contrast to the highly restricted sequence diversity of the 5''NCR and adjacent core region, the two putative envelope genes are highly divergent between different variants of HCV (Table III) 111-114 and show a three-to-four-times higher rate of sequence change with time in persistently infected patients, ll5 Because these proteins are likely to lie on the outside of the virus, they would be the principal targets of the humoral immune response to HCV elicited on infection. abstract: Hepatitis C virus (HCV) has been identified as the main causative agent of post-transfusion non-A, non-B hepatitis. Through recently developed diagnostic assays, routine serologic screening of blood donors has prevented most cases of post-transfusion hepatitis. The purpose of this paper is to comprehensively review current information regarding the virology of HCV. Recent findings on the genome organization, its relationship to other viruses, the replication of HCV ribonucleic acid, HCV translation, and HCV polyprotein expression and processing are discussed. Also reviewed are virus assembly and release, the variability of HCV and its classification into genotypes, the geographic distribution of HCV genotypes, and the biologic differences between HCV genotypes. The assays used in HCV genotyping are discussed in terms of reliability and consistency of results, and the molecular epidemiology of HCV infection is reviewed. These approaches to HCV epidemiology will prove valuable in documenting the spread of HCV in different risk groups, evaluating alternative (nonparenteral) routes of transmission, and in understanding more about the origins and evolution of HCV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173289/ doi: 10.1016/s0149-2918(96)80193-7 id: cord-283756-ycjzitlk author: Simons, Robin R. L. title: Potential for Introduction of Bat-Borne Zoonotic Viruses into the EU: A Review date: 2014-05-16 words: 14415.0 sentences: 605.0 pages: flesch: 53.0 cache: ./cache/cord-283756-ycjzitlk.txt txt: ./txt/cord-283756-ycjzitlk.txt summary: Bat-borne viruses can pose a serious threat to human health, with examples including Nipah virus (NiV) in Bangladesh and Malaysia, and Marburg virus (MARV) in Africa. In assessing the risks of introduction of these bat-borne zoonotic viruses to the EU, it is important to consider the location and range of bat species known to be susceptible to infection, together with the virus prevalence, seasonality of viral pulses, duration of infection and titre of virus in different bat tissues. Bats are known to have varying degrees of contact with domestic animals and commercial food crops [20, 21] , in particular contact of Pteropus giganteus bats with date palm sap producing trees in Bangladesh is considered a risk factor for human NiV infection [22] . It can be seen that while recent human infections of both NiV and MARV appear to be limited in geographical range (the red areas in Figure 2 ), there are a number of countries where bats have been identified as having the virus, but no human infection has been reported. abstract: Bat-borne viruses can pose a serious threat to human health, with examples including Nipah virus (NiV) in Bangladesh and Malaysia, and Marburg virus (MARV) in Africa. To date, significant human outbreaks of such viruses have not been reported in the European Union (EU). However, EU countries have strong historical links with many of the countries where NiV and MARV are present and a corresponding high volume of commercial trade and human travel, which poses a potential risk of introduction of these viruses into the EU. In assessing the risks of introduction of these bat-borne zoonotic viruses to the EU, it is important to consider the location and range of bat species known to be susceptible to infection, together with the virus prevalence, seasonality of viral pulses, duration of infection and titre of virus in different bat tissues. In this paper, we review the current scientific knowledge of all these factors, in relation to the introduction of NiV and MARV into the EU. url: https://doi.org/10.3390/v6052084 doi: 10.3390/v6052084 id: cord-285148-bch7814v author: Singanayagam, Aran title: Viruses exacerbating chronic pulmonary disease: the role of immune modulation date: 2012-03-15 words: 7923.0 sentences: 393.0 pages: flesch: 35.0 cache: ./cache/cord-285148-bch7814v.txt txt: ./txt/cord-285148-bch7814v.txt summary: However in vitro RV infection of epithelial cells from COPD patients resulted in higher virus load and increased inflammatory mediators, but no differences in interferon production compared to cells from control subjects [87] . List of abbreviations ATF: activating transcription factor; BAL: bronchoalveolar lavage; CF: cystic fibrosis; CFTR: cystic fibrosis transmembrane regulator; COPD: chronic obstructive pulmonary disease; ENA-78: epithelial-derived neutrophilactivating peptide 78; ICAM-1: intercellular adhesion molecule; IFN-α: interferon-alpha; IFN-β: interferon-beta; IFN-λ: interferon-lambda; IFN-γ: interferon-gamma; IL: interleukin; IP-10: IFN-γ-induced protein-10; IRF: interferon regulatory factor; ISG: interferon stimulated genes; MDA-5: melanoma differentiation-associated protein-5; NF-κB: nuclear factor-kappa B; NO: nitric oxide; NOS2: nitric oxide synthase 2; PCR: polymerase chain reaction; PEF: peak expiratory flow; PIV: parainfluenza virus; RANTES: regulated on activation: normal T-cell expressed and secreted; RIG-I: retinoic acid inducible gene I; RSV: respiratory syncytial virus; RV: rhinovirus; SLPI: secretory leukoprotease inhibitor; SOCS: suppressor of cytokine signaling family; Th1/2: T helper 1/2; TLR: toll-like receptors; TNF-α: tumor necrosis factor-alpha -1. abstract: Chronic pulmonary diseases are a major cause of morbidity and mortality and their impact is expected to increase in the future. Respiratory viruses are the most common cause of acute respiratory infections and it is increasingly recognized that respiratory viruses are a major cause of acute exacerbations of chronic pulmonary diseases such as asthma, chronic obstructive pulmonary disease and cystic fibrosis. There is now increasing evidence that the host response to virus infection is dysregulated in these diseases and a better understanding of the mechanisms of abnormal immune responses has the potential to lead to the development of new therapies for virus-induced exacerbations. The aim of this article is to review the current knowledge regarding the role of viruses and immune modulation in chronic pulmonary diseases and discuss avenues for future research and therapeutic implications. url: https://doi.org/10.1186/1741-7015-10-27 doi: 10.1186/1741-7015-10-27 id: cord-263245-2qub96mz author: Singh, D. title: Alcohol-based hand sanitisers as first line of defence against SARS-CoV-2: a review of biology, chemistry and formulations date: 2020-09-29 words: 4779.0 sentences: 234.0 pages: flesch: 41.0 cache: ./cache/cord-263245-2qub96mz.txt txt: ./txt/cord-263245-2qub96mz.txt summary: This review summarises the studies on alcohol-based hand sanitisers and their disinfectant activity against SARS-CoV-2 and related viruses. The literature shows that the type and concentration of alcohol, formulation and nature of product, presence of excipients, applied volume, contact time and viral contamination load are critical factors that determine the effectiveness of hand sanitisers. When soap and water are not available, the Food and Drug Administration (FDA) recommends sanitising of non-visibly soiled hands with an alcoholbased agent containing 80% v/v ethanol or 75% v/v isopropanol [4] . This review assesses available information on the composition, formulation and effectiveness of alcohol-based hand disinfection products with specific reference to their activity against SARS-CoV-2. Alcohol-based hand rubs in the form of foam, rinse and gel did not differ significantly in trials of antimicrobial activity but the application volume and drying time had a profound effect on their efficacy [54] . abstract: The pandemic due to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has emerged as a serious global public health issue. Since the start of the outbreak, the importance of hand-hygiene and respiratory protection to prevent the spread of the virus has been the prime focus for infection control. Health regulatory organisations have produced guidelines for the formulation of hand sanitisers to the manufacturing industries. This review summarises the studies on alcohol-based hand sanitisers and their disinfectant activity against SARS-CoV-2 and related viruses. The literature shows that the type and concentration of alcohol, formulation and nature of product, presence of excipients, applied volume, contact time and viral contamination load are critical factors that determine the effectiveness of hand sanitisers. url: https://doi.org/10.1017/s0950268820002319 doi: 10.1017/s0950268820002319 id: cord-349249-jwvz1ux2 author: Singh, Gagandeep title: A Minimally Replicative Vaccine Protects Vaccinated Piglets Against Challenge With the Porcine Epidemic Diarrhea Virus date: 2019-10-22 words: 6553.0 sentences: 314.0 pages: flesch: 46.0 cache: ./cache/cord-349249-jwvz1ux2.txt txt: ./txt/cord-349249-jwvz1ux2.txt summary: To combine the safety and efficacy advantages of inactivated and attenuated PEDV vaccines, respectively, in this study, we tested the hypothesis that subjecting PEDV virions to heat treatment at 44°C for 10 min to reversibly unfold structural proteins, followed by exposure to RNAse to fragment the genome, would result in a vaccine preparation with intact viral structure/antigenicity but highly diminished replicative abilities. to that of the spike protein-specific Abs. Strong virus neutralizing Ab responses, were detected in animals vaccinated with the heat and RNAse treated virions but not in the pigs which received the irradiated viral vaccine. Although the heat and RNAse treated virus culture was amplified after 3 passages in cell culture (Figure 2) , the absence its detection by RT-qPCR (Figure 4) , or immunohistochemistry (Table 1 and Figure 5 ) and the lack of strong Ab responses to the non-structural NP (Figure 3) , in vaccinated pigs prior to challenge indicates that active vaccine viral replication was absent in the host or was undetectable by the techniques used. abstract: Porcine epidemic diarrhea virus (PEDV), is an economically important enteric coronavirus, with over a 90% mortality rate in neonatal piglets. The virus emerged in the US in 2013, resulting in severe production losses. Effective vaccine development against PEDV is a challenge. Inactivated vaccines are of questionable efficacy. Attenuated vaccines, while more effective, require a relatively long lead development time, are associated with safety concerns and are also unable to prevent new field outbreaks. To combine the safety and efficacy advantages of inactivated and attenuated PEDV vaccines, respectively, in this study, we tested the hypothesis that subjecting PEDV virions to heat treatment at 44°C for 10 min to reversibly unfold structural proteins, followed by exposure to RNAse to fragment the genome, would result in a vaccine preparation with intact viral structure/antigenicity but highly diminished replicative abilities. We expected the vaccine to be both safe and effective in a piglet challenge model. Following the heat and RNAse treatment, PEDV virions had an intact electron microscopic ultrastructure and were amplified only in the 3rd passage in Vero cells, indicating that diminished replication was achieved in vitro. Strong PEDV spike-protein specific and virus neutralizing antibody responses were elicited in vaccinated piglets. Upon challenge, all vaccinated pigs were protected against fecal viral shedding and intestinal pathology, while the unvaccinated controls were not. The vaccine virus was not detected in the fecal matter of vaccinated pigs prior to challenge; nor did they develop intestinal lesions. Thus, the described approach has significant promise in improving current approaches for PEDV immunization. url: https://doi.org/10.3389/fvets.2019.00347 doi: 10.3389/fvets.2019.00347 id: cord-275013-na6319rg author: Singh, Indra P. title: Innate defences against viraemia date: 2000-11-23 words: 3294.0 sentences: 168.0 pages: flesch: 42.0 cache: ./cache/cord-275013-na6319rg.txt txt: ./txt/cord-275013-na6319rg.txt summary: Recently, two naturally occurring nonspecific broad‐spectrum antiviral agents, University of Texas Inhibitor β (UTIβ) glycoprotein and high density lipoprotein, have been described in human serum. In this review, we emphasise the properties of broadly active antiviral molecules in human serum and explore the possibility that they can be important as natural defence mechanisms. Based on this protection and other correlations, the authors suggested a natural defensive role for this broadly antiviral inhibitor that is present widely and in high concentration in tissues and extracellular¯uid of human nervous system [25] . The mechanisms of action of these inhibitors are competitive inhibition of virus attachment to cells and neutralisation of viral infectivity by a mechanism unlike classical antibody because complement is not needed for their activity. These observations point to a relationship in vivo between the level of serum inhibitors and in¯uenza virus multiplication and thus support the notion that the narrowly active, nonspeci®c viral inhibitors can be a factor in innate resistance to speci®c viruses. abstract: Human blood plasma has been reported to possess nonspecific antiviral activity. This activity is due to several preexisting naturally occurring molecules that are either active against individual members or a family of viruses. These molecules, however, have not been adequately studied to reveal their molecular structures and mechanisms of action presumably because of their low and nonspecific antiviral action. Therefore, their possible role against viraemia remains unknown. Recently, two naturally occurring nonspecific broad‐spectrum antiviral agents, University of Texas Inhibitor β (UTIβ) glycoprotein and high density lipoprotein, have been described in human serum. They are active against DNA and RNA viruses and one of them, UTIβ, possesses significant antiviral activity of 40 units/mL. Since preexisting antiviral molecules in serum appear to be the only defence mechanisms available at the onset of viral infection they may have protective significance against viraemia. In view of this potential, we have undertaken to review the properties of these innate viral inhibitory molecules. Copyright © 2000 John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/11114078/ doi: 10.1002/1099-1654(200011/12)10:6<395::aid-rmv298>3.0.co;2-v id: cord-026340-2nf97zvc author: Singh, Ranjana title: Chloroquine: A Potential Drug in the COVID-19 Scenario date: 2020-06-07 words: 7542.0 sentences: 412.0 pages: flesch: 55.0 cache: ./cache/cord-026340-2nf97zvc.txt txt: ./txt/cord-026340-2nf97zvc.txt summary: In this review article, we have systematically searched for details of COVID-19 pandemic till May 2020 and assembled few data pertaining to (i) Corona viruses; (ii) SARS-CoV2, the virus that causes COVID-19'' and (iii) How chloroquine and hydroxychloroquine mediates anti-viral effect in both prophylactic and therapeutic setting. The Corona Study Group (CSG) of the International Committee on Taxonomy of Viruses (ICTV) after assessing the etiological agent named it SARS-CoV2 (Severe Acute Respiratory Syndrome Corona Virus2) and the disease outbreak as COVID-19 (Corona Virus Disease-Year of Identification). During COVID-19, SARS-CoV2 S-protein binds to host cell''s receptor ACE2 (Belouzard et al. As for the case of SARS-CoV, it was shown that the binding specificity of virus to host cell was due to 3 prime amino acid residues in S1 protein at positions 360, 479, and 487. abstract: Today, the whole world is fighting a public health emergency called ‘COVID-19’ caused by a new infectious virus called SARS-CoV2. Any person can catch COVID-19 from an infected person via aerosol droplets when the person coughs, sneezes, or speaks. To limit such a transmission, World Health Organization (WHO) has recommended people to wear masks and physically distance themselves by staying at least 1 m (3 feet) away from others. As aerosol droplets (by cough or sneeze) land on objects and surfaces around the person such as tables, doorknobs and handrails, and remain active on these surfaces for hours to days, people are advised to use soaps for at least 20 s. and alcohol-based sanitizers as well. As the public made efforts, clinicians and researchers investigated and found that drugs which were initially used to treat other diseases may work as a treatment option for COVID-19. One of those drugs was Chloroquine and its related derivative called hydroxychloroquine. In this review article, we have systematically searched for details of COVID-19 pandemic till May 2020 and assembled few data pertaining to (i) Corona viruses; (ii) SARS-CoV2, the virus that causes COVID-19’ and (iii) How chloroquine and hydroxychloroquine mediates anti-viral effect in both prophylactic and therapeutic setting. These data have been acquired mostly from PubMed and websites of WHO and Indian Council for Medical Research (ICMR). We did a systematic search and found that the properties of chloroquine are very much essential for the COVID-19 scenario. We also bring to you some evidence that the anti-lysosomal activity of chloroquine may be increased by botanicals like betulinic acid. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7275976/ doi: 10.1007/s41403-020-00114-w id: cord-336554-n8n5ii5k author: Singh, Thakur Uttam title: Drug repurposing approach to fight COVID-19 date: 2020-09-05 words: 13032.0 sentences: 690.0 pages: flesch: 44.0 cache: ./cache/cord-336554-n8n5ii5k.txt txt: ./txt/cord-336554-n8n5ii5k.txt summary: Number of drugs such as remdesivir, favipiravir, ribavirin, lopinavir, ritonavir, darunavir, arbidol, chloroquine, hydroxychloroquine, tocilizumab and interferons have shown inhibitory effects against the SARS-CoV2 in-vitro as well as in clinical conditions. Outbreaks of novel emerging infections such as coronavirus disease 2019 (COVID19) have unique challenges in front of the health professionals to select appropriate therapeutics/pharmacological treatments in the clinical setup with very little time available for the new drug discovery [3] . Currently, with the lack of effective agents against SARS-CoV2 as well as public-health emergency, WHO has identified some therapies which doctors and researchers believe are the most promising, such as a combination of two HIV drugs (lopinavir and ritonavir), anti-malarial drugs (chloroquine and hydroxychloroquine), and an experimental antiviral compound remdesivir. Ribavirin at a dose rate of 500 mg 2-3 times/day in combination with other drugs such as lopinavir/ritonavir or interferon (IFN)-α through intravenous route for not more than 10 days made the SARS-CoV2 infected patients more resistant to respiratory distress syndrome as well as death [41] . abstract: Currently, there are no treatment options available for the deadly contagious disease, coronavirus disease 2019 (COVID-19). Drug repurposing is a process of identifying new uses for approved or investigational drugs and it is considered as a very effective strategy for drug discovery as it involves less time and cost to find a therapeutic agent in comparison to the de novo drug discovery process. The present review will focus on the repurposing efficacy of the currently used drugs against COVID-19 and their mechanisms of action, pharmacokinetics, dosing, safety, and their future perspective. Relevant articles with experimental studies conducted in-silico, in-vitro, in-vivo, clinical trials in humans, case reports, and news archives were selected for the review. Number of drugs such as remdesivir, favipiravir, ribavirin, lopinavir, ritonavir, darunavir, arbidol, chloroquine, hydroxychloroquine, tocilizumab and interferons have shown inhibitory effects against the SARS-CoV2 in-vitro as well as in clinical conditions. These drugs either act through virus-related targets such as RNA genome, polypeptide packing and uptake pathways or target host-related pathways involving angiotensin-converting enzyme-2 (ACE2) receptors and inflammatory pathways. Using the basic knowledge of viral pathogenesis and pharmacodynamics of drugs as well as using computational tools, many drugs are currently in pipeline to be repurposed. In the current scenario, repositioning of the drugs could be considered the new avenue for the treatment of COVID-19. url: https://doi.org/10.1007/s43440-020-00155-6 doi: 10.1007/s43440-020-00155-6 id: cord-280427-smqc23vr author: Singla, Rubal title: Human animal interface of SARS-CoV-2 (COVID-19) transmission: a critical appraisal of scientific evidence date: 2020-09-14 words: 7194.0 sentences: 381.0 pages: flesch: 58.0 cache: ./cache/cord-280427-smqc23vr.txt txt: ./txt/cord-280427-smqc23vr.txt summary: The various evidence from the past clearly suggest that the evolution of the virus in both reservoir and intermediate animal hosts needs to be explored to better evaluate the emergence of SARS-CoV-2 in humans. The qPCR and virus titration test conducted on the various isolated organs of the ferrets on day 4 post inoculation detected infectious virus in the nasal turbinate, soft palate and tonsils of ferrets indicating the possible replication of the virus in the upper respiratory tract of the ferrets while no infection was found in other organs such as trachea, lung, heart, spleen, kidneys, pancreas, small intestine, brain and liver of the ferrets (Kim et al. This study results stipulate ferret to have high susceptibility for the SARS-CoV-2 and this infectious virus sheds by multiple routes of body discharge specimens such as urine and faeces of the infected ferrets which serve as a potential source of viral transmission to close contact. abstract: Coronaviruses are a large family of viruses that are known to infect both humans and animals. However, the evidence of inter-transmission of coronavirus between humans and companion animals is still a debatable issue. There is substantial evidence that the virus outbreak is fueled by zoonotic transmission because this new virus belongs to the same family of viruses as SARS-CoV associated with civet cats, and MERS-CoV associated with dromedary camels. While the whole world is investigating the possibility about the transmission of this virus, the transmission among humans is established, but the interface between humans and animals is not much evident. Not only are the lives of human beings at risk, but there is an equal potential threat to the animal world. With multiple reports claiming about much possibility of transmission of COVID-19 from humans to animals, there has been a significant increase in the number of pets being abandoned by their owners. Additionally, the risk of reverse transmission of COVID-19 virus from companion pets like cats and dogs at home is yet another area of concern. The present article highlights different evidence of human-animal interface and necessitates the precautionary measures required to combat with the consequences of this interface. The Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) have suggested various ways to promote awareness and corroborate practices for helping people as well as animals to stay secure and healthy. url: https://www.ncbi.nlm.nih.gov/pubmed/32926266/ doi: 10.1007/s11259-020-09781-0 id: cord-010248-ln800g5z author: Sissons, J.G. Patrick title: Antibody-Mediated Destruction of Virus-Infected Cells date: 2008-02-29 words: 14994.0 sentences: 687.0 pages: flesch: 44.0 cache: ./cache/cord-010248-ln800g5z.txt txt: ./txt/cord-010248-ln800g5z.txt summary: When lz5I-1abeled IgG antibody was bound to the surface of measles virus-infected cells at the start of the culture period, under the conditions described above for antigenic modulation, about 40% of the radioactivity was still cell associated at 12 hours and nearly all was protein bound Perrin and Oldstone, 1977) . Lysis by human serum of cells infected with HSV types 1 and 2, influenza A, parainfluenza 1, 2, 3, and 4, mumps, and measles viruses was dependent on the presence in serum of IgG antibody specific for the relevant virus and of complement (reviewed by Oldstone and Lampert, 1979) . The use of this system, composed of 11 highly purified complement proteins, provided conclusive evidence that the known proteins of the alternative and membrane attack pathways with IgG antibody are sufficient for lysis of the measles virus-infected cell, without other serum factors. It is apparent that considerably more surface-bound IgG is required to induce complement-dependent lysis of virus-infected cells than is required for antigenic modulation or antibody-dependent cell-mediated cytotoxicity. abstract: This chapter describes the effect of antibody on virus-infected cells with special reference to the human system. The destruction by antibody of the infected cells through the mediation of complement is described in detail based in considerable part on the contributions of the authors. Activation of the alternative pathway by the various infected cells is of special interest. The interesting effect of the antibody-dependent cell-mediated cytotoxicity (ADCC) system involving viral antigens in cell killing is also presented. Multiple additional topics are also covered, such as the effect of antibody on the expression of viral proteins both on the surface of the cell and intracellularly. Serum antibody, produced in response to virus infections, is of major importance in preventing the spread of infection by virtue of neutralizing free virus in extracellular fluids. Virus neutralization by antibody is enhanced by complement. Antibody binding to the surface of virus-infected cells can affect virus production and release in the absence of an effector system. Immunoglobulin (IgG) antibody can mediate the destruction of virus-infected cells in conjunction with complement or cytotoxic lymphocytes. In addition, at a conceptual level there is evidence to suggest that antibody may enhance and confer specificity on basic nonspecific humoral and cell-mediated defense mechanisms. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173112/ doi: 10.1016/s0065-2776(08)60045-0 id: cord-258333-jmk8hdk2 author: Sivier, V title: Place des viroses respiratoires dans les hyperthermies de sujets âgés hospitalisés au cours d’une saison hivernale date: 2001-12-10 words: 2657.0 sentences: 232.0 pages: flesch: 59.0 cache: ./cache/cord-258333-jmk8hdk2.txt txt: ./txt/cord-258333-jmk8hdk2.txt summary: Sur les 129 malades ayant présenté une hyperthermie, 12 décès ont été observés, soit un taux de mortalité de 9,3 % : un décès dans le groupe « virose respiratoire » par surinfection bactérienne pulmonaire, sept décès dans le groupe « infection respiratoire non virale » (un choc septique, cinq décompensations respiratoires aiguës, une décompensation cardiaque aiguë) et quatre décès dans le groupe « autre » (deux cancers en phase terminale, un accident vasculaire cérébral et une cause indéterminée). L''épidémie nosocomiale de virus respiratoire syncytial est survenue dans un service de long séjour avec des locaux communs et exigus, chez des patients porteurs de multiples maladies et souvent déments. En conclusion, les infections respiratoires, qu''elles soient virales, bactériennes ou non documentées, apparaissent comme la principale cause d''hyperthermie chez le sujet âgé institutionnalisé pendant la saison hivernale et sont à l''origine de nombreuses complications, voire de décès. abstract: Purpose. – In the geriatric units of the University Hospital of Saint-Etienne, 129 cases of fever (38° C or more) were recorded prospectively during the 1995–1996 winter period in a population of 503 hospitalised patients (25.6%), and were investigated for the detection of a viral aetiology. Methods. – In febrile patients, a standard form was used to record clinical and biological parameters, including the results of investigations for respiratory viruses from a nasal swab and dual serum specimens. Results. – A clinical or radiological respiratory infection was found in 69 cases (53.5% of all cases of fever), including 14 respiratory syncytial virus (RSV) infections. In comparison to nonviral respiratory infections, the RSV infections were characterised by the prevalence of anorexia (57% vs 20%, P < 0,05) and rhinorrhea (64% vs 5%, P < 0,01). No influenza infection was recorded despite the concomitant circulation of influenza virus in the community. A nosocomial outbreak of RSV infection (nine cases, attack rate of 18.7%) was identified in a long-stay care unit. Conclusion. – This study illustrates the high prevalence (10.9%) of RSV infections in elderly patients with fever during this season and the importance of hygienic measures to control the spread of nosocomial outbreaks. url: https://api.elsevier.com/content/article/pii/S0248866301004891 doi: 10.1016/s0248-8663(01)00489-1 id: cord-011917-6u0t4hy8 author: Skarlupka, Amanda L. title: Immune Imprinting in the Influenza Ferret Model date: 2020-04-08 words: 7904.0 sentences: 456.0 pages: flesch: 37.0 cache: ./cache/cord-011917-6u0t4hy8.txt txt: ./txt/cord-011917-6u0t4hy8.txt summary: Therefore, the use of naïve ferret sera for vaccine strain selection is potentially misrepresentative of the pre-immune human population that receives each season''s influenza virus vaccines, contributing to the observed VE. Unique to sequentially infected ferrets, the elicited antibody profile was broader and interacted with pandemic A(H1N1) HA compared to the single pre-immunity groups as measured with HA-specific ELISA binding. In contrast to previous reports that pre-immunity induced protection does not wane [68] , the boosts in anti-HA stalk antibodies and the cross-reactivity induced from sequential infection with antigenically distinct seasonal A(H1N1) declined over time [74] . The current pre-immunity models are moving away from investigating the differences in disease symptoms and vaccine effectiveness observed in the human population in response to the pandemic virus. Pre-immunity to a historical A(H3N2) virus helped boost the magnitude and breadth of the broadly neutralizing antibodies elicited by computationally optimized broadly reactive antigen (COBRA) immunogens compared to a naïve ferret group [37] . abstract: The initial exposure to influenza virus usually occurs during childhood. This imprinting has long-lasting effects on the immune responses to subsequent infections and vaccinations. Animal models that are used to investigate influenza pathogenesis and vaccination do recapitulate the pre-immune history in the human population. The establishment of influenza pre-immune ferret models is necessary for understanding infection and transmission and for designing efficacious vaccines. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7348859/ doi: 10.3390/vaccines8020173 id: cord-325325-xw7627x9 author: Skeik, Nedaa title: Influenza viruses and the evolution of avian influenza virus H5N1 date: 2007-10-02 words: 4079.0 sentences: 254.0 pages: flesch: 51.0 cache: ./cache/cord-325325-xw7627x9.txt txt: ./txt/cord-325325-xw7627x9.txt summary: While the clock is still ticking towards what seems to be inevitable pandemic influenza, on April 17, 2007 the U.S. Food and Drug Administration (FDA) approved the first vaccine against the avian influenza virus H5N1 for humans at high risk. While the clock is still ticking towards what seems to be inevitable pandemic influenza, on April 17, 2007 the U.S. Food and Drug Administration (FDA) approved the first vaccine against the avian influenza virus H5N1 for humans at high risk. [8] [9] [10] [11] The 1957 pandemic was caused by the H2N2 subtype, a product of genetic reassortment in hosts infected with both an avian and human influenza virus. Although immunization with human influenza vaccine will not protect against avian influenza strains, it should be considered in poultry workers, and also be given to those traveling to affected areas, two weeks ahead of departure, to prevent co-infection and reassortment. abstract: Although small in size and simple in structure, influenza viruses are sophisticated organisms with highly mutagenic genomes and wide antigenic diversity. They are species-specific organisms. Mutation and reassortment have resulted in newer viruses such as H5N1, with new resistance against anti-viral medications, and this might lead to the emergence of a fully transmissible strain, as occurred in the 1957 and 1968 pandemics. Influenza viruses are no longer just a cause of self-limited upper respiratory tract infections; the H5N1 avian influenza virus can cause severe human infection with a mortality rate exceeding 50%. The case death rate of H5N1 avian influenza infection is 20 times higher than that of the 1918 infection (50% versus 2.5%), which killed 675 000 people in the USA and almost 40 million people worldwide. While the clock is still ticking towards what seems to be inevitable pandemic influenza, on April 17, 2007 the U.S. Food and Drug Administration (FDA) approved the first vaccine against the avian influenza virus H5N1 for humans at high risk. However, more research is needed to develop a more effective and affordable vaccine that can be given at lower doses. url: https://www.sciencedirect.com/science/article/pii/S1201971207001531 doi: 10.1016/j.ijid.2007.07.002 id: cord-021770-zn7na974 author: Slifka, Mark K. title: Passive Immunization date: 2017-07-17 words: 12134.0 sentences: 610.0 pages: flesch: 31.0 cache: ./cache/cord-021770-zn7na974.txt txt: ./txt/cord-021770-zn7na974.txt summary: [26] [27] [28] [29] Recent studies verify these earlier results, demonstrating a 90% to 91% vaccine efficacy against whooping cough among infants younger than 2 months of nonlymphoid tissues and to penetrate mucosal sites of infection is likely to explain why it is often considered the best immunoglobulin isotype for routine passive immunization and has shown clinical benefit ranging from reduced clinical symptoms to nearly complete protection from lethal infection in a number of infectious disease models (Table 8 .3). 118 With the recent development of polyclonal and monoclonal antibodies that show protective efficacy against tularemia in animal models, [119] [120] [121] it may be possible to incorporate both passive immunotherapy and antibiotic treatment into clinical practice not only for tularemia, but for other bacterial diseases, especially in cases in which antibiotic resistance is becoming more widespread. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151993/ doi: 10.1016/b978-0-323-35761-6.00008-0 id: cord-003767-9xbu4hnq author: Slingenbergh, Jan title: Animal Virus Ecology and Evolution Are Shaped by the Virus Host-Body Infiltration and Colonization Pattern date: 2019-05-25 words: 6287.0 sentences: 311.0 pages: flesch: 48.0 cache: ./cache/cord-003767-9xbu4hnq.txt txt: ./txt/cord-003767-9xbu4hnq.txt summary: The synthesis of the findings reveals a predictive virus evolution framework, based on the outerto inner-body changes in the interplay of host environment-transmission modes-organ system involvement-host cell infection cycle-virus genome. Pieced together on this basis was an outer-to inner-body line-up of viruses by organ system or combination of organ systems, guided by the one-to-four virus infiltration score, the corresponding virus organ system tropism, the matching virus transmission modes, length of the infection and shedding periods, infection severity level, and virus environmental survival rate, see Figure 3 and, also, Figure S1d . Pieced together on this basis was an outer-to inner-body line-up of viruses by organ system or combination of organ systems, guided by the one-to-four virus infiltration score, the corresponding virus organ system tropism, the matching virus transmission modes, length of the infection and shedding periods, infection severity level, and virus environmental survival rate, see Figure 3 and, also, Figure S1d . abstract: The current classification of animal viruses is largely based on the virus molecular world. Less attention is given to why and how virus fitness results from the success of virus transmission. Virus transmission reflects the infection-shedding-transmission dynamics, and with it, the organ system involvement and other, macroscopic dimensions of the host environment. This study describes the transmission ecology of the world main livestock viruses, 36 in total, a mix of RNA, DNA and retroviruses. Following an iterative process, the viruses are virtually ranked in an outer- to inner-body fashion, by organ system, on ecological grounds. Also portrayed are the shifts in virus host tropism and virus genome. The synthesis of the findings reveals a predictive virus evolution framework, based on the outer- to inner-body changes in the interplay of host environment-transmission modes-organ system involvement-host cell infection cycle-virus genome. Outer-body viruses opportunistically respond to the variation in the external environment. For example, respiratory and enteric viruses tend to be associated with poultry and pig mass rearing. Ruminant and equine viruses tend to be more deep-rooted and host-specific, and also establish themselves in the vital inner-body systems. It is concluded that the framework may assist the study of new emerging viruses and pandemic risks. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6631033/ doi: 10.3390/pathogens8020072 id: cord-341155-3d64mso0 author: Slots, Jørgen title: Bacterial and viral pathogens in saliva: disease relationship and infectious risk date: 2010-12-07 words: 9332.0 sentences: 447.0 pages: flesch: 36.0 cache: ./cache/cord-341155-3d64mso0.txt txt: ./txt/cord-341155-3d64mso0.txt summary: Human viruses are also frequent inhabitants of the human mouth, and their presence in saliva may be caused by the direct transfer of saliva from infected individuals, a bloodborne infection of the salivary glands, infection of the oral mucosa, or serumal exudates from diseased periodontal sites. Caries risk is assessed by the levels of mutans streptococci and lactobacilli in stimulated saliva (94, 96) , and salivary transmission of cariogenic bacteria frequently occurs from the mother to her child (92, 100) . As high quantities of salivary Epstein-Barr virus DNA can be recovered from fully edentulous patients (155) , the occurrence of the virus in saliva may not be a reliable indicator of its subgingival level or of the periodontitis disease status. Taken together, the saliva of HIV-infected persons is a risk factor for the transmission of several virulent herpesvirus species, and patients receiving HAART cannot be assumed to be less infectious for herpesviruses than individuals not receiving HAART. abstract: nan url: https://doi.org/10.1111/j.1600-0757.2010.00361.x doi: 10.1111/j.1600-0757.2010.00361.x id: cord-333853-p2kbjwpy author: Smee, Donald F. title: Therapy and Long-Term Prophylaxis of Vaccinia Virus Respiratory Infections in Mice with an Adenovirus-Vectored Interferon Alpha (mDEF201) date: 2011-10-13 words: 4585.0 sentences: 222.0 pages: flesch: 48.0 cache: ./cache/cord-333853-p2kbjwpy.txt txt: ./txt/cord-333853-p2kbjwpy.txt summary: title: Therapy and Long-Term Prophylaxis of Vaccinia Virus Respiratory Infections in Mice with an Adenovirus-Vectored Interferon Alpha (mDEF201) An adenovirus 5 vector encoding for mouse interferon alpha, subtype 5 (mDEF201) was evaluated for efficacy against lethal vaccinia virus (WR strain) respiratory infections in mice. Lung virus titers were significantly (>100-fold) lower than in the placebo group, and the other infection parameters in mDEF201 treated mice were nearly at baseline. Ad5-vectored mouse interferon (mDEF201) resulted in sustained IFN levels [16] , that completely protected mice from a lethal Western equine encephalitis virus infection when given intramuscularly at 10 7 plaque forming units (PFU)/ mouse up to 7 days prior to virus challenge [16] . The extent of inhibition of lung Intranasal treatments with mDEF201 (10 7 PFU/mouse) were given one time only on the indicated day prior to virus exposure. abstract: An adenovirus 5 vector encoding for mouse interferon alpha, subtype 5 (mDEF201) was evaluated for efficacy against lethal vaccinia virus (WR strain) respiratory infections in mice. mDEF201 was administered as a single intranasal treatment either prophylactically or therapeutically at doses of 10(6) to 10(8) plaque forming units/mouse. When the prophylactic treatment was given at 56 days prior to infection, it protected 90% of animals from death (100% protection for treatments given between 1–49 days pre-infection), with minimal weight loss occurring during infection. Surviving animals re-challenged with virus 22 days after the primary infection were protected from death, indicating that mDEF201 did not compromise the immune response against the initial infection. Post-exposure therapy was given between 6–24 h after vaccinia virus exposure and protection was afforded by a 10(8) dose of mDEF201 given at 24 h, whereas a 10(7) dose was effective up to 12 h. Comparisons were made of the ability of mDEF201, given either 28 or 1 day prior to infection, to inhibit tissue virus titers and lung infection parameters. Lung, liver, and spleen virus titers were inhibited to nearly the same extent by either treatment, as were lung weights and lung hemorrhage scores (indicators of pneumonitis). Lung virus titers were significantly (>100-fold) lower than in the placebo group, and the other infection parameters in mDEF201 treated mice were nearly at baseline. In contrast, viral titers and lung infection parameters were high in the placebo group on day 5 of the infection. These results demonstrate the long-acting prophylactic and treatment capacity of mDEF201 to combat vaccinia virus infections. url: https://www.ncbi.nlm.nih.gov/pubmed/22022603/ doi: 10.1371/journal.pone.0026330 id: cord-006285-kkxdmzk9 author: Smirnova, S. S. title: Long-Term Maintenance of the Functional Changes Induced by Influenza A Virus and/or LPS in Human Endothelial ECV-304 Cell Sublines date: 2019-08-26 words: 4686.0 sentences: 175.0 pages: flesch: 43.0 cache: ./cache/cord-006285-kkxdmzk9.txt txt: ./txt/cord-006285-kkxdmzk9.txt summary: The present work reports the comparative assessment of the functional changes which take place in human ECV-304 endothelial cell sublines obtained previously by the long-term culturing of cells after exposure to varying infectious doses (IDs) of influenza A virus, and/or bacterial lipopolysaccharide (LPS). It has been demonstrated that, in the course of long-term culturing (six passages) after exposure to pathogenic agents (influenza virus and/or LPS), endothelial cells maintain changes in their migratory activity, permeability, and expression of mRNA for cytokines TNFα and TGFβ (along with the changes in their proliferation activity, which has been demonstrated earlier). The comparative study of the human endothelial ECV-304 cell sublines carried out in the present work and in our previous work (Smirnova et al., 2018) has demonstrated that the infection of nonpermissive cells with influenza A virus (both in high and in very low doses) and exposure to LPS can change migratory, proliferation, and apoptotic activity of cells and impair cell barrier function. abstract: Influenza A virus and secondary bacterial infection may have remote effects in the form of cardiovascular complications or fibrosis in different organs. However, the mechanisms governing the development of complications remain poorly studied. The present work reports the comparative assessment of the functional changes which take place in human ECV-304 endothelial cell sublines obtained previously by the long-term culturing of cells after exposure to varying infectious doses (IDs) of influenza A virus, and/or bacterial lipopolysaccharide (LPS). It has been demonstrated that, in the course of long-term culturing (six passages) after exposure to pathogenic agents (influenza virus and/or LPS), endothelial cells maintain changes in their migratory activity, permeability, and expression of mRNA for cytokines TNFα and TGFβ (along with the changes in their proliferation activity, which has been demonstrated earlier). The pattern of changes depended on the type of the agent (agents) to which the cells were exposed. The differences in migratory activity (which was at its maximum 4 h after wounding) between the cell sublines at the sixth passage correlated with the differences in their proliferation activity at the first passage (proliferation data were obtained previously). In particular, an increase in migration and proliferation was observed in the sublines exposed to low virus doses (ECV-1ID), as well as exposed to LPS (ECV-LPS), while the suppression of migration and proliferation was observed in the subline exposed to high virus doses (ECV-1000ID). In the ECV-1ID, ECV-LPS, and most notably in ECV-1ID + LPS sublines, we detected an increase in the expression of mRNA for cytokines TNFα and TGFβ, which, however, didn’t lead to the induction of apoptosis. We have also demonstrated an increase in cell permeability in the analyzed sublines, which was indicated by a decrease in the expression of the mRNAs for the genes encoding occludin and ZO-1, the tight junctions proteins . This paper also reports an evaluation of the effects of the antiviral preparations rimantadine and alpisarin on the functional state of cell sublines. As a result, it has been demonstrated that these drugs may be able to prevent the development of the pathological changes caused by influenza A virus and/or LPS in endothelial cells. The results obtained in the present work may be of use when studying the mechanisms of development of the influenza A virus and secondary bacterial infection complications. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101551/ doi: 10.1134/s1990519x19040084 id: cord-339230-cc7gcy5b author: Smith, Amber M. title: Secondary Bacterial Infections in Influenza Virus Infection Pathogenesis date: 2014-07-16 words: 10381.0 sentences: 576.0 pages: flesch: 34.0 cache: ./cache/cord-339230-cc7gcy5b.txt txt: ./txt/cord-339230-cc7gcy5b.txt summary: Several different animal models have been used to study the effect that influenza viruses have on bacterial transmission and colonization and on invasive diseases, such as acute otitis media and pneumonia (Wherry and Butterfield 1921; Shope 1931; Francis and de Torregrosa 1945; Berendt et al. Although the precise mechanisms responsible for enhancing the transmission profile that influenza viruses provide pneumococci are currently unknown, it is likely due to an increase in pathogen density and frequency of secretion events (e.g., sneezing and coughing) in the infected individual combined with a decrease in immunity and resistance from natural barriers breaking down in the person who is newly exposed. The PB1-F2 protein of some influenza viruses increases pathologic effects by causing cell death, increasing viral replication, and altering inflammatory responses to primary viral infections and to bacterial coinfections (Conenello et al. abstract: Influenza is often complicated by bacterial pathogens that colonize the nasopharynx and invade the middle ear and/or lung epithelium. Incidence and pathogenicity of influenza-bacterial coinfections are multifactorial processes that involve various pathogenic virulence factors and host responses with distinct site- and strain-specific differences. Animal models and kinetic models have improved our understanding of how influenza viruses interact with their bacterial co-pathogens and the accompanying immune responses. Data from these models indicate that considerable alterations in epithelial surfaces and aberrant immune responses lead to severe inflammation, a key driver of bacterial acquisition and infection severity following influenza. However, further experimental and analytical studies are essential to determining the full mechanistic spectrum of different viral and bacterial strains and species and to finding new ways to prevent and treat influenza-associated bacterial coinfections. Here, we review recent advances regarding transmission and disease potential of influenza-associated bacterial infections and discuss the current gaps in knowledge. url: https://doi.org/10.1007/82_2014_394 doi: 10.1007/82_2014_394 id: cord-007764-7750z41g author: Smith, M. L. title: Display of Peptides on the Surface of Tobacco Mosaic Virus Particles date: 2009 words: 7201.0 sentences: 336.0 pages: flesch: 42.0 cache: ./cache/cord-007764-7750z41g.txt txt: ./txt/cord-007764-7750z41g.txt summary: In this review, we focus on the potential that tobacco mosaic virus (TMV) has as a carrier for immunogenic epitopes, and the factors that must be considered in order to bring products based on this platform to the market. There are well-established methodologies for recombinant production of VLP-epitope display systems that use self-assembling capsid proteins of several different viruses, most notably papillomaviruses, hepatitis B core and surface antigens, and various bacteriophages, including the leviviruses MS2 and Qβ. The focus of this review is on some of the practical issues that must be considered in order to bring plant-produced virus particle and VLP-based epitope display systems into commercial use. Commercial-scale biomanufacturing allows translation of the body of data providing proof of the concept that TMV can function as an effective carrier for antigenic peptides into vaccine products for human and veterinary applications (Pogue et al. abstract: In this review, we focus on the potential that tobacco mosaic virus (TMV) has as a carrier for immunogenic epitopes, and the factors that must be considered in order to bring products based on this platform to the market. Large Scale Biology Corporation developed facile and scaleable methods for manufacture of candidate peptide display vaccines based on TMV. We describe how rational design of peptide vaccines can improve the manufacturability of particular TMV products. We also discuss downstream processing and purification of the vaccine products, with particular attention to the metrics that a product must attain in order to meet criteria for regulatory approval as injectable biologics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122513/ doi: 10.1007/978-3-540-70868-1_2 id: cord-256837-100ir651 author: Smith, Steven B. title: Identification of Common Biological Pathways and Drug Targets Across Multiple Respiratory Viruses Based on Human Host Gene Expression Analysis date: 2012-03-14 words: 8447.0 sentences: 415.0 pages: flesch: 38.0 cache: ./cache/cord-256837-100ir651.txt txt: ./txt/cord-256837-100ir651.txt summary: Several recent studies have generated multiple mRNA microarray gene expression datasets derived from experiments involving the infection of human cell-lines or animal models with one or more of the major respiratory viruses [21] [22] [23] . Through a systematic analysis of these respiratory virus-human host gene expression datasets, we determined common sets of genes and pathways involved in host responses to viral infections. A total of seven different respiratory viruses were analyzed, represented by fifteen unique Gene Expression Omnibus (GEO) datasets (indicated by GEO Series or GSE accession numbers), nine different human cell types, and seven different array platforms for a total of 28 unique comparisons. This assumption is based on the occurrence of genes that are differentially expressed in infection models for at least five of the seven respiratory viruses, have involvement in a number of relevant pathways related to host immune response, and encode for known drug targets. abstract: BACKGROUND: Pandemic and seasonal respiratory viruses are a major global health concern. Given the genetic diversity of respiratory viruses and the emergence of drug resistant strains, the targeted disruption of human host-virus interactions is a potential therapeutic strategy for treating multi-viral infections. The availability of large-scale genomic datasets focused on host-pathogen interactions can be used to discover novel drug targets as well as potential opportunities for drug repositioning. METHODS/RESULTS: In this study, we performed a large-scale analysis of microarray datasets involving host response to infections by influenza A virus, respiratory syncytial virus, rhinovirus, SARS-coronavirus, metapneumonia virus, coxsackievirus and cytomegalovirus. Common genes and pathways were found through a rigorous, iterative analysis pipeline where relevant host mRNA expression datasets were identified, analyzed for quality and gene differential expression, then mapped to pathways for enrichment analysis. Possible repurposed drugs targets were found through database and literature searches. A total of 67 common biological pathways were identified among the seven different respiratory viruses analyzed, representing fifteen laboratories, nine different cell types, and seven different array platforms. A large overlap in the general immune response was observed among the top twenty of these 67 pathways, adding validation to our analysis strategy. Of the top five pathways, we found 53 differentially expressed genes affected by at least five of the seven viruses. We suggest five new therapeutic indications for existing small molecules or biological agents targeting proteins encoded by the genes F3, IL1B, TNF, CASP1 and MMP9. Pathway enrichment analysis also identified a potential novel host response, the Parkin-Ubiquitin Proteasomal System (Parkin-UPS) pathway, which is known to be involved in the progression of neurodegenerative Parkinson's disease. CONCLUSIONS: Our study suggests that multiple and diverse respiratory viruses invoke several common host response pathways. Further analysis of these pathways suggests potential opportunities for therapeutic intervention. url: https://doi.org/10.1371/journal.pone.0033174 doi: 10.1371/journal.pone.0033174 id: cord-323930-pl3qlcpo author: Sohail, Ayesha title: Forecasting the timeframe of coronavirus and human cells interaction with reverse engineering date: 2020-04-29 words: 1497.0 sentences: 95.0 pages: flesch: 53.0 cache: ./cache/cord-323930-pl3qlcpo.txt txt: ./txt/cord-323930-pl3qlcpo.txt summary: The purpose of this article is to review and investigate further the molecular mechanism by which the SARS-CoV2 virus infection proceeds via the formation of a hetero-trimer between its protein S, the ACE2 receptor and the B0AT1 protein, which is the "entry receptor" for the infection process involving membrane fusion [10]. The purpose 11 of this article is to review and investigate further the molecular mechanism by which the SARS-CoV2 12 virus infection proceeds via the formation of a hetero-trimer between its protein S, the ACE2 receptor 13 and the B0AT1 protein, which is the "entry receptor" for the infection process involving membrane "animal to man" and then "man to man " transmission. Our hypothesis is supported by 128 the need for activation of the infection system by the virus, given by the particular molecular kinetics that 129 leads to the formation of the "infection trimer" given by the viral S1 protein and the ACE-2 receptor While developing the computational framework, the virus-target cell interaction was studied in depth. abstract: In December 2019, an atypical pneumonia invaded the city of Wuhan, China, and the causative agent of this disease turned out to be a new coronavirus. In January 2020, the World Health Organization named the new coronavirus 2019-nCoV and subsequently it is referred to as SARS-CoV2 and the related disease as CoViD-19 [9]. Very quickly, the epidemic led to a pandemic and it is now a worldwide emergency requiring the creation of new antiviral therapies and a related vaccine. The purpose of this article is to review and investigate further the molecular mechanism by which the SARS-CoV2 virus infection proceeds via the formation of a hetero-trimer between its protein S, the ACE2 receptor and the B0AT1 protein, which is the “entry receptor” for the infection process involving membrane fusion [10]. A reverse engineering process uses the formalism of the Hill function to represent the functions related to the dynamics of the biochemical interactions of the viral infection process. Then, using a logical evaluation of viral density that measures the rate at which the cells are hijacked by the virus (and they provide a place for the virus to replicate) and considering the “time delay” given by the interaction between cell and virus, the expected duration of the incubation period is predicted. The conclusion is that the density of the virus varies from the “exposure time” to the “interaction time” (virus-cells). This model can be used both to evaluate the infectious condition and to analyze the incubation period. BACKGROUND: The ongoing threat of the new coronavirus SARS-CoV2 pandemic is alarming and strategies for combating infection are highly desired. This RNA virus belongs to the β-coronavirus genus and is similar in some features to SARS-CoV. Currently, no vaccine or approved medical treatment is available. The complex dynamics of the rapid spread of this virus can be demonstrated with the aid of a computational framework. METHODS: A mathematical model based on the principles of cell-virus interaction is developed in this manuscript. The amino acid sequence of S proein and its interaction with the ACE-2 protein is mimicked with the aid of Hill function. The mathematical model with delay is solved with the aid of numerical solvers and the parametric values are obtained with the help of MCMC algorithm. RESULTS: A delay differential equation model is developed to demonstrate the dynamics of target cells, infected cells and the SARS-CoV2. The important parameters and coefficients are demonstrated with the aid of numerical computations. The resulting thresholds and forecasting may prove to be useful tools for future experimental studies and control strategies. CONCLUSIONS: From the analysis, I is concluded that control strategy via delay is a promising technique and the role of Hill function formalism in control strategies can be better interpreted in an inexpensive manner with the aid of a theoretical framework. url: https://api.elsevier.com/content/article/pii/S0079610720300262 doi: 10.1016/j.pbiomolbio.2020.04.002 id: cord-022348-w7z97wir author: Sola, Monica title: Drift and Conservatism in RNA Virus Evolution: Are They Adapting or Merely Changing? date: 2007-09-02 words: 10892.0 sentences: 671.0 pages: flesch: 56.0 cache: ./cache/cord-022348-w7z97wir.txt txt: ./txt/cord-022348-w7z97wir.txt summary: An analysis of proteins derived from complete potyvirus genomes, positive-stranded RNA viruses, yielded highly significant linear relationships. Under the rubric replication, a virus could vary to increase its fitness, exploit different target cells or evade adaptive immune responses. For a given virus, different protein sequence sets were compared to a given reference such as RT in the case of HIV/SIV. Although these data were derived from completely sequenced primate immunodeficiency viral genomes, analyses on larger data sets, such as p17 Gag/p24 Gag or gp120/gp41, yielded relative values that differed from those given in Table 6 .1 by at most 14%. An analysis of proteins derived from complete potyvirus genomes, positive-stranded RNA viruses, yielded highly significant linear relationships (Table 6 .1). In the clear cases where genetic variation is exploited by RNA viruses, it is used to overcome barriers to transmission set up by the host population, e.g. herd immunity. abstract: This chapter argues that the vast majority of genetic changes or mutations fixed by RNA viruses are essentially neutral or nearly neutral in character. In molecular evolution one of the remarkable observations has been the uniformity of the molecular clock. An analysis of proteins derived from complete potyvirus genomes, positive-stranded RNA viruses, yielded highly significant linear relationships. These analyses indicate that viral protein diversification is essentially a smooth process, the major parameter being the nature of the protein more than the ecological niche it finds itself in. Synonymous changes are invariably more frequent than nonsynonymous changes. Positive selection exploits a small proportion of genetic variants, while functional sequence space is sufficiently dense, allowing viable solutions to be found. Although evolution has connotations of change, what has always counted is natural selection or adaptation. It is the only force for the genesis of a novel replicon. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155598/ doi: 10.1016/b978-012220360-2/50007-6 id: cord-006790-lye0qjw8 author: Song, R. title: Surveillance of the first case of human avian influenza A (H7N9) virus in Beijing, China date: 2013-10-16 words: 2779.0 sentences: 191.0 pages: flesch: 58.0 cache: ./cache/cord-006790-lye0qjw8.txt txt: ./txt/cord-006790-lye0qjw8.txt summary: A number of specimens from the environment of this cluster and from the feces specimens tested positive for viral RNA of the H7N9 virus on the fourth day following onset of the index case''s illness. A number of specimens from the environment of this cluster and from the feces specimens tested positive for viral RNA of the H7N9 virus on the fourth day following onset of the index case''s illness. Fifteen hours after the fever began, the pharyngeal swab collected from the index case tested positive for the H7N9 virus by RT-time PCR. Pharyngeal swabs collected from the index case''s mother tested positive for the H7N9 virus on 12 April and 14 April and were negative after 15 April. Although the family members of the index case were all exposed to asymptomatic chickens infected with H7N9 virus, they presented with distinct outcomes. abstract: PURPOSE: Human infections with avian influenza A (H7N9) virus manifested in China in March 2013. The first case infected with H7N9 virus in Beijing involved a family member of a chicken dealer and was reported in April 2013. The clinical and epidemiological characteristics of this case and her parents were examined to illustrate some key traits regarding this novel H7N9 virus. METHODS: The index case was subjected to intensive clinical examination in order to observed the clinical process. Real-time PCR was used to confirm cases infected with H7N9 virus. The index case was administered oseltamivir (45 mg, twice daily) at the early stage of the infection. Sera were collected from the index case and her parents from the onset of illness onwards. The subjects were followed for 4 weeks. RESULTS: The sera were confirmed by neutralizing antibody tests. The index case’s clinical manifestation progressed quickly. The pharyngeal swab tested positive for influenza A based on the detection of influenza A antigen (rapid influenza diagnostic test) 15 h after the onset of fever and was positive for H7N9 virus. The patient’s temperature dropped to 36.2 °C 18 h after treatment by oseltamivir (32 h after fever). Cough and other symptoms alleviated rapidly. A number of specimens from the environment of this cluster and from the feces specimens tested positive for viral RNA of the H7N9 virus on the fourth day following onset of the index case’s illness. Pharyngeal swabs of the mother tested positive for H7N9 virus twice, but she showed no clinical symptoms. Four weeks after disease onset, the family did not present any clinical symptoms, and the results of the physical examination and blood tests were normal. The mother and the case’s sera had a fourfold increased neutralizing antibody titer. CONCLUSION: Early diagnosis and early initiation of the treatment of confirmed infections is the most effective strategy for managing H7N9 virus infection. Human beings exposed to H7N9 virus may develop asymptomatic infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102393/ doi: 10.1007/s15010-013-0533-9 id: cord-288945-c9ow1q5c author: Spengler, Ulrich title: Liver Disease Associated with Non-Hepatitis Viruses date: 2019-11-01 words: 7425.0 sentences: 443.0 pages: flesch: 39.0 cache: ./cache/cord-288945-c9ow1q5c.txt txt: ./txt/cord-288945-c9ow1q5c.txt summary: Although exotic diseases, in particular viral hemorrhagic fevers are a severe threat in certain regions of the world, liver disease due to exotic infections such as Ebola virus, Rift valley fever or Lassa fever have been reported only sporadically but do not represent a frequent health problem in returning travelers. Clinically more severe diseases, for example, dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS) can follow from secondary infection with dengue virus of different serotype. Herpes simplex virus (HSV), varizella zoster virus (VZV), Epstein-Barr virus (EBV), cytomegalovirus (CMV) and Human Herpesvirus type 6 or 7 (HHV6, HHV7) can directly affect the liver and are infections in the human population usually acquired during childhood or adolescence. In patients with severe immunodeficiency lymphomatoid granulomatosis is a further unusual complication of Epstein-Barr virus infection leading to granuloma formation in multiple organs including the liver, which may require interferon-alpha antiviral therapy (Wilson et al., 1996) . abstract: Hepatitis is commonly associated with certain viruses labeled as “Hepatitis” viruses. However, many other viral infections can also affect the liver ranging from mild asymptomatic elevations of aminotransferases to fulminant hepatic failure. This article will provide a brief overview on a variety of different viral infections that may be associated with significant liver pathology at least under certain conditions, for example, immunosuppression. This overview discusses key virological features, clinical presentation of associated liver disease and provides some information on diagnosis and an outline of treatment options. Thus, the overview can provide first orientation when infectious hepatitis is encountered in a patient that cannot be explained by the usual hepatitis viruses. url: https://www.sciencedirect.com/science/article/pii/B9780128012383657823 doi: 10.1016/b978-0-12-801238-3.65782-3 id: cord-009589-xfdgk2j6 author: Spradbrow, P. B. title: VIRUS DISEASES OF DOMESTIC ANIMALS date: 2008-03-10 words: 926.0 sentences: 57.0 pages: flesch: 53.0 cache: ./cache/cord-009589-xfdgk2j6.txt txt: ./txt/cord-009589-xfdgk2j6.txt summary: Viruses multiply solely from their genetic material of DNA or RNA when this is introduced into a susceptible cell and provides a code for the production of new virus genetic material and structural components. Much progress has been made towards the grouping (classifying) of related viruses by a consideration of the nature of their genetic material and of certain stable features of the infectious particle or virion. Surprisingly, many veterinary viruses that produce severe disease in conventional animals cause only mild disease in the germ-free host. In fact, the herpesvirus of feline rhinotracheitis is an unusual virus in producing a disease in germ-free animals comparable in severity with that seen naturally (Hoover et a1 1970) . group of agents, and the relative importance of the various defence mechanisms will probably vary with the nature of the infecting virus and of the host. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159752/ doi: 10.1111/j.1751-0813.1972.tb05117.x id: cord-327392-9psblokc author: Srivastava, A.K. title: Potential of Graphene-based Materials to Combat COVID-19: Properties, Perspectives and Prospects date: 2020-10-21 words: 4055.0 sentences: 218.0 pages: flesch: 52.0 cache: ./cache/cord-327392-9psblokc.txt txt: ./txt/cord-327392-9psblokc.txt summary: Graphene and graphene-related materials (GRMs) exhibit extraordinary physicochemical, electrical, optical, antiviral, antimicrobial, and other fascinating properties that warrant them as potential candidates for designing and development of high-performance components and devices required for COVID-19 pandemic and other futuristic calamities. Thus, the effectiveness of graphene-based electrochemical biosensors for the detection of biomolecules, in particular for the viruses, suggests that these biosensors have the potential to effectively detect the novel coronavirus SARS-CoV-2 as well [51] but a lot of high-end research needs to be performed to develop reliable diagnostic devices. We present a hypothetical mechanism in Figure 4 that shows how electrochemical biosensors based on graphene and GRMs could be used for the detection of SARS-CoV-2 virus. These findings reinforce that graphene-based SPR substrates could be used for designing and development of the sensitivity devices for the detection of SARS-CoV-2 and other viruses. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a new virus in coronavirus family that causes coronavirus disease (COVID-19), emerges as a big threat to the human race. To date, there is no medicine and vaccine available for COVID-19 treatment. While the development of medicines and vaccines are essentially and urgently required, what is also extremely important is the repurposing of smart materials to design effective systems for combating COVID-19. Graphene and graphene-related materials (GRMs) exhibit extraordinary physicochemical, electrical, optical, antiviral, antimicrobial, and other fascinating properties that warrant them as potential candidates for designing and development of high-performance components and devices required for COVID-19 pandemic and other futuristic calamities. In this article, we discuss the potential of graphene and GRMs for healthcare applications and how they may contribute to fighting against COVID-19. url: https://www.sciencedirect.com/science/article/pii/S2468519420301452?v=s5 doi: 10.1016/j.mtchem.2020.100385 id: cord-263868-ewnf96cz author: Srivastava, Mayank title: Chemical proteomics tracks virus entry and uncovers NCAM1 as Zika virus receptor date: 2020-08-04 words: 7614.0 sentences: 429.0 pages: flesch: 52.0 cache: ./cache/cord-263868-ewnf96cz.txt txt: ./txt/cord-263868-ewnf96cz.txt summary: ZIKV was labeled on its surface with a chemical probe, which carries a photocrosslinker to covalently link virus-interacting proteins in living cells on UV exposure at different time points, and a biotin tag for subsequent enrichment and mass spectrometric identification of the receptor or other host proteins critical for virus internalization. We used the labeled ZIKV to infect Vero cells and interacting proteins were crosslinked at fixed time points to identify the virus-host factors and elucidate the virus entry mechanism (Fig. 1c) . To further investigate whether the strategy was also capable of correlating spatial information with the virus crosslinked proteins, we performed the STRING analysis to determine whether there is statistical overrepresentation of specific genes or proteins in the sample at specific time points and identify proteins specific at the attachment or cellular entry stages ( Supplementary Fig. 6 ). abstract: The outbreak of Zika virus (ZIKV) in 2016 created worldwide health emergency which demand urgent research efforts on understanding the virus biology and developing therapeutic strategies. Here, we present a time-resolved chemical proteomic strategy to track the early-stage entry of ZIKV into host cells. ZIKV was labeled on its surface with a chemical probe, which carries a photocrosslinker to covalently link virus-interacting proteins in living cells on UV exposure at different time points, and a biotin tag for subsequent enrichment and mass spectrometric identification of the receptor or other host proteins critical for virus internalization. We identified Neural Cell Adhesion Molecule (NCAM1) as a potential ZIKV receptor and further validated it through overexpression, knockout, and inhibition of NCAM1 in Vero cells and human glioblastoma cells U-251 MG. Collectively, the strategy can serve as a universal tool to map virus entry pathways and uncover key interacting proteins. url: https://doi.org/10.1038/s41467-020-17638-y doi: 10.1038/s41467-020-17638-y id: cord-007731-wu7i548j author: Sriwilaijaroen, Nongluk title: Molecular Basis of a Pandemic of Avian-Type Influenza Virus date: 2014-05-27 words: 9917.0 sentences: 484.0 pages: flesch: 49.0 cache: ./cache/cord-007731-wu7i548j.txt txt: ./txt/cord-007731-wu7i548j.txt summary: Change in HA antigen either by accumulation of mutations in HA1 of fi ve proposed antigenic sites (based on amino acid sequence comparison among viruses isolated from different years or among variants grown in the presence of mouse monoclonal antibodies) as shown in Fig. 7c [ 56 -59 ] or by intrasubtypic reassortment between distinct clades of co-circulating infl uenza A viruses [ 35 ] is responsible for evasion of recognition by the host antibodies and thus Cleavage site 324P-X-X/R/K-X-X-R/K↓GLF X = nonbasic residue 324P-X-R/K-X-R/K-R↓GLF (due to insertion/substitution) Host proteases Extracellular tissue-restricted trypsin-like proteases Ubiquitously expressed intracellular proteases (e.g., furin and PC6) continuous circulation of the virus in host populations. However, highly mutable avian infl uenza A viruses that have sporadically continued direct transmission to and infection in humans have raised concerns for pandemic potential with unpredictable pathogenesis (depending on virus-host interactions). abstract: Despite heroic efforts to prevent the emergence of an influenza pandemic, avian influenza A virus has prevailed by crossing the species barriers to infect humans worldwide, occasionally with morbidity and mortality at unprecedented levels, and the virus later usually continues circulation in humans as a seasonal influenza virus, resulting in health-social-economic problems each year. Here, we review current knowledge of influenza viruses, their life cycle, interspecies transmission, and past pandemics and discuss the molecular basis of pandemic acquisition, notably of hemagglutinin (lectin) acting as a key contributor to change in host specificity in viral infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121456/ doi: 10.1007/978-1-4939-1292-6_38 id: cord-253705-utp8po48 author: Sriwilaijaroen, Nongluk title: Sialoglycovirology of Lectins: Sialyl Glycan Binding of Enveloped and Non-enveloped Viruses date: 2020-04-19 words: 20192.0 sentences: 863.0 pages: flesch: 46.0 cache: ./cache/cord-253705-utp8po48.txt txt: ./txt/cord-253705-utp8po48.txt summary: While HEF glycoproteins of influenza C and D viruses attach to 9-O-acetyl-Neu5Accarrying sugar chains found in the respiratory tract of animals [31] as a receptor determinant for infection in cattle and pigs (only C virus has been detected in humans), HAs of influenza A (Fig. 3a) and B viruses recognize α2-6Neu5Ac-carrying sugar chains and Fig. 3 (continued) σ1 containing a Sia-binding site in its body) interacts with a sialoglycan on a glycoprotein/ glycolipid (a brown dash), which is anchored to the host cell membrane. Variants with the HE gene, which have become circulating strains, could be explained by the finding that the HE protein increases the efficiency of production of infectious virus [78] possibly by acting as a lectin for enhancing viral binding and as an enzyme that destroys receptors by de-O-acetylation (esterase) for enhancing release of trapped virions from the host mucosa and of budding virions from infected cells. abstract: On the cell sur “face”, sialoglycoconjugates act as receptionists that have an important role in the first step of various cellular processes that bridge communication between the cell and its environment. Loss of Sia production can cause the developmental of defects and lethality in most animals; hence, animal cells are less prone to evolution of resistance to interactions by rapidly evolved Sia-binding viruses. Obligative intracellular viruses mostly have rapid evolution that allows escape from host immunity, leading to an epidemic variant, and that allows emergence of a novel strain, occasionally leading to pandemics that cause health-social-economic problems. Recently, much attention has been given to the mutual recognition systems via sialosugar chains between viruses and their host cells and there has been rapid growth of the research field “sialoglycovirology.” In this chapter, the structural diversity of sialoglycoconjugates is overviewed, and enveloped and non-enveloped viruses that bind to Sia are reviewed. Also, interactions of viral lectins-host Sia receptors, which determine viral transmission, host range, and pathogenesis, are presented. The future direction of new therapeutic routes targeting viral lectins, development of easy-to-use detection methods for diagnosis and monitoring changes in virus binding specificity, and challenges in the development of suitable viruses to use in virus-based therapies for genetic disorders and cancer are discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/32306355/ doi: 10.1007/978-1-0716-0430-4_47 id: cord-261961-u4d0vvmq author: St-Germain, Jonathan R. title: A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research date: 2020-08-28 words: 2735.0 sentences: 147.0 pages: flesch: 41.0 cache: ./cache/cord-261961-u4d0vvmq.txt txt: ./txt/cord-261961-u4d0vvmq.txt summary: To this end, we conducted a mass spectrometry-based characterization of the SARS-CoV-2 virion and infected cell lysates, identifying 189 unique high-confidence virus tryptic peptides derived from 17 different virus proteins, to create a high quality resource for use in targeted proteomics approaches. The resulting viral tryptic peptides were identified using nanoflow liquid chromatography -tandem mass spectrometry (LC-MS/MS; Fig 1A, Together, these data confirm and expand upon previous proteomic analyses of SARS-CoV-2 virions, infected cells 4, 7-11 and patient samples [12] [13] [14] , and provide a library of high quality virus peptide spectra covering 17 virus proteins that can be used for the creation of peptide spectral libraries and targeted proteomics approaches. To this end, we also undertook an analysis of SARS-CoV-2 virions and infected Vero cell lsyates using data-dependent acquisition tandem mass spectrometry, and identified 189 unique tryptic peptides, assigned to 17 different virus proteins. abstract: Key steps of viral replication take place at host cell membranes, but the detection of membrane-associated protein-protein interactions using standard affinity-based approaches (e.g. immunoprecipitation coupled with mass spectrometry, IP-MS) is challenging. To learn more about SARS-CoV-2 - host protein interactions that take place at membranes, we utilized a complementary technique, proximity-dependent biotin labeling (BioID). This approach uncovered a virus-host topology network comprising 3566 proximity interactions amongst 1010 host proteins, highlighting extensive virus protein crosstalk with: (i) host protein folding and modification machinery; (ii) membrane-bound vesicles and organelles, and; (iii) lipid trafficking pathways and ER-organelle membrane contact sites. The design and implementation of sensitive mass spectrometric approaches for the analysis of complex biological samples is also important for both clinical and basic research proteomics focused on the study of COVID-19. To this end, we conducted a mass spectrometry-based characterization of the SARS-CoV-2 virion and infected cell lysates, identifying 189 unique high-confidence virus tryptic peptides derived from 17 different virus proteins, to create a high quality resource for use in targeted proteomics approaches. Together, these datasets comprise a valuable resource for MS-based SARS-CoV-2 research, and identify novel virus-host protein interactions that could be targeted in COVID-19 therapeutics. url: https://doi.org/10.1101/2020.08.28.269175 doi: 10.1101/2020.08.28.269175 id: cord-002933-zmx4k46v author: Stabell, Alex C title: Dengue viruses cleave STING in humans but not in nonhuman primates, their presumed natural reservoir date: 2018-03-20 words: 9265.0 sentences: 506.0 pages: flesch: 55.0 cache: ./cache/cord-002933-zmx4k46v.txt txt: ./txt/cord-002933-zmx4k46v.txt summary: The dengue virus 2 (DENV2) encoded protease cleaves human STING, reducing type I interferon production and boosting viral titers in humans. We show that an ''RG'' motif at positions 78/79 of STING is critical for susceptibility to cleavage, and conversion of these residues to ''RG'' renders all nonhuman primate STING proteins tested, as well as mouse STING, sensitive to dengue virus proteases. Out of the entire Genbank database, along with our sequencing of STING from 16 additional primate species, we identify only a small number of apes (gorillas, orangutans, and gibbons), and three small rodent species (chinchillas, naked mole rats, and desert woodrats) as encoding a functional dengue virus cleavage determinant in STING. Further, the restoration of the ''RG'' motif at positions 78/79 again renders all of these STING proteins susceptible to cleavage ( Figure 5B) , indicating that the sylvatic protease is targeting (i.e. binding or cleaving) the same cleavage determinant as the proteases from human dengue viruses. abstract: Human dengue viruses emerged from primate reservoirs, yet paradoxically dengue does not reach high titers in primate models. This presents a unique opportunity to examine the genetics of spillover versus reservoir hosts. The dengue virus 2 (DENV2) - encoded protease cleaves human STING, reducing type I interferon production and boosting viral titers in humans. We find that both human and sylvatic (reservoir) dengue viruses universally cleave human STING, but not the STING of primates implicated as reservoir species. The special ability of dengue to cleave STING is thus specific to humans and a few closely related ape species. Conversion of residues 78/79 to the human-encoded ‘RG’ renders all primate (and mouse) STINGs sensitive to viral cleavage. Dengue viruses may have evolved to increase viral titers in the dense and vast human population, while maintaining decreased titers and pathogenicity in the more rare animals that serve as their sustaining reservoir in nature. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860865/ doi: 10.7554/elife.31919 id: cord-329493-ueqlhgn0 author: Stadler, Konrad title: SARS — beginning to understand a new virus date: 2003 words: 5146.0 sentences: 248.0 pages: flesch: 51.0 cache: ./cache/cord-329493-ueqlhgn0.txt txt: ./txt/cord-329493-ueqlhgn0.txt summary: A new infectious disease, known as severe acute respiratory syndrome (SARS), appeared in the Guangdong province of southern China in 2002. When Thiel and colleagues 20 isolated one genomic and eight subgenomic RNAs from the FRA strain and sequenced their 5′ ends, they identified a conserved sequence (5′ACGAAC3′) that was located in coronaviruses: S, spike protein; E, envelope protein; M, membrane glycoprotein; and N, nucleocapsid protein. Alternatively, these antigens could be delivered by DNA immunization by Figure 6 | The S1 domain of SARS-CoV spike is structurally related to group 2 coronaviruses. Schematic representation of cysteine positions in the S1 domains of group 1, 2 and 3 coronaviruses, compared with the SARS-CoV spike protein. The complete genome sequence of a SARS-CoV isolate (FRA) and experimental data on its key RNA elements and protein functions are described. Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection abstract: The 114-day epidemic of the severe acute respiratory syndrome (SARS) swept 29 countries, affected a reported 8,098 people, left 774 patients dead and almost paralysed the Asian economy. Aggressive quarantine measures, possibly aided by rising summer temperatures, successfully terminated the first eruption of SARS and provided at least a temporal break, which allows us to consolidate what we have learned so far and plan for the future. Here, we review the genomics of the SARS coronavirus (SARS-CoV), its phylogeny, antigenic structure, immune response and potential therapeutic interventions should the SARS epidemic flare up again. url: https://www.ncbi.nlm.nih.gov/pubmed/15035025/ doi: 10.1038/nrmicro775 id: cord-302021-42vqmndl author: Stanley, Mathew title: Synthesis and inhibitory activity of sialic acid derivatives targeted at viral sialate-O-acetylesterases date: 2011-04-08 words: 3461.0 sentences: 207.0 pages: flesch: 55.0 cache: ./cache/cord-302021-42vqmndl.txt txt: ./txt/cord-302021-42vqmndl.txt summary: Besides sialidases, the haemagglutinin-esterases (HE) of influenza C virus, isavirus, betacoronaviruses and toroviruses represent another class of RDEs. They are sialate-O-acetylesterases (SOAE) hydrolysing O-acetyl esters of O-acetylated sialic acid derivatives (Fig. 1) . Alkylation of 7 under Williamson-conditions followed by acid-mediated ketal hydrolysis and basic saponification of the methyl ester gave crude inhibitor 1 which was purified by gel permeation chromatography. Inhibition of the SOAE activity of three viruses, influenza C virus (INF-C), bovine coronavirus (BCoV) and mouse hepatitis virus strain S (MHV-S) and of two chimeric recombinant viral haemagglutinin esterases, from influenza C/Cal/78 virus (HE12-GFP) and sialodacryoadenitis virus (SDAV-HE) was investigated. The crude product was purified by flash chromatography (EA / EA:MeOH; 5:1) to yield the 9-O-methyl ether ( The ether (5 mg, 0.0132 mmol) was dissolved in dioxane (0.5 mL) and NaOH (0.05M, 0.5 mL) was added with stirring. abstract: A series of sialosides modified at the 4- and 9-hydroxy group were synthesised and tested for inhibition of the viral haemagglutinin-esterase activity from various Orthomyxoviruses and Coronaviruses. While no inhibition of the sialate-4-O-acetylesterases from mouse hepatitis virus strain S or sialodacryoadenitis virus was found, a 9-O-methyl derivative displayed inhibitory activity against recombinant sialate-9-O-acetylesterase from influenza C virus. url: https://doi.org/10.1016/j.ejmech.2011.04.008 doi: 10.1016/j.ejmech.2011.04.008 id: cord-271927-u8p6c9w4 author: Stefanacci, Richard G. title: Learnings to Operate LTC Better from the COVID-19 Crisis date: 2020-09-07 words: 3454.0 sentences: 167.0 pages: flesch: 57.0 cache: ./cache/cord-271927-u8p6c9w4.txt txt: ./txt/cord-271927-u8p6c9w4.txt summary: But the indirect impact of COVID and LTC residents from social isolation causing weight loss, falls, delirium, dementia and depression as well as staff burn out will likely cause early deaths that may be even more significant. And what I mean by that it''s an opportunity to do things you think you could not do before.‖ This COVID-19 is a serious crisis that we should not let go to waste but rather use as an opportunity operate differently around improving socialization, senses and staff support. For residents of health care facilities and staff the COVID-19 pandemic has added to our existing burden of daily stressors. As we navigate the COVID-19 pandemic, the need or deprescribing and optimizing medication management is more critical than it has ever been as reducing medications will potentially reduce opportunities for transmission of the virus between staff and residents. abstract: • Following is our ALC/LTC column titled - Learningsto Operate LTC Better from the COVID-19 Crisis from Drs. Stefanacci & Riddle. url: https://www.ncbi.nlm.nih.gov/pubmed/32948341/ doi: 10.1016/j.gerinurse.2020.07.014 id: cord-287151-4hlvrfeh author: Steinmann, J title: Surrogate viruses for testing virucidal efficacy of chemical disinfectants date: 2004-04-30 words: 2911.0 sentences: 173.0 pages: flesch: 43.0 cache: ./cache/cord-287151-4hlvrfeh.txt txt: ./txt/cord-287151-4hlvrfeh.txt summary: Abstract Since important agents of viral nosocomial infections like hepatitis B and C viruses and norovirus do not replicate sufficiently in cell culture systems, disinfectants with suspected efficacy against these viruses must be evaluated by different methods. Besides molecular approaches and indirect tests, the use of surrogate viruses with similar biophysical properties and genomic structure allows the assessment of virucidal efficacy of chemical disinfectants in quantitative suspension tests. By including these viruses in inactivation experiments, valuable data from suspension tests can be derived on the virucidal efficacy of chemical disinfectants. Besides the viruses mentioned in the guidelines, there are other important pathogens such as Hepatitis B virus (HBV), Hepatitis C virus (HCV) and norovirus which cause nosocomial infections but cannot be propagated sufficiently by cell culture techniques. Inactivation of hepatitis B virus in plasma by hospital in-use chemical disinfectant assessed by a modified HepG2 cell culture abstract: Abstract Since important agents of viral nosocomial infections like hepatitis B and C viruses and norovirus do not replicate sufficiently in cell culture systems, disinfectants with suspected efficacy against these viruses must be evaluated by different methods. Besides molecular approaches and indirect tests, the use of surrogate viruses with similar biophysical properties and genomic structure allows the assessment of virucidal efficacy of chemical disinfectants in quantitative suspension tests. Furthermore, insights into the survival of these viruses in the environment are possible. In recent years, duck hepatitis B virus and bovine viral diarrhoea virus have been tested as surrogates for hepatitis B and C viruses. Feline calicivirus serves as a surrogate for the group of norovirus. By including these viruses in inactivation experiments, valuable data from suspension tests can be derived on the virucidal efficacy of chemical disinfectants. Even in vivo tests using fingerpads of adult volunteers can be performed with these animal viruses without risk of infection. In contrast to in vitro examinations, the results of these tests allow use recommendations of chemical disinfectants for outbreak situations and daily routine disinfection. url: https://www.sciencedirect.com/science/article/pii/S0195670103005188 doi: 10.1016/j.jhin.2003.12.030 id: cord-331244-zaguyxm5 author: Stephenson, Iain title: Confronting the avian influenza threat: vaccine development for a potential pandemic date: 2004-07-30 words: 8192.0 sentences: 452.0 pages: flesch: 38.0 cache: ./cache/cord-331244-zaguyxm5.txt txt: ./txt/cord-331244-zaguyxm5.txt summary: In clinical trials, conventional surfaceantigen influenza virus vaccines produced from avian viruses have proved poorly immunogenic in immunologically naive populations. In clinical trials, conventional surfaceantigen influenza virus vaccines produced from avian viruses have proved poorly immunogenic in immunologically naive populations. The main antigenic determinants of influenza A and B viruses are two surface glycoproteins: the neuraminidase and the haemagglutinin, both capable of eliciting immune responses in human beings. Pandemic influenza viruses arise by this process of "antigenic shift", when a virus with a new haemagglutinin subtype emerges and spreads efficiently in a naive human population. 14 These reassortant viruses have haemagglutinin receptor-binding sequences potentially capable of human infection, suggesting that new viruses may emerge directly from the avian pool. Improved understanding of the antigenic and molecular associations between potential pandemic strains of same subtype Improved understanding of immunogenicity against drifted avian influenza strains is required as the ability to generate broad crossprotective immunity is desirable in vaccine candidate. abstract: Sporadic human infection with avian influenza viruses has raised concern that reassortment between human and avian subtypes could generate viruses of pandemic potential. Vaccination is the principal means to combat the impact of influenza. During an influenza pandemic the immune status of the population would differ from that which exists during interpandemic periods. An emerging pandemic virus will create a surge in worldwide vaccine demand and new approaches in immunisation strategies may be needed to ensure optimum protection of unprimed individuals when vaccine antigen may be limited. The manufacture of vaccines from pathogenic avian influenza viruses by traditional methods is not feasible for safety reasons as well as technical issues. Strategies adopted to overcome these issues include the use of reverse genetic systems to generate reassortant strains, the use of baculovirusexpressed haemagglutinin or related non-pathogenic avian influenza strains, and the use of adjuvants to enhance immunogenicity. In clinical trials, conventional surfaceantigen influenza virus vaccines produced from avian viruses have proved poorly immunogenic in immunologically naive populations. Adjuvanted or whole-virus preparations may improve immunogenicity and allow sparing of antigen. url: https://api.elsevier.com/content/article/pii/S1473309904011053 doi: 10.1016/s1473-3099(04)01105-3 id: cord-316894-zhmuzv7z author: Stetzenbach, L.D. title: Airborne Infectious Microorganisms date: 2009-02-17 words: 4393.0 sentences: 259.0 pages: flesch: 40.0 cache: ./cache/cord-316894-zhmuzv7z.txt txt: ./txt/cord-316894-zhmuzv7z.txt summary: Viral diseases presented are influenza, severe acute respiratory syndrome (SARS), Norwalk-like viruses (NLVs) and hantavirus disease, measles, and varicella. Exposure to some Gram-negative and Gram-positive bacteria, endotoxin, and actinomycetes when dispersed through the air can result in disease following inhalation. Inhalation of microbial aerosols can elicit adverse human health effects including infection, allergic reaction, inflammation, and respiratory disease. Inhalation of microbial aerosols can elicit adverse human health effects including infection, allergic reaction, inflammation, and respiratory disease. The illnesses resulting from avian influenza infection in humans range from typical mild influenza-like symptoms (e.g., fever, sore throat, cough, and muscle aches) and conjunctivitis to more serious cases of pneumonia, acute respiratory distress, and other severe and life-threatening complications. Disease is spread by aerosol dissemination of the virus during coughing and sneezing by an infected person or it may become airborne directly from the skin lesions. abstract: Inhalation exposes the upper and lower respiratory tracts of humans to a variety of airborne particles and vapors. Airborne transmission of pathogenic microorganisms to humans from the environment, animals, or other humans can result in disease. Inhalation is an important route of exposure as the lung is more susceptible to infection than the gastrointestinal tract. Ingested microorganisms must past through the acidic environment of the stomach before they can colonize tissue while inhaled microorganisms are deposited directly on the moist surfaces of the respiratory tract. Inhalation of microbial aerosols can elicit adverse human health effects including infection, allergic reaction, inflammation, and respiratory disease. Following inhalation, infectious viruses, bacteria, and fungi can establish in host cells of the respiratory tract. Some are translocated and infect the gastrointestinal tract and other tissues. This chapter discusses human viral, bacterial, and fungal diseases transmitted via aerosols. Viral diseases presented are influenza, severe acute respiratory syndrome (SARS), Norwalk-like viruses (NLVs) and hantavirus disease, measles, and varicella. Bacterial diseases are Legionnaires’ disease, tuberculosis, and nontubercule mycobacterial disease. Exposure to some Gram-negative and Gram-positive bacteria, endotoxin, and actinomycetes when dispersed through the air can result in disease following inhalation. Fungal diseases included are histoplasmosis, coccidiomycosis, blastomycosis, cryptococcosis, and aspergillosis. The threat of bioterrorism with airborne infectious agents is also briefly presented. url: https://www.sciencedirect.com/science/article/pii/B9780123739445001772 doi: 10.1016/b978-012373944-5.00177-2 id: cord-006089-08g206kf author: Stevens, James title: Glycan microarray technologies: tools to survey host specificity of influenza viruses date: 2006-10-02 words: 6075.0 sentences: 255.0 pages: flesch: 41.0 cache: ./cache/cord-006089-08g206kf.txt txt: ./txt/cord-006089-08g206kf.txt summary: These proteins are rich in α2-3-linked sialosides (sialylated glycans), and function to trap avian influenza viruses and prevent their attachment to epithelial cells 12 Recent studies have revealed that some human epithelial cells in the lower respiratory tract contain α2-3-linked sialic acids and can be directly infected by avian influenza viruses 10, 11, 13 . Therefore, it is clear that, although human and avian virus HAs have a primary specificity for either α2-6or α2-3-linked sialosides, each virus might use a different range of glycan receptors for cell entry, and the ability of a virus to infect a host cell might depend on features in the glycan structure, other than simply the type of sialic-acid linkage. By working together, future development of DNA and glycan microarray technologies could enable rapid assessment of emerging viruses to detect virus subtypes and receptor specificities that increase the risk to the human population, and to eliminate guesswork from sequence analyses alone. abstract: New technologies are urgently required for rapid surveillance of the current H5N1 avian influenza A outbreaks to gauge the potential for adaptation of the virus to the human population, a crucial step in the emergence of pandemic influenza virus strains. Owing to the species-specific nature of the interaction between the virus and host glycans, attention has recently focused on novel glycan array technologies that can rapidly assess virus receptor specificity and the potential emergence of human-adapted H5N1 viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7097745/ doi: 10.1038/nrmicro1530 id: cord-256325-q70rky3r author: Stewart, Cameron R. title: A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease date: 2017-07-04 words: 8310.0 sentences: 409.0 pages: flesch: 43.0 cache: ./cache/cord-256325-q70rky3r.txt txt: ./txt/cord-256325-q70rky3r.txt summary: title: A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease Here we largely focus on findings from two recent RNAi screens to identify protein-coding genes and host-encoded microRNAs impacting the henipavirus infection cycle in human cells. X-ray data have suggested that the methylation of rRNA requires the formation of this complex with involvement of four fibrillarin molecules interacting with different regions of the target rRNAs. The yeast equivalent of fibrillarin, NOP1, has been more extensively studied than the human counterpart but fibrillarin is a well-conserved protein in most organisms, reinforcing the notion that all post-transcriptional processes involving fibrillarin such as chemical modification (methylation) of rRNA, pre-rRNA cleavage and ribosome assembly are essential for proper cellular functioning (Rodriguez-Corona et al. Deffrasnes and colleagues showed that siRNA-mediated knockdown of fibrillarin expression dramatically reduced HeV protein production and viral genome replication but did not impact viral fusion, and that fibrillarin catalytic activity was essential to henipavirus infection. abstract: Hendra and Nipah viruses (family Paramyxoviridae, genus Henipavirus) are zoonotic RNA viruses that cause lethal disease in humans and are designated as Biosafety Level 4 (BSL4) agents. Moreover, henipaviruses belong to the same group of viruses that cause disease more commonly in humans such as measles, mumps and respiratory syncytial virus. Due to the relatively recent emergence of the henipaviruses and the practical constraints of performing functional genomics studies at high levels of containment, our understanding of the henipavirus infection cycle is incomplete. In this chapter we describe recent loss-of-function (i.e. RNAi) functional genomics screens that shed light on the henipavirus–host interface at a genome-wide level. Further to this, we cross-reference RNAi results with studies probing host proteins targeted by henipavirus proteins, such as nuclear proteins and immune modulators. These functional genomics studies join a growing body of evidence demonstrating that nuclear and nucleolar host proteins play a crucial role in henipavirus infection. Furthermore these studies will underpin future efforts to define the role of nucleolar host–virus interactions in infection and disease. url: https://doi.org/10.1007/82_2017_28 doi: 10.1007/82_2017_28 id: cord-018724-ss8x2g3b author: Stobbe, Anthony title: Plant Virus Diversity and Evolution date: 2016-06-22 words: 7456.0 sentences: 360.0 pages: flesch: 47.0 cache: ./cache/cord-018724-ss8x2g3b.txt txt: ./txt/cord-018724-ss8x2g3b.txt summary: The variation we see within a single plant host has profound effects on the how the virus responds to selective pressures associated with new hosts, and factors such as the bottleneck events associated with cell-to-cell movement or vectoring. However, several forms of virus variation, such as the high mutation rates of RNA and some DNA viruses, recombination, and reassortment lead to resistance breaking (Duffy and Holmes 2008; McDonald and Linde 2002; Harrison 2002) . For example, genetic diversity (heterosis) induced tolerance to Turnip mosaic virus in wild cress (Lepidium sp.) hybrids, while plants that were selfed were more susceptable to disease, suggesting that small populations with low genetic diversity could lead to increased disease symptoms, and infection rates (Houliston et al. Genetic bottlenecks during systemic movement of Cucumber mosaic virus vary in different host plants Role of recombination in the evolution of natural populations of Cucumber mosaic virus, a tripartite RNA plant virus abstract: Historically, the majority of plant virology focused on agricultural systems. Recent efforts have expanded our knowledge of the true diversity of plant viruses by studying those viruses that infect wild, undomesticated plants. Those efforts have provided answers to basic ecological questions regarding viruses in the wild, and insights into evolutionary questions, regarding the origins of viruses. While much work has been done, we have merely scratched the surface of the diversity that is estimated to exist. In this chapter we discuss the state of our knowledge of virus diversity, both in agricultural systems as well as in native wild systems, the border between these two systems and how viruses adapt and move across this border into an artificial, domesticated environment. We look at how this diversity has affected our outlook on viruses as a whole, shifting our past view of viruses as purely antagonistic entities of destruction to one where viruses are in a mutually beneficial relationship with their hosts. Additionally, we discuss the current work that plant virology has put forth regarding the evolutionary mechanisms, the life histories, and the deep evolution of viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123681/ doi: 10.1007/978-3-319-32919-2_8 id: cord-280781-u3wd27rn author: Stohlman, S. A. title: Stability of neurotropic mouse hepatitis virus (JHM strain) during chronic infection of neuroblastoma cells date: 1978 words: 3509.0 sentences: 184.0 pages: flesch: 50.0 cache: ./cache/cord-280781-u3wd27rn.txt txt: ./txt/cord-280781-u3wd27rn.txt summary: title: Stability of neurotropic mouse hepatitis virus (JHM strain) during chronic infection of neuroblastoma cells A line of mouse neuroblastoma cells which was chronically infected with the neurotropic strain (JHM) of MHV, a member of the coronavirus group, was established. The addition of low concentration antiviral antibody modulated the infection to a carrier culture with viral antigen in the cytoplasm of the cells, but no infectious virus was produced, and the cells lacked both surface viral antigen and CPE. Following incubation at room temperature for 30 minutes in the presence of anti-JHM hyperimmune aseitie fluid (50 per cent plaque reduction neutralization titer = 1/1~00), serial dilutions were plated on the indicator monolayers and fixed with 0.5 ml of DMEM plus 5 per cent FBS containing 0.6 per cent agarose. Figure 3 shows that following the initial passage in the presence of antibody, there was an increase in both the supernatant and cell associated virus titer, which rapidly declined until after 4 serial passages no infectious virus was detectable. abstract: A line of mouse neuroblastoma cells which was chronically infected with the neurotropic strain (JHM) of MHV, a member of the coronavirus group, was established. These cells, designated N(J), exhibited typical MHV cytopathic effects (CPE) at all passage levels along with the continual production of infectious virus. Most cells were positive for viral antigen by immunofluorescence. Viral particles consistent with the morphology of MHV were found by electron microscopy. The uninfected neuroblastoma cell line did not contain a detectable population of cells resistant to JHM, and persistence did not elicit the production of interferon. No plaque morphology or temperature sensitive mutants were selected for in the N(J) culture, and we were unable to detect the presence of either a defective or defective interfering virus population. The addition of low concentration antiviral antibody modulated the infection to a carrier culture with viral antigen in the cytoplasm of the cells, but no infectious virus was produced, and the cells lacked both surface viral antigen and CPE. Possible mechanisms of viral persistencein vitro are discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/207241/ doi: 10.1007/bf01315637 id: cord-009615-xcz8m9a7 author: Stoner, Gerald L. title: Polyomavirus Models of Brain Infection and the Pathogenesis of Multiple Sclerosis date: 2008-01-28 words: 6395.0 sentences: 329.0 pages: flesch: 44.0 cache: ./cache/cord-009615-xcz8m9a7.txt txt: ./txt/cord-009615-xcz8m9a7.txt summary: Animal models of viral demyelination and studies showing that JC virus (JCV), the polyomavirus which causes progressive multifocal leukoencephalopathy (PML), may be latent in some normal human brains suggest another possibility. It is thought that an MS virus could be one of two basic types: 1) A rare agent which infects relatively few individuals but is frequently pathogenic, or 2) A common agent which infects a majority of the population and perhaps a significant number of normal brains, but, in which the virus expression and the host response to the infection ( Immunocytochemical studies in our laboratory indicate that perivascular cellular infiltration, apparently due to immunological reactivity to SV40 antigens, occurs in this model (Fig. 1) . Thus, simian immunodeficiency virus (S1V)-infected macaques should be observed regularly for the possible occurrence of MS-like signs with demyelination attributable to mononuclear cell infiltration in response to abortively infected glial cells, rather twa-stage process of deletion and duplication known as "brain adaptation" to generate the progressive multifocal leukoencephalopathy (PML)-type viral genome capable of replicating in glial cells of the human brain. abstract: Multiple sclerosis (MS) is generally considered to be an autoimmune disorder with myelin as the target and with several unidentified viruses playing ancillary roles, possibly through molecular mimicry. Although this paradigm has led to important progress on potential mechanisms of myelin loss, neither a target antigen in myelin nor a triggering mechanism has yet been identified, leaving the etiology of MS still unknown. Animal models of viral demyelination and studies showing that JC virus (JCV), the polyomavirus which causes progressive multifocal leukoencephalopathy (PML), may be latent in some normal human brains suggest another possibility. A host immune response targeting proteins expressed at low levels from viral DNA latent in the central nervous system (CNS) might underlie a focal demyelinating disease such as MS. A shift from autoimmunity to a latent‐virus model is not a trivial substitution of target antigens. This shift would expand the search for a definitive laboratory test for MS and could lead to improved therapeutic and preventive approaches. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7161790/ doi: 10.1111/j.1750-3639.1993.tb00748.x id: cord-281158-vjh9z7l4 author: Storch, Gregory A title: Respiratory Viruses in Babies: Important Insights From Down Under date: 2018-02-01 words: 1578.0 sentences: 69.0 pages: flesch: 44.0 cache: ./cache/cord-281158-vjh9z7l4.txt txt: ./txt/cord-281158-vjh9z7l4.txt summary: Impressive study attributes include large size, community base, enrollment from birth, scheduled frequent longitudinal sampling with or without illness, high percentage of specimen acquisition rate, even enrollment of subjects throughout the year to account for virus seasonality, and testing of samples with an extensive panel of real-time polymerase chain reaction (PCR) assays. This intensive prospective study of respiratory viruses in infants finds that human rhinovirus (HRV) is by far the most frequent virus detected in the infant respiratory tract. Of the 152 infants followed, 81% experienced a first infection with HRV by 6 months of age, compared to 8.5% for RSV, and 0.7%-9.4% for the other respiratory viruses. Timing of first respiratory virus detection in infants: a community-based birth cohort study Viral etiology of acute respiratory infections with cough in infancy: a community-based birth cohort study Etiology of acute respiratory infections in infants: a prospective birth cohort study abstract: nan url: https://doi.org/10.1093/infdis/jix600 doi: 10.1093/infdis/jix600 id: cord-293375-qcy56ui7 author: Strauss, Ellen G. title: Identification of the active site residues in the nsP2 proteinase of sindbis virus date: 1992-12-31 words: 5192.0 sentences: 265.0 pages: flesch: 56.0 cache: ./cache/cord-293375-qcy56ui7.txt txt: ./txt/cord-293375-qcy56ui7.txt summary: coma-, nepo-, and potyviruses; coronaviruses; and flaviviruses (and their proposed relatives pestiviruses and hepatitis C virus.) Originally these domains were predicted to have proteolytic activity based on the presence of certain conserved amino acid residues and on the basis of protein-modeling studies (Bazan and Fletterick, 1989; Boege et a/., 1981; Gorbalenya et al., 1989; Hahn eta/., 1985) . Furthermore, we present data to show that none of the asparagine residues in the proteinase domain of Sindbis nsP2 that are conserved among alphaviruses are absolutely required for proteolytic activity, but that Trp-559, adjacent to His-558, is essential for function. We also examined the effect of changing Cys-525, one of the two remaining conserved cysteine residues in the C-terminal half of nsP2, to serine or arginine, as well as changing Ser-535, which is found in a domain of limited similarity to the active site serine of serine proteinases, to threonine. abstract: Abstract The nonstructural polyproteins of Sindbis virus are processed by a virus-encoded proteinase which is located in the C-terminal domain of nsP2. Here we have performed a mutagenic analysis to identify the active site residues of this proteinase. Substitution of other amino acids for either Cys-481 or His-558 completely abolished proteolytic processing of Sindbis virus polyproteins in vitro. Substitutions within this domain for a second cysteine conserved among alphaviruses, for four other conserved histidines, or for a conserved serine did not affect the activity of the enzyme. These results suggest that nsP2 is a papain-like proteinase whose catalytic dyad is composed of Cys-481 and His-558. Since an asparagine residue has been implicated in the active site of papain, we changed the four conserved asparagine residues in the C-terminal half of nsP2 and found that all could be substituted without total loss of activity. Among papain-like proteinases, the residue following the catalytic histidine is alanine or glycine in the plant and animal enzymes, and the presence of Trp-559 in alphaviruses is unusual. A mutant enzyme containing Ala-559 was completely inactive, implying that Trp-559 is essential for a functional proteinase. All of these mutations were introduced into a full-length clone of Sindbis virus from which infectious RNA could be transcribed in vitro, and the effects of these changes on viability were tested. In all cases it was found that mutations which abolished proteolytic activity were lethal, whether or not these mutations were in the catalytic residues, indicating that proteolysis of the nonstructural polyprotein is essential for Sindbis replication. url: https://www.sciencedirect.com/science/article/pii/004268229290268T doi: 10.1016/0042-6822(92)90268-t id: cord-267261-8z4aqfff author: Su, John R. title: Emerging viral infections date: 2005-03-01 words: 6882.0 sentences: 400.0 pages: flesch: 45.0 cache: ./cache/cord-267261-8z4aqfff.txt txt: ./txt/cord-267261-8z4aqfff.txt summary: In 1999, a similar outbreak in pigs caused an outbreak of human encephalitis in Malaysia with a case-fatality rate approaching 40% [70] ; the causative agent was identified as a distinct but Hendra-like virus later named Nipah virus (NiV) [70] . In November 2002, cases of a new pulmonary disease, later named severe acute respiratory syndrome (SARS), were noted in the Guandong Province of China. In humans, about 20% of cases of infection with WNV lead to clinical disease, typically after an incubation period of 2 to 6 days. Virological features and clinical manifestations associated with human metapneumovirus: a new paramyxovirus responsible for acute respiratory-tract infections in all age groups Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome Detection of Severe Acute Respiratory Syndrome coronavirus in blood of infected patients abstract: "Emerging infections" have been defined as infections that have newly appeared, that have appeared previously but are expanding in incidence and geographic range, or that threaten to increase in the near future. This article focuses on nine emerging viral infectious agents. These viruses illustrate how such agents emerge: by encroaching on previously unvisited habitats (eg, hantaviruses), by air travel (eg, SARS), and by accidental importation (eg, monkeypox). Additionally, the example of SARS demonstrates not only how quickly emerging viral infections can spread but also how quickly they can be identified and contained with motivated cooperation. url: https://www.sciencedirect.com/science/article/pii/S0272271204000587 doi: 10.1016/j.cll.2004.05.002 id: cord-002757-upwe0cpj author: Sullivan, Kathleen E. title: Emerging Infections and Pertinent Infections Related to Travel for Patients with Primary Immunodeficiencies date: 2017-08-07 words: 24212.0 sentences: 1364.0 pages: flesch: 40.0 cache: ./cache/cord-002757-upwe0cpj.txt txt: ./txt/cord-002757-upwe0cpj.txt summary: The first section addresses general considerations, the second section profiles specific infections organized according to mechanism of transmission, and the third section focuses on unique phenotypes and unique susceptibilities in patients with PIDDs. This review does not address most parasitic diseases. In developing countries where polio is still endemic and oral polio vaccine is essential for eradicating the disease, it is of utmost importance that all PIDD patients and family members should not receive live oral polio (OPV) because of the reported prolonged excretion of the virus for months and even years [24] . As for host factors, although severe and fatal cases have been described in healthy immunocompetent hosts [129, 130] , there is evidence to suggest that children under the age of 10 [130] and immunocompromised hosts either secondary to hematologic malignancies, immunosuppressant treatment for organ transplantation, or HIV infection are at a greater risk to develop more severe disease with higher case fatality rates [131, 132] . abstract: In today’s global economy and affordable vacation travel, it is increasingly important that visitors to another country and their physician be familiar with emerging infections, infections unique to a specific geographic region, and risks related to the process of travel. This is never more important than for patients with primary immunodeficiency disorders (PIDD). A recent review addressing common causes of fever in travelers provides important information for the general population Thwaites and Day (N Engl J Med 376:548-560, 2017). This review covers critical infectious and management concerns specifically related to travel for patients with PIDD. This review will discuss the context of the changing landscape of infections, highlight specific infections of concern, and profile distinct infection phenotypes in patients who are immune compromised. The organization of this review will address the environment driving emerging infections and several concerns unique to patients with PIDD. The first section addresses general considerations, the second section profiles specific infections organized according to mechanism of transmission, and the third section focuses on unique phenotypes and unique susceptibilities in patients with PIDDs. This review does not address most parasitic diseases. Reference tables provide easily accessible information on a broader range of infections than is described in the text. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5693703/ doi: 10.1007/s10875-017-0426-2 id: cord-003503-t6cnjwpd author: Sung, Ming-Hua title: Phylogeographic investigation of 2014 porcine epidemic diarrhea virus (PEDV) transmission in Taiwan date: 2019-03-06 words: 3362.0 sentences: 182.0 pages: flesch: 46.0 cache: ./cache/cord-003503-t6cnjwpd.txt txt: ./txt/cord-003503-t6cnjwpd.txt summary: Acknowledging the absence of a thorough investigation at the geographic level, we used 2014 outbreak sequence information from the Taiwan government''s open access databases plus GenBank records to analyze PEDV dissemination among Taiwanese pig farms. The data indicate that the 2014 Taiwan PEDV epidemic resulted from the spread of multiple strains, with strong correlations identified with pig farm numbers and sizes (measured as animal concentrations), feed mill numbers, and the number of slaughterhouses in a specifically defined geographic area. To determine specific temporal and geographic relationships associated with PEDV strain transmission, we used phylogenetic, phylodynamic and phylogeographic methods to systematically evaluate potential temporal and spatial transmission routes among Taiwanese swine farms during the 2014 outbreak. However, to date very few research efforts in Asia have utilized full genome sequencing for determining geographic structures due to the high costs and enormous amounts of computational time Phylogeographic investigation of 2014 porcine epidemic diarrhea virus transmission in Taiwan required for analyses [33, 34] . abstract: The porcine epidemic diarrhea virus (PEDV) that emerged and spread throughout Taiwan in 2014 triggered significant concern in the country’s swine industry. Acknowledging the absence of a thorough investigation at the geographic level, we used 2014 outbreak sequence information from the Taiwan government’s open access databases plus GenBank records to analyze PEDV dissemination among Taiwanese pig farms. Genetic sequences, locations, and dates of identified PEDV-positive cases were used to assess spatial, temporal, clustering, GIS, and phylogeographic factors affecting PEDV dissemination. Our conclusion is that S gene sequences from 2014 PEDV-positive clinical samples collected in Taiwan were part of the same Genogroup 2 identified in the US in 2013. According to phylogenetic and phylogeographic data, viral strains collected in different areas were generally independent of each other, with certain clusters identified across different communities. Data from GIS and multiple potential infection factors were used to pinpoint cluster dissemination in areas with large numbers of swine farms in southern Taiwan. The data indicate that the 2014 Taiwan PEDV epidemic resulted from the spread of multiple strains, with strong correlations identified with pig farm numbers and sizes (measured as animal concentrations), feed mill numbers, and the number of slaughterhouses in a specifically defined geographic area. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6402684/ doi: 10.1371/journal.pone.0213153 id: cord-001834-6xf4o3oy author: Sung, Pil Soo title: Interferon Response in Hepatitis C Virus (HCV) Infection: Lessons from Cell Culture Systems of HCV Infection date: 2015-10-07 words: 4039.0 sentences: 230.0 pages: flesch: 44.0 cache: ./cache/cord-001834-6xf4o3oy.txt txt: ./txt/cord-001834-6xf4o3oy.txt summary: In HCV-infected cells, viral RNA is sensed by retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated protein 5 (MDA-5) in the cytoplasm and Toll-like receptor 3 (TLR3) in the endosome, which leads to downstream signaling that results in the induction of type III and I IFNs and other inflammatory cytokines [28, [36] [37] [38] [39] . Intracellular signals from RIG-I, MDA-5, and TLR3 are transmitted via mitochondrial antiviral signaling protein (MAVS) and Toll/IL-1 receptor domain-containing adaptor inducing IFN- (TRIF), respectively, which leads to the interferon regulatory factor-3 (IRF-3)-dependent induction of IFNs and NF-κB activation in HCV-infected cells [38, 39] . IFN-s activate the same JAK-STAT pathway as type I IFNs [48] [49] [50] , thereby inducing a similar set of ISGs. Although the exact source of IFN-s in HCV-infected liver remains to be clarified, it seems that the production of IFN-s by HCV-infected hepatocytes results in the expression of ISGs, presumably through autocrine and/or paracrine signaling via the IFN-λ receptor [28, [44] [45] [46] . HCV infection induces a unique hepatic innate immune response associated with robust production of type III interferons abstract: Hepatitis C virus (HCV) is a positive-stranded RNA virus that infects approximately 130–170 million people worldwide. In 2005, the first HCV infection system in cell culture was established using clone JFH-1, which was isolated from a Japanese patient with fulminant HCV infection. JFH-1 replicates efficiently in hepatoma cells and infectious virion particles are released into the culture supernatant. The development of cell culture-derived HCV (HCVcc) systems has allowed us to understand how hosts respond to HCV infection and how HCV evades host responses. Although the mechanisms underlying the different outcomes of HCV infection are not fully understood, innate immune responses seem to have a critical impact on the outcome of HCV infection, as demonstrated by the prognostic value of IFN-λ gene polymorphisms among patients with chronic HCV infection. Herein, we review recent research on interferon response in HCV infection, particularly studies using HCVcc infection systems. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632721/ doi: 10.3390/ijms161023683 id: cord-255096-27dfbhsl author: Sweet, Michael J. title: Reprint of ‘Diseases in marine invertebrates associated with mariculture and commercial fisheries’ date: 2016-06-19 words: 18108.0 sentences: 1017.0 pages: flesch: 52.0 cache: ./cache/cord-255096-27dfbhsl.txt txt: ./txt/cord-255096-27dfbhsl.txt summary: Interestingly, although there are countless examples of the spread of disease usually associated with transportation of specific infected hosts for development of aquaculture practices, this process appears to be continuing with no real sign of effective management and mitigation strategies being implicated. In this review, we are not listing all known diseases for the three main commercially important phyla/ sub-phyla and/or class (echinoderms, crustaceans and molluscs), but instead focus on those which likely pose a major threat and/or are infecting large populations of both wild and farmed organisms around the world. Hosts affected: Again, this disease predominantly occurs during the auricularia stages of development of many different sea cucumber species, with mortality being recorded as high as 90% in certain cases (Zhang et al., 2010) . Furthermore, diseases caused by Platyhelminthiasis have been shown to infect both aestivated juveniles (larger than 1 cm) and adults of many different sea cucumber species. abstract: Diseases in marine invertebrates are increasing in both frequency and intensity around the globe. Diseases in individuals which offer some commercial value are often well documented and subsequently well studied in comparison to those wild groups offering little commercial gain. This is particularly the case with those associated with mariculture or the commercial fisheries. Specifically, these include many Holothuroidea, and numerous crustacea and mollusca species. Pathogens/parasites consisting of both prokaryotes and eukaryotes from all groups have been associated with diseases from such organisms, including bacteria, viruses, fungi and protozoa. Viral pathogens in particular, appear to be an increasingly important group and research into this group will likely highlight a larger number of diseases and pathogens being described in the near future. Interestingly, although there are countless examples of the spread of disease usually associated with transportation of specific infected hosts for development of aquaculture practices, this process appears to be continuing with no real sign of effective management and mitigation strategies being implicated. Notably, even in well developed countries such as the UK and the US, even though live animal trade may be well managed, the transport of frozen food appears to be less well so and as evidence suggests, even these to have the potential to transmit pathogens when used as a food source for example. url: https://doi.org/10.1016/j.seares.2016.06.001 doi: 10.1016/j.seares.2016.06.001 id: cord-351170-belbcrcd author: Symonds, Erin M. title: Affordable Enteric Virus Detection Techniques Are Needed to Support Changing Paradigms in Water Quality Management date: 2014-10-16 words: 3018.0 sentences: 135.0 pages: flesch: 29.0 cache: ./cache/cord-351170-belbcrcd.txt txt: ./txt/cord-351170-belbcrcd.txt summary: Although this method is known to be flawed (see below), FIB are still widely used as an indicator of enteric pathogens and human health risks due to their consistent presence in wastewater and the readily available, low cost, culture-based methods for detection that require minimal laboratory training [14] [15] [16] [17] . As a result of the inadequacy of FIB monitoring to determine human health risks associated with enteric pathogens, particularly viruses, alternative approaches to traditional microbial quality monitoring have been recommended (Fig. 1C) . Finally, the utility of incorporating specific enteric viruses and/or a viral indicator to identify wastewater pollution/poor microbial quality and to better predict human health risks related to wastewater exposure has been demonstrated throughout the world [14-16, 22, 24, 25] . In conjunction with water management advances, the development of simple, affordable, lab-free tests for the rapid detection of enteric viruses and/or viral indicators is essential for ensuring worldwide improvements in microbial safety. abstract: In light of water quality monitoring paradigms shifting to a more holistic approach, it is essential that environmental microbiologists embrace new methodological developments in clinical virology to create rapid, laboratory‐free methods for the identification of wastewater pollution. It is widely accepted that routine monitoring of fecal indicator bacteria (FIB) does not adequately reflect human health risks associated with fecal pollution, especially risks posed by viruses. Enteric viruses are typically more resistant to wastewater treatment and persist longer in the environment than FIB. Furthermore, enteric viruses often have extremely low infectious doses. Currently, the incorporation of sanitary surveys, short‐term monitoring of reference pathogens, exploratory quantitative microbial risk assessments, and predictive ecological models is being championed as the preferred approach to water management. In addition to improved virus concentration methods, simple, point‐of‐use tests for enteric viruses and/or improved viral indicators are needed to complement this emerging paradigm and ensure microbial safety worldwide. url: https://www.ncbi.nlm.nih.gov/pubmed/32313585/ doi: 10.1002/clen.201400235 id: cord-265642-7mu530yp author: Syomin, B. V. title: Virus-Like Particles as an Instrument of Vaccine Production date: 2019-06-17 words: 7107.0 sentences: 325.0 pages: flesch: 41.0 cache: ./cache/cord-265642-7mu530yp.txt txt: ./txt/cord-265642-7mu530yp.txt summary: Using protein expression systems it is possible to produce virus-like particles (VLPs), which are made up of monomers, which are able to multimerize into VLPs, and display the antigenic determinants of target pathogens on their surface. For example, in different laboratories different eukaryotic systems for viral protein expression, including plant cells, are used to produce VLPs which are used for vaccination against the hepatitis C virus (HCV) [36] . Antigen of the duck hepatitis A virus produced in the baculovirus expression system assembles into VLPs immediately in the cultured Spodoptera frugiperda (sf9) cells, while immunization of ducklings with the obtained VLPs induces a high level humoral immune response and protects them from developing the disease [46] . Expression vectors for foreign protein production in plants have been developed based on plant viruses, which allows obtaining plant-producing recombinant viruses or VLPs displaying the target antigen on their surface [101, 102] . abstract: The paper discusses the techniques which are currently implemented for vaccine production based on virus-like particles (VLPs). The factors which determine the characteristics of VLP monomers assembly are provided in detail. Analysis of the literature demonstrates that the development of the techniques of VLP production and immobilization of target antigens on their surface have led to the development of universal platforms which make it possible for virtually any known antigen to be exposed on the particle surface in a highly concentrated form. As a result, the focus of attention has shifted from the approaches to VLP production to the development of a precise interface between the organism’s immune system and the peptides inducing a strong immune response to pathogens or the organism’s own pathological cells. Immunome-specified methods for vaccine design and the prospects of immunoprophylaxis are discussed. Certain examples of vaccines against viral diseases and cancers are considered. url: https://doi.org/10.1134/s0026893319030154 doi: 10.1134/s0026893319030154 id: cord-004034-mjkixqhs author: Szilasi, Anna title: Prevalence of feline immunodeficiency virus and feline leukaemia virus in domestic cats in Hungary date: 2019-12-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: Feline immunodeficiency virus (FIV) and feline leukaemia virus (FeLV) are retroviruses affecting cats worldwide. The objectives of the study were to estimate the prevalence of these retroviruses in domestic cats in Hungary and to characterise the phylogenetic relationships of FIV strains. METHODS: A total of 335 anticoagulated whole-blood samples obtained from both a healthy and ill cat population were examined for the presence of FIV and FeLV with two methods: ELISA and PCR. Statistical analysis was carried out to analyse the data obtained. Sequencing and phylogenetic analysis of partial polymerase (pol) gene sequences was performed to describe circulating FIV subtypes. RESULTS: Statistical analysis showed 11.8% and 9.9% true prevalence of FeLV and FIV, respectively, with ELISA. The apparent prevalence calculated from the PCR results were 17.3% for FeLV and 13.1% for FIV. Phylogenetic analysis of partial pol gene sequences obtained from 22 FIV strains showed that all observed Hungarian strains belonged to FIV subtype B. The strains were grouped into several monophyletic subgroups reflecting the geographic locations of the origin of the samples. The overall mean genetic similarity between the analysed strains was 98.2%. CONCLUSIONS AND RELEVANCE: We report the first thorough overview of the prevalence of FeLV and FIV in Hungary, which is relatively high, and give insight into the genetic diversity of Hungarian strains of FIV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6904780/ doi: 10.1177/2055116919892094 id: cord-260014-q5sug7uu author: Szűcs, Zsolt title: Reprogramming of the Antibacterial Drug Vancomycin Results in Potent Antiviral Agents Devoid of Antibacterial Activity date: 2020-06-29 words: 5179.0 sentences: 333.0 pages: flesch: 51.0 cache: ./cache/cord-260014-q5sug7uu.txt txt: ./txt/cord-260014-q5sug7uu.txt summary: We prepared six vancomycin aglycone hexapeptide derivatives with the aim of obtaining compounds having anti-influenza virus but no antibacterial activity. On the other hand, this result is in line with our previous findings on ristocetin and teicoplanin aglycone derivatives, indicating that even minor structural differences in the peptide core can lead to significantly different anti-influenza virus activity [27] . On the other hand, this result is in line with our previous findings on ristocetin and teicoplanin aglycone derivatives, indicating that even minor structural differences in the peptide core can lead to significantly different anti-influenza virus activity [27] . Hence, we established, by virus yield assays, that compound 6 suppresses the replication of influenza virus and coronavirus, and for the other viruses, activity was indicated by the protection against viral CPE. Diazo transfer-click reaction route to new, lipophilic teicoplanin and ristocetin aglycon derivatives with high antibacterial and anti-influenza virus activity: An aggregation and receptor binding study abstract: Influenza A and B viruses are a global threat to human health and increasing resistance to the existing antiviral drugs necessitates new concepts to expand the therapeutic options. Glycopeptide derivatives have emerged as a promising new class of antiviral agents. To avoid potential antibiotic resistance, these antiviral glycopeptides are preferably devoid of antibiotic activity. We prepared six vancomycin aglycone hexapeptide derivatives with the aim of obtaining compounds having anti-influenza virus but no antibacterial activity. Two of them exerted strong and selective inhibition of influenza A and B virus replication, while antibacterial activity was successfully eliminated by removing the critical N-terminal moiety. In addition, these two molecules offered protection against several other viruses, such as herpes simplex virus, yellow fever virus, Zika virus, and human coronavirus, classifying these glycopeptides as broad antiviral molecules with a favorable therapeutic index. url: https://www.ncbi.nlm.nih.gov/pubmed/32610683/ doi: 10.3390/ph13070139 id: cord-017287-70lk77zb author: Sánchez, Gloria title: Survival of Enteric Viruses in the Environment and Food date: 2016-08-26 words: 8962.0 sentences: 450.0 pages: flesch: 44.0 cache: ./cache/cord-017287-70lk77zb.txt txt: ./txt/cord-017287-70lk77zb.txt summary: In the last decade, epidemiological reports indicate that enteric viruses, in particular human noroviruses (NoV), which cause acute gastroenteritis, and hepatitis A virus (HAV), are the leading cause of foodborne illness in developed countries (Koopmans and Duizer 2004 ; EFSA 2015 ) . While consumption of ready-to-eat foods contaminated by infected food handlers remains the major risk factor for viral foodborne outbreaks, many types of food products are being recognized as vehicles of viruses in causing gastroenteritis or hepatitis A outbreaks (Table 13 .1 ). These data suggest that temperature, and probably relative humidity, may be meaningful in the seasonal distribution of outbreaks of certain human enteric viruses (Enright 1954 ) , due to the infl uence of these factors on virus persistence. Survival of enteric viruses in the environment and different food products has been well studied employing cell-adapted virus strains. abstract: Enteric viruses are those human viruses that are primarily transmitted by the fecal-oral route, either by person-to-person contact or by ingestion of contaminated food or water. The importance of viral foodborne diseases is increasingly being recognized, and several international organizations have found that there is an upward trend in their incidence. Thus, in this review, state-of-the-art information regarding virus persistence in food and the environment is compiled. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121804/ doi: 10.1007/978-3-319-30723-7_13 id: cord-009504-sn00p8iw author: Taguchi, Fumihiro title: Pathogenesis of Mouse Hepatitis Virus Infection: The Role of Nasal Epithelial Cells as a Primary Target of Low‐Virulence Virus, MHV‐S date: 2013-11-14 words: 3453.0 sentences: 170.0 pages: flesch: 54.0 cache: ./cache/cord-009504-sn00p8iw.txt txt: ./txt/cord-009504-sn00p8iw.txt summary: The pathogenesis of mouse hepatitis virus (MHV‐S) infection in suckling and weanling mice was comparatively studied after intranasal inoculation. In the posterior part of the brain and spinal cord, virus was detected on days 3 to 4 postinoculation when viral growth was clearly demonstrable in the liver, spleen and intestines. In weanling mice, however, neither infectious virus nor viral antigen was detected in the liver or other visceral organs, while serum neutralizing antibody became detectable on day 5 postinoculation, increasing in titer thereafter. 2A and 2B , significant viral growth was observed in the brain, spinal cord ( Fig. 2A) and head without brain (Fig. 2B) , whereas no virus was demonstrated in the spleen or liver of the infected mice with a few exceptions (not included in the figures). In 4-week-old mice, however, no or little infectious virus was detected in the liver or other visceral organs, although high titered virus demonstrable in the brain was probably disseminated from the nasal mucosa as was observed in suckling mice. abstract: The pathogenesis of mouse hepatitis virus (MHV‐S) infection in suckling and weanling mice was comparatively studied after intranasal inoculation. In sucklings, infectious virus as well as specific antigen was first detected in the nasal mucosa at 12 hr, then in the nerve cells of the olfactory bulbs. At this stage viral particles were demonstrated both in the supporting cells and olfactory cells of the nasal mucosa. In the posterior part of the brain and spinal cord, virus was detected on days 3 to 4 postinoculation when viral growth was clearly demonstrable in the liver, spleen and intestines. In weanlings too, infection was first established in the nasal mucosa, shedding infectious virus in the nasal washing until day 6 postinoculation, and later infection spread to the brain and spinal cord. In weanling mice, however, neither infectious virus nor viral antigen was detected in the liver or other visceral organs, while serum neutralizing antibody became detectable on day 5 postinoculation, increasing in titer thereafter. Histopathologically degenerative and necrotic changes were observed in the nasal mucosa and central nervous system of both age groups of animals coincidentally with the presence of viral specific antigen, while inflammatory response was much less prominent in sucklings. In the liver, spleen and intestines, however, some lesions were observed only in sucklings. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159379/ doi: 10.1111/j.1348-0421.1979.tb00461.x id: cord-004771-4yinnncj author: Tajima, M. title: Morphology of transmissible gastroenteritis virus of pigs: A possible member of coronaviruses date: 1970 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086923/ doi: 10.1007/bf01253886 id: cord-011106-h20vbmbo author: Takeda, Yohei title: Antiviral Activities of Hibiscus sabdariffa L. Tea Extract Against Human Influenza A Virus Rely Largely on Acidic pH but Partially on a Low-pH-Independent Mechanism date: 2019-10-16 words: 5362.0 sentences: 330.0 pages: flesch: 54.0 cache: ./cache/cord-011106-h20vbmbo.txt txt: ./txt/cord-011106-h20vbmbo.txt summary: Here, we analyzed the antiviral activity of hibiscus (Hibiscus sabdariffa L.) tea extract against human IAV and evaluated its potential as a novel anti-IAV drug and a safe inactivating agent for whole inactivated vaccine. In addition, we assessed hibiscus tea extract''s potential as a candidate for novel anti-IAV drug and as an inactivating agent for whole-virus vaccines. PR8 virus propagated in allantoic fluid was mixed with an equal amount of neutral and acidic pH PBS, Hib[crude], frHibis, or PCA. 50 μl PBS, formalin-, β-PL-, or acidic Hib[crude]-inactivated PR8 virus vaccine was intranasally administered in mice (first vaccination) under light anesthesia with isolflurane (Intervet K.K., Tokyo, Japan). The neutralized Hib[crude] in the blood loses potent anti-IAV activity due to acid, and the low-pH-independent antiviral activity is inadequate to inactivate virus in vivo. abstract: Influenza A virus (IAV) infection is perennially one of the leading causes of death worldwide. Effective therapy and vaccination are needed to control viral expansion. However, current anti-IAV drugs risk inducing drug-resistant virus emergence. Although intranasal administration of whole inactivated virus vaccine can induce efficient protective immunity, formalin and β-propiolactone are the currently used and harmful inactivating agents. Here, we analyzed the antiviral activity of hibiscus (Hibiscus sabdariffa L.) tea extract against human IAV and evaluated its potential as a novel anti-IAV drug and a safe inactivating agent for whole inactivated vaccine. The in vitro study revealed that the pH of hibiscus tea extract is acidic, and its rapid and potent antiviral activity relied largely on the acidic pH. Furthermore, the mouse study showed that the acidic extract was not effective for either therapeutic or vaccination purposes. However, hibiscus tea extract and protocatechuic acid, one of the major components of the extract, showed not only potent acid-dependent antiviral activity but also weak low-pH-independent activity. The low-pH-independent activity did not affect the conformation of immunodominant hemagglutinin protein. Although this low-pH-independent activity is very limited, it may be suitable for the application to medication and vaccination because this activity is not affected by the neutral blood environment and does not lose antigenicity of hemagglutinin. Further study of the low-pH-independent antiviral mechanism and attempts to enhance the antiviral activity may establish a novel anti-IAV therapy and vaccination strategy. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223586/ doi: 10.1007/s12560-019-09408-x id: cord-325280-4whzcmqv author: Takizawa, Naoki title: Current landscape and future prospects of antiviral drugs derived from microbial products date: 2017-10-11 words: 6601.0 sentences: 365.0 pages: flesch: 34.0 cache: ./cache/cord-325280-4whzcmqv.txt txt: ./txt/cord-325280-4whzcmqv.txt summary: In this review, we summarize antiviral microbial products discovered by Institute of Microbial Chemistry (IMC) and discuss antiviral compounds against influenza virus and HBV, because these two viruses threaten global human health now and antiviral drug against these two viruses have been developed. THE CONTRIBUTIONS OF IMC TO ANTIVIRAL RESEARCH Nucleos(t)ide analogs are a major class of approved antiviral drugs that exert therapeutic effects through incorporation into viral DNA and RNA to inhibit virus replication. Viral polymerase complex is a promising target for the development of anti-influenza drugs, because transcription and replication are critical steps for virus propagation. Potential applications of microbial products in anti-HBV drug development Approved nucleos(t)ide analogs competitively inhibit DNA elongation of viral polymerase after the conversion to triphosphate form by cellular enzymes. abstract: Viral infections are a major global health threat. Over the last 50 years, significant efforts have been devoted to the development of antiviral drugs and great success has been achieved for some viruses. However, other virus infections, such as epidemic influenza, still spread globally and new threats continue to arise from emerging and re-emerging viruses and drug-resistant viruses. In this review, the contributions of microbial products isolated in Institute of Microbial Chemistry for antiviral research are summarized. In addition, the current state of development of antiviral drugs that target influenza virus and hepatitis B virus, and the future prospects for antivirals from natural products are described and discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/29018267/ doi: 10.1038/ja.2017.115 id: cord-342151-1e6x589e author: Talbot, Pierre J. title: Hemagglutination by Murine Hepatitis Viruses date: 2008-07-29 words: 1218.0 sentences: 79.0 pages: flesch: 54.0 cache: ./cache/cord-342151-1e6x589e.txt txt: ./txt/cord-342151-1e6x589e.txt summary: Erythrocytes from twelve mammalian and avian sources in ten different buffers at three incubation temperatures could not be hemagglutinated with murine hepatitis virus (MHV) strains 3, A59, or S grown on DBT cells. Viral antigen preparation in the absence of fetal calf serum, partial virus purification, or various concentrations of red blood cells still failed to yield detectable hemagglutinating activity. For use as antigen for hemag glutination assays, MHV-3 was grown in the absence of fetal calf serum (FCS) and har vested from clarified medium by precipita tion with 10% (w/v) polyethylene glycol in 0.5 M NaCl. After centrifugation at 10,000 g for 30 min, the pellet was resuspended and dialyzed against TMEN buffer: 50 mM Tris-HCi (pH 6.2), 0.1 M NaCl, 1 m M EDTA. Control hemagglutinating antigens were either rabbit enteric coronavirus (titer 1/64 with rabbit red blood cells ) or pneumonia virus of mice (titer 1/320 with CDI mouse erythrocytes). abstract: Erythrocytes from twelve mammalian and avian sources in ten different buffers at three incubation temperatures could not be hemagglutinated with murine hepatitis virus (MHV) strains 3, A59, or S grown on DBT cells. Viral antigen preparation in the absence of fetal calf serum, partial virus purification, or various concentrations of red blood cells still failed to yield detectable hemagglutinating activity. Thus, the newly described MHV-DVIM remains the only hemagglutinating strain of murine coronavirus. url: https://www.ncbi.nlm.nih.gov/pubmed/2542182/ doi: 10.1159/000150083 id: cord-254100-u6x5zd4i author: Taliansky, M.E. title: Involvement of the Plant Nucleolus in Virus and Viroid Infections: Parallels with Animal Pathosystems date: 2010-10-15 words: 13988.0 sentences: 662.0 pages: flesch: 40.0 cache: ./cache/cord-254100-u6x5zd4i.txt txt: ./txt/cord-254100-u6x5zd4i.txt summary: An increasing number of reports reveal that similar to the proteins of animal viruses, many plant virus proteins localize in the nucleolus to divert host nucleolar proteins from their natural functions in order to exert novel role(s) in the virus infection cycle. An increasing number of reports reveal that similar to the proteins of animal viruses, many plant virus proteins localize in the nucleolus to divert host nucleolar proteins from their natural functions in order to exert novel role(s) in the virus infection cycle. As their name suggests, MPs are involved in virus spread in infected plants, and the potential role of fibrillarin in this process will be discussed in Section IV.B. The multifunctional PVA (potato virus A)-encoded viral genomelinked protein (VPg) is also able to interact with fibrillarin (Rajamäki and Bonfiglioli et al. abstract: The nucleolus is a dynamic subnuclear body with roles in ribosome subunit biogenesis, mediation of cell-stress responses, and regulation of cell growth. An increasing number of reports reveal that similar to the proteins of animal viruses, many plant virus proteins localize in the nucleolus to divert host nucleolar proteins from their natural functions in order to exert novel role(s) in the virus infection cycle. This chapter will highlight studies showing how plant viruses recruit nucleolar functions to facilitate virus translation and replication, virus movement and assembly of virus-specific ribonucleoprotein (RNP) particles, and to counteract plant host defense responses. Plant viruses also provide a valuable tool to gain new insights into novel nucleolar functions and processes. Investigating the interactions between plant viruses and the nucleolus will facilitate the design of novel strategies to control plant virus infections. url: https://www.ncbi.nlm.nih.gov/pubmed/20951872/ doi: 10.1016/b978-0-12-385034-8.00005-3 id: cord-253143-73dsc6q3 author: Tang, Julian W. title: Emerging, Novel, and Known Influenza Virus Infections in Humans date: 2010-08-02 words: 5007.0 sentences: 248.0 pages: flesch: 45.0 cache: ./cache/cord-253143-73dsc6q3.txt txt: ./txt/cord-253143-73dsc6q3.txt summary: Nevertheless, the plethora of epidemiologic, diagnostic, mathematical and phylogenetic modeling, and investigative methodologies developed since the severe acute respiratory syndrome outbreak of 2003 and the subsequent sporadic human cases of avian influenza have been applied effectively and rapidly to the emergence of this novel pandemic virus. 3 In addition, sporadic, generally mild (although there has been at least 1 recorded death because of H7N7) human infections resulting from occasional bird-to-human transmissions, with low pathogenic avian influenza strains (eg, subtypes H9N2, H7N7, H7N2, and H7N3) have been ongoing since 1997, when heightened surveillance for avian influenza viruses began (Fig. 2) . Analyses of the viruses that caused the 1957 and 1968 influenza pandemics therefore proved that zoonotic transmissions of influenza viruses (ie, from animals to man) with gene reassortment were capable of generating antigenically new influenza strains, novel to human immunity, with significant effects on the public health. abstract: Influenza viruses continue to cause yearly epidemics and occasional pandemics in humans. In recent years, the threat of a possible influenza pandemic arising from the avian influenza A(H5N1) virus has prompted the development of comprehensive pandemic preparedness programs in many countries. The recent emergence of the pandemic influenza A(H1N1) 2009 virus from the Americas in early 2009, although surprising in its geographic and zoonotic origins, has tested these preparedness programs and revealed areas in which further work is necessary. Nevertheless, the plethora of epidemiologic, diagnostic, mathematical and phylogenetic modeling, and investigative methodologies developed since the severe acute respiratory syndrome outbreak of 2003 and the subsequent sporadic human cases of avian influenza have been applied effectively and rapidly to the emergence of this novel pandemic virus. This article summarizes some of the findings from such investigations, including recommendations for the management of patients infected with this newly emerged pathogen. url: https://doi.org/10.1016/j.idc.2010.04.001 doi: 10.1016/j.idc.2010.04.001 id: cord-255734-038xu4hq author: Taylor, Deborah R. title: Obstacles and advances in SARS vaccine development date: 2006-02-13 words: 5334.0 sentences: 263.0 pages: flesch: 44.0 cache: ./cache/cord-255734-038xu4hq.txt txt: ./txt/cord-255734-038xu4hq.txt summary: 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. Spike-specific monoclonal and polyclonal antibodies that neutralize the virus have been developed [51, 52] and passive transfer of immune serum into naive mice protected them from infection with SARS-CoV [18] . Mice immunized with a plasmid containing the S protein produced anti-SARS-CoV IgG [64] and developed neutralizing antibodies and a T-cell mediated response resulting in a six-fold reduction in viral titer in the lungs [65] . Inactivation of the coronavirus that induces severe acute respiratory syndrome, SARS-CoV Severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice Immunization with modified vaccinia virus Ankara-based recombinant vaccine against severe acute respiratory syndrome is associated with enhanced hepatitis in ferrets 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-018164-h5k1zsyg author: Taylor, Milton W. title: What Is a Virus? date: 2014-07-22 words: 4769.0 sentences: 260.0 pages: flesch: 60.0 cache: ./cache/cord-018164-h5k1zsyg.txt txt: ./txt/cord-018164-h5k1zsyg.txt summary: Studies of viral replication indicate that most viruses self-assemble as a result of interactions between the viral proteins to form a viral capsid that interacts with the nucleic acid to form the whole. The viral proteins are produced in one part of the cell, the replicated nucleic acid in another, and somehow they find each other, interact, and form virus particles that are expelled from the cell. Indirect contact spread includes cases where mucus from a runny nose may get onto the hands, or virus may be left on a surface such as a doorknob, telephone, or countertops, and is picked up by a second individual, who then touches his eyes or nose, resulting in infection. Vector transmission is a very common means of transmission; the best studied cases include yellow fever, dengue virus, and West Nile fever-viruses all transmitted by mosquitoes. As many as 400 million people are infected annually by dengue virus, which is caused by any one of four related viruses transmitted by mosquitoes. abstract: Viruses are built from short sequences of nucleic acid, either DNA or RNA wrapped in a protein shell. Until the invention of the electron microscope, it was impossible to visualize a virus. The first viruses to be visualized were bacteriophage, which appeared to have a head and tail-like structure. Only the nucleic acid entered the bacterial cell through the tail. Animal viruses were described as spherical or rod-shaped; they were bound to receptors and were taken up by the cell. After the crystallization of the tobacco mosaic virus, there was much discussion as to whether viruses were “living” organisms; the controversy continues to this day. Although viruses were defined in part on the basis of size and filterability, viruses much larger than the traditional viruses have recently been isolated. Studies of viral replication indicate that most viruses self-assemble as a result of interactions between the viral proteins to form a viral capsid that interacts with the nucleic acid to form the whole. The viral replication cycle and synthesis is presented in this chapter. Viral classification into a Linnaean scheme has been proposed, but newer methods using nucleic acid homologies are changing classification. Viruses are spread in the human population by various means, including airborne particles, fecal-oral contact, clothing, insects, and contact with other animals (zoonosis). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122971/ doi: 10.1007/978-3-319-07758-1_2 id: cord-018441-r6wwpfcy author: Taylor, Milton W. title: Emerging Viruses date: 2014-07-22 words: 3674.0 sentences: 210.0 pages: flesch: 63.0 cache: ./cache/cord-018441-r6wwpfcy.txt txt: ./txt/cord-018441-r6wwpfcy.txt summary: Most of these viruses are terrifying, and cause hemorrhagic fever, a complete destruction of the circulation system; they include Lassa fever, Nipah virus, Ebola, HIV, Severe acute respiratory syndrome (SARS), and, recently, Middle East respiratory syndrome (MERS), which is the latest in a series of "new" respiratory viruses infecting man. From 2001 to 2012 there were 280 cases of Nipah virus infections in humans, with 211 deaths-a mortality rate of 75 %. Ebola outbreaks occur with ferocity and suddenness, and with high mortality; they may originate from bats, and the virus spreads easily to a susceptible human population. Ebola is the most lethal human viral infection known, First identified in 1976 in Zaire and the Sudan, it causes hemorrhagic fever (internal bleeding) with a mortality rate of 88 %. The SARS epidemic also showed how international cooperation among health care experts can effectively contain the The virus spread from southern China to Singapore, Taiwan, the U.S. and Canada (Ontario). abstract: Emerging viruses are viruses that appear suddenly in the human population. These are viruses to which man has no history of exposure and thus no or limited immunity; they are not new evolutionary creations, but are viruses than man meets due to environmental changes, such as deforestation, entering into new habitats, or viruses that are transmitted from one species of animal to humans. Most of these viruses are terrifying, and cause hemorrhagic fever, a complete destruction of the circulation system; they include Lassa fever, Nipah virus, Ebola, HIV, Severe acute respiratory syndrome (SARS), and, recently, Middle East respiratory syndrome (MERS), which is the latest in a series of “new” respiratory viruses infecting man. It is possible that unknown emerging viruses are the cause of death, often listed as “death due to an unknown cause,” as in the retrospective cases of HIV. Emerging viruses might also include poliovirus and influenza, since their introduction into the human population is (was) often sudden and due to changes in the environment or due to contact with other animal species. For examples, polio was a result of changes in sanitation in the countries of North America and Western Europe, and influenza is constantly jumping from aquatic birds to man and other animal species where genomic reassortment occurs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123315/ doi: 10.1007/978-3-319-07758-1_20 id: cord-278482-j5zlismf author: Taylor, Raymond title: BCX4430 – A broad-spectrum antiviral adenosine nucleoside analog under development for the treatment of Ebola virus disease date: 2016-06-30 words: 2543.0 sentences: 131.0 pages: flesch: 47.0 cache: ./cache/cord-278482-j5zlismf.txt txt: ./txt/cord-278482-j5zlismf.txt summary: Summary The adenosine nucleoside analog BCX4430 is a direct-acting antiviral drug under investigation for the treatment of serious and life-threatening infections from highly pathogenic viruses, such as the Ebola virus. The adenosine nucleoside analog BCX4430 is a direct-acting antiviral drug under investigation for the treatment of serious and life-threatening infections from highly pathogenic viruses, such as the Ebola virus. In a study in cynomolgus macaques infected with MARV [5] , 0/6 controls survived compared to 17/18 animals treated with a 15 mg/kg BD dose of The maximum viral load, as measured by quantitation of viral RNA copies in the peripheral blood, was reduced by ∼600-fold (geometric mean 0.008 × 10 9 compared to 4.79 × 10 9 copies/mL, p < 0.0005). The slope of the relationship of the dose of BCX4430 to both antiviral effect and survival in nonclinical models of lethal viral infections is steep. abstract: Summary The adenosine nucleoside analog BCX4430 is a direct-acting antiviral drug under investigation for the treatment of serious and life-threatening infections from highly pathogenic viruses, such as the Ebola virus. Cellular kinases phosphorylate BCX4430 to a triphosphate that mimics ATP; viral RNA polymerases incorporate the drug's monophosphate nucleotide into the growing RNA chain, causing premature chain termination. BCX4430 is active in vitro against many RNA viral pathogens, including the filoviruses and emerging infectious agents such as MERS-CoV and SARS-CoV. In vivo, BCX4430 is active after intramuscular, intraperitoneal, and oral administration in a variety of experimental infections. In nonclinical studies involving lethal infections with Ebola virus, Marburg virus, Rift Valley fever virus, and Yellow Fever virus, BCX4430 has demonstrated pronounced efficacy. In experiments conducted in several models, both a reduction in the viral load and an improvement in survival were found to be related to the dose of BCX4430. A Phase 1 clinical trial of intramuscular administration of BCX4430 in healthy subjects is currently ongoing. url: https://api.elsevier.com/content/article/pii/S1876034116300193 doi: 10.1016/j.jiph.2016.04.002 id: cord-016663-qnp99m7o author: Taylor, Robert B. title: Medical Words Linked to Places date: 2017-02-01 words: 4835.0 sentences: 251.0 pages: flesch: 63.0 cache: ./cache/cord-016663-qnp99m7o.txt txt: ./txt/cord-016663-qnp99m7o.txt summary: In addition to causing fever and malaise, when the patient is pregnant, the Zika virus may also cause birth defects, notably microcephaly (from Greek words meaning "small" and "head"). In addition to mosquito-borne infection, we now have discovered sexually transmitted Zika virus disease and continue to learn more each year. The West Nile virus is a member of the family Flaviviridae, from the Latin flavus, meaning "yellow." The family was named for the yellow fever virus, which tends to cause liver damage, giving its victims a yellow jaundiced appearance ( Fig. 5.2 ). The disease is caused by Borrelia bacteria, notably Borrelia burgdorferi, and is spread by the same vector as Nantucket fever/babesiosis: the Ixodes tick, also called the deer tick. Also sometimes called tick typhus or blue disease, Rocky Mountain spotted fever was first recognized in 1896 in the Snake River Valley in the Rocky Mountains of the Western United States. abstract: Many medical terms come from places: towns, rivers, islands, forests, mountains, valleys, countries, and continents. These toponymous diseases, syndromes, descriptors, and other entities bring us colorful names that help us recall some of their history. Today we have Zika virus, its name coming from the Zika Forest in Ghana. Caucasian comes from the Caucasus Mountains, lesbian from the island of Lesbos, and Epsom salts from a mineral spring in Epsom, Surrey, England. Chapter 10.1007/978-3-319-50328-8_5 tells the stories behind these place-named diseases and how many of them affect us today. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121021/ doi: 10.1007/978-3-319-50328-8_5 id: cord-344576-upsc9cf8 author: Taylor-Robinson, Andrew W title: A vaccine effective against Zika virus is theoretically possible but may not be delivered anytime soon date: 2016-07-05 words: 2604.0 sentences: 154.0 pages: flesch: 52.0 cache: ./cache/cord-344576-upsc9cf8.txt txt: ./txt/cord-344576-upsc9cf8.txt summary: In February this year, the World Health Organization declared that further to the then unconfirmed association between the virus and the clinical manifestations of microcephaly and also Guillain-Barré syndrome, the Zika epidemic was a "public health emergency of international concern". No anti-Zika therapy, vaccine or drug, is currently available and while the production of the former has now been prioritized by multiple funding agencies, the history of infectious disease vaccine development indicates that this may take several years to reach the market place. A more rapid spread of the virus via the intercontinental travel of infected persons is an additional concern, although for Zika to become established in a location distant to an endemic area requires local transmission of the initially imported focus of infection; this is dependent on the availability of the vector. Local transmission of Zika virus infection is possible in Australia but should be contained by current vector control measures abstract: Following the first report in May 2015 of the unexpected emergence of Zika in north east Brazil, there has been an explosive epidemic of this infection across Latin America. The outbreak has caused alarm among social and news media as to the virulence and transmission potential of the Aedes mosquito-borne virus. This debate is heightened by the proximity, both in time and distance, to the forthcoming Olympic Games to be held in Rio de Janeiro this August, provoking fears for the safety of athletes and spectators alike. The threat, real or perceived, is exacerbated by the movement between nations in the same or separate continents of persons who act unwittingly as asymptomatic carriers. Pregnant females are considered at greatest risk because microcephaly in newborn infants is linked to, if not yet proven as caused by, Zika infection. In February this year, the World Health Organization declared that further to the then unconfirmed association between the virus and the clinical manifestations of microcephaly and also Guillain-Barré syndrome, the Zika epidemic was a “public health emergency of international concern”. No anti-Zika therapy, vaccine or drug, is currently available and while the production of the former has now been prioritized by multiple funding agencies, the history of infectious disease vaccine development indicates that this may take several years to reach the market place. The fact that Zika is a close relative of yellow fever and Japanese encephalitis viruses, for both of which there are already effective vaccines, provides a rational basis for the fast-tracked laboratory-based preparation of a candidate vaccine. However, undertaking clinical trials on pregnant females provides ethical and practical hurdles to overcome before licensure is granted for public administration. Meanwhile, public health management strategies, including mosquito control programs to reduce breeding, are needed to limit the global spread of this re-emerging disease. url: https://www.ncbi.nlm.nih.gov/pubmed/30050335/ doi: 10.2147/rrtm.s108992 id: cord-017824-0pinevfc author: Tekes, Gergely title: Vaccinia Virus-Based Reverse Genetics for Feline Coronaviruses date: 2015-09-10 words: 3190.0 sentences: 253.0 pages: flesch: 57.0 cache: ./cache/cord-017824-0pinevfc.txt txt: ./txt/cord-017824-0pinevfc.txt summary: The main focus of this chapter is the vaccinia virus-based reverse genetic system for FCoVs. Here we present protocols for (1) the generation of a full-length cDNA clone, (2) the manipulation of the FCoV genome, and (3) the rescue of recombinant FCoVs. The establishment of a reverse genetic system for feline coronaviruses (FCoVs), which allows to modify the entire coronaviral genome, was successfully achieved for the fi rst time in 2008 [ 1 ] . Regardless of the applied strategy, viral RNA serves as a starting material for the generation of all FCoV-sequence containing plasmids (sections "First Step", 3.1.1.3, "Generation of plasmids suitable for vaccinia virus-mediated homologous recombination"). In order to integrate the full-length FCoV cDNA, fragments 1-8 are introduced via four rounds of vaccinia virus-mediated homologous recombination using GPT as a positive and a negative selection marker. abstract: For decades, the genetic modification of coronavirus genomes and the generation of recombinant coronaviruses have been hampered mostly due to the extraordinary large size of the coronaviral genome. The very first reverse genetic system for feline coronaviruses (FCoVs) was established in the early 2000s; the respective approach exclusively enabled the manipulation of the 3′-third of the viral genome. Later on, vaccinia virus- and bacterial artificial chromosome (BAC)-based systems have been developed. Both systems have the advantage that the entire FCoV genome is amenable for mutagenesis. The main focus of this chapter is the vaccinia virus-based reverse genetic system for FCoVs. Here we present protocols for (1) the generation of a full-length cDNA clone, (2) the manipulation of the FCoV genome, and (3) the rescue of recombinant FCoVs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122496/ doi: 10.1007/978-1-4939-3414-0_7 id: cord-311382-ioemd0ij author: Tellier, Raymond title: Recognition of aerosol transmission of infectious agents: a commentary date: 2019-01-31 words: 5339.0 sentences: 235.0 pages: flesch: 39.0 cache: ./cache/cord-311382-ioemd0ij.txt txt: ./txt/cord-311382-ioemd0ij.txt summary: For example, when the infectious dose (the number of infectious agents required to cause disease) of an organism is low, and where large numbers of pathogen-laden droplets are produced in crowded conditions with poor ventilation (in hospital waiting rooms, in lecture theatres, on public transport, etc.), explosive outbreaks can still occur, even with pathogens whose airborne transmission capacity is controversial, e.g. the spread of influenza in a grounded plane where multiple secondary cases were observed in the absence of any ventilation [11] . For example, tighter control of the environment may reduce or prevent airborne transmission by: 1) isolating infectious patients in a single-bed, negative pressure isolation room [25] ; 2) controlling environmental relative humidity to reduce airborne influenza survival [59] ; 3) reducing exposure from aerosols produced by patients through coughing, sneezing or breathing with the use of personal protective equipment (wearing a mask) on the patient (to reduce source emission) and/or the healthcare worker (to reduce recipient exposure) [60] ; 4) carefully controlling the use and exposure to any respiratory assist devices (high-flow oxygen masks, nebulizers) by only allowing their use in designated, containment areas or rooms [61] . abstract: Although short-range large-droplet transmission is possible for most respiratory infectious agents, deciding on whether the same agent is also airborne has a potentially huge impact on the types (and costs) of infection control interventions that are required. The concept and definition of aerosols is also discussed, as is the concept of large droplet transmission, and airborne transmission which is meant by most authors to be synonymous with aerosol transmission, although some use the term to mean either large droplet or aerosol transmission. However, these terms are often used confusingly when discussing specific infection control interventions for individual pathogens that are accepted to be mostly transmitted by the airborne (aerosol) route (e.g. tuberculosis, measles and chickenpox). It is therefore important to clarify such terminology, where a particular intervention, like the type of personal protective equipment (PPE) to be used, is deemed adequate to intervene for this potential mode of transmission, i.e. at an N95 rather than surgical mask level requirement. With this in mind, this review considers the commonly used term of ‘aerosol transmission’ in the context of some infectious agents that are well-recognized to be transmissible via the airborne route. It also discusses other agents, like influenza virus, where the potential for airborne transmission is much more dependent on various host, viral and environmental factors, and where its potential for aerosol transmission may be underestimated. url: https://doi.org/10.1186/s12879-019-3707-y doi: 10.1186/s12879-019-3707-y id: cord-310140-h7uwl0pb author: Templeton, K.E. title: A multi-centre pilot proficiency programme to assess the quality of molecular detection of respiratory viruses date: 2005-07-12 words: 4186.0 sentences: 205.0 pages: flesch: 50.0 cache: ./cache/cord-310140-h7uwl0pb.txt txt: ./txt/cord-310140-h7uwl0pb.txt summary: STUDY DESIGN: Respiratory virus proficiency panels were produced from diluted stocks of respiratory viruses provided and tested by four reference laboratories. Laboratories performing respiratory molecular tests want to report accurate and reliable results regardless of the type of assay in use and one of the best ways to assess performance is to participate in proficiency programmes, enabling laboratories to evaluate their performance (Schirm et al., 2002; Schloss et al., 2003; Noordhoek et al., 2004; Verkooyen et al., 2003) . Laboratories who had expressed an interest to QCMD in participating in a proficiency programme for molecular detection of respiratory viruses were asked to complete a questionnaire detailing technical aspects of the assays they had applied. In this study, samples were grown in cell culture and dilutions were made so sensitivity and limited specificity of assays for these viruses could be assessed. abstract: OBJECTIVES: To assess the quality of molecular detection of respiratory viruses in clinical diagnostic laboratories. STUDY DESIGN: Respiratory virus proficiency panels were produced from diluted stocks of respiratory viruses provided and tested by four reference laboratories. The panels consisted of strong positive, positive, low positive and negative samples for influenza viruses A and B, respiratory syncytial virus, parainfluenza viruses 1 and 3, adenovirus serotypes 4 and 7, human rhinovirus serotypes 16, 72 and 90, human coronaviruses OC43 and 229E. The panels were sent to 17 participants; results and information on methodology was collected. RESULTS: All laboratories returned results, of which five submitted complete data sets. So, for analysis all results were combined. Samples were correctly identified by participants in 93.75%, 76.75% and 47.03% for the high positive, positive and low positive samples, respectively. One false positive was reported for all data sets (1.1%). The overall score for all assays using different methodologies was 78.8%. Laboratory performance was not dependant on methodology as all in-house methodologies could achieve optimal results, but dependant on careful optimisation and procedures specific to the laboratory. CONCLUSIONS: The first proficiency panel showed that in general all participants performed well. Although, it also highlights areas for improvement for all participants in order to generate robust results for use in clinical diagnostics. url: https://www.ncbi.nlm.nih.gov/pubmed/16019258/ doi: 10.1016/j.jcv.2005.05.005 id: cord-339288-y8woqsii author: Tews, Birke Andrea title: Self-Replicating RNA date: 2016-06-11 words: 7567.0 sentences: 338.0 pages: flesch: 44.0 cache: ./cache/cord-339288-y8woqsii.txt txt: ./txt/cord-339288-y8woqsii.txt summary: Self-replicating RNA derived from the genomes of positive strand RNA viruses represents a powerful tool for both molecular studies on virus biology and approaches to novel safe and effective vaccines. Three years later, the performance of poliovirus cDNA clones could be significantly ameliorated through the introduction of SV40 transcription and replication signals and transfection of the resulting construct into cells expressing the SV40 large T antigen [14] , thus ensuring replication of the DNA-plasmid in eukaryotic cells leading to a higher yield of viral RNA and recovered virus (Fig. 2, left part) . The resulting virus CP7_E2alf was only able to infect pigs and thus displayed the Fig. 3 Generation of a chimeric viral genome from two parental RNAs. On the level of a cDNA construct, one protein-coding sequence is replaced by the corresponding gene of the other virus (principle used for the pestivirus vaccine CP7_E2alf [58] ). abstract: Self-replicating RNA derived from the genomes of positive strand RNA viruses represents a powerful tool for both molecular studies on virus biology and approaches to novel safe and effective vaccines. The following chapter summarizes the principles how such RNAs can be established and used for design of vaccines. Due to the large variety of strategies needed to circumvent specific pitfalls in the design of such constructs the technical details of the experiments are not described here but can be found in the cited literature. url: https://www.ncbi.nlm.nih.gov/pubmed/27987141/ doi: 10.1007/978-1-4939-6481-9_2 id: cord-268788-jcu3pasy author: Thor, Sharmi W. title: Recombination in Avian Gamma-Coronavirus Infectious Bronchitis Virus date: 2011-09-23 words: 4426.0 sentences: 219.0 pages: flesch: 49.0 cache: ./cache/cord-268788-jcu3pasy.txt txt: ./txt/cord-268788-jcu3pasy.txt summary: In this study, the full-length genomes of eight avian gamma-coronavirus infectious bronchitis virus (IBV) isolates were sequenced and along with other full-length IBV genomes available from GenBank were analyzed for recombination. In this study we sequenced and analyzed the entire genome of eight IBV strains that represent different serotypes that have not been previously sequenced, and we compared these sequences with other gamma-coronavirus full-length genome sequences available in GenBank for evidence of recombination [16] . A phylogenetic compatibility matrix constructed at the 70% bootstrap level for 250 bp sequence fragments at 100 bp intervals also showed that recombination breakpoints were distributed throughout the IBV genomes (data not shown). Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus Complete genome sequence and recombination analysis of infectious bronchitis virus attenuated vaccine strain H120 abstract: Recombination in the family Coronaviridae has been well documented and is thought to be a contributing factor in the emergence and evolution of different coronaviral genotypes as well as different species of coronavirus. However, there are limited data available on the frequency and extent of recombination in coronaviruses in nature and particularly for the avian gamma-coronaviruses where only recently the emergence of a turkey coronavirus has been attributed solely to recombination. In this study, the full-length genomes of eight avian gamma-coronavirus infectious bronchitis virus (IBV) isolates were sequenced and along with other full-length IBV genomes available from GenBank were analyzed for recombination. Evidence of recombination was found in every sequence analyzed and was distributed throughout the entire genome. Areas that have the highest occurrence of recombination are located in regions of the genome that code for nonstructural proteins 2, 3 and 16, and the structural spike glycoprotein. The extent of the recombination observed, suggests that this may be one of the principal mechanisms for generating genetic and antigenic diversity within IBV. These data indicate that reticulate evolutionary change due to recombination in IBV, likely plays a major role in the origin and adaptation of the virus leading to new genetic types and strains of the virus. url: https://doi.org/10.3390/v3091777 doi: 10.3390/v3091777 id: cord-319208-jrxz59bb author: Ting, Chun Yi title: Are identity badges and lanyards in pediatrics potentially contaminated with viral pathogens? date: 2015-11-01 words: 2011.0 sentences: 113.0 pages: flesch: 47.0 cache: ./cache/cord-319208-jrxz59bb.txt txt: ./txt/cord-319208-jrxz59bb.txt summary: Identity (ID) badges and lanyards worn by pediatric health care workers (HCWs) have been shown to be potential vectors of nosocomial bacterial infections. This cross-sectional study determined the contamination of ID badges and lanyards worn by pediatric HCWs with common respiratory and gastrointestinal viruses. The results showed that ID badges and lanyards are not significantly contaminated with common respiratory or gastrointestinal viruses and are unlikely to be a significant vector for nosocomial infection. The principal aim of this study was to determine the contamination rates of ID badges and lanyards worn by pediatric HCWs with common respiratory and gastrointestinal viruses to evaluate their potential as vectors for both nosocomial and patient-topatient transmission of viruses. HCW ID samples were tested for respiratory viruses using viral PCR technique after an automated DNA-RNA extraction procedure, an identical process to routine clinical samples collected from pediatric patients. abstract: Identity (ID) badges and lanyards worn by pediatric health care workers (HCWs) have been shown to be potential vectors of nosocomial bacterial infections. This cross-sectional study determined the contamination of ID badges and lanyards worn by pediatric HCWs with common respiratory and gastrointestinal viruses. The results showed that ID badges and lanyards are not significantly contaminated with common respiratory or gastrointestinal viruses and are unlikely to be a significant vector for nosocomial infection. url: https://www.ncbi.nlm.nih.gov/pubmed/26300101/ doi: 10.1016/j.ajic.2015.06.024 id: cord-282628-6uoberfu author: Tiwari, Bhagyashree title: Future impacts and trends in treatment of hospital wastewater date: 2020-05-01 words: 5920.0 sentences: 286.0 pages: flesch: 35.0 cache: ./cache/cord-282628-6uoberfu.txt txt: ./txt/cord-282628-6uoberfu.txt summary: The causative agent of most emerging infectious diseases is viruses; every year approximately more than two novel viral pathogens are identified, which can cause illness in a human. Factors for emergence include natural process (evolution of pathogen), infectious agents transfer from vertebrate to mammals, antimicrobial resistance (AMR), and climate change. The factors responsible for the emergence of infectious diseases such as (1) the evolution of new strain, (2) the introduction of a host to enzootic, (3) translocation of infected wildlife, (4) farming practices, and (5) others were provided. Due to emergence of antibiotic-resistant pathogens and unavoidable use of antibiotics, concomitant environmental perturbation caused by climate change might make the earth is not suitable for humans and other livings. Increasing resistance to antibiotics and the emergence of "superbugs" that are resistant to drugs of last resort have highlighted the great need for alternative treatments of bacterial disease. Furthermore, development of drug-resistant organisms and increased pathogen survival rate, only raising panic about the human, animal, and environmental health. abstract: The world’s population growth and economic development result in the increased requirement of land, water, and energy. This increased demand leads to the deforestation, loss in biodiversity, imbalance in agriculture and food supply, climate change, and increase in food and travel trade, which result in emergence and reemergence of infectious diseases. This chapter discussed various emerging infectious diseases and their causative agents (Buruli ulcer and Bunyvirus). Furthermore, this chapter further illustrates the emergence of superbugs and the associated threat due to the presence of pharmaceutical compounds in the environment. The prevalence of pharmaceuticals in the environment exerts ecotoxic effects on living organisms and causes thousands of death every year. The threats associated with the pharmaceutical presence in the environment were briefly discussed in this chapter. Finally, this chapter provides the alternative methods to avoid the use of antibiotics and to develop novel treatment technologies (such as Phage therapy) to degrade and remove the pharmaceutical compounds. url: https://api.elsevier.com/content/article/pii/B9780128197226000171 doi: 10.1016/b978-0-12-819722-6.00017-1 id: cord-280878-1kt51viz author: To, Janet title: Targeting the Channel Activity of Viroporins date: 2016-01-07 words: 15297.0 sentences: 701.0 pages: flesch: 47.0 cache: ./cache/cord-280878-1kt51viz.txt txt: ./txt/cord-280878-1kt51viz.txt summary: For other viroporins, these studies are still mostly in their infancy, although a highresolution structure of the hepatitis C virus (HCV) p7 protein has been recently described (Ouyang et al., 2013) that may be useful for the rational design of p7 channel inhibitors in the future. Structure and ion channel activity of the human respiratory syncytial virus (hRSV) small hydrophobic protein transmembrane domain The small hydrophobic protein of the human respiratory syncytial virus forms pentameric ion channels NMR structure and ion channel activity of the p7 protein from hepatitis C virus Influenza B virus BM2 protein has ion channel activity that conducts protons across membranes Identification of an ion channel activity of the Vpu transmembrane domain and its involvement in the regulation of virus release from HIV-1-infected cells Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus abstract: Since the discovery that certain small viral membrane proteins, collectively termed as viroporins, can permeabilize host cellular membranes and also behave as ion channels, attempts have been made to link this feature to specific biological roles. In parallel, most viroporins identified so far are virulence factors, and interest has focused toward the discovery of channel inhibitors that would have a therapeutic effect, or be used as research tools to understand the biological roles of viroporin ion channel activity. However, this paradigm is being shifted by the difficulties inherent to small viral membrane proteins, and by the realization that protein–protein interactions and other diverse roles in the virus life cycle may represent an equal, if not, more important target. Therefore, although targeting the channel activity of viroporins can probably be therapeutically useful in some cases, the focus may shift to their other functions in following years. Small-molecule inhibitors have been mostly developed against the influenza A M2 (IAV M2 or AM2). This is not surprising since AM2 is the best characterized viroporin to date, with a well-established biological role in viral pathogenesis combined the most extensive structural investigations conducted, and has emerged as a validated drug target. For other viroporins, these studies are still mostly in their infancy, and together with those for AM2, are the subject of the present review. url: https://doi.org/10.1016/bs.apcsb.2015.12.003 doi: 10.1016/bs.apcsb.2015.12.003 id: cord-340194-ibli36rq author: To, Kelvin K.W. title: Ebola virus disease: a highly fatal infectious disease reemerging in West Africa date: 2014-11-29 words: 8870.0 sentences: 485.0 pages: flesch: 51.0 cache: ./cache/cord-340194-ibli36rq.txt txt: ./txt/cord-340194-ibli36rq.txt summary: Ebolavirus has been known to cause outbreaks of severe hemorrhagic fever with high fatality in Africa since 1976 [1] . Zaire and Sudan ebolavirus are responsible for most outbreaks, and these species are associated with highest case-fatality rates, ranging from 44e100% and 41e69%, respectively. In addition to clinically apparent EVD outbreaks, seroepidemiology studies showed that there is a high prevalence seropositive individuals, suggesting that asymptomatic or mild infection can occur [15] . The only human case of ebolavirus infection in West Africa before the 2014 outbreak occurred 20 years ago. During the 1976 EVD outbreak, the index case had transmitted the virus to healthcare workers and hospitalized patients with at least 15 generations of person-to-person transmission [29] . Human fatal zaire ebola virus infection is associated with an aberrant innate immunity and with massive lymphocyte apoptosis Analysis of human peripheral blood samples from fatal and nonfatal cases of Ebola (Sudan) hemorrhagic fever: cellular responses, virus load, and nitric oxide levels abstract: Ebolavirus can cause a highly fatal and panic-generating human disease which may jump from bats to other mammals and human. High viral loads in body fluids allow efficient transmission by contact. Lack of effective antivirals, vaccines and public health infrastructures in parts of Africa make it difficult to health workers to contain the outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/25456100/ doi: 10.1016/j.micinf.2014.11.007 id: cord-345168-3w32v2fm author: To, Kelvin K.W. title: Viral load in patients infected with pandemic H1N1 2009 influenza A virus date: 2009-11-30 words: 3774.0 sentences: 202.0 pages: flesch: 48.0 cache: ./cache/cord-345168-3w32v2fm.txt txt: ./txt/cord-345168-3w32v2fm.txt summary: Comparison was made between patients with pandemic H1N1 virus and seasonal influenza virus infection regarding their demographics, underlying diseases, presenting symptoms, total white blood cell counts, absolute lymphocyte counts, and initial pre-treatment viral load in respiratory specimens on the day of diagnosis. Among patients with pandemic H1N1 virus infection, the same parameters was compared between those with longer duration (!5 days) and shorter duration ( 4 days) of viral shedding, as defined by the time from onset of symptoms to the last positive sample by RT-PCR. For both pandemic H1N1 cases and seasonal influenza historical controls, respiratory specimens collected on the day of onset of symptoms (day 0) had the highest mean viral load (Fig. 1 ). For patients who presented to hospital between days 0 and 3 after onset of symptoms, the initial pre-treatment viral load in pandemic H1N1 cases was lower than the seasonal influenza historical controls. abstract: Viral shedding profile of infections caused by the pandemic H1N1 2009 influenza A virus has not been reported. The aim of this study was to determine the viral load in different body sites. Viral loads of pandemic H1N1 virus in respiratory specimens, stool, urine, and serum were determined by quantitative reverse transcriptase‐polymerase chain reaction (RT‐PCR). Respiratory specimens from patients with seasonal influenza were used as historical controls. Initial pre‐treatment viral load were compared between these two groups. Serial respiratory specimens from patients with pandemic H1N1 virus infection were obtained for analysis of viral dynamics. Twenty‐two pandemic H1N1 cases and 44 seasonal influenza historical controls were included. The mean initial viral load before oseltamivir therapy was 1.84 × 10(8) copies/ml for pandemic H1N1 virus compared with 3.28 × 10(8) copies/ml in seasonal influenza historical controls (P = 0.085). Among patients with pandemic H1N1 virus infection, peak viral load occurred on the day of onset of symptoms, and declined gradually afterwards, with no virus being detectable in respiratory specimens by RT‐PCR 8 days and by culture 5 days after the onset of symptoms respectively, except in one patient. Pandemic H1N1 virus was detected in stool and in urine from 4/9 and 1/14 patients, respectively. Viral culture was also positive from the stool sample with the highest viral load. Younger age was associated with prolonged shedding in the respiratory tract and higher viral load in the stool. Data from this quantitative analysis of viral shedding may have implications for formulating infection control measures. J. Med. Virol. 82:1–7, 2010. © 2009 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/19950247/ doi: 10.1002/jmv.21664 id: cord-325969-9zhmmvdg author: To, Kelvin KW title: Additional molecular testing of saliva specimens improves the detection of respiratory viruses date: 2017-06-07 words: 4543.0 sentences: 250.0 pages: flesch: 48.0 cache: ./cache/cord-325969-9zhmmvdg.txt txt: ./txt/cord-325969-9zhmmvdg.txt summary: In the first cohort of 159 patients whose nasopharyngeal aspirates (NPAs) tested positive for respiratory viruses during routine testing, the viral load was measured using quantitative reverse transcription PCR. Although NPAs have high viral loads and remain the specimen of choice for most patients with respiratory virus infections, supplementary molecular testing of saliva can improve the clinical management of these patients. The first part of the study consisted of patients whose NPA samples tested positive for respiratory viruses by DFA or the influenza A virus M gene by real-time RT-PCR during routine respiratory virus testing in our clinical microbiology laboratory ( Figure 1 ). In the first part of this study, saliva had a higher viral load than NPA in 17.0% of the patients who tested positive for respiratory viruses by DFA or influenza A virus by RT-PCR in their NPA samples. abstract: Emerging infectious diseases in humans are often caused by respiratory viruses such as pandemic or avian influenza viruses and novel coronaviruses. Microbiological testing for respiratory viruses is important for patient management, infection control and epidemiological studies. Nasopharyngeal specimens are frequently tested, but their sensitivity is suboptimal. This study evaluated the incremental benefit of testing respiratory viruses in expectorated saliva using molecular assays. A total of 258 hospitalized adult patients with suspected respiratory infections were included. Their expectorated saliva was collected without the use of any special devices. In the first cohort of 159 patients whose nasopharyngeal aspirates (NPAs) tested positive for respiratory viruses during routine testing, the viral load was measured using quantitative reverse transcription PCR. Seventeen percent of the patients (27/159) had higher viral loads in the saliva than in the NPA. The second cohort consisted of 99 patients whose NPAs tested negative for respiratory viruses using a direct immunofluorescence assay. Their NPA and saliva specimens were additionally tested using multiplex PCR. In these patients, the concordance rate by multiplex PCR between NPA and saliva was 83.8%. Multiplex PCR detected viruses in saliva samples from 16 patients, of which nine (56.3%) had at least one virus that was not detected in the NPA. Decisions on antiviral or isolation precautions would be affected by salivary testing in six patients. Although NPAs have high viral loads and remain the specimen of choice for most patients with respiratory virus infections, supplementary molecular testing of saliva can improve the clinical management of these patients. url: https://www.ncbi.nlm.nih.gov/pubmed/28588283/ doi: 10.1038/emi.2017.35 id: cord-270772-zshjrc87 author: To, Kelvin Kai-Wang title: Host genes and influenza pathogenesis in humans: an emerging paradigm date: 2015-06-14 words: 4110.0 sentences: 228.0 pages: flesch: 35.0 cache: ./cache/cord-270772-zshjrc87.txt txt: ./txt/cord-270772-zshjrc87.txt summary: The emergence of the pandemic influenza virus A(H1N1)pdm09 in 2009 and avian influenza virus A(H7N9) in 2013 provided unique opportunities for assessing genetic predispositions to severe disease because many patients did not have any underlying risk factor or neutralizing antibody against these agents, in contrast to seasonal influenza viruses. Integration of knowledge from genetic and phenotypic studies is essential to identify important gene targets for treatment and prevention of influenza virus infection. Specific amino acid changes in the viral proteins have been associated with increased disease severity in humans or adaptation of avian influenza viruses in humans [13] . High-throughput screening platforms have allowed researchers to systematically screen a large number of genes associated with influenza virus infection in vitro, in animals or in humans. 9 Host genetic determinants of influenza virus disease severity identified in humans. Surfactant protein A genetic variants associate with severe respiratory insufficiency in pandemic influenza A virus infection This study incorporated in vitro, animal and human data to prioritize genes for future research on genetic susceptibility to severe influenza abstract: The emergence of the pandemic influenza virus A(H1N1)pdm09 in 2009 and avian influenza virus A(H7N9) in 2013 provided unique opportunities for assessing genetic predispositions to severe disease because many patients did not have any underlying risk factor or neutralizing antibody against these agents, in contrast to seasonal influenza viruses. High-throughput screening platforms and large human or animal databases from international collaborations allow rapid selection of potential candidate genes for confirmatory functional studies. In the last 2 years, at least seven new human susceptibility genes have been identified in genetic association studies. Integration of knowledge from genetic and phenotypic studies is essential to identify important gene targets for treatment and prevention of influenza virus infection. url: https://www.sciencedirect.com/science/article/pii/S1879625715000760 doi: 10.1016/j.coviro.2015.04.010 id: cord-341923-jwckbdnb author: To, Kelvin Kai-Wang title: Pathogenesis of pandemic H1N1 2009 influenza virus infection and the implication on management date: 2010-04-28 words: 5849.0 sentences: 306.0 pages: flesch: 44.0 cache: ./cache/cord-341923-jwckbdnb.txt txt: ./txt/cord-341923-jwckbdnb.txt summary: Although most patients infected with this novel strain present with mild upper respiratory tract symptoms [6] , the higher fatality rate in children and young adults clearly differentiate this virus from seasonal influenza virus [7, 8] . Known virulence factors in H5N1 virus include Lys627 of PB2, which increases the viral replication; an Asn66Ser substitution in PB1-F2, a protein that induces apoptosis, enhances inflammation in mice, and predisposes to secondary bacterial infection; NS1, which antagonizes the antiviral effect of interferon; and a multibasic HA cleavage sequence, which allows cleavage by ubiquitous proteases [36] . A higher viral load in respiratory tract samples was associated with fatal disease from H5N1 [41] and with disease severity in infection due to respiratory syncytial virus and human metapneumovirus [42] . Delayed clearance of viral load and marked cytokine activation in severe cases of pandemic H1N1 2009 influenza virus infection abstract: The pandemic H1N1 2009 influenza virus has caused the first influenza pandemic of the 21st century, leading to disproportionate fatalities in the low-risk population despite the generally mild nature of the illness. Advances in science and technology have allowed very detailed study on the pathogenesis of this novel virus, and many have already been published in less than a year after the start of the pandemic. Information generated from cell lines, animal models, and clinical data analysis has provided us with greater understanding of the behavior of this virus and the associated host response. The new knowledge will allow us to formulate scientifically sound and evidence-based management plans. url: https://doi.org/10.1007/s11684-010-0030-9 doi: 10.1007/s11684-010-0030-9 id: cord-351365-dc9t3vh3 author: Todt, Daniel title: Mutagenic Effects of Ribavirin on Hepatitis E Virus—Viral Extinction versus Selection of Fitness-Enhancing Mutations date: 2016-10-13 words: 6318.0 sentences: 320.0 pages: flesch: 40.0 cache: ./cache/cord-351365-dc9t3vh3.txt txt: ./txt/cord-351365-dc9t3vh3.txt summary: Consequently, the onset of RBV treatment in chronically HEV-infected individuals can result in two divergent outcomes: viral extinction versus selection of fitness-enhanced viruses. Following an overview of RNA viruses treated with RBV in clinics and a summary of the different antiviral modes of action of this drug, we focus on the mutagenic effect of RBV on HEV intrahost populations, and how HEV is able to overcome lethal mutagenesis. Figure 1 provides an overview of a selection of RNA viruses against which RBV was shown to be active: hepatitis C virus (HCV, Flaviviridae), dengue virus (DENV, Flaviviridae), respiratory syncytial virus (RSV, Paramyxoviridae), influenza A and B virus (Orthomyxoviridae), chikungunya virus (CHIKV, Togaviridae), poliovirus (Picornaviridae), Hantaan virus (Bunyaviridae), and Lassa virus (Arenaviridae) [28, 29] ( Figure 1 ). Furthermore, mechanisms on the virus itself were described by inhibition of the capping efficiency, the viral polymerase, and a mutagenic effect on newly synthesized RNA genomes. A Mutation in the hepatitis E virus RNA polymerase promotes its replication and associates with ribavirin treatment failure in organ transplant recipients abstract: Hepatitis E virus (HEV), an important agent of viral hepatitis worldwide, can cause severe courses of infection in pregnant women and immunosuppressed patients. To date, HEV infections can only be treated with ribavirin (RBV). Major drawbacks of this therapy are that RBV is not approved for administration to pregnant women and that the virus can acquire mutations, which render the intra-host population less sensitive or even resistant to RBV. One of the proposed modes of action of RBV is a direct mutagenic effect on viral genomes, inducing mismatches and subsequent nucleotide substitutions. These transition events can drive the already error-prone viral replication beyond an error threshold, causing viral population extinction. In contrast, the expanded heterogeneous viral population can facilitate selection of mutant viruses with enhanced replication fitness. Emergence of these mutant viruses can lead to therapeutic failure. Consequently, the onset of RBV treatment in chronically HEV-infected individuals can result in two divergent outcomes: viral extinction versus selection of fitness-enhanced viruses. Following an overview of RNA viruses treated with RBV in clinics and a summary of the different antiviral modes of action of this drug, we focus on the mutagenic effect of RBV on HEV intrahost populations, and how HEV is able to overcome lethal mutagenesis. url: https://www.ncbi.nlm.nih.gov/pubmed/27754363/ doi: 10.3390/v8100283 id: cord-340331-51yq1rdo author: Tonelli, Michele title: Host dihydrofolate reductase (DHFR)-directed cycloguanil analogues endowed with activity against influenza virus and respiratory syncytial virus date: 2017-07-28 words: 6160.0 sentences: 285.0 pages: flesch: 42.0 cache: ./cache/cord-340331-51yq1rdo.txt txt: ./txt/cord-340331-51yq1rdo.txt summary: We have identified a series of 1-aryl-4,6-diamino-1,2-dihydrotriazines, structurally related to the antimalarial drug cycloguanil, as new inhibitors of influenza A and B virus and respiratory syncytial virus (RSV) via targeting of the host dihydrofolate reductase (DHFR) enzyme. The compounds, object of the present study, are characterized by the 1-aryl-4,6-diamino-1,2-dihydrotriazine scaffold, such as the cited cycloguanil, which was identified by us as prototype (1) of a new class of antiviral agents exploiting a host DHFR inhibition mechanism. Since host cell DHFR inhibition seemed the plausible explanation for the observed antiviral effect, we performed a combination experiment in which RSV-infected HeLa cells were exposed to compound 14 in combination with different concentrations of the natural DHFR substrate dihydrofolic acid ( reaction has a much higher impact on virus replication than on cell growth, which concurs with the promising antiviral selectivity of our host-directed DHFR inhibitors. The interesting dual activity of the 1-aryl-4,6-diamino-1,2dihydrotriazines against influenza and respiratory syncytial viruses, via inhibition of the cellular (human) DHFR enzyme, points to this host factor as a new therapeutic target for these two respiratory viruses. abstract: We have identified a series of 1-aryl-4,6-diamino-1,2-dihydrotriazines, structurally related to the antimalarial drug cycloguanil, as new inhibitors of influenza A and B virus and respiratory syncytial virus (RSV) via targeting of the host dihydrofolate reductase (DHFR) enzyme. Most analogues proved active against influenza B virus in the low micromolar range, and the best compounds (11, 13, 14 and 16) even reached the sub-micromolar potency of zanamivir (EC(50) = 0.060 μM), and markedly exceeded (up to 327 times) the antiviral efficacy of ribavirin. Activity was also observed for two influenza A strains, including a virus with the S31N mutant form of M2 proton channel, which is the most prevalent resistance mutation for amantadine. Importantly, the compounds displayed nanomolar activity against RSV and a superior selectivity index, since the ratio of cytotoxic to antiviral concentration was >10,000 for the three most active compounds 11, 14 and 16 (EC(50) ∼0.008 μM), far surpassing the potency and safety profile of the licensed drug ribavirin (EC(50) = 5.8 μM, SI > 43). url: https://doi.org/10.1016/j.ejmech.2017.04.070 doi: 10.1016/j.ejmech.2017.04.070 id: cord-271650-biq0chyn author: Torres, Juan M title: Safety evaluation of a recombinant myxoma-RHDV virus inducing horizontal transmissible protection against myxomatosis and rabbit haemorrhagic disease date: 2000-09-15 words: 4589.0 sentences: 226.0 pages: flesch: 45.0 cache: ./cache/cord-271650-biq0chyn.txt txt: ./txt/cord-271650-biq0chyn.txt summary: title: Safety evaluation of a recombinant myxoma-RHDV virus inducing horizontal transmissible protection against myxomatosis and rabbit haemorrhagic disease Safety evaluation of a recombinant myxoma-RHDV virus inducing horizontal transmissible protection against myxomatosis and rabbit haemorrhagic disease In order to protect wild rabbits against both myxomatosis and RHD, we constructed a recombinant virus based on the naturally attenuated MV ®eld strain 6918 [24] , that expressed the RHDV VP60 protein [25] . Groups of eight wild rabbits (2 month old, weighing around 0.8 kg) free from MV and RHDV antibodies, were inoculated at the back by intradermic (i.d.) or subcutaneous (s.c.) route with dierent doses of the vaccine (10 4 , 10 5 , 10 6 pfu of 6918VP60-T2 recombinant virus). Treated rabbits were inoculated (by s.c or i.d. route) with 10 4 pfu of 6918VP60-T2 virus, and clinical signs due to virus infection were compared with those induced in control rabbits, which were vaccinated but not treated with prednisolone (Fig 2, Table 3 ). abstract: We have recently developed a transmissible vaccine to immunize rabbits against myxomatosis and rabbit haemorrhagic disease based on a recombinant myxoma virus (MV) expressing the rabbit haemorrhagic disease virus (RHDV) capsid protein [Bárcena et al. Horizontal transmissible protection against myxomatosis and rabbit haemorragic disease using a recombinant myxoma virus. J. Virol. 2000;74:1114–23]. Administration of the recombinant virus protects rabbits against lethal RHDV and MV challenges. Furthermore, the recombinant virus is capable of horizontal spreading promoting protection of contact animals, thus providing the opportunity to immunize wild rabbit populations. However, potential risks must be extensively evaluated before considering its field use. In this study several safety issues concerning the proposed vaccine have been evaluated under laboratory conditions. Results indicated that vaccine administration is safe even at a 100-fold overdose. No undesirable effects were detected upon administration to immunosuppressed or pregnant rabbits. The recombinant virus maintained its attenuated phenotype after 10 passages in vivo. url: https://www.sciencedirect.com/science/article/pii/S0264410X00001833 doi: 10.1016/s0264-410x(00)00183-3 id: cord-271884-86yl9ren author: Traavik, T. title: Development of a modified immunoelectroosmophoresis method for Uukuniemi and Runde virus serology date: 1977 words: 3120.0 sentences: 239.0 pages: flesch: 56.0 cache: ./cache/cord-271884-86yl9ren.txt txt: ./txt/cord-271884-86yl9ren.txt summary: In search for a suitable method for sero-ecological screenings for arboviruses in Norway, efforts were undertaken to make the immunoelectroosmophoresis technique more sensitive than here to fare in detection of antibodies. The isolation of Uukuniemi (UUK) group viruses and a new coronavirus-like agent, Runde virus, from Norwegian Ixodes ticks (19, 21, 22, 23) , were intended to be followed up promptly by sero-ecological surveys by a standard haemagglutination inhibition test (HAI). B y using a gel composed of 0.4 per cent agar and 0.6 per cent agarose, and concentrated B H K antigens, results comparable to the H A I titers were obtained for the reference sera with all the viruses tested. Provided the opportunity to concentrate the antigen, the modifications used in this work to obtain a sensitive I E O P for antibody detection might prove valuable also with other viruses. abstract: In search for a suitable method for sero-ecological screenings for arboviruses in Norway, efforts were undertaken to make the immunoelectroosmophoresis technique more sensitive than here to fare in detection of antibodies. The aim was to make it comparable to haemagglutination inhibition test in sensitivity, retaining the advantages in specificity, simplicity and capacity. This has been achieved by: 1. Using concentrated virus as antigen. 2. Performing electrophoresis in a gel consisting of an agar-agarose mixture in optimal concentrations. 3. “Sandwiching” the first specific electrophoretic run with an anti-species antiserum to the tested sample. url: https://www.ncbi.nlm.nih.gov/pubmed/889446/ doi: 10.1007/bf01314789 id: cord-333043-fe24ezt6 author: Traavik, T. title: “Runde“ virus, a coronavirus-like agent associated with seabirds and ticks date: 1977 words: 4191.0 sentences: 318.0 pages: flesch: 63.0 cache: ./cache/cord-333043-fe24ezt6.txt txt: ./txt/cord-333043-fe24ezt6.txt summary: uriae collected in the seabird colonies at Runde, Norway, two identical virus strains demonstrating no antigenic relationships to major arbovirus groups were isolated. Until then., no arbovirus isolates had been reported from this country, although ecological and cli-nicaI/epidemiological considerations (3, 24, 26) and a limited serological survey on bovine sera (28) indicated the existence of Central-European tick-borne encephalitis virus fool. uriae ticks collected at Runde in late September 1973, three virus strains have been isolated. Cells were washed with saline, virus was diluted ~enfold from 10 -1 to t0 -6 in the medium, A volume of 0.2 ml of each dilution was inoculated into three tubes and allowed to adsorb for 1 hour at room temperature before washing with saline and addition, of new medium, Culture tubes were incubated for 8 days at 37 ° C and inspected daily for a Cytopathie effect (CPE). Virus from mouse brains and cell culture demonstrated total i d e n t i t y b y these methods. abstract: From 206I. uriae collected in the seabird colonies at Runde, Norway, two identical virus strains demonstrating no antigenic relationships to major arbovirus groups were isolated. The new strains demonstrated a corona-virus like morphology, haemagglutinated chicken red cells and were sensitive to sodium desoxycholate. Multiplication with CPE was demonstrated in BHK 21/c13 and BSC-1 cells, and without CPE in Vero and GMK cell cultures. The mouse pathogenicity was relatively low. In gel precipitation three to five specific lines were seen. Precipitating antibodies have been found in seabird species commonly infested byI. uriae. The ecological circumstances of the isolates indicate an earlier unrecognized arbovirus circulating between seabirds andI. uriae. This corona-like virus has been tentatively termed Runde virus. url: https://www.ncbi.nlm.nih.gov/pubmed/72555/ doi: 10.1007/bf01314476 id: cord-339152-wfakzb6w author: Trovato, Maria title: Viral Emerging Diseases: Challenges in Developing Vaccination Strategies date: 2020-09-03 words: 12000.0 sentences: 540.0 pages: flesch: 38.0 cache: ./cache/cord-339152-wfakzb6w.txt txt: ./txt/cord-339152-wfakzb6w.txt summary: Ebola and Marburg hemorrhagic fevers, Lassa fever, Dengue fever, Yellow fever, West Nile fever, Zika, and Chikungunya vector-borne diseases, Swine flu, Severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and the recent Coronavirus disease 2019 (COVID-19) are examples of zoonoses that have spread throughout the globe with such a significant impact on public health that the scientific community has been called for a rapid intervention in preventing and treating emerging infections. The occurrence of significant disease outbreaks-such as SARS (severe acute respiratory syndrome) originating in China in 2002 (8) , the 2009 H1N1 swine flu pandemic from Mexico (9) , MERS (Middle East respiratory syndrome) that occurred in Saudi Arabia in 2012 (10) , the West African outbreak of Ebola virus (EBOV) in late 2013 (11) , the Zika virus (ZIKV) outbreak originating in Brazil in 2015 (12) , the 2018 health emergence in Nigeria caused by Lassa virus (13) , and the ongoing Coronavirus disease 2019 (COVID19) pandemic (14) -has renewed interests in developing strategies to faster prevent, treat, and/or control emerging and re-emerging viruses with high epidemic potential. abstract: In the last decades, a number of infectious viruses have emerged from wildlife or re-emerged, generating serious threats to the global health and to the economy worldwide. Ebola and Marburg hemorrhagic fevers, Lassa fever, Dengue fever, Yellow fever, West Nile fever, Zika, and Chikungunya vector-borne diseases, Swine flu, Severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and the recent Coronavirus disease 2019 (COVID-19) are examples of zoonoses that have spread throughout the globe with such a significant impact on public health that the scientific community has been called for a rapid intervention in preventing and treating emerging infections. Vaccination is probably the most effective tool in helping the immune system to activate protective responses against pathogens, reducing morbidity and mortality, as proven by historical records. Under health emergency conditions, new and alternative approaches in vaccine design and development are imperative for a rapid and massive vaccination coverage, to manage a disease outbreak and curtail the epidemic spread. This review gives an update on the current vaccination strategies for some of the emerging/re-emerging viruses, and discusses challenges and hurdles to overcome for developing efficacious vaccines against future pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/33013898/ doi: 10.3389/fimmu.2020.02130 id: cord-331652-oc5s1if2 author: Trudeau, Michaela P. title: Comparison of Thermal and Non-Thermal Processing of Swine Feed and the Use of Selected Feed Additives on Inactivation of Porcine Epidemic Diarrhea Virus (PEDV) date: 2016-06-24 words: 5988.0 sentences: 294.0 pages: flesch: 52.0 cache: ./cache/cord-331652-oc5s1if2.txt txt: ./txt/cord-331652-oc5s1if2.txt summary: title: Comparison of Thermal and Non-Thermal Processing of Swine Feed and the Use of Selected Feed Additives on Inactivation of Porcine Epidemic Diarrhea Virus (PEDV) Feed samples were spiked with PEDV and then heated to 120–145°C for up to 30 min or irradiated at 0–50 kGy. Another set of feed samples spiked with PEDV and mixed with Ultracid P (Nutriad), Activate DA (Novus International), KEM-GEST (Kemin Agrifood), Acid Booster (Agri-Nutrition), sugar or salt was incubated at room temperature (~25°C) for up to 21 days. Therefore, the objective of this study was to determine if thermal and non-thermal methods of microbial inactivation, as well as the use of selected feed additives, are effective in reducing the survival of PEDV in experimentally contaminated swine feed. The PEDV showed a high thermal resistance in the dry feed samples and it was completely inactivated (3.0 log reduction) at each of the tested temperatures within 30 min. abstract: Infection with porcine epidemic diarrhea virus (PEDV) causes diarrhea, vomiting, and high mortality in suckling pigs. Contaminated feed has been suggested as a vehicle of transmission for PEDV. The objective of this study was to compare thermal and electron beam processing, and the inclusion of feed additives on the inactivation of PEDV in feed. Feed samples were spiked with PEDV and then heated to 120–145°C for up to 30 min or irradiated at 0–50 kGy. Another set of feed samples spiked with PEDV and mixed with Ultracid P (Nutriad), Activate DA (Novus International), KEM-GEST (Kemin Agrifood), Acid Booster (Agri-Nutrition), sugar or salt was incubated at room temperature (~25°C) for up to 21 days. At the end of incubation, the virus titers were determined by inoculation of Vero-81 cells and the virus inactivation kinetics were modeled using the Weibull distribution model. The Weibull kinetic parameter delta represented the time or eBeam dose required to reduce virus concentration by 1 log. For thermal processing, delta values ranged from 16.52 min at 120°C to 1.30 min at 145°C. For eBeam processing, a target dose of 50 kGy reduced PEDV concentration by 3 log. All additives tested were effective in reducing the survival of PEDV when compared with the control sample (delta = 17.23 days). Activate DA (0.81) and KEM-GEST (3.28) produced the fastest inactivation. In conclusion, heating swine feed at temperatures over 130°C or eBeam processing of feed with a dose over 50 kGy are effective processing steps to reduce PEDV survival. Additionally, the inclusion of selected additives can decrease PEDV survivability. url: https://www.ncbi.nlm.nih.gov/pubmed/27341670/ doi: 10.1371/journal.pone.0158128 id: cord-267140-vdcf6vok author: Trudel, M. title: Purification of infectious rubella virus by gel filtration on sepharose 2B compared to gradient centrifugation in sucrose, sodium metrizoate and metrizamide date: 1981-02-28 words: 1718.0 sentences: 105.0 pages: flesch: 45.0 cache: ./cache/cord-267140-vdcf6vok.txt txt: ./txt/cord-267140-vdcf6vok.txt summary: title: Purification of infectious rubella virus by gel filtration on sepharose 2B compared to gradient centrifugation in sucrose, sodium metrizoate and metrizamide Yields were lower in sucrose and metrizamide, while sodium metrizoate reduced the infectivity of the virus below detectable levels. This report describes the application of Sepharose 2B gel fitration for the purification of infectious rubella virus in comparison to centrifugation on sucrose, metrizamide and sodium metrizoate. Aliquots of 5 ml of viruses were purified by two cycles of density gradient centrifugation in sucrose, metrizoic acid (sodium salt) or metrizamide (Sigma Chemical Co., St. Louis, MO). Density gradient centrifugation of rubella virus on sucrose, metrizamide or sodium a Virus (5 ml, 65,566 HAU and 109*6TCID,,) was purified by ultracentrifugation or chromatography as described in Material and methods. Purification of rubella virus yielded similar results in sucrose and metrizamide but the infectivity was reduced to undetectable levels in sodium metrizoate. abstract: Abstract Rubella virus was purified by chromatography on Sepharose 2B after concentration by ultrafiltration on hollow fibers and hydroextraction with PEG 20,000. Yields of 40% infectivity and 70% hemagglutinating activity were routinely obtained. Chromatographie purification was compared to ultracentrifugation in sucrose, metrizamide and sodium metrizoate. Yields were lower in sucrose and metrizamide, while sodium metrizoate reduced the infectivity of the virus below detectable levels. These results demonstrate the advantage of Sepharose 2B for the purification of infectious rubella virus. url: https://api.elsevier.com/content/article/pii/016609348190032X doi: 10.1016/0166-0934(81)90032-x id: cord-333730-qsx0m68e author: Tsai, Y. C. title: Oral disease-modifying antirheumatic drugs and immunosuppressants with antiviral potential, including SARS-CoV-2 infection: a review date: 2020-09-03 words: 4920.0 sentences: 297.0 pages: flesch: 35.0 cache: ./cache/cord-333730-qsx0m68e.txt txt: ./txt/cord-333730-qsx0m68e.txt summary: However, some immunosuppressants or disease-modifying antirheumatic drugs (DMARDs) show antiviral activity and may be safely used or even beneficial in patients with selected concomitant viral infections. In vitro anti-CMV properties of leflunomide were not through blocking the replication of viral DNA, so it is effective even in patients with direct antiviral drug-resistance history. The combination of MMF and highly active antiretroviral therapy improved the control of viral replication and delayed viral-load rebound in a randomized pilot study (n = 17 The effectiveness of thalidomide for KS might be related to anti-angiogenesis, and experts hypothesized the modulation of the immune system to trigger an antiviral action. Although in most instances, the antiviral activity of DMARDs is based on in vitro or small-scale controlled studies, this property would be useful in the choice of DMARDs for patients with concomitant viral infections. Effects of hydroxychloroquine on immune activation and disease progression among HIV-infected patients not receiving antiretroviral therapy: a randomized controlled trial abstract: There have been several episodes of viral infection evolving into epidemics in recent decades, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the latest example. Its high infectivity and moderate mortality have resulted in an urgent need to find an effective treatment modality. Although the category of immunosuppressive drugs usually poses a risk of infection due to interference of the immune system, some of them have been found to exert antiviral properties and are already used in daily practice. Recently, hydroxychloroquine and baricitinib have been proposed as potential drugs for SARS-CoV-2. In fact, there are other immunosuppressants known with antiviral activities, including cyclosporine A, hydroxyurea, minocycline, mycophenolic acid, mycophenolate mofetil, leflunomide, tofacitinib, and thalidomide. The inherent antiviral activity could be a treatment choice for patients with coexisting rheumatological disorders and infections. Clinical evidence, their possible mode of actions and spectrum of antiviral activities are included in this review article. LAY SUMMARY: Immunosuppressants often raise the concern of infection risks, especially for patients with underlying immune disorders. However, some disease-modifying antirheumatic drugs (DMARDs) with inherent antiviral activity would be a reasonable choice in the situation of concomitant viral infections and flare up of autoimmune diseases. This review covers DMARDs of treatment potential for SARS-CoV-2 in part I, and antiviral mechanisms plus trial evidence for viruses other than SARS-CoV-2 in part II. url: https://www.ncbi.nlm.nih.gov/pubmed/32952617/ doi: 10.1177/1759720x20947296 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-279617-xuzu55cg author: Tuladhar, E. title: Thermal stability of structurally different viruses with proven or potential relevance to food safety date: 2012-03-30 words: 4595.0 sentences: 278.0 pages: flesch: 54.0 cache: ./cache/cord-279617-xuzu55cg.txt txt: ./txt/cord-279617-xuzu55cg.txt summary: Methods and Results: Suspensions with poliovirus Sabin1, adenovirus type5, parechovirus1, human norovirus (NoV) GII.4, murine NoV (MNV1) and human influenza A (H1N1) viruses were heated at 56 and 73°C. The viral stocks titres used were as follows: poliovirus Sabin 1: 6AE3 · 10 8 50% Tissue Culture Infective Dose (TCID 50 ) ml )1 (1AE6 · 10 10 PCR unit (PCRU) ml )1 ), adenovirus type 5: 6AE3 · 10 7 TCID 50 ml )1 (3AE2 · 10 9 PCRU ml )1 ), parechovirus 1: 1AE3 · 10 8 TCID 50 ml )1 (2AE0 · 10 9 PCRU ml )1 ), influenza A (H1N1) virus: 1AE3 · 10 6 TCID 50 ml )1 (1AE5 · 10 8 PCRU ml )1 ), MNV1: 1AE7 · 10 7 PFU ml )1 (5AE0 · 10 8 PCRU ml )1 ) and human NoV GII.4 was at a concentration of 1 · 10 8 PCRU ml )1 . abstract: Aims: To collect comparative data on thermal stability of structurally different viruses with proven or potential relevance to food safety. Methods and Results: Suspensions with poliovirus Sabin1, adenovirus type5, parechovirus1, human norovirus (NoV) GII.4, murine NoV (MNV1) and human influenza A (H1N1) viruses were heated at 56 and 73°C. Infectivity was tested by culture assay for all but human NoV GII.4 that cannot be cultivated in vitro. Time to first log(10) reduction (TFL‐value) was calculated based on best fit using the monophasic, biphasic or Weibull models. The Weibull model provided the best fit at 56°C for all viruses except influenza virus. The TFL at 56°C varied between a high of 27 min (parechovirus) to a low of 10 s (adenovirus) and ranked parechovirus > influenza > MNV1 > poliovirus > adenovirus. The monophasic model best described the behaviour of the viruses at 73°C, in which case the TFL was MNV1(62s) > influenza > adenovirus > parechovirus > poliovirus(14s). Conclusions: Viruses do not follow log‐linear thermal inactivation kinetics and the thermostability of parechovirus and influenza virus is similar to that of proven foodborne viruses. Significance and Impact of the Study: Resistant fractions of viruses may remain infectious in thermal inactivation processes and inactivation of newly discovered or enveloped viruses in thermal food preparation processes should not be assumed without further testing. url: https://www.ncbi.nlm.nih.gov/pubmed/22404161/ doi: 10.1111/j.1365-2672.2012.05282.x id: cord-291707-dzmvjh7j author: Tupper, G. T. title: Antigenic and biological diversity of feline coronaviruses: feline infectious peritonitis and feline enteritis virus date: 1987 words: 2789.0 sentences: 179.0 pages: flesch: 60.0 cache: ./cache/cord-291707-dzmvjh7j.txt txt: ./txt/cord-291707-dzmvjh7j.txt summary: FIPV grows to higher titer, forms larger plaques and switches off host cell protein synthesis more effectively than FECV. It was reported that both virus strains produce relatively large plaques in cell culture and grew to fairly high titers (1) . This indicated the differences were consistent and were not due to maturation artitSct. There was a cell protein band just above the nucleoprotein of the FECV 79-1683 of the radiolabelled virus. The FIPV strains produced larger plaques in CrFK cells and half a log higher titer of virus than the FECV strain. Host cell protein synthesis was also shut offby infection with murine coronavirus and different strains vary in the extent to which they do it, (25) . In this study, all 3 st, ruetural polypeptides appeared synchronously in cells infected with FIPV or FECV strains. Viral protein synthesis in mouse hepatitis virus strain A 59-infected cells: effect oftunieamyein abstract: Antigenically related feline coronaviruses cause two distinct disease manifestations in infected cats. The diseases are feline infectious peritonitis (FIP), in which the virus is widely disseminated, and feline enteric coronavirus (FECV), a mild disease in which the virus is usually limited to the villi. These two viruses were found to differ in their growth in cell culture. FIPV grows to higher titer, forms larger plaques and switches off host cell protein synthesis more effectively than FECV. Cross neutralization studies showed antigenic differences between the strains. There also appeared to be a difference in the nucleoprotein molecular weight of the viruses causing these two different disease syndromes. url: https://www.ncbi.nlm.nih.gov/pubmed/3619653/ doi: 10.1007/bf01310988 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-280987-uhxk5b1b author: Turtle, L. title: Encephalitis, Viral date: 2014-05-01 words: 2266.0 sentences: 120.0 pages: flesch: 33.0 cache: ./cache/cord-280987-uhxk5b1b.txt txt: ./txt/cord-280987-uhxk5b1b.txt summary: Encephalitis is inflammation and swelling of the brain, often caused by an acute viral infection, or a paraor postinfectious phenomenon known as acute disseminated encephalomyelitis (ADEM). The term includes both viral infections of the brain with predominantly gray matter disease and acute disseminated encephalomyelitis (ADEM), an immune-mediated demyelinating disease. Clinically, acute viral encephalitis and ADEM usually manifest with fever, severe headache, neck stiffness, alterations of consciousness, focal neurological signs, and often seizures, especially in children. Once permissive host cells are infected in the subcutaneous tissue, the mucous membranes, or the hematopoietic system (particularly macrophages), viruses replicate usually locally before there is invasion of the central nervous system (CNS). Enteroviruses and mumps virus infect primarily meningeal and ependymal cells; therefore, they usually cause benign meningitis and only rarely are associated with encephalitis. On rare occasions when arboviruses infect the brain, they usually cause encephalitis with a significant death rate; thus, these viruses are not highly neuroinvasive but are highly neurotropic (and neuronotropic) and neurovirulent. abstract: Encephalitis is inflammation and swelling of the brain, often caused by an acute viral infection, or a para- or postinfectious phenomenon known as acute disseminated encephalomyelitis (ADEM). The most common sporadic viral cause is herpes simplex virus, but arthropodborne viruses, such as Japanese encephalitis virus, are a major cause in some settings, and rabies in others. Herpes simplex encephalitis is treated with acyclovir; rabies and Japanese encephalitis are preventable with vaccines. With the reduction in measles through vaccination, the incidence of ADEM, which often follows measles, has also reduced. url: https://api.elsevier.com/content/article/pii/B9780123851574003754 doi: 10.1016/b978-0-12-385157-4.00375-4 id: cord-021990-a8ku5rke author: Tyring, Stephen K. title: Syndromal Tropical Dermatology date: 2016-12-02 words: 7077.0 sentences: 390.0 pages: flesch: 46.0 cache: ./cache/cord-021990-a8ku5rke.txt txt: ./txt/cord-021990-a8ku5rke.txt summary: With increasing numbers of persons from industrialized, temperate countries traveling and / or working in tropical lands, there is a marked need for physicians to be able to diagnose accurately and treat tropical diseases with mucocutaneous manifestations. An example of a mosquito-borne disease that was considered primarily "tropical" in the recent past but is now relatively common in much of North America is infection with the West Nile virus (Fig. 1-3) . When one STD is confirmed, there is an increased possibility of acquisition of additional STDs. Not only is this the case because the source partner(s) may have had multiple STDs, but also because having certain STDs makes a person more susceptible to other STDs. The best example of this phenomenon is the two-to fivefold greater risk of acquiring HIV if the person with a genital ulcer disease (GUD) has sex with an HIV-positive individual. If at least 3 months separate travel from fever / rash, the following infections should be considered: bartonellosis, filariasis, gnathostomiasis, hepatitis viruses (B and C), histoplasmosis, HIV, leishmaniasis, Lyme disease, melioidosis, penicilliosis, syphilis, trypanosomiasis, and tuberculosis. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152309/ doi: 10.1016/b978-0-323-29634-2.00001-8 id: cord-298733-jole21wq author: Tyrrell, D.A.J. title: A view from the common cold unit date: 1992-06-30 words: 9565.0 sentences: 394.0 pages: flesch: 50.0 cache: ./cache/cord-298733-jole21wq.txt txt: ./txt/cord-298733-jole21wq.txt summary: Furthermore, the old empirical idea of the existence of ''the common cold virus'' was soon replaced by data collected by epidemiologically controlled field studies in which infection was detected with a range of viruses following which their pathogenicity was confirmed and studied by inoculating them into volunteers and observing their effects. Thus, after years of frustration the work of the Unit developed to the point where relevant human infections could be produced at will and precisely documented by clinical and laboratory methods -this was the ideal setting for preliminary trials of the efficacy of antiviral drugs or vaccines without which nowadays it would rarely be justifiable to go on to a field study of naturally acquired colds. When natural and recombinant interferons were tested in this way against experimental influenza and rhinovirus infections in volunteers, they were no longer effective, possibly because by then the subject was already producing substantial amounts. abstract: Abstract I have been asked to stand back and describe in broad terms the view I have had of common colds — probably the most frequent of acute human diseases and a long-lasting scientific problem — and in particular our recent work on antivirals. I should be able to do this for two reasons. Like everyone else I have suffered from colds, but in addition I have been studying the problem from the virological and clinical point of view for over 35 years — for the last 31 at the Common Cold Unit, Salisbury. As a result I may have problems with perspective — it is not possible to give a personal view and at the same time to describe something from every possible angle, and quite impossible to be comprehensive, but I have done my best and readers will make their own judgements and corrections. url: https://api.elsevier.com/content/article/pii/016635429290032Z doi: 10.1016/0166-3542(92)90032-z id: cord-264264-7j3xirfg author: TüRsen, Ümit title: CORONAVIRUS‐DAYS IN DERMATOLOGY date: 2020-04-15 words: 2144.0 sentences: 128.0 pages: flesch: 49.0 cache: ./cache/cord-264264-7j3xirfg.txt txt: ./txt/cord-264264-7j3xirfg.txt summary: Soap works better than alcohol and disinfectants at destroying the structure of viruses. Soap dissolves the fat membrane, and the virus falls apart like a house of cards and "dies," or rather, it becomes inactive as viruses aren''t really alive. Apart from alcohol and soap, antibacterial agents in those products don''t affect the virus structure much. However, it was observed that washing hands with soap is better than using alcohol-based disinfectants in removing the noroviruses, rhinovirus and H1N1 influenza virus from hands (Tuladhar 2015, Kopra 2012, Grayson 2009 ). Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial Efficacy of soap and water and alcohol-based hand-rub preparations against live H1N1 influenza virus on the hands of human volunteers Single treatment with ethanol hand rub is ineffective against human rhinovirus--hand washing with soap and water removes the virus efficiently abstract: Severe acute respiratory syndrome‐corona virus‐2 (SARS‐CoV‐2), which causes coronavirus disease 2019 (COVID‐19), is highly contagious and a particularly popular problem in all around the World and also in all departments of every hospital. In order to protect the well‐being of healthcare providers while providing a sufficient workforce to respond to the coronavirus disease (COVID‐19) are vital for pandemic planning. In this article, we will discuss this problem from a dermatological aspect. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1111/dth.13421 doi: 10.1111/dth.13421 id: cord-307364-j86t65qu author: Uccellini, Lorenzo title: Identification of a novel nidovirus in an outbreak of fatal respiratory disease in ball pythons (Python regius) date: 2014-08-08 words: 1917.0 sentences: 110.0 pages: flesch: 45.0 cache: ./cache/cord-307364-j86t65qu.txt txt: ./txt/cord-307364-j86t65qu.txt summary: In situ hybridization confirmed the presence of intracellular, intracytoplasmic viral nucleic acids in the lungs of infected snakes. Phylogenetic analysis based on a 1,136 amino acid segment of the polyprotein suggests that this virus may represent a new species in the subfamily Torovirinae. CONCLUSIONS: This report of a novel nidovirus in ball pythons may provide insight into the pathogenesis of respiratory disease in this species and enhances our knowledge of the diversity of nidoviruses. Here we report the discovery of a novel nidovirus in a collection of ball pythons (Python regius) in upstate New York with pneumonia, tracheitis and esophagitis. Based on the phylogenetic position and the genetic distances between In situ hybridization to a 934 nt fragment of the genomic polyprotein 1ab region was used to assess viral infection and distribution in the lung tissue. Identification of a novel nidovirus in an outbreak of fatal respiratory disease in ball pythons (Python regius) abstract: BACKGROUND: Respiratory infections are important causes of morbidity and mortality in reptiles; however, the causative agents are only infrequently identified. FINDINGS: Pneumonia, tracheitis and esophagitis were reported in a collection of ball pythons (Python regius). Eight of 12 snakes had evidence of bacterial pneumonia. High-throughput sequencing of total extracted nucleic acids from lung, esophagus and spleen revealed a novel nidovirus. PCR indicated the presence of viral RNA in lung, trachea, esophagus, liver, and spleen. In situ hybridization confirmed the presence of intracellular, intracytoplasmic viral nucleic acids in the lungs of infected snakes. Phylogenetic analysis based on a 1,136 amino acid segment of the polyprotein suggests that this virus may represent a new species in the subfamily Torovirinae. CONCLUSIONS: This report of a novel nidovirus in ball pythons may provide insight into the pathogenesis of respiratory disease in this species and enhances our knowledge of the diversity of nidoviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/25106433/ doi: 10.1186/1743-422x-11-144 id: cord-299207-lw0cv74b author: Upadhyay, Ranjit Kumar title: Modeling the spread of bird flu and predicting outbreak diversity date: 2007-05-08 words: 4388.0 sentences: 252.0 pages: flesch: 58.0 cache: ./cache/cord-299207-lw0cv74b.txt txt: ./txt/cord-299207-lw0cv74b.txt summary: We have designed a statistical transmission model of bird flu taking into account the factors that affect the epidemic transmission such as source of infection, social and natural factors and various control measures are suggested. Among these researches, an important approach to study bird flu is to establish a statistical transmission model, from which the general trends of epidemics can be predicted, and the effect of various control measures can be assessed [13] . We know the major factors that play an important role in the transmission of bird flu are the way the infected poultry products are transported, air temperature, the control measures (for example, culling the poultry in the infected form, introducing compulsory vaccination to enhance the resistibility of poultry in the non-infected farms forbidding live birds being sold under crowded and unsanitary conditions, etc.), migratory birds and other infected transportation vehicles (which means the vehicles carry infected poultry or bird dropping or contaminated soil, etc.). abstract: Avian influenza, commonly known as bird flu, is an epidemic caused by H5N1 virus that primarily affects birds like chickens, wild water birds, etc. On rare occasions, these can infect other species including pigs and humans. In the span of less than a year, the lethal strain of bird flu is spreading very fast across the globe mainly in South East Asia, parts of Central Asia, Africa and Europe. In order to study the patterns of spread of epidemic, we made an investigation of outbreaks of the epidemic in one week, that is from February 13–18, 2006, when the deadly virus surfaced in India. We have designed a statistical transmission model of bird flu taking into account the factors that affect the epidemic transmission such as source of infection, social and natural factors and various control measures are suggested. For modeling the general intensity coefficient [Formula: see text] , we have implemented the recent ideas given in the article Fitting the Bill, Nature [R. Howlett, Fitting the bill, Nature 439 (2006) 402], which describes the geographical spread of epidemics due to transportation of poultry products. Our aim is to study the spread of avian influenza, both in time and space, to gain a better understanding of transmission mechanism. Our model yields satisfactory results as evidenced by the simulations and may be used for the prediction of future situations of epidemic for longer periods. We utilize real data at these various scales and our model allows one to generalize our predictions and make better suggestions for the control of this epidemic. url: https://api.elsevier.com/content/article/pii/S1468121807000879 doi: 10.1016/j.nonrwa.2007.04.009 id: cord-001985-iwfidoer author: Urayama, Syun-ichi title: FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance date: 2016-02-13 words: 5007.0 sentences: 281.0 pages: flesch: 50.0 cache: ./cache/cord-001985-iwfidoer.txt txt: ./txt/cord-001985-iwfidoer.txt summary: This method revealed a previously unidentified viral RNA diversity of more than 20 complete RNA viral genomes including dsRNA and ssRNA viruses associated with an environmental diatom colony. We herein established a novel strategy to obtain full-length RNA virus sequences with extremely high efficiency by applying a short dsRNA full-length cloning method (8) for physically fragmented dsRNAs. The improved method, named FLDS (fragmented and loop primer ligated dsRNA sequencing), was applied to a diatom colony in a tide pool and revealed previously unidentified RNA viruses. These results indicated that FLDS effectively enriched dsRNA reads, thereby allowing the retrieval of complete genome sequences including terminal regions without the requirement for the additional rapid amplification of cDNA ends (RACE). A phylogenetic analysis of RdRp in DCASSRV-2 suggested that the RNA virus was classified into the genus Mitovirus, which has a non-segmented ssRNA genome, infects the mitochondria of fungi, and lacks viral particles (Fig. S4E) . abstract: Knowledge of the distribution and diversity of RNA viruses is still limited in spite of their possible environmental and epidemiological impacts because RNA virus-specific metagenomic methods have not yet been developed. We herein constructed an effective metagenomic method for RNA viruses by targeting long double-stranded (ds)RNA in cellular organisms, which is a hallmark of infection, or the replication of dsRNA and single-stranded (ss)RNA viruses, except for retroviruses. This novel dsRNA targeting metagenomic method is characterized by an extremely high recovery rate of viral RNA sequences, the retrieval of terminal sequences, and uniform read coverage, which has not previously been reported in other metagenomic methods targeting RNA viruses. This method revealed a previously unidentified viral RNA diversity of more than 20 complete RNA viral genomes including dsRNA and ssRNA viruses associated with an environmental diatom colony. Our approach will be a powerful tool for cataloging RNA viruses associated with organisms of interest. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791113/ doi: 10.1264/jsme2.me15171 id: cord-293097-poh1y6o7 author: V, Antony Aroul Raj title: The contribution of dry indoor built environment on the spread of Coronavirus: Data from various Indian states date: 2020-07-02 words: 3072.0 sentences: 139.0 pages: flesch: 53.0 cache: ./cache/cord-293097-poh1y6o7.txt txt: ./txt/cord-293097-poh1y6o7.txt summary: This concept is assessed using four major parameters such as population density, climate severity, the volume of indoor spaces, and air-conditioning usage which affect the infection spread and mortality using the data available for various states of India. Hence the major objective of the present work is to propose the mechanism of virus spread under various climates and the indoor environment conditions maintained through the existing theory of respiratory droplet drying. Further, it is aimed to perform a statistical study on the dependence of mortality and infection in the Indian States with respect to four major parameters such as population density, climate severity, volume of indoor spaces, and air-conditioning usage based on monthly data for March and April. In an environment with low humidity and low temperature, due to combined high heat and mass transfer potential leads to fast drying and size reduction of the respiratory droplets and the virus is almost active in all the locations. abstract: Coronavirus spread is more serious in urban metropolitan cities compared to rural areas. It is observed from the data on the infection rate available in the various sources that the cold and dry conditions accelerate the spread of coronavirus. In the present work, the existing theory of respiratory droplet drying is used to propose the mechanism of virus spread under various climates and the indoor environment conditions which plays a greater role in the virus spread. This concept is assessed using four major parameters such as population density, climate severity, the volume of indoor spaces, and air-conditioning usage which affect the infection spread and mortality using the data available for various states of India. Further, it is analysed using the data from various states in India along with the respective climatic conditions. It is found that under some indoor scenarios, the coronaviruses present in the respiratory droplets become active due to size reduction that occurs both in sessile and airborne droplet nuclei causing an increase in the spread. Understanding this mechanism will be very useful to take the necessary steps to reduce the rate of transmission by initiating corrective measures and maintaining the required conditions in the indoor built environment. url: https://www.sciencedirect.com/science/article/pii/S2210670720305928?v=s5 doi: 10.1016/j.scs.2020.102371 id: cord-003639-bjtxf1y8 author: Vahey, Michael D title: Influenza A virus surface proteins are organized to help penetrate host mucus date: 2019-05-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Influenza A virus (IAV) enters cells by binding to sialic acid on the cell surface. To accomplish this while avoiding immobilization by sialic acid in host mucus, viruses rely on a balance between the receptor-binding protein hemagglutinin (HA) and the receptor-cleaving protein neuraminidase (NA). Although genetic aspects of this balance are well-characterized, little is known about how the spatial organization of these proteins in the viral envelope may contribute. Using site-specific fluorescent labeling and super-resolution microscopy, we show that HA and NA are asymmetrically distributed on the surface of filamentous viruses, creating a spatial organization of binding and cleaving activities that causes viruses to step consistently away from their NA-rich pole. This Brownian ratchet-like diffusion produces persistent directional mobility that resolves the virus’s conflicting needs to both penetrate mucus and stably attach to the underlying cells, potentially contributing to the prevalence of the filamentous phenotype in clinical isolates of IAV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6516830/ doi: 10.7554/elife.43764 id: cord-283641-2u16otbf author: Vainionpää, R. title: Diagnostic Techniques: Serological and Molecular Approaches date: 2015-03-06 words: 4400.0 sentences: 222.0 pages: flesch: 40.0 cache: ./cache/cord-283641-2u16otbf.txt txt: ./txt/cord-283641-2u16otbf.txt summary: For diagnostic purposes the following approaches can be used: demonstration of presence of infectious virus or its structural components directly from a patient''s specimens or investigation of specific antibody response in serum specimens. Glossary EIA Enzyme immunoassays are methods used to estimate virus-specific IgG and IgM antibodies or virus antigens by enzyme-labeled conjugates. Nucleic acid testing has become the main approach for the demonstration of the presence of virus while cultivation is used by fewer specialized laboratories and antigen detection methods have moved to the point of care. Diagnostic applications of the measurement of the avidity of IgG antibodies against specific antigens have been developed to help distinguish serological responses due to acute infections from those of chronic or past infections. In immunofluorescence tests, cells from a clinical specimen are fixed on a glass slide and viral antigens present in the cells are detected by fluorescein-labeled virus-specific antibodies. abstract: Virus laboratory diagnostics has an increasingly important role in modern patient care. Virological methods are needed to investigate the etiology of acute viral infection or the reactivation of a latent infection, as well as to follow virus load in antiviral treatments. Serological assays are also used for screening of blood products for the risk of certain chronic infections, evaluation of the immune status, and need for prophylactic treatments in connection with organ transplantations. For diagnostic purposes the following approaches can be used: demonstration of presence of infectious virus or its structural components directly from a patient's specimens or investigation of specific antibody response in serum specimens. Amplification techniques, most commonly polymerase chain reaction (PCR) is currently the workhorse of nucleic acid testing for the detection and quantitation of virus genomes. Virus isolation is used to demonstrate infectious virus in a patient's specimens, whereas virus antigens are investigated by antigen detection assays. Serological diagnosis is based on either the demonstration of the presence of virus-specific IgM antibodies or a significant increase in the levels and/or avidity of specific IgG antibodies. Immunoassays are the most commonly used serological assays. Point-of-care tests (POC tests), for antigens, antibodies, and also nucleic acids are also becoming more and more common in diagnostic use. In order to reach the best diagnostic efficiency for each patient it is important to select the most suitable method using the right sample collected at the right time. url: https://www.sciencedirect.com/science/article/pii/B9780128012383025587 doi: 10.1016/b978-0-12-801238-3.02558-7 id: cord-323195-buzcb8ya author: Valtonen, Maarit title: Common cold in Team Finland during 2018 Winter Olympic Games (PyeongChang): epidemiology, diagnosis including molecular point-of-care testing (POCT) and treatment date: 2019-05-29 words: 4234.0 sentences: 285.0 pages: flesch: 54.0 cache: ./cache/cord-323195-buzcb8ya.txt txt: ./txt/cord-323195-buzcb8ya.txt summary: title: Common cold in Team Finland during 2018 Winter Olympic Games (PyeongChang): epidemiology, diagnosis including molecular point-of-care testing (POCT) and treatment 13 14 The aim of our prospective observational study was to investigate the occurrence and aetiology of the common cold in Team Finland during the 2018 Winter Olympic Games. Six days later, the neighbouring team member in the aeroplane developed symptomatic respiratory syncytial virus A -infection. One subject developed nasal congestion during the 9-hour flight, later detected to be a respiratory syncytial virus B infection. First, 45% of the elite athletes and 32% of the staff members suffered from the symptoms of the common cold during the median stay of 3 weeks at the Winter Olympic Games. Our study is the first to detect the aetiology of respiratory infections in elite athletes using molecular POCT at a major event. abstract: OBJECTIVES: The common cold is the main cause of medical time loss in elite sport. Rapid diagnosis has been a challenge that may be amenable to molecular point-of-care testing (POCT). METHODS: We performed a prospective observational study of the common cold in Team Finland during the 2018 Winter Olympic Games. There were 44 elite athletes and 68 staff members. The chief physician recorded the symptoms of the common cold daily on a standardised form. Two nasal swabs were taken at the onset of symptoms. One swab was analysed within 45 min using a molecular POCT for respiratory syncytial virus and influenza A and B viruses. After the Games, the other swab was tested for 16 possible causative respiratory viruses using PCR in laboratory-based testing. RESULTS: 20 out of 44 (45%) athletes and 22 out of 68 (32%) staff members experienced symptoms of the common cold during a median stay of 21 days. Eleven (26%) samples tested virus-positive using POCT. All subjects with influenza (n=6) and 32 close contacts were treated with oseltamivir. The aetiology of the common cold was finally detected in 75% of the athletes and 68 % of the staff members. Seven virus clusters were identified. They were caused by coronaviruses 229E, NL63 and OC43, influenza B virus, respiratory syncytial virus A, rhinovirus and human metapneumovirus. The virus infections spread readily within the team, most commonly within the same sport discipline. CONCLUSIONS: The cold was indeed a common illness in Team Finland during the Winter Olympic Games. POCT proved to be clinically valuable, especially for influenza. The aetiology of the common cold was identified in most cases. url: https://doi.org/10.1136/bjsports-2018-100487 doi: 10.1136/bjsports-2018-100487 id: cord-333655-lylt7qld author: Van Breedam, Wander title: Bitter‐sweet symphony: glycan–lectin interactions in virus biology date: 2013-12-06 words: 18667.0 sentences: 875.0 pages: flesch: 42.0 cache: ./cache/cord-333655-lylt7qld.txt txt: ./txt/cord-333655-lylt7qld.txt summary: In sum, it appears that the dimeric lectin galectin-1 can enhance HIV-1 infection efficiency by cross-linking viral and host cell glycans and thereby promoting firmer adhesion of the virus to the target cell surface and facilitating virus-receptor interactions (Ouellet et al., 2005; Mercier et al., 2008; St-Pierre et al., 2011; Sato et al., 2012) . As has been shown for IAV, acquisition or deletion of glycosylation sites may affect crucial steps in the viral infection/replication process (e.g. receptor binding, fusion, release of newly formed virions) (Ohuchi et al., 1997; Wagner et al., 2000; Tsuchiya et al., 2002; Kim & Park, 2012) , alter the capacity of the virus to avoid induction of/recognition by virus-specific antibodies (glycan shielding) Wei et al., 2010; Wanzeck et al., 2011; Kim & Park, 2012; Job et al., 2013; Sun et al., 2013) , and modulate viral interaction with various immune system lectins (Reading et al., 2007; Vigerust et al., 2007; Reading et al., 2009; Tate et al., 2011a, b) . abstract: Glycans are carbohydrate modifications typically found on proteins or lipids, and can act as ligands for glycan‐binding proteins called lectins. Glycans and lectins play crucial roles in the function of cells and organs, and in the immune system of animals and humans. Viral pathogens use glycans and lectins that are encoded by their own or the host genome for their replication and spread. Recent advances in glycobiological research indicate that glycans and lectins mediate key interactions at the virus‐host interface, controlling viral spread and/or activation of the immune system. This review reflects on glycan–lectin interactions in the context of viral infection and antiviral immunity. A short introduction illustrates the nature of glycans and lectins, and conveys the basic principles of their interactions. Subsequently, examples are discussed highlighting specific glycan–lectin interactions and how they affect the progress of viral infections, either benefiting the host or the virus. Moreover, glycan and lectin variability and their potential biological consequences are discussed. Finally, the review outlines how recent advances in the glycan–lectin field might be transformed into promising new approaches to antiviral therapy. url: https://www.ncbi.nlm.nih.gov/pubmed/24188132/ doi: 10.1111/1574-6976.12052 id: cord-350964-0jtfc271 author: Van Nguyen, Dung title: Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam date: 2018-02-28 words: 4803.0 sentences: 246.0 pages: flesch: 51.0 cache: ./cache/cord-350964-0jtfc271.txt txt: ./txt/cord-350964-0jtfc271.txt summary: In this study of pegivirus and human hepatitis-related viruses, liver and serum samples from Vietnamese rodents and bats were examined by PCR and sequencing. Nucleic acids homologous to human hepatitis B, C, E viruses were detected in liver samples of 2 (1.3%) of 157 bats, 38 (8.1%), and 14 (3%) of 470 rodents, respectively. Hepacivirus-like viruses were frequently detected (42.7%) in the bamboo rat, Rhizomys pruinosus, while pegivirus RNA was only evident in 2 (0.3%) of 638 rodent serum samples. Nucleic acid that was extracted from liver samples of 157 bats (29 species; Table S1 ) and 470 rodents (six species) was screened for pegivirus and human hepatitis B, C, E viruses and their homologues ( Table 1 ) by nested and semi-nested PCR assays with degenerate primers. abstract: Rodents and bats are now widely recognised as important sources of zoonotic virus infections in other mammals, including humans. Numerous surveys have expanded our knowledge of diverse viruses in a range of rodent and bat species, including their origins, evolution, and range of hosts. In this study of pegivirus and human hepatitis-related viruses, liver and serum samples from Vietnamese rodents and bats were examined by PCR and sequencing. Nucleic acids homologous to human hepatitis B, C, E viruses were detected in liver samples of 2 (1.3%) of 157 bats, 38 (8.1%), and 14 (3%) of 470 rodents, respectively. Hepacivirus-like viruses were frequently detected (42.7%) in the bamboo rat, Rhizomys pruinosus, while pegivirus RNA was only evident in 2 (0.3%) of 638 rodent serum samples. Complete or near-complete genome sequences of HBV, HEV and pegivirus homologues closely resembled those previously reported from rodents and bats. However, complete coding region sequences of the rodent hepacivirus-like viruses substantially diverged from all of the currently classified variants and potentially represent a new species in the Hepacivirus genus. Of the viruses identified, their routes of transmission and potential to establish zoonoses remain to be determined. url: https://doi.org/10.3390/v10030102 doi: 10.3390/v10030102 id: cord-337149-cjon7ihb author: Van Vliet, Kim M. title: The Role of the Adeno-Associated Virus Capsid in Gene Transfer date: 2008 words: 10774.0 sentences: 681.0 pages: flesch: 52.0 cache: ./cache/cord-337149-cjon7ihb.txt txt: ./txt/cord-337149-cjon7ihb.txt summary: Adeno-associated virus (AAV) is one of the most promising viral gene transfer vectors that has been shown to effect long-term gene expression and disease correction with low toxicity in animal models, and is well tolerated in human clinical trials. Prior to developing a gene therapy strategy that utilizes AAV, the serotype should be carefully considered since each capsid exhibits a unique tissue tropism and transduction efficiency. Several approaches have been undertaken in an effort to target AAV vectors to specific cell types, including utilizing natural serotypes that target a desired cellular receptor, producing pseudotyped vectors, and engineering chimeric and mosaic AAV capsids. The atomic structure of adeno-associated virus (AAV-2), a vector for human gene therapy Adeno-associated virus serotypes 1 to 5 mediated tumor cell directed gene transfer and improvement of transduction efficiency Adeno-associated virus vectors serotyped with AAV8 capsid are more efficient than AAV-1 or -2 serotypes for widespread gene delivery to the neonatal mouse brain abstract: Adeno-associated virus (AAV) is one of the most promising viral gene transfer vectors that has been shown to effect long-term gene expression and disease correction with low toxicity in animal models, and is well tolerated in human clinical trials. The surface of the AAV capsid is an essential component that is involved in cell binding, internalization, and trafficking within the targeted cell. Prior to developing a gene therapy strategy that utilizes AAV, the serotype should be carefully considered since each capsid exhibits a unique tissue tropism and transduction efficiency. Several approaches have been undertaken in an effort to target AAV vectors to specific cell types, including utilizing natural serotypes that target a desired cellular receptor, producing pseudotyped vectors, and engineering chimeric and mosaic AAV capsids. These capsid modifications are being incorporated into vector production and purification methods that provide for the ability to scale-up the manufacturing process to support human clinical trials. Protocols for small-scale and large-scale production of AAV, as well as assays to characterize the final vector product, are presented here. The structures of AAV2, AAV4, and AAV5 have been solved by X-ray crystallography or cryo-electron microscopy (cryo-EM), and provide a basis for rational vector design in developing customized capsids for specific targeting of AAV vectors. The capsid of AAV has been shown to be remarkably stable, which is a desirable characteristic for a gene therapy vector; however, recently it has been shown that the AAV serotypes exhibit differential susceptibility to proteases. The capsid fragmentation pattern when exposed to various proteases, as well as the susceptibility of the serotypes to a series of proteases, provides a unique fingerprint for each serotype that can be used for capsid identity validation. In addition to serotype identification, protease susceptibility can also be utilized to study dynamic structural changes that must occur for the AAV capsid to perform its various functions during the virus life cycle. The use of proteases for structural studies in solution complements the crystal structural studies of the virus. A generic protocol based on proteolysis for AAV serotype identification is provided here. url: https://doi.org/10.1007/978-1-59745-210-6_2 doi: 10.1007/978-1-59745-210-6_2 id: cord-353609-no3mbg5d author: Vandegrift, Kurt J. title: An Ecological and Conservation Perspective on Advances in the Applied Virology of Zoonoses date: 2011-04-15 words: 6925.0 sentences: 350.0 pages: flesch: 42.0 cache: ./cache/cord-353609-no3mbg5d.txt txt: ./txt/cord-353609-no3mbg5d.txt summary: Conducting viral surveillance in animal reservoirs and invertebrate vectors can help explain circulation within host species; observed patterns of zoonotic transmission; and even allow for the prediction of periods of increased risk of zoonotic transmission (e.g., Rift valley fever and rainfall [25] ; West Nile virus (WNV) and American robin (Turdus turdus) migration [26] ; as well as hantavirus in mice [27, 28] ). Globalization, host ecology, host-virus dynamics, climate change, and anthropogenic landscape changes all contribute to the complexity of zoonotic viral emergence and disease, and create significant conservation and public health challenges. While the lasting efficacy of wildlife vaccination efforts has yet to be demonstrated with either endangered species or in breaking the transmission cycle of human pathogens, an increasing number of researchers are drawing attention to systems where it seems feasible [99, 103] ; demonstrating that intricate knowledge of host and virus ecology can greatly reduce the amount of vaccine coverage that is necessary to control these viruses. abstract: The aim of this manuscript is to describe how modern advances in our knowledge of viruses and viral evolution can be applied to the fields of disease ecology and conservation. We review recent progress in virology and provide examples of how it is informing both empirical research in field ecology and applied conservation. We include a discussion of needed breakthroughs and ways to bridge communication gaps between the field and the lab. In an effort to foster this interdisciplinary effort, we have also included a table that lists the definitions of key terms. The importance of understanding the dynamics of zoonotic pathogens in their reservoir hosts is emphasized as a tool to both assess risk factors for spillover and to test hypotheses related to treatment and/or intervention strategies. In conclusion, we highlight the need for smart surveillance, viral discovery efforts and predictive modeling. A shift towards a predictive approach is necessary in today’s globalized society because, as the 2009 H1N1 pandemic demonstrated, identification post-emergence is often too late to prevent global spread. Integrating molecular virology and ecological techniques will allow for earlier recognition of potentially dangerous pathogens, ideally before they jump from wildlife reservoirs into human or livestock populations and cause serious public health or conservation issues. url: https://doi.org/10.3390/v3040379 doi: 10.3390/v3040379 id: cord-314166-79323mzd author: Vanderford, Thomas H. title: Adaptation of a Diverse Simian Immunodeficiency Virus Population to a New Host Is Revealed through a Systematic Approach to Identify Amino Acid Sites under Selection date: 2006-12-11 words: 6453.0 sentences: 275.0 pages: flesch: 45.0 cache: ./cache/cord-314166-79323mzd.txt txt: ./txt/cord-314166-79323mzd.txt summary: Here, employing previously unused numerical analyses and a more comprehensive phylogenetic analysis of the same viral sequence data, we detect strong RM-specific selection in the V2 loop at days 40 and 70 p.i., which underscores this region''s importance in adaptation to the RMs. Most prominently, changes in the position and frequency of an N-glyc motif in the V2 loop likely represent an adaptation either to a divergent CD4 or chemokine coreceptor or to an as-of-yet undetermined target cell population. Taken together, these data suggest that in addition to overall differences in the allelic structure of the SIVsm populations between the 2 host species, the viruses replicating in RMs are significantly more diverged from the SI than viruses replicating in the newly infected SMs. To identify specific amino acid sites that may be responsible for the disparate evolutionary patterns of viruses replicating in the 2 monkey species, we applied 3 site-bysite analyses to detect particular codons under selection. abstract: Simian immunodeficiency viruses (SIV) have had considerable success at crossing species barriers; both human immunodeficiency virus (HIV)-1 and HIV-2 have been transmitted on multiple occasions from SIV-infected natural host species. However, the precise evolutionary and ecological mechanisms characterizing a successful cross-species transmission event remain to be elucidated. Here, in addition to expanding and clarifying our previous description of the adaptation of a diverse, naturally occurring SIVsm inoculum to a new rhesus macaque host, we present an analytical framework for understanding the selective forces driving viral adaptation to a new host. A preliminary analysis of large-scale changes in virus population structure revealed that viruses replicating in the macaques were subject to increasing levels of selection through day 70 postinfection (p.i.), whereas contemporaneous viruses in the mangabeys remained similar to the source inoculum. Three different site-by-site methods were employed to identify the amino acid sites responsible for this macaque-specific selection. Of 124 amino acid sites analyzed, 3 codons in V2, a 2–amino acid shift in an N-linked glycosylation site, and variation at 2 sites in the highly charged region were consistently evolving under either directional or diversifying selection at days 40 and 70 p.i. This strong macaque-specific selection on the V2 loop underscores the importance of this region in the adaptation of SIVsm to rhesus macaques. Due to the extreme viral diversity already extant in the naturally occurring viral inoculum, we employed a broad range of phylogenetic and numerical tools in order to distinguish the signatures of past episodes of selection in viral sequences from more recent selection pressures. url: https://www.ncbi.nlm.nih.gov/pubmed/17159231/ doi: 10.1093/molbev/msl194 id: cord-335647-dhcxj7cj author: Vanderlinden, Evelien title: Emerging Antiviral Strategies to Interfere with Influenza Virus Entry date: 2013-06-25 words: 15104.0 sentences: 870.0 pages: flesch: 43.0 cache: ./cache/cord-335647-dhcxj7cj.txt txt: ./txt/cord-335647-dhcxj7cj.txt summary: We here focus on emerging options to interfere with the influenza virus entry process, which consists of the following steps: attachment of the viral hemagglutinin to the sialylated host cell receptors, endocytosis, M2‐mediated uncoating, low pH‐induced membrane fusion, and, finally, import of the viral ribonucleoprotein into the nucleus. There are three conceivable strategies for inhibiting attachment of influenza virus to its target cell: (i) an antiviral compound binding to the HA RBS; (ii) an inhibitor blocking the sialic acid-containing receptors on the epithelial cell membrane; or (iii) a receptor-destroying agent. 91 Regarding potential antiviral use, design of modified forms of the porcine SP-D lectin (which has higher anti-influenza virus activity than its human counterpart) is aided by the growing insight into how its carbohydrate recognition domain (CRD) precisely interacts with the high-mannose glycans attached near the RBS of HA. abstract: Influenza A and B viruses are highly contagious respiratory pathogens with a considerable medical and socioeconomical burden and known pandemic potential. Current influenza vaccines require annual updating and provide only partial protection in some risk groups. Due to the global spread of viruses with resistance to the M2 proton channel inhibitor amantadine or the neuraminidase inhibitor oseltamivir, novel antiviral agents with an original mode of action are urgently needed. We here focus on emerging options to interfere with the influenza virus entry process, which consists of the following steps: attachment of the viral hemagglutinin to the sialylated host cell receptors, endocytosis, M2‐mediated uncoating, low pH‐induced membrane fusion, and, finally, import of the viral ribonucleoprotein into the nucleus. We review the current functional and structural insights in the viral and cellular components of this entry process, and the diverse antiviral strategies that are being explored. This encompasses small molecule inhibitors as well as macromolecules such as therapeutic antibodies. There is optimism that at least some of these innovative concepts to block influenza virus entry will proceed from the proof of concept to a more advanced stage. Special attention is therefore given to the challenging issues of influenza virus (sub)type‐dependent activity or potential drug resistance. url: https://www.ncbi.nlm.nih.gov/pubmed/23801557/ doi: 10.1002/med.21289 id: cord-264291-0czphube author: Varfolomeev, S. D. title: Kinetic model of development of acute viral infection in the human body. Critical conditions, control mechanisms, “thermoheliox” date: 2020-07-20 words: 3008.0 sentences: 174.0 pages: flesch: 50.0 cache: ./cache/cord-264291-0czphube.txt txt: ./txt/cord-264291-0czphube.txt summary: A kinetic model of the development of acute viral infection is proposed and the dynamic behavior of key variables, including the concentrations of viral particles, infected cells, and pathogenic microorganisms, is described. The most important parameters determining the process dynamics are the concentration of the infecting viral agent, the concentration of pathogenic microfl ora, which develops symbiotrophically on the aff ected cells, and physical conditions of the process such as temperature and pH of the medium. Quite a few publications of the last decade describe modeling of the dynamics of viral growth in the body, taking account of the production of pathogenic microfl ora and human immune system response. Most of mathematical models describe the incubation, the viral growth, activation of the immune system, and treatment of infection, but they do not consider the causes for collapse of the system, that is, molecular causes for the death of an organism related to the disease. abstract: A kinetic model of the development of acute viral infection is proposed and the dynamic behavior of key variables, including the concentrations of viral particles, infected cells, and pathogenic microorganisms, is described. The change in the hydrogen ion concentration in the lungs and pH dependence of the activity of carbonic anhydrase, a key respiration enzyme, are critical factors. An acute bifurcation transition determining either the life or collapse of the system is demonstrated. The transition is associated with exponential increase in the concentrations of participants in the process and with functioning of the key enzyme, carbonic anhydrase. A physicochemical interpretation is given for the therapeutic effect of temperature rise and potential therapeutic effect of “thermoheliox”, that is, breathing by heated helium-oxygen mixture. url: https://www.ncbi.nlm.nih.gov/pubmed/32834708/ doi: 10.1007/s11172-020-2886-4 id: cord-005876-d8sid7gd author: Varnholt, V. title: ARDS infolge schwerer RSV-Infektion Therapeutische Optionen: Therapeutische Optionen date: 1996 words: 2394.0 sentences: 308.0 pages: flesch: 55.0 cache: ./cache/cord-005876-d8sid7gd.txt txt: ./txt/cord-005876-d8sid7gd.txt summary: Wir berichten im folgenden ü ber eine auffallende Hä ufung schwerster RS-Virus-Pneumonien mit konsekutivem ARDS im Winterhalbjahr 1994/1995 in unserer Klinik und den Verlauf bei den betroffenen Patienten -nach der vergeblichen Anwendung "ü blicher" Behandlungsmethoden -wä hrend der Anwendung alternativer Therapieverfahren [NO-Inhalation, Hochfrequenzoszillationsbeatmung (HFOV), extrakorporale Membranoxygenierung (ECMO)]. Respiratory syncytial virus (RSV) -ARDS -Inhaled nitric oxide (NO) -High frequency oscillatory ventilation (HFOV) -Extracorporeal membrane oxygenation (ECMO) [10] . Krankheitsverlauf bei 10 Patienten mit RSV-Pneumonie unter alternativen Therapieverfahren wurden -in den verlegenden Institutionen -in 50 % der Fä lle eingesetzt, nach Ü bernahme von uns nur noch bei 2 Kindern: Die mö gliche obstruktive Komponente einer RSV-Infektion stand bei unseren Patienten nicht im Vordergrund, ersichtlich auch an den teilweise sehr niedrigen pCO 2 -Werten. Durch den Einsatz von NO oder/und HFOV kann bei schwer verlaufenden RSV-Infektionen -wie bei anderen Formen des kindlichen Lungenversagens -eine ECMO-Therapie manchmal vermieden werden. Ob bei beatmungspflichtigen Kindern mit RSV-Pneumonie ein frü herer Einsatz von NO und/oder HFOV zu einer weiteren Senkung der Letalität fü hrt, mü ssen weitere Beobachtungen zeigen. abstract: We report on a strikingly frequent referral of former preterm babies with respiratory syncytial virus (RSV) infection and subsequent ARDS in our hospital during the winter 1994/95 with regard to the clinical course under application of alternative treatment modalities. Treatment modalities like inhalational ribavirin, use of bronchodilators and instillation of surfactant had been tried without success. All children (age: 1–43 months) were ventilated for 6.6 (1–17) days with FiO(2) = 1.0 and a mean airway pressure of 16.4 (10–24) cm H(2)O. Mean arterial blood gases were 49 (paO(2)) and 41 (pCO(2)) mm Hg, the OI was 33.4. By inhalational NO in combination with IPPV or HFOV 4 patients could be stabilized, in the other 6 ECMO became necessary. Two of them died in spite of several weeks on ECMO; 8 children survived and could be discharged home after a mean hospital stay of 3 months. Even in very severe cases of RSV infection treatment modalities like NO, HFOV and ECMO can be used successfully. The use of these treatment modalities must be considered before the lung damage is irreversible; in those cases a pre-existing BPD is no contraindication even for extracorporeal lung support. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095882/ doi: 10.1007/s001120050095 id: cord-307046-ko3bdvo0 author: Vasilakis, Nikos title: Exploiting the Legacy of the Arbovirus Hunters date: 2019-05-23 words: 17749.0 sentences: 879.0 pages: flesch: 44.0 cache: ./cache/cord-307046-ko3bdvo0.txt txt: ./txt/cord-307046-ko3bdvo0.txt summary: Complete genome sequences are now available for many of the archived isolates, allowing more accurate taxonomic assignments, analysis of their phylogenetic and evolutionary relationships with other viruses, and evaluation of the potential risks they may present to humans and wild or domestic animal populations. Scientists in these field laboratories were involved in the detection and investigation of human diseases in their respective geographic regions, surveying human and animal populations for serologic evidence of past viral infection, and searching for viruses in a wide variety of arthropods, mammals, birds, reptiles, and amphibians [2] . The family contains several serious human pathogens, including dengue, yellow fever, Zika, Japanese encephalitis, West Nile, and tick-borne encephalitis viruses (all arboviruses in the genus Flavivirus) and the hepatitis C virus (a member of the genus Hepacivirus). abstract: In recent years, it has become evident that a generational gap has developed in the community of arbovirus research. This apparent gap is due to the dis-investment of training for the next generation of arbovirologists, which threatens to derail the rich history of virus discovery, field epidemiology, and understanding of the richness of diversity that surrounds us. On the other hand, new technologies have resulted in an explosion of virus discovery that is constantly redefining the virosphere and the evolutionary relationships between viruses. This paradox presents new challenges that may have immediate and disastrous consequences for public health when yet to be discovered arboviruses emerge. In this review we endeavor to bridge this gap by providing a historical context for the work being conducted today and provide continuity between the generations. To this end, we will provide a narrative of the thrill of scientific discovery and excitement and the challenges lying ahead. url: https://doi.org/10.3390/v11050471 doi: 10.3390/v11050471 id: cord-339209-oe8onyr9 author: Vasilakis, Nikos title: Mesoniviruses are mosquito-specific viruses with extensive geographic distribution and host range date: 2014-05-20 words: 5817.0 sentences: 272.0 pages: flesch: 46.0 cache: ./cache/cord-339209-oe8onyr9.txt txt: ./txt/cord-339209-oe8onyr9.txt summary: The organization of each genome was similar to that described previously for the mesoniviruses (NDiV, CavV, HanaV, NseV and MenoV), featuring a long 5''-untranslated region (5''-UTR) of 359 to 370 nt, six major long open reading frames (ORFs), and a long terminal region of 1780 to 1804 nt preceding the poly[A] tail ( Figure 2 ). To determine the phylogenetic relationships of the newly identified insect viruses, maximum likelihood (ML) phylogenetic trees were constructed based on the amino acid alignments of ORF2a (unprocessed S protein) and a concatenated region of the highly conserved domains within ORF1ab (3CL pro , RdRp and ZnHel1). A Clustal X alignment of the mesonivirus ORF3a proteins and individual structural analyses using SignalP and TMHMM and NetNGlyc (www.expasy.org) indicated that each is a class I transmembrane glycoprotein with a predicted N-termimal signal peptide, an ectodomain containing a conserved set of 6 cysteine residues and a single conserved N-glycosylation site, a transmembrane domain and a C-terminal cytoplasmic domain ( Figure 4A, 4D) . abstract: BACKGROUND: The family Mesoniviridae (order Nidovirales) comprises of a group of positive-sense, single-stranded RNA ([+]ssRNA) viruses isolated from mosquitoes. FINDINGS: Thirteen novel insect-specific virus isolates were obtained from mosquitoes collected in Indonesia, Thailand and the USA. By electron microscopy, the virions appeared as spherical particles with a diameter of ~50 nm. Their 20,129 nt to 20,777 nt genomes consist of positive-sense, single-stranded RNA with a poly-A tail. Four isolates from Houston, Texas, and one isolate from Java, Indonesia, were identified as variants of the species Alphamesonivirus-1 which also includes Nam Dinh virus (NDiV) from Vietnam and Cavally virus (CavV) from Côte d’Ivoire. The eight other isolates were identified as variants of three new mesoniviruses, based on genome organization and pairwise evolutionary distances: Karang Sari virus (KSaV) from Java, Bontag Baru virus (BBaV) from Java and Kalimantan, and Kamphaeng Phet virus (KPhV) from Thailand. In comparison with NDiV, the three new mesoniviruses each contained a long insertion (180 – 588 nt) of unknown function in the 5’ region of ORF1a, which accounted for much of the difference in genome size. The insertions contained various short imperfect repeats and may have arisen by recombination or sequence duplication. CONCLUSIONS: In summary, based on their genome organizations and phylogenetic relationships, thirteen new viruses were identified as members of the family Mesoniviridae, order Nidovirales. Species demarcation criteria employed previously for mesoniviruses would place five of these isolates in the same species as NDiV and CavV (Alphamesonivirus-1) and the other eight isolates would represent three new mesonivirus species (Alphamesonivirus-5, Alphamesonivirus-6 and Alphamesonivirus-7). The observed spatiotemporal distribution over widespread geographic regions and broad species host range in mosquitoes suggests that mesoniviruses may be common in mosquito populations worldwide. url: https://doi.org/10.1186/1743-422x-11-97 doi: 10.1186/1743-422x-11-97 id: cord-023925-qrr7jcwe author: Verhoef, Jan title: A8 Immune response in human pathology: Infections caused by bacteria, viruses, fungi, and parasites date: 2011-07-12 words: 5499.0 sentences: 282.0 pages: flesch: 42.0 cache: ./cache/cord-023925-qrr7jcwe.txt txt: ./txt/cord-023925-qrr7jcwe.txt summary: 128 Immune response in human pathology: infections caused by bacteria, viruses, fungi, and parasites Micro-organisms that succeed in penetrating the first line of defence are ingested, killed, and degraded by phagocytic cells [polymorphonuclear leukocytes (PMN) or neutrophils, monocytes, and macrophages], which are attracted to a microbial infection through chemotaxis. Intracellular signalling involves several kinases depending on 132 Immune response in human pathology: infections caused by bacteria, viruses, fungi, and parasites Genotypical characteristics: chromosomal DNA fragment analysis, nucleic acid sequence analysis, probes Phenotypical characteristics: morphology, biotyping, serotyping, antibiotic resistance Analytical characteristics: cell-wall analysis, lipid and protein analysis, enzyme typing (catalase) Gram staining positive or negative Aerobic, anaerobic: Fermentation of different sugars Naming and classification of viruses according to: Structure: size, morphology (naked, enveloped), nucleic acid (RNA, DNA) Molecular aspects: mode of replication, assembly and budding Disease: encephalitis, hepatitis Means of transmission: droplets, water, blood, insects Host range: animal, plant, bacteria Classification of fungi according to: Structure: macroscopic morphology of hyphae (mycelium); microscopic morphology of hyphae, conidophores and conidia (spores); and shape and size Cell features: nucleus, cytosol, plasmalemma (cell membrane which contains cholesterol), physiology, staining properties Sexual characteristics: sexual and /or asexual reproduction, extended dikaryotic phase, basidium formation Genotypical characteristics: chromosomal DNA fragment analysis, nucleic acid sequence analysis, probes abstract: In the middle of the 19th century, it became clear that micro-organisms could cause disease. Effective treatment, however, was not possible at that time; prevention and spread of infectious diseases depended solely on proper hygienic means. At the beginning of the 20th century, passive and active vaccination procedures were developed against a number of these PATHOGENIC MICRO-ORGANISMS to prevent the diseases in question (rabies, diphtheria, tetanus, etc.). Thanks to the discovery of antimicrobial chemicals (by Paul Ehrlich) and antibiotics (by Sir Alexander Fleming), the threat of infectious diseases seemed to be minimised. Large scale vaccination programmes against childhood diseases (diphtheria, whooping cough and polio), started in the early 1950s, raised hopes of finally being able to eradicate these diseases from the planet. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7178827/ doi: 10.1007/978-3-0346-0136-8_8 id: cord-258389-1u05w7r4 author: Verma, Anju title: Animal tissue culture principles and applications date: 2020-06-26 words: 12098.0 sentences: 740.0 pages: flesch: 49.0 cache: ./cache/cord-258389-1u05w7r4.txt txt: ./txt/cord-258389-1u05w7r4.txt summary: The development of basic culture media has enabled scientists to work with a wide variety of cells under controlled conditions; this has played an important role in advancing our understanding of cell growth and differentiation, identification of growth factors, and understanding of mechanisms underlying the normal functions of various cell types. Many animal cells can be induced to grow outside of their organ or tissue of origin under defined conditions when supplemented with a medium containing nutrients and growth factors. With advancements in animal cell culture technology, a number of cell lines have evolved and are used for vaccine production, therapeutic proteins, pharmaceutical agents, and anticancerous agents. The animal cell culture can be grown for a wide variety of cell-based assays to investigate morphology, protein expression, cell growth, differentiation, apoptosis, and toxicity in different environments. abstract: Animal cell culture technology in today’s scenario has become indispensable in the field of life sciences, which provides a basis to study regulation, proliferation, and differentiation and to perform genetic manipulation. It requires specific technical skills to carry out successfully. This chapter describes the essential techniques of animal cell culture as well as its applications. url: https://www.sciencedirect.com/science/article/pii/B9780128117101000124 doi: 10.1016/b978-0-12-811710-1.00012-4 id: cord-283405-aozxvxxs author: Vermillion, Meghan S. title: Pregnancy and infection: using disease pathogenesis to inform vaccine strategy date: 2018-02-01 words: 8428.0 sentences: 431.0 pages: flesch: 33.0 cache: ./cache/cord-283405-aozxvxxs.txt txt: ./txt/cord-283405-aozxvxxs.txt summary: Pregnant women, unborn fetuses, and neonates represent three populations of high-risk individuals that can all be simultaneously protected from vaccine-preventable infectious disease with strategic maternal immunization protocols. Third are neonatal and infant infections, which are not considered to pose significant risk to pregnant women or unborn fetuses, but can cause severe, and sometimes fatal disease in neonates and infants that lack protective maternal immunity following birth. Studies in pregnant nonhuman primates have been instrumental for the identification of CD4 + T cell responses as critical for early control of CMV infection and transmission during pregnancy, 100 and studies in guinea pigs have demonstrated that a single-cycle infectious CMV vaccine induces immune responses similar to natural infection and protects against congenital infection. 125 Vaccine candidates have been developed using diverse platforms, including DNA, mRNA, and purified inactivated and live-attenuated virus, many of which have been tested in non-pregnant mouse and nonhuman primate models for their ability to generate immune responses that mimic responses to natural infection and protected against ZIKV challenge. abstract: Vaccination is the mainstay of preventative medicine for many infectious diseases. Pregnant women, unborn fetuses, and neonates represent three at-risk populations that can be simultaneously protected by strategic vaccination protocols. Because the pathogenesis of different infectious microbes varies based on tissue tropism, timing of infection, and host susceptibility, the goals of immunization are not uniform across all vaccines. Mechanistic understanding of infectious disease pathogenesis and immune responses is therefore essential to inform vaccine design and the implementation of appropriate immunization protocols that optimize protection of pregnant women, fetuses, and neonates. url: https://doi.org/10.1038/s41541-017-0042-4 doi: 10.1038/s41541-017-0042-4 id: cord-336929-2rnkotqy author: Vieira, Flávia Sarmento title: Host‐cell lipid rafts: a safe door for micro‐organisms? date: 2012-01-03 words: 9925.0 sentences: 494.0 pages: flesch: 41.0 cache: ./cache/cord-336929-2rnkotqy.txt txt: ./txt/cord-336929-2rnkotqy.txt summary: In addition to the lipid components, a variety of cell receptors and signalling proteins are known to be associated with membrane rafts. Many animal viruses exploit the endocytic machinery of their host cell for infection, and lipid rafts are often a site for entry, assembly and budding of microbial pathogens, as confirmed by biochemical approaches and microscopy evidence (Kovbasnjuk et al., 2001; Suomalainen, 2002; Lu et al., 2008) . Interestingly, it had already been demonstrated that Brucella abortus infection is related with PrP C (cellular PrP), one of the lipid raft-associated molecules on the plasma membrane of different cell types. In the macrophage-like cell line RAW 264.7, for example, LPS stimulation induces translocation of CD14, ERK-2 (extracellular-signalregulated kinase 2) and p38 to lipid rafts, but other proteins also involved in the LPS signalling response do not migrate within these microdomains (Triantafilou et al., 2007; Olsson and Sundler, 2006) . abstract: The lipid raft hypothesis proposed that these microdomains are small (10–200 nM), highly dynamic and enriched in cholesterol, glycosphingolipids and signalling phospholipids, which compartmentalize cellular processes. These membrane regions play crucial roles in signal transduction, phagocytosis and secretion, as well as pathogen adhesion/interaction. Throughout evolution, many pathogens have developed mechanisms to escape from the host immune system, some of which are based on the host membrane microdomain machinery. Thus lipid rafts might be exploited by pathogens as signalling and entry platforms. In this review, we summarize the role of lipid rafts as players in the overall invasion process used by different pathogens to escape from the host immune system. url: https://doi.org/10.1042/bc20090138 doi: 10.1042/bc20090138 id: cord-318495-1w74wf02 author: Vignuzzi, Marco title: Defective viral genomes are key drivers of the virus–host interaction date: 2019-06-03 words: 8876.0 sentences: 429.0 pages: flesch: 33.0 cache: ./cache/cord-318495-1w74wf02.txt txt: ./txt/cord-318495-1w74wf02.txt summary: The demonstration of hotspots for the generation of copyback DVGs from respiratory syncytial virus (RSV) and the identification of specific nucleotides that determine where copy-back DVGs rejoin further demonstrate that the generation of copy-back DVGs is not completely random, but instead that specific sequences encoded in the viral genome direct or facilitate their formation 50 in some infections, DVG generation is not a completely stochastic process and, instead, virus-encoded sequences favour the production and/or amplification of predominant DVGs. It remains to be determined whether conservation is a property of certain DVG types and which specific sequences and/or RNA structures lead to DVG generation in these conditions. Persistent infection with infectious pancreatic necrosis virus mediated by defective-interfering (DI) virus particles in a cell line showing strong interference but little DI replication I Interferon-inducing defective-interfering particles as mediators of cell sparing: possible role in persistent infection by vesicular stomatitis virus abstract: Viruses survive often harsh host environments, yet we know little about the strategies they utilize to adapt and subsist given their limited genomic resources. We are beginning to appreciate the surprising versatility of viral genomes and how replication-competent and -defective virus variants can provide means for adaptation, immune escape and virus perpetuation. This Review summarizes current knowledge of the types of defective viral genomes generated during the replication of RNA viruses and the functions that they carry out. We highlight the universality and diversity of defective viral genomes during infections and discuss their predicted role in maintaining a fit virus population, their impact on human and animal health, and their potential to be harnessed as antiviral tools. url: https://doi.org/10.1038/s41564-019-0465-y doi: 10.1038/s41564-019-0465-y id: cord-264884-ydkigome author: Villarreal, Luis P. title: The Widespread Evolutionary Significance of Viruses date: 2008-07-05 words: 23138.0 sentences: 1203.0 pages: flesch: 47.0 cache: ./cache/cord-264884-ydkigome.txt txt: ./txt/cord-264884-ydkigome.txt summary: For example, common structural motifs from phage to eukaryotic DNA viruses (T4 and herpesvirus) suggest very ancient links in virus evolution that span all domains of life (see below). On an evolutionary time-scale, the majority of viral lineages tend to exist as species-specifi c persistent (aka temperate, latent, and chronic) infections in which individual hosts will be colonized by mostly silent (asymptomatic) viruses for the duration of their life . It has distinct genetic, fi tness, and evolutionary characteristics that require intimate, host (tissue)-specifi c viral strategies and precise gene functions to attain stable maintenance in the presence of immunity and to allow biologically controlled reactivation. Thus, the phycodnaviruses appear to represent a basal but diverse viral lineage that has both acute and persistent lifestyle and have some clear relationships to most large eukaryotic DNA viruses and many phage. abstract: In the last 30 years, the study of virus evolution has undergone a transformation. Originally concerned with disease and its emergence, virus evolution had not been well integrated into the general study of evolution. This chapter reviews the developments that have brought us to this new appreciation for the general significance of virus evolution to all life. We now know that viruses numerically dominate all habitats of life, especially the oceans. Theoretical developments in the 1970s regarding quasispecies, error rates, and error thresholds have yielded many practical insights into virus–host dynamics. The human diseases of HIV-1 and hepatitis C virus cannot be understood without this evolutionary framework. Yet recent developments with poliovirus demonstrate that viral fitness can be the result of a consortia, not one fittest type, a basic Darwinian concept in evolutionary biology. Darwinian principles do apply to viruses, such as with Fisher population genetics, but other features, such as reticulated and quasispecies-based evolution distinguish virus evolution from classical studies. The available phylogenetic tools have greatly aided our analysis of virus evolution, but these methods struggle to characterize the role of virus populations. Missing from many of these considerations has been the major role played by persisting viruses in stable virus evolution and disease emergence. In many cases, extreme stability is seen with persisting RNA viruses. Indeed, examples are known in which it is the persistently infected host that has better survival. We have also recently come to appreciate the vast diversity of phage (DNA viruses) of prokaryotes as a system that evolves by genetic exchanges across vast populations (Chapter 10). This has been proposed to be the “big bang” of biological evolution. In the large DNA viruses of aquatic microbes we see surprisingly large, complex and diverse viruses. With both prokaryotic and eukaryotic DNA viruses, recombination is the main engine of virus evolution, and virus host co-evolution is common, although not uniform. Viral emergence appears to be an unending phenomenon and we can currently witness a selective sweep by retroviruses that infect and become endogenized in koala bears. url: https://api.elsevier.com/content/article/pii/B9780123741530000217 doi: 10.1016/b978-0-12-374153-0.00021-7 id: cord-281281-knelqmzx author: Villas-Boas, Gustavo R. title: The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents date: 2020-09-07 words: 15780.0 sentences: 708.0 pages: flesch: 42.0 cache: ./cache/cord-281281-knelqmzx.txt txt: ./txt/cord-281281-knelqmzx.txt summary: The use of bioinformatics and other computational tools in addition to molecular modeling has helped researchers from different areas in the search for strategies for diagnosing viral infection, in the development of vaccines for its prevention, as well as in the discovery of new anti-SARS-CoV-2 agents. In the context of COVID-19, this characteristic was important for a better understanding of the origin of SARS-CoV-2 from the comparative analysis of genomic data of the new virus with others from the same family, suggesting its origin from natural selection, with modifications in its spike protein, more specifically in the host receptor binding domain, which may have enhanced its interaction and recognition by the human cell [83, 91] . The contributions of bioinformatics and molecular modeling in elucidating essential targets for the planning and development of new drugs, and the analysis of already known compounds, support the search for safer and more effective treatments against SARS-CoV-2 infection. abstract: On March 11, 2020, the World Health Organization (WHO) officially declared the outbreak caused by the new coronavirus (SARS-CoV-2) a pandemic. The rapid spread of the disease surprised the scientific and medical community. Based on the latest reports, news, and scientific articles published, there is no doubt that the coronavirus has overloaded health systems globally. Practical actions against the recent emergence and rapid expansion of the SARS-CoV-2 require the development and use of tools for discovering new molecular anti-SARS-CoV-2 targets. Thus, this review presents bioinformatics and molecular modeling strategies that aim to assist in the discovery of potential anti-SARS-CoV-2 agents. Besides, we reviewed the relationship between SARS-CoV-2 and innate immunity, since understanding the structures involved in this infection can contribute to the development of new therapeutic targets. Bioinformatics is a technology that assists researchers in coping with diseases by investigating genetic sequencing and seeking structural models of potential molecular targets present in SARS-CoV2. The details provided in this review provide future points of consideration in the field of virology and medical sciences that will contribute to clarifying potential therapeutic targets for anti-SARS-CoV-2 and for understanding the molecular mechanisms responsible for the pathogenesis and virulence of SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32906733/ doi: 10.3390/molecules25184086 id: cord-004477-qu2o2iu1 author: Vlasova, Anastasia N. title: Editorial: Porcine Anti-Viral Immunity date: 2020-03-06 words: 1583.0 sentences: 88.0 pages: flesch: 45.0 cache: ./cache/cord-004477-qu2o2iu1.txt txt: ./txt/cord-004477-qu2o2iu1.txt summary: Immediately following viral infection, neonatal survival depends on innate immunity and passive protection by lactogenic immune factors such as pathogen-specific antibodies, until an adaptive immune response can develop. Wide-spread porcine reproductive and respiratory syndrome virus (PRRSV) and swine influenza virus (SIV) represent major health challenges in the large US swine production systems and possibly worldwide. In introducing the topic of anti-viral immunity, we emphasize the genetic diversity of viruses, the virus life cycle and the pathology that viral infection can cause. A more tedious procedure is to use only parts of the virus as the vaccine (subunit vaccines) that target the immune response to those viral epitopes that elicit VN antibodies. A second approach to vaccine development is use of live attenuated virus that has been genetically modified or cell culture adapted and cannot produce a disease in the host but can still replicate. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7067899/ doi: 10.3389/fimmu.2020.00399 id: cord-021375-lca26xum author: Voelkner, Nadine title: Riding the Shi: From Infection Barriers to the Microbial City date: 2019-08-23 words: 9599.0 sentences: 443.0 pages: flesch: 49.0 cache: ./cache/cord-021375-lca26xum.txt txt: ./txt/cord-021375-lca26xum.txt summary: Taking its cue from the currently accepted germ theory of disease, such mechanisms render a global city like Hong Kong not only pervasively "on alert" and under threat of unpredictable and pathogenic viruses and other microbes, it also gives rise to a hygiene and antimicrobial politics that is never entirely able to control pathogenic circulation. Considering recent advances in gene sequencing in microbiology, through which a "vast diversity of microbial life in, on and around the human body" (Lorimer 2017, 544) has been identified as residing in complex relationality with one another, how befitting is it to fight infectious diseases by indiscriminately eliminating microbes through the use of antimicrobials and practicing urban hygiene as in the case of Hong Kong? Various scholars have noted how, much like Hong Kong in the face of SARS, global public health programs adopt an antimicrobial stance to the control and/or elimination of infectious diseases, however, which might prove to be counterproductive in securing human life (Macphail 2014; Methot and Alizon 2014; Fishel 2015 Fishel , 2017 White 2015; Hinchliffe et al. abstract: How can a microbial approach to global health security protect life? Contemporary infection control mechanisms set the human and the pathogenic microbe against each other, as the victim versus the menace. This biomedical polarization persistently runs through the contemporary dominant mode of thinking about public health and infectious disease governance. Taking its cue from the currently accepted germ theory of disease, such mechanisms render a global city like Hong Kong not only pervasively “on alert” and under threat of unpredictable and pathogenic viruses and other microbes, it also gives rise to a hygiene and antimicrobial politics that is never entirely able to control pathogenic circulation. The article draws on recent advances in medical microbiology, which depart from germ theory, to invoke an ecological understanding of the human-microbe relation. Here, while a small number of viruses are pathogenic, the majority are benign; some are even essential to human life. Disease is not just the outcome of a pathogenic microbe infecting a human host but emerges from socioeconomic relations, which exacerbate human-animal-microbial interactions. In a final step, the article draws on Daoist thought to reflect on the ways that such a microbial understanding translates into life and city dwelling. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149467/ doi: 10.1093/ips/olz016 id: cord-276193-cngz535o author: Volz, A. title: Modified Vaccinia Virus Ankara: History, Value in Basic Research, and Current Perspectives for Vaccine Development date: 2016-08-01 words: 17857.0 sentences: 787.0 pages: flesch: 36.0 cache: ./cache/cord-276193-cngz535o.txt txt: ./txt/cord-276193-cngz535o.txt summary: Safety tested Modified Vaccinia virus Ankara (MVA) is licensed as third-generation vaccine against smallpox and serves as a potent vector system for development of new candidate vaccines against infectious diseases and cancer. Immunizations with this MVA deletion mutant led to significantly enhanced virus-specific CD8+ T-cell responses and increased protective capacity against lethal challenge infection with virulent VACV strain Western Reserve (WR) . Upon prime-boost vaccinations in BALB/c mice, all four MVA-WNV candidate vaccines elicited circulating serum antibodies binding to recombinant WNV-E protein and neutralizing WNV in tissue culture infections In addition, immunizations in HLA-A2.1-/HLA-DR1-transgenic H-2 class I-/class II-knockout mice efficiently induced WNV-E-specific CD8+ T-cell responses. At the moment, recombinant MVA viruses expressing various heterologous antigens are among the most promising vector candidates to develop innovative vaccination strategies to protect against complex infections such as AIDS, tuberculosis, or malaria, or against rare but threatening emerging diseases. abstract: Safety tested Modified Vaccinia virus Ankara (MVA) is licensed as third-generation vaccine against smallpox and serves as a potent vector system for development of new candidate vaccines against infectious diseases and cancer. Historically, MVA was developed by serial tissue culture passage in primary chicken cells of vaccinia virus strain Ankara, and clinically used to avoid the undesirable side effects of conventional smallpox vaccination. Adapted to growth in avian cells MVA lost the ability to replicate in mammalian hosts and lacks many of the genes orthopoxviruses use to conquer their host (cell) environment. As a biologically well-characterized mutant virus, MVA facilitates fundamental research to elucidate the functions of poxvirus host-interaction factors. As extremely safe viral vectors MVA vaccines have been found immunogenic and protective in various preclinical infection models. Multiple recombinant MVA currently undergo clinical testing for vaccination against human immunodeficiency viruses, Mycobacterium tuberculosis or Plasmodium falciparum. The versatility of the MVA vector vaccine platform is readily demonstrated by the swift development of experimental vaccines for immunization against emerging infections such as the Middle East Respiratory Syndrome. Recent advances include promising results from the clinical testing of recombinant MVA-producing antigens of highly pathogenic avian influenza virus H5N1 or Ebola virus. This review summarizes our current knowledge about MVA as a unique strain of vaccinia virus, and discusses the prospects of exploiting this virus as research tool in poxvirus biology or as safe viral vector vaccine to challenge existing and future bottlenecks in vaccinology. url: https://doi.org/10.1016/bs.aivir.2016.07.001 doi: 10.1016/bs.aivir.2016.07.001 id: cord-347727-wka9q98s author: Vong, Sirenda title: Assessment of Ebola virus disease preparedness in the WHO South-East Asia Region date: 2016-12-01 words: 4899.0 sentences: 266.0 pages: flesch: 46.0 cache: ./cache/cord-347727-wka9q98s.txt txt: ./txt/cord-347727-wka9q98s.txt summary: OBJECTIVE: To conduct assessments of Ebola virus disease preparedness in countries of the World Health Organization (WHO) South-East Asia Region. 2 In January 2015, nine of the 11 countries from the WHO South-East Asia Region agreed to a joint assessment by WHO and ministries of health of their preparedness and operational readiness for Ebola virus disease. Each assessment component comprised several Objective To conduct assessments of Ebola virus disease preparedness in countries of the World Health Organization (WHO) South-East Asia Region. However, only seven of the countries had developed a specific, written Ebola virus disease preparedness plan (task A1), including four that had detailed a risk-based approach and some level of linkage with their pandemic influenza preparedness plans. Our review showed that risk assessment (i.e. evaluating the likelihood of Ebola virus disease being imported or introduced into a non-affected country) had been formally or informally conducted in six countries (Bhutan, Indonesia, Maldives, Sri Lanka, Thailand and Timor-Leste). abstract: OBJECTIVE: To conduct assessments of Ebola virus disease preparedness in countries of the World Health Organization (WHO) South-East Asia Region. METHODS: Nine of 11 countries in the region agreed to be assessed. During February to November 2015 a joint team from WHO and ministries of health conducted 4–5 day missions to Bangladesh, Bhutan, Indonesia, Maldives, Myanmar, Nepal, Sri Lanka, Thailand and Timor-Leste. We collected information through guided discussions with senior technical leaders and visits to hospitals, laboratories and airports. We assessed each country’s Ebola virus disease preparedness on 41 tasks under nine key components adapted from the WHO Ebola preparedness checklist of January 2015. FINDINGS: Political commitment to Ebola preparedness was high in all countries. Planning was most advanced for components that had been previously planned or tested for influenza pandemics: multilevel and multisectoral coordination; multidisciplinary rapid response teams; public communication and social mobilization; drills in international airports; and training on personal protective equipment. Major vulnerabilities included inadequate risk assessment and risk communication; gaps in data management and analysis for event surveillance; and limited capacity in molecular diagnostic techniques. Many countries had limited planning for a surge of Ebola cases. Other tasks needing improvement included: advice to inbound travellers; adequate isolation rooms; appropriate infection control practices; triage systems in hospitals; laboratory diagnostic capacity; contact tracing; and danger pay to staff to ensure continuity of care. CONCLUSION: Joint assessment and feedback about the functionality of Ebola virus preparedness systems help countries strengthen their core capacities to meet the International Health Regulations. url: https://www.ncbi.nlm.nih.gov/pubmed/27994284/ doi: 10.2471/blt.16.174441 id: cord-255479-yd5cbwnx author: Vu, David M. title: Chikungunya Virus date: 2017-06-30 words: 4097.0 sentences: 232.0 pages: flesch: 45.0 cache: ./cache/cord-255479-yd5cbwnx.txt txt: ./txt/cord-255479-yd5cbwnx.txt summary: Anti-CHIKV antibodies directed against the envelope protein that neutralize the virus in vitro also protect neonatal mice from lethal CHIKV infection in vivo, suggesting that these proteins may be important antigenic lethal targets for development of naturally acquired, or vaccine-elicited protection. Stedman, who reported this "anomalous disease" called "dandy fever" by local residents, noted that the illness "attacked almost every individual in the town," had "extremely low mortality," and was associated with "pains in the joints for weeks after recovery from the acute stage," which were key differences between the 1827 and 1828 West Indies epidemic and previous descriptions of a "break-bone fever" (referring to modern-day dengue fever). For diagnostic confirmation of current and recent infection, a molecular test (typically polymerase chain reaction [PCR]) for the virus and an assay for the presence of specific IgM antibody are required. abstract: For chikungunya virus (CHIKV), the long-term sequelae from infection are yet ill-defined. The prolonged debilitating arthralgia associated with CHIKV infection has tremendous potential for impacting the global economy and should be considered when evaluating the human burden of disease and the allocation of resources. There is much still unknown about CHIKV and the illnesses that it causes. Developing a better understanding of the pathogenesis of CHIKV infection is a priority and forms the basis for developing effective strategies at infection prevention and disease control. url: https://www.ncbi.nlm.nih.gov/pubmed/28457355/ doi: 10.1016/j.cll.2017.01.008 id: cord-010016-fs8pjy1z author: WEBB, H. E. title: CAN VIRAL ENVELOPE GLYCOLIPIDS PRODUCE AUTO‐IMMUNITY, WITH REFERENCE TO THE CNS AND MULTIPLE SCLEROSIS? date: 2008-05-12 words: 2976.0 sentences: 154.0 pages: flesch: 47.0 cache: ./cache/cord-010016-fs8pjy1z.txt txt: ./txt/cord-010016-fs8pjy1z.txt summary: In this paper it is proposed that CNS demyelination could arise in susceptible individuals (HLA type) from an immune response to glycolipids, triggered by the carrier effect of one or more enveloped neurotropic viruses. The demyelination is dependent upon T-lymphocytes probably cytotoxic cells (Jagelman et al., 1978; Fazakerley, Amor & Webb 1983; Pathak et al., 1983) and probably results from an immune reaction against viral antigens on the surface of oligodendrocytes or myelin. Since all are budding viruses they will have a similar host derived viral envelope provided the virus replicates in the same cell type. It is an intriguing possibility that CNS demyelination in diseases such as MS, arises as a result of an auto-immune reaction against specific glycolipids, induced by the carrier effect of a budding neurotropic virus. I n this way any number of enveloped neurotropic viruses could be involved in initiating and restimulating a n autoimmune response to the same brain cell membrane specific glycolipid(s). abstract: Many viruses, with lipid envelopes derived from the host cell membranes, have been implicated in the aetiology of multiple sclerosis (MS), and epidemiological studies support an infectious agent. Alternatively the disease is thought by other workers to be auto‐immune in nature, and recently much attention has been focused on immunological sensitivity to glycolipids in MS patients. In this paper it is proposed that CNS demyelination could arise in susceptible individuals (HLA type) from an immune response to glycolipids, triggered by the carrier effect of one or more enveloped neurotropic viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7168014/ doi: 10.1111/j.1365-2990.1984.tb00335.x id: cord-000359-y0m1utug author: Walpita, Pramila title: Vaccine Potential of Nipah Virus-Like Particles date: 2011-04-06 words: 7808.0 sentences: 334.0 pages: flesch: 46.0 cache: ./cache/cord-000359-y0m1utug.txt txt: ./txt/cord-000359-y0m1utug.txt summary: Co-expression of these proteins under optimized conditions resulted in quantifiable amounts of VLPs with many virus-like/vaccine desirable properties including some not previously described for VLPs of any paramyxovirus: The particles were fusogenic, inducing syncytia formation; PCR array analysis showed NiV VLP-induced activation of innate immune defense pathways; the surface structure of NiV VLPs imaged by cryoelectron microscopy was dense, ordered, and repetitive, and consistent with similarly derived structure of paramyxovirus measles virus. Plasmid-mediated expression of selected viral proteins results in the spontaneous assembly and release of VLPs. These particles make highly effective immunogens because they possess several features of the authentic virus such as their surface structure and dimensions [31, 36] . In preliminary studies it was found that co-expression of NiV G, F and M proteins in 293T cells resulted in the formation of VLPs that bud out into the transfected cell SUP and that they can be harvested, concentrated and purified as described under Methods. abstract: Nipah virus (NiV) was first recognized in 1998 in a zoonotic disease outbreak associated with highly lethal febrile encephalitis in humans and a predominantly respiratory disease in pigs. Periodic deadly outbreaks, documentation of person-to-person transmission, and the potential of this virus as an agent of agroterror reinforce the need for effective means of therapy and prevention. In this report, we describe the vaccine potential of NiV virus-like particles (NiV VLPs) composed of three NiV proteins G, F and M. Co-expression of these proteins under optimized conditions resulted in quantifiable amounts of VLPs with many virus-like/vaccine desirable properties including some not previously described for VLPs of any paramyxovirus: The particles were fusogenic, inducing syncytia formation; PCR array analysis showed NiV VLP-induced activation of innate immune defense pathways; the surface structure of NiV VLPs imaged by cryoelectron microscopy was dense, ordered, and repetitive, and consistent with similarly derived structure of paramyxovirus measles virus. The VLPs were composed of all the three viral proteins as designed, and their intracellular processing also appeared similar to NiV virions. The size, morphology and surface composition of the VLPs were consistent with the parental virus, and importantly, they retained their antigenic potential. Finally, these particles, formulated without adjuvant, were able to induce neutralizing antibody response in Balb/c mice. These findings indicate vaccine potential of these particles and will be the basis for undertaking future protective efficacy studies in animal models of NiV disease. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071823/ doi: 10.1371/journal.pone.0018437 id: cord-347710-ff64y6ef author: Wan, Qianya title: Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development date: 2020-07-13 words: 36567.0 sentences: 2487.0 pages: flesch: 46.0 cache: ./cache/cord-347710-ff64y6ef.txt txt: ./txt/cord-347710-ff64y6ef.txt summary: hnRNPs involve in a large number of cellular processes, including chromatin remodelling, transcription regulation, RNP assembly and stabilization, RNA export, virus replication, histone-like nucleoid structuring, and even intracellular immunity. 6, 13 It is well known that Hsp90 not only interacts and contributes to RNA polymerase assembly and nuclear import of some (−) ssRNA viruses (e.g., PB2 of influenza virus), but plays crucial roles in the folding process of viral capsid proteins and virion assemblies as well. 17, 18 As a critical component of cellular protein surveillance, the ATP-dependent molecular chaperone protects cells from damage caused by stress and takes part in a number of folding processes, including folding of newly synthesized polypeptides, recognition and refolding of misfolded or aggregated proteins, solubilization or degradation of proteins, transporting proteins, assembly or disassembly of oligomeric protein complexes, and the regulation of certain natively folded proteins. abstract: Stress proteins (SPs) including heat-shock proteins (HSPs), RNA chaperones, and ER associated stress proteins are molecular chaperones essential for cellular homeostasis. The major functions of HSPs include chaperoning misfolded or unfolded polypeptides, protecting cells from toxic stress, and presenting immune and inflammatory cytokines. Regarded as a double-edged sword, HSPs also cooperate with numerous viruses and cancer cells to promote their survival. RNA chaperones are a group of heterogeneous nuclear ribonucleoproteins (hnRNPs), which are essential factors for manipulating both the functions and metabolisms of pre-mRNAs/hnRNAs transcribed by RNA polymerase II. hnRNPs involve in a large number of cellular processes, including chromatin remodelling, transcription regulation, RNP assembly and stabilization, RNA export, virus replication, histone-like nucleoid structuring, and even intracellular immunity. Dysregulation of stress proteins is associated with many human diseases including human cancer, cardiovascular diseases, neurodegenerative diseases (e.g., Parkinson’s diseases, Alzheimer disease), stroke and infectious diseases. In this review, we summarized the biologic function of stress proteins, and current progress on their mechanisms related to virus reproduction and diseases caused by virus infections. As SPs also attract a great interest as potential antiviral targets (e.g., COVID-19), we also discuss the present progress and challenges in this area of HSP-based drug development, as well as with compounds already under clinical evaluation. url: https://www.ncbi.nlm.nih.gov/pubmed/32661235/ doi: 10.1038/s41392-020-00233-4 id: cord-305263-fgwf6wy3 author: Wang, Ben X. title: The yin and yang of viruses and interferons date: 2012-02-07 words: 6285.0 sentences: 294.0 pages: flesch: 38.0 cache: ./cache/cord-305263-fgwf6wy3.txt txt: ./txt/cord-305263-fgwf6wy3.txt summary: IFN therapy therefore has the advantage over DAA treatments in that, in addition to stimulating genes that block viral replication in infected cells, IFNs activate other innate and adaptive immune responses to combat the virus. For example, polymorphisms in host genes encoding proteins associated with regulation of an IFN response such as interferon receptor a-chain (IFNAR1) [10] , the IFN-inducible myxovirus resistance GTPase protein, Mx [11] , the IFN-inducible 2 0 ,5 0 -oligoadenylate synthetase (OAS) [12] and the suppressor of cytokine signaling (SOCS) 3 associated with regulation of an IFN response [13] , are predictive markers linked with the rate of sustained virological response (SVR) to HCV infection following IFN-a treatment. Remarkably, distinct highly pathogenic respiratory viruses, namely influenza viruses and the SARS-CoV, encode nonstructural proteins in their genomes that function as virulence factors that specifically target the host innate IFN response, further emphasizing the importance of IFNs as broad-spectrum antivirals. abstract: Interferons (IFNs)-α/β are critical effectors of the innate immune response to virus infections. Through activation of the IFN-α/β receptor (IFNAR), they induce expression of IFN-stimulated genes (ISGs) that encode antiviral proteins capable of suppressing viral replication and promoting viral clearance. Many highly pathogenic viruses have evolved mechanisms to evade an IFN response and the balance between the robustness of the host immune response and viral antagonistic mechanisms determines whether or not the virus is cleared. Here, we discuss IFNs as broad-spectrum antivirals for treatment of acute virus infections. In particular, they are useful for treatment of re-emerging virus infections, where direct-acting antivirals (DAAs) have limited utility due to DAA-resistant mutations, and for newly emerging virus strains in which the time to vaccine availability precludes vaccination at the onset of an outbreak. url: https://doi.org/10.1016/j.it.2012.01.004 doi: 10.1016/j.it.2012.01.004 id: cord-278511-je1509ar author: Wang, David title: 5 challenges in understanding the role of the virome in health and disease date: 2020-03-26 words: 2166.0 sentences: 107.0 pages: flesch: 38.0 cache: ./cache/cord-278511-je1509ar.txt txt: ./txt/cord-278511-je1509ar.txt summary: An even more significant problem is that in most virome studies, more than 50% of the sequences in virus-enriched preparations have no detectable sequence similarity to any known reference sequences; these unalignable sequences are referred to as viral "dark matter" [8] and may include novel, highly divergent viruses that are unrecognizable. To illustrate this point, the United States National Institutes of Health (NIH) virology study sections address only "non-bacteriophage viral genetics, infection and replication, cellular and host responses to viral infections, and mechanisms of viral disease pathogenesis." Thus, there is a great need to bring these disparate communities together in order to collectively attack questions associated with the virome, especially as more complex trans-kingdom interactions are identified linking phages, bacteria, eukaryotic viruses, and eukaryotic cells. With new cell-culture systems and animal models for novel viruses, there will ideally be studies that attribute causal roles for some of the associations. abstract: nan url: https://doi.org/10.1371/journal.ppat.1008318 doi: 10.1371/journal.ppat.1008318 id: cord-340610-ex2yjyum author: Wang, De-Yun title: Upper Airway Stem Cells: Understanding the Nose and Role for Future Cell Therapy date: 2014-11-28 words: 5235.0 sentences: 195.0 pages: flesch: 32.0 cache: ./cache/cord-340610-ex2yjyum.txt txt: ./txt/cord-340610-ex2yjyum.txt summary: In addition to the physical barrier, nasal epithelial cells are known to play an active role in both the innate and acquired immune responses, which have been summarized in the European Position paper on rhinosinusitis and nasal polyps 2012 (EPOS 2012) [1••] as (l) expressing membrane-bound and cytoplasmic pattern recognition receptors (PRRs) that recognize pathogen-associated molecular patterns (PAMPs), which are conserved molecular patterns found in parasites, viruses, yeasts, bacteria, and mycobacteria; (2) secreting a vast arsenal of host defense molecules, such as antimicrobial molecules in several classes of enzymes (lysozyme, chitinases, and peroxidases), opsonins (complement and pentraxin-3), permeabilizing proteins (A defensins, B defensins, and cathelicidins such as LL-37), collectins (surfactant protein-A, surfactant protein-D, and mannose-binding lectin), and binding proteins (lactoferrin and mucins); (3) producing a variety of inflammatory cytokines, such as IL-1, TNF-α, IFNα/β, GM-CSF, eotaxins, RANTES, IP-10, IL-6, IL-8, GRO-α, MDC, SCF, TARC, MCP-4, BAFF, osteopontin, IL-25, IL-32, IL-33, and thymic stromal lymphopoietin (TSLP), in response to stimulation of the antigens. abstract: The nose together with the paranasal sinuses has an approximate surface area of 100 to 200 cm(2) in adults, which is lined with pseudostratified columnar ciliated epithelium. It serves several important physiological functions such as conditioning and filtration of the inspired air and the provision of end organ for the sense of smell. It is also a physical and immunological barrier as it is the first site of interaction between the host tissue and foreign invaders (viruses, bacteria, and allergens). Our understanding of the complex cellular events occurring in response to inhaled agents during the development of common airway diseases has been significantly enhanced by the current status of in vivo and in vitro nasal experimental models. This will allow the development of novel therapeutic strategies designed to improve the physiological and immune defense functions of the nasal epithelium, as well as novel therapies for other common nasal diseases. url: https://doi.org/10.1007/s11882-014-0490-0 doi: 10.1007/s11882-014-0490-0 id: cord-295445-f4p00yaw author: Wang, Hao title: Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments date: 2018-02-01 words: 6889.0 sentences: 284.0 pages: flesch: 48.0 cache: ./cache/cord-295445-f4p00yaw.txt txt: ./txt/cord-295445-f4p00yaw.txt summary: Previous studies conducted in wastewater treatment plants have shown that ozone disinfection might be highly efficient in inactivating bacteria and bacteriophages after conventional sewage treatments (Kim et al., 1999; Tyrrell et al., 1995) , but knowledge regarding its effect for reducing human enteric viruses is relatively scarce. The four concentrated water samples (incoming sewage, conventionally treated, ozone treated, and outlet water) from each of the three weeks were also analyzed by qPCR for 14 common enteric viruses (adenovirus, astrovirus, hepatitis A virus, hepatitis E virus, norovirus GI, norovirus GII, norovirus GIV, parechovirus, sapovirus, aichivirus, mengovirus, torovirus, enterovirus, and rotavirus). However, in this study some viruses that were undetectable in the ozone-treated samples reoccurred in the outlet water, including parvovirus, norovirus GII, human feces pecovirus, parvovirus-like virus, gokushovirus, and HAdV-F41, although the amounts were significantly lower compared with raw sewage. abstract: Sewage contains a mixed ecosystem of diverse sets of microorganisms, including human pathogenic viruses. Little is known about how conventional as well as advanced treatments of sewage, such as ozonation, reduce the environmental spread of viruses. Analyses for viruses were therefore conducted for three weeks in influent, after conventional treatment, after additional ozonation, and after passing an open dam system at a full-scale treatment plant in Knivsta, Sweden. Viruses were concentrated by adsorption to a positively charged filter, from which they were eluted and pelleted by ultracentrifugation, with a recovery of about 10%. Ion Torrent sequencing was used to analyze influent, leading to the identification of at least 327 viral species, most of which belonged to 25 families with some having unclear classification. Real-time PCR was used to test for 21 human-related viruses in inlet, conventionally treated, and ozone-treated sewage and outlet waters. The viruses identified in influent and further analyzed were adenovirus, norovirus, sapovirus, parechovirus, hepatitis E virus, astrovirus, pecovirus, picobirnavirus, parvovirus, and gokushovirus. Conventional treatment reduced viral concentrations by one to four log10, with the exception of adenovirus and parvovirus, for which the removal was less efficient. Ozone treatment led to a further reduction by one to two log10, but less for adenovirus. This study showed that the amount of all viruses was reduced by conventional sewage treatment. Further ozonation reduced the amounts of several viruses to undetectable levels, indicating that this is a promising technique for reducing the transmission of many pathogenic human viruses. url: https://api.elsevier.com/content/article/pii/S1438463917307307 doi: 10.1016/j.ijheh.2018.01.012 id: cord-030961-5gzc7193 author: Wang, Jiajun title: Adhesive contact between cylindrical (Ebola) and spherical (SARS-CoV-2) viral particles and a cell membrane date: 2020-08-28 words: 4335.0 sentences: 260.0 pages: flesch: 55.0 cache: ./cache/cord-030961-5gzc7193.txt txt: ./txt/cord-030961-5gzc7193.txt summary: In the limit where bending dominates, for sufficiently large values of normalized bending stiffness, there is no adhesion between viral particles and the cell membrane without applied force. In this work, we create a continuum model for the small-deflection adhesive contact mechanics of virus particle attachment onto the host cell membrane in terms of the principal biophysical properties of the virus, membrane, and their interaction. These results also help to retrieve conditions for lack of adhesion, pull-off force, and contact area between the virus particle and cell membrane. We now describe in outline the continuum models for adhesive contact between the virus and cell membrane, driven by adhesion and external displacement or force, and resisted by tension and elastic bending. In our models, the parameters that govern the adhesive contact mechanics are (more in Table 1 ) bending rigid κ, tension σ, adhesion free energy per receptor β, binding receptor density ρ, and the radius of the virus, R. abstract: A critical event during the process of cell infection by a viral particle is attachment, which is driven by adhesive interactions and resisted by bending and tension. The biophysics of this process has been studied extensively, but the additional role of externally applied force or displacement has generally been neglected. In this work, we study the adhesive force-displacement response of viral particles against a cell membrane. We have built two models: one in which the viral particle is cylindrical (say, representative of a filamentous virus such as Ebola) and another in which it is spherical (such as SARS-CoV-2 and Zika). Our interest is in initial adhesion, in which case deformations are small, and the mathematical model for the system can be simplified considerably. The parameters that characterize the process combine into two dimensionless groups that represent normalized membrane bending stiffness and tension. In the limit where bending dominates, for sufficiently large values of normalized bending stiffness, there is no adhesion between viral particles and the cell membrane without applied force. (The zero external force contact width and pull-off force are both zero.) For large values of normalized membrane tension, the adhesion between virus and cell membrane is weak but stable. (The contact width at zero external force has a small value.) Our results for pull-off force and zero force contact width help to quantify conditions that could aid the development of therapies based on denying the virus entry into the cell by blocking its initial adhesion. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s42558-020-00026-3) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7453191/ doi: 10.1007/s42558-020-00026-3 id: cord-017568-8fnr4zzv author: Wang, Lin-Fa title: Disease Outbreaks Caused by Emerging Paramyxoviruses of Bat Origin date: 2008 words: 6817.0 sentences: 345.0 pages: flesch: 53.0 cache: ./cache/cord-017568-8fnr4zzv.txt txt: ./txt/cord-017568-8fnr4zzv.txt summary: They are Hendra virus (HeV), Nipah virus (NiV), and Menangle virus (MenV), isolated from infected horses and humans in Australia in 1994 , humans and pigs in Malaysia in 1999 , and pigs in Australia in 1997 , respectively (Chua et al., 2000 Murray et al., 1995b; Philbey et al., 1998) . In addition to the emergence of paramyxoviruses from frugivorous Pteropus bats, insectivorous Rhinolophus species have been identified as natural hosts of SARS-like viruses (Lau et al., 2005; Li et al., 2005) , and Ebola virus has been shown to have fruit bat reservoir hosts (Leroy et al., 2005) . The identification of fruit bats in the genus Pteropus as the reservoir hosts of HeV and NiV in Australia and Malaysia, respectively, prompted searches for related viruses in other nations in the region. Case-control study of risk factors for human infection with a new zoonotic paramyxovirus, Nipah virus, during a 1998-1999 outbreak of severe encephalitis in Malaysia abstract: Newly emerging and re-emerging infections are recognized as a global problem and 75% of these are potentially zoonotic (Woolhouse & Gowtage-Sequeria, 2005). Emergence of a new “killer” disease in any part of the world is likely to be a threat world wide in today’s society with very rapid means of transportation of both human and animal/animal products. Recent examples include the global outbreaks of severe acute respiratory syndrome (SARS), H5N1 avian influenza, and the outbreaks of West Nile virus in United States. The rapid economic development in the Asian region during the last few decades was accompanied by massive urbanization and environmental changes, which are believed to be one of the triggers leading to the emergence of new zoonotic diseases. Wildlife animals play an ever-increasing role in the emergence of zoonotic diseases, and bats have been identified as natural reservoir host of several lethal zoonotic viruses that emerged in recent times. This review will focus on the disease outbreaks caused by emerging bat viruses in the family Paramyxoviridae. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122158/ doi: 10.1007/978-0-387-75722-3_12 id: cord-270803-jtv5jmkn author: Wang, Lin-Fa title: Mass extinctions, biodiversity and mitochondrial function: are bats ‘special’ as reservoirs for emerging viruses? date: 2011-11-09 words: 5612.0 sentences: 256.0 pages: flesch: 47.0 cache: ./cache/cord-270803-jtv5jmkn.txt txt: ./txt/cord-270803-jtv5jmkn.txt summary: This has been due to a combination of factors including the emergence of highly virulent zoonotic pathogens, such as Hendra, Nipah, SARS and Ebola viruses, and the high rate of detection of a large number of previously unknown viral sequences in bat specimens. This has been due to a combination of factors including the emergence of highly virulent zoonotic pathogens, such as Hendra, Nipah, SARS and Ebola viruses, and the high rate of detection of a large number of previously unknown viral sequences in bat specimens. Bats (order Chiroptera), one of the most abundant, diverse and geographically dispersed vertebrates on earth, have recently been shown to be reservoir hosts of a number of emerging viruses responsible for severe disease outbreaks in humans and livestock [1 ,2,3]. abstract: For the past 10–15 years, bats have attracted growing attention as reservoirs of emerging zoonotic viruses. This has been due to a combination of factors including the emergence of highly virulent zoonotic pathogens, such as Hendra, Nipah, SARS and Ebola viruses, and the high rate of detection of a large number of previously unknown viral sequences in bat specimens. As bats have ancient evolutionary origins and are the only flying mammals, it has been hypothesized that some of their unique biological features may have made them especially suitable hosts for different viruses. So the question ‘Are bats different, special or exceptional?’ has become a focal point in the field of virology, bat biology and virus-host co-evolution. In this brief review, we examine the topic in a relatively unconventional way, that is, our discussion will be based on both scientific discoveries and theoretical predictions. This approach was chosen partially because the data in this field are so limited that it is impossible to conduct a useful review based on published results only and also because we believe it is important to provoke original, speculative or even controversial ideas or theories in this important field of research. url: https://api.elsevier.com/content/article/pii/S1879625711001325 doi: 10.1016/j.coviro.2011.10.013 id: cord-277309-kelebqr6 author: Wang, Lin-Fa title: Viruses in bats and potential spillover to animals and humans date: 2019-01-18 words: 6080.0 sentences: 299.0 pages: flesch: 49.0 cache: ./cache/cord-277309-kelebqr6.txt txt: ./txt/cord-277309-kelebqr6.txt summary: While it is not easy to assess the spillover potential of many SARS-CoV related bat CoVs due to unsuccessful attempts to isolate the viruses, it should be noted that a ''consensus'' virus constructed via reverse genetics pointed to a high probability of human infection [19] . Further study is required to determine the true zoonotic potential of SADS-CoV and closely related bat CoVs. For unknown reasons, despite of the wide presence of CoVs in bats of different locations and species with relative high viral genome levels, multiple attempts by different international groups to isolate bat CoVs have been largely unsuccessful. The genetic and functional Viruses in bats and potential spillover to animals and humans Wang and Anderson 81 Aside from MenPV and TioPV, other paramyxoviruses from the genus Rubulavirus have been isolated from or detected in bats without evidence of zoonotic transmission. abstract: In the last two decades, several high impact zoonotic disease outbreaks have been linked to bat-borne viruses. These include SARS coronavirus, Hendra virus and Nipah virus. In addition, it has been suspected that ebolaviruses and MERS coronavirus are also linked to bats. It is being increasingly accepted that bats are potential reservoirs of a large number of known and unknown viruses, many of which could spillover into animal and human populations. However, our knowledge into basic bat biology and immunology is very limited and we have little understanding of major factors contributing to the risk of bat virus spillover events. Here we provide a brief review of the latest findings in bat viruses and their potential risk of cross-species transmission. url: https://www.sciencedirect.com/science/article/pii/S187962571830107X doi: 10.1016/j.coviro.2018.12.007 id: cord-103688-n7hzpbyf author: Wang, Lina title: VirusDIP: Virus Data Integration Platform date: 2020-06-09 words: 1286.0 sentences: 81.0 pages: flesch: 47.0 cache: ./cache/cord-103688-n7hzpbyf.txt txt: ./txt/cord-103688-n7hzpbyf.txt summary: Results To facilitate virus research and promote the global sharing of virus data, we present here VirusDIP, a one-stop service platform for archive, integration, access, analysis of virus data. It accepts the submission of viral sequence data from all over the world and currently integrates data resources from the National GeneBank Database (CNGBdb), Global initiative on sharing all influenza data (GISAID), and National Center for Biotechnology Information (NCBI). Moreover, based on the comprehensive data resources, BLAST sequence alignment tool and multi-party security computing tools are deployed for multi-sequence alignment, phylogenetic tree building and global trusted sharing. For data compatibility, the virus data standard integrates the virus and pathogen sample data standard of The International Nucleotide Sequence Database Collaboration (INSDC) (Karsch-Mizrachi et al., 2018) , the hCoV-19 data standard of GISAID, and the sample data standard of COVID-19 Genomics UK (COG-UK) Consortium. VirusDIP is committed to building a comprehensive virus data platform for archive, integration, access, and analysis. abstract: Motivation The Coronavirus Disease 2019 (COVID-19) pandemic poses a huge threat to human public health. Viral sequence data plays an important role in the scientific prevention and control of epidemics. A comprehensive virus database will be vital useful for virus data retrieval and deep analysis. To promote sharing of virus data, several virus databases and related analyzing tools have been created. Results To facilitate virus research and promote the global sharing of virus data, we present here VirusDIP, a one-stop service platform for archive, integration, access, analysis of virus data. It accepts the submission of viral sequence data from all over the world and currently integrates data resources from the National GeneBank Database (CNGBdb), Global initiative on sharing all influenza data (GISAID), and National Center for Biotechnology Information (NCBI). Moreover, based on the comprehensive data resources, BLAST sequence alignment tool and multi-party security computing tools are deployed for multi-sequence alignment, phylogenetic tree building and global trusted sharing. VirusDIP is gradually establishing cooperation with more databases, and paving the way for the analysis of virus origin and evolution. All public data in VirusDIP are freely available for all researchers worldwide. Availability https://db.cngb.org/virus/ Contact weixiaofeng@cngb.org url: https://doi.org/10.1101/2020.06.08.139451 doi: 10.1101/2020.06.08.139451 id: cord-268593-rvxxv1dn author: Wang, Mingyang title: Hemagglutinin-esterase-fusion (HEF) protein of influenza C virus date: 2015-07-28 words: 10152.0 sentences: 468.0 pages: flesch: 50.0 cache: ./cache/cord-268593-rvxxv1dn.txt txt: ./txt/cord-268593-rvxxv1dn.txt summary: Influenza C virus is unique since it contains only one spike protein, the hemagglutinin-esterase-fusion glycoprotein HEF that possesses receptor binding, receptor destroying and membrane fusion activities, thus combining the functions of Hemagglutinin (HA) and Neuraminidase (NA) of influenza A and B viruses. While influenza A and B virus contain the two glycoproteins Hemagglutinin (HA) and Neuraminidase (NA) inserted into the viral membrane, influenza C virus possesses only one spike designated Hemagglutinin-Esterase-Fusion (HEF) protein which combines the functions of both HA and NA (Herrler et al., 1988a; Herrler and Klenk, 1991) . Although there is only 12% amino acid identity between HA and HEF, the overall structure of both molecules as well as folds of individual segments are quite similar, except an additional bulge, which is located at the lower part of the globular domain and contains the esterase region that is not present in HA (Fig. 3) . abstract: Influenza C virus, a member of the Orthomyxoviridae family, causes flu-like disease but typically only with mild symptoms. Humans are the main reservoir of the virus, but it also infects pigs and dogs. Very recently, influenza C-like viruses were isolated from pigs and cattle that differ from classical influenza C virus and might constitute a new influenza virus genus. Influenza C virus is unique since it contains only one spike protein, the hemagglutinin-esterase-fusion glycoprotein HEF that possesses receptor binding, receptor destroying and membrane fusion activities, thus combining the functions of Hemagglutinin (HA) and Neuraminidase (NA) of influenza A and B viruses. Here we briefly review the epidemiology and pathology of the virus and the morphology of virus particles and their genome. The main focus is on the structure of the HEF protein as well as on its co- and post-translational modification, such as N-glycosylation, disulfide bond formation, S-acylation and proteolytic cleavage into HEF1 and HEF2 subunits. Finally, we describe the functions of HEF: receptor binding, esterase activity and membrane fusion. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s13238-015-0193-x) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s13238-015-0193-x doi: 10.1007/s13238-015-0193-x id: cord-306983-6w2fvtfy author: Wang, Siye title: Influenza Virus—Cytokine-Protease Cycle in the Pathogenesis of Vascular Hyperpermeability in Severe Influenza date: 2010-10-01 words: 3808.0 sentences: 223.0 pages: flesch: 39.0 cache: ./cache/cord-306983-6w2fvtfy.txt txt: ./txt/cord-306983-6w2fvtfy.txt summary: Influenza A virus infection resulted in significant increases in TNF-α, IL-6, IL-1β, viral hemagglutininprocessing protease trypsin levels, and viral replication with vascular hyperpermeability in lung and brain in the first 6 days of infection. The present study reports several new observations: (1) proinflammatory cytokines, TNF-a, IL-1b, and IL-6, when upregulated by influenza A virus infection, induce trypsin expression in various organs and human endothelial cells; (2) the upregulated trypsin induces [Ca 2+ ] i mobilization via activation of the PAR-2, followed by loss of zonula occludens-1 and vascular hyperpermeability; (3) inhibitors of NF-kB and activator protein 1 effectively suppress the upregulation of proinflammatory cytokines and trypsin and improve the survival rates of infected mice. The present results allow us to propose a new mechanism of junctional permeability regulation: upregulated trypsin by influenza A virus and/or proinflammatory cytokines induces increase in [Ca 2+ ] i and loss of zonula occludens-1 in endothelial cells via PAR-2 signaling. abstract: Background. Severe influenza is characterized by cytokine storm and multiorgan failure with edema. The aim of this study was to define the impact of the cytokine storm on the pathogenesis of vascular hyperpermeability in severe influenza. Methods. Weanling mice were infected with influenza A WSN/33(H1N1) virus. The levels of proinflammatory cytokines, tumor necrosis factor (TNF) α, interleukin (IL) 6, IL-1β, and trypsin were analyzed in the lung, brain, heart, and cultured human umbilical vein endothelial cells. The effects of transcriptional inhibitors on cytokine and trypsin expressions and viral replication were determined. Results. Influenza A virus infection resulted in significant increases in TNF-α, IL-6, IL-1β, viral hemagglutininprocessing protease trypsin levels, and viral replication with vascular hyperpermeability in lung and brain in the first 6 days of infection. Trypsin upregulation was suppressed by transcriptional inhibition of cytokines in vivo and by anti-cytokine antibodies in endothelial cells. Calcium mobilization and loss of tight junction constituent, zonula occludens-1, associated with cytokine- and trypsin-induced endothelial hyperpermeability were inhibited by a protease-activated receptor-2 antagonist and a trypsin inhibitor. Conclusions. The influenza virus-cytokine-protease cycle is one of the key mechanisms of vascular hyperpermeability in severe influenza. url: https://www.ncbi.nlm.nih.gov/pubmed/20731583/ doi: 10.1086/656044 id: cord-295640-mhfu0e9r author: Wang, Wenling title: Improving Cross-Protection against Influenza Virus Using Recombinant Vaccinia Vaccine Expressing NP and M2 Ectodomain Tandem Repeats date: 2019-06-25 words: 4793.0 sentences: 305.0 pages: flesch: 51.0 cache: ./cache/cord-295640-mhfu0e9r.txt txt: ./txt/cord-295640-mhfu0e9r.txt summary: Therefore, the cross-protection potentially correlates with both NP and M2e-specific humoral and cellular immune responses induced by RVJ-4M2eNP, which expresses a fusion antigen of full-length NP preceded by four M2e repeats. Previously, we expressed a fusion protein of NP and M2e (NM2e) in Escherichia coli and showed that immunization with NM2e formulated with aluminum hydroxide gel protected mice from a lethal challenge with heterologous influenza virus . BALB/c mice were immunized with the recombinant viruses to measure NP-and M2e-specific humoral and cellular immune responses as well as protective effect against lethal challenge with a heterologous influenza virus. Mice immunized with the recombinant vaccinia virus RVJ-NPM2e and RVJ-M2eNP showed strong antibody responses against NP, with lower titers of antibodies against M2e (Fig. 3A) . The recombinant vaccinia virus expressing 4M2e and full-length NP fusion antigen induced strong cross-protection (92%) against a lethal heterosubtypic PR8 challenge at 20 MLD 50 and thus regarded as the optimal one among the four constructs. abstract: Conventional influenza vaccines need to be designed and manufactured yearly. However, they occasionally provide poor protection owing to antigenic mismatch. Hence, there is an urgent need to develop universal vaccines against influenza virus. Using nucleoprotein (NP) and extracellular domain of matrix protein 2 (M2e) genes from the influenza A virus A/Beijing/30/95 (H3N2), we constructed four recombinant vaccinia virus-based influenza vaccines carrying NP fused with one or four copies of M2e genes in different orders. The recombinant vaccinia viruses were used to immunize BALB/C mice. Humoral and cellular responses were measured, and then the immunized mice were challenged with the influenza A virus A/Puerto Rico/8/34 (PR8). NP-specific humoral response was elicited in mice immunized with recombinant vaccinia viruses carrying full-length NP, while robust M2e-specific humoral response was elicited only in the mice immunized with recombinant vaccinia viruses carrying multiple copies of M2e. All recombinant viruses elicited NP- and M2e-specific cellular immune responses in mice. Only immunization with RVJ-4M2eNP induced remarkably higher levels of IL-2 and IL-10 cytokines specific to M2e. Furthermore, RVJ-4M2eNP immunization provided the highest cross-protection in mice challenged with 20 MLD(50) of PR8. Therefore, the cross-protection potentially correlates with both NP and M2e-specific humoral and cellular immune responses induced by RVJ-4M2eNP, which expresses a fusion antigen of full-length NP preceded by four M2e repeats. These results suggest that the rational fusion of NP and multiple M2e antigens is critical toward inducing protective immune responses, and the 4M2eNP fusion antigen may be employed to develop a universal influenza vaccine. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12250-019-00138-9) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/31240620/ doi: 10.1007/s12250-019-00138-9 id: cord-260554-nao59qx4 author: Wargo, Andrew R title: Viral fitness: definitions, measurement, and current insights date: 2012-09-15 words: 2898.0 sentences: 134.0 pages: flesch: 38.0 cache: ./cache/cord-260554-nao59qx4.txt txt: ./txt/cord-260554-nao59qx4.txt summary: Important recent trends include increasing use of in vivo systems to assess vertebrate virus fitness, and a broadening of research beyond replicative fitness to also investigate transmission fitness and epidemiologic fitness. The majority of viral fitness study systems are based on RNA viruses, and the highest numbers of publications in recent years involves human pathogens associated with major disease emergence events, such as human immunodeficiency virus-1 (HIV-1), influenza virus, and dengue virus (DENV). In many cases the ultimate goal of replicative and transmission fitness studies is to understand the epidemiology 540 Virus evolution and population level processes governing viral evolution, emergence, and displacement in the field. For vertebrate viruses the recent increase of in vivo virus fitness research is encouraging, but the majority of studies still remain in vitro. abstract: Viral fitness is an active area of research, with recent work involving an expanded number of human, non-human vertebrate, invertebrate, plant, and bacterial viruses. Many publications deal with RNA viruses associated with major disease emergence events, such as HIV-1, influenza virus, and Dengue virus. Study topics include drug resistance, immune escape, viral emergence, host jumps, mutation effects, quasispecies diversity, and mathematical models of viral fitness. Important recent trends include increasing use of in vivo systems to assess vertebrate virus fitness, and a broadening of research beyond replicative fitness to also investigate transmission fitness and epidemiologic fitness. This is essential for a more integrated understanding of overall viral fitness, with implications for disease management in the future. url: https://www.sciencedirect.com/science/article/pii/S1879625712001290 doi: 10.1016/j.coviro.2012.07.007 id: cord-002932-5e7xrd1y author: Watanabe, Tokiko title: Experimental infection of Cynomolgus Macaques with highly pathogenic H5N1 influenza virus through the aerosol route date: 2018-03-19 words: 4497.0 sentences: 212.0 pages: flesch: 44.0 cache: ./cache/cord-002932-5e7xrd1y.txt txt: ./txt/cord-002932-5e7xrd1y.txt summary: In the ferret model, these studies demonstrated that the inoculation of animals with highly pathogenic avian influenza H5N1 virus via the aerosol route led to higher nasal wash virus titers, earlier onset of clinical signs, and/or a broader spectrum of disease compared with infection via intranasal inoculation despite no difference in lethality [9] [10] [11] . On day 3 post-infection, VN3040 virus was recovered from nasal swabs of two and three animals in the conventional and aerosol method groups, respectively, and the mean virus titers were comparable between the two groups. Cynomolgus macaques were inoculated with 4 ml of a 10 7 PFU/ml solution of the highly pathogenic H5N1 avian influenza virus A/Vietnam/ UT3040/2004 strain (VN3040) through the aerosol route by using the ultrasonic nebulizer NE-U17 (defined as "the aerosol method group"). In contrast, VN3040 replicated well in the right-and left-lower lung lobes of the infected animals in the conventional method group [the virus mean titers were 3.51 and 4.75 log 10 (PFU/g), respectively]. abstract: Several animal models are used to study influenza viruses. Intranasal inoculation of animals with a liquid inoculum is one of the main methods used to experimentally infect animals with influenza virus; however, this method does not reflect the natural infection with influenza virus by contact or aerosol route. Aerosol inhalation methods have been established with several influenza viruses for mouse and ferret models, but few studies have evaluated inoculation routes in a nonhuman primates (NHP) model. Here, we performed the experimental infection of NHPs with a highly pathogenic H5N1 influenza virus via the aerosol route and demonstrated that aerosol infection had no effect on clinical outcome, but caused broader infection throughout all of the lobes of the lung compared with a non-aerosolized approach. Aerosol infection therefore represents an option for inoculation of NHPs in future studies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859186/ doi: 10.1038/s41598-018-23022-0 id: cord-290548-0wezrr1b author: Watanabe, Tokiko title: Villains or heroes? The raison d''être of viruses date: 2020-02-19 words: 2919.0 sentences: 171.0 pages: flesch: 42.0 cache: ./cache/cord-290548-0wezrr1b.txt txt: ./txt/cord-290548-0wezrr1b.txt summary: For example, Ebola virus disease and acquired immunodeficiency syndrome emerged in 1976 and 1981, respectively, 5-9 and more recently, severe acute respiratory syndrome (SARS), highly pathogenic avian influenza viruses and Middle East respiratory syndrome (MERS) have appeared in human society. In traditional virology, most viruses found in humans are considered to be pathogenic to their hosts; however, recent studies have shown that there are some viruses that have symbiotic relationships with their hosts and do not cause disease. 44 In the last a few decades, emerging infectious diseases caused by newly identified viruses, such as Ebola virus, 5-8 SARS and MERS coronaviruses, [10] [11] [12] human immunodeficiency virus (HIV), 9 Nipah virus and Hendra virus, [45] [46] [47] [48] have appeared in human society. To date, the PREDICT programme has found over 1100 viruses in animals and humans, including a new Ebola virus and MERSand SARS-like coronaviruses. abstract: The relationship between humans and viruses has a long history. Since the first identification of viruses in the 19th century, we have considered them to be ‘pathogens’ and have studied their mechanisms of replication and pathogenicity to combat the diseases that they cause. However, the relationships between hosts and viruses are various and virus infections do not necessarily cause diseases in their hosts. Rather, recent studies have shown that viral infections sometimes have beneficial effects on the biological functions and/or evolution of hosts. Here, we provide some insight into the positive side of viruses. url: https://doi.org/10.1002/cti2.1114 doi: 10.1002/cti2.1114 id: cord-281061-uoszpnst author: Watanabe, Yohei title: A novel immunochromatographic system for easy-to-use detection of group 1 avian influenza viruses with acquired human-type receptor binding specificity date: 2015-03-15 words: 4300.0 sentences: 188.0 pages: flesch: 54.0 cache: ./cache/cord-281061-uoszpnst.txt txt: ./txt/cord-281061-uoszpnst.txt summary: A biotinylated anti-hemagglutinin antibody that bound a broad range of group 1 influenza A viruses and latex-conjugated α2,3 (blue) and α2,6 (red) sialylglycopolymers were used in an immunochromatographic strip test, with avidin and lectin immobilized on a nitrocellulose membrane at test and control lines, respectively. The strip test could detect the receptor binding specificity of a wide range of influenza viruses, as well as small increases in the binding affinity of variant H5N1 viruses to α2,6 sialylglycans at viral titers >128 hemagglutination units. In conclusion, the immunochromatographic strip test developed in this study should be useful for monitoring potential changes in the receptor binding specificity of group 1 influenza A viruses in the field. In this study, we developed a new easy-to-use immunochoromatographic strip test to detect the emergence of AI viruses with increased human-type receptor specificity and confirmed the applicability of this test using AI viruses isolated in several different geographic areas. abstract: A switch of viral hemagglutinin receptor binding specificity from bird-type α2,3- to human-type α2,6-linked sialic acid is necessary for an avian influenza virus to become a pandemic virus. In this study, an easy-to-use strip test to detect receptor binding specificity of influenza virus was developed. A biotinylated anti-hemagglutinin antibody that bound a broad range of group 1 influenza A viruses and latex-conjugated α2,3 (blue) and α2,6 (red) sialylglycopolymers were used in an immunochromatographic strip test, with avidin and lectin immobilized on a nitrocellulose membrane at test and control lines, respectively. Accumulation of a sialylglycopolymer–virus–antibody complex at the test line was visualized by eye. The strip test could be completed in 30 min and did not require special equipment or skills, thereby avoiding some disadvantages of current methods for analyzing receptor binding specificity of influenza virus. The strip test could detect the receptor binding specificity of a wide range of influenza viruses, as well as small increases in the binding affinity of variant H5N1 viruses to α2,6 sialylglycans at viral titers >128 hemagglutination units. The strip test results were in agreement with those of ELISA virus binding assays, with correlations >0.95. In conclusion, the immunochromatographic strip test developed in this study should be useful for monitoring potential changes in the receptor binding specificity of group 1 influenza A viruses in the field. url: https://www.sciencedirect.com/science/article/pii/S0956566314008355 doi: 10.1016/j.bios.2014.10.036 id: cord-321481-vrfwczve author: Watashi, Koichi title: NTCP and Beyond: Opening the Door to Unveil Hepatitis B Virus Entry date: 2014-02-19 words: 4936.0 sentences: 247.0 pages: flesch: 39.0 cache: ./cache/cord-321481-vrfwczve.txt txt: ./txt/cord-321481-vrfwczve.txt summary: Recently, sodium taurocholate cotransporting polypeptide (NTCP) was identified as an HBV entry receptor and enabled the establishment of a susceptible cell line that can efficiently support HBV infection. HBV infection into host hepatocytes follows a multiple step process: (1) initially, HBV reversibly attaches to host cell surface proteoglycans with a low affinity; (2) this is followed by the process involving more specific receptor(s) with high affinity to mediate the early entry step; and (3) after endocytosis-mediated internalization, the virus fuses with the cellular membrane compartment, probably in an endosomal compartment, although the mechanisms are not fully understood. A myristoylated peptide encompassing amino acids 2-48 of the preS1 region turned out to be the most efficient in infection inhibition of HBV and also the envelope protein-related hepatitis D virus (HDV) [30, 31] . Cyclosporin A and its analogs inhibit hepatitis B virus entry into cultured hepatocytes through targeting a membrane transporter NTCP abstract: Chronic hepatitis B virus (HBV) infection, affecting approximately 240 million people worldwide, is a major public health problem that elevates the risk of developing liver cirrhosis and hepatocellular carcinoma. Given that current anti-HBV drugs are limited to interferon-based regimens and nucleos(t)ide analogs, the development of new anti-HBV agents is urgently needed. The viral entry process is generally an attractive target implicated in antiviral strategies. Using primary cells from humans and Tupaia belangeri, as well as HepaRG cells, important determinants of viral entry have been achieved. Recently, sodium taurocholate cotransporting polypeptide (NTCP) was identified as an HBV entry receptor and enabled the establishment of a susceptible cell line that can efficiently support HBV infection. This finding will allow a deeper understanding of the requirements for efficient HBV infection, including the elucidation of the molecular entry mechanism. In addition, pharmacological studies suggest that NTCP is able to serve as a therapeutic target. This article summarizes our current knowledge on the mechanisms of HBV entry and the role of NTCP in this process. url: https://doi.org/10.3390/ijms15022892 doi: 10.3390/ijms15022892 id: cord-271122-3fsl5589 author: Wathes, D. Claire title: Importance of Viral Disease in Dairy Cow Fertility date: 2019-07-24 words: 7111.0 sentences: 346.0 pages: flesch: 44.0 cache: ./cache/cord-271122-3fsl5589.txt txt: ./txt/cord-271122-3fsl5589.txt summary: Acute infection with non-cytopathic bovine viral diarrhea virus (BVDV) in mid-gestation increases abortion rates or causes the birth of persistently infected calves. In cultured bovine endometrial cells, experimental infection with ncp BVDV inhibited a variety of immune pathways normally activated in response to a challenge with bacterial lipopolysaccharide (LPS), including downregulation of many interferon-stimulated genes (ISGs), which are an important part of uterine defense mechanisms [40, 41] . Establishment of persistent infection with non-cytopathic bovine viral diarrhoea virus in cattle is associated with a failure to induce type I interferon A field investigation of the effects of bovine viral diarrhea virus infection around the time of insemination on the reproductive performance of cattle The effect of infection with bovine viral diarrhea virus on the fertility of Swiss dairy cattle Embryos produced from fertilization with bovine viral diarrhea virus (BVDV)-infected semen and the risk of disease transmission to embryo transfer (ET) recipients and offspring abstract: Many viral diseases are endemic in cattle populations worldwide. The ability of many viruses to cross the placenta and cause abortions and fetal malformations is well understood. There is also significant evidence that viral infections have additional actions in dairy cows, which are reflected in reduced conception rates. These effects are, however, highly dependent on the time at which an individual animal first contracts the disease and are less easy to quantify. This paper reviews the evidence relating to five viruses that can affect fertility, together with their potential mechanisms of action. Acute infection with non-cytopathic bovine viral diarrhea virus (BVDV) in mid-gestation increases abortion rates or causes the birth of persistently infected calves. BVDV infections closer to the time of breeding can have direct effects on the ovaries and uterine endometrium, which cause estrous cycle irregularities and early embryo mortality. Fertility may also be reduced by BVDV-induced immunosuppression, which increases the susceptibility to bacterial infections. Bovine herpesvirus (BHV)-1 is most common in pre-pubertal heifers, and can slow their growth, delay breeding, and increase the age at first calving. Previously infected animals subsequently show reduced fertility. Although this may be associated with lung damage, ovarian lesions have also been reported. Both BHV-1 and BHV-4 remain latent in the host following initial infection and may be reactivated later by stress, for example associated with calving and early lactation. While BHV-4 infection alone may not reduce fertility, it appears to act as a co-factor with established bacterial pathogens such as Escherichia coli and Trueperella pyogenes to promote the development of endometritis and delay uterine repair mechanisms after calving. Both Schmallenberg virus (SBV) and bluetongue virus (BTV) are transmitted by insect vectors and lead to increased abortion rates and congenital malformations. BTV-8 also impairs the development of hatched blastocysts; furthermore, infection around the time of breeding with either virus appears to reduce conception rates. Although the reductions in conception rates are often difficult to quantify, they are nevertheless sufficient to cause economic losses, which help to justify the benefits of vaccination and eradication schemes. url: https://doi.org/10.1016/j.eng.2019.07.020 doi: 10.1016/j.eng.2019.07.020 id: cord-275602-cog4nma0 author: Watkins, Kevin title: Emerging Infectious Diseases: a Review date: 2018-06-22 words: 4672.0 sentences: 278.0 pages: flesch: 49.0 cache: ./cache/cord-275602-cog4nma0.txt txt: ./txt/cord-275602-cog4nma0.txt summary: SUMMARY: In addition to the aforementioned pathogens, the Severe Acute Respiratory Syndrome, Middle East Respiratory Syndrome, Nipah virus, New Delhi metallo-ß-lactamase-1 Enterobacteriaceae, Rift Valley Fever virus, and Crimean-Congo Hemorrhagic Fever virus are reviewed. In 1992, an expert committee that produced the Institute of Medicine report on emerging infections defined them as "new, reemerging, or drug-resistant infections whose incidence in humans has increased within the past two decades or whose incidence threatens to increase in the near future." Additionally, six major contributors to these diseases were presented and included changes in human demographics and behavior, advances in technology and changes in industry practices, economic development and changes in land-use patterns, dramatic increases in volume and speed of international travel and commerce, microbial adaptation and change, and breakdown of public health capacity [1] . The World Health Organization has prioritized a number of infectious diseases as requiring urgent need for research and development given the concern for potential of severe outbreaks. abstract: PURPOSE OF REVIEW: This review highlights some of the recent concerning emerging infectious diseases, a number of them specifically that the World Health Organization has categorized as priorities for research. RECENT FINDINGS: Emerging and reemerging infectious diseases account for significant losses in not only human life, but also financially. There are a number of contributing factors, most commonly surrounding human behavior, that lead to disease emergence. Zoonoses are the most common type of infection, specifically from viral pathogens. The most recent emerging diseases in the USA are Emergomyces canadensis, the Heartland virus, and the Bourbon virus. SUMMARY: In addition to the aforementioned pathogens, the Severe Acute Respiratory Syndrome, Middle East Respiratory Syndrome, Nipah virus, New Delhi metallo-ß-lactamase-1 Enterobacteriaceae, Rift Valley Fever virus, and Crimean-Congo Hemorrhagic Fever virus are reviewed. These pathogens are very concerning with a high risk for potential epidemic, ultimately causing both significant mortality and financial costs. Research should be focused on monitoring, prevention, and treatment of these diseases. url: https://doi.org/10.1007/s40138-018-0162-9 doi: 10.1007/s40138-018-0162-9 id: cord-339062-tq0f6d01 author: Weaver, Scott C. title: Transmission cycles, host range, evolution and emergence of arboviral disease date: 2004 words: 7314.0 sentences: 379.0 pages: flesch: 43.0 cache: ./cache/cord-339062-tq0f6d01.txt txt: ./txt/cord-339062-tq0f6d01.txt summary: RNA viruses, including HIV 1,2 , dengue virus (DENV) 3, 4 and possibly the severe acute respiratory syndrome (SARS) coronavirus [5] [6] [7] , have caused recent pandemics by changing their host range to amplify in humans. In this review, we focus on selected viruses such as Venezuelan equine and Japanese encephalitis viruses (VEEV and JEV, respectively), which cause epidemics by adapting to domestic animals and exploiting them as amplification hosts. After identification of VEEV as a cause of human disease, experimental animal models revealed that equine infection results in a high titre VIRAEMIA; the animals therefore serve as highly efficient amplification hosts in the presence of abundant competent mosquito vectors 12 However, studies of dengue virus ecology in sylvatic habitats of west Africa 72 and Malaysia 73, 74 have identified transmission cycles involving non-human primates as reservoir hosts and arboreal, tree-hole dwelling Aedes (Stegomyia) spp. abstract: Many pandemics have been attributed to the ability of some RNA viruses to change their host range to include humans. Here, we review the mechanisms of disease emergence that are related to the host-range specificity of selected mosquito-borne alphaviruses and flaviviruses. We discuss viruses of medical importance, including Venezuelan equine and Japanese encephalitis viruses, dengue viruses and West Nile viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/15378043/ doi: 10.1038/nrmicro1006 id: cord-274112-6t0wpiqy author: Webby, RJ title: Responsiveness to a pandemic alert: use of reverse genetics for rapid development of influenza vaccines date: 2004-04-03 words: 4199.0 sentences: 206.0 pages: flesch: 48.0 cache: ./cache/cord-274112-6t0wpiqy.txt txt: ./txt/cord-274112-6t0wpiqy.txt summary: INTERPRETATION: The ability to produce a candidate reference virus in such a short period of time sets a new standard for rapid response to emerging infectious disease threats and clearly shows the usefulness of reverse genetics for influenza vaccine development. The agent must be handled only under conditions of at least biosafety level 3 (BSL3), and it can kill fertilised chicken eggs, the standard medium for the reassortment and Responsiveness to a pandemic alert: use of reverse genetics for rapid development of influenza vaccines propagation of influenza virus before its inactivation and formulation for use in vaccines. The vaccine-candidate reference virus stock described in this report has been produced entirely on a cell substrate licensed for the manufacture of human vaccine, and as such, is-to our knowledge-the first reverse genetically derived influenza vaccine suitable for testing in clinical trials. Recombinant influenza A virus vaccines for the pathogenic human A/Hong Kong/97 (H5N1) viruses abstract: BACKGROUND: In response to the emergence of severe infection capable of rapid global spread, WHO will issue a pandemic alert. Such alerts are rare; however, on Feb 19, 2003, a pandemic alert was issued in response to human infections caused by an avian H5N1 influenza virus, A/Hong Kong/213/03. H5N1 had been noted once before in human beings in 1997 and killed a third (6/18) of infected people.1, 2 The 2003 variant seemed to have been transmitted directly from birds to human beings and caused fatal pneumonia in one of two infected individuals. Candidate vaccines were sought, but no avirulent viruses antigenically similar to the pathogen were available, and the isolate killed embryonated chicken eggs. Since traditional strategies of vaccine production were not viable, we sought to produce a candidate reference virus using reverse genetics. METHODS: We removed the polybasic aminoacids that are associated with high virulence from the haemagglutinin cleavage site of A/Hong Kong/213/03 using influenza reverse genetics techniques. A reference vaccine virus was then produced on an A/Puerto Rico/8/34 (PR8) backbone on WHO-approved Vero cells. We assessed this reference virus for pathogenicity in in-vivo and in-vitro assays. FINDINGS: A reference vaccine virus was produced in Good Manufacturing Practice (GMP)-grade facilities in less than 4 weeks from the time of virus isolation. This virus proved to be non-pathogenic in chickens and ferrets and was shown to be stable after multiple passages in embryonated chicken eggs. INTERPRETATION: The ability to produce a candidate reference virus in such a short period of time sets a new standard for rapid response to emerging infectious disease threats and clearly shows the usefulness of reverse genetics for influenza vaccine development. The same technologies and procedures are currently being used to create reference vaccine viruses against the 2004 H5N1 viruses circulating in Asia. url: https://www.sciencedirect.com/science/article/pii/S0140673604158923 doi: 10.1016/s0140-6736(04)15892-3 id: cord-280130-ewqe9edq author: Weber, Friedemann title: Viral suppression of the interferon system date: 2007-01-27 words: 4298.0 sentences: 224.0 pages: flesch: 39.0 cache: ./cache/cord-280130-ewqe9edq.txt txt: ./txt/cord-280130-ewqe9edq.txt summary: In most nucleated body cells, viral infections activate transcription of the ''''classic'''' IFN-b gene [1] by a signaling chain which is initiated by the RNA sensors RIG-I and MDA-5, which in turn act trough the adaptor IPS-1 and the kinases TBK-1 and IKK-3 to activate the transcription factor IRF-3 (see reviews by P. Many RNA and DNA viruses therefore express proteins which bind this key molecule to avoid both IFN induction and activation of dsRNA-dependent antiviral enzymes [7, 8] . Binding of the influenza virus NS1 protein to double-stranded RNA inhibits the activation of the protein kinase that phosphorylates the elF-2 translation initiation factor Ebola virus VP35 protein binds double-stranded RNA and inhibits alpha/beta interferon production induced by RIG-I signaling Double-stranded RNA binding of influenza B virus nonstructural NS1 protein inhibits protein kinase R but is not essential to antagonize production of alpha/beta interferon abstract: Type I interferons (IFN-α/β) were originally discovered by their strong and direct antiviral activity [A. Isaacs, J. Lindenmann, Virus interference. I. The interferon, Proc. R. Soc. Lond. B Biol. Sci. 147 (1957) 258–267]. (see review by J. Lindenmann on p. 719, in this issue). Nevertheless, only very recently it was entirely realized that viruses would not succeed without efficient tools to undermine this potent host defense system. Current investigations are revealing an astonishing variety of viral IFN antagonistic strategies targeting virtually all parts of the IFN system, often in a highly specific manner. Viruses were found to interfere with induction of IFN synthesis, IFN-induced signaling events, the antiviral effector proteins, or simply shut off the host cell macromolecule synthesis machinery to avoid booting of the antiviral host defense. Here, we will describe a few well-characterized examples to illustrate the sophisticated and often multi-layered anti-IFN mechanisms employed by viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/17336442/ doi: 10.1016/j.biochi.2007.01.005 id: cord-018078-clxzp1ph author: Weber, Olaf title: Coronavirus infections in veterinary medicine date: 2005 words: 4430.0 sentences: 278.0 pages: flesch: 43.0 cache: ./cache/cord-018078-clxzp1ph.txt txt: ./txt/cord-018078-clxzp1ph.txt summary: Some important viruses that are discussed below belong to group I and include the canine enteric coronavirus (CECoV), the transmissible gastroenteritis virus (TGEV) of swine, the porcine epidemic diarrhoea virus (PEDV), the porcine respiratory coronavirus (PRCoV) and the feline coronaviruses (FCoVs). The clinical symptoms of endemic/enzootic TGE are usually less severe in the older pigs, making a clinical differentiation between TGE and other infectious enteric diseases, like that caused by rotaviruses and/or clostridia, impossible. Bovine coronavirus (BCoV) is an important cause of neonatal calf diarrhea [33] but may also infect the respiratory tract and has been recognized as the causing agent especially for winter dysentery in adult cattle. As for other coronaviruses, seasonal changes in temperature, environmental factors but also the immune status play an important role in the transmission of the virus and the clinical outcome of the infection. Two amino acid changes at the N-terminus of transmissible gastroenteritis coronavirus spike protein result in the loss of enteric tropism abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122866/ doi: 10.1007/3-7643-7339-3_2 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: 12321.0 sentences: 734.0 pages: flesch: 44.0 cache: ./cache/cord-019051-gtruu1op.txt txt: ./txt/cord-019051-gtruu1op.txt summary: Viruses with an established role in common cold are rhinoviruses, adenoviruses, parainfluenza viruses, coronaviruses and the respiratory syncytial virus, and these are reviewed in greater detail here. Therefore, the viral etiology and the role of viruses in the pathogenesis of common cold is complex and it is safe to say, not fully understood for each and every virus that is linked to respiratory tract infection. RSV infection is assumed to be frequently misdiagnosed, particularly in adults [56] , because the symptoms are similar to those caused by other respiratory viruses like influenza. Human parainfluenza viruses (HPIV) are important causes of respiratory diseases in infants and children. HMPV is thought to be the second or third cause of severe acute respiratory tract infection in children, just ranking behind RSV and influenza virus [146, 148] . Retinoic acid-inducible gene I mediates early Antiviral Response and Toll-like receptor 3 expression in respiratory syncytial virus-infected airway epithelial cells 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-266138-yibbiiij author: Wege, Helmut title: Immunopathological aspects of coronavirus infections date: 1995 words: 6899.0 sentences: 398.0 pages: flesch: 37.0 cache: ./cache/cord-266138-yibbiiij.txt txt: ./txt/cord-266138-yibbiiij.txt summary: Murine coronaviruses (mouse hepatitis virus, MHV) can spread inapparently or may hide as persistent infections that modulate the immune response [38, 100] . Suppression of immune response induction in Peyer''s patch lymphoid cells from mice infected with mouse hepatitis virus Infection of BALB/cByJ mice with the JHM strain of mouse hepatitis virus alters in vitro splenic T cell proliferation and cytokine production Interaction of immune and central nervous systems: contribution of anti-viral Thy-1 + cells to demyelination induced by coronavirus JHM Impaired T and B cell subpopulations involved in a chronic disease induced by mouse hepatitis virus type 3 Identification of antigenic sites mediating antibody-dependent enhancement of feline infectious peritonitis virus infectivity The pathogenic role of virus-specific antibody-secreting cells in the central nervous system of rats with different susceptibility to coronavirus-induced demyelinating encephalitis Demyelination induced by murine hepatitis virus JHM strain (MHV-4) is immunologically mediated abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/8571165/ doi: 10.1007/bf00196162 id: cord-272981-8gahvdt0 author: Wege, Helmut title: Relapsing subacute demyelinating encephalomyelitis in rats during the course of coronavirus JHM infection date: 1984-08-31 words: 3725.0 sentences: 295.0 pages: flesch: 57.0 cache: ./cache/cord-272981-8gahvdt0.txt txt: ./txt/cord-272981-8gahvdt0.txt summary: These results demonstrate that mutants of JHM virus can induce a relapsing demyelinating disease process, associated with a persistent infection, which possesses some similarities to chronic experimental allergic encephalomyelitis. It has been shown that an autoimmune reaction against CNS tissue can lead to 6hronic relapsing demyelination as seen in chronic experimental allergic encephalomyelitis (EAE) whereas the role of a virus infection in the induction of such a condition has not so far been directly demonstrated (McFarlin et al. After virus infection in rats inflammatory disseminating CNS lesions of marked demyelination develop accompanied by clinical signs of a subacute disease after varying incubation times. The induction of a progressive demyelinating, or relapsing demyelinating, disease process, in JHM virus-infected rats has ~me parallels to chronic EAE, an animal model based on sensitation ~8ainst CNS tissue extracts or myelin basic protein (McFarlin et al. abstract: Abstract Temperature-sensitive mutants of the murine coronavirus JHM induced a subacute demyelinating encephalomyelitis (SDE) in young rats. Neurological symptoms were associated with marked lesions of primary demyelination in the white matter of the central nervous system (CNS), and developing after an incubation time of several weeks to months. Many rats survived this infection and recovered completely from this CNS disease. Among 43 survivors of SDE, 9 rats developed a relapse 27–153 days after onset of the first attack. Neuropathological examination of these animals revealed areas of fresh demyelination together with old remyelinated lesions. Viral antigens were detectable in the neighbourhood of fresh lesions and in some cases infectious virus was re-isolated from rats revealing low antibody titers to JHM virus. These results demonstrate that mutants of JHM virus can induce a relapsing demyelinating disease process, associated with a persistent infection, which possesses some similarities to chronic experimental allergic encephalomyelitis. url: https://www.sciencedirect.com/science/article/pii/0165572884900225 doi: 10.1016/0165-5728(84)90022-5 id: cord-276212-ys5njiw0 author: Wei, L. title: Burden, seasonal pattern and symptomatology of acute respiratory illnesses with different viral aetiologies in children presenting at outpatient clinics in Hong Kong date: 2015-05-30 words: 2860.0 sentences: 117.0 pages: flesch: 40.0 cache: ./cache/cord-276212-ys5njiw0.txt txt: ./txt/cord-276212-ys5njiw0.txt summary: authors: Wei, L.; Chan, K.-H.; Ip, D.K.M.; Fang, V.J.; Fung, R.O.P.; Leung, G.M.; Peiris, M.J.S.; Cowling, B.J. title: Burden, seasonal pattern and symptomatology of acute respiratory illnesses with different viral aetiologies in children presenting at outpatient clinics in Hong Kong In this study, we aimed to investigate the burden of ARIs caused by different respiratory viral pathogens among children aged 15 years in a community outpatient setting, to describe their seasonal patterns of occurrence, and to characterize their clinical characteristics at presentation. The specimens were tested for eight common respiratory viruses (including types and subtypes), namely IFVA (subtypes H1 and H3), influenza virus B (IFVB), RSV (subtypes A and B), PIV (types 1-4), metapneumovirus (MPV), enterovirus (EnV)/RhV, AdV, bocavirus (BoV), and coronavirus (CoV) (types NL63, HKU1, 229E, and OC43), with the xTAG RVP FAST version 2.0 multiplex assay (Luminex Molecular Diagnostics, Toronto, Ontario, Canada), and this was followed by product detection and identification with a Luminex suspension microarray [7] . abstract: Respiratory viruses cause acute respiratory diseases with a broad and overlapping spectrum of symptoms. We examined the clinical symptoms and explored the patterns of various respiratory viral infections in children in Hong Kong. Among 2090 specimens collected from outpatient care (2007–2010), 1343 (64.3%) were positive for any virus by the xTAG assay, and 81 (3.9%) were positive for co-infection. The most frequently detected viruses among children aged 6–15 years were enterovirus/rhinovirus and influenza virus A, whereas most non-influenza viruses were more frequently detected in younger children. Higher body temperature was more common for illnesses associated with influenza viruses than for those associated with non-influenza viruses, but other symptoms were largely similar across all infections. The seasonality pattern varied among different viruses, with influenza virus A being the predominant virus detected in winter, and enterovirus/rhinovirus being more commonly detected than influenza virus A in the other three seasons, except for 2009. url: https://www.ncbi.nlm.nih.gov/pubmed/26033670/ doi: 10.1016/j.cmi.2015.05.027 id: cord-004775-foaf3vyl author: Weiss, Marianne title: The proposed family toroviridae: Agents of enteric infections date: 1987 words: 3946.0 sentences: 231.0 pages: flesch: 56.0 cache: ./cache/cord-004775-foaf3vyl.txt txt: ./txt/cord-004775-foaf3vyl.txt summary: A morphologically similar virus (Lyon 4 virus) detected in cattle in Lyon, France (6, 7) , was shown later to possess an antigenic relatedness to the Berne (BEV) and Breda (BRV) viruses. In thin sections through BEV infected cells (horse kidney, embryonic mule skin, equine dermal cells) densely staining spherical, elliptieM and elongated particles were detected (2, 9) . Thin sections through BRV infected intestinal cells of calves (10, 11, 12) showed elongated viral particles with rounded ends measuring 42 × 100.5 nm. The high molecular weight virion protein in the range of 75-100 kD of BEV is glycosylated, probably by N-linked oligosaccharides since tunicamycin, an antibiotic known to inhibit N-linked oligosaccharide synthesis, prevented the formation of infectious virus as well as appearance of the 75-100 kD band in PAGE of infected cells (20) . Evidence of a reaction of the particles in human feces with sera containing antibodies against BRV and BEV, respectively, were obtained in IEM (8), (Flewett personal communication). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086944/ doi: 10.1007/bf01310058 id: cord-290133-4ou7ubb4 author: Weiss, Martin M. title: Rethinking Smallpox date: 2004-12-01 words: 3976.0 sentences: 244.0 pages: flesch: 51.0 cache: ./cache/cord-290133-4ou7ubb4.txt txt: ./txt/cord-290133-4ou7ubb4.txt summary: The last recorded death due to smallpox, according to World Health Organization investigators, was likely associated with virus that had been transmitted by aerosol [16] . Such observations-along with the long incubation period of smallpox (mean, 12-14 days; range, 7-21 days)suggest that there would be adequate time to vaccinate the public and prevent a more widespread outbreak. Nonetheless, these masks, if distributed to the public, could prove to be critical for the control of a smallpox epidemic that was overwhelming our health care system, and they might also prove to be effective in limiting contagion of smaller viruses, such as influenza virus (either natural virus, as in 1918, or engineered virus [61] ). Because of the possibility of an attack involving bioengineered smallpox virus that is resistant to the current vaccine, methisazone should be reexamined, and research should be continued on other antiviral agents. abstract: The potential consequences of a competently executed smallpox attack have not been adequately considered by policy makers. The possibility of release of an aerosolized and/or bioengineered virus must be anticipated and planned for. The transmission and infectivity of variola virus are examined. Arguments for and against pre-event vaccination are offered. The likely morbidity and mortality that would ensue from implementation of a mass pre-event vaccination program, within reasonable boundaries, are known. The extent of contagion that could result from an aerosolized release of virus is unknown and may have been underestimated. Pre-event vaccination of first responders is urged, and voluntary vaccination programs should be offered to the public. Two defenses against a vaccine-resistant, engineered variola virus are proposed for consideration. Methisazone, an overlooked drug, is reported to be effective for prophylaxis only. The extent of reduction in the incidence of smallpox with use of this agent is uncertain. It is useless for treatment of clinical smallpox. N-100 respirators (face masks) worn by uninfected members of the public may prevent transmission of the virus. url: https://www.ncbi.nlm.nih.gov/pubmed/15578369/ doi: 10.1086/425745 id: cord-008333-1wepke2o author: Weisz, Ora A. title: Chapter 7 Use of Recombinant Vaccinia Virus Vectors for Cell Biology date: 2008-02-28 words: 7465.0 sentences: 461.0 pages: flesch: 56.0 cache: ./cache/cord-008333-1wepke2o.txt txt: ./txt/cord-008333-1wepke2o.txt summary: The recombinant virus is selected, expanded, and used to infect cells, which then express high levels of the foreign protein. Transfection of cells immediately after infection with a vector containing the gene of interest cloned behind a T7 promoter results in rapid and efficient expression of the encoded protein. The use of an early vaccinia promoter to drive the foreign gene is essential for cell biology applications, since the protein will be expressed before most of the cytopathic effects of the virus infection become evident. Before growing a large-scale preparation of the recombinant, we also test that the expressed protein is the correct size by immunoprecipitation from radiolabeled infected cells, followed by electrophoresis in SDS polyacrylamide gels (see Section IV,C,l). Expression is mediated by co-infecting the cells with another vaccinia virus encoding T7 RNA polymerase (vTF7-3). This chapter has discussed the preparation and use of recombinant vaccinia viruses to express proteins in mammalian cells. abstract: This chapter describes the use of several of the recombinant vaccinia expression systems, focuses on the systems that are most useful for cell biologists, and discusses their advantages and limitations. Vaccinia-mediated expression can be used for assessing cellular localization, posttranslational modifications, oligomerization, and transport and turnover rates. The system provides a rapid method for screening mutant proteins for expression and targeting. It is an excellent way of quickly deciding which mutant proteins might be worth further studying using stable expression systems. Expression of foreign genes using Vaccinia virus is based on recombinant viruses constructed by insertion of complementary DNA (cDNA) into the nonessential thymidine kinase (TK) gene. Both direct and indirect methods of expression are possible. The foreign gene can be inserted into the vaccinia genome by homologous recombination using a plasmid with flanking regions of vaccinia DNA. The recombinant virus is selected, expanded, and used to infect cells, which then express high levels of the foreign protein. Recombinant vaccinia viruses are generated by subcloning the foreign gene into a plasmid transfer vector so it is flanked by DNA from the vaccinia (TK) gene, which is nonessential for growth of the virus in tissue culture. This plasmid is then transfected into vaccinia-infected cells. Homologous recombination of the plasmid and the vaccinia genome generates a recombinant virus with an inactive TK gene. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7130382/ doi: 10.1016/s0091-679x(08)60602-0 id: cord-002874-9rxv6fy9 author: Welch, David title: Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases date: 2018-02-09 words: 3266.0 sentences: 166.0 pages: flesch: 47.0 cache: ./cache/cord-002874-9rxv6fy9.txt txt: ./txt/cord-002874-9rxv6fy9.txt summary: Here we applied this approach to test the efficacy of the 222-nm far-UVC light to inactivate influenza A virus (H1N1) carried by aerosols in a benchtop aerosol UV irradiation chamber, which generated aerosol droplets of sizes similar to those generated by human coughing and breathing. If these results are confirmed in other scenarios, it follows that the use of overhead low-level far-UVC light in public locations may represent a safe and efficient methodology for limiting the transmission and spread of airborne-mediated microbial diseases such as influenza and tuberculosis. In conclusion, we have shown for the first time that very low doses of far-UVC light efficiently inactivate airborne viruses carried by aerosols. If these results are confirmed in other scenarios, it follows that the use of overhead very low level far-UVC light in public locations may represent a safe and efficient methodology for limiting the transmission and spread of airborne-mediated microbial diseases. abstract: Airborne-mediated microbial diseases such as influenza and tuberculosis represent major public health challenges. A direct approach to prevent airborne transmission is inactivation of airborne pathogens, and the airborne antimicrobial potential of UVC ultraviolet light has long been established; however, its widespread use in public settings is limited because conventional UVC light sources are both carcinogenic and cataractogenic. By contrast, we have previously shown that far-UVC light (207–222 nm) efficiently inactivates bacteria without harm to exposed mammalian skin. This is because, due to its strong absorbance in biological materials, far-UVC light cannot penetrate even the outer (non living) layers of human skin or eye; however, because bacteria and viruses are of micrometer or smaller dimensions, far-UVC can penetrate and inactivate them. We show for the first time that far-UVC efficiently inactivates airborne aerosolized viruses, with a very low dose of 2 mJ/cm(2) of 222-nm light inactivating >95% of aerosolized H1N1 influenza virus. Continuous very low dose-rate far-UVC light in indoor public locations is a promising, safe and inexpensive tool to reduce the spread of airborne-mediated microbial diseases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5807439/ doi: 10.1038/s41598-018-21058-w id: cord-277010-2iecsho0 author: Wen, Xiaohong title: Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study date: 2019-01-08 words: 3100.0 sentences: 153.0 pages: flesch: 47.0 cache: ./cache/cord-277010-2iecsho0.txt txt: ./txt/cord-277010-2iecsho0.txt summary: title: Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study Similarly, the positive rate of cases with a single virus infection was highest in the young children (65.5%) and lowest in adults of 18-60 years of age (38.5%). The proportion of respiratory viruses notably differed across different age groups; the virus positive rate was the highest in young children under 5 years but was lowest in adults (18~60 years) in this study. Therefore, all positive RhV and/or EV specimens and 10 FluA virus specimens with random selection were identified Table 2 Age distribution of viruses from outpatients with ARIs ARIs, acute respiratory infections by sequencing assay, respectively, and among them, four RhV positive and 3 EV positive specimens were not sequenced due to low viral load in the specimens. In summary, this study provides important epidemiologic data regarding the clinical characteristics, viral spectrum, age distribution and seasonality of viruses in outpatients with ARIs in Huzhou, China. abstract: BACKGROUND: Viruses are commonly found in patients with acute respiratory infections (ARIs). However, the viral etiologies and clinical characteristics of outpatients with ARIs are poorly understood in China. Here, we identified the viral etiologies in outpatients with ARIs in Huzhou, China. RESULTS: Our results indicated that of 426 outpatients, 246 were positive for viruses. Of them, 221 were positive for a single virus, including influenza A, which comprised H3N2 (28.5%) and pandemic H1N1 (2009) (19.0%), enterovirus (10.4%), and influenza B (8.6%). Other single viruses were detected at less than 8.0%. Twenty-five patients were positively coinfected with two viruses. The prevalent viruses in coinfections were rhinovirus and H3N2 virus (28.0%). Viruses were major pathogens in young children (< 5 years) (75.0%). Coinfections were prevalent in older adults (11.9%) and young children (9.5%). Virus-positive outpatients presented higher temperatures and more sore throat, fatigue and shortness of breath than virus-negative outpatients. ARIs and most virus detections peaked during the winter, but enteroviruses emerged between April and September. CONCLUSION: Viruses are major agents of ARIs among outpatients in Huzhou, China. There was a variation in the distribution of viruses across different age groups and seasons. These findings are beneficial for planning prevention and treatment services for outpatients with ARIs. url: https://www.ncbi.nlm.nih.gov/pubmed/30621623/ doi: 10.1186/s12879-018-3668-6 id: cord-267671-ys43n672 author: Whary, Mark T. title: Biology and Diseases of Mice date: 2015-07-10 words: 63666.0 sentences: 3678.0 pages: flesch: 40.0 cache: ./cache/cord-267671-ys43n672.txt txt: ./txt/cord-267671-ys43n672.txt summary: Clinical Signs MCMV causes subclinical infection in adult immunocompetent mice, but experimental inoculation of neonates can cause lethal disease due to multisystemic necrosis and inflammation. Diagnosis Because infected mice do not manifest signs or lesions and the virus is very difficult to propagate in cell culture, detection and diagnosis rely on serology and molecular methods. Differential Diagnosis Reovirus infection must be differentiated from other diarrheal diseases of infant mice, including those caused by mouse coronaviruses, EDIM virus, Salmonella spp., or Clostridium piliforme. Epizootiology EDIM virus appears to be infectious only for mice and occurs episodically in mouse colonies, and infection is probably widespread geographically (Livingston and Riley, 2003; Pritchett-Corning LABORATORY ANIMAL MEDICINE et al., 2009) . Sentinel mouse surveillance, using soiled bedding, is an effective strategy for detecting MNV (Manuel et al., 2008) Differential Diagnosis The mild change in fecal consistency associated with MNV in adult mice may mimic rotavirus, coronavirus, Helicobacter spp., Citrobacter rodentium, or other enteric diseases. abstract: Today’s laboratory mouse, Mus musculus, has its origins as the ‘house mouse’ of North America and Europe. Beginning with mice bred by mouse fanciers, laboratory stocks (outbred) derived from M. musculus musculus from eastern Europe and M. m. domesticus from western Europe were developed into inbred strains. Since the mid-1980s, additional strains have been developed from Asian mice (M. m. castaneus from Thailand and M. m. molossinus from Japan) and from M. spretus which originated from the western Mediterranean region. url: https://api.elsevier.com/content/article/pii/B9780124095274000031 doi: 10.1016/b978-0-12-409527-4.00003-1 id: cord-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-263017-rh86g4jk author: Wigginton, Krista Rule title: Virus disinfection mechanisms: the role of virus composition, structure, and function date: 2011-12-09 words: 3710.0 sentences: 186.0 pages: flesch: 34.0 cache: ./cache/cord-263017-rh86g4jk.txt txt: ./txt/cord-263017-rh86g4jk.txt summary: Non-culturable virus disinfection kinetics must be either determined with human charge studies or predicted using surrogate viruses that can be cultured in vitro but that differ in composition, structure, and function. Coupling structure and composition information aids in our understanding of virus reactivity X-ray crystal structures have been published for numerous enteric viruses [25,26 ,27] and with these reports have come a windfall of valuable information including the location and orientation of capsid protein residues. Specific questions include: 1) Which virus protein residues are involved with fundamental functions and how do these vary amongst different strains and species; 2) What specific chemical modifications take place in the genome and capsid during disinfection and what effects do these modifications have on virus structure and function; 3) How similar are disinfectant-induced modifications amongst various enteric viruses? abstract: Drinking waters are treated for enteric virus via a number of disinfection techniques including chemical oxidants, irradiation, and heat, however the inactivation mechanisms during disinfection remain elusive. Owing to the fact that a number of significant waterborne virus strains are not readily culturable in vitro at this time (e.g. norovirus, hepatitis A), the susceptibility of these viruses to disinfection is largely unknown. An in-depth understanding of the mechanisms involved in virus inactivation would aid in predicting the susceptibility of non-culturable virus strains to disinfection and would foster the development of improved disinfection methods. Recent technological advances in virology research have provided a wealth of information on enteric virus compositions, structures, and biological functions. This knowledge will allow for physical/chemical descriptions of virus inactivation and thus further our understanding of virus disinfection to the most basic mechanistic level. url: https://doi.org/10.1016/j.coviro.2011.11.003 doi: 10.1016/j.coviro.2011.11.003 id: cord-278465-tjjkz16y author: Wille, Michelle title: Urbanization and the dynamics of RNA viruses in Mallards (Anas platyrhynchos) date: 2017-03-18 words: 5890.0 sentences: 307.0 pages: flesch: 52.0 cache: ./cache/cord-278465-tjjkz16y.txt txt: ./txt/cord-278465-tjjkz16y.txt summary: Recent studies have been instrumental in starting to describe dynamics and ecology of AMPV-1 and CoV in wild birds; 9-12% of migrating Mallards have CoV infections, compared to a lower prevalence (2%) of AMPV-1 towards the end of the migratory season in Sweden (Tolf et al., 2013b; Wille et al., 2015) . In context of IAV, and to a lesser degree CoV and APMV-1, an assessment of virus prevalence and diversity in an urban population will further allow us to assess if dynamics in wild birds are reflected in an urban setting. In comparing prevalence [Sept-Dec] between our urban dataset and a wild bird dataset from southern Sweden using the same qPCR methods (Wille et al., 2015) , autumnal prevalence for IAV (p b 0.0010) and CoV (p b 0.0010) is significantly different, where prevalence for both these viruses is lower in urban Mallards (Fig. 2) . abstract: Urbanization is intensifying worldwide, and affects the epidemiology of infectious diseases. However, the effect of urbanization on natural host-pathogen systems remains poorly understood. Urban ducks occupy an interesting niche in that they directly interact with both humans and wild migratory birds, and either directly or indirectly with food production birds. Here we have collected samples from Mallards (Anas platyrhynchos) residing in a pond in central Uppsala, Sweden, from January 2013 to January 2014. This artificial pond is kept ice-free during the winter months, and is a popular location where the ducks are fed, resulting in a resident population of ducks year-round. Nine hundred and seventy seven (977) fecal samples were screened for RNA viruses including: influenza A virus (IAV), avian paramyxovirus 1, avian coronavirus (CoV), and avian astrovirus (AstroV). This intra-annual dataset illustrates that these RNA viruses exhibit similar annual patterns to IAV, suggesting similar ecological factors are at play. Furthermore, in comparison to wild ducks, autumnal prevalence of IAV and CoV are lower in this urban population. We also demonstrate that AstroV might be a larger burden to urban ducks than IAV, and should be better assessed to demonstrate the degree to which wild birds contribute to the epidemiology of these viruses. The presence of economically relevant viruses in urban Mallards highlights the importance of elucidating the ecology of wildlife pathogens in urban environments, which will become increasingly important for managing disease risks to wildlife, food production animals, and humans. url: https://www.ncbi.nlm.nih.gov/pubmed/28323070/ doi: 10.1016/j.meegid.2017.03.019 id: cord-302047-vv5gpldi author: Willemsen, Anouk title: On the stability of sequences inserted into viral genomes date: 2019-11-14 words: 12557.0 sentences: 598.0 pages: flesch: 43.0 cache: ./cache/cord-302047-vv5gpldi.txt txt: ./txt/cord-302047-vv5gpldi.txt summary: Viruses are widely used as vectors for heterologous gene expression in cultured cells or natural hosts, and therefore a large number of viruses with exogenous sequences inserted into their genomes have been engineered. Viruses genera covered in relevant studies Conclusions of this review All viruses • Inserted sequences are often unstable and rapidly lost upon passaging of an engineered virus • The position at which a sequence is integrated in the genome can be important for stability • Sequence stability is not an intrinsic property of genomes because demographic parameters, such as population size and bottleneck size, can have important effects on sequence stability • The multiplicity of cellular infection affects sequence stability, and can in some cases directly affect whether there is selection for deletion variants • Deletions are not the only class of mutations that can reduce the cost of inserted sequences, although they are the most common I: dsDNA abstract: Viruses are widely used as vectors for heterologous gene expression in cultured cells or natural hosts, and therefore a large number of viruses with exogenous sequences inserted into their genomes have been engineered. Many of these engineered viruses are viable and express heterologous proteins at high levels, but the inserted sequences often prove to be unstable over time and are rapidly lost, limiting heterologous protein expression. Although virologists are aware that inserted sequences can be unstable, processes leading to insert instability are rarely considered from an evolutionary perspective. Here, we review experimental work on the stability of inserted sequences over a broad range of viruses, and we present some theoretical considerations concerning insert stability. Different virus genome organizations strongly impact insert stability, and factors such as the position of insertion can have a strong effect. In addition, we argue that insert stability not only depends on the characteristics of a particular genome, but that it will also depend on the host environment and the demography of a virus population. The interplay between all factors affecting stability is complex, which makes it challenging to develop a general model to predict the stability of genomic insertions. We highlight key questions and future directions, finding that insert stability is a surprisingly complex problem and that there is need for mechanism-based, predictive models. Combining theoretical models with experimental tests for stability under varying conditions can lead to improved engineering of viral modified genomes, which is a valuable tool for understanding genome evolution as well as for biotechnological applications, such as gene therapy. url: https://www.ncbi.nlm.nih.gov/pubmed/31741748/ doi: 10.1093/ve/vez045 id: cord-337659-x4oywbrj author: Wilson, Brenda A. title: Global biosecurity in a complex, dynamic world date: 2008-07-31 words: 10626.0 sentences: 469.0 pages: flesch: 45.0 cache: ./cache/cord-337659-x4oywbrj.txt txt: ./txt/cord-337659-x4oywbrj.txt summary: Although one might argue that the principal difference in the infectious disease threat today versus say 10, 25, or 50 years ago is bioterrorism, the resources spend on preparing for a bioterror attack is viewed by most scientists as grossly exorbitant [6] , particularly considering the small numbers of individuals who have been or could be affected by this type of attack and considering the relatively low medical relevance or prevalence of the diseases caused by the limited number of highpriority bioterror bioagents, the socalled ''''category A select agents.'''' And, while admittedly the preparedness and surveillance measures put in place for one has certainly helped to protect against the other (the improved global response to and curtailment of SARS coming after the anthrax bioterrorist attacks is a prime example of this), most scientists feel that the limited resources available from an already overburdened system should instead be used for studying and preparing against the looming and potentially more devastating infectious disease threats from natural or accidental exposure [7] , which could affect millions of people and animals and could have huge health and economic consequences. abstract: Biosecurity is emerging as a major global health priority for which innovative and unprecedented solutions are needed. Biosecurity is a challenging biocomplexity problem involving multifaceted processes such as interactions between humans and nonhuman biota, anthropogenic environmental and ecological factors, and socioeconomic and political pressures. Key to an effective biosecurity strategy will be fundamental understanding of evolutionary, anthropogenic and environmental driving forces at play in transmission and perpetuation of infectious diseases. Biosecurity solutions will depend on increased support of basic biomedical research and public education, enhanced healthcare preparedness, alternative strategies for ensuringsafety, and improved interagency cooperation regarding global health policy. © 2008 Wiley Periodicals, Inc. Complexity, 2008. url: https://www.ncbi.nlm.nih.gov/pubmed/32313416/ doi: 10.1002/cplx.20246 id: cord-281332-5mddyv0n author: Wilson, Michael R. title: A novel cause of chronic viral meningoencephalitis: Cache Valley virus date: 2017-07-25 words: 4008.0 sentences: 232.0 pages: flesch: 42.0 cache: ./cache/cord-281332-5mddyv0n.txt txt: ./txt/cord-281332-5mddyv0n.txt summary: Interpretation: Cache Valley virus, a mosquito-borne orthobunyavirus, has only been identified in 3 immunocompetent North American patients with acute neuroinvasive disease. This report demonstrates that metagenomic next generation sequencing allows for unbiased pathogen identification, the early detection of emerging viruses as they spread to new locales, and the discovery of novel disease phenotypes. This report demonstrates that metagenomic next generation sequencing allows for unbiased pathogen identification, the early detection of emerging viruses as they spread to new locales, and the discovery of novel disease phenotypes. Here, we report the effective deployment of metagenomic next generation sequencing (mNGS) to diagnose Cache Valley virus (CVV), a mosquito-borne orthobunyavirus, 4 in an Australian patient with a primary immunodeficiency suffering from chronic meningoencephalitis. 41 Because CVV is rarely identified as a cause of human disease and has not been reported in Australia previously, there are no traditional candidate-based diagnostic tests for this virus available in Australia. abstract: OBJECTIVE: Immunodeficient patients are particularly vulnerable to neuroinvasive infections that can be challenging to diagnose. Metagenomic next generation sequencing can identify unusual or novel microbes and is therefore well suited for investigating the etiology of chronic meningoencephalitis in immunodeficient patients. METHODS: We present the case of a 34‐year‐old man with X‐linked agammaglobulinemia from Australia suffering from 3 years of meningoencephalitis that defied an etiologic diagnosis despite extensive conventional testing, including a brain biopsy. Metagenomic next generation sequencing of his cerebrospinal fluid and brain biopsy tissue was performed to identify a causative pathogen. RESULTS: Sequences aligning to multiple Cache Valley virus genes were identified via metagenomic next generation sequencing. Reverse transcription polymerase chain reaction and immunohistochemistry subsequently confirmed the presence of Cache Valley virus in the brain biopsy tissue. INTERPRETATION: Cache Valley virus, a mosquito‐borne orthobunyavirus, has only been identified in 3 immunocompetent North American patients with acute neuroinvasive disease. The reported severity ranges from a self‐limiting meningitis to a rapidly fatal meningoencephalitis with multiorgan failure. The virus has never been known to cause a chronic systemic or neurologic infection in humans. Cache Valley virus has also never previously been detected on the Australian continent. Our research subject traveled to North and South Carolina and Michigan in the weeks prior to the onset of his illness. This report demonstrates that metagenomic next generation sequencing allows for unbiased pathogen identification, the early detection of emerging viruses as they spread to new locales, and the discovery of novel disease phenotypes. Ann Neurol 2017;82:105–114 url: https://doi.org/10.1002/ana.24982 doi: 10.1002/ana.24982 id: cord-018463-a6qu0cuv author: Wimmer, Eckard title: Synthetic Biology, Dual Use Research, and Possibilities for Control date: 2018-03-23 words: 1970.0 sentences: 107.0 pages: flesch: 48.0 cache: ./cache/cord-018463-a6qu0cuv.txt txt: ./txt/cord-018463-a6qu0cuv.txt summary: The anthrax attack coincided with the first report in 2002 of the de novo synthesis in the test tube of a pathogenic human virus, poliovirus, that was equally shocking because it indicated that dangerous infectious agents could be produced in laboratories outside of government control. These events were synchronous with the advent of a new discipline, Synthetic Biology, which was an emerging area of research that can broadly be described "as the design and construction of novel artificial biological pathways, organisms or devices, or the redesign of existing natural biological systems." The synthesis of viruses, or more broadly expressed: each experiment in Synthetic Biology, fits the definition of "Dual Use Research" – the dual use dilemma in which the same technologies can be used for the good of humans and misused for bioterrorism. abstract: The anthrax attack on the human population in the United States in 2001/2002 may be considered the naissance of modern bioterrorism. This attack, e.g. the planned killing by means of deadly microorganisms (Bacillus anthracis) caused enormous public concern, because, numerous other deadly agents, now known as “select agents”, occur in nature and are available for misuse. The anthrax attack coincided with the first report in 2002 of the de novo synthesis in the test tube of a pathogenic human virus, poliovirus, that was equally shocking because it indicated that dangerous infectious agents could be produced in laboratories outside of government control. These events were synchronous with the advent of a new discipline, Synthetic Biology, which was an emerging area of research that can broadly be described “as the design and construction of novel artificial biological pathways, organisms or devices, or the redesign of existing natural biological systems.” The synthesis of viruses, or more broadly expressed: each experiment in Synthetic Biology, fits the definition of “Dual Use Research” – the dual use dilemma in which the same technologies can be used for the good of humans and misused for bioterrorism. In view of these threats the US Government has formulated rules that can lower the chances of misuse of biological research. That includes all research with select agents or the modification of agents to acquire dangerous traits (“Gain of Function”). It also calls for the continuous education of all generations entering research: to be aware that results of research can be dangerous, if not immediately then possibly at later times. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123342/ doi: 10.1007/978-94-024-1263-5_2 id: cord-350151-s75d1hat author: Wiramus, S. title: Rianimazione e influenza grave: pandemia influenzale A (H1N1) date: 2013-04-30 words: 6539.0 sentences: 767.0 pages: flesch: 61.0 cache: ./cache/cord-350151-s75d1hat.txt txt: ./txt/cord-350151-s75d1hat.txt summary: A causa delle mutazioni costanti dei virus influenzali, la composizione del vaccino è generalmente diversa da un anno all''altro: ogni anno, l''Organizzazione Mondiale della Sanità (OMS) emette una raccomandazione sui ceppi che devono essere inclusi nel vaccino. • personale paramedico e medico: rischio importante di riduzione del personale disponibile negli ospedali e rischio maggiore di infettare dei pazienti fragili; • donne gravide: rischio elevato di complicanze gravi e di morte; • bambini di meno di 6 mesi e persone che se ne occupano; • persone da 6 mesi a 24 anni; • persone da 25 a 64 anni che hanno delle comorbilità: enfisema polmonare, broncopneumopatia cronica ostruttiva (BPCO), asma, obesità patologica, insufficienza cardiaca, diabete instabile, immunodepressione e malattie neurologiche. Solo i soggetti poco o non immuni nei confronti del virus sono suscettibili di essere colpiti in questa maniera ed è per questo che la vaccinazione contro l''influenza stagionale sembra conferire una protezione contro queste forme più gravi [6] . abstract: Durante la pandemia influenzale A (H1N1) nel 2009-2010, il 20% dei pazienti ospedalizzati ha presentato delle forme gravi con trasferimento in rianimazione. L’età mediana di questi pazienti era di circa 30 anni, con una percentuale leggermente inferiore al 10% di donne gravide. Si riscontrava circa un 80% di comorbilità, essenzialmente malattie cardiorespiratorie e obesità. Il tempo mediano tra la comparsa della sindrome influenzale e il trasferimento in rianimazione era di un giorno. I test di diagnosi rapida sono realizzabili a partire da semplici campioni respiratori, ma la loro sensibilità rimane bassa. La durata mediana del ricovero in rianimazione era dell’ordine di 11 giorni. Circa il 70% dei pazienti ha richiesto una ventilazione meccanica (durata mediana di dieci giorni). Oltre il 95% di questi pazienti ha ricevuto un trattamento antivirale e oltre il 95% degli antibiotici, a fronte di un 20% soltanto di infezioni batteriche documentate, soprattutto da Streptococcus pneumoniae e Staphylococcus aureus. La mortalità globale a 28 giorni era del 17%. Il tempo mediano tra la comparsa della sindrome influenzale e il decesso era di 14 giorni. Fra questi decessi, la maggior parte dei pazienti aveva ricevuto un trattamento antivirale, ma non sempre nelle prime 48 ore, il che appare un fattore prognostico infausto. Così, il trattamento antivirale è consigliato nelle forme gravi; il virus pandemico A (H1N1) era sensibile ai due inibitori della neuraminidasi. Sono stati riscontrati dei casi sporadici di resistenza, il che spinge a sviluppare altre molecole attive sui virus influenzali. url: https://www.sciencedirect.com/science/article/pii/S1283077113645028 doi: 10.1016/s1283-0771(13)64502-8 id: cord-325915-dw989txm author: Wolf, Michael W title: Downstream processing of cell culture-derived virus particles date: 2014-01-09 words: 11861.0 sentences: 655.0 pages: flesch: 34.0 cache: ./cache/cord-325915-dw989txm.txt txt: ./txt/cord-325915-dw989txm.txt summary: The number of publications [24, [38] [39] [40] [41] [42] [43] [44] [45] [46] and patents [301] [302] [303] describing the purification or concentration of virus particles by centrifugation methods demonstrates that these procedures are extensively used at industrial-and small-scale levels for viral vectors and vaccine production processes. In summary, the main advantages of ultrafiltration compared with other methods are their high-throughput and (for the concentration of active virus particles) the gentle processing at optimal operating conditions [43, 47] that results in improved efficacies for purification of viral vectors for gene therapy. Considering a complete purification train for the production of vaccines or gene therapy vectors (Figure 1) , current improvements of the dynamic binding capacities in chromatography media might facilitate the removal of the initial concentration step within the downstream process. abstract: Manufacturing of cell culture-derived virus particles for vaccination and gene therapy is a rapidly growing field in the biopharmaceutical industry. The process involves a number of complex tasks and unit operations ranging from selection of host cells and virus strains for the cultivation in bioreactors to the purification and formulation of the final product. For the majority of cell culture-derived products, efforts focused on maximization of bioreactor yields, whereas design and optimization of downstream processes were often neglected. Owing to this biased focus, downstream procedures today often constitute a bottleneck in various manufacturing processes and account for the majority of the overall production costs. For efficient production methods, particularly in sight of constantly increasing economic pressure within human healthcare systems, highly productive downstream schemes have to be developed. Here, we discuss unit operations and downstream trains to purify virus particles for use as vaccines and vectors for gene therapy. url: https://doi.org/10.1586/erv.11.111 doi: 10.1586/erv.11.111 id: cord-327660-p1b07b4t author: Wolf, Yuri I. title: Origins and Evolution of the Global RNA Virome date: 2018-11-27 words: 13927.0 sentences: 658.0 pages: flesch: 45.0 cache: ./cache/cord-327660-p1b07b4t.txt txt: ./txt/cord-327660-p1b07b4t.txt summary: The current RdRp tree topology combined with gene gain-loss reconstruction suggests the following evolutionary scenario for branch 1 ( Fig. 2A) : a levivirus-like ancestor that, like the extant members of the Leviviridae, possessed a capsid protein unrelated to SJR-CP (19, 52) gave rise to naked eukaryotic RNA replicons known as "mitoviruses" and "narnaviruses." These replicons consist of a single RdRp gene (Fig. 2B ) and replicate in mitochondria and in the cytosol of the host cells of fungal and invertebrate hosts, respectively (the latter hosts were identified in metaviromic holobiont analyses) (14, 53) . This genome architecture could hint at an ancestral flavivirus genome that was assembled from genes borrowed from preexisting viruses, one of which possessed a divergent "tombus-like virus" RdRp. Although the origins of branch 3 are murky, major trends in its subsequent evolution clearly included lineage-specific gene capture, starting with helicases and CapEs in the ancestors of the major lineages and followed by diverse genes in smaller groups (Fig. 4B) . abstract: Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants. The recent advances of metaviromics prompted us to perform a detailed phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. The only universal gene among RNA viruses is the gene encoding the RNA-dependent RNA polymerase (RdRp). We developed an iterative computational procedure that alternates the RdRp phylogenetic tree construction with refinement of the underlying multiple-sequence alignments. The resulting tree encompasses 4,617 RNA virus RdRps and consists of 5 major branches; 2 of the branches include positive-sense RNA viruses, 1 is a mix of positive-sense (+) RNA and double-stranded RNA (dsRNA) viruses, and 2 consist of dsRNA and negative-sense (−) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from +RNA viruses on at least two independent occasions, whereas −RNA viruses evolved from dsRNA viruses. Reconstruction of RNA virus evolution using the RdRp tree as the scaffold suggests that the last common ancestors of the major branches of +RNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, in particular, those encoding distinct RNA helicases, enabling replication of larger RNA genomes and facilitating virus genome expression and virus-host interactions. Phylogenomic analysis reveals extensive gene module exchange among diverse viruses and horizontal virus transfer between distantly related hosts. Although the network of evolutionary relationships within the RNA virome is bound to further expand, the present results call for a thorough reevaluation of the RNA virus taxonomy. url: https://www.ncbi.nlm.nih.gov/pubmed/30482837/ doi: 10.1128/mbio.02329-18 id: cord-303186-2hxlx1j2 author: Won, Hokeun title: Generation and protective efficacy of a cold-adapted attenuated genotype 2b porcine epidemic diarrhea virus date: 2019-07-09 words: 8115.0 sentences: 320.0 pages: flesch: 45.0 cache: ./cache/cord-303186-2hxlx1j2.txt txt: ./txt/cord-303186-2hxlx1j2.txt summary: In this study, we generated a cold-adapted live attenuated vaccine candidate (Aram-P29-CA) by short-term passage of a virulent PEDV isolate at successively lower temperatures in Vero cells. In this study, we sought to create a cold-adapted attenuated G2b PEDV low-passage strain by progressively decreasing growth temperatures to 32°C in Vero cells and then attempted to evaluate its protective efficacy on neonatal piglets against virulent PEDV challenge. Overall, the quantities of viruses in the feces of animals of group 2 significantly declined compared to those in group 1, with wide Ct ranges of 34.46-24.34 ( Efficacy of cold-adapted attenuated PEDV vaccine All animals in the parental Aram-P5-infected group were necropsied upon death at 4 or 5 DPI, while piglets in the remaining groups were euthanized at the end of the study for postmortem examinations (Fig. 7) . abstract: The recent emergence and re-emergence of porcine epidemic diarrhea virus (PEDV) underscore the urgent need for the development of novel, safe, and effective vaccines against the prevailing strain. In this study, we generated a cold-adapted live attenuated vaccine candidate (Aram-P29-CA) by short-term passage of a virulent PEDV isolate at successively lower temperatures in Vero cells. Whole genome sequencing identified 12 amino acid changes in the cold-adapted strain with no insertions and deletions throughout the genome. Animal inoculation experiments confirmed the attenuated phenotype of Aram-P29-CA virus in the natural host. Pregnant sows were orally administered P29-CA live vaccines two doses at 2-week intervals prior to parturition, and the newborn piglets were challenged with the parental virus. The oral homologous prime-boost vaccination of P29-CA significantly improved the survival rate of the piglets and notably mitigated the severity of diarrhea and PEDV fecal shedding after the challenge. Furthermore, strong antibody responses to PEDV were detected in the sera and colostrum of immunized sows and in the sera of their offspring. These results demonstrated that the cold-adapted attenuated virus can be used as a live vaccine in maternal vaccination strategies to provide durable lactogenic immunity and confer passive protection to litters against PEDV. url: https://www.ncbi.nlm.nih.gov/pubmed/31364317/ doi: 10.4142/jvs.2019.20.e32 id: cord-276364-zyw5aukk author: Wong, Ho Him title: Manipulation of autophagy by (+) RNA viruses date: 2019-08-08 words: 6884.0 sentences: 360.0 pages: flesch: 33.0 cache: ./cache/cord-276364-zyw5aukk.txt txt: ./txt/cord-276364-zyw5aukk.txt summary: Over the past few decades, a growing body of research has defined the critical role of this pathway in facilitating infection by numerous +RNA RNA viruses, including poliovirus (PV) [7, 8] , Coxsackievirus B3 (CVB3) [9, 10] , CVB4 [11] , Enterovirus 71 (EV71) [12] , Human rhinovirus (HRV) [13] , Foot-and-mouth disease virus (FMDV) [14] , encephalomyocarditis virus (EMCV) [15] , Dengue virus (DENV) [16, 17] , Zika virus (ZIKV) [18, 19] , Hepatitis C virus (HCV) [20] , Mouse hepatitic virus (MHV), Newcastle disease virus (NDV) [21] , Severe and acute respiratory syndrome coronavirus (SARS-CoV) [22] , Chikungunya virus (ChikV) [23] , and Japanese encephalitis virus (JEV) [24] . Delineating the process of viral assembly from replication is technically challenging, especially since both processes would very likely Induces formation of autophagosome-like double-membrane liposomes [112] Summary of Interactions between proteins from positive strand RNA viruses and host autophagy machinery. abstract: Autophagy is an evolutionarily conserved process central to host metabolism. Among its major functions are conservation of energy during starvation, recycling organelles, and turnover of long-lived proteins. Besides, autophagy plays a critical role in removing intracellular pathogens and very likely represents a primordial intrinsic cellular defence mechanism. More recent findings indicate that it has not only retained its ability to degrade intracellular pathogens, but also functions to augment and fine tune antiviral immune responses. Interestingly, viruses have also co-evolved strategies to manipulate this pathway and use it to their advantage. Particularly intriguing is infection-dependent activation of autophagy with positive stranded (+)RNA virus infections, which benefit from the pathway without succumbing to lysosomal degradation. In this review we summarise recent data on viral manipulation of autophagy, with a particular emphasis on +RNA viruses and highlight key unanswered questions in the field that we believe merit further attention. url: https://www.sciencedirect.com/science/article/pii/S1084952118302222 doi: 10.1016/j.semcdb.2019.07.013 id: cord-343963-99rd3o79 author: Wong, Mun-Teng title: Emerging roles of interferon-stimulated genes in the innate immune response to hepatitis C virus infection date: 2014-12-29 words: 17253.0 sentences: 1074.0 pages: flesch: 42.0 cache: ./cache/cord-343963-99rd3o79.txt txt: ./txt/cord-343963-99rd3o79.txt summary: 13, 14 Upon infection by viruses such as HCV, viral RNA is first sensed by cellular pattern recognition receptors (PRRs), and the PRR-mediated recruitment of adaptor proteins and the activation of downstream signaling lead to IFN production. First, we briefly discuss the signaling triggered by the retinoic acid-inducible gene 1-like receptor (RLR) and the Toll-like receptor (TLR), which leads to type I IFN synthesis and IFN-mediated signaling pathway activation, resulting in the expression of a variety of effector ISGs. We also summarize the strategies that HCV uses to escape IFN antiviral surveillance. 156 demonstrated that HCVinduced SG formation is IFN-and PKR-dependent and is inversely correlated with the induction of ISG proteins, such as myxovirus resistance gene A (MxA) and Ub-like (UBL)specific protease 18 (USP18), in HCV-infected cells without affecting the mRNA levels of these ISGs. Furthermore, the SG proteins TIA-1, TIAR and G3BP1 have been shown to play a critical role in HCV replication and infectious virus production. abstract: Infection with hepatitis C virus (HCV), a major viral cause of chronic liver disease, frequently progresses to steatosis and cirrhosis, which can lead to hepatocellular carcinoma. HCV infection strongly induces host responses, such as the activation of the unfolded protein response, autophagy and the innate immune response. Upon HCV infection, the host induces the interferon (IFN)-mediated frontline defense to limit virus replication. Conversely, HCV employs diverse strategies to escape host innate immune surveillance. Type I IFN elicits its antiviral actions by inducing a wide array of IFN-stimulated genes (ISGs). Nevertheless, the mechanisms by which these ISGs participate in IFN-mediated anti-HCV actions remain largely unknown. In this review, we first outline the signaling pathways known to be involved in the production of type I IFN and ISGs and the tactics that HCV uses to subvert innate immunity. Then, we summarize the effector mechanisms of scaffold ISGs known to modulate IFN function in HCV replication. We also highlight the potential functions of emerging ISGs, which were identified from genome-wide siRNA screens, in HCV replication. Finally, we discuss the functions of several cellular determinants critical for regulating host immunity in HCV replication. This review will provide a basis for understanding the complexity and functionality of the pleiotropic IFN system in HCV infection. Elucidation of the specificity and the mode of action of these emerging ISGs will also help to identify novel cellular targets against which effective HCV therapeutics can be developed. url: https://www.ncbi.nlm.nih.gov/pubmed/25544499/ doi: 10.1038/cmi.2014.127 id: cord-330647-w1bpeqzg author: Wong, Samson Sai-Yin title: Ebola virus disease in nonendemic countries date: 2015-05-31 words: 8637.0 sentences: 507.0 pages: flesch: 41.0 cache: ./cache/cord-330647-w1bpeqzg.txt txt: ./txt/cord-330647-w1bpeqzg.txt summary: The largest outbreak of Ebola virus disease (EVD) in history has renewed interest in filoviruses and has provided an unprecedented impetus to the development of new therapeutics and vaccines for this highly lethal infection. Nucleic acid amplification is the diagnostic test of choice because of its high sensitivity (especially in the early phase of illness); its ability to differentiate between different agents of viral hemorrhagic fever; and its relatively lower biohazard, if the viruses are appropriately inactivated; and because antigen and antibody assays are often unavailable in laboratories in nonendemic countries. 119e123 Animal studies also demonstrate the efficacy of favipiravir in the treatment of Junín virus, arenavirus, and EBOV hemorrhagic fevers, and the drug was used to treat human EVD in the 2014 West African epidemic. abstract: The 2014 West African outbreak of Ebola virus disease was unprecedented in its scale and has resulted in transmissions outside endemic countries. Clinicians in nonendemic countries will most likely face the disease in returning travelers, either among healthcare workers, expatriates, or visiting friends and relatives. Clinical suspicion for the disease must be heightened for travelers or contacts presenting with compatible clinical syndromes, and strict infection control measures must be promptly implemented to minimize the risk of secondary transmission within healthcare settings or in the community. We present a concise review on human filoviral disease with an emphasis on issues that are pertinent to clinicians practicing in nonendemic countries. url: https://api.elsevier.com/content/article/pii/S0929664615000637 doi: 10.1016/j.jfma.2015.01.012 id: cord-293387-0m1ngob3 author: Wood, A. title: The action of three antiseptics/disinfectants against enveloped and non-enveloped viruses date: 1998-04-30 words: 2917.0 sentences: 141.0 pages: flesch: 45.0 cache: ./cache/cord-293387-0m1ngob3.txt txt: ./txt/cord-293387-0m1ngob3.txt summary: Four antiseptic/disinfectant solutions with chloroxylenol, benzalkonium chloride, cetrimide/ chlorhexidme and povidone-iodine were also assessed for antiviral effect against human immunodeficiency virus in the presence of whole human blood. Four antiseptic/disinfectant solutions with chloroxylenol, benzalkonium chloride, cetrimide/ chlorhexidine and povidone-iodine were also assessed for antiviral effect against human immunodeficiency virus in the presence of whole human blood. Virucidal activity of the antiseptic/disinfectants in the presence of albumin/ yeast extract The virucidal activity of Dettol, Dettol Hospital Concentrate and Savlon was compared to that of water of standard hardness against all the test viruses. The exception was Dettol Hospital Concentrate (active agent benzalkonium chloride) which was effective in the inactivation of the non-enveloped human coxsackie virus with a reduction of >5 log,,, after the 1 min timepoint. In conclusion, the solutions tested at their recommended concentrations for antiseptic use were very effective in inactivating the non-enveloped viruses, human immunodeficiency virus type 1 and herpes simplex virus type 1 in the presence of significant levels of organic soil. abstract: Abstract The antiviral action of chloroxylenol, benzalkonium chloride and cetrimide/chlorhexidine was assessed against a range of enveloped and non-enveloped human viruses using a suspension test method. Viral suspensions of 106–107 pfu/TCID50 or sfu were prepared in each of the antiseptic/ disinfectant solutions in the presence of a bovine serum/yeast extract mixture to simulate ‘dirty conditions’. During incubation, aliquots were removed at predetermined timepoints up to 10 min to assess the kinetics of inactivation. Results indicate that all products were effective in inactivating the enveloped viruses herpes simplex virus type 1 and human immunodeficiency virus type 1, whilst being ineffective in inactivating human coronavirus, also enveloped, and the non-enveloped viruses. The exception to this was the benzalkonium chloride-based product (Dettol Hospital Concentrate) which was active against the non-enveloped human coxsackie virus. Four antiseptic/disinfectant solutions with chloroxylenol, benzalkonium chloride, cetrimide/ chlorhexidme and povidone-iodine were also assessed for antiviral effect against human immunodeficiency virus in the presence of whole human blood. All four solutions proved to be effective within l min despite the cytotoxic nature of the compounds to the detection system. url: https://api.elsevier.com/content/article/pii/S0195670198900779 doi: 10.1016/s0195-6701(98)90077-9 id: cord-009846-o6wj8z6e author: Wroblewska, Zofia title: Rat tracheal organ culture supports replication of parainfluenza 1 (6/94) virus and promotes 6/94 virus rescue from latently infected human brain cells date: 2005-12-06 words: 2471.0 sentences: 138.0 pages: flesch: 54.0 cache: ./cache/cord-009846-o6wj8z6e.txt txt: ./txt/cord-009846-o6wj8z6e.txt summary: title: Rat tracheal organ culture supports replication of parainfluenza 1 (6/94) virus and promotes 6/94 virus rescue from latently infected human brain cells For example, Cytochalasin treatment of indicator cells has been shown to enhance the rescue of 6/94 virus from latently infected human brain cells [Wroblewska et al, 19781 after cocultivation. For these reasons, we decided to study the replication of 6/94 virus in rat TOC and to determine its applicability for rescue of 6/94 virus from latently infected human brain cell cultures. The ability of rat TOC to promote 6/94 virus rescue from latently infected human brain cells is shown in Table 1 . Transfer of rat TOC that had been cocultivated with normal human brain cells to CV, cells did not result in 6/94 virus detection. TOC provides a favorable growth environment for a large number of viruses as well as a system that is capable of rescuing virus from latently infected human brain cells. abstract: Rat tracheal organ culture (TOC) supported replication of parainfluenza 1 (6/94) virus. Cell‐associated and cell‐free viruses were found after primary infection of TOC. In contrast to other mammalian systems, rat TOC was capable of maintaining 6/94 virus infectivity after primary infection. Rat TOC may be considered a potential indicator system that could be used to detect virus latent in human tissue. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7166323/ doi: 10.1002/jmv.1890030204 id: cord-337673-1nau263l author: Wu, Chang-Jer title: Antiviral applications of RNAi for coronavirus date: 2006-01-24 words: 4329.0 sentences: 253.0 pages: flesch: 52.0 cache: ./cache/cord-337673-1nau263l.txt txt: ./txt/cord-337673-1nau263l.txt summary: Recently, small interfering RNA (siRNA) has shown promise in the protection from viral invasion, as it can inhibit the expression of viral antigens and accessory genes as well as control the transcription and replication of the viral genome. Genes encoding vital proteins in reproducing SARS-CoV virions can be chosen for chemotherapeutic intervention (e.g., those coding for S, 3C-like protease [3CLpro], RNA-dependent RNA polymerase and possibly other gene products involved in viral-protein-mediated processes) [81] first demonstrated that siRNA was able to silence the replicase of SARS-CoV (1a region of the genome) and that this approach was effective in vitro against SARS-CoV. [82] subsequently observed that vector-based siRNAs could inhibit the replication of SARS-CoV, and showed that expression in the plasmid, pSUPER, of siRNAs specifically targeting viral RNA polymerases could block the cytopathic effects of SARS-CoV on Vero cells. [86] showed that three chemically synthesised siRNA duplexes targeting viral RNA polymerases, and one targeting the S gene potently inhibited SARS-CoV infection and replication in fetal rhesus kidney cells (FRhK-4) . abstract: Until the appearance of severe acute respiratory syndrome (SARS), caused by the SARS coronavirus (SARS-CoV) in early 2003, coronavirus infection was not considered to be serious enough to be controlled by either vaccination or specific antiviral therapy. It is now believed that the availability of antiviral drugs effective against SARS-CoV will be crucial for the control of future SARS outbreaks. Recently, RNA interference has been successfully used as a more specific and efficient method for gene silencing. RNA interference induced by small interfering RNA can inhibit the expression of viral antigens and so provides a new approach to the therapy of pathogenic viruses. This review provides an overview of current information on coronavirus and the application of small interfering RNA in viral therapeutics, with particular reference to SARS-CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/16433589/ doi: 10.1517/13543784.15.2.89 id: cord-309635-1tgovkr7 author: Wu, Nicholas C. title: Structural Biology of Influenza Hemagglutinin: An Amaranthine Adventure date: 2020-09-22 words: 5497.0 sentences: 289.0 pages: flesch: 42.0 cache: ./cache/cord-309635-1tgovkr7.txt txt: ./txt/cord-309635-1tgovkr7.txt summary: Hemagglutinin (HA) glycoprotein is an important focus of influenza research due to its role in antigenic drift and shift, as well as its receptor binding and membrane fusion functions, which are indispensable for viral entry. Similarly, RBS of influenza B HA is composed of the 140-loop, 190-helix, and 240-loop, which are structurally equivalent to the 130-loop, 150-loop, and 190-helix Receptor specificity can also continue to evolve when seasonal viruses circulate in the human population, due to natural mutations that are likely a response to immune selection pressure. A broadly neutralizing human monoclonal antibody that recognizes a conserved, novel epitope on the globular head of the influenza H1N1 virus hemagglutinin Broadly neutralizing human antibody that recognizes the receptor-binding pocket of influenza virus hemagglutinin Design of nanoparticulate group 2 influenza virus hemagglutinin stem antigens that activate unmutated ancestor B cell receptors of broadly neutralizing antibody lineages abstract: Hemagglutinin (HA) glycoprotein is an important focus of influenza research due to its role in antigenic drift and shift, as well as its receptor binding and membrane fusion functions, which are indispensable for viral entry. Over the past four decades, X-ray crystallography has greatly facilitated our understanding of HA receptor binding, membrane fusion, and antigenicity. The recent advances in cryo-EM have further deepened our comprehension of HA biology. Since influenza HA constantly evolves in natural circulating strains, there are always new questions to be answered. The incessant accumulation of knowledge on the structural biology of HA over several decades has also facilitated the design and development of novel therapeutics and vaccines. This review describes the current status of the field of HA structural biology, how we got here, and what the next steps might be. url: https://www.ncbi.nlm.nih.gov/pubmed/32971825/ doi: 10.3390/v12091053 id: cord-268645-5op2m7pu author: Wu, Zhiqiang title: Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases date: 2015-08-11 words: 5949.0 sentences: 277.0 pages: flesch: 49.0 cache: ./cache/cord-268645-5op2m7pu.txt txt: ./txt/cord-268645-5op2m7pu.txt summary: However, the understanding of the viral population and the ecological diversity residing in bat populations is unclear, which complicates the determination of the origins of certain EIDs. Here, using bats as a typical wildlife reservoir model, virome analysis was conducted based on pharyngeal and anal swab samples of 4440 bat individuals of 40 major bat species throughout China. Based on the partial genomic sequences of the viruses obtained by the assembly, we designed specific nested primers for PCR or reverse trancriptase-PCR to screen for each virus in individual samples from each bat species (the primer sequences for each virus are available in Supplementary Table S2 ). The diverse BtCoVs were grouped into several novel evolutionary clades that significantly differed from those of all known αand β-CoVs, providing additional evidence to support investigations of the evolution of bat-originated CoVs. With regard to BtParaVs, a previous study has revealed that bats host major mammalian ParaVs in the genera Rubulavirus, Morbillivirus, Henipavirus and the subfamily Pneumovirinae (Drexler et al., 2012) . abstract: Studies have demonstrated that ~60%–80% of emerging infectious diseases (EIDs) in humans originated from wild life. Bats are natural reservoirs of a large variety of viruses, including many important zoonotic viruses that cause severe diseases in humans and domestic animals. However, the understanding of the viral population and the ecological diversity residing in bat populations is unclear, which complicates the determination of the origins of certain EIDs. Here, using bats as a typical wildlife reservoir model, virome analysis was conducted based on pharyngeal and anal swab samples of 4440 bat individuals of 40 major bat species throughout China. The purpose of this study was to survey the ecological and biological diversities of viruses residing in these bat species, to investigate the presence of potential bat-borne zoonotic viruses and to evaluate the impacts of these viruses on public health. The data obtained in this study revealed an overview of the viral community present in these bat samples. Many novel bat viruses were reported for the first time and some bat viruses closely related to known human or animal pathogens were identified. This genetic evidence provides new clues in the search for the origin or evolution pattern of certain viruses, such as coronaviruses and noroviruses. These data offer meaningful ecological information for predicting and tracing wildlife-originated EIDs. url: https://www.ncbi.nlm.nih.gov/pubmed/26262818/ doi: 10.1038/ismej.2015.138 id: cord-307632-x9bxnrtn author: Wu, Zhiqiang title: Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases date: 2018-10-03 words: 7230.0 sentences: 397.0 pages: flesch: 50.0 cache: ./cache/cord-307632-x9bxnrtn.txt txt: ./txt/cord-307632-x9bxnrtn.txt summary: Five virus strains identified from Microtus clarkei, Eothenomys inez, Eothenomys melanogaster, Myodes rufocanus, and Cricetulus longicaudatus in five provinces appeared to be closely related to porcine reproductive and respiratory syndrome virus (PRRSV) with higher sequence similarity than those with other members of the family Arteriviridae (60.1-73.7% versus 25.7-54.2% aa identity for ORF1b, compared with equine arteritis virus, lactate dehydrogenase-elevating virus (LDV) of mice, simian hemorrhagic fever virus, and wobbly possum disease virus; Additional file 1: Table S6 ). Pairwise similarity and phylogenetic analysis ( Fig. 5a and Additional file 3: Figure S6 ) revealed that 29 viruses formed diverse evolutionary clades in lineage A under the genus Betacoronavirus, with sequence identities between 88.1 and 98.9% (RdRp aa identity). abstract: BACKGROUND: Rodents represent around 43% of all mammalian species, are widely distributed, and are the natural reservoirs of a diverse group of zoonotic viruses, including hantaviruses, Lassa viruses, and tick-borne encephalitis viruses. Thus, analyzing the viral diversity harbored by rodents could assist efforts to predict and reduce the risk of future emergence of zoonotic viral diseases. RESULTS: We used next-generation sequencing metagenomic analysis to survey for a range of mammalian viral families in rodents and other small animals of the orders Rodentia, Lagomorpha, and Soricomorpha in China. We sampled 3,055 small animals from 20 provinces and then outlined the spectra of mammalian viruses within these individuals and the basic ecological and genetic characteristics of novel rodent and shrew viruses among the viral spectra. Further analysis revealed that host taxonomy plays a primary role and geographical location plays a secondary role in determining viral diversity. Many viruses were reported for the first time with distinct evolutionary lineages, and viruses related to known human or animal pathogens were identified. Phylogram comparison between viruses and hosts indicated that host shifts commonly happened in many different species during viral evolutionary history. CONCLUSIONS: These results expand our understanding of the viromes of rodents and insectivores in China and suggest that there is high diversity of viruses awaiting discovery in these species in Asia. These findings, combined with our previous bat virome data, greatly increase our knowledge of the viral community in wildlife in a densely populated country in an emerging disease hotspot. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s40168-018-0554-9) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s40168-018-0554-9 doi: 10.1186/s40168-018-0554-9 id: cord-354035-i3sl2r0k author: Wylie, Kristine M. title: The Virome of the Human Respiratory Tract date: 2016-12-10 words: 3901.0 sentences: 215.0 pages: flesch: 46.0 cache: ./cache/cord-354035-i3sl2r0k.txt txt: ./txt/cord-354035-i3sl2r0k.txt summary: Sensitive, culture-independent molecular assays (polymerase chain reaction and high-throughput sequencing) reveal that in addition to common viruses that cause acute, symptomatic infections the virome also includes viruses that do not cause clinical symptoms, have unknown pathogenic effect, or cause symptoms but are not among the most common viral respiratory tract pathogens. However, as characterization of the respiratory tract virome using molecular methods is a relatively new area of exploration, these studies can be useful in order to determine if viruses beyond the common, known respiratory pathogens are detected. In a study of 71 patients, viruses were assessed in nasal swabs using a panel of targeted PCR assays for common respiratory pathogens. Another study tested 89 nasopharyngeal swabs from adults with upper respiratory tract infections using reverse transcription (RT)-PCR assays for a series of common viruses, including human rhinoviruses, coronaviruses, influenza viruses and others, and by RNA sequencing. abstract: The human respiratory tract virome is defined here as the viruses present in the human respiratory tract that can infect human cells. Sensitive, culture-independent molecular assays (polymerase chain reaction and high-throughput sequencing) reveal that in addition to common viruses that cause acute, symptomatic infections the virome also includes viruses that do not cause clinical symptoms, have unknown pathogenic effect, or cause symptoms but are not among the most common viral respiratory tract pathogens. These molecular tools provide means for better defining the virome and studying the effects of viral infections on the dynamics of chronic lung diseases. url: https://doi.org/10.1016/j.ccm.2016.11.001 doi: 10.1016/j.ccm.2016.11.001 id: cord-352200-i05h8csb author: Xu, Yi title: Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus date: 2012-04-27 words: 5286.0 sentences: 278.0 pages: flesch: 47.0 cache: ./cache/cord-352200-i05h8csb.txt txt: ./txt/cord-352200-i05h8csb.txt summary: title: Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus METHODOLOGY/PRINCIPAL FINDINGS: By de novo transcriptome assembling and massive parallel pyrosequencing, we constructed two transcriptomes of WBPH and profiled the alternation of gene expression in response to SRBSDV infection in transcriptional level. As a whole, 81388 distinct unigenes have been identified and the results indicated that SRBSDV infection can potentially perturb primary metabolism and the ubiquitin-proteasome pathway of WBPH and activate immune regulatory systems, such as RNA interfering, autophagy and antimicrobial peptide production. However, some unigenes were obtained only from viruliferous or non-viruliferous samples (data not shown) and we believe these differences may be caused by distinctions that arise from long-term ecological adaptation to virus infection. In addition, GO analysis also showed a similar distribution of gene functions for non-viruliferous and viruliferous WBPH (Figure 4 ), indicating that the number of genes expressed in each GO category was not significantly affected by SRBSDV infection. abstract: BACKGROUND: The white backed planthopper (WBPH), Sogatella furcifera (Horváth), causes great damage to many crops by direct feeding or transmitting plant viruses. Southern rice black-streaked dwarf virus (SRBSDV), transmitted by WBPH, has become a great threat to rice production in East Asia. METHODOLOGY/PRINCIPAL FINDINGS: By de novo transcriptome assembling and massive parallel pyrosequencing, we constructed two transcriptomes of WBPH and profiled the alternation of gene expression in response to SRBSDV infection in transcriptional level. Over 25 million reads of high-quality DNA sequences and 81388 different unigenes were generated using Illumina technology from both viruliferous and non-viruliferous WBPH. WBPH has a very similar gene ontological distribution to other two closely related rice planthoppers, Nilaparvata lugens and Laodelphax striatellus. 7291 microsatellite loci were also predicted which could be useful for further evolutionary analysis. Furthermore, comparative analysis of the two transcriptomes generated from viruliferous and non-viruliferous WBPH provided a list of candidate transcripts that potentially were elicited as a response to viral infection. Pathway analyses of a subset of these transcripts indicated that SRBSDV infection may perturb primary metabolism and the ubiquitin-proteasome pathways. In addition, 5.5% (181 out of 3315) of the genes in cell cytoskeleton organization pathway showed obvious changes. Our data also demonstrated that SRBSDV infection activated the immunity regulatory systems of WBPH, such as RNA interference, autophagy and antimicrobial peptide production. CONCLUSIONS/SIGNIFICANCE: We employed massively parallel pyrosequencing to collect ESTs from viruliferous and non-viruliferous samples of WBPH. 81388 different unigenes have been obtained. We for the first time described the direct effects of a Reoviridae family plant virus on global gene expression profiles of its insect vector using high-throughput sequencing. Our study will provide a road map for future investigations of the fascinating interactions between Reoviridae viruses and their insect vectors, and provide new strategies for crop protection. url: https://www.ncbi.nlm.nih.gov/pubmed/22558400/ doi: 10.1371/journal.pone.0036238 id: cord-262748-v4xue7ha author: Xu, Yongtao title: Identification of Peptide Inhibitors of Enveloped Viruses Using Support Vector Machine date: 2015-12-04 words: 4636.0 sentences: 253.0 pages: flesch: 40.0 cache: ./cache/cord-262748-v4xue7ha.txt txt: ./txt/cord-262748-v4xue7ha.txt summary: Here we developed a support vector machine model using sequence-based statistical scores of self-derived peptide inhibitors as input features to correlate with their activities. The predictive support vector machine model for selfderived peptides of envelope proteins would be useful in development of antiviral peptide inhibitors targeting the virus fusion process. In view of the important role of E proteins in virus fusion process and common mechanism of action of self-derived peptides, we developed a SVM model to predict the antiviral activities of self-derived peptides using sequence-based statistical scores as input features. Because similar sequences are often associated with similar structure and function, the sequence-based property AVPalign would account for the activities of the self-derived peptide inhibitors which regulate the virus fusion by mimicking the binding to E proteins. The prominent performance of EAPscoring model indicates the sequence-based stability feature of self-derived peptides may reflect their potential of binding to E proteins so as to regulate the virus entry process. abstract: The peptides derived from envelope proteins have been shown to inhibit the protein-protein interactions in the virus membrane fusion process and thus have a great potential to be developed into effective antiviral therapies. There are three types of envelope proteins each exhibiting distinct structure folds. Although the exact fusion mechanism remains elusive, it was suggested that the three classes of viral fusion proteins share a similar mechanism of membrane fusion. The common mechanism of action makes it possible to correlate the properties of self-derived peptide inhibitors with their activities. Here we developed a support vector machine model using sequence-based statistical scores of self-derived peptide inhibitors as input features to correlate with their activities. The model displayed 92% prediction accuracy with the Matthew’s correlation coefficient of 0.84, obviously superior to those using physicochemical properties and amino acid decomposition as input. The predictive support vector machine model for self- derived peptides of envelope proteins would be useful in development of antiviral peptide inhibitors targeting the virus fusion process. url: https://www.ncbi.nlm.nih.gov/pubmed/26636321/ doi: 10.1371/journal.pone.0144171 id: cord-018706-gykw2nvt author: Yadav, Mahendra Pal title: Emerging and Transboundary Animal Viral Diseases: Perspectives and Preparedness date: 2020-02-23 words: 9686.0 sentences: 390.0 pages: flesch: 41.0 cache: ./cache/cord-018706-gykw2nvt.txt txt: ./txt/cord-018706-gykw2nvt.txt summary: The factors driving the emergence of different emerging infectious disease (EID) interfaces include global travel, urbanisation and biomedical manipulations for human EIDs; agricultural intensification for domestic animal EIDs; translocation for wildlife EIDs; human encroachment, ex situ contact and ecological manipulation for wildlife–human EIDs; encroachment, new introductions and ''spill-over'' and ''spill-back''; and technology and industry for domestic animal–human EIDs. The concepts of sanitary and phytosanitary (SPS) measures and biosecurity have gained recognition globally in almost all the realms of human activities, including livestock health and production management. Among the TADs having zoonotic manifestations, a number of infectious diseases, such as highly pathogenic avian influenza (HPAI), BSE (Mad cow disease caused by prion), West Nile fever, Rift Valley fever, SARS coronavirus, Hendra virus, Nipah virus, Ebola virus, Zika virus and CCHF, to name a few, adversely affecting animal and human health have been in the news in recent times (Malik and Dhama 2015; Munjal et al. abstract: The epidemics and pandemics of a few infectious diseases during the past couple of decades have accentuated the significance of emerging infectious diseases (EIDs) due to their influence on public health. Although Asia region has been identified as the epicentre of many EIDs and upcoming infections, several new pathogens have also emerged in the past in other parts of the world. Furthermore, the emergence of new viral diseases/infections, such as Rift Valley fever, West Nile fever, SARS coronavirus, Hendra virus, avian influenza A (H5N1), Nipah virus, Zika virus and swine influenza A (H1N1) virus, from time to time is a glaring example threatening adversely both animal and public health globally. Infectious diseases are dynamic and concerning due to their epidemiology and aetiological agents, which is manifested within a host, pathogen and environment continuum involving domestic animals, wildlife and human populations. The complex relationship among host populations and other environmental factors creates conditions for the emergence of diseases. The factors driving the emergence of different emerging infectious disease (EID) interfaces include global travel, urbanisation and biomedical manipulations for human EIDs; agricultural intensification for domestic animal EIDs; translocation for wildlife EIDs; human encroachment, ex situ contact and ecological manipulation for wildlife–human EIDs; encroachment, new introductions and ‘spill-over’ and ‘spill-back’; and technology and industry for domestic animal–human EIDs. The concepts of sanitary and phytosanitary (SPS) measures and biosecurity have gained recognition globally in almost all the realms of human activities, including livestock health and production management. This chapter provides the experience gained in the control and management of a few important TADs and EIDs along with the successes, constraints, limitations and future research needs for developing better control approaches. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123659/ doi: 10.1007/978-981-15-0402-0_1 id: cord-276052-gk6n8slx author: Yadav, Pragya title: Isolation of Tioman virus from Pteropus giganteus bat in North-East region of India date: 2016-09-09 words: 3005.0 sentences: 164.0 pages: flesch: 51.0 cache: ./cache/cord-276052-gk6n8slx.txt txt: ./txt/cord-276052-gk6n8slx.txt summary: During the survey for Nipah virus among bats at North-East region of India; Tioman virus (TioV), a new member of the Paramyxoviridae family was isolated from tissues of Pteropus giganteus bats for the first time in India. While investigating NiV in urine samples of giant fruit bats of the Pteropus genus on Tioman Island, Malaysia, in 2001, researchers isolated a novel virus which was placed in the Rubulavirus genus of the Paramyxoviridae family. In order to study susceptibility of different vertebrate cells to TioV, the infectious virus titer was determined by estimating 50% tissue culture infective dose (TCID 50 ) using Reed and Muench method (Reed and Muench, 1938) . Negative contrast electron microscopy of the cell supernatant of Vero CCL-81 infected with virus isolate showed the presence of virus particles with the typical paramyxovirus morphology. TioV isolated from kidney tissue homogenate of bat showed a titer of 10 4.61 /100 μL by TCID 50 in Vero CCL-81 cell line. abstract: Bat-borne viral diseases are a major public health concern among newly emerging infectious diseases which includes severe acute respiratory syndrome, Nipah, Marburg and Ebola virus disease. During the survey for Nipah virus among bats at North-East region of India; Tioman virus (TioV), a new member of the Paramyxoviridae family was isolated from tissues of Pteropus giganteus bats for the first time in India. This isolate was identified and confirmed by RT-PCR, sequence analysis and electron microscopy. A range of vertebrate cell lines were shown to be susceptible to Tioman virus. Negative electron microscopy study revealed the “herringbone” morphology of the nucleocapsid filaments and enveloped particles with distinct envelope projections a characteristic of the Paramyxoviridae family. Sequence analysis of Nucleocapsid gene of TioV demonstrated sequence identity of 99.87% and 99.99% nucleotide and amino acid respectively with of TioV strain isolated in Malaysia, 2001. This report demonstrates the first isolation of Tioman virus from a region where Nipah virus activity has been noticed in the past and recent years. Bat-borne viruses have become serious concern world-wide. A Survey of bats for novel viruses in this region would help in recognizing emerging viruses and combating diseases caused by them. url: https://api.elsevier.com/content/article/pii/S1567134816303926 doi: 10.1016/j.meegid.2016.09.010 id: cord-014908-jys1y0k9 author: Yadav, Rakesh title: Trends and Perspectives of Biosensors for Food and Environmental Virology date: 2010-05-19 words: 5113.0 sentences: 259.0 pages: flesch: 32.0 cache: ./cache/cord-014908-jys1y0k9.txt txt: ./txt/cord-014908-jys1y0k9.txt summary: Unluckily, the PCR-based tools do not persistently amplify nucleic acids if viruses are found in infected food or environmental samples at critically low level. Another successful innovative biosensor with combined microfluidics and biosensing capabilities, furnish real time and automated affinity bioanalysis (e.g. for antigen-antibody assays) through surface plasmon resonance (SPR)-based original optical transduction mechanism. Since molecular recognition trait is central in the biosensing systems, all the structural components can be targeted to device a biosensor for detection of the specific virion particles present in food and environment samples. Molecular nanotechnology-based new nanostructures/nanomaterials such as aptamers are capable for developing highly specific biosensor for target elements detection. DNA-based biosensors have great applications in food and environmental analysis including determination of the pathogenic bacteria , and virus DNA sequence such as that of SARS virus (Abad-Valle et al. Quartz crystal microbalance (QCM)-based piezoelectric sensors can detect the hybridized viral DNA and also the capsid protein-ligand interactions. abstract: Food and environmental virology has become a very important and interesting area of research because of food safety and public health concerns. During the last few decades, increasing foodborne diseases and environmental generated illnesses are considered to be highly challenging issues. Biosensor technology holds great promise for the healthcare market, and the security sector. Similar to clinical diagnostic tools, biosensors are being developed for the rapid, reliable, yet inexpensive identification and enumeration of pathogenic viruses which are adulterating environment, food and feed commodities. In this modern era, bio-and nano-technologies play a pivotal role in virological diagnostics of food industry, environmental and veterinary samples. This review covers the recent advances and future prospects of nanotechnology-based bioanalytical microsystems for food and environmental virology. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7090531/ doi: 10.1007/s12560-010-9034-5 id: cord-010189-makhaypd author: Yamashita, Teruo title: VI, 3. Molecular biology and epidemiology of Aichi virus and other diarrhoeogenic enteroviruses date: 2004-09-14 words: 3009.0 sentences: 157.0 pages: flesch: 50.0 cache: ./cache/cord-010189-makhaypd.txt txt: ./txt/cord-010189-makhaypd.txt summary: Stool samples from adult patients in six oyster-associated gastroenteritis outbreaks were examined for variation, based on their reactivity with a monoclonal antibody raised against the standard strain (A486/88) and on reverse transcription–polymerase chain reactions (RT-PCR) of three genomic regions. Aichi virus was isolated in Vero cells from 7 (12.5%) of 56 patients in 6 gastroenteritis outbreaks, 5 (0.7%) of 722 Japanese travelers returning from tours to Southeast Asian countries and complaining of gastrointestinal symptoms at the quarantine station of Nagoya International Airport in Japan, and 5(2.3%) of 222 Pakistani children with gastroenteritis (Yamashita et al., 1993; Yamashita et al., 1995) . In the ELISA, 15 (26.8%) of 56 stool samples from adult patients in six oyster-associated gastroenteritis outbreaks were found to be positive for Aichi virus. The Aichi virus RNA was detected in 54 (55%) of 99 fecal specimens from patients in 12 (32%) of 37 outbreaks of gastroenteritis in Japan. abstract: The virion of the Aichi virus contains a single-stranded RNA molecule as the genome. The homology of Aichi virus structural proteins (VP0, VP3, and VP1) with corresponding polypeptides of other picornaviruses varies between 19% and 32%. The epidemiology of the Aichi virus as a medically important pathogen has not been well defined. Stool samples from adult patients in six oyster-associated gastroenteritis outbreaks were examined for variation, based on their reactivity with a monoclonal antibody raised against the standard strain (A486/88) and on reverse transcription–polymerase chain reactions (RT-PCR) of three genomic regions. Antibody to the Aichi virus could be detected using a neutralization test and an enzyme-linked immunosorbent assay (ELISA). These methods were used for the identification of Aichi virus infection in paired serum samples. The chapter concludes with a discussion on other diarrheagenic enteroviruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172506/ doi: 10.1016/s0168-7069(03)09040-2 id: cord-277107-gs7j6fxo author: Yamin, Mohammad title: Counting the cost of COVID-19 date: 2020-05-13 words: 4178.0 sentences: 236.0 pages: flesch: 64.0 cache: ./cache/cord-277107-gs7j6fxo.txt txt: ./txt/cord-277107-gs7j6fxo.txt summary: Coronavirus disease 2019 (COVID-19) is the name given by the World Health Organization (WHO) to the highly contagious and infectious disease caused by the Novel Corona Virus or SARS-CoV-2, which was first reported on 31 December 2019 in Wuhan city of the capital of China''s Hubei province. In recent years we have witnessed an increased growth and spread of communicable and highly contagious viruses and diseases like EBOLA [3] , HIV Aids [4] , Swine Influenza (H1N1, H1N2) [5] , various strands of Flu [6] , Severe Acute Respiratory Syndrome (SARS) [7] and Middle Eastern Respiratory Syndrome (MERS) [8] in Africa, the Middle East and several other parts of the world. The coronavirus disease COVID-19 is a highly transmittable and pathogenic viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ( Fig. 1) , which is resulting in a heavy toll on people''s lives and colossal economic damage. abstract: Coronavirus disease 2019 (COVID-19) is the name given by the World Health Organization (WHO) to the highly contagious and infectious disease caused by the Novel Corona Virus or SARS-CoV-2, which was first reported on 31 December 2019 in Wuhan city of the capital of China's Hubei province. Due to the rapid increase in the number of infections worldwide, the WHO in March 2020, declared COVID-19 as a pandemic. Historically, first coronavirus had surfaced in 1965 with symptoms of common cold. Since then five different strands of this virus have emerged, most lethal of them was the Severe Acute Respiratory Syndrome (SARS), which infected about eight thousand people, killing ten percent of them. The COVID-19 is not the most deadly pandemic world has ever witnessed as the Spanish influenza pandemic, during 1918–19, killed more than fifty million people. Indeed COVID-19 has turned out to be the most lethal of all coronaviruses as it has infected at least three million people killing more than two hundred thousands of them in the first 4 months of its spread. Many politicians and social scientists have dubbed the depression, being caused by COVID-19, worse than that caused by the Second World War. In this article, we shall analyze economic, social, cultural, educational and political impact of the COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32412538/ doi: 10.1007/s41870-020-00466-0 id: cord-308385-bcph664h author: Yan, Zishuo title: Modeling COVID-19 infection in a confined space date: 2020-07-15 words: 3529.0 sentences: 182.0 pages: flesch: 57.0 cache: ./cache/cord-308385-bcph664h.txt txt: ./txt/cord-308385-bcph664h.txt summary: In our model, states of individuals with diverse physiological conditions are subject to dynamic changes according to their interaction with viruses in a closed environment, where spatial factors play an essential role in that the spreading of the virus and the infection of human are tightly correlated in both space and time. Based on the SEIR model, Joseph T Wu [7] estimated the basic regeneration number as 2.68 and the doubling time as 6.4 days; Qun Li [18] analyzed data on the first 425 confirmed cases in the early stage and found that the epidemic is doubled in size every 7.4 days with a mean serial interval of 7.5 days. Through the newly constructed virus infection model, we provide useful guidance for effective prevention and control of the COVID-19 spreading, such as restricting the movement of people and placing the ventilation opening in the right position, reducing the releasing of the virus and the contact of susceptibles with unfriendly environment. abstract: In this paper, we construct a stochastic model of the 2019-nCoV transmission in a confined space, which gives a detailed account of the interaction between the spreading virus and mobile individuals. Different aspects of the interaction at mesoscopic level, such as the human motion, the shedding and spreading of the virus, its contamination and invasion of the human body and the response of the human immune system, are touched upon in the model, their relative importance during the course of infection being evaluated. The model provides a bridge linking the epidemic statistics to the physiological parameters of individuals and may serve a theoretical guidance for epidemic prevention and control. url: https://doi.org/10.1007/s11071-020-05802-4 doi: 10.1007/s11071-020-05802-4 id: cord-254090-x8tnweih author: Yang, Szu-Chi title: Efficient Structure Resonance Energy Transfer from Microwaves to Confined Acoustic Vibrations in Viruses date: 2015-12-09 words: 6073.0 sentences: 302.0 pages: flesch: 53.0 cache: ./cache/cord-254090-x8tnweih.txt txt: ./txt/cord-254090-x8tnweih.txt summary: It is interesting to notice that the required threshold electric field magnitudes at the resonant frequency (86.9 V/m) to fracture H3N2 viruses as shown in Fig. 3 (c) are within the IEEE Microwave Safety Standard (106 V/m), indicating high SRET efficiency, even though the quality factor of the H3N2 virus is low. To further investigate the efficiency of this SRET effect from microwave to virus and the threshold effect, we further measured the inactivation ratio of H3N2 virus with different power densities at the resonant frequency ~8 GHz of the confined acoustic dipolar mode. Second, at the resonant frequency, we do observe H3N2 virus inactivation by illuminating 82 W/m 2 (lower than the IEEE safety standard in public space) 8 GHz microwaves on our viral solution, corresponding to an average 87 V/m electric field intensity inside the solution, confirming that our proposed simple model to estimate the field threshold (86.9 V/m) to structurally fracture the virus is quantitatively correct, especially combining the observed threshold effect as discussed above. abstract: Virus is known to resonate in the confined-acoustic dipolar mode with microwave of the same frequency. However this effect was not considered in previous virus-microwave interaction studies and microwave-based virus epidemic prevention. Here we show that this structure-resonant energy transfer effect from microwaves to virus can be efficient enough so that airborne virus was inactivated with reasonable microwave power density safe for the open public. We demonstrate this effect by measuring the residual viral infectivity of influenza A virus after illuminating microwaves with different frequencies and powers. We also established a theoretical model to estimate the microwaves power threshold for virus inactivation and good agreement with experiments was obtained. Such structure-resonant energy transfer induced inactivation is mainly through physically fracturing the virus structure, which was confirmed by real-time reverse transcription polymerase chain reaction. These results provide a pathway toward establishing a new epidemic prevention strategy in open public for airborne virus. url: https://www.ncbi.nlm.nih.gov/pubmed/26647655/ doi: 10.1038/srep18030 id: cord-355259-779czzzx author: Yang, Xiaoyun title: A Beneficiary Role for Neuraminidase in Influenza Virus Penetration through the Respiratory Mucus date: 2014-10-15 words: 6143.0 sentences: 324.0 pages: flesch: 47.0 cache: ./cache/cord-355259-779czzzx.txt txt: ./txt/cord-355259-779czzzx.txt summary: Swine influenza virus (SIV) has a strong tropism for pig respiratory mucosa, which consists of a mucus layer, epithelium, basement membrane and lamina propria. The microscopic diffusion of SIV particles in the mucus was analyzed by single particle tracking (SPT), and the macroscopic penetration of SIV through mucus was studied by a virus in-capsule-mucus penetration system, followed by visualizing the translocation of the virions with time by immunofluorescence staining. These findings clearly show that the neuraminidase helps SIV move through the mucus, which is important for the virus to reach and infect epithelial cells and eventually become shed into the lumen of the respiratory tract. To this purpose, we applied swine influenza virus to a model we previously set up using porcine respiratory mucus, pseudorabies virus (PRV) and single particle tracking (SPT) [20] . This does not only confirm the beneficial effect of neuraminidase on releasing SIV from respiratory mucus, but also highlights bidirectional synergistic interactions between influenza virus and bacterial infections. abstract: Swine influenza virus (SIV) has a strong tropism for pig respiratory mucosa, which consists of a mucus layer, epithelium, basement membrane and lamina propria. Sialic acids present on the epithelial surface have long been considered to be determinants of influenza virus tropism. However, mucus which is also rich in sialic acids may serve as the first barrier of selection. It was investigated how influenza virus interacts with the mucus to infect epithelial cells. Two techniques were applied to track SIV H1N1 in porcine mucus. The microscopic diffusion of SIV particles in the mucus was analyzed by single particle tracking (SPT), and the macroscopic penetration of SIV through mucus was studied by a virus in-capsule-mucus penetration system, followed by visualizing the translocation of the virions with time by immunofluorescence staining. Furthermore, the effects of neuraminidase on SIV getting through or binding to the mucus were studied by using zanamivir, a neuraminidase inhibitor (NAI), and Arthrobacter ureafaciens neuraminidase. The distribution of the diffusion coefficient shows that 70% of SIV particles were entrapped, while the rest diffused freely in the mucus. Additionally, SIV penetrated the porcine mucus with time, reaching a depth of 65 µm at 30 min post virus addition, 2 fold of that at 2 min. Both the microscopic diffusion and macroscopic penetration were largely diminished by NAI, while were clearly increased by the effect of exogenous neuraminidase. Moreover, the exogenous neuraminidase sufficiently prevented the binding of SIV to mucus which was reversely enhanced by effect of NAI. These findings clearly show that the neuraminidase helps SIV move through the mucus, which is important for the virus to reach and infect epithelial cells and eventually become shed into the lumen of the respiratory tract. url: https://doi.org/10.1371/journal.pone.0110026 doi: 10.1371/journal.pone.0110026 id: cord-297662-slmlhqnb author: Yap, Sally S. L. title: Dengue Virus Glycosylation: What Do We Know? date: 2017-07-25 words: 11116.0 sentences: 526.0 pages: flesch: 48.0 cache: ./cache/cord-297662-slmlhqnb.txt txt: ./txt/cord-297662-slmlhqnb.txt summary: In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis. Since high mannose binding DC-SIGN interacts only with N67 glycans on the viral surface (Pokidysheva et al., 2006) and N153-glycan is dispensable for virus production in mosquito and mammalian cells (Bryant et al., 2007) , this suggests that N153 glycans may serve a distinct function from N67 glycans in DEN pathogenesis possibly via interaction with an unknown fucose binder or act as a viral glycan shield. Finally, N153 deglycosylated (N153 − ) DENV mutant displayed reduced infectivity (10-fold lower) in both mammalian and mosquito cells compared to WT, possibly due to impaired virus entry process (Lee et al., 1997; Hacker et al., 2009) , whereby loss of the N153-glycan affected the conformational stability of E proteins and led to premature exposure of the fusion peptide (Yoshii et al., 2013) . N-linked glycosylation of dengue virus NS1 protein modulates secretion, cell-surface expression, hexamer stability, and interactions with human complement abstract: In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis. url: https://doi.org/10.3389/fmicb.2017.01415 doi: 10.3389/fmicb.2017.01415 id: cord-322748-a5131tv9 author: Yates, Mary K. title: Flex-nucleoside analogues – Novel therapeutics against filoviruses date: 2017-06-15 words: 1492.0 sentences: 78.0 pages: flesch: 53.0 cache: ./cache/cord-322748-a5131tv9.txt txt: ./txt/cord-322748-a5131tv9.txt summary: Most recently GS-5734, a monophosphoramidate prodrug adenosine analogue which targets EBOV RNA-dependent RNA polymerase (RdRp), exhibited very potent activity against both EBOV and MARV, 17, 18 further demonstrating the potential for finding effective nucleoside inhibitors of filoviruses. After the successful synthesis of the three Flex-analogues 1, 2, and 3, the compounds were screened against a panel of filoviruses including EBOV, MARV, and SUDV, as well as other hemorrhagic fever viruses such as Lassa and Rift Valley Fever. The second series of assays utilized Huh7 cells infected with recombinant reporter EBOV, Lassa, and Rift Valley Fever viruses. Within this study we found that both compounds 1 and 3 exhibited antiviral activity against a recombinant reporter EBOV in Huh7 cells, though surprisingly the McGuigan prodrug was 10-fold less potent (EC 50 = 2.2 ± 0.3 lM and 27.2 ± 2.2 lM respectively). abstract: Abstract Fleximers, a novel type of flexible nucleoside that have garnered attention due to their unprecedented activity against human coronaviruses, have now exhibited highly promising levels of activity against filoviruses. The Flex-nucleoside was the most potent against recombinant Ebola virus in Huh7 cells with an EC50 =2μM, while the McGuigan prodrug was most active against Sudan virus-infected HeLa cells with an EC50 of 7μM. url: https://www.ncbi.nlm.nih.gov/pubmed/28465098/ doi: 10.1016/j.bmcl.2017.04.069 id: cord-003961-gs75ebo4 author: Yin, Xin title: Hepatitis E Virus Entry date: 2019-09-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Hepatitis E virus (HEV) infection is a major cause of acute hepatitis worldwide. It is transmitted enterically but replicates in the liver. Recent studies indicate that HEV exists in two forms: naked, nonenveloped virions that are shed into feces to mediate inter-host transmission, and membrane-cloaked, quasienveloped virions that circulate in the bloodstream to mediate virus spread within a host. Both virion types are infectious, but differ in the way they infect cells. Elucidating the entry mechanism for both virion types is essential to understand HEV biology and pathogenesis, and is relevant to the development of treatments and preventions for HEV. This review summarizes the current understanding of the cell entry mechanism for these two HEV virion types. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6832200/ doi: 10.3390/v11100883 id: cord-255137-utg8k7qs author: Yinda, Claude Kwe title: Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses date: 2019-01-23 words: 9528.0 sentences: 861.0 pages: flesch: 51.0 cache: ./cache/cord-255137-utg8k7qs.txt txt: ./txt/cord-255137-utg8k7qs.txt summary: Previously, we identified a plethora of known and novel eukaryotic viruses in Cameroonian fruit bats using a viral metagenomics approach, including viruses known to cause gastroenteritis in humans (sapovirus, sapelovirus, and rotaviruses A and H) and Astroviridae (Mamastrovirus), Calciviridae (Sapovirus), Picornaviridae (Parechovirus), and Reoviridae (Rotavirus), viral families known to cause gastroenteritis in humans, were identified in both bat and human pools from the same region. In this study, we focused on viruses from which near-complete genomes were obtained, particularly those that are known to cause viral gastroenteritis (belonging to the Astroviridae, Caliciviridae [norovirus and sapovirus] , Picornaviridae [enterovirus, parechovirus, cosavirus] , Parvoviridae, Reoviridae, and Adenoviridae [human mastadenovirus]). Recently, we thoroughly investigated the gut virome of fruit bats from Cameroon (20) (21) (22) (23) 63) and showed the presence of many novel and divergent eukaryotic viral families, including viruses known to cause gastroenteritis in humans. abstract: Diarrhea remains one of the most common causes of deaths in children. A limited number of studies have investigated the prevalence of enteric pathogens in Cameroon, and as in many other African countries, the cause of many diarrheal episodes remains unexplained. A proportion of these unknown cases of diarrhea are likely caused by yet-unidentified viral agents, some of which could be the result of (recent) interspecies transmission from animal reservoirs, like bats. Using viral metagenomics, we screened fecal samples of 221 humans (almost all with gastroenteritis symptoms) between 0 and 89 years of age with different degrees of bat contact. We identified viruses belonging to families that are known to cause gastroenteritis such as Adenoviridae, Astroviridae, Caliciviridae, Picornaviridae, and Reoviridae. Interestingly, a mammalian orthoreovirus, picobirnaviruses, a smacovirus, and a pecovirus were also found. Although there was no evidence of interspecies transmission of the most common human gastroenteritis-related viruses (Astroviridae, Caliciviridae, and Reoviridae), the phylogenies of the identified orthoreovirus, picobirnavirus, and smacovirus indicate a genetic relatedness of these viruses identified in stools of humans and those of bats and/or other animals. These findings points out the possibility of interspecies transmission or simply a shared host of these viruses (bacterial, fungal, parasitic, …) present in both animals (bats) and humans. Further screening of bat viruses in humans or vice versa will elucidate the epidemiological potential threats of animal viruses to human health. Furthermore, this study showed a huge diversity of highly divergent novel phages, thereby expanding the existing phageome considerably. IMPORTANCE Despite the availability of diagnostic tools for different enteric viral pathogens, a large fraction of human cases of gastroenteritis remains unexplained. This could be due to pathogens not tested for or novel divergent viruses of potential animal origin. Fecal virome analyses of Cameroonians showed a very diverse group of viruses, some of which are genetically related to those identified in animals. This is the first attempt to describe the gut virome of humans from Cameroon. Therefore, the data represent a baseline for future studies on enteric viral pathogens in this area and contribute to our knowledge of the world’s virome. The studies also highlight the fact that more viruses may be associated with diarrhea than the typical known ones. Hence, it provides meaningful epidemiological information on diarrhea-related viruses in this area. url: https://www.ncbi.nlm.nih.gov/pubmed/30674646/ doi: 10.1128/msphere.00585-18 id: cord-307813-elom30nx author: Yip, Tsz-Fung title: Advancements in Host-Based Interventions for Influenza Treatment date: 2018-07-10 words: 15075.0 sentences: 735.0 pages: flesch: 38.0 cache: ./cache/cord-307813-elom30nx.txt txt: ./txt/cord-307813-elom30nx.txt summary: Besides controlling virus replication, potential targets for drug development include controlling virus-induced host immune responses such as the recently suggested involvement of innate lymphoid cells and NADPH oxidases in influenza virus pathogenesis and immune cell metabolism. Besides controlling virus replication, potential targets for drug development include controlling virus-induced host immune responses such as the recently suggested involvement of innate lymphoid cells and NADPH oxidases in influenza virus pathogenesis and immune cell metabolism. A recent study using RNAi also demonstrated that cholesterol homeostasis can be regulated via acid phosphatase 2 (ACP2)-mediated Niemann-Pick C2 activity and impaired the membrane fusion of IAV and influenza B virus (IBV) (52) , further suggesting the importance of controlling cholesterol homeostasis in the release of viral genome to cytoplasm. Furthermore, FPR2 antagonists have been described to possess antiviral activity against not only IAV but also IBV infection (111) , promoting the idea that antagonizing FPR2 to suppress Raf/MEK/ERK signaling cascade could potentially be a novel approach for the treatment of a broad spectrum of influenza viruses. abstract: Influenza is a major acute respiratory infection that causes mortality and morbidity worldwide. Two classes of conventional antivirals, M2 ion channel blockers and neuraminidase inhibitors, are mainstays in managing influenza disease to lessen symptoms while minimizing hospitalization and death in patients with severe influenza. However, the development of viral resistance to both drug classes has become a major public health concern. Vaccines are prophylaxis mainstays but are limited in efficacy due to the difficulty in matching predicted dominant viral strains to circulating strains. As such, other potential interventions are being explored. Since viruses rely on host cellular functions to replicate, recent therapeutic developments focus on targeting host factors involved in virus replication. Besides controlling virus replication, potential targets for drug development include controlling virus-induced host immune responses such as the recently suggested involvement of innate lymphoid cells and NADPH oxidases in influenza virus pathogenesis and immune cell metabolism. In this review, we will discuss the advancements in novel host-based interventions for treating influenza disease. url: https://doi.org/10.3389/fimmu.2018.01547 doi: 10.3389/fimmu.2018.01547 id: cord-252466-usrpodjx author: Yun, Nadezhda E. title: Pathogenesis of Lassa Fever date: 2012-10-09 words: 5668.0 sentences: 290.0 pages: flesch: 40.0 cache: ./cache/cord-252466-usrpodjx.txt txt: ./txt/cord-252466-usrpodjx.txt summary: Apparently, failure to develop the cellular immune response that would control dissemination of LASV, which is indicated by high serum virus titers, combined with disseminated replication in tissues and absence of neutralizing antibodies, leads to the development of fatal Lassa fever [64] . Downregulation of immune responses caused by LASV infection demonstrated in vitro is also in agreement with the results of clinical observations showing that fatal outcome of Lassa fever correlates with low levels or absence of interleukin (IL) 8 and IFN inducible protein 10 (IP-10) in circulation [70] . These data indicate that T cells are essential for rapid resolution of LASV infection; however, if the host fails to control virus replication due to inadequate activation of the immune system, T lymphocytes may play a key role in Lassa fever pathogenesis. abstract: Lassa virus, an Old World arenavirus (family Arenaviridae), is the etiological agent of Lassa fever, a severe human disease that is reported in more than 100,000 patients annually in the endemic regions of West Africa with mortality rates for hospitalized patients varying between 5-10%. Currently, there are no approved vaccines against Lassa fever for use in humans. Here, we review the published literature on the life cycle of Lassa virus with the specific focus put on Lassa fever pathogenesis in humans and relevant animal models. Advancing knowledge significantly improves our understanding of Lassa virus biology, as well as of the mechanisms that allow the virus to evade the host’s immune system. However, further investigations are required in order to design improved diagnostic tools, an effective vaccine, and therapeutic agents. url: https://doi.org/10.3390/v4102031 doi: 10.3390/v4102031 id: cord-272829-i4jh6bcn author: ZANETTI, A. R. title: Emerging and re‐emerging infections at the turn of the millennium date: 2010-01-04 words: 4100.0 sentences: 180.0 pages: flesch: 50.0 cache: ./cache/cord-272829-i4jh6bcn.txt txt: ./txt/cord-272829-i4jh6bcn.txt summary: Globalization changes promote the emergence of new infections and pandemics; international deliveries and travelling facilitate the dissemination of infectious agents; man‐induced environmental changes create new opportunities for contacts between species, leading to infections in aberrant hosts, including man; global warming enables insects, a major vector of pathogens, to thrive in more countries. What is more, a number of other factors promote not only the dissemination but also the emergence of new infectious diseases: intensive farming and breeding associated with crowding promote the development of foci of infection; global warming has modified the climate, making insects, a major vector of pathogens, able to thrive in countries where the climate was previously hostile; the exploitation of natural resources has produced environmental changes that create opportunities for new contacts between species leading to emergence of infections in new hosts. abstract: Summary. After World War II, mankind believed that infectious diseases were on the way to being defeated. Unfortunately, they still are the second worldwide cause of death. Globalization changes promote the emergence of new infections and pandemics; international deliveries and travelling facilitate the dissemination of infectious agents; man‐induced environmental changes create new opportunities for contacts between species, leading to infections in aberrant hosts, including man; global warming enables insects, a major vector of pathogens, to thrive in more countries. The main pandemics have been caused by viruses, such as HIV and novel subtypes of influenza viruses. In addition, prion proteins are a threat. The transmission of the Creutzfeld Jakob disease variant through blood transfusion and the recent discovery of prion protein in the spleen of a haemophilia patient are a matter of further concern. The end of the war against infectious diseases is not in sight. Mankind’s battle with pathogens has lasted millennia and is destined to continue. url: https://www.ncbi.nlm.nih.gov/pubmed/20059563/ doi: 10.1111/j.1365-2516.2009.02174.x id: cord-292286-ygomb3oi author: Zakaryan, Hovakim title: Flavonoids: promising natural compounds against viral infections date: 2017-05-25 words: 6064.0 sentences: 327.0 pages: flesch: 37.0 cache: ./cache/cord-292286-ygomb3oi.txt txt: ./txt/cord-292286-ygomb3oi.txt summary: Flavonoids are widely distributed as secondary metabolites produced by plants and play important roles in plant physiology, having a variety of potential biological benefits such as antioxidant, anti-inflammatory, anticancer, antibacterial, antifungal and antiviral activity. The antiviral activity of flavones is known from the 1990s, when it was showed that the simultaneous application of apigenin with acyclovir resulted in an enhanced antiviral effect on herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) in cell culture [92] . Besides these DNA viruses, apigenin was found to exert antiviral effect against African swine fever virus (ASFV), by suppressing the viral protein synthesis and reducing the ASFV yield by 3 log [46]. Besides these viruses, EGCG has been found to exert antiviral activity against HCV by preventing the attachment of the virus to the cell surface and suppressing RNA replication steps [8, 15] . Antiviral activity of baicalin against influenza A (H1N1/ H3N2) virus in cell culture and in mice and its inhibition of neuraminidase abstract: Flavonoids are widely distributed as secondary metabolites produced by plants and play important roles in plant physiology, having a variety of potential biological benefits such as antioxidant, anti-inflammatory, anticancer, antibacterial, antifungal and antiviral activity. Different flavonoids have been investigated for their potential antiviral activities and several of them exhibited significant antiviral properties in in vitro and even in vivo studies. This review summarizes the evidence for antiviral activity of different flavonoids, highlighting, where investigated, the cellular and molecular mechanisms of action on viruses. We also present future perspectives on therapeutic applications of flavonoids against viral infections. url: https://www.ncbi.nlm.nih.gov/pubmed/28547385/ doi: 10.1007/s00705-017-3417-y id: cord-016990-ot1wi3xi author: Zaki, Sherif R. title: Viral Infections of the Lung date: 2008 words: 19585.0 sentences: 1132.0 pages: flesch: 36.0 cache: ./cache/cord-016990-ot1wi3xi.txt txt: ./txt/cord-016990-ot1wi3xi.txt summary: 105, [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] The pathology is more prominent in larger bronchi, and inflammation may vary in intensity in individual patients, Viral inclusions cannot be identified by light microscopy (Fig, 11 .8D), Secondary bacterial infections with organisms such as Streptococcus pneumoniae (group A streptococcus [GAS]), Staphylococcus aureus, and Haemophilus influenzae may occur as a complication in about 50% to 75% of fatal cases and make it difficult to recognize the pathologic changes associated with the primary viral infec-445 tion ,190,192,193 The histopathologic features in other organs may include myocarditis, cerebral edema, rhabdomyolysis, and hemophagocytosis (Figs, 11.8H and 11.9E,F), Immunohistochemistry and ISH assays demonstrate that viral antigens and nucleic acids are usually sparse and are primarily seen in the bronchioepithelial cells of larger bronchioles (Figs. 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-340907-j9i1wlak author: Zarai, Yoram title: Evolutionary selection against short nucleotide sequences in viruses and their related hosts date: 2020-04-27 words: 8162.0 sentences: 415.0 pages: flesch: 45.0 cache: ./cache/cord-340907-j9i1wlak.txt txt: ./txt/cord-340907-j9i1wlak.txt summary: Here, based on a novel statistical framework and a large-scale genomic analysis of 2,625 viruses from all classes infecting 439 host organisms from all kingdoms of life, we identify short nucleotide sequences that are under-represented in the coding regions of viruses and their hosts. Figure 3A and B depicts the average number of under-represented sequences of size m ¼ 3, 4, and 5 nucleotides, identified in few subsets of viruses in both the original and random variants of the virus. A sampling analysis that we performed (see Supplementary document, Section 2.8) suggests that the number of under-represented sequences identified in dsDNA viruses matches their genomic size, when compared with RNA viruses. To show that the correspondence between selection against short palindromic sequences in viruses and restriction sites cannot be explained by basic coding region features such as amino-acid content and order, codon usage bias and dinucleotide distribution, we also evaluated the overlap between restriction sites and common under-represented sequences of random variants of viruses. abstract: Viruses are under constant evolutionary pressure to effectively interact with the host intracellular factors, while evading its immune system. Understanding how viruses co-evolve with their hosts is a fundamental topic in molecular evolution and may also aid in developing novel viral based applications such as vaccines, oncologic therapies, and anti-bacterial treatments. Here, based on a novel statistical framework and a large-scale genomic analysis of 2,625 viruses from all classes infecting 439 host organisms from all kingdoms of life, we identify short nucleotide sequences that are under-represented in the coding regions of viruses and their hosts. These sequences cannot be explained by the coding regions’ amino acid content, codon, and dinucleotide frequencies. We specifically show that short homooligonucleotide and palindromic sequences tend to be under-represented in many viruses probably due to their effect on gene expression regulation and the interaction with the host immune system. In addition, we show that more sequences tend to be under-represented in dsDNA viruses than in other viral groups. Finally, we demonstrate, based on in vitro and in vivo experiments, how under-represented sequences can be used to attenuated Zika virus strains. url: https://www.ncbi.nlm.nih.gov/pubmed/32339222/ doi: 10.1093/dnares/dsaa008 id: cord-348867-c0xpzd4d author: Zhai, Jun-Qiong title: First complete genome sequence of parainfluenza virus 5 isolated from lesser panda date: 2017-01-30 words: 1980.0 sentences: 117.0 pages: flesch: 54.0 cache: ./cache/cord-348867-c0xpzd4d.txt txt: ./txt/cord-348867-c0xpzd4d.txt summary: In this study, a PIV5 variant (named ZJQ-221) was isolated from a lesser panda with respiratory disease in Guangzhou zoo in Guangdong province, southern China. Sequence alignment and genetic analysis revealed that ZJQ-221 shared a close relationship with a PIV5 strain of canine-origin (1168-1) from South Korea. In this study, a novel variant of PIV5 (designated as ZJQ-221) was isolated from a lesser panda with respiratory disease in Guangzhou zoo in Guangdong province, southern China. Fourteen samples were tested for the possible presence of three respiratory-related pathogens (including PIV5, canine distemper virus, and coronavirus) by RT-PCR according to previous studies [27, 28] . In summary, we have identified a novel PIV5 isolate in lesser panda and performed whole genome sequencing, indicating that this mammal may act as a possible natural reservoir for this virus. The complete genome sequencing and analysis of canine parainfluenza virus strain CC-14 abstract: Parainfluenza virus 5 (PIV5) is widespread in mammals and humans. Up to now, there is little information about PIV5 infection in lesser pandas. In this study, a PIV5 variant (named ZJQ-221) was isolated from a lesser panda with respiratory disease in Guangzhou zoo in Guangdong province, southern China. The full-length genome of ZJQ-221 was found to be 15,246 nucleotides and consisted of seven non-overlapping genes encoding eight proteins (i.e., NP, V, P, M, F, SH, HN and L). Sequence alignment and genetic analysis revealed that ZJQ-221 shared a close relationship with a PIV5 strain of canine-origin (1168-1) from South Korea. The findings of this study confirm the presence of PIV5 in lesser panda and indicate this mammal as a possible natural reservoir. Furthermore they highlight the urgent need to strengthen viral surveillance and control of PIV5 in zoo animals. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-017-3245-0) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-017-3245-0 doi: 10.1007/s00705-017-3245-0 id: cord-339885-mpzgrogd author: Zhan, Yangqing title: Respiratory virus is a real pathogen in immunocompetent community-acquired pneumonia: comparing to influenza like illness and volunteer controls date: 2014-09-02 words: 3889.0 sentences: 244.0 pages: flesch: 46.0 cache: ./cache/cord-339885-mpzgrogd.txt txt: ./txt/cord-339885-mpzgrogd.txt summary: title: Respiratory virus is a real pathogen in immunocompetent community-acquired pneumonia: comparing to influenza like illness and volunteer controls In order to better understand the real role of respiratory virus in pneumonia and better manage the patients, we conducted a prospective observational study to reveal the viral etiology of adult CAP in Guangzhou, as compared with etiology of patients diagnosed with influenza like illness (ILI) and with volunteer controls. Obviously, considering the high prevalence of viral CAP in Guangzhou and influenza infection as an independent variable in the severe disease model, routine laboratory detection should be taken in hospitalized CAP patients at admission for an adequate diagnosis of respiratory viruses, especially influenza virus in severe individuals. Another question was that did all patients with viral community-acquired pneumonia, especially those without evidence of bacteria infection, need to be treated with antibiotics? abstract: BACKGROUND: Viral pathogens were more commonly reported than previously estimated in community-acquired pneumonia (CAP) patients. However, the real role of virus was still controversial. METHODS: Consecutive adult patients with CAP between April and December, 2009 were prospectively enrolled. A four-fold or greater increase of IgG-titres against respiratory viruses in pair sera was tested by means of hemagglutination inhibition assay or indirect immunofluorescence. Swab samples were tested by cell culture and/or nucleic amplification tests. Viral etiology was considered definitive if at least one of the above tests was positive. RESULTS: Viral etiology was established in fifty-two (34.9%) of 149 CAP patients, twenty-two (81.5%) of 27 influenza like illness patients, and none of 75 volunteer controls. Forty-seven CAP patients were infected by a single virus (24 influenza A virus, 5 influenza B, 10 parainfluenza virus type 3 [PIV-3], 2 PIV-1, 2 adenovirus, 2 human rhinovirus and 2 coronavirus OC43), five cases by two or three viruses co-infection. Fever ≥ 39°C (66.7%), fatigue (64.6%), and purulent sputum (52.1%) was the most common symptoms in viral pneumonia patients. On multivariate analysis, myalgia was included in the model for pneumonia associated with influenza infection. In the CURB-65 model only influenza infection was found independently associated with severe disease (CURB-65 score ≥ 3) out of variables, including age(years), sex, current smoking status, sick contact with febrile patients, numbers of comorbidity, presence of influenza infection, presence of PIV infection, with P = 0.021, OR 7.86 (95% CI 1.37-45.04). CONCLUSION: Respiratory virus was not a bystander, but pathogenic in pneumonia and was a common cause of CAP. url: https://www.ncbi.nlm.nih.gov/pubmed/25178477/ doi: 10.1186/1471-2466-14-144 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-344782-ond1ziu5 author: Zhang, Jing title: Identification of a novel nidovirus as a potential cause of large scale mortalities in the endangered Bellinger River snapping turtle (Myuchelys georgesi) date: 2018-10-24 words: 6003.0 sentences: 280.0 pages: flesch: 49.0 cache: ./cache/cord-344782-ond1ziu5.txt txt: ./txt/cord-344782-ond1ziu5.txt summary: Nucleic acid sequencing of the virus isolate has identified the entire genome and indicates that this is a novel nidovirus that has a low level of nucleotide similarity to recognised nidoviruses. Following the detection of the novel virus, in November 2015 (about 6 months after the cessation of the outbreak) an intensive survey of the parts of the river where affected turtles had been detected [2] was undertaken by groups of biologists and ecologists and samples collected from a wide range of aquatic species and some terrestrial animals (n = 360) to establish the size of the remaining population and whether any other animals were carrying this virus. BRV, as a novel nidovirus, was isolated from tissues of diseased animals, very high levels of viral RNA were detected in tissues with marked pathological changes and in situ hybridisation assays demonstrated the presence of specific viral RNA in lesions in kidneys and eye tissue-two of the main affected organs. abstract: In mid-February 2015, a large number of deaths were observed in the sole extant population of an endangered species of freshwater snapping turtle, Myuchelys georgesi, in a coastal river in New South Wales, Australia. Mortalities continued for approximately 7 weeks and affected mostly adult animals. More than 400 dead or dying animals were observed and population surveys conducted after the outbreak had ceased indicated that only a very small proportion of the population had survived, severely threatening the viability of the wild population. At necropsy, animals were in poor body condition, had bilateral swollen eyelids and some animals had tan foci on the skin of the ventral thighs. Histological examination revealed peri-orbital, splenic and nephric inflammation and necrosis. A virus was isolated in cell culture from a range of tissues. Nucleic acid sequencing of the virus isolate has identified the entire genome and indicates that this is a novel nidovirus that has a low level of nucleotide similarity to recognised nidoviruses. Its closest relatives are nidoviruses that have recently been described in pythons and lizards, usually in association with respiratory disease. In contrast, in the affected turtles, the most significant pathological changes were in the kidneys. Real time PCR assays developed to detect this virus demonstrated very high virus loads in affected tissues. In situ hybridisation studies confirmed the presence of viral nucleic acid in tissues in association with pathological changes. Collectively these data suggest that this virus is the likely cause of the mortalities that now threaten the survival of this species. Bellinger River Virus is the name proposed for this new virus. url: https://doi.org/10.1371/journal.pone.0205209 doi: 10.1371/journal.pone.0205209 id: cord-299549-bjqwwzam author: Zhang, Lei title: Against Ebola: type I interferon guard risk and mesenchymal stromal cell combat sepsis date: 2015-01-01 words: 3644.0 sentences: 191.0 pages: flesch: 47.0 cache: ./cache/cord-299549-bjqwwzam.txt txt: ./txt/cord-299549-bjqwwzam.txt summary: When the viral infection proceeds to the terminal stage, the key factor would be applying a non-specific immune modulation approach to suppress the cytokine storm that causes multiple organ failure, in an attempt to open a time window for the host''s immune system to recover. In most patients, Ebola viral burden elevates by time and triggers an extremely strong immune attack-a phenomenon called ''cytokine storm'' (Sullivan et al., 2003) , during which monocytes and/or macrophages produce a massive amount of pro-inflammatory cytokines, including tumor necrosis factor-α (TNF-α) and interleukins (ILs), and The virus burden, inflammatory response, and specific antibodies are the main contributors to different outcomes: mortality, survival, or symptomless infection (Fig. 2) , suggesting that the appropriate intervention strategy in each stage would accordingly be able to control the Ebola virus. Nonetheless, this phenomenon does give clues to the treatment against Ebola virus disease (EVD)-early activated innate immune responses may prevent the viral infection. abstract: The 2014 Ebola outbreak in West Africa triggered a global crisis. Nine countries have reported more than 20 000 infection cases in total and nearly 8000 lives have been lost. The actual death toll is likely much higher than this figure; the death rate is as high as 70%, considering confirmed cases. The Ebola virus launches its destruction by shutting down the host’s innate and adaptive immune systems. The virus then replicates itself out of control and causes a cytokine storm in the host. Consequently, the host’s overdriven immune system attacks its own endothelial cells and this leads to multiple organ hemorrhagic damage, the host dies of septic shock finally. Under current circumstances where no specific interventions have shown effectiveness against the virus, our opinions are justified in applying a non-specific anti-viral approach during the incubation period of virus infection as an essential protection to put the host’s immune system into an alert state and henceforth to slow down the viral replication. When the viral infection proceeds to the terminal stage, the key factor would be applying a non-specific immune modulation approach to suppress the cytokine storm that causes multiple organ failure, in an attempt to open a time window for the host’s immune system to recover. url: https://www.ncbi.nlm.nih.gov/pubmed/25559950/ doi: 10.1631/jzus.b1400365 id: cord-263785-0iift8zy author: Zhang, Xiaorong title: Evaluation of the reproductive system development and egg-laying performance of hens infected with TW I-type infectious bronchitis virus date: 2020-07-31 words: 3690.0 sentences: 171.0 pages: flesch: 50.0 cache: ./cache/cord-263785-0iift8zy.txt txt: ./txt/cord-263785-0iift8zy.txt summary: title: Evaluation of the reproductive system development and egg-laying performance of hens infected with TW I-type infectious bronchitis virus Our findings suggest that TW I-type IBV is deadly to chickens and could cause permanent damage to the oviduct, resulting in the poor laying performance of female survivors and decreasing the breeding value and welfare of the infected flock. In this study, the pathogenicity of TW I-type IBV was evaluated by examining clinical symptoms, mortality rates, virus shedding, lesions, and laying performance in terms of egg quantity and quality in infected chickens. The pathogenicity of TW I-type IBV in the early stage post-infection was evaluated via the clinical symptoms, pathological lesions, and virus shedding from trachea and cloaca. Abbreviations IBV: infectious bronchitis virus; SPF: specific-pathogen-free; dpi: days post infection; RT-qPCR: reverse transcription-quantitative polymerase chain reaction. abstract: The prevalence of TW I-type infectious bronchitis virus (IBV) has been increasing rapidly, and it has become the second most common genotype of IBV in China threatening the poultry industry. In this study, 1-day-old specific-pathogen-free (SPF) chickens infected with TW I-type IBV were continuously observed for 200 days. TW I-type IBV affected the respiratory, urinary, and female reproductive systems, resulting in a mortality rate of 10% as well as a decrease in egg quantity and an increase in inferior eggs. During the monitoring period, serious lesions occurred in the female reproductive system, such as yolk peritonitis, a shortened oviduct, and cysts of different sizes with effusion in the degenerated right oviduct. The infective viruses persisted in vivo for a long time, and due to the stress of laying, virus shedding was detected again after the onset of egg production. Our findings suggest that TW I-type IBV is deadly to chickens and could cause permanent damage to the oviduct, resulting in the poor laying performance of female survivors and decreasing the breeding value and welfare of the infected flock. url: https://www.ncbi.nlm.nih.gov/pubmed/32736651/ doi: 10.1186/s13567-020-00819-4 id: cord-317412-f3ua8ks3 author: Zhang, Xing title: Characterization of the lipidomic profile of BmN cells in response to Bombyx mori cytoplasmic polyhedrosis virus infection date: 2020-08-15 words: 2584.0 sentences: 186.0 pages: flesch: 47.0 cache: ./cache/cord-317412-f3ua8ks3.txt txt: ./txt/cord-317412-f3ua8ks3.txt summary: Here, the lipid metabolism in BmCPV-infected BmN cells was studied by lipidomics analysis. Our previous studies have found alterations in a large number of genes related to important signaling pathways, including those associated with innate immunity, development and metabolism following BmCPV infection [3, 5] . An increasing number of studies in recent years have demonstrated changes of lipid metabolism in host cells after virus infection. It has been shown that infection by some single-stranded RNA(ssRNA) viruses can alter the lipid metabolism and other biological processes of the host cells to facilitate the completion of the virus life cycle [11] . Analysis of differential expressed circRNAs has revealed changes in the metabolism of fatty acids upon BmCPV infection [5] . In addition, fatty acid metabolism has been observed to be significantly changed by the differentially expressed circRNAs in the midgut of silkworms infected by BmCPV [5] . abstract: Bombyx mori cytoplasmic polyhedrosis virus (BmCPV)that belongs to the genus Cypovirus in the family of Reoviridae is one of the problematic pathogens in sericulture. In our previous study, we have found that lipid-related constituents in the host cellular membrane are associated with the BmCPV life cycle. It is important to note that the lipids not only affect the cellular biological processes, they also impact the virus life cycle. However, the intracellular lipid homeostasis in BmN cells after BmCPV infection remains unclear. Here, the lipid metabolism in BmCPV-infected BmN cells was studied by lipidomics analysis. Our results revealed that the intracellular lipid homeostasis was disturbed in BmN cells upon BmCPV infection. Major lipids constituents in cellular membrane were found to be significantly induced upon BmCPV infection, which included triglycerides, phosphatidylcholine, phosphatidylethanolamine, sphingomyelin, phospholipids, glucoside ceramide, monoetherphosphatidylcholin, ceramide, ceramide phosphoethanolamineand cardiolipin. Further analysis of the pathways related to these altered lipids (such as PE and PC) showed that glycerophospholipid metabolism was one of the most enriched pathways. These results suggested that BmCPV may manipulate the lipid metabolism of cells for their own interest. The findings may facilitate a better understanding of the roles of lipid metabolic changes during virus infection in future studies. url: https://www.sciencedirect.com/science/article/pii/S0145305X20303773?v=s5 doi: 10.1016/j.dci.2020.103822 id: cord-000539-uh3q65we author: Zhang, Yi title: Acute Respiratory Distress Syndrome Induced by a Swine 2009 H1N1 Variant in Mice date: 2012-01-03 words: 4620.0 sentences: 247.0 pages: flesch: 51.0 cache: ./cache/cord-000539-uh3q65we.txt txt: ./txt/cord-000539-uh3q65we.txt summary: BACKGROUND: Acute respiratory distress syndrome (ARDS) induced by pandemic 2009 H1N1 influenza virus has been widely reported and was considered the main cause of death in critically ill patients with 2009 H1N1 infection. Mice infected with SD/09 virus showed typical ARDS symptoms characterized by 60% lethality on days 8–10 post-inoculation, highly edematous lungs, inflammatory cellular infiltration, alveolar and interstitial edema, lung hemorrhage, progressive and severe hypoxemia, and elevated levels of proinflammatory cytokines and chemokines. In the present mouse model, the number of leukocytes observed in the BALF of virus-infected mice significantly increased compared with the control mice on day 8 p.i. Different counts in BALF showed that the proportion of neutrophils dramatically increased. abstract: BACKGROUND: Acute respiratory distress syndrome (ARDS) induced by pandemic 2009 H1N1 influenza virus has been widely reported and was considered the main cause of death in critically ill patients with 2009 H1N1 infection. However, no animal model has been developed for ARDS caused by infection with 2009 H1N1 virus. Here, we present a mouse model of ARDS induced by 2009 H1N1 virus. METHODOLOGY PRINCIPAL FINDINGS: Mice were inoculated with A/swine/Shandong/731/2009 (SD/09), which was a 2009 H1N1 influenza variant with a G222D mutation in the hemagglutinin. Clinical symptoms were recorded every day. Lung injury was assessed by lung water content and histopathological observation. Arterial blood gas, leukocyte count in the bronchial alveolar lavage fluid and blood, virus titers, and cytokine levels in the lung were measured at various times post-inoculation. Mice infected with SD/09 virus showed typical ARDS symptoms characterized by 60% lethality on days 8–10 post-inoculation, highly edematous lungs, inflammatory cellular infiltration, alveolar and interstitial edema, lung hemorrhage, progressive and severe hypoxemia, and elevated levels of proinflammatory cytokines and chemokines. CONCLUSIONS/SIGNIFICANCE: These results suggested that we successfully established an ARDS mouse model induced by a virulent 2009 H1N1 variant without previous adaptation, which may be of benefit for evaluating the pathogenesis or therapy of human ARDS caused by 2009 H1N1 virus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3250439/ doi: 10.1371/journal.pone.0029347 id: cord-257652-ndt8f812 author: Zhang, Yong-Zhen title: The diversity, evolution and origins of vertebrate RNA viruses date: 2018-08-13 words: 4249.0 sentences: 171.0 pages: flesch: 40.0 cache: ./cache/cord-257652-ndt8f812.txt txt: ./txt/cord-257652-ndt8f812.txt summary: In addition, despite frequent cross-species transmission, the RNA viruses in vertebrates generally follow the evolutionary history of their hosts, which began in the oceans and then moved to terrestrial habitats over timescales covering hundreds of millions of years. In addition, despite frequent cross-species transmission, the RNA viruses in vertebrates generally follow the evolutionary history of their hosts, which began in the oceans and then moved to terrestrial habitats over timescales covering hundreds of millions of years. However, following the extensive use of PCR and the Sanger sequencing methods for virus identification over the past decade, the number of RNA viruses sampled from lower vertebrates has steadily increased [28] , with notable examples being arenavirus and paramyxoviruses in reptiles [29] , and novirhabdoviruses and other RNA viruses from fish [30] , although these numbers were still very limited compared to the viruses described in birds and mammals. abstract: Despite a substantial increase in our knowledge of the biodiversity and evolution of vertebrate RNA viruses, far less is known about the diversity, evolution and origin of RNA viruses across the diverse phylogenetic range of viruses, and particularly in healthy animals that are often only rarely utilized for virological sampling. Fortunately, recent advances in virus discovery using metagenomic approaches are beginning to reveal a multitude of RNA viruses in vertebrates other than birds and mammals. In particular, fish harbor a remarkable array of RNA viruses, including the relatives of important pathogens. In addition, despite frequent cross-species transmission, the RNA viruses in vertebrates generally follow the evolutionary history of their hosts, which began in the oceans and then moved to terrestrial habitats over timescales covering hundreds of millions of years. url: https://api.elsevier.com/content/article/pii/S1879625718300622 doi: 10.1016/j.coviro.2018.07.017 id: cord-011438-imbpgsub author: Zhang, Yun title: Host–Virus Interaction: How Host Cells Defend against Influenza A Virus Infection date: 2020-03-29 words: 9294.0 sentences: 567.0 pages: flesch: 41.0 cache: ./cache/cord-011438-imbpgsub.txt txt: ./txt/cord-011438-imbpgsub.txt summary: Upon IAV infection, host innate immune system is triggered and activated to restrict virus replication and clear pathogens. In the current review, we present a general description on recent work regarding different host cells and molecules facilitating antiviral defenses against IAV infection and how IAVs antagonize host immune responses. Host innate immunity, including phagocytic cells, interferons (IFNs), proinflammatory cytokines, etc., applies multiple mechanisms in defending IAV infection [105] . Influenza A virus nucleoprotein induces apoptosis in human airway epithelial cells: Implications of a novel interaction between nucleoprotein and host protein Clusterin Antiviral response elicited against avian influenza virus infection following activation of toll-like receptor (TLR)7 signaling pathway is attributable to interleukin (IL)-1β production The human interferon-induced MxA protein inhibits early stages of influenza A virus infection by retaining the incoming viral genome in the cytoplasm Cell death regulation during influenza A virus infection by matrix (M1) protein: A model of viral control over the cellular survival pathway abstract: Influenza A viruses (IAVs) are highly contagious pathogens infecting human and numerous animals. The viruses cause millions of infection cases and thousands of deaths every year, thus making IAVs a continual threat to global health. Upon IAV infection, host innate immune system is triggered and activated to restrict virus replication and clear pathogens. Subsequently, host adaptive immunity is involved in specific virus clearance. On the other hand, to achieve a successful infection, IAVs also apply multiple strategies to avoid be detected and eliminated by the host immunity. In the current review, we present a general description on recent work regarding different host cells and molecules facilitating antiviral defenses against IAV infection and how IAVs antagonize host immune responses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7232439/ doi: 10.3390/v12040376 id: cord-348876-v55piprx author: Zhao, Guangyu title: An M2e-based multiple antigenic peptide vaccine protects mice from lethal challenge with divergent H5N1 influenza viruses date: 2010-01-18 words: 3571.0 sentences: 185.0 pages: flesch: 49.0 cache: ./cache/cord-348876-v55piprx.txt txt: ./txt/cord-348876-v55piprx.txt summary: In the present study, we designed a tetra-branched multiple antigenic peptide (MAP)-based vaccine, designated M2e-MAP, which contains the sequence overlapping the highly conserved extracellular domain of matrix protein 2 (M2e) of a HPAI H5N1 virus, and investigated its immune responses and cross-protection against different clades of H5N1 viruses. In the present study, we designed and synthesized a tetra-branched multiple antigenic peptide (MAP) derived from the M2e sequence of H5N1 virus VN/1194 strain, denoted as M2e-MAP, with an aim to develop a M2e-based vaccine for induction of M2e-specific immune responses and cross-protection of the vaccinated animals against lethal challenge of divergent H5N1 virus strains. After receiving the lethal dose (10 LD 50 ) of two H5N1 virus strains, the M2e-MAP vaccinated mice were further evaluated in terms of cross-protective ability by daily observation of the clinical symptoms, including weight loss and survival rate for two weeks, and then histopathological examination following removal of lung tissues. abstract: BACKGROUND: A growing concern has raised regarding the pandemic potential of the highly pathogenic avian influenza (HPAI) H5N1 viruses. Consequently, there is an urgent need to develop an effective and safe vaccine against the divergent H5N1 influenza viruses. In the present study, we designed a tetra-branched multiple antigenic peptide (MAP)-based vaccine, designated M2e-MAP, which contains the sequence overlapping the highly conserved extracellular domain of matrix protein 2 (M2e) of a HPAI H5N1 virus, and investigated its immune responses and cross-protection against different clades of H5N1 viruses. RESULTS: Our results showed that M2e-MAP vaccine induced strong M2e-specific IgG antibody responses following 3-dose immunization of mice with M2e-MAP in the presence of Freunds' or aluminium (alum) adjuvant. M2e-MAP vaccination limited viral replication and attenuated histopathological damage in the challenged mouse lungs. The M2e-MAP-based vaccine protected immunized mice against both clade1: VN/1194 and clade2.3.4: SZ/406H H5N1 virus challenge, being able to counteract weight lost and elevate survival rate following lethal challenge of H5N1 viruses. CONCLUSIONS: These results suggest that M2e-MAP presenting M2e of H5N1 virus has a great potential to be developed into an effective subunit vaccine for the prevention of infection by a broad spectrum of HPAI H5N1 viruses. url: https://doi.org/10.1186/1743-422x-7-9 doi: 10.1186/1743-422x-7-9 id: cord-000902-ew8orn0z author: Zhao, Xiangyan title: Coevolution between simple sequence repeats (SSRs) and virus genome size date: 2012-08-30 words: 5822.0 sentences: 302.0 pages: flesch: 53.0 cache: ./cache/cord-000902-ew8orn0z.txt txt: ./txt/cord-000902-ew8orn0z.txt summary: The results showed that simple sequence repeats (SSRs) is strongly, positively and significantly correlated with genome size. While, relative abundance and relative density were examined to make the SSRs comparison parallel among differently sized species genomes; principal component analysis (PCA) was designed to investigate which repeat class(es) made a greater contribution to the variance among virus species as well as the relationships between repeat classes. Therefore, the 257 genome sequences were selected as samples for the analysis of relationship between SSRs distribution and genome size in the level of the whole virus. We surveyed the distribution of different SSR classes in virus genomes to investigate the relationship between repeat classes (mono-, di-, tri-, tetra-, penta-and hexa-) and genome sequence length. Coevolution between simple sequence repeats (SSRs) and virus genome size abstract: BACKGROUND: Relationship between the level of repetitiveness in genomic sequence and genome size has been investigated by making use of complete prokaryotic and eukaryotic genomes, but relevant studies have been rarely made in virus genomes. RESULTS: In this study, a total of 257 viruses were examined, which cover 90% of genera. The results showed that simple sequence repeats (SSRs) is strongly, positively and significantly correlated with genome size. Certain repeat class is distributed in a certain range of genome sequence length. Mono-, di- and tri- repeats are widely distributed in all virus genomes, tetra- SSRs as a common component consist in genomes which more than 100 kb in size; in the range of genome < 100 kb, genomes containing penta- and hexa- SSRs are not more than 50%. Principal components analysis (PCA) indicated that dinucleotide repeat affects the differences of SSRs most strongly among virus genomes. Results showed that SSRs tend to accumulate in larger virus genomes; and the longer genome sequence, the longer repeat units. CONCLUSIONS: We conducted this research standing on the height of the whole virus. We concluded that genome size is an important factor in affecting the occurrence of SSRs; hosts are also responsible for the variances of SSRs content to a certain degree. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3585866/ doi: 10.1186/1471-2164-13-435 id: cord-321112-w7x1dkds author: Zhao, Xuesen title: IFITM Genes, Variants, and Their Roles in the Control and Pathogenesis of Viral Infections date: 2019-01-08 words: 6973.0 sentences: 350.0 pages: flesch: 43.0 cache: ./cache/cord-321112-w7x1dkds.txt txt: ./txt/cord-321112-w7x1dkds.txt summary: Similar to many other host defense genes that evolve under the selective pressure of microorganism infection, IFITM genes evolved in an accelerated speed in vertebrates and many single-nucleotide polymorphisms (SNPs) have been identified in the human population, some of which have been associated with severity and prognosis of viral infection (e.g., influenza A virus). Similar to many other host defense genes that evolve under the selective pressure of microorganism infection, IFITM genes evolved in an accelerated speed in vertebrates and many single-nucleotide polymorphisms (SNPs) have been identified in the human population, some of which have been associated with severity and prognosis of viral infection (e.g., influenza A virus). Among the number of single-nucleotide polymorphisms (SNPs) in IFITM3 gene that have been identified in human populations, several are associated with disease severity and prognosis of influenza A virus (IAV) and other viral infections (Everitt et al., 2012; Zhang et al., 2015; Xu-Yang et al., 2016; Allen et al., 2017) . abstract: Interferon-induced transmembrane proteins (IFITMs) are a family of small proteins that localize in the plasma and endolysosomal membranes. IFITMs not only inhibit viral entry into host cells by interrupting the membrane fusion between viral envelope and cellular membranes, but also reduce the production of infectious virions or infectivity of progeny virions. Not surprisingly, some viruses can evade the restriction of IFITMs and even hijack the antiviral proteins to facilitate their infectious entry into host cells or promote the assembly of virions, presumably by modulating membrane fusion. Similar to many other host defense genes that evolve under the selective pressure of microorganism infection, IFITM genes evolved in an accelerated speed in vertebrates and many single-nucleotide polymorphisms (SNPs) have been identified in the human population, some of which have been associated with severity and prognosis of viral infection (e.g., influenza A virus). Here, we review the function and potential impact of genetic variation for IFITM restriction of viral infections. Continuing research efforts are required to decipher the molecular mechanism underlying the complicated interaction among IFITMs and viruses in an effort to determine their pathobiological roles in the context of viral infections in vivo. url: https://doi.org/10.3389/fmicb.2018.03228 doi: 10.3389/fmicb.2018.03228 id: cord-355535-01h8yyqj author: Zheng, Xue-yan title: Regional, age and respiratory-secretion-specific prevalence of respiratory viruses associated with asthma exacerbation: a literature review date: 2018-01-11 words: 3290.0 sentences: 179.0 pages: flesch: 39.0 cache: ./cache/cord-355535-01h8yyqj.txt txt: ./txt/cord-355535-01h8yyqj.txt summary: The primary focus was on the prevalence of respiratory viruses, including AdV (adenovirus), BoV (bocavirus), CoV (coronavirus), CMV (cytomegalovirus), EnV (enterovirus), HSV (herpes simplex virus), IfV (influenza virus), MpV (metapneumovirus), PiV (parainfluenzavirus), RV (rhinovirus) and RSV (respiratory syncytial virus) during asthma exacerbations. A standardized form was used for data extraction, including the main characteristics (author, year of publication, sample size, age, definition of exacerbation, quality, detection method, study design and season), primary outcome (the prevalence of viral infection during asthma exacerbations), and secondary outcomes (the prevalence of viruses in different strata). We also did a subgroup analysis to assess the weight of viral infection on asthma exacerbations with respect to geographic region, population, type of respiratory tract secretion examined, and detection method. Because difference in the geographic regions, age, study population, type of respiratory tract secretion, and detection method significantly confound the determination of the prevalence of individual viruses, heterogeneity was not assessed in this study. abstract: Despite increased understanding of how viral infection is involved in asthma exacerbations, it is less clear which viruses are involved and to what extent they contribute to asthma exacerbations. Here, we sought to determine the prevalence of different respiratory viruses during asthma exacerbations. Systematic computerized searches of the literature up to June 2017 without language limitation were performed. The primary focus was on the prevalence of respiratory viruses, including AdV (adenovirus), BoV (bocavirus), CoV (coronavirus), CMV (cytomegalovirus), EnV (enterovirus), HSV (herpes simplex virus), IfV (influenza virus), MpV (metapneumovirus), PiV (parainfluenzavirus), RV (rhinovirus) and RSV (respiratory syncytial virus) during asthma exacerbations. We also examined the prevalence of viral infection stratified by age, geographic region, type of respiratory secretion, and detection method. Sixty articles were included in the final analysis. During asthma exacerbations, the mean prevalence of AdV, BoV, CoV, CMV, EnV, HSV, IfV, MpV, PiV, RV and RSV was 3.8%, 6.9%, 8.4%, 7.2%, 10.1%, 12.3%, 10.0%, 5.3%, 5.6%, 42.1% and 13.6%, respectively. EnV, MPV, RV and RSV were more prevalent in children, whereas AdV, BoV, CoV, IfV and PiV were more frequently present in adults. RV was the major virus detected globally, except in Africa. RV could be detected in both the upper and lower airway. Polymerase chain reaction was the most sensitive method for detecting viral infection. Our findings indicate the need to develop prophylactic polyvalent or polyvirus (including RV, EnV, IfV and RSV) vaccines that produce herd immunity and reduce the healthcare burden associated with virus-induced asthma exacerbations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-017-3700-y) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-017-3700-y doi: 10.1007/s00705-017-3700-y id: cord-025181-eg108wcd author: Zheng, Zhihang title: Establishment of Murine Infection Models with Biological Clones of Dengue Viruses Derived from a Single Clinical Viral Isolate date: 2020-05-25 words: 5919.0 sentences: 340.0 pages: flesch: 59.0 cache: ./cache/cord-025181-eg108wcd.txt txt: ./txt/cord-025181-eg108wcd.txt summary: In this study, with biologically cloned viruses from a single clinical isolate, we have established two mouse models of DENV infection, one is severe lethal infection in immunocompromised mice, and the other resembles self-limited disease manifestations in Balb/c mice with transient blockage of type I IFN responses. Further, we compared the infectivity of these two viral variants in a self-limited infection model, in which type I IFN receptor of wild-type Balb/c mice had been transiently blocked before infection, and found only the virus strain exhibiting larger plaque size caused infectious viral particles in sera. We have recently developed a ZIKV infection model in Balb/c mice with transient blockage of type I IFN Fig. 2 Phylogenetic analysis of DENV-2 1D4-5-SP and DENV-2 8H2-7-LP with representative serotype-2 dengue viruses of different genotypes isolated from different geographical regions. abstract: Dengue virus (DENV) is a single-stranded RNA virus transmitted by mosquitoes in tropical and subtropical regions. It causes dengue fever, dengue hemorrhagic fever and dengue shock syndrome in patients. Each year, 390 million people are estimated to be infected by four serotypes of dengue virus, creating a great burden on global public health and local economy. So far, no antiviral drug is available for dengue disease, and the newly licensed vaccine is far from satisfactory. One large obstacle for dengue vaccine and drug development is the lack of suitable small animal models. Although some DENV infection models have been developed, only a small number of viral strains can infect immunodeficient mice. In this study, with biologically cloned viruses from a single clinical isolate, we have established two mouse models of DENV infection, one is severe lethal infection in immunocompromised mice, and the other resembles self-limited disease manifestations in Balb/c mice with transient blockage of type I IFN responses. This study not only offers new small animal models of dengue viral infection, but also provides new viral variants for further investigations on dengue viral pathogenesis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7246292/ doi: 10.1007/s12250-020-00229-y id: cord-270911-z637eh2z author: Zhou, Jie title: Differentiated human airway organoids to assess infectivity of emerging influenza virus date: 2018-06-26 words: 5003.0 sentences: 274.0 pages: flesch: 47.0 cache: ./cache/cord-270911-z637eh2z.txt txt: ./txt/cord-270911-z637eh2z.txt summary: title: Differentiated human airway organoids to assess infectivity of emerging influenza virus airway organoid | proximal differentiation | influenza virus | infectivity I nfluenza A viruses (IAVs) can infect a diversity of avian and mammalian species, including humans, and have the remarkable capacity to evolve and adapt to new hosts (1) . Current in vitro models for studying influenza infection in the human respiratory tract involve shortterm cultures of human lung explants and primary airway epithelial cells. We chose to compare the infectivity of H7N2 with that of H7N9/Ah in the PD organoids as a proof of concept, to verify that the differentiated AOs can indeed simulate human airway epithelium in the context of influenza virus infection. Fig. 4 shows that viral loads in the cell lysate and medium of H7N9/ Ah-infected organoids increased gradually after inoculation; the viral titer increased more than 3 log 10 units within 24 h, indicating a robust viral replication. abstract: Novel reassortant avian influenza H7N9 virus and pandemic 2009 H1N1 (H1N1pdm) virus cause human infections, while avian H7N2 and swine H1N1 virus mainly infect birds and pigs, respectively. There is no robust in vitro model for assessing the infectivity of emerging viruses in humans. Based on a recently established method, we generated long-term expanding 3D human airway organoids which accommodate four types of airway epithelial cells: ciliated, goblet, club, and basal cells. We report differentiation conditions which increase ciliated cell numbers to a nearly physiological level with synchronously beating cilia readily discernible in every organoid. In addition, the differentiation conditions induce elevated levels of serine proteases, which are essential for productive infection of human influenza viruses and low-pathogenic avian influenza viruses. We also established improved 2D monolayer culture conditions for the differentiated airway organoids. To demonstrate the ability of differentiated airway organoids to identify human-infective virus, 3D and 2D differentiated airway organoids are applied to evaluate two pairs of viruses with known distinct infectivity in humans, H7N9/Ah versus H7N2 and H1N1pdm versus an H1N1 strain isolated from swine (H1N1sw). The human-infective H7N9/Ah virus replicated more robustly than the poorly human-infective H7N2 virus; the highly human-infective H1N1pdm virus replicated to a higher titer than the counterpart H1N1sw. Collectively, we developed differentiated human airway organoids which can morphologically and functionally simulate human airway epithelium. These differentiated airway organoids can be applied for rapid assessment of the infectivity of emerging respiratory viruses to human. url: https://doi.org/10.1073/pnas.1806308115 doi: 10.1073/pnas.1806308115 id: cord-255075-6azu6k3h author: Zhuang, Jianjian title: Advanced “lab-on-a-chip” to detect viruses – Current challenges and future perspectives date: 2020-05-12 words: 3141.0 sentences: 230.0 pages: flesch: 49.0 cache: ./cache/cord-255075-6azu6k3h.txt txt: ./txt/cord-255075-6azu6k3h.txt summary: Multiplexed efficient on-chip sample preparation 613 and sensitive amplification-free detection of Ebola virus A bead-based 689 immunofluorescence-assay on a microfluidic dielectrophoresis platform for rapid dengue virus 690 detection Fast and Parallel Detection of Four Ebola Virus Species on a Microfluidic-Chip-Based Portable 770 An integrated self-driven microfluidic device for rapid 781 detection of the influenza A (H1N1) virus by reverse transcription loop-mediated isothermal 782 amplification Paper-based RNA detection and 785 multiplexed analysis for Ebola virus diagnostics Multiplex microfluidic paper-based 805 immunoassay for the diagnosis of hepatitis C virus infection Simultaneous and automated detection of influenza A virus hemagglutinin H7 and H9 based on 965 magnetism and size mediated microfluidic chip A 1026 point of care platform based on microfluidic chip for nucleic acid extraction in less than 1 minute D: Schematic of a 1149 paper-based chip for the detection of HIV developed by Li et al. abstract: Massive viral outbreaks draw attention to viruses that have not been thoroughly studied or understood. In recent decades, microfluidic chips, known as “lab-on-a-chip”, appears as a promising tool for the detection of viruses. Here, we review the development of microfluidic chips that could be used in response to viral detection, specifically for viruses involved in more recent outbreaks. The advantages as well as the disadvantages of microfluidic systems are discussed and analyzed. We also propose ideas for future development of these microfluidic chips and we expect this advanced technology to be used in the future for viral outbreaks. url: https://doi.org/10.1016/j.bios.2020.112291 doi: 10.1016/j.bios.2020.112291 id: cord-264916-c4n0kyog author: Zimmerman, Keith title: Natural protection of ocular surface from viral infections – a hypothesis date: 2020-07-09 words: 4671.0 sentences: 225.0 pages: flesch: 46.0 cache: ./cache/cord-264916-c4n0kyog.txt txt: ./txt/cord-264916-c4n0kyog.txt summary: A pandemic outbreak of a viral respiratory infection (COVID-19) caused by a coronavirus (SARS-CoV-2) prompted a multitude of research focused on various aspects of this disease. In this work, we discuss the significance of natural protective factors related to anatomical and physiological properties of the eyes and preventing the deposition of large number of virus-loaded particles on the ocular surface. Specifically, we advance the hypothesis that the standing potential of the eye plays an important role in repelling aerosol particles (microdroplets) from the surface of the eye and discuss factors associated with this hypothesis, possible ways to test it and its implications in terms of prevention of ocular infections. This hypothesis could be tested by measuring the electrical charge of bioaerosol generated by normal breathing in healthy subjects and in patients with viral infections caused by different viruses, causing respiratory infections or with suspected aerosol transmission pathway. abstract: A pandemic outbreak of a viral respiratory infection (COVID-19) caused by a coronavirus (SARS-CoV-2) prompted a multitude of research focused on various aspects of this disease. One of the interesting aspects of the clinical manifestation of the infection is an accompanying ocular surface viral infection, viral conjunctivitis. Although occasional reports of viral conjunctivitis caused by this and the related SARS-CoV virus (causing the SARS outbreak in the early 2000s) are available, the prevalence of this complication among infected people appears low (∼1%). This is surprising, considering the recent discovery of the presence of viral receptors (ACE2 and TMPRSS2) in ocular surface tissue. The discrepancy between the theoretically expected high rate of concurrence of viral ocular surface inflammation and the observed relatively low occurrence can be explained by several factors. In this work, we discuss the significance of natural protective factors related to anatomical and physiological properties of the eyes and preventing the deposition of large number of virus-loaded particles on the ocular surface. Specifically, we advance the hypothesis that the standing potential of the eye plays an important role in repelling aerosol particles (microdroplets) from the surface of the eye and discuss factors associated with this hypothesis, possible ways to test it and its implications in terms of prevention of ocular infections. url: https://www.ncbi.nlm.nih.gov/pubmed/32679424/ doi: 10.1016/j.mehy.2020.110082 id: cord-284523-lknyehsa author: da Mata, Élida Cleyse Gomes title: Antiviral activity of animal venom peptides and related compounds date: 2017-01-06 words: 7073.0 sentences: 347.0 pages: flesch: 43.0 cache: ./cache/cord-284523-lknyehsa.txt txt: ./txt/cord-284523-lknyehsa.txt summary: This review provides a panorama of peptides described from animal venoms that present antiviral activity, thereby reinforcing them as important tools for the development of new therapeutic drugs. Synthetic hybrid peptides, namely cecropin A (1-8)-magainin 2 (1-12), exhibited potent antiviral activity by a mechanism mainly based on the compound hydrophobicity and α-helical content, inhibiting the virushost cell fusion [85] (Table 2) . Other peptides from marine sponges that inhibit HIV-1 entry into host cells are: callipeltin A, isolated from sponges of the genus Callipelta, which displayed antiviral activity with a high selectivity index (29) between the virus and host cells (SI ratio 50% cytotoxic dose [CD 50 ]/ED 50 ) [109] ; celebesides A-C from Siliquariaspongia mirabilis [108] ; neamphamide A, from Neamphius huxleyi, a compound with structural similarities to callipeptins and papuamides that exhibited low toxicity to host cells and a selectivity index above 10 [110] ; and microspinosamide, isolated from Sidonops microspinosa [111] . abstract: Viruses exhibit rapid mutational capacity to trick and infect host cells, sometimes assisted through virus-coded peptides that counteract host cellular immune defense. Although a large number of compounds have been identified as inhibiting various viral infections and disease progression, it is urgent to achieve the discovery of more effective agents. Furthermore, proportionally to the great variety of diseases caused by viruses, very few viral vaccines are available, and not all are efficient. Thus, new antiviral substances obtained from natural products have been prospected, including those derived from venomous animals. Venoms are complex mixtures of hundreds of molecules, mostly peptides, that present a large array of biological activities and evolved to putatively target the biochemical machinery of different pathogens or host cellular structures. In addition, non-venomous compounds, such as some body fluids of invertebrate organisms, exhibit antiviral activity. This review provides a panorama of peptides described from animal venoms that present antiviral activity, thereby reinforcing them as important tools for the development of new therapeutic drugs. url: https://www.ncbi.nlm.nih.gov/pubmed/28074089/ doi: 10.1186/s40409-016-0089-0 id: cord-350925-1h6pbfwp author: da Silva, Priscilla Gomes title: Airborne spread of infectious SARS-CoV-2: moving forward using lessons from SARS-CoV and MERS-CoV date: 2020-10-08 words: 5221.0 sentences: 279.0 pages: flesch: 49.0 cache: ./cache/cord-350925-1h6pbfwp.txt txt: ./txt/cord-350925-1h6pbfwp.txt summary: Transmission of viruses through air can happen via droplets or aerosols generated during coughing, sneezing, talking, singing or breathing (Jones and CoV-2 is that most studies performed only focused on the detection of viral RNA and do not correlate to the infectivity of these viral particles. Therefore, in this systematic review, the viability/stability of aerosols containing SARS-CoV and MERS-CoV viruses will be discussed to provide information on potential mitigation strategies for SARS-CoV-2 airborne transmission. The presence of MERS-CoV was also confirmed by RT-PCR of viral cultures of 4 out of 7 air samples from two hospitals in South Korea (Kim et al., 2016) , and showed to be very stable in aerosol at 20°C and 40% relative humidity (van Doremalen et al., 2013) . abstract: Background Although an increasing body of data reports the detection of SARS-CoV-2 RNA in air, this does not correlate to the presence of infectious viruses, thus not evaluating the risk for airborne COVID-19. Hence there is a marked knowledge gap that requires urgent attention. Therefore, in this systematic review, viability/stability of airborne SARS-CoV-2, SARS-CoV and MERS-CoV viruses is discussed. Methods A systematic literature review was performed on PubMed/MEDLINE, Web of Science and Scopus to assess the stability and viability of SARS-CoV, MERS-CoV and SARS-CoV-2 on air samples. Results and discussion The initial search identified 27 articles. Following screening of titles and abstracts and removing duplicates, 11 articles were considered relevant. Temperatures ranging from 20 °C to 25 °C and relative humidity ranging from 40% to 50% were reported to have a protective effect on viral viability for airborne SARS-CoV and MERS-CoV. As no data is yet available on the conditions influencing viability for airborne SARS-CoV-2, and given the genetic similarity to SARS-CoV and MERS-CoV, one could extrapolate that the same conditions would apply. Nonetheless, the effect of these conditions seems to be residual considering the increasing number of cases in the south of USA, Brazil and India, where high temperatures and humidities have been observed. Conclusion Higher temperatures and high relative humidity can have a modest effect on SARS-CoV-2 viability in the environment, as reported in previous studies to this date. However, these studies are experimental, and do not support the fact that the virus has efficiently spread in the tropical regions of the globe, with other transmission routes such as the contact and droplet ones probably being responsible for the majority of cases reported in these regions, along with other factors such as human mobility patterns and contact rates. Further studies are needed to investigate the extent of aerosol transmission of SARS-CoV-2 as this would have important implications for public health and infection-control policies. url: https://www.sciencedirect.com/science/article/pii/S0048969720363312?v=s5 doi: 10.1016/j.scitotenv.2020.142802 id: cord-259233-smmhhroe author: de Armas‐Rillo, Laura title: Membrane dynamics associated with viral infection date: 2016-01-28 words: 7086.0 sentences: 374.0 pages: flesch: 40.0 cache: ./cache/cord-259233-smmhhroe.txt txt: ./txt/cord-259233-smmhhroe.txt summary: Several RNA viruses induce the formation of these autophagosome-like vesicles (also referred to as DMVs) to enhance viral replication and non-lytic egression, such as poliovirus and CVB3, HIV-1 and HCV. Indeed, autophagosome-like vesicles may represent a trafficking pathway for these viruses, connecting to multivesicular bodies (MVBs), and assuring virus assembly and budding at the cell surface while protecting them from intrinsic antiviral factors and immune responses. Trogocytosis involves the exchange of cell surface membrane patches that may contain receptor clusters associated to viral particles, while exosomes are vesicles formed from MVBs that could participate in viral infection and spreading between cells of the Alphavirus group of this family [12] , couple their RNA synthesis to endosome and lysosome membranes modified by the association of virus specific components. It remains unclear how proteins from distinct viruses and host cells use the same intracellular membrane compartments or events (e.g. autophagy) to achieve viral replication, without affecting important cellular processes. abstract: Viral replication and spreading are fundamental events in the viral life cycle, accounting for the assembly and egression of nascent virions, events that are directly associated with viral pathogenesis in target hosts. These processes occur in cellular compartments that are modified by specialized viral proteins, causing a rearrangement of different cell membranes in infected cells and affecting the ER, mitochondria, Golgi apparatus, vesicles and endosomes, as well as processes such as autophagic membrane flux. In fact, the activation or inhibition of membrane trafficking and other related activities are fundamental to ensure the adequate replication and spreading of certain viruses. In this review, data will be presented that support the key role of membrane dynamics in the viral cycle, especially in terms of the assembly, egression and infection processes. By defining how viruses orchestrate these events it will be possible to understand how they successfully complete their route of infection, establishing viral pathogenesis and provoking disease. © 2015 The Authors Reviews in Medical Virology Published by John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/26817660/ doi: 10.1002/rmv.1872 id: cord-289593-81vu2kbu author: de Blic, J. title: Interactions micro-organismes et voies aériennes distales : spécificités pédiatriques date: 2017-03-03 words: 5325.0 sentences: 526.0 pages: flesch: 65.0 cache: ./cache/cord-289593-81vu2kbu.txt txt: ./txt/cord-289593-81vu2kbu.txt summary: Les relations entre bronchiolites virales et asthme, la place des virus à tropisme respiratoire dans l''histoire naturelle de l''asthme ont fait l''objet de nombreuses études, d''abord concentrées sur le virus respiratoire syncytial humain (hVRS) et plus récemment sur le rhinovirus humain (hRV). D''autres IAV aviaires ont pu contaminer l''homme ces dernières années, mais c''est du porc en 2009 qu''une pandémie grippale a éclos avec un virus influenza A triple réassortant (H 1 N 1pdm09 ), heureusement d''une pathogénicité moindre que celle imaginée lors des premières transmissions au Mexique puis de son expansion pandémique dans l''hémisphère sud [3] . En effet, à partir de la cohorte Childhood Origins of ASThma (COAST) constituée de 285 nouveau-nés, ayant au moins un parent atopique (1 Prick test positif) et/ou asthmatique, les auteurs ont évalué la prévalence des manifestations sifflantes dans les 6 premières années de la vie, en regard des antécédents de bronchiolite à VRS et à hRV [17, 28] . abstract: The spectrum of respiratory viruses is expanding and emerging diseases have been described regularly over the last fifteen years. The origin of these emerging respiratory viruses may be zoonotic (by crossing species barrier, after changes to RNA viruses such as avian influenza virus type A or coronaviruses), or related to the use of new identification techniques (metapneumovirus, bocavirus). The relationship between bronchiolitis and asthma is now better understood thanks to prospective follow up of birth cohorts. The role of rhinovirus has become predominant with respect to respiratory syncytial virus. The identification of predisposing factors immunological, functional, atopic and genetic, for the onset of asthma after rhinovirus infection suggests that viral infection reveals a predisposition rather than itself being a cause of asthma. The role of bacteria in the natural history of asthma is also beginning to be better understood. The results of the COPSAC Danish cohort have shown the frequency of bacterial identification during wheezy episodes before 3 years, and the impact of bacterial colonization at the age of one month on the onset of asthma by age 5 years. The role of bacterial infections in severe asthma in young children is also discussed. url: https://doi.org/10.1016/j.rmr.2016.02.012 doi: 10.1016/j.rmr.2016.02.012 id: cord-256510-orr2roxz author: de Castro, Isabel Fernández title: Virus factories: biogenesis and structural design date: 2012-10-04 words: 5188.0 sentences: 259.0 pages: flesch: 43.0 cache: ./cache/cord-256510-orr2roxz.txt txt: ./txt/cord-256510-orr2roxz.txt summary: For example, transmission electron microscopy (TEM) of cells infected with coxsackievirus showed intracellular organized lattices (Fig. 1E) , very similar to those assembled by the viral RNA polymerase in vitro (Kemball et al., 2010) close relationship between self-interaction and replication activity is reported for viral polymerases of other viruses such as FHV (Dye et al., 2005) , hepatitis C virus (Qin et al., 2002) and RUBV (Risco et al., 2012) . For viral genome replication, the virus first assembles cytoplasmic mini-nuclei with attached mitochondria (Tolonen et al., 2001) ; virus morphogenesis then starts an aggresome-like structure (Risco et al., 2002) , where immature viruses assemble using an atypical membrane remodelling mechanism that has been characterized by ET (Chlanda et al., 2009) . Although we are beginning to understand how replication organelles are assembled, information is still limited about how cell organelles are recruited, about the mechanisms of macromolecular transport between compartments, and about the signals that regulate the major structural changes in the factory during distinct stages in the virus life cycle. abstract: Replication and assembly of many viruses occur in specific intracellular compartments known as ‘virus factories’. Our knowledge of the biogenesis and architecture of these unique structures has increased considerably in the last 10 years, due to technical advances in cellular, molecular and structural biology. We now know that viruses build replication organelles, which recruit cell and viral components in a macrostructure in which viruses assemble and mature. Cell membranes and cytoskeleton participate in the biogenesis of these scaffolds and mitochondria are present in many factories, where they might supply energy and other essential factors. New inter‐organelle contacts have been visualized within virus factories, whose structure is very dynamic, as it changes over time. There is increasing interest in identifying the factors involved in their biogenesis and functional architecture, and new microscopy techniques are helping us to understand how these complex entities are built and work. In this review, we summarize recent findings on the cell biology, biogenesis and structure of virus factories. url: https://www.ncbi.nlm.nih.gov/pubmed/22978691/ doi: 10.1111/cmi.12029 id: cord-290352-0pc5eji4 author: de Jong, Menno D. title: Avian influenza A (H5N1) date: 2005-10-06 words: 9156.0 sentences: 412.0 pages: flesch: 41.0 cache: ./cache/cord-290352-0pc5eji4.txt txt: ./txt/cord-290352-0pc5eji4.txt summary: Since their reemergence in 2003, highly pathogenic avian influenza A (H5N1) viruses have reached endemic levels among poultry in several southeast Asian countries and have caused a still increasing number of more than 100 reported human infections with high mortality. However, occurrences of direct bird-to-human transmission of avian influenza viruses have increasingly been reported in recent years, culminating in the ongoing outbreak of influenza A (H5N1) among poultry in several Asian countries with associated human infections. The "Asian influenza" pandemic of 1957 was caused by an H2N2 virus that had acquired three genes (H2, N2, and PB1) from avian viruses infecting wild ducks, in a backbone of the circulating H1N1 human influenza strain. Furthermore, these infections were associated with severe hemorrhagic pneumonia and the induction of high levels of macrophage-derived cytokines and chemokines, strikingly reminiscent of clinical observations in humans during the Spanish flu pandemic, as well as of recent in vitro and in vivo observations of infections with highly pathogenic avian influenza H5N1 viruses (Cheung et al., 2002; Oxford, 2000; Peiris et al., 2004; To et al., 2001) . abstract: Since their reemergence in 2003, highly pathogenic avian influenza A (H5N1) viruses have reached endemic levels among poultry in several southeast Asian countries and have caused a still increasing number of more than 100 reported human infections with high mortality. These developments have ignited global fears of an imminent influenza pandemic. The current knowledge of the virology, clinical spectrum, diagnosis and treatment of human influenza H5N1 virus infections is reviewed herein. url: https://www.ncbi.nlm.nih.gov/pubmed/16213784/ doi: 10.1016/j.jcv.2005.09.002 id: cord-020756-d9f5fd7x author: de Jong, Menno Douwe title: Avian Influenza Viruses and Pandemic Influenza date: 2007 words: 15047.0 sentences: 677.0 pages: flesch: 41.0 cache: ./cache/cord-020756-d9f5fd7x.txt txt: ./txt/cord-020756-d9f5fd7x.txt summary: This is illustrated by the fact that during its evolution in humans, the NA of H2N2 viruses, which were of avian origin and therefore highly specific for hydrolization of α2,3-linked sialic acids, acquired high affinity for the human α2,6-linked sialic acids (Baum and Paulson, 1991) In addition to the surface glycoproteins, laboratory experiments with reassortant viruses suggest that the genes encoding internal proteins, such as M, NP, PB1 and PB2, may also play a role in determining the host range (Almond 1977; Scholtissek et al., 1978a; Snyder et al., 1987; Subbarao et al., 1993) . By reverse genetics experiments, it has been shown that a lysine residue at position 627 (Lys627) of PB2 seems essential for high virulence and systemic replication in mice of highly pathogenic influenza H5N1 viruses responsible for the outbreak among poultry and humans in Hong Kong in 1997 (H5N1/97) (Hatta et al., 2001) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147437/ doi: 10.1007/978-0-387-32830-0_9 id: cord-259235-p0yj9qug author: de Lamballerie, Xavier title: Diagnostic et traitement des viroses émergentes : comment aller de l’avant ? date: 2016-12-31 words: 1633.0 sentences: 178.0 pages: flesch: 60.0 cache: ./cache/cord-259235-p0yj9qug.txt txt: ./txt/cord-259235-p0yj9qug.txt summary: (ii) l''émergence dans une population donnée d''un pathogène déjà impliqué en pathologie humaine dans un contexte épidémiologique différent (on parle ici plus proprement de pathologie « ré-émergente » et l''arrivée des virus Chikungunya [2] ou Zika [3] dans le Nouveau Monde constituent des exemples récents ayant provoqué des épidémies massives) ; À titre d''exemple, le seul arbovirus dont la circulation avait été prouvée en République du Congo jusqu''à une période récente était le virus de la fièvre jaune, alors qu''une simple étude de séroprévalence a permis de préciser l''importance de la circulation de la dengue, du chikungunya, de la fièvre de la vallée du Rift, de la fièvre de West Nile (Dr. Nanikaly Moyen, données personnelles Un cas particulier de thérapeutique antivirale applicable aux infections émergentes et ré-émergentes est constitué par la sérothérapie au sens large qui inclut l''usage d''immunoglobulines humaines ou animales (ces dernières pouvant être « humanisées ») monoclonales ou polyclonales [19] . abstract: SUMMARY Virus emergence episodes follow one another at a steady pace. The medical and scientific community responds to needs as and when they arise but finds difficult to propose a global strategy in the medium and long term. Regarding diagnosis, priority should be given to anticipating the management of re-emerging pathogens, to developing capacities of real-time molecular diagnosis, and to preserving reference expertise and reference biological materials. This effort should also include sero-epidemiological studies aiming at obtaining a more accurate mapping of the circulation of potentially re-emerging pathogens. Regarding therapeutics (with the exception of vaccines which are addressed in another presentation), the expected improvements are the advance implementation of ready-to-use protocol frames for clinical trials and that of an ambitious strategy aiming at gradually covering the taxonomic spectrum of evolutionary virus groups infecting vertebrates. url: https://api.elsevier.com/content/article/pii/S0001407919305710 doi: 10.1016/s0001-4079(19)30571-0 id: cord-332992-8rmqg4rf author: de Vries, A. A. F. title: SARS-CoV-2/COVID-19: a primer for cardiologists date: 2020-07-15 words: 9182.0 sentences: 433.0 pages: flesch: 39.0 cache: ./cache/cord-332992-8rmqg4rf.txt txt: ./txt/cord-332992-8rmqg4rf.txt summary: Although SARS-CoV-2 particles/components have been detected in, for example, endothelial cells, the digestive tract and the liver, not all extrarespiratory manifestations of COVID-19 are necessarily caused by direct viral injury but may also be the consequence of the hypoxaemia, (hyper)inflammatory response, neuroendocrine imbalance and other pathophysiological changes induced by the airway infection [43] . Factors that may contribute to the thrombophilia observed in severely ill COVID-19 patients include the following: (1) a disturbed balance between pro-and anticoagulant activities due to excessive production of proinflammatory cytokines, activation of complement, formation of neutrophil extracellular traps and activation of platelets; (2) inflammation-related endothelial activation; (3) death of SARS-CoV-2-infected endothelial cells; (4) endothelial dysfunction caused by unbalanced angiotensin IIangiotensin II type-1 receptor signalling; (5) formation of prothrombotic antiphospholipid antibodies; (6) immobility-associated reduction of blood flow; (7) hypoxia due to respiratory impairment resulting from SARS-CoV-2-induced lung injury [79] [80] [81] . abstract: In the late autumn of 2019, a new potentially lethal human coronavirus designated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China. The pandemic spread of this zoonotic virus has created a global health emergency and an unprecedented socioeconomic crisis. The severity of coronavirus disease 2019 (COVID-19), the illness caused by SARS-CoV‑2, is highly variable. Most patients (~85%) develop no or mild symptoms, while others become seriously ill, some succumbing to disease-related complications. In this review, the SARS-CoV‑2 life cycle, its transmission and the clinical and immunological features of COVID-19 are described. In addition, an overview is presented of the virological assays for detecting ongoing SARS-CoV‑2 infections and the serological tests for SARS-CoV-2-specific antibody detection. Also discussed are the different approaches to developing a COVID-19 vaccine and the perspectives of treating COVID-19 with antiviral drugs, immunomodulatory agents and anticoagulants/antithrombotics. Finally, the cardiovascular manifestations of COVID-19 are briefly touched upon. While there is still much to learn about SARS-CoV‑2, the tremendous recent advances in biomedical technology and knowledge and the huge amount of research into COVID-19 raise the hope that a remedy for this disease will soon be found. COVID-19 will nonetheless have a lasting impact on human society. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12471-020-01475-1) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s12471-020-01475-1 doi: 10.1007/s12471-020-01475-1 id: cord-002327-tocqabgu author: de Vries, Rory D. title: Viral vector-based influenza vaccines date: 2016-07-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Antigenic drift of seasonal influenza viruses and the occasional introduction of influenza viruses of novel subtypes into the human population complicate the timely production of effective vaccines that antigenically match the virus strains that cause epidemic or pandemic outbreaks. The development of game-changing vaccines that induce broadly protective immunity against a wide variety of influenza viruses is an unmet need, in which recombinant viral vectors may provide. Use of viral vectors allows the delivery of any influenza virus antigen, or derivative thereof, to the immune system, resulting in the optimal induction of virus-specific B- and T-cell responses against this antigen of choice. This systematic review discusses results obtained with vectored influenza virus vaccines and advantages and disadvantages of the currently available viral vectors. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5137548/ doi: 10.1080/21645515.2016.1210729 id: cord-326160-mf0vh6iu author: de Wit, Emmie title: Influenza Virus A/Anhui/1/2013 (H7N9) Replicates Efficiently in the Upper and Lower Respiratory Tracts of Cynomolgus Macaques date: 2014-08-12 words: 6428.0 sentences: 318.0 pages: flesch: 42.0 cache: ./cache/cord-326160-mf0vh6iu.txt txt: ./txt/cord-326160-mf0vh6iu.txt summary: Given the public health importance of this virus, we performed a pathogenicity study of the H7N9 virus in the cynomolgus macaque model, focusing on clinical aspects of disease, radiographic, histological, and gene expression profile changes in the upper and lower respiratory tracts, and changes in systemic cytokine and chemokine profiles during infection. To elucidate global host responses specifically associated with sites of virus-induced airway injury in influenza virus A/Anhui/1/2013-infected macaques, we used microarrays to assess transcriptional profiles induced in lung lesions compared to the adjacent lung tissue. We identified ten compounds in IPA (Table 1) , four of which were perturbagens listed in CMap. We identified two compounds that met our criteria in IPA and CMap, rosiglitazone and simvastatin, predicted to have inhibitory effects on pathological host responses associated with lesions in influenza virus A/Anhui/1/2013-infected animals ( Table 1) . abstract: In March 2013, three fatal human cases of infection with influenza A virus (H7N9) were reported in China. Since then, human cases have been accumulating. Given the public health importance of this virus, we performed a pathogenicity study of the H7N9 virus in the cynomolgus macaque model, focusing on clinical aspects of disease, radiographic, histological, and gene expression profile changes in the upper and lower respiratory tracts, and changes in systemic cytokine and chemokine profiles during infection. Cynomolgus macaques developed transient, mild to severe disease with radiographic evidence of pulmonary infiltration. Virus replicated in the upper as well as lower respiratory tract, with sustained replication in the upper respiratory tract until the end of the experiment at 6 days after inoculation. Virus shedding occurred mainly via the throat. Histopathological changes in the lungs were similar to those observed in humans, albeit less severe, with diffuse alveolar damage, infiltration of polymorphonuclear cells, formation of hyaline membranes, pneumocyte hyperplasia, and fibroproliferative changes. Analysis of gene expression profiles in lung lesions identified pathways involved in tissue damage during H7N9 infection as well as leads for development of therapeutics targeting host responses rather than virus replication. Overall, H7N9 infection was not as severe in cynomolgus macaques as in humans, supporting the possible role of underlying medical complications in disease severity as discussed for human H7N9 infection (H. N. Gao et al., N. Engl. J. Med. 368:2277–2285, 2013, doi:10.1056/NEJMoa1305584). url: https://www.ncbi.nlm.nih.gov/pubmed/25118237/ doi: 10.1128/mbio.01331-14 id: cord-332457-gan10za0 author: de Ángel Solá, David E. title: Weathering the pandemic: How the Caribbean Basin can use viral and environmental patterns to predict, prepare and respond to COVID‐19 date: 2020-04-10 words: 2867.0 sentences: 168.0 pages: flesch: 39.0 cache: ./cache/cord-332457-gan10za0.txt txt: ./txt/cord-332457-gan10za0.txt summary: On March 12, 2020, the World Health Organization (WHO) declared a pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, the pathogen responsible for the clinical disease known as COVID-19. Recently, a pattern favoring cold, dry weather was also observed in Hong Kong in a 6-year-long study, though in this case coronaviruses were found yearround 48 Therefore, data from other coronaviruses and the similar portal of infection discussed above do support the idea that SARS-CoV-2 may follow the same patterns as influenza, and that timing interventions around influenza peaks in the Caribbean would be reasonable. If SARS-CoV-2 interacts with climate and weather as theorized above, it is likely that areas in the Greater Caribbean with Air Surface Temperatures (AST) >25°C and RH>70% might be considered areas of relatively decreased environmental risk (Figure 1 ) 53 . abstract: The 2020 coronavirus pandemic is developing at different paces throughout the world. Some areas, like the Caribbean Basin, have yet to see the virus strike at full force. When it does, there is reasonable evidence to suggest the consequent COVID‐19 outbreaks will overwhelm healthcare systems and economies. This is particularly concerning in the Caribbean as pandemics can have disproportionately higher mortality impacts on lower and middle income countries. Preliminary observations from our team and others suggest that temperature and climatological factors could influence the spread of this novel coronavirus, making spatiotemporal predictions of its infectiousness possible. This review studies geographic and time‐based distribution of known respiratory viruses in the Caribbean Basin in an attempt to foresee how the pandemic will develop in this region. This review is meant to aid in planning short‐ and long‐term interventions to manage outbreaks at the international, national and sub‐national levels in the region. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.25864 doi: 10.1002/jmv.25864 id: cord-001521-l36f1gp7 author: nan title: Oral and Poster Manuscripts date: 2011-04-08 words: 183363.0 sentences: 11362.0 pages: flesch: 53.0 cache: ./cache/cord-001521-l36f1gp7.txt txt: ./txt/cord-001521-l36f1gp7.txt summary: The IC 50 values determined in functional NI assays provide valuable information for detection of resistant viruses, but should not be used to draw direct correlations with drug concentrations needed to inhibit virus replication in the infected human host, as clinical data to support such inferences are inadequate. • Standardized reagents and protocols • Choice of detection technology • Simple instrumentation requirements • High sensitivity for use with low virus concentrations • Compatibility with batch-mode processing and largescale assay throughput • Broad specificity of influenza detection • Flexibility in assay format • Additional NA assay applications -cell-based viral assays, screening for new NIs, detection of NA from other organisms Functional neuraminidase inhibition assays enable detection of any resistance mutation and are extremely important in conjunction with sequence-based screening assays for global monitoring of virus isolates for NI resistance mutations, including known and new mutations. Such new assays need to include methods to measure local antibodies and virus-specific lymphocytes, especially in the case of live attenuated influenza vaccines, because of their potential to induce such broad-based immune responses. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313891/ doi: 10.1111/j.1750-2659.2011.00209.x id: cord-004608-3u00cpsc author: nan title: Arboviren—durch Arthropoden übertragbare Viren: Stellungnahmen des Arbeitskreises Blut des Bundesministeriums für Gesundheit und Soziale Sicherung date: 2004 words: 2798.0 sentences: 356.0 pages: flesch: 48.0 cache: ./cache/cord-004608-3u00cpsc.txt txt: ./txt/cord-004608-3u00cpsc.txt summary: Unter dem Oberbegriff Arboviren (arthropod-borne viruses) werden diejenigen Viren zusammengefasst, die sich sowohl in Arthropoden wie Mücken oder Zecken als auch in Vertebraten (Vögeln, Säugetieren) vermeh-ren. Hantaviren, die zum Genus Hantavirus der Bunyaviridae gehören, werden dagegen nicht von Arthropoden auf den Menschen übertragen, sondern durch dessen Kontakt mit Ausscheidungen der natürlichen Wirte, Mäuse und Ratten. In Deutschland spielt nach dem heutigen Wissensstand nur das Virus der Frühsommermeningoenzephalitis (FSME), das durch Zecken (Ixodes ricinus) übertragen wird, epidemiologisch eine wesentliche Rolle. Für einige Viren, wie etwa West-Nil-Virus (WNV) und St.-Louis-Enzephalitis-Virus (SLEV), wurde nachgewiesen, dass die Virusvermehrung in den Mücken abhängig ist von der durchschnittlichen Umgebungstemperatur. Für verschiedene Erreger wurde gezeigt, dass einerseits infizierte Mücken überwintern können; annahme an Krankheitsfällen bei Menschen in den USA Das Verhältnis von Infektionen zu Erkrankungen wird dabei je nach Erreger und untersuchtem Kollektiv mit 20:1 bis 1.000:1 angegeben. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080098/ doi: 10.1007/s00103-004-0890-8 id: cord-008764-j9qmw4zy author: nan title: Chapter 1 The need for chemotherapy and prophylaxis against viral diseases date: 2008-05-29 words: 6399.0 sentences: 273.0 pages: flesch: 47.0 cache: ./cache/cord-008764-j9qmw4zy.txt txt: ./txt/cord-008764-j9qmw4zy.txt summary: We shall examine the methods developed for the prevention of measles, influenza, polio and rotaviruses later on (Chapters 8, 7, 4 and 9, respectively) but it may be mentioned here that live polio vaccines used so successfully in industrialized countries are much more difficult to apply successfully in third world countries where problems of vaccine administration, heat lability control and viral interference become very important. The greatest challenges and probably the most difficult and medically important areas for prophylaxis and therapy of viral diseases are those viruses which are rapidly changing in antigenic composition and/or viruses with animal reservoirs (influenza and arboviruses) and also those forming latent infections (herpesviruses). The greatest challenges and probably the most difficult and medically important areas for prophylaxis and therapy of viral diseases are those viruses which are rapidly changing in antigenic composition and/or viruses with animal reservoirs (influenza and arboviruses) and also those forming latent infections (herpesviruses). abstract: The chapter discusses the need for chemotherapy and prophylaxis against viral diseases. It briefly mentions clinical diseases and syndromes such as influenza, respiratory tract infections, hepatitis, and arbovirus infections resulting from virus infections. Viruses causing respiratory diseases, as well as many other diseases in humans are also discussed in the chapter. It describes the vaccines that are used to check the attack of different viruses as well as their cost-effectiveness. There is a list of some viruses that have been ranked according to different variables in an attempt to select a good candidate for an antiviral drug. The incidence of the viral disease is naturally an important factor, as is the severity of the disease. The incidence can be obtained for diseases being reported in accordance with local regulations, but in many cases viral diseases are not reported and the incidence has to be calculated from different surveys. Also, a grading of the severity is not easy and an example is when herpesvirus infections are handled as a group, which includes both herpes encephalitis and cold sores. The greatest challenges and probably the most difficult and medically important areas for prophylaxis and therapy of viral diseases are the viruses that are rapidly changing in antigenic composition and/or viruses with animal reservoirs (influenza and arboviruses) and those forming latent infections (herpesviruses). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7134146/ doi: 10.1016/s0168-7069(08)70009-0 id: cord-014462-11ggaqf1 author: nan title: Abstracts of the Papers Presented in the XIX National Conference of Indian Virological Society, “Recent Trends in Viral Disease Problems and Management”, on 18–20 March, 2010, at S.V. University, Tirupati, Andhra Pradesh date: 2011-04-21 words: 35453.0 sentences: 1711.0 pages: flesch: 49.0 cache: ./cache/cord-014462-11ggaqf1.txt txt: ./txt/cord-014462-11ggaqf1.txt summary: Molecular diagnosis based on reverse transcription (RT)-PCR s.a. one step or nested PCR, nucleic acid sequence based amplification (NASBA), or real time RT-PCR, has gradually replaced the virus isolation method as the new standard for the detection of dengue virus in acute phase serum samples. Non-genetic methods of management of these diseases include quarantine measures, eradication of infected plants and weed hosts, crop rotation, use of certified virus-free seed or planting stock and use of pesticides to control insect vector populations implicated in transmission of viruses. The results of this study indicate that NS1 antigen based ELISA test can be an useful tool to detect the dengue virus infection in patients during the early acute phase of disease since appearance of IgM antibodies usually occur after fifth day of the infection. The studies showed high level of expression in case of constructed vector as compared to infected virus for the specific protein. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3639731/ doi: 10.1007/s13337-011-0027-2 id: cord-015619-msicix98 author: nan title: Virus Structure & Assembly date: 2009-02-24 words: 3302.0 sentences: 164.0 pages: flesch: 45.0 cache: ./cache/cord-015619-msicix98.txt txt: ./txt/cord-015619-msicix98.txt summary: The studies were performed with nanoindentation techniques using an Atomic Force Microscope (AFM), an approach which is becoming a standard method to measure the mechanical properties of viral particles (1, 2) . Using molecular dynamics simulations of the connector in complex with DNA, and aiming at distinguishing between these three models, we calculated mechanical properties of this system. The bacteriophage lambda is composed of an icosahedral capsid, into which a 48.5 kbp double-stranded DNA genome is packaged, and a long non-contractile tail consisting of 34 disk-like structures. The relative probabilities of fusion and endocytosis of a virus particle initially nonspecifically adsorbed on the host cell membrane are computed as functions of receptor concentration, binding strength, and number of spikes. As revealed by techniques of structural biology and single-molecule experimentation, the capsids of viruses are some of nature''s best examples of highly symmetric multiscale self-assembled structures with impressive mechanical properties of strength and elasticity. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7111173/ doi: 10.1016/s0006-3495(08)79065-9 id: cord-017752-ofzm3x3a author: nan title: Theories of Carcinogenesis date: 2007 words: 12289.0 sentences: 692.0 pages: flesch: 47.0 cache: ./cache/cord-017752-ofzm3x3a.txt txt: ./txt/cord-017752-ofzm3x3a.txt summary: Others attributed the simplified enzyme patterns of cancerous cells to a regression of the tumor tissues to early embryonal stages of development. Viral DNA is frequently integrated into the cancer cells, but additional agents or factors may be involved at various stages of the progression to invasive carcinoma. The encounter with a family, in which many members developed breast or liver cancer, led Pierre Paul Broca to hypothesize, in 1866, that an inherited abnormality within the affected tissue caused the tumor development [Broca 1866 Theodor Boveri (1862 Boveri ( -1915 then proposed that defects in chromosomes lead to malignancy [Boveri 1914 ]. Any mutation of cancer associated genes can be handed on to following generations and predispose the affected cells to malignant transformation in the case of additional DNA damage. Further developments in tumor immunology have led to models of selection and evolution of cancer cells. abstract: The oldest description of human cancer, referring to eight cases of tumors of the breast, was found in the Egyptian Edwin Smith Papyrus, written around 3000–1500 BC. The oldest specimens of human cancers were detected in the remains of a female skull dating back to the Bronze Age (1900–1600 BC), and in fossilized bones of ancient Egypt. The mummified skeletal remains of Peruvian Incas, dating about 2,400 years ago, contained lesions suggestive of malignant melanoma. The term “cancer” goes back to Hippocrates (460–370 BC), who named a group of diseases καρκινοσ and καρκινομα, the ancient Greek word for crab. It is a metaphor for the hard center and spiny projections of the tumors he studied. Cancer is the Latin word for crab and its use has been traced back to Galen (AD 129–199). A snapshot of theories of carcinogenesis, devised in the course of the last two centuries, reflects the progress of insight from the cellular level via biochemistry to an understanding of damaging influences and oncogenes, and to a more wholistic approach in the regulatory theory. It shows the relative success of reductionism as well as the current need to put the insights of various research endeavors into broader paradigmatic contexts. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122402/ doi: 10.1007/978-1-4020-6016-8_1 id: cord-020010-q58x6xb0 author: nan title: 19th ICAR Abstracts: date: 2006-03-13 words: 46663.0 sentences: 2181.0 pages: flesch: 44.0 cache: ./cache/cord-020010-q58x6xb0.txt txt: ./txt/cord-020010-q58x6xb0.txt summary: In the present study we reported the antiviral activity of neuraminidase inhibitor oseltamivir against lethal H5N1 influenza virus infection in ferrets, an appropriate animal model that closely resembles clinical signs of human influenza. Earl Kern 1 , Kathy Keith 2 , Robert Jordan 2 , Dennis Hruby 2 , Debra Quenelle 2 1 Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL, USA; 2 SIGA Technologies, Inc., Corvallis, OR, USA Although cidofovir (CDV) has been approved as an investigational new drug for emergency treatment of smallpox, its lack of oral activity and dose limiting toxicity dictates a need for continued development of better therapeutic agents for this potential bioterror disease. The in vitro antiviral activity of one of the most selective compounds, i.e. CHI-033, was assessed by (i) MTS-based cytopathic effect assays, (ii) virus yield reduction assays, (iii) real-time quantitative PCR (RT-QPCR) and (iv) by monitoring viral antigen expression. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133865/ doi: 10.1016/j.antiviral.2006.02.001 id: cord-020087-gs0pc6ee author: nan title: Cumulative Contents for 2010 date: 2010-11-18 words: 479.0 sentences: 43.0 pages: flesch: 37.0 cache: ./cache/cord-020087-gs0pc6ee.txt txt: ./txt/cord-020087-gs0pc6ee.txt summary: Myristoylation of the small envelope protein of porcine reproductive and respiratory syndrome virus is non-essential for virus infectivity but promotes its growth 294 Porcine reproductive and respiratory syndrome virus (PRRSV) could be sensed by professional beta interferon-producing Hikichi (Japan) The 126-and/or 183-kDa replicases or their coding regions are responsible both for inefficient local and for systemic movements of Paprika mild mottle virus Japanese strain in tomato plants USA) Genetic control of host resistance to porcine reproductive and respiratory syndrome virus (PRRSV) infection Porcine reproductive and respiratory syndrome virus (PRRSV) in serum and oral fluid samples from individual boars: Will oral fluid replace serum for PRRSV surveillance USA) Use of a production region model to assess the efficacy of various air filtration systems for preventing airborne transmission of porcine reproductive and respiratory syndrome virus and Mycoplasma hyopneumoniae: Results from a 2-year study 177 Morrison (USA) Control and elimination of porcine reproductive and respiratory syndrome virus 185 Cumulative Author Index for abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7134101/ doi: 10.1016/s0168-1702(10)00397-7 id: cord-020097-eh5deunk author: nan title: Cumulative Author Index for 2006 (Volumes 115–122) date: 2006-10-27 words: 1481.0 sentences: 87.0 pages: flesch: 28.0 cache: ./cache/cord-020097-eh5deunk.txt txt: ./txt/cord-020097-eh5deunk.txt summary: Modulation of PKR activity in cells infected by bovine viral diarrhea virus Complete genome analysis of RFLP 184 isolates of porcine reproductive and respiratory syndrome virus Phylogenetic analysis of the gag region encoding the matrix protein of small ruminant lentiviruses: Comparative analysis and molecular epidemiological applications TATAbinding protein and TBP-associated factors during herpes simplex virus type 1 infection: Localization at viral DNA replication sites Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein Efficient inhibition of hepatitis B virus replication by small interfering RNAs targeted to the viral X gene in mice Preparation and characterization of a novel monoclonal antibody specific to severe acute respiratory syndrome-coronavirus nucleocapsid protein A deletion and point mutation study of the human papillomavirus type 16 major capsid gene Sequencing and comparative analysis of a pig bovine viral diarrhea virus genome Antigenic structure analysis of glycosylated protein 3 of porcine reproductive and respiratory syndrome virus abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7134138/ doi: 10.1016/s0168-1702(06)00318-2 id: cord-020101-5rib7pe8 author: nan title: Cumulative Author Index for 2008 date: 2008-11-17 words: 2140.0 sentences: 126.0 pages: flesch: 29.0 cache: ./cache/cord-020101-5rib7pe8.txt txt: ./txt/cord-020101-5rib7pe8.txt summary: Cauliflower mosaic virus gene VI product N-terminus contains regions involved in resistance-breakage, self-association and interactions with movement protein Intrahost evolution of envelope glycoprotein and OrfA sequences after experimental infection of cats with a molecular clone and a biological isolate of feline immunodeficiency virus DC-SIGN enhances infection of cells with glycosylated West Nile virus in vitro and virus replication in human dendritic cells induces production of Increase in proto-oncogene mRNA transcript levels in bovine lymphoid cells infected with a cytopathic type 2 bovine viral diarrhea virus Complete genome sequence analysis of dengue virus type 2 isolated in Modulation of hepatitis B virus replication by expression of polymerasesurface fusion protein through splicing: Implications for viral persistence Induction of apoptosis in Vero cells by Newcastle disease virus requires viral replication, de-novo protein synthesis and caspase activation Mechanisms of inhibition of HIV replication by non-nucleoside reverse transcriptase inhibitors abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7134142/ doi: 10.1016/s0168-1702(08)00367-5 id: cord-020235-stcrozdw author: nan title: Abstracts of Papers Presented at the 38th Meeting of the Deutsche Gesellschaft für Hygiene und Mikrobiologie, Virology Section, Göttingen, 5.–8.10.1981 date: 2012-03-15 words: 13494.0 sentences: 843.0 pages: flesch: 58.0 cache: ./cache/cord-020235-stcrozdw.txt txt: ./txt/cord-020235-stcrozdw.txt summary: Hepatitis A virus (HAV) was isolated directly from human stool in diploid human fibroplasrs, Viral antigen was expressed only after 210 days of incubation of the infected cultures. Univ., 0-8700 Wiirzburg Effect of Measles (SSPE) Antiserum on Viral Surface Proteins and Hormone Receptor Activity in C6/SSPE Persistently Infected Cells BARRETT, P. Inst, of Genetics, Univ., 0-5000 Co logne Virus-Cell DNA Recombinants in Human Cells Lytically Infected by Ad2 NEUMANN, R., WEYER, U., and DOERFLER, W. In vitro, however, the gag-specific peptide sequences are cleaved off upon addition of the purified viral piS protease; in the case of the replication-defective, transforming avian sarcoma virus PRC II the cleaved nongag part has a ryrosine-phosphorylaring kinase activity similar to that described for the RSV src-gene product pp60 src . f. Virologie, Univ., D·6300 Giefen, 3 A protein of a molecular weight of about 38.000 d has been found to be phosphorylated 1 h after the onset of cell transformation by Rous sarcoma virus (RSV). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7134445/ doi: 10.1016/s0174-3031(82)80128-5 id: cord-022822-7346069t author: nan title: Infections, Immunity & their Effects on Asthma date: 2006-10-02 words: 3292.0 sentences: 148.0 pages: flesch: 30.0 cache: ./cache/cord-022822-7346069t.txt txt: ./txt/cord-022822-7346069t.txt summary: The mechanisms underlying the association between RSV bronchiolitis and the later development of wheezing are incompletely understood, though there is increasing evidence that impaired antiviral immunity is likely to play an important role in increasing susceptibility to virus infections early in life, as well as perhaps the later development of asthma [3] . Areas that particularly require attention include interplay between the innate and acquired immune responses in host defence; the role of viral persistence in development of wheezing illness and asthma; the roles of antigen presenting cells and other specific cell compartments such as epithelial cells, T cells, neutrophils, eosinophils and non T cell lymphocytes in host protection and disease severity. Further studies investigating the importance of different virus types in the association between lower respiratory infection in infancy and wheezing illness in asthma are required to clarify the relationships, including rhinovirus, human metapneumoviruses, coronaviruses and bocaviruses. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162137/ doi: 10.1111/j.1365-2222.2006.02583_7.x id: cord-022980-tkii8se4 author: nan title: Diarrhea date: 2008-03-05 words: 303.0 sentences: 19.0 pages: flesch: 52.0 cache: ./cache/cord-022980-tkii8se4.txt txt: ./txt/cord-022980-tkii8se4.txt summary: Nevertheless, until recently gastro-enteritis provided a poor hunting ground for virologists for, although such viruses as adenoviruses, echoviruses and Coxsackie viruses could be isolated from the stools of patients with acute gastro-enteritis, they could often be recovered with almost equal frequency from those without diarrhoeal disease, particularly in developing countries. However, the examination of negatively stained faecal preparations from patients witb gastro-enteritis by electron microscopy has resulted in the discovery of many viruses, some of which, for example, rotaviruses and such parovirus-like viruses as the Norwalk agent, are undoubtedly the cause of acute gastroenteritis. In general, in vitro cultivation of viruses causing gastroenteritis in humans is either not possible or extremely difficult and of little value for routine diagnostic purposes but, since they are often excreted in very high titres, they may be detected without difficulty by electron microscopic examination of faecal extracts,-Banatvala jE: Viruses and Diarrhoes, Trans R Soc Trop Med Hyg 73: 503, 1979. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165543/ doi: 10.1111/j.1365-4362.1980.tb00268.x id: cord-023143-fcno330z author: nan title: Molecular aspects of viral immunity date: 2004-02-19 words: 43425.0 sentences: 2056.0 pages: flesch: 47.0 cache: ./cache/cord-023143-fcno330z.txt txt: ./txt/cord-023143-fcno330z.txt summary: Based on a variety of experimental evidence, it is clear that demyelination induced in SJUJ mice by infection with the BeAn strain of TMEV is a Thl-mediated event: (a) disease induction is suppressed in T cell-deprived mice and by in vivo treatment with anti-I-A and anti-CD4 antibodies; (b) disease susceptibility correlates temporally with the development of TMEV-specific, MHC-class Il-restricted DTH responses and with a predominance of anti-viral lgG2a antibody; (c) activated (Le., lL-2RC) T cells infiltrating the CNS are exclusively of the CD4+ phenotype, and (d) proinflammatory cytokines (IFNq and TNF-p) are predominantly produced in the CNS. These results have important implications for a possible viral trigger in MS as they indicate that chronic demyelination in TMEV-infected mice is initiated in the absence of demonstrable neuroantigen-specific autoimmune responses and are consistent with a model wherein early myelin damage is mediated via primarily by mononuclear phagocytes recruited to the CNS and activated by pro-inflammatory cytokines produced by TMEV-specific Thl cells. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167094/ doi: 10.1002/jcb.240591009 id: cord-023564-kpqvyxxe author: nan title: Viral gastroenteritis: Causes, pathophysiology, immunology, treatment, and epidemiology date: 2004-09-14 words: 2512.0 sentences: 145.0 pages: flesch: 45.0 cache: ./cache/cord-023564-kpqvyxxe.txt txt: ./txt/cord-023564-kpqvyxxe.txt summary: This chapter discusses the causes, pathophysiology, immunology, treatment, and epidemiology of viral gastroenteritis. Infection with gastroenteritis agents can be asymptomatic or can be followed by mild or severe disease, including vomiting or diarrhea or both, and can be fatal because of severe dehydration. Infection with gastroenteritis agents can be asymptomatic, or be followed by mild or severe disease including vomiting or diarrhoea or both, and can be fatal as a consequence of severe dehydration. The main diarrhoeogenic agents comprise four virus families: rotaviruses, enteric adenoviruses, human caliciviruses (Norwalk-and Sapporo-like viruses, now termed noro-and sapoviruses) and astroviruses, and cause diarrhoea at frequencies of 20-30%, 5%, 5-10%, and 5%, respectively. By contrast, epidemic disease is found in all ages, mainly caused by Norwalk-and Sapporo-like viruses (human caliciviruses), rotaviruses of group B (in China), and sometimes astroviruses. Systemic and intestinal antibody secreting cell responses and correlates of protective immunity to human rotaviruses in a gnotobiotic pigs model of disease abstract: This chapter discusses the causes, pathophysiology, immunology, treatment, and epidemiology of viral gastroenteritis. Acute gastroenteritis is one of the most common illnesses affecting humans and may be caused by a large variety of different microbes. Infection with gastroenteritis agents can be asymptomatic or can be followed by mild or severe disease, including vomiting or diarrhea or both, and can be fatal because of severe dehydration. The spectrum of causative agents differs in developed and developing countries. Besides rotaviruses (RVs) as the main etiologic agent, there are many other viral causes of diarrhea. The main diarrheagenic agents comprise four virus families: RVs, enteric adenoviruses (Ads), human caliciviruses (CVs), and astroviruses. Treatment of infantile diarrhea is mainly by oral or intravenous rehydration. Several formulas of oral rehydration solution (ORS) have been devised and are recommended. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172247/ doi: 10.1016/s0168-7069(03)09001-3 id: cord-023608-w2g7v7g1 author: nan title: ISAR News date: 2017-10-20 words: 6059.0 sentences: 284.0 pages: flesch: 48.0 cache: ./cache/cord-023608-w2g7v7g1.txt txt: ./txt/cord-023608-w2g7v7g1.txt summary: ICAR retains its flavor and personality, providing an interdisciplinary forum at which investigators involved in basic, translational, and clinical research worldwide meet to review recent developments in all areas of antiviral research, drug and vaccine development. Additionally, satellite activities such as the Women in Science Roundtable, the Career Development Panel and the New Member and First Time Attendee luncheon (The Happy Hour) provided an opportunity to discuss other issues of relevance. With so many different competing conferences and meetings to attend and a long economic crisis of which scientific research did not escape, ISAR has gone through great financial efforts to continue supporting the participation of students, postdocs and young investigators. The TCFF Awards support the professional development of women with potential to make significant contributions to the field of Antiviral Research by providing funds to attend a conference, visit another laboratory, take a course, or acquire specialized training. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172721/ doi: 10.1016/s0166-3542(17)30664-2 id: cord-023622-tul7bonh author: nan title: Rotaviruses of Man and Animals date: 1975-02-01 words: 1952.0 sentences: 100.0 pages: flesch: 51.0 cache: ./cache/cord-023622-tul7bonh.txt txt: ./txt/cord-023622-tul7bonh.txt summary: Certainly bacterial pathogens may cause both sporadic and epidemic gastroenteritis in children, but they cannot be isolated in up to 75% of cases.2, 3 Whilst it is true that some investigations suggest that enteroviruses or adenoviruses may occasionally cause localised outbreaks of gastroenteritis,4-7 others have shown that these viruses may be detected almost as frequently in controls as among patients. Employing negativestaining techniques on fsecal extracts, FLEWETT and his colleagues found similar particles in children with gastroenteritis in Birmingham 13; indeed, if virologists had only looked at such simply prepared specimens, there is no technical reason why these viruses could not have been detected, say, 15 years ago. Thus, existing evidence suggests that rotaviruses are the most important cause of infantile gastroenteritis throughout the world, but as yet only a limited number of specimens have been examined from those tropical areas where mortality-rates are particularly high. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172916/ doi: 10.1016/s0140-6736(75)91148-4 id: cord-327883-s9nbr5y8 author: nan title: Section Virology date: 1990-03-31 words: 10576.0 sentences: 571.0 pages: flesch: 48.0 cache: ./cache/cord-327883-s9nbr5y8.txt txt: ./txt/cord-327883-s9nbr5y8.txt summary: By improving the enzyme-linked immunosorbent assay (ELISA) for HSV-2-antibodies and additional testing of sera by Western blot, we were able to specifically identify HSV-l-and HSV-2-antibodies in serum samples. To get some insight into the molecular basis of processes controlling the viral expression we studied the sequence-specific DNA-protein interactions within the genomic regulatory regions. for Med. Microbiology, Univ., D-5300 Bonn Semiquantitative detection of Hepatitis B Virus (HBV) DNA in sera of infected individuals has become an important means of modern serological hepatitis diagnostics. THOMSSEN 1 In the course of acute Epstein-Barr virus (EBV) infection IgM antibodies always occur against two cellular antigens that were characterized as proteins with a molecular weight of 26 kD (p26) and 29 kD (p29), respectively. The frequency and specificity of antibodies to P-gene encoded proteins of human hepatitis B virus was tested in sera of acute and chronically infected patients with and without hepatocellular carcinoma (HCC). abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0934884011800393 doi: 10.1016/s0934-8840(11)80039-3 id: cord-340489-yo3cp5vs author: nan title: KAPITEL 13 Infektionskrankheiten date: 2008-12-31 words: 26536.0 sentences: 3917.0 pages: flesch: 45.0 cache: ./cache/cord-340489-yo3cp5vs.txt txt: ./txt/cord-340489-yo3cp5vs.txt summary: Die Wirksamkeit von BVDU bei VZV-Infektionen (Varizellen und Zoster) immunkompromittierter Patienten ist durchaus sehr gut und vergleichbar der von i.v. verabreichtem Aciclovir, jedoch fällt die Nutzen-Risiko-Betrachtung insgesamt auch bei VZV-Therapie zu Gunsten von Aciclovir aus, da BVDU eher mutagen zu sein scheint und nicht zusammen mit 5-Fluorouracil (Zytostatikum) gegeben werden darf. In klinischen Studien konnte durch Anwendung von ACV bei EBV-Infektionen auch die Virusausscheidung deutlich vermindert werden, ein wesentlicher Einfluss auf den Krankheitsverlauf ließ sich nicht erreichen. Typisch für viele opportunistische Erreger ist, dass sie weit verbreitet sind und nach einer Primärinfektion, die bereits vor der HIV-Infektion stattfindet, zu latenten Infektionen führen. Die Prophylaxe von Infektionen bereits vor deren erstem Auftreten (Primärprophylaxe) oder nach der ersten Episode (Sekundärprophylaxe) ist weiterhin eine wichtige Aufgabe bei der Betreuung HIV-positiver Patienten, auch wenn opportunistische Infektionen durch die antiretrovirale Therapie insgesamt seltener geworden sind. abstract: Zur Orientierung Infektionskrankheiten werden durch Pathogene verursacht, die sich im Wirt vermehren: Ektoparasiten, Helminthen, Protozoen, Pilze, Bakterien, Viren, Prionen. Infektionskrankheiten können alle Organe bzw. Organsysteme befallen. Entstehung und Verlauf werden durch Faktoren beeinflusst, die sich grob einteilen lassen in Erreger- und Wirtsfaktoren. Die Kenntnis und richtige Einschätzung dieser Faktoren sind entscheidend für Diagnostik und Therapie dieser Erkrankungen. url: https://api.elsevier.com/content/article/pii/B9783437428319100130 doi: 10.1016/b978-3-437-42831-9.10013-0 id: cord-350703-vrqltz3s author: nan title: ISAR News date: 2016-01-31 words: 11202.0 sentences: 497.0 pages: flesch: 45.0 cache: ./cache/cord-350703-vrqltz3s.txt txt: ./txt/cord-350703-vrqltz3s.txt summary: She is studying the response of primary human mononuclear cells to dengue virus infection, aiming to establish a more relevant in vitro model for antiviral drug testing and to identify potential new antiviral targets, using genome-wide transcriptomic analysis. According to ISAR member Robert Jordan, who heads the Gilead team developing antivirals against respiratory viruses, the parent compound was originally discovered as part of the hepatitis C program, targeting the HCV polymerase, but the strong clinical efficacy of sofosbuvir, especially in combination with ledipasvir, resulted in the molecule being evaluated for other indications, including respiratory viruses such as respiratory syncytial virus (RSV). ISAR members know Andrea (standing, above, with Cardiff colleague Salvatore Ferla) as the winner of the 2013 Prusoff Young Investigator Award, but not all of us are familiar with the direction of his career, which has increasingly explored the use of computer-based methods to design new antivirals and anticancer drugs. abstract: nan url: https://api.elsevier.com/content/article/pii/S0166354215002867 doi: 10.1016/s0166-3542(15)00286-7 id: cord-257019-lj1yzjn0 author: ter MEULEN, V. title: Mechanisms and Consequences of Virus Persistence in the Human Nervous System date: 2006-12-16 words: 5189.0 sentences: 304.0 pages: flesch: 44.0 cache: ./cache/cord-257019-lj1yzjn0.txt txt: ./txt/cord-257019-lj1yzjn0.txt summary: Virus penetration may result in acute encephalitis, but occasionally a persistent infection is established that leads to a fatal slowly progressing disease, subacute sclerosing panencephalitis (SSPE). However, virus expression may sometimes be rescued from this infected tissue by co-cultivation procedure^.''^ These experiments have therefore confirmed that measles virus is the etiological agent of SSPE and also indicated that virus persistence may be based on some defect in the virus maturation process that could involve some form of host effect. The case of PRP is an exception; infectious virus may be isolated directly despite a strong antibody response in both serum and CSF.M Similarly, the cell-mediated immune system does not show any specific deficien~y.*~.~'' However, the site of rubella virus antigen expression has not yet been identified during this disease process. Similarly, chronic echovirus infection is associated with immune deficiency, and although inflammatory processes are observed in extraneural tissue, it seems unlikely that C N S damage is largely caused by virus-mediated cell destruction. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/6398025/ doi: 10.1111/j.1749-6632.1984.tb14778.x id: cord-288111-0ufc54kw author: ter MEULEN, VOLKER title: Autoimmune Reactions Against Myelin Basic Protein Induced by Corona and Measles Viruses date: 2006-12-17 words: 2851.0 sentences: 153.0 pages: flesch: 37.0 cache: ./cache/cord-288111-0ufc54kw.txt txt: ./txt/cord-288111-0ufc54kw.txt summary: What apparently happens is that the viruses themselves induce Ia expression on the astrocytes, enabling these cells to present the viral antigens to the lymphocytes and allowing the host to mount an effective immune response to control the infection. However, in extremely high constitutive levels of class I1 expression on astrocytes, an inappropriate or excessive presentation of self-antigens and viral antigens may develop, similar to that in autoimmune processes directed against the thyroid gland.''" This mechanism could well play a role in the JHM-and measles-virus-induced CNS disease in Lewis rats, because as recently shown by us," these hyperexpressions of Ia molecules on astrocytes after contact with gamma-interferon or viral particles are genetically regulated. JHM and measles virus infections in rats are models of a persistent viral infection of the CNS with and without demyelination, associated with a cell-mediated immune reaction to MBP. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/2462802/ doi: 10.1111/j.1749-6632.1988.tb27062.x id: cord-354151-psog34u3 author: van Asten, Liselotte title: Early occurrence of influenza A epidemics coincided with changes in occurrence of other respiratory virus infections date: 2015-12-11 words: 4227.0 sentences: 203.0 pages: flesch: 40.0 cache: ./cache/cord-354151-psog34u3.txt txt: ./txt/cord-354151-psog34u3.txt summary: METHODS: We investigated time trends of and the correlation between positive laboratory diagnoses of eight common viruses in the Netherlands over a 10‐year time period (2003–2012): influenza viruses types A and B, respiratory syncytial virus (RSV), rhinovirus, coronavirus, norovirus, enterovirus, and rotavirus. [1] [2] [3] [4] A few population-level studies in Europe were based on observations in one respiratory season only (the 2009 H1N1 pandemic) in which the annually recurring influenza epidemic occurred relatively early. Almost all of the included respiratory viruses (influenza A and B virus, RSV, coronavirus) except rhinovirus showed very clear seasonality in their reporting over time. Viruses that showed a shifted trend of reporting during years with early influenza A epidemics were of respiratory nature with clear winter seasonality and with epidemics occurring relatively close in time to influenza A virus epidemics. abstract: BACKGROUND: Viral interaction in which outbreaks of influenza and other common respiratory viruses might affect each other has been postulated by several short studies. Regarding longer time periods, influenza epidemics occasionally occur very early in the season, as during the 2009 pandemic. Whether early occurrence of influenza epidemics impacts outbreaks of other common seasonal viruses is not clear. OBJECTIVES: We investigated whether early occurrence of influenza outbreaks coincides with shifts in the occurrence of other common viruses, including both respiratory and non‐respiratory viruses. METHODS: We investigated time trends of and the correlation between positive laboratory diagnoses of eight common viruses in the Netherlands over a 10‐year time period (2003–2012): influenza viruses types A and B, respiratory syncytial virus (RSV), rhinovirus, coronavirus, norovirus, enterovirus, and rotavirus. We compared trends in viruses between early and late influenza seasons. RESULTS: Between 2003 and 2012, influenza B, RSV, and coronavirus showed shifts in their occurrence when influenza A epidemics occurred earlier than usual (before week 1). Although shifts were not always consistently of the same type, when influenza type A hit early, RSV outbreaks tended to be delayed, coronavirus outbreaks tended to be intensified, and influenza virus type B tended not to occur at all. Occurrence of rhinovirus, norovirus, rotavirus, and enterovirus did not change. CONCLUSION: When influenza A epidemics occured early, timing of the epidemics of several respiratory winter viruses usually occurring close in time to influenza A was affected, while trends in rhinoviruses (occurring in autumn) and trends in enteral viruses were not. url: https://doi.org/10.1111/irv.12348 doi: 10.1111/irv.12348 id: cord-261241-eqf6ame6 author: van Beek, Josine title: Influenza-like Illness Incidence Is Not Reduced by Influenza Vaccination in a Cohort of Older Adults, Despite Effectively Reducing Laboratory-Confirmed Influenza Virus Infections date: 2017-08-15 words: 4445.0 sentences: 243.0 pages: flesch: 49.0 cache: ./cache/cord-261241-eqf6ame6.txt txt: ./txt/cord-261241-eqf6ame6.txt summary: The aim of this prospective observational study was to determine the relative contribution of influenza virus and other respiratory pathogens to ILI in older adults (aged ≥60 years) in 2 consecutive seasons in the Netherlands. In 60.8% (2011-2012) and 44.7% (2012-2013) of ILI samples, potential pathogens other than influenza virus were detected (Figure 3 ; Supplementary Table 1 ). Coronaviruses of all 4 common human subtypes (18.2% in 2011-2012 and 11.3% in 2012-2013), human metapneumovirus (hMPV) (20.3% and 3.6%), rhinoviruses (8.4% and 21.1%), respiratory syncytial virus (RSV) (4.9% and 6.5%), and parainfluenza viruses (2.8% and 5.1%) were detected in >5% of the ILI samples in at least 1 season. In this study in a cohort of community-dwelling older adults in the Netherlands, we show that influenza virus was present in 18.9% and 34.2% of ILI cases in 2 consecutive seasons and that influenza vaccination significantly reduced laboratory-confirmed influenza virus infection. Effectiveness of seasonal influenza vaccine in community-dwelling elderly people: a meta-analysis of test-negative design case-control studies abstract: BACKGROUND: Data on the relative contribution of influenza virus and other respiratory pathogens to respiratory infections in community-dwelling older adults (≥60 years) are needed. METHODS: A prospective observational cohort study was performed in the Netherlands during 2 winters. Nasopharyngeal and oropharyngeal swabs were collected during influenza-like illness (ILI) episodes and from controls. Viruses and bacteria were identified by multiplex ligation–dependent probe amplification assay and conventional bacterial culture. RESULTS: The ILI incidence in the consecutive seasons was 7.2% and 11.6%, and influenza virus caused 18.9% and 34.2% of ILI episodes. Potential pathogen were detected in 80% of the ILI events with influenza virus, coronaviruses, rhinoviruses, human metapneumovirus, respiratory syncytial virus, parainfluenza viruses, and Haemophilus influenzae being the most common. Influenza vaccination reduced influenza virus infection by 73% (95% confidence interval [CI], 26%–90%) and 51% (95% CI, 7%–74%) in ILI patients. However, ILI incidence was similar between vaccinated (7.6% and 10.8%) and nonvaccinated (4.2% and 11.4%) participants in 2011–2012 and 2012–2013, respectively (P > .05). CONCLUSIONS: Influenza virus is a frequent pathogen in older adults with ILI. Vaccination reduces the number of influenza virus infections but not the overall number of ILI episodes: other pathogens fill the gap. We suggest the existence of a pool of individuals with high susceptibility to respiratory infections. CLINICAL TRIALS REGISTRATION: NTR3386. url: https://doi.org/10.1093/infdis/jix268 doi: 10.1093/infdis/jix268 id: cord-291860-dw1sfzqx author: van Boheemen, Sander title: Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients date: 2019-12-16 words: 5398.0 sentences: 276.0 pages: flesch: 40.0 cache: ./cache/cord-291860-dw1sfzqx.txt txt: ./txt/cord-291860-dw1sfzqx.txt summary: Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. Clinical sensitivity was analyzed using the optimized procedure, which in short consisted of total nucleic acid extraction, including internal controls (1:100 dilution); the adapted New England Biolabs Next library preparation protocol, including fragmentation with zinc, for combined RNA and DNA detection (see Library Preparation); and sequencing of 10 million reads (Illumina NextSeq 500). The Centrifuge default settings, with NCBI''s nucleotide database and assignment of sequence reads to a maximum of five labels per sequence, resulted in various spurious classifications ( Figure 4) [eg, Lassa virus ( Figure 5 ), evidently highly unlikely to be present in patient samples from the Netherlands with respiratory complaints]. abstract: Viruses are the main cause of respiratory tract infections. Metagenomic next-generation sequencing (mNGS) enables unbiased detection of all potential pathogens. To apply mNGS in viral diagnostics, sensitive and simultaneous detection of RNA and DNA viruses is needed. Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. The sequencing protocol and bioinformatics analysis were designed and optimized, including exogenous internal controls. Subsequently, the protocol was retrospectively validated using 25 clinical respiratory samples. The developed protocol using Illumina NextSeq 500 sequencing showed high repeatability. Use of the National Center for Biotechnology Information’s RefSeq database as opposed to the National Center for Biotechnology Information’s nucleotide database led to enhanced specificity of classification of viral pathogens. A correlation was established between read counts and PCR cycle threshold value. Sensitivity of mNGS, compared with PCR, varied up to 83%, with specificity of 94%, dependent on the cutoff for defining positive mNGS results. Viral pathogens only detected by mNGS, not present in the routine diagnostic workflow, were influenza C, KI polyomavirus, cytomegalovirus, and enterovirus. Sensitivity and analytical specificity of this mNGS protocol were comparable to PCR and higher when considering off-PCR target viral pathogens. One single test detected all potential viral pathogens and simultaneously obtained detailed information on detected viruses. url: https://www.sciencedirect.com/science/article/pii/S1525157819304325 doi: 10.1016/j.jmoldx.2019.10.007 id: cord-330508-uilejxmi author: van den Hoogen, Bernadette title: Immunometabolism pathways as the basis for innovative anti-viral strategies (INITIATE): A Marie Sklodowska-Curie innovative training network date: 2020-07-28 words: 1781.0 sentences: 80.0 pages: flesch: 30.0 cache: ./cache/cord-330508-uilejxmi.txt txt: ./txt/cord-330508-uilejxmi.txt summary: While molecular details of the innate immune response are well characterized, this research field is now being revolutionized with the recognition that cell metabolism has a major impact on the antiviral and inflammatory responses to virus infections. While molecular details of the innate immune response are well characterized, this research field is now being revolutionized with the recognition that cell metabolism has a major impact on the antiviral and inflammatory responses to virus infections. A detailed understanding of the role of metabolic regulation with respect to antiviral and inflammatory responses, together with knowledge of the strategies used by viruses to exploit immunometabolic pathways, will ultimately change our understanding and treatment of pathogenic viral diseases. A detailed understanding of the role of metabolic regulation with respect to antiviral and inflammatory responses, together with knowledge of the strategies used by viruses to exploit immunometabolic pathways, will ultimately change our understanding and treatment of pathogenic viral diseases. abstract: The past century has witnessed major advances in the control of many infectious diseases, yet outbreaks and epidemics caused by (re-) emerging RNA viruses continue to pose a global threat to human health. As illustrated by the global COVID19 pandemic, high healthcare costs, economic disruption and loss of productivity reinforce the unmet medical need to develop new antiviral strategies to combat not only the current pandemic but also future viral outbreaks. Pivotal for effective anti-viral defense is the innate immune system, a first line host response that senses and responds to virus infection. While molecular details of the innate immune response are well characterized, this research field is now being revolutionized with the recognition that cell metabolism has a major impact on the antiviral and inflammatory responses to virus infections. A detailed understanding of the role of metabolic regulation with respect to antiviral and inflammatory responses, together with knowledge of the strategies used by viruses to exploit immunometabolic pathways, will ultimately change our understanding and treatment of pathogenic viral diseases. INITIATE is a Marie Sklodowska-Curie Actions Innovative Training Network (MSCA-ITN), with the goal to train 15 early stage PhD researchers (ESRs) to become experts in antiviral immunometabolism (https://initiate-itn.eu/). To this end, INITIATE brings together a highly complementary international team of academic and corporate leaders from 7 European countries, with outstanding track records in the historically distinct research fields of virology, immunology and metabolism. The ESRs of INITIATE are trained in these interdisciplinary research fields through individual investigator-driven research projects, specialized scientific training events, workshops on academia-industry interactions, outreach & communication. INITIATE will deliver a new generation of creative and entrepreneurial researchers who will be able to face the inevitable future challenges in combating viral diseases. url: https://www.sciencedirect.com/science/article/pii/S0168170220309400?v=s5 doi: 10.1016/j.virusres.2020.198094 id: cord-295792-hajvtzj9 author: Álvez, Fernando title: SARS-CoV2 coronavirus: So far polite with children. Debatable immunological and non-immunological evidence date: 2020-07-03 words: 4504.0 sentences: 196.0 pages: flesch: 46.0 cache: ./cache/cord-295792-hajvtzj9.txt txt: ./txt/cord-295792-hajvtzj9.txt summary: In short, the purpose of this first defensive barrier for early control during the incubation period and the first symptoms of SAR-CoV2 infection is to inhibit viral replication, promote elimination of the virus, induce tissue repair and trigger a specific adaptive immune response (AIR) (12) . Furthermore, this enzyme also plays an important role in the immune response, especially in inflammation, and is involved in the defensive mechanisms of the lung -protecting it from severe injury induced by respiratory viruses (11, 18) . However, serological studies evaluating the immune response to respiratory infections including CovH have shown steadily increasing seroprevalence of antibodies to CovH in both children and young adults, as well as cross-reactivity, such as between antibodies to the previous SARS-CoV and CovH (25) (26) . Cell Responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-Infected mice abstract: Abstract The reasons for the relative resistance of children to certain infections such as that caused by coronavirus SARS- CoV2 are not yet fully clear. Deciphering these differences can provide important information about the pathogenesis of the disease. Regarding the SARS-CoV2 virus, children are at the same risk of infection as the general population of all ages, with the most serious cases being found in infants. However, it has been reported that the disease is much less frequent than in adults and that most cases are benign or moderate (even with high viral loads), provided there are no other risk factors or underlying diseases. It is not clear why they have lower morbidity and virtually no mortality. A series of findings, relationships and behavioral patterns between the infectious agent and the child host may account for the lower incidence and a greatly attenuated clinical presentation of the disease in children. url: https://www.sciencedirect.com/science/article/pii/S0301054620301075?v=s5 doi: 10.1016/j.aller.2020.05.003 id: cord-258027-f3rr5el1 author: Østby, Anne‐Cathrine title: Respiratory virology and microbiology in intensive care units: a prospective cohort study date: 2013-05-18 words: 5259.0 sentences: 268.0 pages: flesch: 38.0 cache: ./cache/cord-258027-f3rr5el1.txt txt: ./txt/cord-258027-f3rr5el1.txt summary: Our aim was to determine the frequency of 12 common respiratory viruses in patients admitted to intensive care units with respiratory symptoms, evaluate the clinical characteristics and to compare the results to routine microbiological diagnostics. The information included the following: age, gender, underlying comorbidity, use of immunosuppressant drugs, respiratory symptoms, diagnoses on admission, diagnoses on discharge, length of hospital stay, ICU stay and intubation, Simplified Acute Physiology Score II (SAPS II)scores, administration of antibiotics, non-invasive ventilation, chest x-ray, laboratory analyses and results of the physical examination, which included temperature, saturation, stethoscopic findings and clinical signs of respiratory infection or distress. Viruses -Of the 122 patients included in the study group, 19 (16%) were positive for a virus, of which the most frequently detected were influenza A (n = 9) and RSV (n = 3, Fig. 2 ). abstract: Our aim was to determine the frequency of 12 common respiratory viruses in patients admitted to intensive care units with respiratory symptoms, evaluate the clinical characteristics and to compare the results to routine microbiological diagnostics. Throat swabs from 122 intensive care‐patients >18 years with acute respiratory symptoms were collected upon admission and analysed with multiplex real‐time polymerase chain reaction, for 12 community respiratory viruses. Blood and respiratory tract specimens were analysed for bacteria and fungi upon clinicians' request. Clinical and paraclinical data were collected. Viruses were detected in 19 (16%) of the 122 study patients. Five virus‐positive patients (26%) had possible clinically relevant bacteria or fungi co‐detected. Patients with exacerbation in COPD were associated with a viral infection (p = 0.02). Other comorbidities, clinical and paraclinical parameters, and death were independent of a viral infection or co‐detection of bacteria/fungi. In conclusion, respiratory viruses were frequently detected in the patients. The investigated clinical and paraclinical parameters were not different in viral infections compared to other agents, thus respiratory viruses likely have similar impact on the clinical course as other agents. In 25% of the virus‐positive patients, polymicrobial aetiology was identified. Comprehensive and sensitive diagnostic methods should be emphasized to enhance respiratory diagnostics. url: https://doi.org/10.1111/apm.12089 doi: 10.1111/apm.12089 id: cord-278635-vwdxr1bl author: Świętoń, Edyta title: Low pathogenic avian influenza virus isolates with different levels of defective genome segments vary in pathogenicity and transmission efficiency date: 2020-08-28 words: 5432.0 sentences: 295.0 pages: flesch: 48.0 cache: ./cache/cord-278635-vwdxr1bl.txt txt: ./txt/cord-278635-vwdxr1bl.txt summary: In the present study we compared the clinical outcome, mortality and transmission in chickens and turkeys infected with the same infectious doses of H7N7 low pathogenic avian influenza virus containing different levels of defective gene segments (95/95(DVG-high) and 95/95(DVG-low)). Virions containing highly deleted forms of genome segments (defective viral genes-DVGs) are able to replicate only in the presence and at the expense of fully infectious virus, hence the term "defective interfering particles" (DIPs) [4] . To evaluate the effect of DIPs on the course of infection with low pathogenic avian influenza virus (LPAIV), a comparison of pathogenicity of two virus stocks of H7N7 LPAIV with different levels of defective genomes was performed in turkeys and chickens. Infected birds received the same infectious dose of the virus but with different amount of DVGs. The semiquantitative analysis of defective particles was done by a combination of RT-PCR, real time RT-PCR and whole genome sequencing and indicated significantly higher amount of truncated gene segments in 95/95(DVG-high). abstract: Defective interfering particles (DIPs) of influenza virus are generated through incorporation of highly truncated forms of genome segments, mostly those coding polymerase complex proteins (PB2, PB1, PA). Such particles are able to replicate only in the presence of a virus with the complete genome, thus DIPs may alter the infection outcome by suppressing production of standard virus particles, but also by stimulating the immune response. In the present study we compared the clinical outcome, mortality and transmission in chickens and turkeys infected with the same infectious doses of H7N7 low pathogenic avian influenza virus containing different levels of defective gene segments (95/95(DVG-high) and 95/95(DVG-low)). No clinical signs, mortality or transmission were noted in SPF chickens inoculated with neither virus stock. Turkeys infected with 95/95(DVG-high) showed only slight clinical signs with no mortality, and the virus was transmitted only to birds in direct contact. In contrast, more severe disease, mortality and transmission to direct and indirect contact birds was observed in turkeys infected with 95/95(DVG-low). Apathy, lower water and food intake, respiratory system disorders and a total mortality of 60% were noted. Shedding patterns in contact turkeys indicated more efficient within- and between-host spread of the virus than in 95/95(DVG-high) group. Sequencing of virus genomes showed no mutations that could account for the observed differences in pathogenicity. The results suggest that the abundance of DIPs in the inoculum was the factor responsible for the mild course of infection and disrupted virus transmission. url: https://doi.org/10.1186/s13567-020-00833-6 doi: 10.1186/s13567-020-00833-6 ==== make-pages.sh questions [ERIC WAS HERE] ==== make-pages.sh search /data-disk/reader-compute/reader-cord/bin/make-pages.sh: line 77: /data-disk/reader-compute/reader-cord/tmp/search.htm: No such file or directory Traceback (most recent call last): File "/data-disk/reader-compute/reader-cord/bin/tsv2htm-search.py", line 51, in with open( TEMPLATE, 'r' ) as handle : htm = handle.read() FileNotFoundError: [Errno 2] No such file or directory: '/data-disk/reader-compute/reader-cord/tmp/search.htm' ==== make-pages.sh topic modeling corpus Zipping study carrel