Carrel name: journal-archVirol-cord Creating study carrel named journal-archVirol-cord Initializing database file: cache/cord-004680-u3cnsdl8.json key: cord-004680-u3cnsdl8 authors: Lin, Z.; Kato, A.; Kudou, Y.; Umeda, K.; Ueda, S. title: Typing of recent infectious bronchitis virus isolates causing nephritis in chicken date: 1991 journal: Arch Virol DOI: 10.1007/bf01310957 sha: doc_id: 4680 cord_uid: u3cnsdl8 file: cache/cord-004673-c8qcjve9.json key: cord-004673-c8qcjve9 authors: Faaberg, K. S.; Plagemann, P. G. W. title: Membrane association of the C-terminal half of the open reading frame 1a protein of lactate dehydrogenase-elevating virus date: 1996 journal: Arch Virol DOI: 10.1007/bf01718835 sha: doc_id: 4673 cord_uid: c8qcjve9 file: cache/cord-003050-n25wnmq5.json key: cord-003050-n25wnmq5 authors: Nibert, Max L.; Manny, Austin R.; Debat, Humberto J.; Firth, Andrew E.; Bertini, Laura; Caruso, Carla title: A barnavirus sequence mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis date: 2018-03-07 journal: Arch Virol DOI: 10.1007/s00705-018-3794-x sha: doc_id: 3050 cord_uid: n25wnmq5 file: cache/cord-004812-ikco4h5k.json key: cord-004812-ikco4h5k authors: Moore, K. M.; Jackwood, M. W.; Hilt, D. A. title: Identification of amino acids involved in a serotype and neutralization specific epitope with in the s1 subunit of avian infectious bronchitis virus date: 1997-04-06 journal: Arch Virol DOI: 10.1007/s007050050239 sha: doc_id: 4812 cord_uid: ikco4h5k file: cache/cord-004793-6yh36r0w.json key: cord-004793-6yh36r0w authors: Choi, C. S.; Joo, H. S.; Molitor, T. W. title: Replication of two porcine parvovirus isolates at non-permissive temperatures date: 1990 journal: Arch Virol DOI: 10.1007/bf01316676 sha: doc_id: 4793 cord_uid: 6yh36r0w file: cache/cord-001274-vz0qvp01.json key: cord-001274-vz0qvp01 authors: Chitray, M.; de Beer, T. A. P.; Vosloo, W.; Maree, F. F. title: Genetic heterogeneity in the leader and P1-coding regions of foot-and-mouth disease virus serotypes A and O in Africa date: 2013-11-13 journal: Arch Virol DOI: 10.1007/s00705-013-1838-9 sha: doc_id: 1274 cord_uid: vz0qvp01 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-004764-tmvebf23.json key: cord-004764-tmvebf23 authors: Stephenson, J. R.; ter Meulen, V. title: A comparative analysis of measles virus RNA by oligonucleotide fingerprinting date: 1982 journal: Arch Virol DOI: 10.1007/bf01315058 sha: doc_id: 4764 cord_uid: tmvebf23 file: cache/cord-004681-02wem2u3.json key: cord-004681-02wem2u3 authors: Wada, R.; Fukunaga, Y.; Kondo, T.; Kanemaru, T. title: Ultrastructure and immuno-cytochemistry of BHK-21 cells infected with a modified Bucyrus strain of equine arteritis virus date: 1995 journal: Arch Virol DOI: 10.1007/bf01322744 sha: doc_id: 4681 cord_uid: 02wem2u3 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-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-004778-xrv0qs6n.json key: cord-004778-xrv0qs6n authors: Smith, C. B.; Wei, L. S.; Griffiths, Marie title: Mouse cytomegalovirus is infectious for rats and alters lymphocyte subsets and spleen cell proliferation date: 1986 journal: Arch Virol DOI: 10.1007/bf01317379 sha: doc_id: 4778 cord_uid: xrv0qs6n file: cache/cord-004831-lu62noak.json key: cord-004831-lu62noak authors: Kempf, C.; Michel, M. R.; Kohler, U.; Koblet, H. title: A novel method for the detection of early events in cell-cell fusion of Semliki Forest virus infected cells growing in monolayer cultures date: 1987 journal: Arch Virol DOI: 10.1007/bf01310786 sha: doc_id: 4831 cord_uid: lu62noak 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-004810-g0y7ied0.json key: cord-004810-g0y7ied0 authors: Lee, S. K.; Sung, H. W.; Kwon, H. M. title: S1 glycoprotein gene analysis of infectious bronchitis viruses isolated in Korea date: 2003-11-13 journal: Arch Virol DOI: 10.1007/s00705-003-0225-3 sha: doc_id: 4810 cord_uid: g0y7ied0 file: cache/cord-004713-gzts5h0y.json key: cord-004713-gzts5h0y authors: Fennestad, K. L. title: Pathogenetic observations on pleural effusion disease in rabbits date: 1985 journal: Arch Virol DOI: 10.1007/bf01378969 sha: doc_id: 4713 cord_uid: gzts5h0y file: cache/cord-011105-or9azf1g.json key: cord-011105-or9azf1g authors: Huang, Zheng; Yao, Dong; Xiao, Shan; Yang, Dong; Ou, Xinhua title: Full-genome sequences of GII.13[P21] recombinant norovirus strains from an outbreak in Changsha, China date: 2020-04-30 journal: Arch Virol DOI: 10.1007/s00705-020-04643-1 sha: doc_id: 11105 cord_uid: or9azf1g 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-004798-5budstbg.json key: cord-004798-5budstbg authors: Takayama, N.; Kirn, A. title: An improved method for titration of mouse hepatitis virus type 3 in a mouse cell culture date: 1976 journal: Arch Virol DOI: 10.1007/bf01315624 sha: doc_id: 4798 cord_uid: 5budstbg file: cache/cord-256859-7ixegm72.json key: cord-256859-7ixegm72 authors: Liu, S. W.; Zhang, Q. X.; Chen, J. D.; Han, Z. X.; Liu, X.; Feng, L.; Shao, Y. H.; Rong, J. G.; Kong, X. G.; Tong, G. Z. title: Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between 1995 and 2004 date: 2006-01-09 journal: Arch Virol DOI: 10.1007/s00705-005-0695-6 sha: doc_id: 256859 cord_uid: 7ixegm72 file: cache/cord-004755-rmnjs1t6.json key: cord-004755-rmnjs1t6 authors: Welch, Siao-Kun Wan; Saif, Linda J. title: Monoclonal antibodies to a virulent strain of transmissible gastroenteritis virus: comparison of reactivity with virulent and attenuated virus date: 1988 journal: Arch Virol DOI: 10.1007/bf01311003 sha: doc_id: 4755 cord_uid: rmnjs1t6 file: cache/cord-004717-41ui4lqc.json key: cord-004717-41ui4lqc authors: Laurin, Marc-André; Dastor, Margaux; L’Homme, Yvan title: Detection and genetic characterization of a novel pig astrovirus: relationship to other astroviruses date: 2011-09-08 journal: Arch Virol DOI: 10.1007/s00705-011-1088-7 sha: doc_id: 4717 cord_uid: 41ui4lqc file: cache/cord-004693-1xglujqk.json key: cord-004693-1xglujqk authors: Chasey, D.; Alexander, D. J. title: Morphogenesis of avian infectious bronchitis virus in primary chick kidney cells date: 1976 journal: Arch Virol DOI: 10.1007/bf01317869 sha: doc_id: 4693 cord_uid: 1xglujqk file: cache/cord-004769-hhge62sl.json key: cord-004769-hhge62sl authors: Remond, M.; Boireau, P.; Lebreton, F. title: Partial DNA cloning and sequencing of a canine parvovirus vaccine strain: application of nucleic acid hybridization to the diagnosis of canine parvovirus disease date: 1992 journal: Arch Virol DOI: 10.1007/bf01309589 sha: doc_id: 4769 cord_uid: hhge62sl file: cache/cord-006459-9kizif98.json key: cord-006459-9kizif98 authors: Deng, Guangcun; Bi, Jianmin; Kong, Fuli; Li, Xuezhu; Xu, Qiang; Dong, Jun; Zhang, Miaojie; Zhao, Lihong; Luan, Zhihua; Lv, Nana; Qiao, Jian title: Acute respiratory distress syndrome induced by H9N2 virus in mice date: 2009-11-28 journal: Arch Virol DOI: 10.1007/s00705-009-0560-0 sha: doc_id: 6459 cord_uid: 9kizif98 file: cache/cord-029775-mntcor5d.json key: cord-029775-mntcor5d authors: Oka, Tomoichiro; Yamamoto, Seiji P.; Iritani, Nobuhiro; Sato, Shigenori; Tatsumi, Chika; Mita, Tetsuo; Yahiro, Shunsuke; Shibata, Shinichiro; Wu, Fang-Tzy; Takagi, Hirotaka title: Polymerase chain reaction primer sets for the detection of genetically diverse human sapoviruses date: 2020-07-27 journal: Arch Virol DOI: 10.1007/s00705-020-04746-9 sha: doc_id: 29775 cord_uid: mntcor5d file: cache/cord-004754-5596p4ma.json key: cord-004754-5596p4ma authors: Duan, X.; Nauwynck, H. J.; Pensaert, M. B. title: Effects of origin and state of differentiation and activation of monocytes/macrophages on their susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) date: 2014-04-06 journal: Arch Virol DOI: 10.1007/s007050050256 sha: doc_id: 4754 cord_uid: 5596p4ma file: cache/cord-004790-69lry0ys.json key: cord-004790-69lry0ys authors: Smith, A. L.; Winograd, Deborah F.; Burrage, T. G. title: Comparative biological characterization of mouse adenovirus strains FL and K 87 and seroprevalence in laboratory rodents date: 1986 journal: Arch Virol DOI: 10.1007/bf01314283 sha: doc_id: 4790 cord_uid: 69lry0ys file: cache/cord-004690-q38ogrem.json key: cord-004690-q38ogrem authors: Barthold, S. W.; Smith, Abigail L. title: Viremic dissemination of mouse hepatitis virus-JHM following intranasal inoculation of mice date: 1992 journal: Arch Virol DOI: 10.1007/bf01321116 sha: doc_id: 4690 cord_uid: q38ogrem file: cache/cord-252232-vgq6gjpx.json key: cord-252232-vgq6gjpx authors: Hou, Yuxuan; Peng, Cheng; Yu, Meng; Li, Yan; Han, Zhenggang; Li, Fang; Wang, Lin-Fa; Shi, Zhengli title: Angiotensin-converting enzyme 2 (ACE2) proteins of different bat species confer variable susceptibility to SARS-CoV entry date: 2010-06-22 journal: Arch Virol DOI: 10.1007/s00705-010-0729-6 sha: doc_id: 252232 cord_uid: vgq6gjpx file: cache/cord-006674-ywzpwlrb.json key: cord-006674-ywzpwlrb authors: Ikeda, T.; Shimokata, K.; Daikoku, T.; Fukatsu, T.; Tsutsui, Y.; Nishiyama, Y. title: Pathogenesis of cytomegalovirus-associated pneumonitis in ICR mice: possible involvement of superoxide radicals date: 1992 journal: Arch Virol DOI: 10.1007/bf01309571 sha: doc_id: 6674 cord_uid: ywzpwlrb file: cache/cord-258768-bjjfkfgg.json key: cord-258768-bjjfkfgg authors: McElligott, Susan; Collins, P. 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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-048485-b8xb1f12.json key: cord-048485-b8xb1f12 authors: Hulst, Marcel; Kerstens, Hinri; de Wit, Agnes; Smits, Mari; van der Meulen, Jan; Niewold, Theo title: Early transcriptional response in the jejunum of germ-free piglets after oral infection with virulent rotavirus date: 2008-06-04 journal: Arch Virol DOI: 10.1007/s00705-008-0118-6 sha: doc_id: 48485 cord_uid: b8xb1f12 file: cache/cord-261749-lq1ah16x.json key: cord-261749-lq1ah16x authors: Mayo, M. A.; Haenni, A.-L. title: Report from the 36(th) and the 37(th) Meetings of the Executive Committee of the International Committee on Taxomony of Viruses date: 2006-03-03 journal: Arch Virol DOI: 10.1007/s00705-006-0728-9 sha: doc_id: 261749 cord_uid: lq1ah16x file: cache/cord-004685-qote5nx2.json key: cord-004685-qote5nx2 authors: Vassão, R. C.; Sant' Anna, O. A.; Pereira, C. 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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-338641-s006a7m0.json key: cord-338641-s006a7m0 authors: Black, W. D.; Hartley, C. A.; Ficorilli, N. P.; Studdert, M. J. title: Reverse transcriptase-polymerase chain reaction for the detection equine rhinitis B viruses and cell culture isolation of the virus date: 2006-08-24 journal: Arch Virol DOI: 10.1007/s00705-006-0810-3 sha: doc_id: 338641 cord_uid: s006a7m0 file: cache/cord-338607-22f04uqe.json key: cord-338607-22f04uqe authors: Verbeek, A.; Dea, S.; Tijssen, P. title: Genomic relationship between turkey and bovine enteric coronaviruses identified by hybridization with BCV or TCV specific cDNA probes date: 1991 journal: Arch Virol DOI: 10.1007/bf01316754 sha: doc_id: 338607 cord_uid: 22f04uqe file: cache/cord-340422-8f5xe4zc.json key: cord-340422-8f5xe4zc authors: Rowland, R. R. R.; Robinson, B.; Stefanick, J.; Kim, T. S.; Guanghua, L.; Lawson, S. R.; Benfield, D. A. title: Inhibition of porcine reproductive and respiratory syndrome virus by interferon-gamma and recovery of virus replication with 2-aminopurine date: 2001 journal: Arch Virol DOI: 10.1007/s007050170161 sha: doc_id: 340422 cord_uid: 8f5xe4zc file: cache/cord-339178-d6f6a5ds.json key: cord-339178-d6f6a5ds authors: Pensaert, M. B.; de Bouck, P. title: A new coronavirus-like particle associated with diarrhea in swine date: 1978 journal: Arch Virol DOI: 10.1007/bf01317606 sha: doc_id: 339178 cord_uid: d6f6a5ds file: cache/cord-332811-kjgah8ts.json key: cord-332811-kjgah8ts authors: Lee, Do Hyun; Jeon, Young-Soo; Park, Choi-Kyu; Kim, Seungjoon; Lee, Du Sik; Lee, Changhee title: Immunoprophylactic effect of chicken egg yolk antibody (IgY) against a recombinant S1 domain of the porcine epidemic diarrhea virus spike protein in piglets date: 2015-06-23 journal: Arch Virol DOI: 10.1007/s00705-015-2494-z sha: doc_id: 332811 cord_uid: kjgah8ts file: cache/cord-334810-hw1aijwf.json key: cord-334810-hw1aijwf authors: Banyard, Ashley C.; Johnson, N.; Voller, K.; Hicks, D.; Nunez, A.; Hartley, M.; Fooks, A. R. title: Repeated detection of European bat lyssavirus type 2 in dead bats found at a single roost site in the UK date: 2009-10-20 journal: Arch Virol DOI: 10.1007/s00705-009-0504-8 sha: doc_id: 334810 cord_uid: hw1aijwf file: cache/cord-334090-66d8c75g.json key: cord-334090-66d8c75g authors: Seger, Waleed; GhalyanchiLangeroudi, Arash; Karimi, Vahid; Madadgar, Omid; Marandi, Mehdi Vasfi; Hashemzadeh, Masoud title: Genotyping of infectious bronchitis viruses from broiler farms in Iraq during 2014-2015 date: 2016-02-18 journal: Arch Virol DOI: 10.1007/s00705-016-2790-2 sha: doc_id: 334090 cord_uid: 66d8c75g file: cache/cord-340905-8nyew5i5.json key: cord-340905-8nyew5i5 authors: Chen, Yi-Ning; Loa, Chien Chang; Ababneh, Mustafa Mohammed-Khair; Wu, Ching Ching; Lin, Tsang Long title: Genotyping of turkey coronavirus field isolates from various geographic locations in the Unites States based on the spike gene date: 2015-08-08 journal: Arch Virol DOI: 10.1007/s00705-015-2556-2 sha: doc_id: 340905 cord_uid: 8nyew5i5 file: cache/cord-339991-k8z6v2vx.json key: cord-339991-k8z6v2vx authors: Rong, Q.; Alexander, T. S.; Koski, G. K.; Rosenthal, K. S. title: Multiple mechanisms for HSV-1 induction of interferon α production by peripheral blood mononuclear cells date: 2003 journal: Arch Virol DOI: 10.1007/s00705-002-0912-5 sha: doc_id: 339991 cord_uid: k8z6v2vx file: cache/cord-340065-f4ffvkr9.json key: cord-340065-f4ffvkr9 authors: Horváth, Trén; Mocsári, E. title: Ultrastructural changes in the small intestinal epithelium of suckling pigs affected with a transmissible gastroenteritis (TGE)-like disease date: 1981 journal: Arch Virol DOI: 10.1007/bf01314440 sha: doc_id: 340065 cord_uid: f4ffvkr9 file: cache/cord-338916-fqxjzavm.json key: cord-338916-fqxjzavm authors: Anindita, Paulina Duhita; Sasaki, Michihito; Setiyono, Agus; Handharyani, Ekowati; Orba, Yasuko; Kobayashi, Shintaro; Rahmadani, Ibnu; Taha, Siswatiana; Adiani, Sri; Subangkit, Mawar; Nakamura, Ichiro; Sawa, Hirofumi; Kimura, Takashi title: Detection of coronavirus genomes in Moluccan naked-backed fruit bats in Indonesia date: 2015-02-04 journal: Arch Virol DOI: 10.1007/s00705-015-2342-1 sha: doc_id: 338916 cord_uid: fqxjzavm file: cache/cord-341278-klv9jdm8.json key: cord-341278-klv9jdm8 authors: Smith, Abigail L.; Barthold, S. W.; de Souza, M. S.; Bottomly, Kim title: The role of gamma interferon in infection of susceptible mice with murine coronavirus, MHV-JHM date: 1991 journal: Arch Virol DOI: 10.1007/bf01316746 sha: doc_id: 341278 cord_uid: klv9jdm8 file: cache/cord-343349-ftzjdvfj.json key: cord-343349-ftzjdvfj authors: Bhatt, P. N.; Jacoby, R. O. title: Experimental infection of adult axenic rats with Parker's Rat Coronavirus date: 1977 journal: Arch Virol DOI: 10.1007/bf01314779 sha: doc_id: 343349 cord_uid: ftzjdvfj file: cache/cord-335690-66t5fjld.json key: cord-335690-66t5fjld authors: Khromykh, A. A.; Westaway, E. G. title: RNA binding properties of core protein of the flavivirus Kunjin date: 1996 journal: Arch Virol DOI: 10.1007/bf01718326 sha: doc_id: 335690 cord_uid: 66t5fjld file: cache/cord-343131-tu6g977q.json key: cord-343131-tu6g977q authors: Cheung, Andrew K.; Ng, Terry F.; Lager, Kelly M.; Bayles, Darrell O.; Alt, David P.; Delwart, Eric L.; Pogranichniy, Roman M.; Kehrli, Marcus E. title: A divergent clade of circular single-stranded DNA viruses from pig feces date: 2013-04-24 journal: Arch Virol DOI: 10.1007/s00705-013-1701-z sha: doc_id: 343131 cord_uid: tu6g977q file: cache/cord-341469-7guojyay.json key: cord-341469-7guojyay authors: Park, Seong-Jun; Kim, Hye-Kwon; Song, Dae-Sub; Moon, Hyoung-Joon; Park, Bong-Kyun title: Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field isolates in Korea date: 2011-01-06 journal: Arch Virol DOI: 10.1007/s00705-010-0892-9 sha: doc_id: 341469 cord_uid: 7guojyay file: cache/cord-343780-084lq92r.json key: cord-343780-084lq92r authors: Hsu, Tien-Huan; Liu, Hao-Ping; Chin, Chieh-Yu; Wang, Chinling; Zhu, Wan-Zhen; Wu, Bing-Lin; Chang, Yu-Chung title: Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan date: 2018-07-26 journal: Arch Virol DOI: 10.1007/s00705-018-3964-x sha: doc_id: 343780 cord_uid: 084lq92r file: cache/cord-341342-kyavg4vu.json key: cord-341342-kyavg4vu authors: Masters, P. S. title: Localization of an RNA-binding domain in the nucleocapsid protein of the coronavirus mouse hepatitis virus date: 1992 journal: Arch Virol DOI: 10.1007/bf01309634 sha: doc_id: 341342 cord_uid: kyavg4vu file: cache/cord-341383-e2jrhycj.json key: cord-341383-e2jrhycj authors: Dong, Wei; Chen, Qianqian; Hu, Yihong; He, Dongping; Liu, Jia; Yan, Huajie; Lan, Ke; Zhang, Chiyu title: Epidemiological and clinical characteristics of respiratory viral infections in children in Shanghai, China date: 2016-05-02 journal: Arch Virol DOI: 10.1007/s00705-016-2866-z sha: doc_id: 341383 cord_uid: e2jrhycj file: cache/cord-346629-770qyee8.json key: cord-346629-770qyee8 authors: Mase, M.; Tsukamoto, K.; Imai, K.; Yamaguchi, S. title: Phylogenetic analysis of avian infectious bronchitis virus strains isolated in Japan date: 2004-07-15 journal: Arch Virol DOI: 10.1007/s00705-004-0369-9 sha: doc_id: 346629 cord_uid: 770qyee8 file: cache/cord-344464-if6js43s.json key: cord-344464-if6js43s authors: Cowley, J. A.; Walker, P. J. title: The complete genome sequence of gill-associated virus of Penaeus monodon prawns indicates a gene organisation unique among nidoviruses(*): Brief Report date: 2002 journal: Arch Virol DOI: 10.1007/s00705-002-0847-x sha: doc_id: 344464 cord_uid: if6js43s file: cache/cord-342568-3sj235rm.json key: cord-342568-3sj235rm authors: Bald-Blume, Niklas; Bergervoet, Jan H. W.; Maiss, Edgar title: Development of a molecular assay for the general detection of tospoviruses and the distinction between tospoviral species date: 2017-02-11 journal: Arch Virol DOI: 10.1007/s00705-017-3256-x sha: doc_id: 342568 cord_uid: 3sj235rm file: cache/cord-343256-n593kh7u.json key: cord-343256-n593kh7u authors: Percy, D. H.; Williams, K. L.; Paturzo, F. X. title: A comparison of the sensitivity and specificity of sialodacryoadenitis virus, Parker's rat coronavirus, and mouse hepatitis virus-infected cells as a source of antigen for the detection of antibody to rat coronaviruses date: 1991 journal: Arch Virol DOI: 10.1007/bf01310668 sha: doc_id: 343256 cord_uid: n593kh7u file: cache/cord-345552-h6fwi0qn.json key: cord-345552-h6fwi0qn authors: Li, Q.-G.; Lindman, K.; Wadell, G. title: Hydropathic characteristics of adenovirus hexons date: 1997-07-01 journal: Arch Virol DOI: 10.1007/s007050050162 sha: doc_id: 345552 cord_uid: h6fwi0qn file: cache/cord-345957-wuk2arf9.json key: cord-345957-wuk2arf9 authors: Mohamed, Fakry F.; Mansour, Shimaa M. G.; Orabi, Ahmed; El-Araby, Iman E.; Ng, Terry Fei Fan; Mor, Sunil K.; Goyal, Sagar M. title: Detection and genetic characterization of bovine kobuvirus from calves in Egypt date: 2018-02-08 journal: Arch Virol DOI: 10.1007/s00705-018-3758-1 sha: doc_id: 345957 cord_uid: wuk2arf9 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-347443-0evqo01m.json key: cord-347443-0evqo01m authors: Litwin, Christine M.; Bosley, James G. title: Seasonality and prevalence of respiratory pathogens detected by multiplex PCR at a tertiary care medical center date: 2013-07-24 journal: Arch Virol DOI: 10.1007/s00705-013-1794-4 sha: doc_id: 347443 cord_uid: 0evqo01m file: cache/cord-345940-adg264vb.json key: cord-345940-adg264vb authors: Wanitchang, Asawin; Saenboonrueng, Janya; Srisutthisamphan, Kanjana; Jongkaewwattana, Anan title: Characterization of influenza A virus pseudotyped with the spike protein of porcine epidemic diarrhea virus date: 2018-08-22 journal: Arch Virol DOI: 10.1007/s00705-018-4001-9 sha: doc_id: 345940 cord_uid: adg264vb 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-348179-i8w7huke.json key: cord-348179-i8w7huke authors: Xue, Yong; Sun, Xiaohua; Li, Yinghui; Liu, Xin; Dong, Chen title: Increased risk of hepatitis E virus infection in schizophrenia date: 2012-10-07 journal: Arch Virol DOI: 10.1007/s00705-012-1494-5 sha: doc_id: 348179 cord_uid: i8w7huke file: cache/cord-349800-s9w2yr08.json key: cord-349800-s9w2yr08 authors: Hohdatsu, T.; Okada, S.; Koyama, H. title: Characterization of monoclonal antibodies against feline infectious peritonitis virus type II and antigenic relationship between feline, porcine, and canine coronaviruses date: 1991 journal: Arch Virol DOI: 10.1007/bf01310494 sha: doc_id: 349800 cord_uid: s9w2yr08 file: cache/cord-349907-dwhyx97y.json key: cord-349907-dwhyx97y authors: Noh, Ji Yeong; Yoon, Sun-Woo; Kim, Doo-Jin; Lee, Moo-Seung; Kim, Ji-Hyung; Na, Woonsung; Song, Daesub; Jeong, Dae Gwin; Kim, Hye Kwon title: Simultaneous detection of severe acute respiratory syndrome, Middle East respiratory syndrome, and related bat coronaviruses by real-time reverse transcription PCR date: 2017-02-20 journal: Arch Virol DOI: 10.1007/s00705-017-3281-9 sha: doc_id: 349907 cord_uid: dwhyx97y file: cache/cord-348147-leni23pa.json key: cord-348147-leni23pa authors: Müller, B.; Klemm, U.; Mas Marques, A.; Schreier, E. title: Genetic diversity and recombination of murine noroviruses in immunocompromised mice date: 2007-05-29 journal: Arch Virol DOI: 10.1007/s00705-007-0989-y sha: doc_id: 348147 cord_uid: leni23pa 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-346321-drhiqch0.json key: cord-346321-drhiqch0 authors: Hohdatsu, T.; Tokunaga, J.; Koyama, H. title: The role of IgG subclass of mouse monoclonal antibodies in antibody-dependent enhancement of feline infectious peritonitis virus infection of feline macrophages date: 1994 journal: Arch Virol DOI: 10.1007/bf01310791 sha: doc_id: 346321 cord_uid: drhiqch0 file: cache/cord-345856-ckm0ol20.json key: cord-345856-ckm0ol20 authors: Zhong, Qiong; Yang, Zhanqiu; Liu, Yuanyuan; Deng, Haiying; Xiao, Hong; Shi, Liqiao; He, Jing title: Antiviral activity of Arbidol against Coxsackie virus B5 in vitro and in vivo date: 2009-03-17 journal: Arch Virol DOI: 10.1007/s00705-009-0346-4 sha: doc_id: 345856 cord_uid: ckm0ol20 file: cache/cord-346928-g1dqiki6.json key: cord-346928-g1dqiki6 authors: Costantini, V.; Lewis, P.; Alsop, J.; Templeton, C.; Saif, L. J. title: Respiratory and fecal shedding of Porcine respiratory coronavirus (PRCV) in sentinel weaned pigs and sequence of the partial S-gene of the PRCV isolates date: 2003-11-26 journal: Arch Virol DOI: 10.1007/s00705-003-0245-z sha: doc_id: 346928 cord_uid: g1dqiki6 file: cache/cord-353797-yb355mxk.json key: cord-353797-yb355mxk authors: Inaba, Y.; Sato, K.; Kurogi, H.; Takahashi, E.; Ito, Y.; Omori, T.; Goto, Y.; Matumoto, M. title: Replication of bovine coronavirus in cell line BEK-1 culture date: 1976 journal: Arch Virol DOI: 10.1007/bf01317959 sha: doc_id: 353797 cord_uid: yb355mxk 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-349964-38rgcc5h.json key: cord-349964-38rgcc5h authors: Pedersen, N. C.; Ward, J.; Mengeling, W. L. title: Antigenic relationship of the feline infectious peritonitis virus to coronaviruses of other species date: 1978 journal: Arch Virol DOI: 10.1007/bf01315534 sha: doc_id: 349964 cord_uid: 38rgcc5h file: cache/cord-355512-tycuoslv.json key: cord-355512-tycuoslv authors: Storz, J.; Zhang, X. M.; Rott, R. title: Comparison of hemagglutinating, receptor-destroying, and acetylesterase activities of avirulent and virulent bovine coronavirus strains date: 1992 journal: Arch Virol DOI: 10.1007/bf01309637 sha: doc_id: 355512 cord_uid: tycuoslv file: cache/cord-356192-8b96rgqa.json key: cord-356192-8b96rgqa authors: Xie, Qian; Cao, Yujuan; Su, Juan; Wu, Jie; Wu, Xianbo; Wan, Chengsong; He, Mingliang; Ke, Changwen; Zhang, Bao; Zhao, Wei title: Two deletion variants of Middle East respiratory syndrome coronavirus found in a patient with characteristic symptoms date: 2017-04-18 journal: Arch Virol DOI: 10.1007/s00705-017-3361-x sha: doc_id: 356192 cord_uid: 8b96rgqa Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named journal-archVirol-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: 60842 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 60745 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 60722 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 60792 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 60572 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 60956 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 61089 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: 61066 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 61133 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 61052 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 61061 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 61076 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 60923 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 61159 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 60648 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 61058 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 61954 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 61951 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 61884 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-004798-5budstbg author: Takayama, N. title: An improved method for titration of mouse hepatitis virus type 3 in a mouse cell culture date: 1976 pages: extension: .txt txt: ./txt/cord-004798-5budstbg.txt cache: ./cache/cord-004798-5budstbg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004798-5budstbg.txt' === file2bib.sh === id: cord-004743-ido065mh author: Nagy, Éva title: Polypeptide patterns of infectious bronchitis virus serotypes fall into two categories date: 1979 pages: extension: .txt txt: ./txt/cord-004743-ido065mh.txt cache: ./cache/cord-004743-ido065mh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004743-ido065mh.txt' === file2bib.sh === id: cord-004680-u3cnsdl8 author: Lin, Z. title: Typing of recent infectious bronchitis virus isolates causing nephritis in chicken date: 1991 pages: extension: .txt txt: ./txt/cord-004680-u3cnsdl8.txt cache: ./cache/cord-004680-u3cnsdl8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004680-u3cnsdl8.txt' === file2bib.sh === id: cord-004681-02wem2u3 author: Wada, R. title: Ultrastructure and immuno-cytochemistry of BHK-21 cells infected with a modified Bucyrus strain of equine arteritis virus date: 1995 pages: extension: .txt txt: ./txt/cord-004681-02wem2u3.txt cache: ./cache/cord-004681-02wem2u3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004681-02wem2u3.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-004812-ikco4h5k author: Moore, K. M. title: Identification of amino acids involved in a serotype and neutralization specific epitope with in the s1 subunit of avian infectious bronchitis virus date: 1997-04-06 pages: extension: .txt txt: ./txt/cord-004812-ikco4h5k.txt cache: ./cache/cord-004812-ikco4h5k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004812-ikco4h5k.txt' === file2bib.sh === id: cord-274780-fmnro0kw author: Hoshino, Y. title: Detection of astroviruses in feces of a cat with diarrhea date: 1981 pages: extension: .txt txt: ./txt/cord-274780-fmnro0kw.txt cache: ./cache/cord-274780-fmnro0kw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274780-fmnro0kw.txt' === file2bib.sh === id: cord-004728-rjl35dpa author: Taguchi, F. title: Asymptomatic infection of mouse hepatitis virus in the rat date: 1979 pages: extension: .txt txt: ./txt/cord-004728-rjl35dpa.txt cache: ./cache/cord-004728-rjl35dpa.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004728-rjl35dpa.txt' === file2bib.sh === id: cord-252037-rj61mzqj author: Gerna, G. title: Changing circulation rate of human metapneumovirus strains and types among hospitalized pediatric patients during three consecutive winter-spring seasons date: 2005-06-28 pages: extension: .txt txt: ./txt/cord-252037-rj61mzqj.txt cache: ./cache/cord-252037-rj61mzqj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252037-rj61mzqj.txt' === file2bib.sh === id: cord-004685-qote5nx2 author: Vassão, R. C. title: A genetic analysis of macrophage activation and specific antibodies in relation to the resistance of heterogeneous mouse populations to MHV3 infection date: 1994 pages: extension: .txt txt: ./txt/cord-004685-qote5nx2.txt cache: ./cache/cord-004685-qote5nx2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004685-qote5nx2.txt' === file2bib.sh === id: cord-004759-jozdnhgy author: Snodgrass, D. R. title: Pathogenesis of diarrhoea caused by astrovirus infections in lambs date: 1979 pages: extension: .txt txt: ./txt/cord-004759-jozdnhgy.txt cache: ./cache/cord-004759-jozdnhgy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004759-jozdnhgy.txt' === file2bib.sh === id: cord-004808-6w9n03fy author: Sekiguchi, K. title: Detection of equine arteritis virus (EAV) by polymerase chain reaction (PCR) and differentiation of EAV strains by restriction enzyme analysis of PCR products date: 1995 pages: extension: .txt txt: ./txt/cord-004808-6w9n03fy.txt cache: ./cache/cord-004808-6w9n03fy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004808-6w9n03fy.txt' === file2bib.sh === id: cord-004838-cdas57cx author: Morozov, I. title: Sequence analysis of open reading frames (ORFs) 2 to 4 of a U.S. isolate of porcine reproductive and respiratory syndrome virus date: 1995 pages: extension: .txt txt: ./txt/cord-004838-cdas57cx.txt cache: ./cache/cord-004838-cdas57cx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004838-cdas57cx.txt' === file2bib.sh === id: cord-265768-hwki5lk2 author: Abi, Keha-mo title: An emerging novel bovine coronavirus with a 4-amino-acid insertion in the receptor-binding domain of the hemagglutinin-esterase gene date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-265768-hwki5lk2.txt cache: ./cache/cord-265768-hwki5lk2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265768-hwki5lk2.txt' === file2bib.sh === id: cord-029775-mntcor5d author: Oka, Tomoichiro title: Polymerase chain reaction primer sets for the detection of genetically diverse human sapoviruses date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-029775-mntcor5d.txt cache: ./cache/cord-029775-mntcor5d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-029775-mntcor5d.txt' === file2bib.sh === id: cord-004831-lu62noak author: Kempf, C. title: A novel method for the detection of early events in cell-cell fusion of Semliki Forest virus infected cells growing in monolayer cultures date: 1987 pages: extension: .txt txt: ./txt/cord-004831-lu62noak.txt cache: ./cache/cord-004831-lu62noak.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004831-lu62noak.txt' === file2bib.sh === id: cord-279676-sk9xyd1r author: Carossino, Mariano title: Detection of SARS-CoV-2 by RNAscope(®)in situ hybridization and immunohistochemistry techniques date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-279676-sk9xyd1r.txt cache: ./cache/cord-279676-sk9xyd1r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-279676-sk9xyd1r.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 9 resourceName b'cord-004724-llex3yed.txt' === file2bib.sh === id: cord-011105-or9azf1g author: Huang, Zheng title: Full-genome sequences of GII.13[P21] recombinant norovirus strains from an outbreak in Changsha, China date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-011105-or9azf1g.txt cache: ./cache/cord-011105-or9azf1g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-011105-or9azf1g.txt' === file2bib.sh === id: cord-255653-0bj5eh5d author: Pensaert, M. B. title: An immunoelectron microscopic and immunofluorescent study on the antigenic relationship between the coronavirus-like agent, CV 777, and several coronaviruses date: 1981 pages: extension: .txt txt: ./txt/cord-255653-0bj5eh5d.txt cache: ./cache/cord-255653-0bj5eh5d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255653-0bj5eh5d.txt' === file2bib.sh === id: cord-004673-c8qcjve9 author: Faaberg, K. S. title: Membrane association of the C-terminal half of the open reading frame 1a protein of lactate dehydrogenase-elevating virus date: 1996 pages: extension: .txt txt: ./txt/cord-004673-c8qcjve9.txt cache: ./cache/cord-004673-c8qcjve9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004673-c8qcjve9.txt' === file2bib.sh === id: cord-004713-gzts5h0y author: Fennestad, K. L. title: Pathogenetic observations on pleural effusion disease in rabbits date: 1985 pages: extension: .txt txt: ./txt/cord-004713-gzts5h0y.txt cache: ./cache/cord-004713-gzts5h0y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004713-gzts5h0y.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 3 resourceName b'cord-004781-ajf9zig0.txt' === file2bib.sh === id: cord-004717-41ui4lqc author: Laurin, Marc-André title: Detection and genetic characterization of a novel pig astrovirus: relationship to other astroviruses date: 2011-09-08 pages: extension: .txt txt: ./txt/cord-004717-41ui4lqc.txt cache: ./cache/cord-004717-41ui4lqc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004717-41ui4lqc.txt' === file2bib.sh === id: cord-261749-lq1ah16x author: Mayo, M. A. title: Report from the 36(th) and the 37(th) Meetings of the Executive Committee of the International Committee on Taxomony of Viruses date: 2006-03-03 pages: extension: .txt txt: ./txt/cord-261749-lq1ah16x.txt cache: ./cache/cord-261749-lq1ah16x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-261749-lq1ah16x.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-003050-n25wnmq5 author: Nibert, Max L. title: A barnavirus sequence mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis date: 2018-03-07 pages: extension: .txt txt: ./txt/cord-003050-n25wnmq5.txt cache: ./cache/cord-003050-n25wnmq5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003050-n25wnmq5.txt' === file2bib.sh === id: cord-263193-paeosfiu author: Zhu, Jinyan title: Infectious bronchitis virus inhibits activation of the TLR7 pathway, but not the TLR3 pathway date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-263193-paeosfiu.txt cache: ./cache/cord-263193-paeosfiu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263193-paeosfiu.txt' === file2bib.sh === id: cord-004693-1xglujqk author: Chasey, D. title: Morphogenesis of avian infectious bronchitis virus in primary chick kidney cells date: 1976 pages: extension: .txt txt: ./txt/cord-004693-1xglujqk.txt cache: ./cache/cord-004693-1xglujqk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-004693-1xglujqk.txt' === file2bib.sh === id: cord-004729-nmkilkcx author: Reynolds, D. J. title: Virus isolation and serum antibody responses after infection of cats with transmissible gastroenteritis virus date: 1979 pages: extension: .txt txt: ./txt/cord-004729-nmkilkcx.txt cache: ./cache/cord-004729-nmkilkcx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004729-nmkilkcx.txt' === file2bib.sh === id: cord-004810-g0y7ied0 author: Lee, S. K. title: S1 glycoprotein gene analysis of infectious bronchitis viruses isolated in Korea date: 2003-11-13 pages: extension: .txt txt: ./txt/cord-004810-g0y7ied0.txt cache: ./cache/cord-004810-g0y7ied0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004810-g0y7ied0.txt' === file2bib.sh === id: cord-004840-4rbrzv5o author: Choudhary, Manohar Lal title: Development of real-time RT-PCR for detection of human metapneumovirus and genetic analysis of circulating strains (2009-2011) in Pune, India date: 2013-08-09 pages: extension: .txt txt: ./txt/cord-004840-4rbrzv5o.txt cache: ./cache/cord-004840-4rbrzv5o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004840-4rbrzv5o.txt' === file2bib.sh === id: cord-004690-q38ogrem author: Barthold, S. W. title: Viremic dissemination of mouse hepatitis virus-JHM following intranasal inoculation of mice date: 1992 pages: extension: .txt txt: ./txt/cord-004690-q38ogrem.txt cache: ./cache/cord-004690-q38ogrem.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004690-q38ogrem.txt' === file2bib.sh === id: cord-252232-vgq6gjpx author: Hou, Yuxuan title: Angiotensin-converting enzyme 2 (ACE2) proteins of different bat species confer variable susceptibility to SARS-CoV entry date: 2010-06-22 pages: extension: .txt txt: ./txt/cord-252232-vgq6gjpx.txt cache: ./cache/cord-252232-vgq6gjpx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252232-vgq6gjpx.txt' === file2bib.sh === id: cord-006459-9kizif98 author: Deng, Guangcun title: Acute respiratory distress syndrome induced by H9N2 virus in mice date: 2009-11-28 pages: extension: .txt txt: ./txt/cord-006459-9kizif98.txt cache: ./cache/cord-006459-9kizif98.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-006459-9kizif98.txt' === file2bib.sh === id: cord-004793-6yh36r0w author: Choi, C. S. title: Replication of two porcine parvovirus isolates at non-permissive temperatures date: 1990 pages: extension: .txt txt: ./txt/cord-004793-6yh36r0w.txt cache: ./cache/cord-004793-6yh36r0w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004793-6yh36r0w.txt' === file2bib.sh === id: cord-004769-hhge62sl author: Remond, M. title: Partial DNA cloning and sequencing of a canine parvovirus vaccine strain: application of nucleic acid hybridization to the diagnosis of canine parvovirus disease date: 1992 pages: extension: .txt txt: ./txt/cord-004769-hhge62sl.txt cache: ./cache/cord-004769-hhge62sl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004769-hhge62sl.txt' === file2bib.sh === id: cord-004778-xrv0qs6n author: Smith, C. B. title: Mouse cytomegalovirus is infectious for rats and alters lymphocyte subsets and spleen cell proliferation date: 1986 pages: extension: .txt txt: ./txt/cord-004778-xrv0qs6n.txt cache: ./cache/cord-004778-xrv0qs6n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004778-xrv0qs6n.txt' === file2bib.sh === id: cord-271831-vekok62k author: Dewerchin, H. L. title: Replication of feline coronaviruses in peripheral blood monocytes date: 2005-08-01 pages: extension: .txt txt: ./txt/cord-271831-vekok62k.txt cache: ./cache/cord-271831-vekok62k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-271831-vekok62k.txt' === file2bib.sh === id: cord-006674-ywzpwlrb author: Ikeda, T. title: Pathogenesis of cytomegalovirus-associated pneumonitis in ICR mice: possible involvement of superoxide radicals date: 1992 pages: extension: .txt txt: ./txt/cord-006674-ywzpwlrb.txt cache: ./cache/cord-006674-ywzpwlrb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006674-ywzpwlrb.txt' === file2bib.sh === id: cord-004849-d64hnqkh author: Choi, C. S. title: Temperature dependent replication of porcine parvovirus isolates date: 1989 pages: extension: .txt txt: ./txt/cord-004849-d64hnqkh.txt cache: ./cache/cord-004849-d64hnqkh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-004849-d64hnqkh.txt' === file2bib.sh === id: cord-258374-qht98q0l author: Takano, Tomomi title: Neutrophil survival factors (TNF-alpha, GM-CSF, and G-CSF) produced by macrophages in cats infected with feline infectious peritonitis virus contribute to the pathogenesis of granulomatous lesions date: 2009-04-03 pages: extension: .txt txt: ./txt/cord-258374-qht98q0l.txt cache: ./cache/cord-258374-qht98q0l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258374-qht98q0l.txt' === file2bib.sh === id: cord-004694-43yvs52a author: Han, Tae-Hee title: Detection of human rhinovirus C in children with acute lower respiratory tract infections in South Korea date: 2009-05-05 pages: extension: .txt txt: ./txt/cord-004694-43yvs52a.txt cache: ./cache/cord-004694-43yvs52a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004694-43yvs52a.txt' === file2bib.sh === id: cord-004764-tmvebf23 author: Stephenson, J. R. title: A comparative analysis of measles virus RNA by oligonucleotide fingerprinting date: 1982 pages: extension: .txt txt: ./txt/cord-004764-tmvebf23.txt cache: ./cache/cord-004764-tmvebf23.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004764-tmvebf23.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-276617-chgjpg0v author: Takano, Tomomi title: B-cell activation in cats with feline infectious peritonitis (FIP) by FIP-virus-induced B-cell differentiation/survival factors date: 2008-11-30 pages: extension: .txt txt: ./txt/cord-276617-chgjpg0v.txt cache: ./cache/cord-276617-chgjpg0v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276617-chgjpg0v.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 2 resourceName b'cord-280781-u3wd27rn.txt' === file2bib.sh === id: cord-004802-rhkrmftn author: Hoshino, Y. title: Isolation and characterization of a canine rotavirus date: 1982 pages: extension: .txt txt: ./txt/cord-004802-rhkrmftn.txt cache: ./cache/cord-004802-rhkrmftn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004802-rhkrmftn.txt' === file2bib.sh === id: cord-266716-pghnl980 author: Wang, Hai-Ming title: Isobavachalcone inhibits post-entry stages of the porcine reproductive and respiratory syndrome virus life cycle date: 2018-02-06 pages: extension: .txt txt: ./txt/cord-266716-pghnl980.txt cache: ./cache/cord-266716-pghnl980.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 133 resourceName b'cord-266716-pghnl980.txt' === file2bib.sh === id: cord-265631-b0kg6qpo author: Saeng-chuto, Kepalee title: Retrospective investigation and evolutionary analysis of a novel porcine deltacoronavirus strain detected in Thailand from 2008 to 2015 date: 2017-03-23 pages: extension: .txt txt: ./txt/cord-265631-b0kg6qpo.txt cache: ./cache/cord-265631-b0kg6qpo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265631-b0kg6qpo.txt' === file2bib.sh === id: cord-254405-yc1q20fz author: Jie, Tao title: Preparation and characterization of an attenuated porcine epidemic diarrhea virus strain by serial passaging date: 2018-07-31 pages: extension: .txt txt: ./txt/cord-254405-yc1q20fz.txt cache: ./cache/cord-254405-yc1q20fz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254405-yc1q20fz.txt' === file2bib.sh === id: cord-004825-cdvnqfjz author: Castilla, V. title: The entry of Junin virus into Vero cells date: 1994 pages: extension: .txt txt: ./txt/cord-004825-cdvnqfjz.txt cache: ./cache/cord-004825-cdvnqfjz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004825-cdvnqfjz.txt' === file2bib.sh === id: cord-004790-69lry0ys author: Smith, A. L. title: Comparative biological characterization of mouse adenovirus strains FL and K 87 and seroprevalence in laboratory rodents date: 1986 pages: extension: .txt txt: ./txt/cord-004790-69lry0ys.txt cache: ./cache/cord-004790-69lry0ys.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004790-69lry0ys.txt' === file2bib.sh === id: cord-012032-zolowuhj author: Yu, Peifa title: 2’-Fluoro-2’-deoxycytidine inhibits murine norovirus replication and synergizes MPA, ribavirin and T705 date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-012032-zolowuhj.txt cache: ./cache/cord-012032-zolowuhj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-012032-zolowuhj.txt' === file2bib.sh === id: cord-004720-r6b34tjm author: Kaiser, C. J. title: Inhibition by monensin of human cytomegalovirus DNA replication date: 1987 pages: extension: .txt txt: ./txt/cord-004720-r6b34tjm.txt cache: ./cache/cord-004720-r6b34tjm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004720-r6b34tjm.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-276630-qci7khki author: Lima, William Gustavo title: The potential of drug repositioning as a short-term strategy for the control and treatment of COVID-19 (SARS-CoV-2): a systematic review date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-276630-qci7khki.txt cache: ./cache/cord-276630-qci7khki.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276630-qci7khki.txt' === file2bib.sh === id: cord-026518-xv03vpji author: Xie, Peng title: Immune effect of a Newcastle disease virus DNA vaccine with IL-12 as a molecular adjuvant delivered by electroporation date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-026518-xv03vpji.txt cache: ./cache/cord-026518-xv03vpji.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-026518-xv03vpji.txt' === file2bib.sh === id: cord-004765-7e4yu2do author: Homberger, F. R. title: Maternally-derived passive immunity to enterotropic mouse hepatitis virus date: 1992 pages: extension: .txt txt: ./txt/cord-004765-7e4yu2do.txt cache: ./cache/cord-004765-7e4yu2do.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004765-7e4yu2do.txt' === file2bib.sh === id: cord-004754-5596p4ma author: Duan, X. title: Effects of origin and state of differentiation and activation of monocytes/macrophages on their susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) date: 2014-04-06 pages: extension: .txt txt: ./txt/cord-004754-5596p4ma.txt cache: ./cache/cord-004754-5596p4ma.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004754-5596p4ma.txt' === file2bib.sh === id: cord-265201-ab67pnct author: Sugiyama, K. title: Hemagglutination and structural polypeptides of a new coronavirus associated with diarrhea in infant mice date: 1980 pages: extension: .txt txt: ./txt/cord-265201-ab67pnct.txt cache: ./cache/cord-265201-ab67pnct.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265201-ab67pnct.txt' === file2bib.sh === id: cord-004755-rmnjs1t6 author: Welch, Siao-Kun Wan title: Monoclonal antibodies to a virulent strain of transmissible gastroenteritis virus: comparison of reactivity with virulent and attenuated virus date: 1988 pages: extension: .txt txt: ./txt/cord-004755-rmnjs1t6.txt cache: ./cache/cord-004755-rmnjs1t6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004755-rmnjs1t6.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 2 resourceName b'cord-004775-foaf3vyl.txt' === file2bib.sh === id: cord-258768-bjjfkfgg author: McElligott, Susan title: Detection and genetic characterization of canine parvoviruses and coronaviruses in southern Ireland date: 2010-11-24 pages: extension: .txt txt: ./txt/cord-258768-bjjfkfgg.txt cache: ./cache/cord-258768-bjjfkfgg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258768-bjjfkfgg.txt' === file2bib.sh === id: cord-256859-7ixegm72 author: Liu, S. W. title: Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between 1995 and 2004 date: 2006-01-09 pages: extension: .txt txt: ./txt/cord-256859-7ixegm72.txt cache: ./cache/cord-256859-7ixegm72.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256859-7ixegm72.txt' === file2bib.sh === id: cord-004738-vnz15x84 author: Chen, H. H. title: The rubella virus nonstructural protease recognizes itself via an internal sequence present upstream of the cleavage site for trans-activity date: 2006-03-27 pages: extension: .txt txt: ./txt/cord-004738-vnz15x84.txt cache: ./cache/cord-004738-vnz15x84.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004738-vnz15x84.txt' === file2bib.sh === id: cord-272973-kzaowysv author: Joshi, Lok R. title: Passive immunity to porcine epidemic diarrhea virus following immunization of pregnant gilts with a recombinant orf virus vector expressing the spike protein date: 2018-05-03 pages: extension: .txt txt: ./txt/cord-272973-kzaowysv.txt cache: ./cache/cord-272973-kzaowysv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272973-kzaowysv.txt' === file2bib.sh === id: cord-004766-gvom0f13 author: Traavik, T. title: Improvement of arbovirus HA antigens by treatment with a colloidal silica gel and sonication date: 1977 pages: extension: .txt txt: ./txt/cord-004766-gvom0f13.txt cache: ./cache/cord-004766-gvom0f13.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004766-gvom0f13.txt' === file2bib.sh === id: cord-262505-1ufgwxxg author: Lai, M. M. C. title: Genetic heterogeneity of murine coronaviruses date: 1983 pages: extension: .txt txt: ./txt/cord-262505-1ufgwxxg.txt cache: ./cache/cord-262505-1ufgwxxg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262505-1ufgwxxg.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-004719-3stcx0dd.txt cache: ./cache/cord-004719-3stcx0dd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004719-3stcx0dd.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-004672-0lf5j8lo.txt cache: ./cache/cord-004672-0lf5j8lo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 11 resourceName b'cord-004672-0lf5j8lo.txt' === file2bib.sh === id: cord-004851-h9ppa064 author: Plagemann, P. G. W. title: Hepatitis C virus date: 1991 pages: extension: .txt txt: ./txt/cord-004851-h9ppa064.txt cache: ./cache/cord-004851-h9ppa064.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004851-h9ppa064.txt' === file2bib.sh === id: cord-264392-he1vekrt author: Lambeth, L. S. title: Complete genome sequence of Nariva virus, a rodent paramyxovirus date: 2008-12-23 pages: extension: .txt txt: ./txt/cord-264392-he1vekrt.txt cache: ./cache/cord-264392-he1vekrt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-264392-he1vekrt.txt' === file2bib.sh === id: cord-048485-b8xb1f12 author: Hulst, Marcel title: Early transcriptional response in the jejunum of germ-free piglets after oral infection with virulent rotavirus date: 2008-06-04 pages: extension: .txt txt: ./txt/cord-048485-b8xb1f12.txt cache: ./cache/cord-048485-b8xb1f12.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-048485-b8xb1f12.txt' === file2bib.sh === id: cord-272955-kkkrkgg1 author: Belsy, Acosta title: Molecular characterization of adenoviral infections in Cuba: report of an unusual association of species D adenoviruses with different clinical syndromes date: 2009-03-12 pages: extension: .txt txt: ./txt/cord-272955-kkkrkgg1.txt cache: ./cache/cord-272955-kkkrkgg1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272955-kkkrkgg1.txt' === file2bib.sh === id: cord-001274-vz0qvp01 author: Chitray, M. title: Genetic heterogeneity in the leader and P1-coding regions of foot-and-mouth disease virus serotypes A and O in Africa date: 2013-11-13 pages: extension: .txt txt: ./txt/cord-001274-vz0qvp01.txt cache: ./cache/cord-001274-vz0qvp01.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-001274-vz0qvp01.txt' === file2bib.sh === id: cord-032801-b2ncmkjg author: Song, Jie title: Transcriptome analysis following enterovirus 71 and coxsackievirus A16 infection in respiratory epithelial cells date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-032801-b2ncmkjg.txt cache: ./cache/cord-032801-b2ncmkjg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-032801-b2ncmkjg.txt' === file2bib.sh === id: cord-281410-y558a5jf author: Akashi, H. title: Propagation of the Kakegawa strain of bovine coronavirus in suckling mice, rats and hamsters date: 1981 pages: extension: .txt txt: ./txt/cord-281410-y558a5jf.txt cache: ./cache/cord-281410-y558a5jf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281410-y558a5jf.txt' === file2bib.sh === id: cord-286794-adbxzgvs author: Du, Juan title: Identification and complete genome characterization of human enterovirus 117 from a child with pneumonia in China date: 2019-03-16 pages: extension: .txt txt: ./txt/cord-286794-adbxzgvs.txt cache: ./cache/cord-286794-adbxzgvs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286794-adbxzgvs.txt' === file2bib.sh === id: cord-285329-62yafd2d author: Tsunemitsu, H. title: Antigenic and biological comparisons of bovine coronaviruses derived from neonatal calf diarrhea and winter dysentery of adult cattle date: 1995 pages: extension: .txt txt: ./txt/cord-285329-62yafd2d.txt cache: ./cache/cord-285329-62yafd2d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285329-62yafd2d.txt' === file2bib.sh === id: cord-282062-h9smg0w9 author: Takano, Tomomi title: Novel single-stranded, circular DNA virus identified in cats in Japan date: 2018-09-14 pages: extension: .txt txt: ./txt/cord-282062-h9smg0w9.txt cache: ./cache/cord-282062-h9smg0w9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282062-h9smg0w9.txt' === file2bib.sh === id: cord-283525-kvcqayl4 author: Wei, Zhan-Yong title: Nitric oxide inhibits the replication cycle of porcine parvovirus in vitro date: 2009-05-13 pages: extension: .txt txt: ./txt/cord-283525-kvcqayl4.txt cache: ./cache/cord-283525-kvcqayl4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283525-kvcqayl4.txt' === file2bib.sh === id: cord-288948-89cdfhi0 author: Campalto, M. title: Divergent minute virus of canines strains identified in illegally imported puppies in Italy date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-288948-89cdfhi0.txt cache: ./cache/cord-288948-89cdfhi0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-288948-89cdfhi0.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 68600 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 68478 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 67698 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 67620 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 67935 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 68077 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-299342-l8ugjou9 author: Yaling, Zhou title: Porcine epidemic diarrhea virus (CV 777) and feline infectious peritonitis virus (FIPV) are antigenically related date: 1988 pages: extension: .txt txt: ./txt/cord-299342-l8ugjou9.txt cache: ./cache/cord-299342-l8ugjou9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299342-l8ugjou9.txt' === file2bib.sh === id: cord-285429-vmnj25b5 author: Saikruang, Wilaiporn title: Detection of diarrheal viruses circulating in adult patients in Thailand date: 2014-07-31 pages: extension: .txt txt: ./txt/cord-285429-vmnj25b5.txt cache: ./cache/cord-285429-vmnj25b5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285429-vmnj25b5.txt' === file2bib.sh === id: cord-294467-kq5wmavt author: Kasai, H. title: Characterization of haemagglutinin-esterase protein (HE) of murine corona virus DVIM by monoclonal antibodies date: 2014-04-08 pages: extension: .txt txt: ./txt/cord-294467-kq5wmavt.txt cache: ./cache/cord-294467-kq5wmavt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294467-kq5wmavt.txt' === file2bib.sh === id: cord-267446-rpv19oy6 author: Park, Jung-Eun title: Receptor-bound porcine epidemic diarrhea virus spike protein cleaved by trypsin induces membrane fusion date: 2011-06-12 pages: extension: .txt txt: ./txt/cord-267446-rpv19oy6.txt cache: ./cache/cord-267446-rpv19oy6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267446-rpv19oy6.txt' === file2bib.sh === id: cord-283804-dje7qbps author: Macnaughton, M. R. title: The polypeptide composition of avian infectious bronchitis virus particles date: 1977 pages: extension: .txt txt: ./txt/cord-283804-dje7qbps.txt cache: ./cache/cord-283804-dje7qbps.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-283804-dje7qbps.txt' === file2bib.sh === id: cord-302871-x3mjov5l author: Ribeiro, Juliane title: Extra-intestinal detection of canine kobuvirus in a puppy from Southern Brazil date: 2016-11-25 pages: extension: .txt txt: ./txt/cord-302871-x3mjov5l.txt cache: ./cache/cord-302871-x3mjov5l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302871-x3mjov5l.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-284087-g2jfnxja author: Falcone, Valeria title: Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season date: 2013-02-09 pages: extension: .txt txt: ./txt/cord-284087-g2jfnxja.txt cache: ./cache/cord-284087-g2jfnxja.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-284087-g2jfnxja.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-291718-cz1bi0ym author: Yu, Liping title: The papain-like protease of avian infectious bronchitis virus has deubiquitinating activity date: 2017-03-18 pages: extension: .txt txt: ./txt/cord-291718-cz1bi0ym.txt cache: ./cache/cord-291718-cz1bi0ym.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-291718-cz1bi0ym.txt' === file2bib.sh === id: cord-291530-ffex7dw9 author: Escutenaire, S. title: Characterization of divergent and atypical canine coronaviruses from Sweden date: 2007-05-29 pages: extension: .txt txt: ./txt/cord-291530-ffex7dw9.txt cache: ./cache/cord-291530-ffex7dw9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291530-ffex7dw9.txt' === file2bib.sh === id: cord-295409-7l0pglef author: Percy, D. title: Replication of sialodacryoadenitis virus in mouse L-2 cells date: 1989 pages: extension: .txt txt: ./txt/cord-295409-7l0pglef.txt cache: ./cache/cord-295409-7l0pglef.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295409-7l0pglef.txt' === file2bib.sh === id: cord-295308-ruwxm4fd author: Chen, S.-P. title: Identification of a recombinant dengue virus type 1 with 3 recombination regions in natural populations in Guangdong province, China date: 2008-04-30 pages: extension: .txt txt: ./txt/cord-295308-ruwxm4fd.txt cache: ./cache/cord-295308-ruwxm4fd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295308-ruwxm4fd.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 4 resourceName b'cord-285547-7m3dh8hu.txt' === file2bib.sh === id: cord-316797-sf2lu45f author: Hirano, N. title: Replication of rat coronavirus in a rat cell line, LBC date: 1985 pages: extension: .txt txt: ./txt/cord-316797-sf2lu45f.txt cache: ./cache/cord-316797-sf2lu45f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-316797-sf2lu45f.txt' === file2bib.sh === id: cord-299763-ttb7o8lv author: Choi, Jeong-Won title: Molecular characteristics of a novel strain of canine minute virus associated with hepatitis in a dog date: 2016-06-01 pages: extension: .txt txt: ./txt/cord-299763-ttb7o8lv.txt cache: ./cache/cord-299763-ttb7o8lv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299763-ttb7o8lv.txt' === file2bib.sh === id: cord-283710-55m16q7c author: Wo, Ying title: Epidemical features of HAdV-3 and HAdV-7 in pediatric pneumonia in Chongqing, China date: 2014-12-12 pages: extension: .txt txt: ./txt/cord-283710-55m16q7c.txt cache: ./cache/cord-283710-55m16q7c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283710-55m16q7c.txt' === file2bib.sh === id: cord-293945-gyb9mjb5 author: Chai, Weidong title: Antiviral effects of a probiotic Enterococcus faecium strain against transmissible gastroenteritis coronavirus date: 2012-11-28 pages: extension: .txt txt: ./txt/cord-293945-gyb9mjb5.txt cache: ./cache/cord-293945-gyb9mjb5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293945-gyb9mjb5.txt' === file2bib.sh === id: cord-290695-ubrqy2zf author: Payne, H. R. title: Analysis of cell fusion induced by bovine coronavirus infection date: 1988 pages: extension: .txt txt: ./txt/cord-290695-ubrqy2zf.txt cache: ./cache/cord-290695-ubrqy2zf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290695-ubrqy2zf.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 4 resourceName b'cord-291707-dzmvjh7j.txt' === file2bib.sh === id: cord-285892-tp6mlqtw author: Li, Yingli title: Isolation of two Chinese bovine enteroviruses and sequence analysis of their complete genomes date: 2012-08-01 pages: extension: .txt txt: ./txt/cord-285892-tp6mlqtw.txt cache: ./cache/cord-285892-tp6mlqtw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285892-tp6mlqtw.txt' === file2bib.sh === id: cord-296167-np0b9a7o author: Mardani, Karim title: Naturally occurring recombination between distant strains of infectious bronchitis virus date: 2010-06-24 pages: extension: .txt txt: ./txt/cord-296167-np0b9a7o.txt cache: ./cache/cord-296167-np0b9a7o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296167-np0b9a7o.txt' === file2bib.sh === id: cord-287275-vwyny1vt author: Zhang, Meng-Jia title: Genomic characterization and pathogenicity of porcine deltacoronavirus strain CHN-HG-2017 from China date: 2018-10-30 pages: extension: .txt txt: ./txt/cord-287275-vwyny1vt.txt cache: ./cache/cord-287275-vwyny1vt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287275-vwyny1vt.txt' === file2bib.sh === id: cord-311773-r9c7sx6r author: Gaertner, Diane J. title: Susceptibility of rodent cell lines to rat coronaviruses and differential enhancement by trypsin or DEAE-dextran date: 1991 pages: extension: .txt txt: ./txt/cord-311773-r9c7sx6r.txt cache: ./cache/cord-311773-r9c7sx6r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-311773-r9c7sx6r.txt' === file2bib.sh === id: cord-305859-vt8vwo3y author: Jung, Kwonil title: Calves are susceptible to infection with the newly emerged porcine deltacoronavirus, but not with the swine enteric alphacoronavirus, porcine epidemic diarrhea virus date: 2017-04-03 pages: extension: .txt txt: ./txt/cord-305859-vt8vwo3y.txt cache: ./cache/cord-305859-vt8vwo3y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305859-vt8vwo3y.txt' === file2bib.sh === id: cord-299345-2i48ld8d author: Nefedeva, Mariia title: Molecular characteristics of a novel recombinant of porcine epidemic diarrhea virus date: 2019-02-06 pages: extension: .txt txt: ./txt/cord-299345-2i48ld8d.txt cache: ./cache/cord-299345-2i48ld8d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299345-2i48ld8d.txt' === file2bib.sh === id: cord-328381-bfvdhai8 author: Hattermann, K. title: Susceptibility of different eukaryotic cell lines to SARS-coronavirus date: 2005-01-13 pages: extension: .txt txt: ./txt/cord-328381-bfvdhai8.txt cache: ./cache/cord-328381-bfvdhai8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328381-bfvdhai8.txt' === file2bib.sh === id: cord-304109-yirs7kjg author: Mueller, Andreas title: Polyomaviruses KI and WU in children with respiratory tract infection date: 2009-09-12 pages: extension: .txt txt: ./txt/cord-304109-yirs7kjg.txt cache: ./cache/cord-304109-yirs7kjg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304109-yirs7kjg.txt' === file2bib.sh === id: cord-294947-g4ntyddb author: Zhu, Yu title: Establishment of a nanoparticle-assisted RT-PCR assay to distinguish field strains and attenuated strains of porcine epidemic diarrhea virus date: 2016-06-10 pages: extension: .txt txt: ./txt/cord-294947-g4ntyddb.txt cache: ./cache/cord-294947-g4ntyddb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294947-g4ntyddb.txt' === file2bib.sh === id: cord-307378-cx1jz7wf author: Dadar, Maryam title: The association between the incidence of COVID-19 and the distance from the virus epicenter in Iran date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-307378-cx1jz7wf.txt cache: ./cache/cord-307378-cx1jz7wf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307378-cx1jz7wf.txt' === file2bib.sh === id: cord-317617-snrumw3x author: Sugiyama, K. title: Morphological and biological properties of a new coronavirus associated with diarrhea in infant mice date: 1981 pages: extension: .txt txt: ./txt/cord-317617-snrumw3x.txt cache: ./cache/cord-317617-snrumw3x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317617-snrumw3x.txt' === file2bib.sh === id: cord-306380-msk9p1yy author: Lee, C.-W. title: Evidence of genetic diversity generated by recombination among avian coronavirus IBV date: 2000 pages: extension: .txt txt: ./txt/cord-306380-msk9p1yy.txt cache: ./cache/cord-306380-msk9p1yy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306380-msk9p1yy.txt' === file2bib.sh === id: cord-316525-uadfehr6 author: Zhang, X. W. title: Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus date: 2004-10-11 pages: extension: .txt txt: ./txt/cord-316525-uadfehr6.txt cache: ./cache/cord-316525-uadfehr6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316525-uadfehr6.txt' === file2bib.sh === id: cord-312338-r6jqmes3 author: Althani, Asma title: Characterisation of winter respiratory viral infections in patients with asthma and COPD in Qatar date: 2012-12-14 pages: extension: .txt txt: ./txt/cord-312338-r6jqmes3.txt cache: ./cache/cord-312338-r6jqmes3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312338-r6jqmes3.txt' === file2bib.sh === id: cord-290546-zu5ns4yq author: Fennestad, K. L. title: Pleural effusion disease in rabbits. Properties of the aetiological agent date: 1983 pages: extension: .txt txt: ./txt/cord-290546-zu5ns4yq.txt cache: ./cache/cord-290546-zu5ns4yq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290546-zu5ns4yq.txt' === file2bib.sh === id: cord-330825-apfcql4m author: Paraguison-Alili, Rubigilda title: Phylogenetic tracking of current porcine epidemic diarrhea virus (PEDV) strains in the Philippines date: 2016-06-28 pages: extension: .txt txt: ./txt/cord-330825-apfcql4m.txt cache: ./cache/cord-330825-apfcql4m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330825-apfcql4m.txt' === file2bib.sh === id: cord-308950-bl83r4v3 author: Miguel, B. title: The role of feline aminopeptidase N as a receptor for infectious bronchitis virus : Brief Review date: 2002 pages: extension: .txt txt: ./txt/cord-308950-bl83r4v3.txt cache: ./cache/cord-308950-bl83r4v3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-308950-bl83r4v3.txt' === file2bib.sh === id: cord-294138-h7sfd1wa author: McIver, David J. title: Coronavirus surveillance of wildlife in the Lao People’s Democratic Republic detects viral RNA in rodents date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-294138-h7sfd1wa.txt cache: ./cache/cord-294138-h7sfd1wa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294138-h7sfd1wa.txt' === file2bib.sh === id: cord-307098-oq7zrnuv author: Taguchi, F. title: Difference in Bgp-independent fusion activity among mouse hepatitis viruses date: 2014-05-20 pages: extension: .txt txt: ./txt/cord-307098-oq7zrnuv.txt cache: ./cache/cord-307098-oq7zrnuv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307098-oq7zrnuv.txt' === file2bib.sh === id: cord-294218-v4gjabp3 author: Dea, S. title: Intracellular synthesis and processing of the structural glycoproteins of turkey enteric coronavirus date: 1989 pages: extension: .txt txt: ./txt/cord-294218-v4gjabp3.txt cache: ./cache/cord-294218-v4gjabp3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294218-v4gjabp3.txt' === file2bib.sh === id: cord-334810-hw1aijwf author: Banyard, Ashley C. title: Repeated detection of European bat lyssavirus type 2 in dead bats found at a single roost site in the UK date: 2009-10-20 pages: extension: .txt txt: ./txt/cord-334810-hw1aijwf.txt cache: ./cache/cord-334810-hw1aijwf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334810-hw1aijwf.txt' === file2bib.sh === id: cord-306725-0vam15pt author: Li, Hao title: First detection and genomic characteristics of bovine torovirus in dairy calves in China date: 2020-05-09 pages: extension: .txt txt: ./txt/cord-306725-0vam15pt.txt cache: ./cache/cord-306725-0vam15pt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-306725-0vam15pt.txt' === file2bib.sh === id: cord-289926-y1rjgbui author: Veretnik, S. title: RNA binding domain of HDV antigen is homologous to the HMG box of SRY date: 2014-05-18 pages: extension: .txt txt: ./txt/cord-289926-y1rjgbui.txt cache: ./cache/cord-289926-y1rjgbui.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289926-y1rjgbui.txt' === file2bib.sh === id: cord-316153-wet0go35 author: Jia, W. title: A novel variant of avian infectious bronchitis virus resulting from recombination among three different strains date: 1995 pages: extension: .txt txt: ./txt/cord-316153-wet0go35.txt cache: ./cache/cord-316153-wet0go35.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316153-wet0go35.txt' === file2bib.sh === id: cord-298883-uiwg482s author: Truong, C. title: Identification of an immunorelevant ORF2 epitope from porcine circovirus type 2 as a serological marker for experimental and natural infection date: 2001 pages: extension: .txt txt: ./txt/cord-298883-uiwg482s.txt cache: ./cache/cord-298883-uiwg482s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-298883-uiwg482s.txt' === file2bib.sh === id: cord-312787-j7ye7ed5 author: Loemba, H. D. title: Kinetics of humoral immune response to the major structural proteins of the porcine reproductive and respiratory syndrome virus date: 1996 pages: extension: .txt txt: ./txt/cord-312787-j7ye7ed5.txt cache: ./cache/cord-312787-j7ye7ed5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312787-j7ye7ed5.txt' === file2bib.sh === id: cord-299428-gon6bzat author: Mondal, Shankar title: Sequence analysis of infectious bronchitis virus isolates from the 1960s in the United States date: 2012-10-11 pages: extension: .txt txt: ./txt/cord-299428-gon6bzat.txt cache: ./cache/cord-299428-gon6bzat.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299428-gon6bzat.txt' === file2bib.sh === id: cord-339178-d6f6a5ds author: Pensaert, M. B. title: A new coronavirus-like particle associated with diarrhea in swine date: 1978 pages: extension: .txt txt: ./txt/cord-339178-d6f6a5ds.txt cache: ./cache/cord-339178-d6f6a5ds.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339178-d6f6a5ds.txt' === file2bib.sh === id: cord-324377-br2uorg8 author: Zhou, Pei title: Antiviral effect of lithium chloride on infection of cells by canine parvovirus date: 2015-08-28 pages: extension: .txt txt: ./txt/cord-324377-br2uorg8.txt cache: ./cache/cord-324377-br2uorg8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-324377-br2uorg8.txt' === file2bib.sh === id: cord-309145-6aqc074e author: Ito, Y. title: Induction of interferon by virus glycoprotein(s) in lymphoid cells through interaction with the cellular receptors via lectin-like action: An alternative interferon induction mechanism date: 1994 pages: extension: .txt txt: ./txt/cord-309145-6aqc074e.txt cache: ./cache/cord-309145-6aqc074e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309145-6aqc074e.txt' === file2bib.sh === id: cord-321471-gev5xq3a author: Zhu, Liqian title: Control of the PI3K/Akt pathway by porcine reproductive and respiratory syndrome virus date: 2013-02-05 pages: extension: .txt txt: ./txt/cord-321471-gev5xq3a.txt cache: ./cache/cord-321471-gev5xq3a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321471-gev5xq3a.txt' === file2bib.sh === id: cord-302323-vvo8a4hp author: Wang, Xiaobo title: Immunogenicity and antigenic relationships among spike proteins of porcine epidemic diarrhea virus subtypes G1 and G2 date: 2015-11-26 pages: extension: .txt txt: ./txt/cord-302323-vvo8a4hp.txt cache: ./cache/cord-302323-vvo8a4hp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302323-vvo8a4hp.txt' === file2bib.sh === id: cord-302063-ct5rvqtd author: Mohamed, Fakry F. title: Molecular detection of enteric viruses from diarrheic calves in Egypt date: 2016-09-29 pages: extension: .txt txt: ./txt/cord-302063-ct5rvqtd.txt cache: ./cache/cord-302063-ct5rvqtd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302063-ct5rvqtd.txt' === file2bib.sh === id: cord-302798-q0mbngqy author: Ge, Junwei title: Genomic characterization of circoviruses associated with acute gastroenteritis in minks in northeastern China date: 2018-06-14 pages: extension: .txt txt: ./txt/cord-302798-q0mbngqy.txt cache: ./cache/cord-302798-q0mbngqy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302798-q0mbngqy.txt' === file2bib.sh === id: cord-310669-6hwq5jfv author: Erles, K. title: Investigation into the causes of canine infectious respiratory disease: antibody responses to canine respiratory coronavirus and canine herpesvirus in two kennelled dog populations date: 2005-04-21 pages: extension: .txt txt: ./txt/cord-310669-6hwq5jfv.txt cache: ./cache/cord-310669-6hwq5jfv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310669-6hwq5jfv.txt' === file2bib.sh === id: cord-307408-6wfx0wey author: Li, Renfeng title: Phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in central China based on the ORF3 gene and the main neutralization epitopes date: 2013-11-30 pages: extension: .txt txt: ./txt/cord-307408-6wfx0wey.txt cache: ./cache/cord-307408-6wfx0wey.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307408-6wfx0wey.txt' === file2bib.sh === id: cord-340905-8nyew5i5 author: Chen, Yi-Ning title: Genotyping of turkey coronavirus field isolates from various geographic locations in the Unites States based on the spike gene date: 2015-08-08 pages: extension: .txt txt: ./txt/cord-340905-8nyew5i5.txt cache: ./cache/cord-340905-8nyew5i5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340905-8nyew5i5.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 2 resourceName b'cord-325827-492xi3ee.txt' === file2bib.sh === id: cord-318731-vlszl0i8 author: Chen, Si title: Molecular characterization of HLJ-073, a recombinant canine coronavirus strain from China with an ORF3abc deletion date: 2019-05-31 pages: extension: .txt txt: ./txt/cord-318731-vlszl0i8.txt cache: ./cache/cord-318731-vlszl0i8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318731-vlszl0i8.txt' === file2bib.sh === id: cord-290819-zhywlf6r author: Wu, Jiaqi title: The antiviral protein viperin interacts with the viral N protein to inhibit proliferation of porcine epidemic diarrhea virus date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-290819-zhywlf6r.txt cache: ./cache/cord-290819-zhywlf6r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290819-zhywlf6r.txt' === file2bib.sh === id: cord-338641-s006a7m0 author: Black, W. D. title: Reverse transcriptase-polymerase chain reaction for the detection equine rhinitis B viruses and cell culture isolation of the virus date: 2006-08-24 pages: extension: .txt txt: ./txt/cord-338641-s006a7m0.txt cache: ./cache/cord-338641-s006a7m0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338641-s006a7m0.txt' === file2bib.sh === id: cord-317009-8tqnt1l9 author: Aita, Tsunehiko title: Characterization of epidemic diarrhea outbreaks associated with bovine torovirus in adult cows date: 2011-12-14 pages: extension: .txt txt: ./txt/cord-317009-8tqnt1l9.txt cache: ./cache/cord-317009-8tqnt1l9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317009-8tqnt1l9.txt' === file2bib.sh === id: cord-322593-bgm6smuo author: Li, Lan title: Antiviral activity of recombinant porcine surfactant protein A against porcine reproductive and respiratory syndrome virus in vitro date: 2016-04-21 pages: extension: .txt txt: ./txt/cord-322593-bgm6smuo.txt cache: ./cache/cord-322593-bgm6smuo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322593-bgm6smuo.txt' === file2bib.sh === id: cord-338607-22f04uqe author: Verbeek, A. title: Genomic relationship between turkey and bovine enteric coronaviruses identified by hybridization with BCV or TCV specific cDNA probes date: 1991 pages: extension: .txt txt: ./txt/cord-338607-22f04uqe.txt cache: ./cache/cord-338607-22f04uqe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338607-22f04uqe.txt' === file2bib.sh === id: cord-334090-66d8c75g author: Seger, Waleed title: Genotyping of infectious bronchitis viruses from broiler farms in Iraq during 2014-2015 date: 2016-02-18 pages: extension: .txt txt: ./txt/cord-334090-66d8c75g.txt cache: ./cache/cord-334090-66d8c75g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334090-66d8c75g.txt' === file2bib.sh === id: cord-314069-8dxzf2ip author: Dongliu, Yuan title: Outbreak of acute febrile respiratory illness caused by human adenovirus B P14H11F14 in a military training camp in Shandong China date: 2016-06-28 pages: extension: .txt txt: ./txt/cord-314069-8dxzf2ip.txt cache: ./cache/cord-314069-8dxzf2ip.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314069-8dxzf2ip.txt' === file2bib.sh === id: cord-343131-tu6g977q author: Cheung, Andrew K. title: A divergent clade of circular single-stranded DNA viruses from pig feces date: 2013-04-24 pages: extension: .txt txt: ./txt/cord-343131-tu6g977q.txt cache: ./cache/cord-343131-tu6g977q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343131-tu6g977q.txt' === file2bib.sh === id: cord-343349-ftzjdvfj author: Bhatt, P. N. title: Experimental infection of adult axenic rats with Parker's Rat Coronavirus date: 1977 pages: extension: .txt txt: ./txt/cord-343349-ftzjdvfj.txt cache: ./cache/cord-343349-ftzjdvfj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343349-ftzjdvfj.txt' === file2bib.sh === id: cord-321195-cndq6aqb author: Xue, Chunyi title: Chimeric influenza-virus-like particles containing the porcine reproductive and respiratory syndrome virus GP5 protein and the influenza virus HA and M1 proteins date: 2014-07-27 pages: extension: .txt txt: ./txt/cord-321195-cndq6aqb.txt cache: ./cache/cord-321195-cndq6aqb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321195-cndq6aqb.txt' === file2bib.sh === id: cord-333403-imx3990a author: Christianson, K. K. title: Characterization of a temperature sensitive feline infectious peritonitis coronavirus date: 1989 pages: extension: .txt txt: ./txt/cord-333403-imx3990a.txt cache: ./cache/cord-333403-imx3990a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333403-imx3990a.txt' === file2bib.sh === id: cord-333331-ddcz7zck author: Yang, Jin title: Detection of hepatitis C virus by an improved loop-mediated isothermal amplification assay date: 2011-05-12 pages: extension: .txt txt: ./txt/cord-333331-ddcz7zck.txt cache: ./cache/cord-333331-ddcz7zck.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333331-ddcz7zck.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-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 4 resourceName b'cord-329145-424vv8a8.txt' === file2bib.sh === id: cord-341278-klv9jdm8 author: Smith, Abigail L. title: The role of gamma interferon in infection of susceptible mice with murine coronavirus, MHV-JHM date: 1991 pages: extension: .txt txt: ./txt/cord-341278-klv9jdm8.txt cache: ./cache/cord-341278-klv9jdm8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341278-klv9jdm8.txt' === file2bib.sh === id: cord-322760-tsxniu3j author: Sha, Jianping title: Fatality risks for nosocomial outbreaks of Middle East respiratory syndrome coronavirus in the Middle East and South Korea date: 2016-09-23 pages: extension: .txt txt: ./txt/cord-322760-tsxniu3j.txt cache: ./cache/cord-322760-tsxniu3j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322760-tsxniu3j.txt' === file2bib.sh === id: cord-315811-wpeac0lk author: Hu, Hui title: Experimental infection of gnotobiotic pigs with the cell-culture-adapted porcine deltacoronavirus strain OH-FD22 date: 2016-09-12 pages: extension: .txt txt: ./txt/cord-315811-wpeac0lk.txt cache: ./cache/cord-315811-wpeac0lk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315811-wpeac0lk.txt' === file2bib.sh === id: cord-314751-i9rxesrg author: Oh, Jongsuk title: Immunogenicity and protective efficacy of recombinant S1 domain of the porcine epidemic diarrhea virus spike protein date: 2014-07-10 pages: extension: .txt txt: ./txt/cord-314751-i9rxesrg.txt cache: ./cache/cord-314751-i9rxesrg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314751-i9rxesrg.txt' === file2bib.sh === id: cord-341469-7guojyay author: Park, Seong-Jun title: Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field isolates in Korea date: 2011-01-06 pages: extension: .txt txt: ./txt/cord-341469-7guojyay.txt cache: ./cache/cord-341469-7guojyay.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341469-7guojyay.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 4 resourceName b'cord-292286-ygomb3oi.txt' === file2bib.sh === id: cord-332811-kjgah8ts author: Lee, Do Hyun title: Immunoprophylactic effect of chicken egg yolk antibody (IgY) against a recombinant S1 domain of the porcine epidemic diarrhea virus spike protein in piglets date: 2015-06-23 pages: extension: .txt txt: ./txt/cord-332811-kjgah8ts.txt cache: ./cache/cord-332811-kjgah8ts.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332811-kjgah8ts.txt' === file2bib.sh === id: cord-339991-k8z6v2vx author: Rong, Q. title: Multiple mechanisms for HSV-1 induction of interferon α production by peripheral blood mononuclear cells date: 2003 pages: extension: .txt txt: ./txt/cord-339991-k8z6v2vx.txt cache: ./cache/cord-339991-k8z6v2vx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339991-k8z6v2vx.txt' === file2bib.sh === id: cord-343780-084lq92r author: Hsu, Tien-Huan title: Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan date: 2018-07-26 pages: extension: .txt txt: ./txt/cord-343780-084lq92r.txt cache: ./cache/cord-343780-084lq92r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343780-084lq92r.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 2 resourceName b'cord-294323-mryiqmsw.txt' === file2bib.sh === id: cord-343256-n593kh7u author: Percy, D. H. title: A comparison of the sensitivity and specificity of sialodacryoadenitis virus, Parker's rat coronavirus, and mouse hepatitis virus-infected cells as a source of antigen for the detection of antibody to rat coronaviruses date: 1991 pages: extension: .txt txt: ./txt/cord-343256-n593kh7u.txt cache: ./cache/cord-343256-n593kh7u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343256-n593kh7u.txt' === file2bib.sh === id: cord-346629-770qyee8 author: Mase, M. title: Phylogenetic analysis of avian infectious bronchitis virus strains isolated in Japan date: 2004-07-15 pages: extension: .txt txt: ./txt/cord-346629-770qyee8.txt cache: ./cache/cord-346629-770qyee8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346629-770qyee8.txt' === file2bib.sh === id: cord-341383-e2jrhycj author: Dong, Wei title: Epidemiological and clinical characteristics of respiratory viral infections in children in Shanghai, China date: 2016-05-02 pages: extension: .txt txt: ./txt/cord-341383-e2jrhycj.txt cache: ./cache/cord-341383-e2jrhycj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-341383-e2jrhycj.txt' === file2bib.sh === id: cord-335690-66t5fjld author: Khromykh, A. A. title: RNA binding properties of core protein of the flavivirus Kunjin date: 1996 pages: extension: .txt txt: ./txt/cord-335690-66t5fjld.txt cache: ./cache/cord-335690-66t5fjld.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335690-66t5fjld.txt' === file2bib.sh === id: cord-344464-if6js43s author: Cowley, J. A. title: The complete genome sequence of gill-associated virus of Penaeus monodon prawns indicates a gene organisation unique among nidoviruses(*): Brief Report date: 2002 pages: extension: .txt txt: ./txt/cord-344464-if6js43s.txt cache: ./cache/cord-344464-if6js43s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-344464-if6js43s.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-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 2 resourceName b'cord-355535-01h8yyqj.txt' === file2bib.sh === id: cord-345552-h6fwi0qn author: Li, Q.-G. title: Hydropathic characteristics of adenovirus hexons date: 1997-07-01 pages: extension: .txt txt: ./txt/cord-345552-h6fwi0qn.txt cache: ./cache/cord-345552-h6fwi0qn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345552-h6fwi0qn.txt' === file2bib.sh === id: cord-349907-dwhyx97y author: Noh, Ji Yeong title: Simultaneous detection of severe acute respiratory syndrome, Middle East respiratory syndrome, and related bat coronaviruses by real-time reverse transcription PCR date: 2017-02-20 pages: extension: .txt txt: ./txt/cord-349907-dwhyx97y.txt cache: ./cache/cord-349907-dwhyx97y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349907-dwhyx97y.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-345957-wuk2arf9 author: Mohamed, Fakry F. title: Detection and genetic characterization of bovine kobuvirus from calves in Egypt date: 2018-02-08 pages: extension: .txt txt: ./txt/cord-345957-wuk2arf9.txt cache: ./cache/cord-345957-wuk2arf9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345957-wuk2arf9.txt' === file2bib.sh === id: cord-347443-0evqo01m author: Litwin, Christine M. title: Seasonality and prevalence of respiratory pathogens detected by multiplex PCR at a tertiary care medical center date: 2013-07-24 pages: extension: .txt txt: ./txt/cord-347443-0evqo01m.txt cache: ./cache/cord-347443-0evqo01m.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-347443-0evqo01m.txt' === file2bib.sh === id: cord-341342-kyavg4vu author: Masters, P. S. title: Localization of an RNA-binding domain in the nucleocapsid protein of the coronavirus mouse hepatitis virus date: 1992 pages: extension: .txt txt: ./txt/cord-341342-kyavg4vu.txt cache: ./cache/cord-341342-kyavg4vu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341342-kyavg4vu.txt' === file2bib.sh === id: cord-353797-yb355mxk author: Inaba, Y. title: Replication of bovine coronavirus in cell line BEK-1 culture date: 1976 pages: extension: .txt txt: ./txt/cord-353797-yb355mxk.txt cache: ./cache/cord-353797-yb355mxk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353797-yb355mxk.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-349800-s9w2yr08 author: Hohdatsu, T. title: Characterization of monoclonal antibodies against feline infectious peritonitis virus type II and antigenic relationship between feline, porcine, and canine coronaviruses date: 1991 pages: extension: .txt txt: ./txt/cord-349800-s9w2yr08.txt cache: ./cache/cord-349800-s9w2yr08.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-349800-s9w2yr08.txt' === file2bib.sh === id: cord-348179-i8w7huke author: Xue, Yong title: Increased risk of hepatitis E virus infection in schizophrenia date: 2012-10-07 pages: extension: .txt txt: ./txt/cord-348179-i8w7huke.txt cache: ./cache/cord-348179-i8w7huke.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348179-i8w7huke.txt' === file2bib.sh === id: cord-348147-leni23pa author: Müller, B. title: Genetic diversity and recombination of murine noroviruses in immunocompromised mice date: 2007-05-29 pages: extension: .txt txt: ./txt/cord-348147-leni23pa.txt cache: ./cache/cord-348147-leni23pa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348147-leni23pa.txt' === file2bib.sh === id: cord-345940-adg264vb author: Wanitchang, Asawin title: Characterization of influenza A virus pseudotyped with the spike protein of porcine epidemic diarrhea virus date: 2018-08-22 pages: extension: .txt txt: ./txt/cord-345940-adg264vb.txt cache: ./cache/cord-345940-adg264vb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345940-adg264vb.txt' === file2bib.sh === id: cord-345856-ckm0ol20 author: Zhong, Qiong title: Antiviral activity of Arbidol against Coxsackie virus B5 in vitro and in vivo date: 2009-03-17 pages: extension: .txt txt: ./txt/cord-345856-ckm0ol20.txt cache: ./cache/cord-345856-ckm0ol20.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345856-ckm0ol20.txt' === file2bib.sh === id: cord-346321-drhiqch0 author: Hohdatsu, T. title: The role of IgG subclass of mouse monoclonal antibodies in antibody-dependent enhancement of feline infectious peritonitis virus infection of feline macrophages date: 1994 pages: extension: .txt txt: ./txt/cord-346321-drhiqch0.txt cache: ./cache/cord-346321-drhiqch0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346321-drhiqch0.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-342568-3sj235rm author: Bald-Blume, Niklas title: Development of a molecular assay for the general detection of tospoviruses and the distinction between tospoviral species date: 2017-02-11 pages: extension: .txt txt: ./txt/cord-342568-3sj235rm.txt cache: ./cache/cord-342568-3sj235rm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-342568-3sj235rm.txt' === file2bib.sh === 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 4 resourceName b'cord-348163-9q1rt8i7.txt' === file2bib.sh === id: cord-355512-tycuoslv author: Storz, J. title: Comparison of hemagglutinating, receptor-destroying, and acetylesterase activities of avirulent and virulent bovine coronavirus strains date: 1992 pages: extension: .txt txt: ./txt/cord-355512-tycuoslv.txt cache: ./cache/cord-355512-tycuoslv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355512-tycuoslv.txt' === file2bib.sh === id: cord-356192-8b96rgqa author: Xie, Qian title: Two deletion variants of Middle East respiratory syndrome coronavirus found in a patient with characteristic symptoms date: 2017-04-18 pages: extension: .txt txt: ./txt/cord-356192-8b96rgqa.txt cache: ./cache/cord-356192-8b96rgqa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356192-8b96rgqa.txt' === file2bib.sh === id: cord-349964-38rgcc5h author: Pedersen, N. C. title: Antigenic relationship of the feline infectious peritonitis virus to coronaviruses of other species date: 1978 pages: extension: .txt txt: ./txt/cord-349964-38rgcc5h.txt cache: ./cache/cord-349964-38rgcc5h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349964-38rgcc5h.txt' === file2bib.sh === id: cord-346928-g1dqiki6 author: Costantini, V. title: Respiratory and fecal shedding of Porcine respiratory coronavirus (PRCV) in sentinel weaned pigs and sequence of the partial S-gene of the PRCV isolates date: 2003-11-26 pages: extension: .txt txt: ./txt/cord-346928-g1dqiki6.txt cache: ./cache/cord-346928-g1dqiki6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346928-g1dqiki6.txt' Que is empty; done journal-archVirol-cord === reduce.pl bib === id = cord-004680-u3cnsdl8 author = Lin, Z. title = Typing of recent infectious bronchitis virus isolates causing nephritis in chicken date = 1991 pages = extension = .txt mime = text/plain words = 860 sentences = 47 flesch = 57 summary = Four isolates of infectious bronchitis viruses (IBV) from chickens with nephritis, were characterized by polymerase chain reaction (PCR) and restriction enzyme fragment length polymorphism (RFLP), and were found to be genetically different from the other twelve strains which we previously studied. HinfI digested pUC 19 DNA was used as the molecular size markers (3//), and their sizes are indicated in base pairs (bp) on the left In this study, essentially the same procedure was used in an attempt to characterize four IBV isolates F-88, Y-4, M-l, and NI-1 from chickens with nephritis in different endemic areas of Japan between 1988 and 1989. The results of the present study, indicate that the four recently obtained IBV isolates causing nephritis are, by our genetic criteria, similar to each other but different from previous isolates, hence are classified together into a new subtype (group VI). Serological comparisons of strains of infectious bronchitis virus using plaque-purified isolants cache = ./cache/cord-004680-u3cnsdl8.txt txt = ./txt/cord-004680-u3cnsdl8.txt === reduce.pl bib === id = cord-004673-c8qcjve9 author = Faaberg, K. S. title = Membrane association of the C-terminal half of the open reading frame 1a protein of lactate dehydrogenase-elevating virus date = 1996 pages = extension = .txt mime = text/plain words = 4647 sentences = 220 flesch = 55 summary = cDNAs encoding ORF 1a protein segments encompassing transmembrane segments 5 to 11 and its amphipathic C-terminal end as well as the N-terminal 80 amino acids of the downstream ORF 1b protein were transcribed and the transcripts in vitro translated in the absence and presence of microsomal membranes. Eisenberg hydrophobic moment analysis of the protein predicted the presence of eleven transmembrane segments in the C-terminal half of the molecule (amino acids 980-1852) that flank the serine protease domain, cDNAs encoding ORF la protein segments encompassing transmembrane segments 5 to 11 and its amphipathic C-terminal end as well as the N-terminal 80 amino acids of the downstream ORF lb protein were transcribed and the transcripts in vitro translated in the absence and presence of microsomal membranes. In the present study we provide strong evidence that the segment of LDV ORF la protein with transmembrane segments 5-11 (see Fig. 1 ) becomes intimately associated with endoplasmic reticulum (ER) membranes during synthesis and that none of its potential N-glycosylation sites becomes glycosylated. cache = ./cache/cord-004673-c8qcjve9.txt txt = ./txt/cord-004673-c8qcjve9.txt === reduce.pl bib === id = cord-004681-02wem2u3 author = Wada, R. title = Ultrastructure and immuno-cytochemistry of BHK-21 cells infected with a modified Bucyrus strain of equine arteritis virus date = 1995 pages = extension = .txt mime = text/plain words = 2044 sentences = 123 flesch = 55 summary = title: Ultrastructure and immuno-cytochemistry of BHK-21 cells infected with a modified Bucyrus strain of equine arteritis virus Morphogenesis of a modified Bucyrus strain of equine arteritis virus (EAV) in BHK-21 cells was studied. Bacillary tubules were first detected in the cytoplasm 8 h after infection, and mature virions 79 to 122 nm in diameter, 101 nm on average, were mostly observed in the cisternae of the rough endoplasmic reticulum (RER) at 12 h or later. Equine arteritis virus (EAV) has been classified into the Togaviridae family [22] on the basis of the virion size and morphology [23] . In the present study a mutant virus showing higher growth on BHK-21 cells than the parental Bucyrus strain of EAV [11] was examined for the fine structure, its morphogenesis and intracellular localization of viral antigen. Through cross-sections of the outer layer of the virion, a grape-like structure seemed to be subunits 13 to 20 nm in diameter around the core (Fig. 3c) . cache = ./cache/cord-004681-02wem2u3.txt txt = ./txt/cord-004681-02wem2u3.txt === reduce.pl bib === id = cord-004793-6yh36r0w author = Choi, C. S. title = Replication of two porcine parvovirus isolates at non-permissive temperatures date = 1990 pages = extension = .txt mime = text/plain words = 3234 sentences = 178 flesch = 57 summary = Previous studies have shown that replication in vitro of the porcine parvovirus (PPV) isolate, KBSH, was restricted at 39°C but not at 37°C. In this study, Kresse and KBSH isolates were passaged up to ten times in swine testicle (ST) cells at non-permissive temperatures, and at subsequent passage viral protein synthesis, viral DNA synthesis, and progeny virus were evaluated. Kresse and KBSH isolates were serially passaged at non-permissive temperatures in an attempt to evaluate the effect of in vitro passages on the pattern of virus replication. KBSH appeared to gain the ability to replicate in swine fetuses following serial cell culture passages at 39 °C evidenced by fetal death and virus detection in fetal tissues. Furthermore, KBSH isolate passaged at 39 °C for 10 times now showed the ability to replicate in swine fetuses, indicating that pathogenicity can be recovered by serial adaptation at the mean body temperature of pigs, 39 °C. cache = ./cache/cord-004793-6yh36r0w.txt txt = ./txt/cord-004793-6yh36r0w.txt === 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 === id = cord-003050-n25wnmq5 author = Nibert, Max L. title = A barnavirus sequence mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis date = 2018-03-07 pages = extension = .txt mime = text/plain words = 3324 sentences = 159 flesch = 53 summary = The 4.2-kb plus-strand sequence of this virus encompasses four main open reading frames (ORFs), as expected for barnaviruses, including ORFs for a protease-containing polyprotein, an RNA-dependent RNA polymerase whose translation appears to rely on − 1 ribosomal frameshifting, and a capsid protein that is likely to be translated from a subgenomic RNA. Based on similar genome sizes, coding organizations, and P2-and P3-region sequence similarities, both MBV and RsBV1 appear to be most closely related to plant viruses in the unassigned genus Sobemovirus [12, 16] . As a result, the consensus sequence for the apparent new barnavirus reported here (GenBank MG686618) is 4206 nt long, appears to be coding complete for ORFs 1-4 ( Fig. 1) , and was newly assembled from a total of 821 individual reads (reads per position: mean, 19; range, 2-35). cache = ./cache/cord-003050-n25wnmq5.txt txt = ./txt/cord-003050-n25wnmq5.txt === 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-004717-41ui4lqc author = Laurin, Marc-André title = Detection and genetic characterization of a novel pig astrovirus: relationship to other astroviruses date = 2011-09-08 pages = extension = .txt mime = text/plain words = 2226 sentences = 115 flesch = 49 summary = Phylogenetic analysis of the 3 0 end of this strain suggests that a novel and possibly fifth lineage of AstV exists in swine and heightens concerns about the role of pigs as a potential source of emerging astrovirus infections. However, a group of four related sequences revealed only approximately 70% nucleotide identity to bat and human AstV sequences in the database, suggesting that these sequences were divergent from known PoAstV strains and possibly novel. Phylogenetic analysis of these sequences, in addition to prototypical animal AstV strains, confirmed their relatedness and grouped them in a unique lineage on a divergent branch distantly related to other known mamastroviruses (PoAstV 5 in Fig. 2a) . Phylogenetic analysis of the complete capsid coding region of PoAstV CC12 confirms that this strain forms a distinct lineage in the family Mamastroviridae, including previously identified porcine astroviruses from different continents (Fig. 2b ). cache = ./cache/cord-004717-41ui4lqc.txt txt = ./txt/cord-004717-41ui4lqc.txt === reduce.pl bib === id = cord-004764-tmvebf23 author = Stephenson, J. R. title = A comparative analysis of measles virus RNA by oligonucleotide fingerprinting date = 1982 pages = extension = .txt mime = text/plain words = 4851 sentences = 374 flesch = 70 summary = In addition to this disorder another CNS disease (subaeute selerosing panencephalitis --SSPE) has been associated with measles virus infection (1--3) . As the methods employed in these previous studies could only detect gross differences in virus-specific products, or examined one protein or ~ small p a r t thereof, we have chosen in this study to analyse the oligonncteotides from a T1 digest of the complete genome. purification scheme is hybridized to unlabelled messenger R N A from infected cells (Table 1) , it can be shown t h a t at, least 85 per cent, is protected from subsequent nuclease digestion and is thus assumed to be negative stranded. In order to compare the genomes of various measles isolates: unlabelled, single stranded, negative sense nueleocapsid I~NA was prepared from infected cell cytoplasm and purified in parallel with similar radio-labelled material as described in the previous section. 85 per cent measles-specific negative sense R N A b y hybridization to infected cell messenger I~NA. cache = ./cache/cord-004764-tmvebf23.txt txt = ./txt/cord-004764-tmvebf23.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 5703 sentences = 298 flesch = 59 summary = In this communication, the structurM proteins of the wfld-ty]pe and mutant, viruses were compared by SDS-PAGE, peptide mapping, and twodimensional gel electrophoresis to determine which of the mutant structural proteins differed from that of wild-type and the extent of homology among analogous proteins. To determine whether the arrangement of the structural proteins on the surface of mutants 205 and 280 was similar to that of wild-type, purified virions were labeled with r25I and analyzed by SDS-PAGE (Fig. 2) . Eight virus-specified intracellular proteins were resolved in wild-type and mutant strain-infected cells: A (1-2 A), B (1), C (3), D (3 CD), 1 ABC, D 2 (1 CD), alpha (1 D), and gamma (1 C). To further examine these viruses for structural differences, surface labeling of intact wild-type and mutant virus particles was done to compare the arrangement of the structural proteins which form the xdral capsids. cache = ./cache/cord-004672-0lf5j8lo.txt txt = ./txt/cord-004672-0lf5j8lo.txt === reduce.pl bib === id = cord-004798-5budstbg author = Takayama, N. title = An improved method for titration of mouse hepatitis virus type 3 in a mouse cell culture date = 1976 pages = extension = .txt mime = text/plain words = 924 sentences = 56 flesch = 73 summary = Plaque assay in DBT cells with DEAE-dextran and trypsin presents a titration system for MHV3 as sensitive as the LD(50) assay in mice. In DBT cells overlaid with ME)/I containing 1 per cent Noble agar, 5 per cent CS, 10 per cent TPB, and 1 : 10,000 neutral red, MHV3-plaques of 0.6--1.4 mm (mean value = 0.9 ram) in diameter could be counted at 40 hours p.i. The plaques were clearly-defined and sometimes contained a deeply-stained area at their center. To ira.prove the sensitivity of the plaque assay we examined the effect of diethylaminoethyl-dextran (DEAE-D) on the plaque formation and plaque diameter of MHV3, as BRADBUllNE and TYRREL]5 had reported that DEAE-D added to overlay agar increased the plaque number of human coronavirus (2). 1%eplication and plaque formation of mouse hepatitis virus (MttV-2) in mouse cell line DBT culture cache = ./cache/cord-004798-5budstbg.txt txt = ./txt/cord-004798-5budstbg.txt === reduce.pl bib === id = cord-011105-or9azf1g author = Huang, Zheng title = Full-genome sequences of GII.13[P21] recombinant norovirus strains from an outbreak in Changsha, China date = 2020-04-30 pages = extension = .txt mime = text/plain words = 2436 sentences = 165 flesch = 58 summary = title: Full-genome sequences of GII.13[P21] recombinant norovirus strains from an outbreak in Changsha, China Further, we determined the full-genome sequences of two strains of GII.13[P21] recombinant noroviruses, which were 7434 nt long. Although those genotypes have not caused severe outbreaks, studying these strains has helped us to obtain more information on the genetic diversity and gene constellation of noroviruses. Hence, we determined the genome sequences of GII.13[P21] recombinant strains isolated in the city of Changsha, China. Although the sporadic norovirus genotypes do not cause serious epidemic worldwide, unlike GII.2[P16] and GII.4[P4], due to these special binding sites, human infections are associated with severe vomiting and diarrhea. Although only a few samples were collected in this outbreak, we obtained the full genome of GII.13[P21] recombinant strains that have rarely been reported in China. Full-genomic analysis of a human norovirus recombinant GII.12/13 novel strain isolated from South Korea Full-genome sequence analysis of an uncommon norovirus genotype, GII.21, from South Korea cache = ./cache/cord-011105-or9azf1g.txt txt = ./txt/cord-011105-or9azf1g.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 6347 sentences = 280 flesch = 44 summary = 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. 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. 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. With representative sequences of plant virus genomes from many groups available, efforts were made to identify regions of similarity between known movement proteins and to predict movement functions for uncharacterized ORFs. Early observations made by this approach have been reviewed previously (e.g. cache = ./cache/cord-004719-3stcx0dd.txt txt = ./txt/cord-004719-3stcx0dd.txt === reduce.pl bib === id = cord-004713-gzts5h0y author = Fennestad, K. L. title = Pathogenetic observations on pleural effusion disease in rabbits date = 1985 pages = extension = .txt mime = text/plain words = 3596 sentences = 193 flesch = 53 summary = A pathogenetic study of pleural effusion disease (PED) in rabbits was made, using the virulent PED agent or virus (PEDV) and an avirulent derivate of this isolate. Support for this contention is the enhancement of virulence of PED virus (PEDV) observed in the "natural" disease and --after its isolation --by continued serial propagation in rabbits at intervals of 3---10 days (Fig. 1) . However, there is also evidence which might suggest that increasing time of persistence of virulent virus in the individual rabbit host may operate in the reverse direction by selecting a population of predominantly avirulent PEDV particles, which appear to be unable to cause disease unless undergoing new rabbit passages at short intervals (t, 6). After infection with the avirulent derivate, the isolates from serum obtained during the entire period of viraemia were demonstrable in serum dilution 10 -1 to 10 -a, but the primary rabbit inoculation of these dilutions never resulted in clinical signs of PED. cache = ./cache/cord-004713-gzts5h0y.txt txt = ./txt/cord-004713-gzts5h0y.txt === reduce.pl bib === id = cord-004693-1xglujqk author = Chasey, D. title = Morphogenesis of avian infectious bronchitis virus in primary chick kidney cells date = 1976 pages = extension = .txt mime = text/plain words = 3300 sentences = 238 flesch = 68 summary = Late in infection large numbers of virus particles were present, mainly in cytoplasmic vacuoles, and the majority were released by cell lysis. Since this mechanism is the reverse of micropinocytosis it was important to establish in which direction the vesicles at the cell surface were moving in order to distinguish outgoing particles from already released progeny virus re-entering the monolayer in a secondary cycle of infection. Virus particles were seen in the process of budding from internal membranes but, unlike strain Beaudette, appeared to form predominantly within pre-existing cytoplasmic vacuoles (Fig. 8) . The method of release of virus particles by fusion of vacuoles with the cell plasma membranes seen in 'T' strain infected cells appears similar to the process described for coronaviruscs from human respiratory infections (12) . cache = ./cache/cord-004693-1xglujqk.txt txt = ./txt/cord-004693-1xglujqk.txt === reduce.pl bib === id = cord-004755-rmnjs1t6 author = Welch, Siao-Kun Wan title = Monoclonal antibodies to a virulent strain of transmissible gastroenteritis virus: comparison of reactivity with virulent and attenuated virus date = 1988 pages = extension = .txt mime = text/plain words = 4962 sentences = 283 flesch = 56 summary = Twelve hybridomas secreting monoclonal antibodies (MAbs) against Miller virulent strain of transmissible gastroenteritis virus (TGEV) were generated and characterized. Two E 2-specific MAbs had higher neutralizing antibody titers (782 to 34,117) and showed 4-to 13-fold differences in titers against the attenuated and virulent TGEV strains. Two E 2-specific MAbs had higher neutralizing antibody titers (782 to 34,117) and showed 4-to 13-fold differences in titers against the attenuated and virulent TGEV strains. In two previous studies, monoclonal antibodies (MAbs) to the structural proteins of the attenuated (Purdue) strain of TGEV were described [9, 12] . These MAbs were further characterized in various comparative assays including cell culture immunofluorescence, virus neutralization, and radioimmunoprecipitation for reactivity against the Miller virulent and Purdue attenuated strains of TGEV. Anti-E 1 MAbs prepared against a mixture of virulent Miller 3 and Purdue attenuated strains of TGEV had virus neutralizing antibody titers only in the presence of guinea pig, rabbit or swine complement [22] . cache = ./cache/cord-004755-rmnjs1t6.txt txt = ./txt/cord-004755-rmnjs1t6.txt === reduce.pl bib === id = cord-004812-ikco4h5k author = Moore, K. M. title = Identification of amino acids involved in a serotype and neutralization specific epitope with in the s1 subunit of avian infectious bronchitis virus date = 1997-04-06 pages = extension = .txt mime = text/plain words = 2731 sentences = 172 flesch = 57 summary = title: Identification of amino acids involved in a serotype and neutralization specific epitope with in the s1 subunit of avian infectious bronchitis virus We identified amino acids involved in a serotype specific, conformationally dependent epitope by analysis of the S1 gene of 13 monoclonal antibody-neutralization-resistant mutants. However, based on data obtained using monoclonal antibodies (Mab), there appears to be at least three to ®ve neutralizing, conformationally dependent epitopes on the S1 subunit in different IBV strains [13, 15, 20] . Mab-neutralization-resistant (NR) mutants have been used to identify amino acids (AA) involved in conformationally dependent epitopes in the spike protein of IBV [5, 12] . Based on AA substitutions in Mab-NR mutants, the S1 subunit was divided into three regions associated with neutralizing, conformationally dependent epitopes. In previous research, AA substitutions in IBV Mab-NR mutants were divided into three regions associated with neutralizing epitopes. cache = ./cache/cord-004812-ikco4h5k.txt txt = ./txt/cord-004812-ikco4h5k.txt === reduce.pl bib === id = cord-004831-lu62noak author = Kempf, C. title = A novel method for the detection of early events in cell-cell fusion of Semliki Forest virus infected cells growing in monolayer cultures date = 1987 pages = extension = .txt mime = text/plain words = 1890 sentences = 119 flesch = 55 summary = title: A novel method for the detection of early events in cell-cell fusion of Semliki Forest virus infected cells growing in monolayer cultures Furthermore, it was shown that potassium cyanide, a potent inhibitor of polykaryon formation in the described system, inhibits an early step of membrane-membrane fusion of neighbouring cells. Furthermore, we show that potassium cyanide, a potent inhibitor of SFV induced polykaryon formation (4) acts at an early stage in the fusion process. The aim of this investigation was to clarify the early events in cell-cell fusion and the action of potassium cyanide an inhibitor of oxidative phosphorylation-which inhibits SFV-induced polykaryon formation [4] -on the fusion process. That this assumption holds true is depicted in Fig. 1A where a single, SFV infected cell was injected with Lucifer yellow 5 minutes after exposure to pH 6. Therefore, it can be concluded that potassium cyanide inhibits SFV-induced polykaryon formation at the level of membrane-membrane fusion. cache = ./cache/cord-004831-lu62noak.txt txt = ./txt/cord-004831-lu62noak.txt === 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 === id = cord-006459-9kizif98 author = Deng, Guangcun title = Acute respiratory distress syndrome induced by H9N2 virus in mice date = 2009-11-28 pages = extension = .txt mime = text/plain words = 3874 sentences = 217 flesch = 52 summary = Clinical signs, pathological changes and viral replication in lungs, arterial blood gas, and cytokines in bronchoalveolar lavage fluid (BALF) were observed at different time points after infection. Our data show that H9N2 viral infection resulted in ARDS in mice, and this may facilitate studies of the pathogenesis of future potential H9N2 disease in humans. Arterial blood gas, white blood cell counts, tumor necrosis factor (TNF)-a and interleukin (IL)-6 levels in bronchoalveolar lavage fluid (BALF), and viral titers in the lungs were measured at different times. In H9N2-virus-infected mice, we observed that circulating leukocytes dramatically decreased in the blood and that a great number of inflammatory cells infiltrated the lungs. Acute respiratory distress syndrome induced by avian influenza A (H5N1) virus in mice cache = ./cache/cord-006459-9kizif98.txt txt = ./txt/cord-006459-9kizif98.txt === reduce.pl bib === id = cord-001274-vz0qvp01 author = Chitray, M. title = Genetic heterogeneity in the leader and P1-coding regions of foot-and-mouth disease virus serotypes A and O in Africa date = 2013-11-13 pages = extension = .txt mime = text/plain words = 6307 sentences = 285 flesch = 52 summary = For this study, the L and P1 coding regions for eight FMDV A and nine FMDV O viruses isolated between 1975 and 2003 were successfully sequenced and analysed using phylogenetic analysis, examination of sequence variability, and identification of highly conserved genomic regions relating to previously identified FMDV functional and structural biological capabilities. The sub-Saharan African isolates included in this study belong to different topotypes of FMDV serotypes A and O as defined by 1D sequencing and represent a broad geographical distribution of viruses within East and West Africa. Characterising sequence variation in the VP1 capsid proteins of foot-and-mouth disease virus (serotype O) with the respect to virion structure Sequence analysis of monoclonal antibody resistant mutants of type O foot and mouth disease virus: evidence for the involvement of the three surface exposed capsid proteins in four antigenic sites cache = ./cache/cord-001274-vz0qvp01.txt txt = ./txt/cord-001274-vz0qvp01.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-252037-rj61mzqj author = Gerna, G. title = Changing circulation rate of human metapneumovirus strains and types among hospitalized pediatric patients during three consecutive winter-spring seasons date = 2005-06-28 pages = extension = .txt mime = text/plain words = 2203 sentences = 116 flesch = 44 summary = In this study, we examined: i) the circulation rate of hMPV among the other respiratory viruses during 3 consecutive winter-spring seasons; ii) the relative circulation of the 2 types and the 4 subtypes of hMPV during the same 3-year period; iii) the relative impact of hMPV as compared to hRSV in determining admission to the hospital of infants with acute respiratory infections. The relative distribution of different respiratory viruses causing severe infections requiring admission to the hospital of infants and young children in three consecutive winter-spring seasons from 2001 through 2004 is reported in Table 2 Within the aliquot of patients found positive for some respiratory virus, no difference in the circulation rate was observed for respiratory virus infections caused by influenzavirus B, hPIVs, hAdVs, hCoVs, and coinfections along the three years studied. cache = ./cache/cord-252037-rj61mzqj.txt txt = ./txt/cord-252037-rj61mzqj.txt === reduce.pl bib === id = cord-004690-q38ogrem author = Barthold, S. W. title = Viremic dissemination of mouse hepatitis virus-JHM following intranasal inoculation of mice date = 1992 pages = extension = .txt mime = text/plain words = 3308 sentences = 154 flesch = 50 summary = Using a sensitive infant mouse bioassay to detect infectious virus, the pattern of mouse hepatitis virus (MHV) JHM dissemination in blood and other tissues was examined during the first 5 days following intranasal inoculation. Previous studies have shown that both of these mouse strains develop disseminated infections between days 3 and 5 after i.n. inoculation, but virus titers and disease are significantly greater in BALB mice compared to SJL mice [5] . The association of interferon-a/~ with viremia was explored initially by analyzing pooled samples of nasal turbinate, blood, liver, brain, or spleen obtained from 3 mice of each genotype on days 0 (controls), 1, 2, 3, and 4 after i.n. inoculation. In the current study, interferon was found in spleen and serum of MHV-JHM-infected BALB mice, but not nose, liver or brain and was not detectable in any tissue of SJL mice. cache = ./cache/cord-004690-q38ogrem.txt txt = ./txt/cord-004690-q38ogrem.txt === reduce.pl bib === id = cord-004769-hhge62sl author = Remond, M. title = Partial DNA cloning and sequencing of a canine parvovirus vaccine strain: application of nucleic acid hybridization to the diagnosis of canine parvovirus disease date = 1992 pages = extension = .txt mime = text/plain words = 3270 sentences = 221 flesch = 62 summary = title: Partial DNA cloning and sequencing of a canine parvovirus vaccine strain: application of nucleic acid hybridization to the diagnosis of canine parvovirus disease The cloning and sequencing of anEco RI-Pst I fragment derived from the replicative form of a canine parvovirus (CPV) vaccine strain are reported. In order to improve CPV diagnosis, radioactively labelled RNA or DNA and biotin labelled DNA obtained by random priming of the recombinant plasmid were used as probes mainly on gut or stool samples from naturally infected dogs. Results of filter hybridization correlated well with histopathological diagnosis of parvovirus infection and with hemagglutination tests performed on dog faeces. To elucidate whether the deletion observed was originally in the vaccine or was generated by cell culture passages in our laboratory, DNA sequence was determined on CPV-b 108 after PCR amplification of a 1000 bp fragment including the deleted region and the two H i n d I I I restriction sites (Fig. 1) . cache = ./cache/cord-004769-hhge62sl.txt txt = ./txt/cord-004769-hhge62sl.txt === reduce.pl bib === id = cord-004778-xrv0qs6n author = Smith, C. B. title = Mouse cytomegalovirus is infectious for rats and alters lymphocyte subsets and spleen cell proliferation date = 1986 pages = extension = .txt mime = text/plain words = 3373 sentences = 172 flesch = 52 summary = The Smith strain of mouse cytomegalovirus (MCMV) was infectious for infant and mature DA strain laboratory rats as judged by development of neutralizing antibodies and specific spleen cell proliferation on stimulation with MCMV antigen. In the following report, we describe a transient, effect of MCMV infections on rat T lymphoc~ helper/suppressor cell ratios and on spleen cell proliferation following stimulation with mitogens and MCMY antigen. Seven days after MCMV infection, a consistently greater proliferation of spleen cells from MCMV infected rats as compared to control animMs was seen with M1 mitogens and also in unstimulated background cultures (Table 2 and Fig. 1 and 2 ). P. route for infants and adults of three strains of laboratory rats as judged by virus isolation, neutralizing antibody response and development of a high level of spleen cell reactivity to MCMV antigen. cache = ./cache/cord-004778-xrv0qs6n.txt txt = ./txt/cord-004778-xrv0qs6n.txt === reduce.pl bib === id = cord-004743-ido065mh author = Nagy, Éva title = Polypeptide patterns of infectious bronchitis virus serotypes fall into two categories date = 1979 pages = extension = .txt mime = text/plain words = 1068 sentences = 68 flesch = 59 summary = authors: Nagy, Éva; Lomniczi, B. title: Polypeptide patterns of infectious bronchitis virus serotypes fall into two categories Molecular weights of six major polypeptides of infectious bronchitis virus (IBV) are: 1. All IBV strains examined showed one of two protein patterns with polypeptides having apparent molecular weights in the range of 20,000 and 110,000 dalton (Fig. 1) . Pattern M (named after Massachusetts) includes strains from two serotypes, Massachusetts and Georgia (SE 17), and here the "broad" protein has an apparent molecular weight of 28,000 dalton. Pattern C (named after Connecticut) is characterized by a smaller "broad" protein of an apparent molecular weight of 24,000 dalton, and includes the five remaining serotypes studied: Connecticut, Delaware (Gray), Iowa 97, Iowa 609 and Australia T. cache = ./cache/cord-004743-ido065mh.txt txt = ./txt/cord-004743-ido065mh.txt === reduce.pl bib === id = cord-029775-mntcor5d author = Oka, Tomoichiro title = Polymerase chain reaction primer sets for the detection of genetically diverse human sapoviruses date = 2020-07-27 pages = extension = .txt mime = text/plain words = 1827 sentences = 100 flesch = 58 summary = For the initial reactivity test, double-stranded DNA fragments (gBlocks® Gene Fragments) including the sequence targeted by the PCR primers (approximately 1700 bp each) of the human sapovirus genotypes GI.1 (GenBank accession number X86560), GI.2 (AB614356), GI.3 (AB623037), GI.4 (AJ606693), GI.5 (DQ366345), GI.6 (AJ606694), GI.7 (AB522390), GII.1 (AJ249939), GII.2 (AY237420), GII.3 (AB630068), GII.4 (AB522397), GII.5 (LC190463), GII.6 (AY646855), GII.7 (AB630067), GII.8 (KX894315), GIV.1 (DQ058829), GV.1 (DQ366344), and GV.2 (AB775659) were synthesized (Integrated DNA Technologies, Coralville, IA), and 1.0 × 10 4 copies of these fragments were used. The target regions of HuSaV-F1, -F2, and -F3 recently designed as forward primers in a broadly reactive real-time PCR for human sapoviruses [11] are similar to those of SV-F13 and SV-F14 (Fig. 2) , and the sapovirus-specific sequence of M13R-HuSaV5498R (5′-CCCCANCCNGCVHACAT-3′) ( [11] are shown in parentheses. The assay including two primers (M13F-HuSaV-5159F and M13R-HuSaV-5498R) generated similar-sized PCR products (approximately 380 bp) for all of the sapovirus genotypes tested (Fig. 1A, right panel, and Fig. 1B) . cache = ./cache/cord-029775-mntcor5d.txt txt = ./txt/cord-029775-mntcor5d.txt === reduce.pl bib === id = cord-004685-qote5nx2 author = Vassão, R. C. title = A genetic analysis of macrophage activation and specific antibodies in relation to the resistance of heterogeneous mouse populations to MHV3 infection date = 1994 pages = extension = .txt mime = text/plain words = 2352 sentences = 113 flesch = 42 summary = The data indicate, among the mechanisms of resistance against the virus infection, a role of IFN gamma macrophage-activation and of antibodies against MHV3 which may delay the mean survival time in susceptible animals. The virus replication in target cells, the antiviral state induced by interferon (IFN) and the expression of a monokine with procoagulant activity (PCA) have been implicated in the resistance/susceptibility of the genetic homogeneous or heterogeneous mouse populations to the MHV3 infection [t, 2, 4, 7, 17, 18, 23, 243 . For the study of the individual correlation between in vivo resistance and in vitro inhibition of virus replication by IFN gamma, peritoneal macrophages from Hm, Lm and F 2 segregants were collected without sacrificing the animals, which were infected with MHV3 a week later. This brings further support to our previous suggestion that one of the main mechanisms involved in the resistance of mice to the MHV3 infection is based on the ability of their macrophages to restrict the virus replication upon IFN gamma activation [10 13, 153 . cache = ./cache/cord-004685-qote5nx2.txt txt = ./txt/cord-004685-qote5nx2.txt === reduce.pl bib === id = cord-004810-g0y7ied0 author = Lee, S. K. title = S1 glycoprotein gene analysis of infectious bronchitis viruses isolated in Korea date = 2003-11-13 pages = extension = .txt mime = text/plain words = 3750 sentences = 190 flesch = 59 summary = The S1 glycoprotein gene of IBV isolates were amplified by reverse transcriptase – polymerase chain reaction (RT-PCR) and analyzed by restriction fragment length polymorphism (RFLP) analysis. And these IBV isolates showed different patterns from each other and non-Korean IBV isolates in reverse transcriptase-polymerase chain reaction-restriction fragment length polymorphism (RT-PCR-RFLP) analysis [29] . Amplified S1 genes were first classified by RFLP analysis and then the representative strains were cloned, sequenced and compared to other non-Korean published IBV sequences. Phylogenetic trees were constructed from the nucleotide and deduced amino acid sequences of the S1 glycoprotein genes of Korean IBV isolates and non-Korean IBV strains (Fig. 3) . Korean IBV K281-01 and K210-02 isolates formed distinct clusters that were related to non-Korean IBV Ark99, Ark DPI, Gray and JMK strains although K281-01 and K210-02 isolates were classified into the Arkansas type by PCR-RFLP analysis. cache = ./cache/cord-004810-g0y7ied0.txt txt = ./txt/cord-004810-g0y7ied0.txt === reduce.pl bib === id = cord-006674-ywzpwlrb author = Ikeda, T. title = Pathogenesis of cytomegalovirus-associated pneumonitis in ICR mice: possible involvement of superoxide radicals date = 1992 pages = extension = .txt mime = text/plain words = 3716 sentences = 193 flesch = 45 summary = When the activity of xanthine oxidase (XO) in lung tissue homogenates was measured, the activity was found to significantly increase after intranasal infection with MCMV irrespective of CP administration and there was a good correlation between the elevation of XO activity and the degree of pathological changes in the lung. Furthermore, recent studies have shown that the enhanced production of superoxide radicals by xanthine oxidase (XO) plays a key role in the pathogenesis of influenza virus-induced pulmonary infection [1, 193. In this study, we have established a model of murine cytomegalovirus (MCMV) pneumonitis in ICR mice, measured XO activity in tung tissues, and evaluated the effect of superoxide dismutase (SOD) and allopurinol in this model. Although the precise role of superoxide radicals in the pathogenesis of MCMV pneumonitis is still unknown, such a process seems to be involved in the formation of pulmonary lesions in MCMV-infected mice. cache = ./cache/cord-006674-ywzpwlrb.txt txt = ./txt/cord-006674-ywzpwlrb.txt === reduce.pl bib === id = cord-004838-cdas57cx author = Morozov, I. title = Sequence analysis of open reading frames (ORFs) 2 to 4 of a U.S. isolate of porcine reproductive and respiratory syndrome virus date = 1995 pages = extension = .txt mime = text/plain words = 2240 sentences = 122 flesch = 60 summary = title: Sequence analysis of open reading frames (ORFs) 2 to 4 of a U.S. isolate of porcine reproductive and respiratory syndrome virus The sequence of ORFs 2 to 4 of a U.S. isolate of porcine reproductive and respiratory syndrome virus (PRRSV), ATCC VR2385, was determined by analysis of a cDNA λ library. No overlap was found between ORFs 4 and 5, and instead there was a 10 bp sequence which separated these two ORFs. The nucleic acid homology with corresponding ORFs of the European PRRSV isolate Lelystad virus (LV) was 65% for ORF 2, 64% for ORF 3 and 66% for ORF 4. Cloning, expression, and sequence analysis of the ORF 4 gene of porcine reproductive and respiratory syndrome virus MN-lb Molecular cloning and nucleotide sequencing of the 3'-terminal genomic RNA of porcine reproductive and respiratory syndrome virus cache = ./cache/cord-004838-cdas57cx.txt txt = ./txt/cord-004838-cdas57cx.txt === reduce.pl bib === id = cord-271831-vekok62k author = Dewerchin, H. L. title = Replication of feline coronaviruses in peripheral blood monocytes date = 2005-08-01 pages = extension = .txt mime = text/plain words = 4704 sentences = 247 flesch = 53 summary = Feline infectious peritonitis virus (FIPV) (Coronaviridae) causes the most lethal viral infection in cats: FIP. In this study, infection kinetics (titres and antigen expression) of FIPV 79-1146, and FECV 79-1683, were determined in peripheral blood monocytes from 3 donor cats and compared to those in Crandell feline kidney (CrFK) cells. Two coronaviruses are described in cats: feline infectious peritonitis virus (FIPV) and feline enteric coronavirus (FECV). Within this population of 19 cats, the monocytes isolated from 9 cats showed a continuous increase in viral antigen positive cells during a 24 hour time span after inoculation with FIPV. Monocytes from 9 cats did not sustain both FIPV and FECV infection since the number of viral antigen positive cells dropped after 6 or 12 hpi (third pattern). In an infection kinetics study where another cell type, feline peritoneal macrophages, was used, different results in the antigen expression kinetics were obtained [29] . cache = ./cache/cord-271831-vekok62k.txt txt = ./txt/cord-271831-vekok62k.txt === reduce.pl bib === id = cord-274780-fmnro0kw author = Hoshino, Y. title = Detection of astroviruses in feces of a cat with diarrhea date = 1981 pages = extension = .txt mime = text/plain words = 1367 sentences = 96 flesch = 52 summary = Astroviruses were detected by electron microscopy in the feces from a 4 month old kitten with diarrhea. Astroviruses were detected by electron microscopy in the feces from a 4 month old kitten with diarrhea. The clinical disease manifested by the cat and the observed morphology of the viral particles are consistent with previous reports on astroviruses of other species. The clinical disease manifested by the cat and the observed morphology of the viral particles are consistent with previous reports on astroviruses of other species. Viral antigen was detected by indirect immunofluorescent staining within the cytoplasm of cultured cells infected with fecal material of human (10, 11) and bovine (23) astroviruses. Studies on the pathogenesis of astrovirus infection in lambs have shown the site of virus multiplication to be the mature villous epithelial cells of the small intestine (21, 22) . cache = ./cache/cord-274780-fmnro0kw.txt txt = ./txt/cord-274780-fmnro0kw.txt === reduce.pl bib === id = cord-004754-5596p4ma author = Duan, X. title = Effects of origin and state of differentiation and activation of monocytes/macrophages on their susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) date = 2014-04-06 pages = extension = .txt mime = text/plain words = 4875 sentences = 252 flesch = 50 summary = title: Effects of origin and state of differentiation and activation of monocytes/macrophages on their susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) To evaluate the effect of maturation of monocytes/macrophages on their susceptibility to PRRSV, freshly isolated AMf, PMf and BMo from ®ve donors were seeded in 24-well tissue culture plates at a concentration of 10 6 cells/ml/well and further incubated in RPMI medium plus 5% of foetal bovine serum at 37 C with 5% CO 2 . The virus titres and percentage of viral antigen positive cells in freshly isolated porcine AMf at 24 and 48 h after inoculation were respectively 1 to 2 log 10 TCID 50 and 5 to 10 times lower than those of one day cultivated ones, which is signi®cantly different (P'0.01). Porcine reproductive and respiratory syndrome virus infection of alveolar macrophages can be blocked by monoclonal antibodies against cell surface surface antigens cache = ./cache/cord-004754-5596p4ma.txt txt = ./txt/cord-004754-5596p4ma.txt === reduce.pl bib === id = cord-258768-bjjfkfgg author = McElligott, Susan title = Detection and genetic characterization of canine parvoviruses and coronaviruses in southern Ireland date = 2010-11-24 pages = extension = .txt mime = text/plain words = 4380 sentences = 220 flesch = 53 summary = Two hundred fifty samples were collected in total, Fig. 2 Phylogenetic tree based on partial S gene nucleotide sequences of CCoVs described in this study and reference strains. As a result of RNA recombination, insertions, deletions and a high susceptibility to frequent mutation, coronaviruses can mutate rapidly, leading to new genotypes (CCoV-I), biotypes (pantropic CCoV) and host variants (canine respiratory coronavirus), all of which may present possible difficulties regarding successful vaccination of dogs. As a result of this study, it can be concluded that although it appears that the viral evolution of CPV type 2 is not yet a significant problem for the canine population in Ireland, vaccine efficacy may need to be re-evaluated by the animal healthcare industry, as it is a possibility that the new CPV-2c strain will eventually emerge into the population as a result of importing dogs from other parts of the world. cache = ./cache/cord-258768-bjjfkfgg.txt txt = ./txt/cord-258768-bjjfkfgg.txt === reduce.pl bib === id = cord-004759-jozdnhgy author = Snodgrass, D. R. title = Pathogenesis of diarrhoea caused by astrovirus infections in lambs date = 1979 pages = extension = .txt mime = text/plain words = 2304 sentences = 139 flesch = 53 summary = Experimental infection of 2-day-old gnotobiotic lambs with lamb astrovirus produced mild diarrhoea after an incubation period of about 48 hours. Astrovirus was not observed in faeces from the lambs killed t4 and 23 hours p.i., but was first seen in the faeces of all other infected lambs between 38 and 48 hours p.i. At necropsy, astrovirus was detected in intestinal contents of all Iambs except that killed 14 hours p.i. The control lambs remained clinically normal, and passed firm brown faeces throughout the duration of the experiment. Specific immunofluorescent staining was detected only in scattered epithelial and subepithelial cells on small intestinal villi (Fig. 1) . Lactase levels in the 6 control lambs were ¢.5±0.5, 5.14-0.6, and 2.44-1.2 units/g tissue for the proximal, mid, and distal small intestinal sites respectively. In midgut of infected lambs, observations were consistently below those of the controls, fMling to a minimum of 1.2 units/g tissue at 23 hours p.i. cache = ./cache/cord-004759-jozdnhgy.txt txt = ./txt/cord-004759-jozdnhgy.txt === reduce.pl bib === id = cord-004851-h9ppa064 author = Plagemann, P. G. W. title = Hepatitis C virus date = 1991 pages = extension = .txt mime = text/plain words = 6835 sentences = 320 flesch = 48 summary = The viral proteins have not been identified, but on the basis of the predicted amino acid sequences, hydrophobicity plots, location of potential glycosylation sites and similarities of these properties to those of pestiand flaviviruses, the following genome organization has been predicted. A recent study of stored blood samples from prospective studies of 15 U.S.A. patients with transfusion-associated chronic hepatitis documented by liver biopsies indicated that the time course of changes in plasma ALT activity and of the formation of anti-HepCV antibodies can vary considerably between patients [4] . The putative nucleocapsid protein sequence derived from PCR products of RNA extracted from healthy Japanese carrier plasma exhibited a 97.4% amino acid identity with the sequence determined for the original chimpanzee HepCV isolate (HepCV-1) but only a 90.5 % identity at the nucleotide level [45] [46] [47] . cache = ./cache/cord-004851-h9ppa064.txt txt = ./txt/cord-004851-h9ppa064.txt === reduce.pl bib === id = cord-263193-paeosfiu author = Zhu, Jinyan title = Infectious bronchitis virus inhibits activation of the TLR7 pathway, but not the TLR3 pathway date = 2020-06-10 pages = extension = .txt mime = text/plain words = 2831 sentences = 163 flesch = 55 summary = Here, primary chicken embryo kidney (CEK) cells and specific-pathogen-free (SPF) chickens were infected with three pathogenic IBV strains, and it was observed that the TLR7-MYD88 pathway was inhibited but the TLR3-TIRF pathway was activated. To investigate the effect of innate immune molecules, agonists of TLR3, TLR7, and MDA5 and inhibitors of key molecules of the TLR3 pathway were added to CEK cells that had grown to 80-90% as instructed by the reagent manufacturer (InvivoGen, CA, USA) as follows: 5 μg of imiquimod (a TLR7 agonist) per mL for 12 h, 10 μg of low-molecular-weight (LMW) polyinosinic-polycytidylic acid (poly(I:C)) (a TLR3 agonist) per mL for 12 h, 0.5 μg of poly (I:C)-LMW/LyoVec (an MDA5 agonist) per mL for 12 h, 10 μM Pepinh-TRIF (a TRIF inhibitor) for 6 h, 5 μM celastrol (an NF-κB inhibitor) for 1 h, 50 μM chloroquine (an inhibitor of endosomal acidification) for 0.5 h, and 5 μM BX795 (a TBK1 inhibitor) for 6 h. cache = ./cache/cord-263193-paeosfiu.txt txt = ./txt/cord-263193-paeosfiu.txt === reduce.pl bib === id = cord-004802-rhkrmftn author = Hoshino, Y. title = Isolation and characterization of a canine rotavirus date = 1982 pages = extension = .txt mime = text/plain words = 2902 sentences = 172 flesch = 47 summary = Replication of the virus in cell culture was found to be less dependent upon trypsin than that of human, bovine and porcine rotaviruses. Reproducible, sharp-edged plaques of various sizes were produced by the canine rotavirus in an established cell line of fetal rhesus monkey kidney, MA104, under overlays of carboxymethyl cellulose or agarose. By plaque reduction neutralization assay, a two-way antigenic relationship was found between the canine (CU-1) and simian (rhesus MMU 18006 and SA-11) rotaviruses. Although canine rotavirus readily replicated and produced CPE in monolayer cultures of MA104 cells in the absence of trypsin, detectable plaques were not formed even 8 D P I under the overlays of CMC or agarose without trypsin. Since both IFT and CFT detect only group-specific antibodies, and rotaviruses from one species can infect another species (5, 8, 34, 36, 46, 50, 51, 52, 55) , it was not clear from these studies whether the antibodies in the dogs resulted from infection with distinctly canine rotavirus or with human or some other rotavirus. cache = ./cache/cord-004802-rhkrmftn.txt txt = ./txt/cord-004802-rhkrmftn.txt === reduce.pl bib === id = cord-254405-yc1q20fz author = Jie, Tao title = Preparation and characterization of an attenuated porcine epidemic diarrhea virus strain by serial passaging date = 2018-07-31 pages = extension = .txt mime = text/plain words = 3450 sentences = 189 flesch = 57 summary = Furthermore, we cultured the virus and screened for attenuated PEDV strains by analyzing the genovariations that occurred during passaging -confirming the results in animal experiments. [27] analyzed a cell culture-adapted PEDV (passage 100) strain with a smaller ORF3 gene and found it to have lower virulence relative to the wild-type virus. Molecular characterization of the ORF3 and S1 genes of porcine epidemic diarrhea virus non S-INDEL strains in seven regions of China Comparative genomic analysis of classical and variant virulent parental/attenuated strains of porcine epidemic diarrhea virus Isolation and identification of porcine epidemic diarrhea virus strain HBMC2012 and its pathogenicity in piglet Cloning and further sequence analysis of the spike gene of attenuated porcine epidemic diarrhea virus DR13 Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China cache = ./cache/cord-254405-yc1q20fz.txt txt = ./txt/cord-254405-yc1q20fz.txt === reduce.pl bib === id = cord-255653-0bj5eh5d author = Pensaert, M. B. title = An immunoelectron microscopic and immunofluorescent study on the antigenic relationship between the coronavirus-like agent, CV 777, and several coronaviruses date = 1981 pages = extension = .txt mime = text/plain words = 2521 sentences = 171 flesch = 52 summary = A possible antigenic relationship between the porcine enteropathogenic coronavirus-like agent (CVLA) and 6 known coronaviruses was examined by immunoelectron microscopy (IEM) and by immunofluorescence (IF). CVLA did not show cross reactivity with infectious bronchitis virus, transmissible gastroenteritis virus (TGEV), canine coronavirus (CCV) hemagglutinating encephalomyelitis virus (HEV), neonatal calf diarrhea coronavirus (NCDCV) or feline infectious peritonitis virus (FIPV). The CVLA was shown by serologic cross protection studies to differ from the two knowm porcine coronaviruses, transmissible gastroenteritis virus (TGEV) and hemagglntinating encephalomyelitis virus (HEV) (4, 14) . The coronaviruses selected for the present study were TGEV, HEV, neonatal calf diarrhea coronavirus (NCDCV), canine coronavirus (CCV), avian infectious bronchitis virus (IBV) and feline infectious peritonitis virus (FIPV). This hyperimmune serum had a virus neutralizing titer of 1:2560 when tested against the cell culture adapted Purdue strain of TGEV. Antiserum to TGEV reacted with CCV, but did not show detectable antigenic cross-reactivity with FIPV. cache = ./cache/cord-255653-0bj5eh5d.txt txt = ./txt/cord-255653-0bj5eh5d.txt === reduce.pl bib === id = cord-004720-r6b34tjm author = Kaiser, C. J. title = Inhibition by monensin of human cytomegalovirus DNA replication date = 1987 pages = extension = .txt mime = text/plain words = 4357 sentences = 246 flesch = 50 summary = Phosphonoacetic acid (PAA) and monensin were purchased from Sigma, Deisenhofen, Federal Republic of Germany, tunieamycin from Calbiochem, La Jolla, U.S.A. In a typicM experiment for the determination of infected cell DNA synthesis in the presence of monensin, parallel cultures of HFF (5 × 106 cells) were infected by HCMV (MOI of 1) and pulse labelled with att-thymidine (5 ~Ci/ml) during the late phase of the consecutive infectious cycle (28) . To examine whether pretreated cells support, viral replication, confluent serum-starved HFF were exposed to various concentrations of monensin prior to virus infection and subsequently pulse labelled with 3H-thymidine during the interval of expected viral DNA synthesis (28; Fig. 2 A) . This protocol again did not prevent subsequent recovery of viral DNA replication within 48-72 hours after removal, an observation which was based on the comparative anMysis by isopycnie centrifugation in CsC1 of DNA samples from untreated and drug-treated infected cultures labelled during corresponding pulse intervals (Fig. 2 B, w/o and monint) . cache = ./cache/cord-004720-r6b34tjm.txt txt = ./txt/cord-004720-r6b34tjm.txt === reduce.pl bib === id = cord-258374-qht98q0l author = Takano, Tomomi title = Neutrophil survival factors (TNF-alpha, GM-CSF, and G-CSF) produced by macrophages in cats infected with feline infectious peritonitis virus contribute to the pathogenesis of granulomatous lesions date = 2009-04-03 pages = extension = .txt mime = text/plain words = 3690 sentences = 198 flesch = 45 summary = title: Neutrophil survival factors (TNF-alpha, GM-CSF, and G-CSF) produced by macrophages in cats infected with feline infectious peritonitis virus contribute to the pathogenesis of granulomatous lesions Furthermore, it was investigated whether macrophages, one of the target cells of FIPV infection, produce neutrophil survival factors (TNF-alpha, GM-CSF, and G-CSF). The neutrophil survival rates were significantly increased in the presence of the culture supernatant of macrophages infected with the mixture of FIPV and MAb 6-4-2 compared to those in the presence of other supernatants (Fig. 5) . When SPF-cat-derived alveolar macrophages were infected with a mixture of FIPV and MAb 6-4-2, the intracellular TNF-alpha, GM-CSF, and G-CSF mRNA levels increased (Fig. 6 ). These cytokine mRNA levels were also elevated in macrophages infected with FIPV and MAb 6-4-2, clarifying the presence of neutrophil survival factors in the macrophage culture supernatant. It was suggested that: (1) FIPV-infected macrophages release TNF-alpha, GM-CSF, and G-CSF in response to virus replication, and (2) these cytokines act on neutrophils and prolong their survival. cache = ./cache/cord-258374-qht98q0l.txt txt = ./txt/cord-258374-qht98q0l.txt === reduce.pl bib === id = cord-012032-zolowuhj author = Yu, Peifa title = 2’-Fluoro-2’-deoxycytidine inhibits murine norovirus replication and synergizes MPA, ribavirin and T705 date = 2020-08-08 pages = extension = .txt mime = text/plain words = 3499 sentences = 197 flesch = 45 summary = To further examine the antiviral effects, another murine macrophage cell line, J774A.1, was used, and a similar inhibitory effect of 2'-FdC on MNV-1 replication was observed, with decreased viral RNA and NS1/2 protein expression ( Supplementary Fig. 1 ). As shown in Fig. 3D and E, the viral NS1/2 protein expression and viral titers were further decreased when the antivirals were used in combination, supporting the synergistic antiviral effects of 2'-FdC with MPA, ribavirin, or T705 against MNV replication. The combined effect of 2'-FdC and ribavirin on viral replication was analyzed using a qRT-PCR assay (n = 2-4) and mathematical modeling using MacSynergy. RAW264.7 cells were infected with MNV-1 at an MOI of 1 for 1 h and then left untreated or treated with 2'-FdC and MPA, ribavirin, or T705 at the indicated concentrations for 20 h, alone or in combination. cache = ./cache/cord-012032-zolowuhj.txt txt = ./txt/cord-012032-zolowuhj.txt === reduce.pl bib === id = cord-276617-chgjpg0v author = Takano, Tomomi title = B-cell activation in cats with feline infectious peritonitis (FIP) by FIP-virus-induced B-cell differentiation/survival factors date = 2008-11-30 pages = extension = .txt mime = text/plain words = 3971 sentences = 216 flesch = 50 summary = The present study shows that: (1) the ratio of peripheral blood sIg(+) CD21(−) B-cells was higher in cats with FIP than in SPF cats, (2) the albumin-to-globulin ratio has negative correlation with the ratio of peripheral blood sIg(+) CD21(−) B-cell, (3) cells strongly expressing mRNA of the plasma cell master gene, B-lymphocyte-induced maturation protein 1 (Blimp-1), were increased in peripheral blood in cats with FIP, (4) mRNA expression of B-cell differentiation/survival factors, IL-6, CD40 ligand, and B-cell-activating factor belonging to the tumor necrosis factor family (BAFF), was enhanced in macrophages in cats with FIP, and (5) mRNAs of these B-cell differentiation/survival factors were overexpressed in antibody-dependent enhancement (ADE)-induced macrophages. We also collected macrophages from FIP cats and measured the expression levels of the viral RNA and mRNA of B-cell differentiation/survival factors: IL-6, CD40 ligand (CD40L), and Bcell-activating factor belonging to the tumor necrosis factor family (BAFF). cache = ./cache/cord-276617-chgjpg0v.txt txt = ./txt/cord-276617-chgjpg0v.txt === reduce.pl bib === id = cord-004728-rjl35dpa author = Taguchi, F. title = Asymptomatic infection of mouse hepatitis virus in the rat date = 1979 pages = extension = .txt mime = text/plain words = 954 sentences = 70 flesch = 59 summary = After intranasal inoculation of suckling rats mouse hepatitis virus multiplied mostly in the nasal epithelium; though there were no symptoms, antibodies were produced. Bar represents 0.1 mm Two-, 4-, 6-and t0-week-old rats were also inoculated i.n. with t05 PFU of MHV-S and infectious viruses were assayed in the lung, brain, salivary glands and liver. So far only mice have been considered to be natural hosts of MHV and rat; has been excluded because highly virulent MHV inoculated by various routes did not cause any sy~lptomatic infection like that produced in the mouse (7, 13) . B~tATT and his eoworkers showed that SDAV multiplied in mice producing some histopathological changes in the respiratory system after i.n. inoculation (3) and we demonstrated in the w e s e n t paper that 3{HV infected rats of any ages. Pathogenicity of mouse hepatitis virus for mice depending upon host age and route of infection cache = ./cache/cord-004728-rjl35dpa.txt txt = ./txt/cord-004728-rjl35dpa.txt === reduce.pl bib === id = cord-004808-6w9n03fy author = Sekiguchi, K. title = Detection of equine arteritis virus (EAV) by polymerase chain reaction (PCR) and differentiation of EAV strains by restriction enzyme analysis of PCR products date = 1995 pages = extension = .txt mime = text/plain words = 2056 sentences = 116 flesch = 59 summary = title: Detection of equine arteritis virus (EAV) by polymerase chain reaction (PCR) and differentiation of EAV strains by restriction enzyme analysis of PCR products A polymerase chain reaction (PCR) based assay capable of detecting and differentiating seven strains of equine arteritis virus (EAV) from around the world was developed. A potymerase chain reaction (PCR) based assay capable of detecting and differentiating seven strains of equine arteritis virus (EAV) from around the world was developed. Viral RNA from cell culture fluids infected with each of the seven EAV strains and RNA from the live vaccine, Arvac, was detected by PCR using four sets of primers. The objective of this study was to detect each of the EAV strains using PCR, and to differentiate the strains through restriction enzyme analysis of their PCR products, based on the M protein nucleotide sequence data of the strains, together with those of the Bucyrus [7] and modified Bucyrus strain [251. cache = ./cache/cord-004808-6w9n03fy.txt txt = ./txt/cord-004808-6w9n03fy.txt === reduce.pl bib === id = cord-276630-qci7khki author = Lima, William Gustavo title = The potential of drug repositioning as a short-term strategy for the control and treatment of COVID-19 (SARS-CoV-2): a systematic review date = 2020-06-08 pages = extension = .txt mime = text/plain words = 3727 sentences = 214 flesch = 49 summary = Due to the evidence of the anti-SARS-CoV-2 activity of various clinically available agents, drug repositioning stands out as a promising strategy for a short-term response in the fight against the novel coronavirus. Only seven drugs (chloroquine, tetrandrine, umifenovir (arbidol), carrimycin, Table 1 Clinical evidence of potential candidates for drug repositioning against COVID-19 (SARS-CoV-2) *Lopinavir (400 mg) + ritonavir (100 mg), q12h, orally; associated with umifenovir (200 mg), q12h, orally. [14] reported that the use of arbidol in combination with lopinavir/ritonavir inhibits the aggravation of pneumonia caused by SARS-CoV-2 and promotes a virus-negative conversion in patients from China. Of these, only six drugs (lopinavir/ritonavir, umifenovir (arbidol), remdesivir, chloroquine, and hydroxychloroquine) have shown promising results in preclinical trials and have clinically lessened the symptoms of COVID-19. Although lopinavir/ ritonavir had low anti-SARS-CoV-2 activity, arbidol, remdesivir, and chloroquine/hydroxychloroquine showed promising effects against this coronavirus. cache = ./cache/cord-276630-qci7khki.txt txt = ./txt/cord-276630-qci7khki.txt === reduce.pl bib === id = cord-252232-vgq6gjpx author = Hou, Yuxuan title = Angiotensin-converting enzyme 2 (ACE2) proteins of different bat species confer variable susceptibility to SARS-CoV entry date = 2010-06-22 pages = extension = .txt mime = text/plain words = 3208 sentences = 159 flesch = 57 summary = Here, we extended our previous study to ACE2 molecules from seven additional bat species and tested their interactions with human SARS-CoV spike protein using both HIV-based pseudotype and live SARS-CoV infection assays. However, although the genetically related SARS-like coronavirus (SL-CoV) has been identified in horseshoe bats of the genus Rhinolophus [5, 8, 12, 18] , its spike protein was not able to use the human ACE2 (hACE2) protein as a receptor [13] . To this end, we have extended our studies to include ACE2 molecules from different bat species and examined their interaction with the human SARS-CoV spike protein. Our results show that there is great genetic diversity among bat ACE2 molecules, especially at the key residues known to be important for interacting with the viral spike protein, and that ACE2s of Myotis daubentoni and Rhinolophus sinicus from Hubei province can support viral entry. cache = ./cache/cord-252232-vgq6gjpx.txt txt = ./txt/cord-252232-vgq6gjpx.txt === reduce.pl bib === id = cord-261749-lq1ah16x author = Mayo, M. A. title = Report from the 36(th) and the 37(th) Meetings of the Executive Committee of the International Committee on Taxomony of Viruses date = 2006-03-03 pages = extension = .txt mime = text/plain words = 2288 sentences = 119 flesch = 60 summary = At EC36 there were extensive discussions of proposals to revise the statutes under which ICTV operates and to revise the International Code for Virus Classification and Nomenclature (ICVCN). In response to the proposal that ICTV should provide for each approved species a latinized binomial name to link its common name(s), the 'type' description and the classification, the EC felt that there was little support in the virology community for using latinized names. The changes proposed further stipulated that ICTV should keep an official list of virus names that were used previously but are no longer in current taxonomy. It was pointed out that fixing these lists of criteria was an important task for individual SGs. It was proposed that the category "tentative species" be eliminated from taxonomic usage because a virus can either be a member of a species or it cannot. cache = ./cache/cord-261749-lq1ah16x.txt txt = ./txt/cord-261749-lq1ah16x.txt === reduce.pl bib === id = cord-026518-xv03vpji author = Xie, Peng title = Immune effect of a Newcastle disease virus DNA vaccine with IL-12 as a molecular adjuvant delivered by electroporation date = 2020-06-09 pages = extension = .txt mime = text/plain words = 5771 sentences = 280 flesch = 52 summary = An additional 52 14-day-old SPF chickens were randomly divided into four equal groups (N = 13) to investigate the effect of chIL-12 used as an adjuvant to the F gene DNA vaccine. Two weeks after booster vaccination, the birds were challenged with NDV and mortality for 14 days was evaluated the two delivery methods might induce different immune responses in chickens. Oladele and colleagues constructed a DNA vaccine based on the HA gene of H5N1 avian influenza virus and found that EP delivery could enhance the antibody response, significantly reduce morbidity, and protect chickens from fatal NDV attack [25] . However, although all of the chickens in the pCAG-F/EP group survived, they did not all have detectable neutralizing antibodies, indicating that antibodies may not be essential for protection and that cell mediated immunity might play an important role in plasmid DNA-induced protection against NDV challenge. cache = ./cache/cord-026518-xv03vpji.txt txt = ./txt/cord-026518-xv03vpji.txt === reduce.pl bib === id = cord-004790-69lry0ys author = Smith, A. L. title = Comparative biological characterization of mouse adenovirus strains FL and K 87 and seroprevalence in laboratory rodents date = 1986 pages = extension = .txt mime = text/plain words = 4411 sentences = 246 flesch = 57 summary = The source of these discrepancies is not immediately apparent; however, our results may explain why seroconversion to mouse adenovirus is not observed among mice thought to be infected with the virus. Finally, we provide serologic evidence that an outbreak of disease in a mouse breeding colony which sustained high infant mortality was associated with the introduction of a mouse adenovirus strain closely related to MAd-K 87. Sera from mice housed in two intramural, barrier-maintained facilities were Mso free of antibody to MAd. Only three mouse sera ofl61 which were tested reacted by IFA with MAd bivalent antigen. (19) for growth of MAd-FL in primary mouse kidney cultures, we have found that the majority of infectious progeny virions (between 90 and 99 percent) are released fl~om infected L 929 or CMT-93 cells. We have provided serologic evidence linking an outbreak of clinical disease in a breeding colony of mice to infection with MAd-K 87 or a very closely related virus. cache = ./cache/cord-004790-69lry0ys.txt txt = ./txt/cord-004790-69lry0ys.txt === reduce.pl bib === id = cord-048485-b8xb1f12 author = Hulst, Marcel title = Early transcriptional response in the jejunum of germ-free piglets after oral infection with virulent rotavirus date = 2008-06-04 pages = extension = .txt mime = text/plain words = 6269 sentences = 313 flesch = 45 summary = RNA pools prepared from two infected piglets were used to compare whole mucosal gene expression at 12 and 18 hpi to expression in uninfected germ-free piglets (n = 3) using a porcine intestinal cDNA microarray. However, the fluorescence intensity was not higher than the background threshold for any of these probes, indicating that mRNA concentrations of these cytokines (including IFN-c) in infected and uninfected mucosal scrapings were too low to detect by microarray analysis, probably due to the relatively low percentage of cytokine-producing (immune) cells present in intestinal mucosa [6] . Using microarray analysis, we detected a set of genes that are differently expressed in rotavirus-infected jejunal mucosa compared to uninfected mucosa. Perhaps, enhanced expression of a PLA2-inh in our study may be a countermeasure of specific intestinal epithelial cells to normalize and/or inhibit PLA2 enzyme activity in response to extra-and intracellular changes in [Ca 2+ ] evoked by rotavirus replication, either to protect specific cells from extra-and intracellular membrane-damage or to negatively regulate A-acid production. cache = ./cache/cord-048485-b8xb1f12.txt txt = ./txt/cord-048485-b8xb1f12.txt === reduce.pl bib === id = cord-256859-7ixegm72 author = Liu, S. W. title = Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between 1995 and 2004 date = 2006-01-09 pages = extension = .txt mime = text/plain words = 5156 sentences = 266 flesch = 56 summary = Except for isolates in genotype V, which included the Mass-type strains, none of the Chinese IBV isolates examined in this study shared more than 83% amino acid similarity in the S1 protein with the H120 vaccine strain. Furthermore, almost all of the Chinese IBV isolates contained deletions and insertions except for those of the Mass-type IBV, which were included in genotype V in this study, and had amino acid sequences similar to those of the H120 strain ( Table 4 ). The low identities (<83%) of amino acid sequences between Chinese IBV isolates and H120, except for those of the Mass-type IBV, which were included in genotype V in this study, may account for the prevalence of the viruses during the past ten years in spite of the extensive use of Mass-type vaccines in the field in China. cache = ./cache/cord-256859-7ixegm72.txt txt = ./txt/cord-256859-7ixegm72.txt === reduce.pl bib === id = cord-266716-pghnl980 author = Wang, Hai-Ming title = Isobavachalcone inhibits post-entry stages of the porcine reproductive and respiratory syndrome virus life cycle date = 2018-02-06 pages = extension = .txt mime = text/plain words = 3385 sentences = 170 flesch = 48 summary = title: Isobavachalcone inhibits post-entry stages of the porcine reproductive and respiratory syndrome virus life cycle Since the first report of a porcine reproductive and respiratory syndrome (PRRS) outbreak, tremendous efforts to control this disease, including various national policies and plans incorporating the use of multiple modified live-virus vaccines, have been made. Western blot analysis revealed that PRRSV N protein levels decreased markedly, indicating that increasing concentrations of IBC significantly inhibited PRRSV replication (Fig. 1F) . The in vitro study established that IBC efficiently inhibited the replication of both HP-PRRSV and the current Chinese epidemic NADC30-like strains without significant drug toxicity. Role of phosphatidylinositol 3-kinase (PI3K) and Akt1 kinase in porcine reproductive and respiratory syndrome virus (PRRSV) replication Pathogenicity and antigenicity of a novel NADC30-like strain of porcine reproductive and respiratory syndrome virus emerged in China NADC30-like strain of porcine reproductive and respiratory syndrome virus cache = ./cache/cord-266716-pghnl980.txt txt = ./txt/cord-266716-pghnl980.txt === reduce.pl bib === id = cord-279676-sk9xyd1r author = Carossino, Mariano title = Detection of SARS-CoV-2 by RNAscope(®)in situ hybridization and immunohistochemistry techniques date = 2020-08-05 pages = extension = .txt mime = text/plain words = 1643 sentences = 94 flesch = 45 summary = In situ hybridization (ISH) and immunohistochemistry (IHC) are essential tools to characterize SARS-CoV-2 infection and tropism in naturally and experimentally infected animals and also for diagnostic purposes. In situ hybridization (ISH) and immunohistochemistry (IHC) techniques allow visualization of viral nucleic acid and protein antigens, respectively, within tissues and cells. For this purpose, the development of SARS-CoV-2-specific ISH and IHC are both critical for the assessment of viral distribution, cell tropism, and cytopathology within tissues, complementing classical histopathology, various molecular tools, and serological assays. Thus, the objective of this study was to develop RNAscope ® ISH and IHC methods for the detection of SARS-CoV-2-specific antigen and RNA in infected cells that can be utilized for both research (e.g., studies involving experimentally and naturally infected animals) and diagnostic purposes. Furthermore, the development of IHC and ISH tools is of utmost significance for understanding the pathogenesis of SARS-CoV-2 by characterizing the viral tissue distribution/cellular tropism in animal models and humans. cache = ./cache/cord-279676-sk9xyd1r.txt txt = ./txt/cord-279676-sk9xyd1r.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-004729-nmkilkcx author = Reynolds, D. J. title = Virus isolation and serum antibody responses after infection of cats with transmissible gastroenteritis virus date = 1979 pages = extension = .txt mime = text/plain words = 1998 sentences = 135 flesch = 54 summary = No clinical disease resulted but infectious virus was isolated from faeces for up to 22 days after infection and serum antibody was detected by neutralisation and immunofluorescence tests. No clinical disease resulted but infectious virus was isolated from faeces for up to 22 days after infection and serum antibody was detected by neutralisation and immunofluorescence tests. Control and infected animals were tested for TGEV excretion by attempted isolation of virus from faeces for up to 35 days after infection; occasionally rectal swabs were used to obtain fresh samples. The medium was changed after 24 hours and 4 days later any viral eytopathic effect was recorded, the medium was removed and passaged in fresh APT/2 cultures and the eoverslips were stained to demonstrate virM antigen by indirect immunofluorescence, using paired sera from a gnotobiotic piglet before and after TGEV infection, followed by FITCconjugated rabbit anti-swine globulin (Nordic Immunological Laboratories, London). cache = ./cache/cord-004729-nmkilkcx.txt txt = ./txt/cord-004729-nmkilkcx.txt === reduce.pl bib === id = cord-265768-hwki5lk2 author = Abi, Keha-mo title = An emerging novel bovine coronavirus with a 4-amino-acid insertion in the receptor-binding domain of the hemagglutinin-esterase gene date = 2020-10-06 pages = extension = .txt mime = text/plain words = 1947 sentences = 91 flesch = 50 summary = title: An emerging novel bovine coronavirus with a 4-amino-acid insertion in the receptor-binding domain of the hemagglutinin-esterase gene We previously reported a novel recombinant bovine coronavirus (BCoV) strain that was circulating in dairy cattle in China, but this virus was not successfully isolated, and the genetic characteristics of BCoV are still largely unknown. A 3D model constructed based on the crystal structure of bovine coronavirus hemagglutinin-esterase (SMTL ID: 3cl4.1) using the online software SWISSMODEL (https ://www.swiss model .expas y.org/inter activ e) showed that the position of the 4-aa insertion in the R3-loop between F 211 and F 212 in HE in the recombinant BCoV strains would alter the spatial conformation of the receptor-binding site relative to that in the HE recombinant strains and prototype strains lacking this insertion ( Fig. 2B and C) . cache = ./cache/cord-265768-hwki5lk2.txt txt = ./txt/cord-265768-hwki5lk2.txt === reduce.pl bib === id = cord-272973-kzaowysv author = Joshi, Lok R. title = Passive immunity to porcine epidemic diarrhea virus following immunization of pregnant gilts with a recombinant orf virus vector expressing the spike protein date = 2018-05-03 pages = extension = .txt mime = text/plain words = 4281 sentences = 210 flesch = 54 summary = PEDV NA, IgG and IgA were detected in the serum of piglets born to immunized gilts, demonstrating the transfer of antibodies through colostrum and milk. In the present study, we investigated the immunogenicity of ORFV-PEDV-S recombinant virus in pregnant gilts and its ability to induce passive immunity and protection in piglets born to immunized animals. Animals in G1 seroconverted to PEDV, presenting detectable levels of IgG, IgA and NA a week after challenge of the piglets (day 7 post-birth; Fig. 1 ). Notably, passive transfer of antibodies from gilts to piglets was observed in both G2 and G3, as PEDV-specific IgG, IgA and NAs were detected in serum of piglets born to immunized gilts following ingestion of colostrum and milk. Additionally, passive transfer of antibodies from gilts to piglets was observed, as PEDV-specific IgG, IgA and NAs were detected in serum of piglets born to immunized gilts following ingestion of colostrum and milk. cache = ./cache/cord-272973-kzaowysv.txt txt = ./txt/cord-272973-kzaowysv.txt === reduce.pl bib === id = cord-004765-7e4yu2do author = Homberger, F. R. title = Maternally-derived passive immunity to enterotropic mouse hepatitis virus date = 1992 pages = extension = .txt mime = text/plain words = 3091 sentences = 182 flesch = 60 summary = Maternally-derived antibody to enterotropic mouse hepatitis virus (MHV) strain Y was transferred to pups by both intrauterine (IgG) and lactogenic (IgA and IgG) routes. MHV-IgG, but not IgA or IgM, could be found in the serum of pups suckling immune dams. Stomach contents of pups suckling immune dams yielded constant IgG titers and gradually declining IgA titers up to the age of 14 days, but neither isotype of MHV antibody was detected at or beyond 21 days (Table 3 ). Pups from three consecutive litters born to immune and naive dams were exsanguated at 2, 4, 6, 8, and 10 weeks of age and sera were tested for MHV-specific IgG. Antibodies persisted for 4 weeks in pups born to dams with low MHV IgG serum titers and then declined to undetectable levels. cache = ./cache/cord-004765-7e4yu2do.txt txt = ./txt/cord-004765-7e4yu2do.txt === reduce.pl bib === id = cord-004840-4rbrzv5o author = Choudhary, Manohar Lal title = Development of real-time RT-PCR for detection of human metapneumovirus and genetic analysis of circulating strains (2009-2011) in Pune, India date = 2013-08-09 pages = extension = .txt mime = text/plain words = 3379 sentences = 186 flesch = 52 summary = title: Development of real-time RT-PCR for detection of human metapneumovirus and genetic analysis of circulating strains (2009-2011) in Pune, India This study describes the development of real time RT-PCR assay for the detection of all four HMPV lineages (A1, A2, B1, B2) in respiratory specimens and genotyping of circulating strains from July 2009 to August 2011 in Pune, western India. [24] designed two sets of primers and probes within the nucleoprotein gene to detect all known genetic lineages of HMPV in a one-step real-time RT-PCR. We have designed a primer-probe set using conserved regions of the nucleoprotein gene to detect all known genetic lineages of HMPV in a one-step real-time RT-PCR. Detection of human metapneumovirus RNA sequences in nasopharyngeal aspirates of young French children with acute bronchiolitis by real-time reverse transcriptase PCR and phylogenetic analysis cache = ./cache/cord-004840-4rbrzv5o.txt txt = ./txt/cord-004840-4rbrzv5o.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-004738-vnz15x84 author = Chen, H. H. title = The rubella virus nonstructural protease recognizes itself via an internal sequence present upstream of the cleavage site for trans-activity date = 2006-03-27 pages = extension = .txt mime = text/plain words = 3966 sentences = 160 flesch = 52 summary = To evaluate the trans-cleavage activity of RV protease on P200-derived substrates, a series of RV P200-related polypeptide expression plasmids that express protein with different N-terminal lengths from the cleavage site (72, 199, 309, and 475 residues) were constructed. To test whether replacement of P200-related sequences C-terminal to the cleavage site by non-rubella sequences affect RV protease trans-activity, the plasmid pRVS-GFP, which contains PCR-amplified RV protease substrate sequences representing polypeptide residues 827-1306 (residues 1302-1306 represent the C-terminal side of the cleavage site), fused at its C-terminus to GFP ORF in-frame, was created (Fig. 1B) . Similarly, to test whether a heterologous sequence on the N-terminal side of the cleavage site affects substrate recognition by the protease trans-activity, GFP ORF was fused in-frame at the N-terminus of the rubella sequence in the plasmid pRVS-1102-1548 to create pRVS-GFP-1102-1548 (Fig. 1B) . In this report, we have shown that RV protease trans-activity demonstrates substrate specificity by requiring an internal sequence within the region that is N-terminal to the cleavage site. cache = ./cache/cord-004738-vnz15x84.txt txt = ./txt/cord-004738-vnz15x84.txt === reduce.pl bib === id = cord-272955-kkkrkgg1 author = Belsy, Acosta title = Molecular characterization of adenoviral infections in Cuba: report of an unusual association of species D adenoviruses with different clinical syndromes date = 2009-03-12 pages = extension = .txt mime = text/plain words = 4219 sentences = 233 flesch = 39 summary = title: Molecular characterization of adenoviral infections in Cuba: report of an unusual association of species D adenoviruses with different clinical syndromes The objectives of this study were to identify and characterize members of different adenovirus species at the molecular level and to describe the correlation between viruses and clinical syndromes during a period of 4 years. Four isolates from clinical materials obtained from patients with encephalitis, acute flaccid paralysis and meningoencephalitis were identified as belonging to the species Human adenovirus D. In the present report, the nested PCR method used was able to detect different HAdVs in clinical samples and supernatant culture with a sensitive internal control system to assure the quality of reaction conditions in each individual tube. Human adenovirus DNA was detected in the supernatant of a cell culture infected with viruses obtained from fecal specimens taken from a patient with acute flaccid paralysis (AFP), as well as in two cases of meningoencephalitis. cache = ./cache/cord-272955-kkkrkgg1.txt txt = ./txt/cord-272955-kkkrkgg1.txt === reduce.pl bib === id = cord-265201-ab67pnct author = Sugiyama, K. title = Hemagglutination and structural polypeptides of a new coronavirus associated with diarrhea in infant mice date = 1980 pages = extension = .txt mime = text/plain words = 3274 sentences = 272 flesch = 69 summary = The hemagglutination (HA) and receptor destroying enzyme (RDE) activities of a newly isolated mouse enteric coronavirus (designated as DVIM) are described. H e madsorbed s y n e y t i u m which were i n c u b a t e d at 37 ° C to release I~BCs for 60 minutes, were exposed to freshly p r e p a r e d RBCs a n d p h o t o g r a p h e d Above results strongly suggest that DVIM possesses an enzymatic activity which reacts with surface components of RBCs. However, this enzymatic action appears to differ from the bacterial neuraminidase and that of Influenza-A virions. A densitometer scan of a stained polyacrylamide gel of the polypeptides of virus particles treated with bromelain (1.0 mg/ml at 37°C for 15 minutes) is shown in Fig. 4 . cache = ./cache/cord-265201-ab67pnct.txt txt = ./txt/cord-265201-ab67pnct.txt === reduce.pl bib === id = cord-004825-cdvnqfjz author = Castilla, V. title = The entry of Junin virus into Vero cells date = 1994 pages = extension = .txt mime = text/plain words = 2668 sentences = 141 flesch = 50 summary = The entry mechanism of Junin virus (JV) into Vero cells was studied analyzing the effect of lysosomotropic compounds and acid pH on JV infection. Vero cells grown in coverslips were infected with JV (moi 1) and 15 mM ammonium chloride was added to the culture medium after adsorption. To reinforce that the membrane fusion activity of Junin virus is expressed at low pH, the formation of JV-induced syncytia in infected Vero cells incubated in medium at pH 5.5 or 7.5 was quantitated. In fact, a bypass of the ammonium chloride block of JV infection was achieved when the extracellular medium was at a pH below 6.1 (Fig. 5) , suggesting that the acidic conditions would probably trigger direct fusion of virus envelope with the cell membrane. cache = ./cache/cord-004825-cdvnqfjz.txt txt = ./txt/cord-004825-cdvnqfjz.txt === reduce.pl bib === id = cord-265631-b0kg6qpo author = Saeng-chuto, Kepalee title = Retrospective investigation and evolutionary analysis of a novel porcine deltacoronavirus strain detected in Thailand from 2008 to 2015 date = 2017-03-23 pages = extension = .txt mime = text/plain words = 1601 sentences = 87 flesch = 52 summary = title: Retrospective investigation and evolutionary analysis of a novel porcine deltacoronavirus strain detected in Thailand from 2008 to 2015 We performed a retrospective investigation of the presence of PDCoV in intestinal samples collected from piglets with diarrhea in Thailand from 2008 to 2015 using RT-PCR. Positive samples were subjected to full-length genome characterization followed by genetic analyses to compare Thai strains of PDCoV to those from other countries and to investigate the genetic similarity and the evolutionary relationships among them. To investigate its evolutionary relationships to foreign PDCoV strains and estimate the divergence time of PDCoV in Thailand, phylogenetic analysis of the full-length nucleotide sequence of the PDCoV isolate collected in this study, together with 21 other PDCoV isolate sequences (Supplementary Table 1 ), was performed using the Bayesian Markov chain Monte Carlo (BMCMC) method implemented in the program BEAST v1.8.3 [2, 3] . cache = ./cache/cord-265631-b0kg6qpo.txt txt = ./txt/cord-265631-b0kg6qpo.txt === reduce.pl bib === id = cord-004694-43yvs52a author = Han, Tae-Hee title = Detection of human rhinovirus C in children with acute lower respiratory tract infections in South Korea date = 2009-05-05 pages = extension = .txt mime = text/plain words = 1987 sentences = 103 flesch = 57 summary = A total of 54 single HRV-positive specimens from children hospitalized with acute LRTIs were sequenced after performing RT-PCR based on the 5 0 NCR region. Recently, novel HRV species were identified and their members were reported to be associated with acute respiratory tract infections with febrile wheeze, asthmatic exacerbation, influenza-like illness, pneumonia and rhinitis [10, 13, 14, 17] . An association of members of novel HRV species with severe respiratory tract infections [19, 20] and a global distribution of members of novel species in respiratory specimens have Fig. 1 Phylogenetic tree of clinical viral isolates (n = 54) based on analysis of *285 bp from the 5 0 noncoding region (nt 178-462 of HRV16 L24917). In the present study, phylogenetic analysis of the 5 0 NCR region showed that QPM, HRV-C strain026 and HRV X1 were grouped into the HRV-C species, but 9 strains could not be identified. cache = ./cache/cord-004694-43yvs52a.txt txt = ./txt/cord-004694-43yvs52a.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 === === reduce.pl bib === id = cord-262505-1ufgwxxg author = Lai, M. M. C. title = Genetic heterogeneity of murine coronaviruses date = 1983 pages = extension = .txt mime = text/plain words = 2559 sentences = 162 flesch = 57 summary = Several mouse hepatitis viruses (MHV) with different pathogenicity were studied by oligonucleotide fingerprinting. The MHVs isolated from separate cloned neuroblastoma cell lines persistently infected with JHM strain were also found to have diverged more markedly than the corresponding virus maintained under the conditions of lytic infection. The viruses maintained under the latter conditions exhibit much more variability, suggesting that persistent infections may be a mechanism contributing to the genetic heterogeneity of the current MHV strains. To study the genetic relationship of different MHV strains causing various diseases in mice, we first examined the oligonucleotide fingerprints of two of the IKHVs isolated in Japan. To assess the genetic stability and variability of MItV and to study the possible mechanism of viral divergence observed as above, we examined the heterogeneity of viral genomic sequences in viruses isolated from persistently and latently infected cells. cache = ./cache/cord-262505-1ufgwxxg.txt txt = ./txt/cord-262505-1ufgwxxg.txt === reduce.pl bib === id = cord-032801-b2ncmkjg author = Song, Jie title = Transcriptome analysis following enterovirus 71 and coxsackievirus A16 infection in respiratory epithelial cells date = 2020-09-29 pages = extension = .txt mime = text/plain words = 4930 sentences = 238 flesch = 48 summary = It was discovered that enriched GO terms (such as histone acetylation and positive regulation of phosphorylation) and pathways (such as glycosylphosphatidylinositol (GPI)-anchor biosynthesis and DNA replication) might be closely associated with the pathogenic mechanism of these two viruses, and key genes (such as TBCK and GPC) might be involved in the progression of HFMD. In the current study, we aimed to discover significant differentially expressed genes in EV-A71-and CV-A16-infected respiratory epithelial cells through transcriptome sequencing. For example, transcriptome analysis revealed differentially expressed genes, including SCARB2, miR-3605-5p, and enriched ECM-receptor interaction and circadian rhythm pathways involved in the pathogenesis of HFMD in CV-A16-infected HEK 293T cells [9] . These 111 common differentially expressed genes were used to perform hierarchical cluster analysis, and the heatmap result showed that these genes were mainly clustered into two categories-either significantly upregulated or significantly downregulated, suggesting that EV-A71 and CV-A16 infections result in largely similar transcriptome-level changes. cache = ./cache/cord-032801-b2ncmkjg.txt txt = ./txt/cord-032801-b2ncmkjg.txt === reduce.pl bib === === 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 === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-264392-he1vekrt author = Lambeth, L. S. title = Complete genome sequence of Nariva virus, a rodent paramyxovirus date = 2008-12-23 pages = extension = .txt mime = text/plain words = 4363 sentences = 204 flesch = 52 summary = This study confirmed the classification of NarPV as a member of the subfamily Paramyxovirinae and established the close genome organization and sequence relationship between the two rodent paramyxoviruses isolated almost a decade apart and from two locations separated by more than 15,000 km. This was then followed by PCR to fill in the ''gaps'' using specific primers designed from NarPV Nariva virus genome 201 sequences obtained from the cDNA subtraction or degenerate primers designed using highly conserved consensus sequences of known paramyxoviruses in the subfamily Paramyxovirinae. Overall comparison of deduced sizes and amino acid sequences of all proteins indicated that NarPV is most closely related to MosPV (Table 1) genome is significantly larger (16,650 nt) than that of NarPV due to the longer untranslated regions (UTRs) located at the 3 0 end of most genes ( Fig. 1b and Table 1 ). cache = ./cache/cord-264392-he1vekrt.txt txt = ./txt/cord-264392-he1vekrt.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-004849-d64hnqkh author = Choi, C. S. title = Temperature dependent replication of porcine parvovirus isolates date = 1989 pages = extension = .txt mime = text/plain words = 2338 sentences = 121 flesch = 48 summary = The replication of four porcine parvovirus isolates, NADL-8, NADL-2, KBSH, and Kresse, in swine testes cells were compared at temperatures of 32, 37, and 39 °C. Similar patterns of cell associated virus were detected from both NADL-8 and NADL-2 infected ceils at the 3 temperatures (Fig. 2 a, b) , whereas marked differences were again observed for Kresse and KBSH-infected cells (Fig. 2 c, d) . Since marked differences in replication of Kresse and KBSH isolates were observed at 37 and 39°C evidenced by both intracellular and extracellular infectious virus and HA antigen, further characterization of viral polypeptide production was attempted. Temperature dependent differences in the number and quantity of viral polypeptides were observed in cells infected with Kresse and KBSH and propagated at either 32, 37 or 39 °C (Fig. 3 A) . To further examine the mechanism of temperature-dependent replication of PPV isolates, the synthesis of viral D N A was evaluated by nucleic acid hybridization of cell extracts (Fig. 4) . cache = ./cache/cord-004849-d64hnqkh.txt txt = ./txt/cord-004849-d64hnqkh.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-004766-gvom0f13 author = Traavik, T. title = Improvement of arbovirus HA antigens by treatment with a colloidal silica gel and sonication date = 1977 pages = extension = .txt mime = text/plain words = 2232 sentences = 167 flesch = 62 summary = A remarkable increase in HA titers for weakly haemagglutinating Norwegian arbovirus strains, Uukuniemi and Runde viruses, was achieved by including treatment with the colloidal silica gel Aerosil in the antigen preparation scheme. Good antigens also were obtained from virus grown in BHK 21/c 13 cell cultures and concentrated by polyethylene glycol 6000/NaCl. Rubella virus HA antigen and HB(s)Ag were adsorbed to the gel, and excluded from a preparation by treatment with Aerosil. For production of arbovirus haemagglutinating (HA) antigens, the classical sucrose-aeeton extraction method (SA) (3) with infected suckling mouse brains has been almost undisputed, although methods based on infected cell culture fluids (2, 12) and infected mouse aseites fluids (8) have also been reported. Infected brain suspensions and PEG treated cell culture concentrates were titrated by intraeerebral inoculation in suckling mice after Aerosil absorption, incubation with shaking in waterbath at 45 ° C and untreated. Simple method for preparation of haemagglutinating arbo-A virus antigens from brains of suckling mice cache = ./cache/cord-004766-gvom0f13.txt txt = ./txt/cord-004766-gvom0f13.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-267446-rpv19oy6 author = Park, Jung-Eun title = Receptor-bound porcine epidemic diarrhea virus spike protein cleaved by trypsin induces membrane fusion date = 2011-06-12 pages = extension = .txt mime = text/plain words = 4075 sentences = 186 flesch = 47 summary = The addition of trypsin was shown to induce fusion of the infected Vero cells, resulting in the formation of multiple syncytia, and produced a significant increase in virus titer after several passages. For example, infection by severe acute respiratory syndrome coronavirus (SARS-CoV) and murine hepatitis virus strain 2 (MHV-2) requires proteolytic cleavage in their target cells, which is mediated by trypsin-like proteases [24, 29, 32] . To investigate the effects of proteolytic cleavage of the surface protein of Vero cells and free virions by trypsin, Vero cells or KPEDV-9 were pre-treated with trypsin prior to infection. These results are consistent with the suggestion that trypsin is not absolutely essential for Vero-cell-adapted PEDV infection, as reported for other group 1 coronaviruses, but the titer increases during infection with trypsin-treated virus. cache = ./cache/cord-267446-rpv19oy6.txt txt = ./txt/cord-267446-rpv19oy6.txt === reduce.pl bib === id = cord-282062-h9smg0w9 author = Takano, Tomomi title = Novel single-stranded, circular DNA virus identified in cats in Japan date = 2018-09-14 pages = extension = .txt mime = text/plain words = 1942 sentences = 124 flesch = 56 summary = We detected a novel feline stool-associated circular DNA virus (FeSCV) in fecal samples from cats with diarrhea using consensus primers matching those of circovirus and cyclovirus. Feline cyclovirus was identified by next-generation sequencing analysis in which the viral gene was detected in a pooled fecal sample collected from 4-5 healthy cats. In this study, we performed nested PCR using Circoviridae family consensus primers and detected novel CRESS DNA viruses in several cats with diarrhea symptoms. However, we concluded that FeSCV is a circular DNA virus based on the following: 1) No Giardia intestinalis was detected in the fecal test, and 2) the complete genome of FeSCV was amplified using the rolling-circle amplification and inverse PCR assays. We detected a novel CRESS DNA virus, FeSCV, in fecal samples from cats. Although it was detected using consensus primers of circovirus and cyclovirus, FeSCV was phylogenetically positioned in a clade different from that of these viruses. cache = ./cache/cord-282062-h9smg0w9.txt txt = ./txt/cord-282062-h9smg0w9.txt === reduce.pl bib === id = cord-285329-62yafd2d author = Tsunemitsu, H. title = Antigenic and biological comparisons of bovine coronaviruses derived from neonatal calf diarrhea and winter dysentery of adult cattle date = 1995 pages = extension = .txt mime = text/plain words = 2453 sentences = 126 flesch = 55 summary = The antigenic and biological properties of 6 strains of bovine coronavirus (BCV) derived from neonatal calf diarrhea (CD) and 8 strains of BCV from winter dysentery (WD) of adult cattle, propagated in HRT-18 cells, were compared to determine if CD and WD strains belong to distinct serotypes or subtypes of BCV. However, in virus neutralization tests, antisera to 1 CD and 2 WD strains had 16-fold or lower antibody titers against 3 WD and 1 CD strains than against the homologous strains, and this variation reflected low antigenic relatedness values (R=13–25%), suggesting the presence of different subtypes among BCV. Receptor-destroying enzyme activity with mouse erythrocytes was not UExpressed as the reciprocal of the highest dilution of virus causing complete disappearance of HA patterns at 4 °C after 2 h incubation at 37 °C ° CD Calf diarrhea, WD winter dysentery of adult cattle dM/C Ratio of HA titer with mouse erythrocytes to HA titer with chicken erythrocytes detected for any strain of BCV. cache = ./cache/cord-285329-62yafd2d.txt txt = ./txt/cord-285329-62yafd2d.txt === reduce.pl bib === id = cord-283525-kvcqayl4 author = Wei, Zhan-Yong title = Nitric oxide inhibits the replication cycle of porcine parvovirus in vitro date = 2009-05-13 pages = extension = .txt mime = text/plain words = 2366 sentences = 124 flesch = 51 summary = This study investigated the inhibitory effect and mechanism of nitric oxide (NO) on porcine parvovirus (PPV) replication in PK-15 cells. The results showed that two NO-generating compounds, S-nitroso-l-acetylpenicillamine (SNAP) and l-arginine (LA), at a noncytotoxic concentration could reduce PPV replication in a dose-dependent manner and that this anti-PPV effect could be reversed by the NO synthase (NOS) inhibitor N-nitro-l-arginine methyl ester (l-NAME). As shown in Fig. 1a , SNAP and LA have the ability to inhibit PPV replication in PK-15 cells, and there is a dose-dependent relationship between the inhibitory effect and the SNAP (or LA) concentration. As shown in Fig. 2 , the PFU value increased with later addition of SNAP (or LA), and adding SNAP (or LA) 6 or 3 h prior to viral infection resulted in the highest level of inhibition. Our results demonstrate that NO specially inhibits the PPV replication cycle during the step of viral protein synthesis (Fig. 3b) . cache = ./cache/cord-283525-kvcqayl4.txt txt = ./txt/cord-283525-kvcqayl4.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-281410-y558a5jf author = Akashi, H. title = Propagation of the Kakegawa strain of bovine coronavirus in suckling mice, rats and hamsters date = 1981 pages = extension = .txt mime = text/plain words = 1120 sentences = 85 flesch = 63 summary = title: Propagation of the Kakegawa strain of bovine coronavirus in suckling mice, rats and hamsters Infected animals died with nervous symptoms, and serial passage was readily accomplished by intracerebral inoculation with brain emulsions. Infected animals died with nervous symptoms, and serial passage was readily accomplished by intraeerebral inoculation with brain emulsions. The present paper describes briefly our recent observation that the Kakegawa strain of BCV readily propagates in suckling mice, rats and hamsters. Four-day-old mouse 3 days after intraeerebral inoculation with the 3rd mouse brain passaged Kakegawa strain (left) and an uninoeulated 4-day-old mouse (right) Four litters (10 to 12/litter) of suckling mice were inoculated intracerebrally with infected tissue culture fluid containing 106-5 TCID50/ml. These findings showed that the viruses recovered from the brains of affected animals were antigenieally the same as the cell culture passaged virus and could be clearly differentiated from the MttV strain 2. cache = ./cache/cord-281410-y558a5jf.txt txt = ./txt/cord-281410-y558a5jf.txt === reduce.pl bib === id = cord-283804-dje7qbps author = Macnaughton, M. R. title = The polypeptide composition of avian infectious bronchitis virus particles date = 1977 pages = extension = .txt mime = text/plain words = 2683 sentences = 221 flesch = 78 summary = The polypeptides of the different density virus particles from the three IBV strains were analysed on polyacrylamide gels. Other studies on the polypeptide composition of eoronaviruses have shown 6 polypeptides in the virus particles of human coronavirus (HCV) strain OC43 (7) a n d t r a n s m i s s i b l e g a s t r o e n t e r i t i s v i r u s ( T G E V ) (5), a n d 7 p o l y p e p t i d e s in t h e v i r u s p a r t i c l e s of H C V s t r a i n 229 E (8) Virus Polypeptide Analysis Figure 2 shows the polsTeptides of the purified major virus species of the IBV strains Beaudette, Connecticut and Massachusetts, on polyaerylamide gels. cache = ./cache/cord-283804-dje7qbps.txt txt = ./txt/cord-283804-dje7qbps.txt === reduce.pl bib === id = cord-287275-vwyny1vt author = Zhang, Meng-Jia title = Genomic characterization and pathogenicity of porcine deltacoronavirus strain CHN-HG-2017 from China date = 2018-10-30 pages = extension = .txt mime = text/plain words = 5181 sentences = 267 flesch = 56 summary = In this study, a Chinese PDCoV strain, designated CHN-HG-2017, was isolated from feces of a suckling piglet with severe watery diarrhea on a farm located in central China. Tissues of small intestines from CHN-HG-2017-infected piglets at 4 DPI displayed significant macroscopic and microscopic lesions with clear viral antigen expression. In addition, it has been reported that newborn piglets inoculated with two recent Chinese PDCoV isolates, named CHN-HN-2014 and CHN-GD-2016, developed clear clinical signs, including severe diarrhea, vomiting, and dehydration [21, 22] . Analysis of the genomic sequence suggested that CHN-HG-2017 is a potential recombinant virus derived from Chinese and Vietnam PDCoV strains. To confirm that virus propagation had occurred, the infectivity of the plaque-purified CHN-HG-2017 strain in LLC-PK1 cells was tested by IFA and western blot with an mAb against the PDCoV N protein. Isolation, genomic characterization, and pathogenicity of a Chinese porcine deltacoronavirus strain CHN-HN-2014 cache = ./cache/cord-287275-vwyny1vt.txt txt = ./txt/cord-287275-vwyny1vt.txt === reduce.pl bib === id = cord-289926-y1rjgbui author = Veretnik, S. title = RNA binding domain of HDV antigen is homologous to the HMG box of SRY date = 2014-05-18 pages = extension = .txt mime = text/plain words = 6679 sentences = 309 flesch = 53 summary = Using sequence analysis methods we have discovered significant sequence similarity between this central domain of HDAg and the HMG (High Mobility Group) box of the SRY gene [40] , whose product binds to DNA and is essential for sex determination. The sequence similarity between the central domain of HDAg and the HMG (High Mobility Group) box of the SRY gene suggests that SRY may be a cellular cognate of HDAg. Another candidate for the 'captured' cellular RNA was recently proposed: a 202 residue cellular protein referred to as DIPA (delta interacting protein A) was identified by co-immunoprecipitation with HDAg and by its in vivo ability to inhibit viral replication [5] . Statistically significant sequence similarities are limited to the functionally essential regions of both genes: in the SRY gene the similarity is confined to the HMG (High Mobility Group) box, a DNA binding motif found in the HMG protein superfamily [24, 31] , in HDAg the similarity is limited to RNA-binding domain. cache = ./cache/cord-289926-y1rjgbui.txt txt = ./txt/cord-289926-y1rjgbui.txt === reduce.pl bib === id = cord-285429-vmnj25b5 author = Saikruang, Wilaiporn title = Detection of diarrheal viruses circulating in adult patients in Thailand date = 2014-07-31 pages = extension = .txt mime = text/plain words = 2186 sentences = 113 flesch = 51 summary = A total of 332 fecal specimens collected during January-December 2008 from adult patients with diarrhea were screened for group A and C rotaviruses, noroviruses GI and GII, sapovirus, Aichi virus, human parechovirus, enterovirus, adenovirus and astrovirus by RT-multiplex PCR. This study provides epidemiological data for a wide variety of diarrheal viruses circulating in adult patients with diarrhea in Chiang Mai, Thailand. Then, the specimens were tested for the presence of SaV, AiV, group A rotavirus (RVA), group C rotavirus (RVC), HPeV, NoV GI and GII, EV, AdV, and AstV by RT-multiplex PCR using the protocol described previously by Khamrin et al. In addition, this study clearly demonstrates that HPeV is an unusual cause of acute gastroenteritis in adults compared to other viruses. The relatively low rate of diarrheal virus detection in adults with diarrhea in this study suggests that acute gastroenteritis in adults in this area may be caused by other pathogens. cache = ./cache/cord-285429-vmnj25b5.txt txt = ./txt/cord-285429-vmnj25b5.txt === reduce.pl bib === id = cord-286794-adbxzgvs author = Du, Juan title = Identification and complete genome characterization of human enterovirus 117 from a child with pneumonia in China date = 2019-03-16 pages = extension = .txt mime = text/plain words = 1172 sentences = 61 flesch = 54 summary = title: Identification and complete genome characterization of human enterovirus 117 from a child with pneumonia in China In this study, human enterovirus C117 (EV-C117) was detected in a 3-month-old boy diagnosed with pneumonia in China. Here, we report the identification and complete genomic sequence of EV-117 in a child with pneumonia in China, which may provide more information for understanding EV-C117 infection. Using multiple primers (Table 1) , we determined the full-length viral genome sequence of the strain detected in patient CQ6747 (GenBank accession no. Conversely, all genome regions of CQ6747 showed less similarity to other EV-C strains (including EV-C104, EV-C105, EV-C109, and EV-C118) ( Table 2) . Complete genomic sequencing shows that polioviruses and members of human enterovirus species C are closely related in the noncapsid coding region Complete genome sequence of a novel human enterovirus C (HEV-C117) identified in a child with communityacquired pneumonia Respiratory infection with enterovirus genotype C117, China and Mongolia cache = ./cache/cord-286794-adbxzgvs.txt txt = ./txt/cord-286794-adbxzgvs.txt === reduce.pl bib === id = cord-293945-gyb9mjb5 author = Chai, Weidong title = Antiviral effects of a probiotic Enterococcus faecium strain against transmissible gastroenteritis coronavirus date = 2012-11-28 pages = extension = .txt mime = text/plain words = 4304 sentences = 199 flesch = 41 summary = Virus yield reduction assay ST cell monolayers were infected with TGEV with or without probiotic bacteria treatment according to the experimental design. faecium (1.00E?07 CFU/ml) when the probiotic was added to the cells together with the virus during the infection period (competition assay). faecium inactivates TGEV particles by direct physical interaction with virus, a cell-free preincubation assay was performed. faecium together with the virus significantly increases mRNA expression levels of the pro-inflammatory cytokines interleukin 6 (IL-6) and IL-8 (an approximately 3-and 13-fold increase, respectively) when compared with TGEV-infected ST cells that had not been exposed to the probiotic (Fig. 6) . faecium (pretreatment), the viability of TGEV-infected cells was protected, and virus yields were reduced (Figs. In this study, the competition assay in which virus and probiotic bacteria are present in the culture medium side by side, exhibited the most pronounced antiviral activity in terms of cell survival (Figs. cache = ./cache/cord-293945-gyb9mjb5.txt txt = ./txt/cord-293945-gyb9mjb5.txt === reduce.pl bib === id = cord-288948-89cdfhi0 author = Campalto, M. title = Divergent minute virus of canines strains identified in illegally imported puppies in Italy date = 2020-10-08 pages = extension = .txt mime = text/plain words = 1924 sentences = 98 flesch = 59 summary = This study reports the characterization of four divergent MVC strains detected between 2012 and 2018, three of which were from dogs illegally imported into Italy, most probably from Eastern Europe, that cluster together phylogenetically but share low genetic similarity with the fourth MVC from an autochthonous dog and other available MVC sequences. In detail: the complete ORF1, encoding the NS1 protein, of three of the four MVC isolates (Italy/4033/2012, BIO-CRIME/2018 and Italy/59116/2017, which had a gap of 17 nt) was sequenced and was 2325 bases in length, corresponding to 774 aa (Fig. 1a) . The phylogenetic tree based on the ORF2 nt sequences encoding the VP1/VP2 proteins (Fig. 2c) , was constructed using all 124 MVC sequences available in the GenBank database and included the only Italian MVC sequence available, Italy/285_11/2011 (JQ612703_Canine_ minute_virus_strain_285_11_Italy_2011), for which only the partial VP1/VP2 sequence is present [9] . cache = ./cache/cord-288948-89cdfhi0.txt txt = ./txt/cord-288948-89cdfhi0.txt === reduce.pl bib === id = cord-299342-l8ugjou9 author = Yaling, Zhou title = Porcine epidemic diarrhea virus (CV 777) and feline infectious peritonitis virus (FIPV) are antigenically related date = 1988 pages = extension = .txt mime = text/plain words = 2974 sentences = 148 flesch = 50 summary = Using gut sections from pigs infected with porcine epidemic diarrhea virus (strain CV 777) and ascitic fluid from cats which had succumbed to feline infectious peritonitis (FIP), a weak cross reaction was found by immunofluorescence. No reaction was found at the nucleocapsid protein position when blots of a mock infected N L F K cell lysate had been incubated with anti-CV 777 antibodies. As shown in figure 3 , results of the RIP confirmed the cross-reaction between pig anti-CV 777 sera and the 43,000 protein of FIPV found in Western blots; the homologous reaction reveals the typical pattern of FIPV structural polypeptides with Mr of 210,000 (peplomer), 45,000 (nucleocapsid) and 25,000 to 32,000 (envelope). We have confirmed the finding of cross reactions within one group, namely between transmissible gastroenteritis virus (TGEV) of swine, FIPV and canine enteric coronavirus, and showed that common determinants are present on all three structural polypeptides [7] . cache = ./cache/cord-299342-l8ugjou9.txt txt = ./txt/cord-299342-l8ugjou9.txt === reduce.pl bib === id = cord-294218-v4gjabp3 author = Dea, S. title = Intracellular synthesis and processing of the structural glycoproteins of turkey enteric coronavirus date = 1989 pages = extension = .txt mime = text/plain words = 5297 sentences = 256 flesch = 49 summary = Pulse labeling of cells with [(35)S]methionine or [(3)H]glucosamine at different times after infection, followed by SDS-PAGE and Western immunoblotting analysis using rabbit anti-TCV hyperimmune serum, was used to resolve and identify TCV-induced intracellular proteins. In the present study, we have investigated the intracellular synthesis and post-translational modifications of virus-coded polypeptides in cultures of HRT-18 infected with TCV in the presence or the absence of glycosylation inhibitors. Radioim-munoprecipitation experiments using the anti-TCV hyperimmune serum, after [35S]methionine and [3H]glucosamine labeling, confirmed the absence of the peplomeric glycoproteins from TM-treated cells, whereas the relative amount of the unglycosylated high mol.wt, polypeptide species increased (Fig. 4A, lanes 5 and 7) . In this paper, we described the identification of virus-induced intracellular polypeptides in TCV-infected HRT-18 cells, the kinetic of their synthesis, their post-translational processing in the presence of glycosylation inhibitors and their significance with respect to the production of mature virions. cache = ./cache/cord-294218-v4gjabp3.txt txt = ./txt/cord-294218-v4gjabp3.txt === reduce.pl bib === id = cord-285892-tp6mlqtw author = Li, Yingli title = Isolation of two Chinese bovine enteroviruses and sequence analysis of their complete genomes date = 2012-08-01 pages = extension = .txt mime = text/plain words = 2956 sentences = 123 flesch = 49 summary = In this study, RNA corresponding to bovine enterovirus (BEV) was detected in 24.6 % of faecal samples (17/69) from diarrheic and healthy cattle in six different areas in China by an RT-PCR screening method. These viruses were characterized molecularly through sequence analysis of complete genomes, and the BHM26 and BJ50 isolates were therefore classified into genotype 2 of the BEV-B cluster. A total of 69 bovine diarrheic and healthy faecal specimens from six different areas were examined by RT-PCR using the primer pair 6424U24 and 7450L24, which cover the highly conserved partial 3D gene and 3 0 UTR of BEVs. The results showed that virus-specific RNA could be detected directly in faecal material in 17 of 69 samples (24.6 %). The results showed that the 3D/3 0 UTR (1026 nt) of BHM26 and BJ50 shared 86 % and 88 % nucleotide sequence identity, respectively, to that of BEV strain Jena38/02 (GenBank accession number: DQ092789), indicating that the two isolates are bovine enterovirus. cache = ./cache/cord-285892-tp6mlqtw.txt txt = ./txt/cord-285892-tp6mlqtw.txt === reduce.pl bib === id = cord-284087-g2jfnxja author = Falcone, Valeria title = Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season date = 2013-02-09 pages = extension = .txt mime = text/plain words = 3417 sentences = 189 flesch = 51 summary = In this study, we investigated the molecular evolution of influenza virus A(H1N1)pdm09 in the 2010/11 influenza season in southern Germany by sequence analysis of the influenza virus hemagglutinin gene from 25 patients with mild, moderate, and severe disease. The H275Y mutation in the influenza virus neuraminidase gene, known to confer resistance to the neuraminidase inhibitor oseltamivir, was detected in one patient. Aim of this study was to investigate the molecular evolution of A(H1N1)pdm09 in the 2010/11 influenza season in southern Germany by sequence analysis of the HA gene of mild, moderate, and severe influenza cases. In order to detect molecular changes in the HA gene of influenza virus, 33 A(H1N1)pdm09 HA sequences representing 25 individual patients were analysed. e., C 2 weeks) of influenza virus in the respiratory tract was observed in 6 of the 25 patients (24 %; 3 with severe, 2 with moderate, and 1 with mild disease). cache = ./cache/cord-284087-g2jfnxja.txt txt = ./txt/cord-284087-g2jfnxja.txt === reduce.pl bib === id = cord-302871-x3mjov5l author = Ribeiro, Juliane title = Extra-intestinal detection of canine kobuvirus in a puppy from Southern Brazil date = 2016-11-25 pages = extension = .txt mime = text/plain words = 2586 sentences = 129 flesch = 45 summary = This study presents the pathological, immunohistochemical, and molecular findings associated with the extra-intestinal detection of canine kobuvirus (CaKV) in a 5-month-old Chihuahua puppy, that had a clinical history of bloody-tinged feces. There are few descriptions of coinfection due to CaKV and other viral agents: a recent study identified CaKV in association with a several agents including canine herpesvirus type 1 (CaHV-1), canine distemper virus (CDV), canine parvovirus (CPV), and canine adenovirus A types 1 (CAdV-1) and 2 (CAdV-2) in diarrheic and non-diarrheic dogs from Korea [19] . Furthermore, widespread viral dissemination was demonstrated in multiple tissues as CaKV nucleic acids were detected in the liver, lung, brain, and tonsils of this Fig. 2 Phylogenetic analysis of a partial nucleotide sequence (nt 201) of the RdRp gene (a) and partial region of the VP1 protein (nt 303) of canine kobuvirus (CaKV) (b). cache = ./cache/cord-302871-x3mjov5l.txt txt = ./txt/cord-302871-x3mjov5l.txt === reduce.pl bib === id = cord-294467-kq5wmavt author = Kasai, H. title = Characterization of haemagglutinin-esterase protein (HE) of murine corona virus DVIM by monoclonal antibodies date = 2014-04-08 pages = extension = .txt mime = text/plain words = 1947 sentences = 116 flesch = 60 summary = title: Characterization of haemagglutinin-esterase protein (HE) of murine corona virus DVIM by monoclonal antibodies We analyzed the characteristics of seven monoclonal antibodies (mAbs) raised against purified HE (hemagglutinin-esterase) glycoprotein of the murine coronavirus DVIM (diarrhea virus of infant mice). Neutralizing activity was shown in group A mAbs exclusively, suggesting that the ratio of HA and/or AE activities may play important roles in the cell fusion activity of DVIM-infected cells. As described in a previous report [8] , by treatment of DVIM with the non-ionic detergent NP-40 we isolated the HE protein, which carries the functional sites for both acetylesterase (AE) and the haemagglutination (HA) activities. We examined the cytopathic effect of mAbs with respect to the formation of syncytia in DVIM-infected cells. The antibodies that had low titers to both activities did not delay the fusion of infected cells. cache = ./cache/cord-294467-kq5wmavt.txt txt = ./txt/cord-294467-kq5wmavt.txt === reduce.pl bib === id = cord-295409-7l0pglef author = Percy, D. title = Replication of sialodacryoadenitis virus in mouse L-2 cells date = 1989 pages = extension = .txt mime = text/plain words = 3069 sentences = 178 flesch = 54 summary = The ability to propagate SDAV to high titers in the widely available L-2 cell line should promote the study of this virus and facilitate its comparison with other murine coronaviruses. In LBC cells inoculated with strain #681 of SDAV, CPE was first detected in infected cultures 48 hours pi, and syncytia were observed by 72 hours pi [11] . Viral antigen and TCIDs0 titers of 107/0.2ml could be detected in inoculated culture fluid at 24 hours pi by the tenth passage of SDAV in LBC cells [11] . Submandibular and parotid salivary glands from animals infected with the eighth pass of SDAV were homogenized to make a 10% (w/v) suspension in PBS, then 0.5 ml was inoculated onto L-2 or L-929 cells, incubated at 37 °C, and observed for evidence of viral antigen and CPE. Following 5-6 serial passages of supernatant fluid from infected cell cultures, viral antigen, infectious virus, and CPE could be readily demonstrated. cache = ./cache/cord-295409-7l0pglef.txt txt = ./txt/cord-295409-7l0pglef.txt === reduce.pl bib === id = cord-291718-cz1bi0ym author = Yu, Liping title = The papain-like protease of avian infectious bronchitis virus has deubiquitinating activity date = 2017-03-18 pages = extension = .txt mime = text/plain words = 3426 sentences = 180 flesch = 54 summary = Furthermore, the IBV replicase-encoded PLP, including the downstream transmembrane (TM) domain, is a DUB enzyme and dramatically reduced the level of Ub-conjugated proteins, while processing both K48and K63-linked polyubiquitin chains. Overall, these results demonstrate that the IBV-encoded PLP-TM functions as a DUB enzyme and suggest that IBV may interfere with the activation of host antiviral signaling pathway by degrading polyubiquitin-associated proteins. Further experiments indicated that the proteinase PLP-TM plays an important role in IBV DUB activity and can process both K48-and K63-linked polyubiquitin chains. Overall, the results of our study show that IBV has DUB activity and confirm that PLP-TM is not only a classic papain-like protease encoded by IBV but is also a multifunctional protein that plays important roles in the regulation of interactions between IBV and host antiviral innate immune response proteins. IBV PLP-TM may prevent the activation of host antiviral signaling pathways by degrading polyubiquitin chains associated with ubiquitin proteins. cache = ./cache/cord-291718-cz1bi0ym.txt txt = ./txt/cord-291718-cz1bi0ym.txt === reduce.pl bib === id = cord-296167-np0b9a7o author = Mardani, Karim title = Naturally occurring recombination between distant strains of infectious bronchitis virus date = 2010-06-24 pages = extension = .txt mime = text/plain words = 2955 sentences = 132 flesch = 50 summary = In the present study, the 3′ terminal 7.2 kb of the genome of a recently isolated variant of IBV (N1/03) was sequenced and compared with the sequences of classical and novel strains of IBV, the two main groups of these viruses in Australia. The 3 0 -terminal 7.2 kb of the genomes of the representative classical and novel Australian IBV strains were aligned with the sequences from the same region of the N1/03 isolate, and the multiple alignment results were introduced into SimPlot version 3.5.1 to identify likely recombination sites [19] . It would be appropriate to sequence and analyse the polymerase genes of classical, novel and new variant strains of IBV to obtain further information about the relationships between the different Australian IBVs. Isolation and characterization of new infectious bronchitis virus variants in Hungary cache = ./cache/cord-296167-np0b9a7o.txt txt = ./txt/cord-296167-np0b9a7o.txt === reduce.pl bib === id = cord-299763-ttb7o8lv author = Choi, Jeong-Won title = Molecular characteristics of a novel strain of canine minute virus associated with hepatitis in a dog date = 2016-06-01 pages = extension = .txt mime = text/plain words = 2615 sentences = 128 flesch = 49 summary = Necropsy performed on the dog revealed that the surgeries were not the cause of death; however, degenerative viral hepatitis, showing intranuclear inclusion bodies in hepatic cells, was observed in histopathologic examination. On analyzing the in situ hybridization images, hepatic cells surrounding the damaged regions and intranuclear inclusion bodies were found positive for MVC nucleic acid (Fig. 1) . However, the NP1 region of the 15D009 strain showed greater nucleotide and amino acid sequence similarity to that of the HM-6 strain (AB158475), which was isolated from a Korean dog in 2004 (99.1 % and 99.4 %, respectively), compared to those of the other MVC strains (mean similarities of 90.9-91.4 % and 93.0 %, respectively) ( Table 1 ). A minute virus of canines (MVC: canine bocavirus) isolated from an elderly dog with severe gastroenteritis, and phylogenetic analysis of MVC strains cache = ./cache/cord-299763-ttb7o8lv.txt txt = ./txt/cord-299763-ttb7o8lv.txt === reduce.pl bib === id = cord-291530-ffex7dw9 author = Escutenaire, S. title = Characterization of divergent and atypical canine coronaviruses from Sweden date = 2007-05-29 pages = extension = .txt mime = text/plain words = 2326 sentences = 129 flesch = 57 summary = Field canine coronaviruses (CCVs) identified during a series of outbreaks of gastroenteritis in Swedish dogs were subjected to genetic analysis involving the open reading frame 1b (ORF1b) and the membrane (M) and spike (S) protein genes. Four field viruses originating from the Stockholm region presented identical sequences and segregated separately from other CCVs characterized so far and from GOT/05, the variant recovered in Western Sweden. In the alignment based on 3 0 S gene sequences, the Swedish field viruses displayed higher ranges of nucleotide and amino acid identity with both CCVs and FCoVs of type II (Table 2 ). Comparable or even higher percentages of nucleotide variation were observed between GOT=05 and the same reference strains, thus suggesting that GOT=05 also constitutes a genetically distinct variant among CCVs. In addition, 5 0 S gene sequences related to CCV type I were identified among the SWE1 viruses and UPPS2=04. cache = ./cache/cord-291530-ffex7dw9.txt txt = ./txt/cord-291530-ffex7dw9.txt === reduce.pl bib === id = cord-283710-55m16q7c author = Wo, Ying title = Epidemical features of HAdV-3 and HAdV-7 in pediatric pneumonia in Chongqing, China date = 2014-12-12 pages = extension = .txt mime = text/plain words = 2891 sentences = 145 flesch = 45 summary = Multivariate analysis showed that single infections with HAdV-7 were associated with a higher prevalence of severe pneumonia. There is therefore a need for continuous surveillance, with extensive molecular characterization, to determine the prevalence and genetic characteristics of the circulating HAdVs. The current study was performed to identify the predominant HAdV types associated with pediatric pneumonia and to trace the new genetic variants that might be derived from recombination of different types. However, HAdV infection was associated with more-severe pneumonia and more frequent transfer to the intensive care unit in comparison with HAdV-negative patients (P \ 0.001 and P = 0.027, respectively) ( Table 1) . These findings have the clinical implication that in patients with severe pneumonia, the contribution of HAdV, especially HAdV-7, should be considered with high priority, regardless of whether another respiratory pathogen has been detected. Identification and typing of adenovirus from acute respiratory infections in pediatric patients in Beijing from cache = ./cache/cord-283710-55m16q7c.txt txt = ./txt/cord-283710-55m16q7c.txt === reduce.pl bib === id = cord-295308-ruwxm4fd author = Chen, S.-P. title = Identification of a recombinant dengue virus type 1 with 3 recombination regions in natural populations in Guangdong province, China date = 2008-04-30 pages = extension = .txt mime = text/plain words = 1499 sentences = 78 flesch = 47 summary = title: Identification of a recombinant dengue virus type 1 with 3 recombination regions in natural populations in Guangdong province, China Using recombination analysis, we identified a recombinant dengue virus type 1 strain, namely, GD23/95, with three recombination regions, located within the sequences of the prM/E junction, NS1, and NS3, respectively. This appears to be the first study to confirm the existence of three recombination regions in a single dengue virus isolate and to report recombination between parent virus strains isolated from the same geographic area (Guangdong province, China). Recombination events have been proven to occur in RNA viruses such as polioviruses [3] , feline calicivirus [4] , Western equine encephalitis virus [6] , severe acute respiratory syndrome coronavirus (SARS-CoV) [20, 21, 25] , and hepatitis C virus (HCV) [2, 9, 10, 12, 17] . cache = ./cache/cord-295308-ruwxm4fd.txt txt = ./txt/cord-295308-ruwxm4fd.txt === reduce.pl bib === id = cord-302323-vvo8a4hp author = Wang, Xiaobo title = Immunogenicity and antigenic relationships among spike proteins of porcine epidemic diarrhea virus subtypes G1 and G2 date = 2015-11-26 pages = extension = .txt mime = text/plain words = 4988 sentences = 231 flesch = 53 summary = To determine whether these mutations lead to changes in antigenicity, as suggested by the failure of PEDV vaccines in China, we first optimized the codons of typical S genes of the CV777 vaccine strain (G1 subtype) and LNCT2 strain (G2 subtype) and expressed the recombinant full-length sequence of the S protein in a eukaryotic expression system. The findings of this study confirmed that the recombinant S protein was highly immunogenic in Cross serum neutralization (SN) between the S proteins of the two PEDV subtypes and anti-S PAbs. Reciprocals of PEDV neutralizing antibody titers were expressed as the dilution inhibiting PEDV infection by 50 %, which was calculated as follows: Log50 % neutralizing titer = L-d (s-0.5), where L is the log of the lowest dilution factor, d is the difference between the dilution factors, and s is the sum of the ratios of positive wells Variation between porcine epidemic diarrhea virus subtypes 545 mice and could effectively induce production of antibodies, especially neutralizing antibodies. cache = ./cache/cord-302323-vvo8a4hp.txt txt = ./txt/cord-302323-vvo8a4hp.txt === reduce.pl bib === id = cord-298883-uiwg482s author = Truong, C. title = Identification of an immunorelevant ORF2 epitope from porcine circovirus type 2 as a serological marker for experimental and natural infection date = 2001 pages = extension = .txt mime = text/plain words = 4158 sentences = 216 flesch = 51 summary = Post-weaning multisystemic wasting syndrome (PMWS) is a recently identified disease of pigs linked to the emergence of a new porcine circovirus (PCV2). We report here the characterization of immunorelevant linear B-cell epitopes of the Open Reading Frame 2-encoded protein (Orf2) from PCV2 by an enzyme-linked immunosorbent assay (ELISA) using experimental antisera collected from pigs inoculated with a PCV2 isolate. Antibodies to the 117 to 131 epitope (B-133) were detected in 22% and 100% of specific pathogen-free (SPF) pig sera 6 and 11 weeks post inoculation, respectively. Here, we describe the characterization of an Orf2 peptide as an immunorelevant PCV2 specific linear B-cell epitope by ELISA, using sera from pigs experimentally inoculated with a PCV2 isolate, and its potential use as a serological marker to detect PCV2 antibodies following natural infection in swine herds. cache = ./cache/cord-298883-uiwg482s.txt txt = ./txt/cord-298883-uiwg482s.txt === reduce.pl bib === id = cord-294947-g4ntyddb author = Zhu, Yu title = Establishment of a nanoparticle-assisted RT-PCR assay to distinguish field strains and attenuated strains of porcine epidemic diarrhea virus date = 2016-06-10 pages = extension = .txt mime = text/plain words = 2849 sentences = 154 flesch = 54 summary = title: Establishment of a nanoparticle-assisted RT-PCR assay to distinguish field strains and attenuated strains of porcine epidemic diarrhea virus In this study, a nanoparticle-assisted polymerase chain reaction (nanoparticle-assisted RT-PCR) assay targeting the ORF3 of PEDV was developed to distinguish PEDV field strains from attenuated strains by using a specific pair of primers. The nanoparticle-assisted RT-PCR assay we describe here can be used to distinguish field strains from vaccine strains of PEDV, and it shows promise for reducing economic loss due to PEDV infection. The results showed that the nanoparticle-assisted RT-PCR assay could distinguish PEDV field strains from the attenuated strain in samples from infected pigs. The present study demonstrated that an effective nanoparticle-assisted RT-PCR assay targeting the ORF3 gene of PEDV was able to distinguish field strains from attenuated vaccine strains. Development of a nanoparticle-assisted PCR assay for detection of porcine epidemic diarrhea virus cache = ./cache/cord-294947-g4ntyddb.txt txt = ./txt/cord-294947-g4ntyddb.txt === reduce.pl bib === id = cord-305859-vt8vwo3y author = Jung, Kwonil title = Calves are susceptible to infection with the newly emerged porcine deltacoronavirus, but not with the swine enteric alphacoronavirus, porcine epidemic diarrhea virus date = 2017-04-03 pages = extension = .txt mime = text/plain words = 3232 sentences = 167 flesch = 56 summary = Fecal virus shedding, seroconversion and histopathology were evaluated in 3-7-year-old gnotobiotic calves orally inoculated with porcine deltacoronavirus (PDCoV) (9.0-9.6 log(10) genomic equivalents [GE] of OH-FD22-P5; n=4) or porcine epidemic diarrhea virus (PEDV) (10.2-12.5 log(10) GE of PC21A; n=3). In PDCoV-inoculated calves, an acute but persisting fecal viral RNA shedding and PDCoV-specific serum IgG antibody responses were observed, but without lesions or clinical disease. Our study demonstrated that Gn calves orally inoculated with the PDCoV strain OH-FD22 (ICs of cell-culture grown PDCoV from infected Gn pigs) develop an acute infection with persistent fecal PDCoV RNA shedding and PDCoVspecific serum IgG antibody responses, but show no signs of significant intestinal lesions or clinical disease [8] . In our study, there were no detectable fecal viral RNA shedding, virus-specific serum IgG antibody responses, histological lesions, and clinical disease in Gn calves orally inoculated with the PEDV strain PC21A (ICs of wild-type PEDV-infected Gn pigs) [6] . cache = ./cache/cord-305859-vt8vwo3y.txt txt = ./txt/cord-305859-vt8vwo3y.txt === reduce.pl bib === id = cord-290695-ubrqy2zf author = Payne, H. R. title = Analysis of cell fusion induced by bovine coronavirus infection date = 1988 pages = extension = .txt mime = text/plain words = 2078 sentences = 109 flesch = 50 summary = Polykaryon formation in bovine fetal spleen (BFS) cells infected with bovine coronavirus L9 occurred only in media supplemented with trypsin. Cell fusion and polykaryon formation in cultures infected with bovine coronavirus (BCV) occur late in the virus replication cycle. We analyzed the trypsin-dependent cell fusion of BCV-infected BFS cells and found that the range of pH 7.5 to 8.0 was optimal for polykaryon formation. The cells were inoculated with BCV at a multiplicity of 2 PFU per cell, incubated in MEM containing trypsin (0.4 ug per ml; Sigma Chemical Company) treated with L-l-tosylamide-2-phenylethyl chloromethyl ketone, an inhibitor of chymotrypsin activity. The ability of anti-BCV IgG to affect polykaryon formation at 37 °C was tested by two procedures: (i) Infected cell monolayers were incubated for 6 h in trypsin-free MEM then exposed to MEM that contained antibody freshly diluted with trypsin containing medium. Trypsin treatments of BCV-infected BFS cells during the time of maximal fusion enhancement were effective only with media of pH levels 7.5 to 8.0. cache = ./cache/cord-290695-ubrqy2zf.txt txt = ./txt/cord-290695-ubrqy2zf.txt === reduce.pl bib === id = cord-290546-zu5ns4yq author = Fennestad, K. L. title = Pleural effusion disease in rabbits. Properties of the aetiological agent date = 1983 pages = extension = .txt mime = text/plain words = 3821 sentences = 403 flesch = 83 summary = The size and heat sensitivity of Pleural effusion disease (PED) agent or virus (PEDV) propagated in rabbits were examined. PEDV and the Stockholm agent appeared identical concerning pathogenic and immunogenic properties by infection experiments and protection tests in rabbits. The third isolate, obtained from the laboratory, which several years previously had supplied material for demonstration of the Stockholm agent, differed from PEDV in pathogenic and immunogenic properties. Stock PEDV consisted of pooled rabbit sera obtained 48 hours after subcutaneous inoculation with pleural fluid or infectious serum. Stocks of the Stockholm agent and the three isolates were from the first or second rabbit passage, prepared in the same manner as for PEDV. HCV229E and CV Paris were used as antigens in E L I S A to detect antibody rises to coronaviruses in paired sere from 20 rabbits infected with the 5 isolates. cache = ./cache/cord-290546-zu5ns4yq.txt txt = ./txt/cord-290546-zu5ns4yq.txt === reduce.pl bib === id = cord-302798-q0mbngqy author = Ge, Junwei title = Genomic characterization of circoviruses associated with acute gastroenteritis in minks in northeastern China date = 2018-06-14 pages = extension = .txt mime = text/plain words = 4343 sentences = 273 flesch = 58 summary = In this study, the role of circoviruses (CVs) in mink acute gastroenteritis was investigated, and the MiCV genome was molecularly characterized through sequence analysis. MiCVs and previously characterized CVs shared genome organizational features, including the presence of (i) a potential stem-loop/nonanucleotide motif that is considered to be the origin of virus DNA replication; (ii) two major inversely arranged open reading frames encoding putative replication-associated proteins (Rep) and a capsid protein; (iii) direct and inverse repeated sequences within the putative 5ʹ region; and (iv) motifs in Rep. Pairwise comparisons showed that the capsid proteins of MiCV shared the highest amino acid sequence identity with those of porcine CV (PCV) 2 (45.4%) and bat CV (BatCV) 1 (45.4%). In our study, sequence analysis confirmed that MiCV genomes displayed the characteristics of members of the genus Circovirus, and the common features included their genome organization, the presence of a potential stem-loop and conserved nonanucleotide motif postulated to be the origin of viral DNA replication, and major ORFs and repeats [26, 27] . cache = ./cache/cord-302798-q0mbngqy.txt txt = ./txt/cord-302798-q0mbngqy.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-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-311773-r9c7sx6r author = Gaertner, Diane J. title = Susceptibility of rodent cell lines to rat coronaviruses and differential enhancement by trypsin or DEAE-dextran date = 1991 pages = extension = .txt mime = text/plain words = 2675 sentences = 150 flesch = 57 summary = Cell lines of rodent origin were tested for susceptibility to infection with rat coronavirus (RCV), including sialodacryoadenitis virus (SDAV) and Parker's rat coronavirus (PRCV). In a single attempt to isolate SDAV-681 from the lung of an experimentally infected rat, syncytia and viral antigen were first seen after 6 passages in untreated L2 (Percy) cells. Based on this finding, a small study was initiated to ascertain the sensitivity of trypsin-treated L2 (Percy) cells for primary isolation of RCVs. Virus isolations were attempted using tissue homogenates previously tested for SDAV-681 by infant mouse inoculation (Table 4 ). Of the cell lines and treatments tested, L2 (Percy) cells treated with trypsin supported maximal growth of RCVs as evidenced by syncytium formation and viral antigen. RCV growth in L2 (Percy) cells was not enhanced by trypsin treatment of later passages when the enzyme was added at the time of virus inoculation. cache = ./cache/cord-311773-r9c7sx6r.txt txt = ./txt/cord-311773-r9c7sx6r.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-290819-zhywlf6r author = Wu, Jiaqi title = The antiviral protein viperin interacts with the viral N protein to inhibit proliferation of porcine epidemic diarrhea virus date = 2020-07-27 pages = extension = .txt mime = text/plain words = 4550 sentences = 249 flesch = 44 summary = title: The antiviral protein viperin interacts with the viral N protein to inhibit proliferation of porcine epidemic diarrhea virus In the early stage of virus infection, the pattern recognition receptor (PRR) signaling pathway of the host cell is activated to induce interferon production, activating interferon-stimulated genes (ISGs) that encode antiviral proteins that exert antiviral effects. Increased expression of interferon and viperin and decreased replication of PEDV with a clear reduction in the viral load were observed in PEDV-infected IPEC-J2 cells. After virus infection, pattern recognition receptors recognize released viral nucleic acids and activate downstream signaling pathways to promote the production of specific transcription factors and type I interferons [25] . These results indicate that PEDV infection upregulates the expression of interferon and viperin in IPEC-J2 cells. This study showed that the expression of type I interferon increases and that of viperin is also upregulated in IPEC-J2 cells infected with PEDV. cache = ./cache/cord-290819-zhywlf6r.txt txt = ./txt/cord-290819-zhywlf6r.txt === reduce.pl bib === id = cord-308950-bl83r4v3 author = Miguel, B. title = The role of feline aminopeptidase N as a receptor for infectious bronchitis virus : Brief Review date = 2002 pages = extension = .txt mime = text/plain words = 2543 sentences = 157 flesch = 56 summary = Our objective was to determine if fAPN can serve as a receptor for infectious bronchitis virus (IBV). Feline kidney cells that express fAPN and hamster kidney fibroblasts that do not express fAPN were inoculated with IBV and monitored for replication by indirect fluorescent assay and confocal microscopy and in chicken embryonated eggs. To evaluate the permissiveness of cells to IBV, monolayers of transfected (pBK-fAPN and pBK-CMV) BHK-21, non-transfected BHK-21 and FEK on coverslips were infected with a 10 3.2 EID 50 of Ark/IBV virus. To test the hypothesis that the feline APN had a role in permissiveness of FEK cells to Ark/IBV, BHK-21 cells were transfected with pBK-CMV plasmid or pBK-fAPN. The BHK-21 cells transfected with pBK-fAPN were shown to express the fAPN receptor on the cell surface (Fig. 3) , and were permissive to Ark/IBV (Figs. cache = ./cache/cord-308950-bl83r4v3.txt txt = ./txt/cord-308950-bl83r4v3.txt === reduce.pl bib === id = cord-294138-h7sfd1wa author = McIver, David J. title = Coronavirus surveillance of wildlife in the Lao People’s Democratic Republic detects viral RNA in rodents date = 2020-06-01 pages = extension = .txt mime = text/plain words = 2780 sentences = 130 flesch = 56 summary = Both countries were involved in the United States Agency for International Development's (USAID) Emerging Pandemic Threats PREDICT program, and surveillance of bats in wildlife markets in rural areas in Laos using family-level PCR assays revealed the presence of CoV RNA in 41 animals [5] . Considering the significant interactions of wildlife and especially rodents with humans in Laos, we were interested in investigating the presence of CoVs in these animals, which can be primary or intermediate hosts for CoVs with zoonotic potential. Since there are abundant contact opportunities for wildlife pathogens and humans in Laos, and considering that coronavirus-zoonotic events can involve intermediate hosts, as in the cases of SARS and MERS, we focused our screening on non-bat species potentially capable of playing that role. It is worth noting that we targeted rodents most likely to be in contact with humans and transmit virus and found fewer CoV-RNA-positive animals than in other studies of rodents in the region or elsewhere. cache = ./cache/cord-294138-h7sfd1wa.txt txt = ./txt/cord-294138-h7sfd1wa.txt === reduce.pl bib === id = cord-299345-2i48ld8d author = Nefedeva, Mariia title = Molecular characteristics of a novel recombinant of porcine epidemic diarrhea virus date = 2019-02-06 pages = extension = .txt mime = text/plain words = 1535 sentences = 114 flesch = 49 summary = Pairwise identity analysis of the whole genome sequences revealed that PEDV/Belgorod/dom/2008 is an intermediate between PEDV and transmissible gastroenteritis virus (TGEV) strains. Based on the phylogenetic analysis of the M gene, the PEDV/Belgorod/ dom/2008 isolate belongs to the same clade as other virulent Russian PEDV strains, indicating a high degree of sequence homogeneity in the M gene (Fig. 3a) isolate is genetically distinct and does not belong to any group (Fig. 3b ). The identification of recombinant regions in PEDV/Belgorod/dom/2008 can be useful for further analysis of evolutionary variability, epidemiology, and development of a new diagnostic gene-based assay for porcine epidemic diarrhea virus. Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China cache = ./cache/cord-299345-2i48ld8d.txt txt = ./txt/cord-299345-2i48ld8d.txt === reduce.pl bib === id = cord-304109-yirs7kjg author = Mueller, Andreas title = Polyomaviruses KI and WU in children with respiratory tract infection date = 2009-09-12 pages = extension = .txt mime = text/plain words = 1935 sentences = 109 flesch = 54 summary = The polyomaviruses KI (KIPyV) and WU (WUPyV) have recently been discovered in specimens from patients with respiratory tract infections. Nasopharyngeal aspirates or bronchoalveolar lavage specimens of 229 children with acute respiratory tract infection were screened for KIPyV and WUPyV using polymerase chain reaction-based methods. Since 2001, an increasing number of ''new'' respiratory viruses have been detected in children with respiratory tract infection (RTI), including the human metapneumovirus (hMPV) and the human bocavirus (hBoV) [4, 15] . The authors amplified and cloned the genome of WU Polyomavirus (WUPyV) from NPA of a 3-year-old patient with pneumonia without detection of other respiratory pathogens. The very low prevalence of polyomavirus KI and WU DNA in NPA specimens of 3 out of 229 pediatric patients with acute RTI in this series does not confirm or exclude a pathogenic role of these newly described viruses. Presence of the newly discovered human polyomaviruses KI and WU in Australian patients with acute respiratory tract infection cache = ./cache/cord-304109-yirs7kjg.txt txt = ./txt/cord-304109-yirs7kjg.txt === reduce.pl bib === id = cord-312338-r6jqmes3 author = Althani, Asma title = Characterisation of winter respiratory viral infections in patients with asthma and COPD in Qatar date = 2012-12-14 pages = extension = .txt mime = text/plain words = 2420 sentences = 140 flesch = 53 summary = This study aimed to identify the most common viral strains responsible for respiratory tract infections in asthma/COPD patients (without exacerbations) in Qatar during the winter season (2008) (2009) . This study aimed to identify the most common viral strains responsible for respiratory tract infections in asthma/COPD patients (without exacerbations) in Qatar during the winter season (2008) (2009) . carried out a study in the UK to investigate the role of viral infections in acute exacerbations of asthma in schoolchildren, and they reported that the most commonly identified virus type in this population was rhinovirus [3] . During October 2008-March 2009, adults with COPD or asthma, seeking care at the Chest clinic of the Hamad Medical Corporation, Qatar, with symptoms of upper respiratory tract infection were eligible for participation. Our study is the first in Qatar to analyse the clinical aetiology of respiratory tract viral infections in adult patients from all age groups with asthma or COPD. cache = ./cache/cord-312338-r6jqmes3.txt txt = ./txt/cord-312338-r6jqmes3.txt === reduce.pl bib === id = cord-306380-msk9p1yy author = Lee, C.-W. title = Evidence of genetic diversity generated by recombination among avian coronavirus IBV date = 2000 pages = extension = .txt mime = text/plain words = 2796 sentences = 146 flesch = 58 summary = Phylogenetic analysis of selected regions of the genome of the DE072 serotype field isolates further support those results and indicate that isolates within the same serotype may have different amounts of nucleotide sequence similarity with each other in individual genes other than the S gene. Further, we conducted sequence analysis of six isolates of the DE072 serotype in order to determine if recombination is frequently occurring in this region in field isolates of IBV. We conducted phylogenetic analysis by dividing 3.8 kb of the 3 end of the genome among five IBV strains at the IG sequences. However, these 6 isolates had a much different level of nucleotide sequence similarity with each other in gene 3 and gene 4, and clustered randomly with other serotypes of IBV (Fig. 3) . Sequence analysis of gene 3, gene 4 and gene 5 of avian infectious bronchitis virus strain CU-T2 Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus cache = ./cache/cord-306380-msk9p1yy.txt txt = ./txt/cord-306380-msk9p1yy.txt === reduce.pl bib === id = cord-302063-ct5rvqtd author = Mohamed, Fakry F. title = Molecular detection of enteric viruses from diarrheic calves in Egypt date = 2016-09-29 pages = extension = .txt mime = text/plain words = 3198 sentences = 227 flesch = 60 summary = RNA was extracted and tested by reverse transcription polymerase chain reaction (RT-PCR) for the presence of rotavirus, norovirus, astrovirus, torovirus, coronavirus and bovine viral diarrhea virus. Bovine rotavirus and bovine coronavirus (BRV and BCV) are the leading causes of viral diarrhea [2] , although bovine viral diarrhea virus (BVDV), bovine norovirus (BNoV), bovine astrovirus (BAstV) and bovine torovirus (BToV) have also been implicated. The phylogenetic analysis of the BRV-VP7 coding sequences revealed that they clustered with the G6 and G10 genotypes of group A rotaviruses (http://rotac.regatools.be/) [19] (Fig. 2) . One of the study sequences (BNoV-4) grouped differently from the remaining sequences, with 87.5 % and 96.7 % nt and aa identity, respectively, and showed maximum identity to isolates from Italy (BEC195), the UK (Aberystwyth24) and Belgium (Florennes-B242). BNoV was molecularly detected (24 %) either alone or as a co-infection with other enteric viruses (BRV and BAstV). cache = ./cache/cord-302063-ct5rvqtd.txt txt = ./txt/cord-302063-ct5rvqtd.txt === reduce.pl bib === id = cord-307408-6wfx0wey author = Li, Renfeng title = Phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in central China based on the ORF3 gene and the main neutralization epitopes date = 2013-11-30 pages = extension = .txt mime = text/plain words = 3224 sentences = 159 flesch = 58 summary = title: Phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in central China based on the ORF3 gene and the main neutralization epitopes In this study, we aimed to investigate the molecular epidemiology and antigenic variability of PEDV field strains based on analysis of ORF3 and a portion of the S gene encoding three neutralizing epitopes (aa 499-638, 748-755, and 764-771) of the S protein. To further investigate the molecular epidemiology of this virus, we chose the ORF3 gene and a partial S gene encoding a region including three neutralization epitopes for studying the evolutionary characteristic and antigenic variation of PEDV. Based on the sequence analysis of ORF3 and partial S genes of PEDV, molecular epidemiology was conducted using 14 field strains from central China. Sequence and phylogenetic analysis of nucleocapsid genes of porcine epidemic diarrhea virus (PEDV) strains in China cache = ./cache/cord-307408-6wfx0wey.txt txt = ./txt/cord-307408-6wfx0wey.txt === reduce.pl bib === id = cord-309145-6aqc074e author = Ito, Y. title = Induction of interferon by virus glycoprotein(s) in lymphoid cells through interaction with the cellular receptors via lectin-like action: An alternative interferon induction mechanism date = 1994 pages = extension = .txt mime = text/plain words = 4391 sentences = 210 flesch = 36 summary = The interferon induction system, in which attachment of virus glycoprotein to the cellular receptor on the cell surface triggers interferon induction in lymphoid cells, is similar to a system in which plant lectins such as concanavalin A (Con-A) and phytohemagglutinin (PHA) stimulate lymphocytes and consequently induce interferon. For example, sialyl-oligosaccharides are receptors for parainfluenza and influenza viruses [62] , human membrane cofactor protein (CD46) for measles virus [13, 58] , MHC class I for Semliki Forest virus (SFV) [24] , MHC class II for lactose dehydrogenase virus (LDH virus) [26] , phosphatidylserine and phosphatidylinositol for vesicular stomatitis virus (VSV) [51] , the CD4 for human immunodeficiency virus (HIV) [11, 43] , the C3d receptor CR2 for Epstein-Barr virus [15, 59, 69] , acetylcholin receptor for rabies virus [47] , the intercellular adhesion molecule-1 (ICAM-1) for the major subgroup of human rhinoviruses [23, 67, 69] , another member of the immunoglobulin superfamily for poliovirus [45, 54-1, a basic amino acid transporter for gibbon ape leukemia virus and feline leukemia virus [1, 40, 68, 70, 71] , aminopeptidase N [13, 75-1 or a member of the carcinoembryonic antigen family of proteins for the coronavirus virus [14] , a high-affinity laminin receptor for sindbis virus [72] , ~2 subunit of human VLA-2 for echoviruses 1 and 8 [5] , erythrocyte P antigen for B19 Parvovirus Viral glycoproteins and interferon induction 193 [6] , and CD13 (human aminopeptidase N) for cytomegalovirus [66] . cache = ./cache/cord-309145-6aqc074e.txt txt = ./txt/cord-309145-6aqc074e.txt === reduce.pl bib === id = cord-315811-wpeac0lk author = Hu, Hui title = Experimental infection of gnotobiotic pigs with the cell-culture-adapted porcine deltacoronavirus strain OH-FD22 date = 2016-09-12 pages = extension = .txt mime = text/plain words = 6500 sentences = 365 flesch = 62 summary = The aims of our current study were to investigate i) the pathogenicity of the tissue-culture-grown PDCoV (TC-PDCoV) strain OH-FD22 at passage 5 (P5), P20, and P40 on LLC-PK cells in 14-day-old Gn pigs compared with that of the wild-type parent virus [12] ; ii) Fecal PDCoV shedding, viremia, and pathology tested at post-inoculation day (PID) 1 to 23-24 or PID 28; iii) possible attenuation of TC-PDCoV OH-FD22 P40, the highest passage in cell culture among the passages tested; iv) serum-PDCoV-specific IgG and IgA and virus neutralization (VN) antibody titers and any differences in the titers among OH-FD22 P5, P20, and P40-inoculated pigs; and v) the genetic stability of TC-and Gn-pig-passaged PDCoV OH-FD22 P5, P20, and P40 by analysis of the complete spike (S) and nucleocapsid (N) gene sequences. Regardless of the cell culture passage number of the virus strains used, serum virus neutralization (VN) antibodies were first detected in all of the original and TC-PDCoV OH-FD22-inoculated pigs at PID 7 (64-256), and thereafter, the titers increased gradually and peaked at PID 23/24. cache = ./cache/cord-315811-wpeac0lk.txt txt = ./txt/cord-315811-wpeac0lk.txt === reduce.pl bib === id = cord-310669-6hwq5jfv author = Erles, K. title = Investigation into the causes of canine infectious respiratory disease: antibody responses to canine respiratory coronavirus and canine herpesvirus in two kennelled dog populations date = 2005-04-21 pages = extension = .txt mime = text/plain words = 4104 sentences = 205 flesch = 60 summary = Two training centres for working dogs were monitored for one year to determine the presence of viruses and viral antibodies and their association with canine infectious respiratory disease (CIRD). Canine herpesvirus (CHV) has been detected in dogs with CIRD [3] the importance of this infection in the pathogenesis of the disease however has not yet been determined. From dogs that were not on the study but showed clinical symptoms of CIRD, both a blood sample and a swab were taken at the time of disease as well as four weeks after. In total twelve out of 54 serum samples (22.2%) obtained from dogs on the day they entered Kennel A were positive for antibodies to CRCoV. None of the samples obtained from dogs at Kennel B tested by PCR for CRCoV (n = 28), CPIV (n = 18), CAV (n = 9) or CHV (n = 26) were found positive. cache = ./cache/cord-310669-6hwq5jfv.txt txt = ./txt/cord-310669-6hwq5jfv.txt === reduce.pl bib === id = cord-307098-oq7zrnuv author = Taguchi, F. title = Difference in Bgp-independent fusion activity among mouse hepatitis viruses date = 2014-05-20 pages = extension = .txt mime = text/plain words = 2676 sentences = 143 flesch = 55 summary = Co-cultivation of MHV-nonpermissive hamster BHK cells devoid of mouse Bgp with mouse DBT cells infected with MHV-A59 or JHMV induces syncytia formation on BHK cells (Bgp-independent fusion). Under a phase contrast microscopy, JHMV (cl-2, sp-4) induced the Bgp-independent syncytia on BHK cells similar to those observed on DBT cells, while such syncytia were not seen with the infection of other MHV strains (MHV-1, MHV-3, MHV-A59, MHV-S, srr7, srr11 and srr18). Interestingly, no syncytia formation was demonstrated on BHK cells with other strains or srr mutants under the phase contrast microscopy, though all of them produced syncytia on Bgp-positive DBT cells [10] . The cl-2 S protein could have a very strong Bgp-independent fusion activity, but its replication in BHK cells could be less efficient than the other MHV strains. Present study showed that JHMV (cl-2 and sp-4) could induce syncytia on BHK cells detectable by microscopy, whereas the other MHVs and srr mutants failed. cache = ./cache/cord-307098-oq7zrnuv.txt txt = ./txt/cord-307098-oq7zrnuv.txt === reduce.pl bib === id = cord-299428-gon6bzat author = Mondal, Shankar title = Sequence analysis of infectious bronchitis virus isolates from the 1960s in the United States date = 2012-10-11 pages = extension = .txt mime = text/plain words = 3262 sentences = 152 flesch = 56 summary = To better understand the molecular epidemiology of infectious bronchitis virus (IBV) in the United States following the introduction of commercial IBV vaccines, we sequenced the S1 and N structural protein genes of thirteen IBV field isolates collected in the 1960s. Analysis of the S1 sequence showed that seven isolates were of the Massachusetts (Mass) genotype, five were SE17, and one was of the Connecticut (Conn) genotype, suggesting that these three IBVs were circulating in commercial poultry raised in different regions in the United States during the 1960s. In addition, the Mass-type isolates had high levels of sequence identity in the S1 gene compared with widely used modified live vaccines (Mass41, Ma5 and H120) and modern field strains from the USA and other countries, suggesting a common ancestor. cache = ./cache/cord-299428-gon6bzat.txt txt = ./txt/cord-299428-gon6bzat.txt === reduce.pl bib === id = cord-316153-wet0go35 author = Jia, W. title = A novel variant of avian infectious bronchitis virus resulting from recombination among three different strains date = 1995 pages = extension = .txt mime = text/plain words = 3917 sentences = 232 flesch = 61 summary = An antigenic variant of avian infectious bronchitis virus (IBV), a coronavirus, was isolated and characterized. Therefore, several recently reported diagnostic and serotyping methods of IBV which are based on dot-blot hybridization, restriction fragment length polymorphism (RFLP), and polymerase chain reaction (PCR), may not reveal the true antigenic and/or genetic nature of IBV isolates, and may in fact yield misleading information. More recently, two American field isolates were found to contain fragments of Mass-like sequences in the S1 gene, which were 94% to 95% homologous to IBV strain Mass41 [38] . Sequence data were obtained from cDNA clones, except for the first 1100 bases of the S gene, the last 200 bases of the N gene, the 3' end non-coding region of CU-T2, and the partial Gene3 of Ark99 and Ho1152, which were obtained from direct sequencing of IBV genomic RNA. Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus cache = ./cache/cord-316153-wet0go35.txt txt = ./txt/cord-316153-wet0go35.txt === reduce.pl bib === id = cord-307378-cx1jz7wf author = Dadar, Maryam title = The association between the incidence of COVID-19 and the distance from the virus epicenter in Iran date = 2020-09-02 pages = extension = .txt mime = text/plain words = 2337 sentences = 112 flesch = 49 summary = Since the first official report of the spread of SARS-CoV-2 infections in the city of Qom in mid-February, Iran has become the country most affected by the COVID-19 epidemic in the Middle East. The aim of the present study was to evaluate whether the distance from the epicenter of the infection (Qom) or demographic factors such as population density and the ratio of the elderly population are associated with the incidence of COVID-19 in different Iranian provinces. Through regression analysis, this study aimed to evaluate whether the distance of different Iranian provinces from the epicenter of the infection (Qom) was associated with the incidence of COVID-19 at the early stages of the epidemic in Iran. COVID-19 has spread to all 31 Iranian provinces, and the city of Tehran, the densely populated capital with over 13 million people located 150 km northeast of Qom, leads the country in COVID-19 cases ( Table 1) . cache = ./cache/cord-307378-cx1jz7wf.txt txt = ./txt/cord-307378-cx1jz7wf.txt === reduce.pl bib === id = cord-317009-8tqnt1l9 author = Aita, Tsunehiko title = Characterization of epidemic diarrhea outbreaks associated with bovine torovirus in adult cows date = 2011-12-14 pages = extension = .txt mime = text/plain words = 3922 sentences = 191 flesch = 57 summary = However, other viruses, including bovine torovirus (BToV), are also suspected to be etiologic agents of diarrhea [14, 15, 21] , although the epidemiological situation of infections caused by these viruses in adult cattle remains unclear. In the present study, we report the epidemiological features of three outbreaks of epidemic diarrhea in adult cows between May 2007 and February 2008 at three dairy farms in Niigata Prefecture, Japan, in which BToV was detected as the only pathogen. Further, we describe the isolation of a cytopathogenic BToV strain from diarrheic feces using HRT-18 cells, as well as the molecular characterization of the detected BToVs. Three epidemic outbreaks of adult cattle diarrhea occurred between May 2007 and February 2008 in Niigata Prefecture, Japan. Here, we examined the etiological agents and conducted detailed serological tests with samples from three outbreaks of adult cattle diarrhea in Niigata, Japan, and found that BToV was the only causative pathogen. cache = ./cache/cord-317009-8tqnt1l9.txt txt = ./txt/cord-317009-8tqnt1l9.txt === reduce.pl bib === id = cord-324377-br2uorg8 author = Zhou, Pei title = Antiviral effect of lithium chloride on infection of cells by canine parvovirus date = 2015-08-28 pages = extension = .txt mime = text/plain words = 2930 sentences = 164 flesch = 58 summary = We determined the antiviral effect of Lithium Chloride on canine parvovirus type 2 in feline kidney cells. These results indicated that lithium chloride could be a potential antiviral drug for curing dogs with canine parvovirus infection. The specific steps of canine parvovirus entry into cells that are affected by lithium chloride and its antiviral effect in vivo should be explored in future studies. As a control, cells infected with the same dose of CPV were not treated with LiCl. Subsequently, the antiviral efficacy was evaluated by analysis of viral RNA levels, protein expression level and CPE. These results indicate that treatment of F81 cells with LiCl inhibits CPV infection and reduces the cytopathic effect in a dose-dependent manner. No significant differences in the relative levels of viral VP2 gene DNA or viral titers were observed between drug-treated and mocktreated cells, indicating that LiCl had no effect on CPV attachment and replication in F81 cells ( Fig. 4A and B) . cache = ./cache/cord-324377-br2uorg8.txt txt = ./txt/cord-324377-br2uorg8.txt === reduce.pl bib === id = cord-306725-0vam15pt author = Li, Hao title = First detection and genomic characteristics of bovine torovirus in dairy calves in China date = 2020-05-09 pages = extension = .txt mime = text/plain words = 3015 sentences = 156 flesch = 58 summary = Sequence analysis showed that the two isolates shared 10 identical amino acid mutations in the S protein compared to the complete S sequences of BToV available in the GenBank database. A phylogenetic analysis based on the complete amino acid sequence of the S protein showed that the BToVs could be separated into four groups (Fig. 2) , designated tentatively as group 1 to group 4. The bovine torovirus strains BToV/SC-1/China and BToV /SC-2/China investigated in this study are indicated by black triangles Fig. 2 Phylogenetic tree based on the deduced 1586-aa sequence of the complete S gene. Moreover, the two Chinese strains shared identical unique amino acid changes in the S and HE genes when compared to the other strains with sequences available in the GenBank database, indicating the unique evolution in Chinese BToV strains. Moreover, two complete BToV genome sequences were obtained from the clinical samples, and these two BToV isolates had unique amino acid changes in the S and HE proteins. cache = ./cache/cord-306725-0vam15pt.txt txt = ./txt/cord-306725-0vam15pt.txt === reduce.pl bib === id = cord-321471-gev5xq3a author = Zhu, Liqian title = Control of the PI3K/Akt pathway by porcine reproductive and respiratory syndrome virus date = 2013-02-05 pages = extension = .txt mime = text/plain words = 3759 sentences = 181 flesch = 50 summary = The activation of PI3K-Akt pathway promotes cell survival by the phosphorylation of numerous substrates such as glycogen synthase kinase-3 (GSK-3), FoxO1, Bad and mTOR [5, 11, 24, 36, 38] . Previous studies have shown that during PRRSV infection of porcine monocyte-derived dendritic cells (Mo-DCs), the PI3K/Akt pathway is activated at 90 min and 4 h postinfection (h p.i.), and it is inhibited at 12 h p.i. A number of studies have shown that the PI3K/Akt signaling pathway is functionally dependent on downstream substrates of Akt such as FoxO1, Bad and mTOR for regulation of cell survival [3, 11, 15, 25] . Since increased phosphorylation of Akt induced by HP-PRRSV was observed at 5 min and 15 min postinfection in virus-infected MARC-145 cells, and at 5, 15 and 30 min postinfection in PAMs, we hypothesized that the virus entry process accounted for this early-stage activation. cache = ./cache/cord-321471-gev5xq3a.txt txt = ./txt/cord-321471-gev5xq3a.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-328381-bfvdhai8 author = Hattermann, K. title = Susceptibility of different eukaryotic cell lines to SARS-coronavirus date = 2005-01-13 pages = extension = .txt mime = text/plain words = 1829 sentences = 103 flesch = 60 summary = In all susceptible cell lines mRNA of the Angiotensin-converting enzyme 2 (ACE2), the functional receptor for SARS-CoV infection, could be detected by RT-PCR. In contrast, 50% of the Huh-7 cells were positive for viral antigen not until 31 h after infection ( The quantification of SARS-CoV RNA by quantitative real-time PCR revealed a significant increase of intracellular viral RNA in Vero E6, Huh-7, POEK, (Fig. 1/I A-C) and PS cells (data not shown). An increase of SARS-CoV RNA was detected in the supernatant of infected Vero E6, Huh-7, POEK ( Fig. 1/I A-C) and PS cells (data not shown). As expected, the investigation of all SARS-CoV susceptible cell lines (Vero E6, Huh-7, POEK and PS) for mRNA of ACE2 was positive in all cases though we failed to detect ACE2 expression by IFA, Western Blot and FACS analysis using commercially available monoclonal and polyclonal antibodies (ALPHA DIAGNOSTICS, San Antonio, USA) against human ACE2 (data not shown). cache = ./cache/cord-328381-bfvdhai8.txt txt = ./txt/cord-328381-bfvdhai8.txt === reduce.pl bib === id = cord-312787-j7ye7ed5 author = Loemba, H. D. title = Kinetics of humoral immune response to the major structural proteins of the porcine reproductive and respiratory syndrome virus date = 1996 pages = extension = .txt mime = text/plain words = 3411 sentences = 149 flesch = 41 summary = coli-expressed ORFs 5 to 7 gene products, suggested that antibodies directed against the envelope E protein appear by day 7 p.i., whereas antibodies directed against the nucleocapsid N and membrane M proteins can only be detected by the end of the second week p.i. No correlation could be demonstrated between VN and IIF antibody titers, viremia, and viral protein specificities of circulating antibodies at various times p.i. Summary. coli-expressed ORFs 5 to 7 gene products, suggested that antibodies directed against the envelope E protein appear by day 7 p.i., whereas antibodies directed against the nucleocapsid N and membrane M proteins can only be detected by the end of the second week p.i. No correlation could be demonstrated between VN and IIF antibody titers, viremia, and viral protein specificities of circulating antibodies at various times p.i. The porcine reproductive and respiratory syndrome virus (PRRSV) is an enveloped RNA virus which has been found to be responsible for reproductive failure in sows of any parities (late-term abortions, increased numbers of stillborn, mummified and weakborn pigs) and respiratory problems affecting pigs of all ages [8, 20] . cache = ./cache/cord-312787-j7ye7ed5.txt txt = ./txt/cord-312787-j7ye7ed5.txt === reduce.pl bib === id = cord-314751-i9rxesrg author = Oh, Jongsuk title = Immunogenicity and protective efficacy of recombinant S1 domain of the porcine epidemic diarrhea virus spike protein date = 2014-07-10 pages = extension = .txt mime = text/plain words = 6006 sentences = 242 flesch = 44 summary = In this study, a codon-optimized PEDV S1 gene containing amino acid residues 25–738 was synthesized based on a multiple alignment of the S amino acid sequences of PEDV field isolates and used to establish a stable porcine cell line constitutively expressing the PEDV S1 protein. In the present study, therefore, we first synthesized a full-length, codon-optimized PEDV S1 gene and then generated a stable porcine-origin cell line constitutively expressing the recombinant S1 protein. These results were coincident with the rabbit study described above, since the rabbit antisera generated by immunization with the recombinant S1 protein also contained low levels of neutralizing antibodies to the heterologous PEDV vaccine strain. In the present study, the first aim was to stably express the full-length, codon-optimized S1 gene of PEDV in porcine-origin cells and to evaluate the immunogenicity and efficacy of the recombinant S1 protein. cache = ./cache/cord-314751-i9rxesrg.txt txt = ./txt/cord-314751-i9rxesrg.txt === reduce.pl bib === id = cord-322593-bgm6smuo author = Li, Lan title = Antiviral activity of recombinant porcine surfactant protein A against porcine reproductive and respiratory syndrome virus in vitro date = 2016-04-21 pages = extension = .txt mime = text/plain words = 4702 sentences = 235 flesch = 54 summary = In this present study, we assessed the antiviral properties of recombinant porcine SP-A (RpSP-A) on PRRSV infection in Marc 145 cells and revealed its antiviral mechanism using a plaque assay, real-time qPCR, western blotting analysis and an attachment and penetration assay. Our results showed that RpSP-A could inhibit the infectivity of PRRSV in Marc 145 cells and could reduce the total RNA and protein level. Notably, porcine ficolin is also a collagenous lectin that was established to reduce PRRSV infection in Marc-145 cells in neutralization assays and to inhibit the replication of infectious viral particles in a GlcNAc-dependent manner [30] . Porcine reproductive and respiratory syndrome virus-infected alveolar macrophages contain no detectable levels of viral proteins in their plasma membrane and are protected against antibody-dependent, complement-mediated cell lysis Recombinant porcine lung surfactant protein A inhibits porcine reproductive and respiratory syndrome virus infection into host cells in vitro cache = ./cache/cord-322593-bgm6smuo.txt txt = ./txt/cord-322593-bgm6smuo.txt === reduce.pl bib === === reduce.pl bib === id = cord-314069-8dxzf2ip author = Dongliu, Yuan title = Outbreak of acute febrile respiratory illness caused by human adenovirus B P14H11F14 in a military training camp in Shandong China date = 2016-06-28 pages = extension = .txt mime = text/plain words = 4283 sentences = 206 flesch = 51 summary = authors: Dongliu, Yuan; Guoliang, Yang; Haocheng, Xu; Shuaijia, Qing; Li, Bing; Yanglei, Jia This study reports an outbreak of acute febrile respiratory illness caused by human adenovirus B [P14H11F14] in a military training center in China between May and June 2014. A HAdV-B [P14H11F14] virus was confirmed as the etiological pathogen of this acute outbreak of febrile respiratory illness based on clinical manifestations, epidemiological characteristics, specific molecular detection results, phylogenetic analysis, and serological assays. In conclusion, the regional CDC officials concluded that a type-55-like human adenovirus B human/CHN/SD77001/ 2014/[P14H11F14] virus was the etiological pathogen responsible for this acute FRI outbreak based on the clinical manifestations in the patients, the epidemiological characteristics of the outbreak, the HAdV-DNA-specific PCR results, isolation of the virus, sequencing and alignment of the PCR amplicons, homology and phylogenetic analyses based on the complete E1A, penton base, hexon, and fiber gene sequences, and serological assays specific for HAdV IgA/IgG. cache = ./cache/cord-314069-8dxzf2ip.txt txt = ./txt/cord-314069-8dxzf2ip.txt === reduce.pl bib === === reduce.pl bib === id = cord-317617-snrumw3x author = Sugiyama, K. title = Morphological and biological properties of a new coronavirus associated with diarrhea in infant mice date = 1981 pages = extension = .txt mime = text/plain words = 2707 sentences = 252 flesch = 74 summary = Recently, a new viral agent (DVIM) was isolated from an infant mouse with diarrhea, by the utilization of cultured cells. It has also been shown by complement fixation tests that this new isolate is antigenically related to known coronaviruses, avian infectious bronchitis virus (IBV) and mouse hepatitis virus strain-2 (MHV-2). A virus isolated from t h e intestine of a n i n f a n t mouse w i t h clinical signs of diarrhea, d e s i g n a t e d DVIM, was generously p r o v i d e d b y Dr. K o z a b u r o Sato (Central L a b o r a t o r y of Shionogi P h a r m . Mouse hepatitis virus (MHV), a member of coronaviruses, has been described as a common cause of enteric infection in baby mice (8, 21) . Lethal enteritis in infant mice caused by mouse hepatitis virus New strain of mouse hepatitis virus as the cause of lethal enteritis in infant mice cache = ./cache/cord-317617-snrumw3x.txt txt = ./txt/cord-317617-snrumw3x.txt === reduce.pl bib === id = cord-316525-uadfehr6 author = Zhang, X. W. title = Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus date = 2004-10-11 pages = extension = .txt mime = text/plain words = 3023 sentences = 152 flesch = 52 summary = Surprisingly, we found that 7 putative recombination regions, located in Replicase 1ab and Spike protein, exist between SARS-CoV and other 6 coronaviruses: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), human coronavirus 229E (HCoV), murine hepatitis virus (MHV), and avian infectious bronchitis virus (IBV). After potential recombination events were identified by at least 3 methods above, separate neighbor joining trees were constructed for each putative recombination region to better evaluate the evidence for conflicting evolutionary histories of different sequence regions. Two regions (13151-13299 and 16051-16449, position in alignment) are identified as putative recombination regions and all 6 coronaviruses are potential parents with SARS-CoV as potential daughter. In this study, seven recombination detection methods and phylogenetic analyses were performed on SARS-CoV and the six coronaviruses identified by BLAST (IBV, BCoV, HCoV, MHV, PEDV and TGEV). cache = ./cache/cord-316525-uadfehr6.txt txt = ./txt/cord-316525-uadfehr6.txt === reduce.pl bib === id = cord-333403-imx3990a author = Christianson, K. K. title = Characterization of a temperature sensitive feline infectious peritonitis coronavirus date = 1989 pages = extension = .txt mime = text/plain words = 4008 sentences = 223 flesch = 56 summary = The characteristics of a temperature sensitive feline infectious peritonitis virus (TS-FIPV) were examined. Viral structural proteins and RNA were synthesized at 39 °C but some undefined maturational defect prevented the formation of infectious TS-FIPV at its nonpermissive temperature. TS-FIPV proteins in supernatants from cells infected at 31 °C and 39 °C were examined by Western blot. Immune sera from both TS-FIPV vaccinated cats and WT-FIPV challenged cats showed the same differences in the envelope protein of the two viruses as did the monoclonal antibody (data not shown). The culture supernatant from TS-FIPV infected cells was monitored for the appearance of structural proteins at both the permissive and nonpermissive temperatures. All three structural proteins of TS-FIPV were detected in the cells by IFA at both the permissive and nonpermissive temperatures ( Table 2 ). Surface expression of TS-FIPV and WT-FIPV peplomer and envelope proteins but not nucleocapsid at the optimal temperature for each virus resembles the situation in FIPV-infected macrophage-like cells [8] . cache = ./cache/cord-333403-imx3990a.txt txt = ./txt/cord-333403-imx3990a.txt === reduce.pl bib === id = cord-322760-tsxniu3j author = Sha, Jianping title = Fatality risks for nosocomial outbreaks of Middle East respiratory syndrome coronavirus in the Middle East and South Korea date = 2016-09-23 pages = extension = .txt mime = text/plain words = 4625 sentences = 207 flesch = 55 summary = Thus, older age, pre-existing concurrent diseases, and delayed confirmation increase the odds of a fatal outcome in nosocomial MERS-CoV outbreaks in the Middle East and South Korea. Information on all laboratory-confirmed MERS cases was obtained from various publicly available sources, including WHO Global Alert and Response updates, documents officially released by the local health bureau, news releases from Middle Eastern and South Korean authorities, the Weekly Epidemiological Record, ProMed posts, and literature published from 1 April 2012 to 29 June 2016 (http:// www.who.int/csr/don/archive/disease/coronavirus_infections/ en/). In this study, we compared the mortality risk factors in two different nosocomial outbreaks, based on 51 nosocomial outbreaks of MERS-CoV infection in the Middle East and one large outbreak identified in South Korea. The severity of nosocomial outbreaks and the risk of fatal infection in HCP were significantly lower than the overall rate in the Middle East and South Korea. Middle East respiratory syndrome coronavirus (MERS-CoV) nosocomial outbreak in South Korea: insights from modeling cache = ./cache/cord-322760-tsxniu3j.txt txt = ./txt/cord-322760-tsxniu3j.txt === reduce.pl bib === id = cord-321195-cndq6aqb author = Xue, Chunyi title = Chimeric influenza-virus-like particles containing the porcine reproductive and respiratory syndrome virus GP5 protein and the influenza virus HA and M1 proteins date = 2014-07-27 pages = extension = .txt mime = text/plain words = 4542 sentences = 229 flesch = 49 summary = In this study, we have developed a chimeric virus-like particle (VLP) vaccine candidate for porcine reproductive and respiratory syndrome virus (PRRSV) and H3N2 influenza virus and investigated its immunogenicity in mice. The HA and M1 proteins from the H3N2 influenza virus and the PRRSV GP5 protein fused to the cytoplasmic and transmembrane domains of the NA protein were both incorporated into the chimeric VLPs. Analysis of the immune responses showed that the chimeric VLPs elicited serum antibodies specific for both PRRSV GP5 and the H3N2 HA protein, and they stimulated cellular immune responses compared to the responses to equivalent amounts of inactivated viruses. Serum samples were collected on the 14th, 28th, and 42nd day after primary immunization of mice (8 per group) vaccinated with chimeric VLPs, inactivated H3N2 virus, or PBS. A trivalent virus-like particle vaccine elicits protective immune responses against seasonal influenza strains in mice and ferrets cache = ./cache/cord-321195-cndq6aqb.txt txt = ./txt/cord-321195-cndq6aqb.txt === reduce.pl bib === id = cord-316797-sf2lu45f author = Hirano, N. title = Replication of rat coronavirus in a rat cell line, LBC date = 1985 pages = extension = .txt mime = text/plain words = 895 sentences = 61 flesch = 65 summary = Rat coronavirus readily propagated and induced marked cytopathic effect in a rat cell line, LBC cell culture, which provided a sensitive, practical assay system for viral infectivity and neutralizing antibody, and a satisfactory source of the virus. The growth of RCV has been reported on a primary rat kidney cell culture but not on any established cell lines. This brief communication recommends a rat cell line, LBC, providing propagation of RCV and useful tool for infectivity assay. The culture fluid sampled at ¢8 hours p.i. was assayed for infectivity by inoculating into LBC cells prepared in 13 × 100 mm test tubes, showing an infectivity titer of i07.5 50 per cent tissue culture infective doses (TCIDs0)/0.2 ml. The LBC cell culture might be a much more useful tool for RCV propagation and assay. The LBC cells can also support growth of siModaeryoadenitis virus of rat, strain 681 (1), but not of MHV strains (unpublished observation). cache = ./cache/cord-316797-sf2lu45f.txt txt = ./txt/cord-316797-sf2lu45f.txt === reduce.pl bib === id = cord-318731-vlszl0i8 author = Chen, Si title = Molecular characterization of HLJ-073, a recombinant canine coronavirus strain from China with an ORF3abc deletion date = 2019-05-31 pages = extension = .txt mime = text/plain words = 2215 sentences = 137 flesch = 57 summary = title: Molecular characterization of HLJ-073, a recombinant canine coronavirus strain from China with an ORF3abc deletion Interestingly, sequence analysis suggested that HLJ-073 contained a 350-nt deletion in ORF3abc compared with reference CCoV isolates, resulting in the loss of portions of ORF3a and ORF3c and the complete loss of ORF3b. This is the first report of the isolation of strain HLJ-073 in China, and this virus has biological characteristics that are different from those of other reported CCoVs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-019-04296-9) contains supplementary material, which is available to authorized users. In the present study, we report the emergence and molecular characterization of an, FCoV-like recombinant CCoV-HLJ-073, which was isolated from a fecal sample from a dead dog that exhibited enteritis. We isolated a canine coronavirus with a deletion in the ORF3abc region from a dead dog in China. cache = ./cache/cord-318731-vlszl0i8.txt txt = ./txt/cord-318731-vlszl0i8.txt === reduce.pl bib === id = cord-330825-apfcql4m author = Paraguison-Alili, Rubigilda title = Phylogenetic tracking of current porcine epidemic diarrhea virus (PEDV) strains in the Philippines date = 2016-06-28 pages = extension = .txt mime = text/plain words = 2175 sentences = 116 flesch = 54 summary = title: Phylogenetic tracking of current porcine epidemic diarrhea virus (PEDV) strains in the Philippines Since the receptor-binding sites and majority of the neutralization epitopes are located in the S1 portion, this region has been subjected to sequencing and molecular analysis to determine the genetic relatedness of different PEDV viruses [1] [2] [3] . Using data from swine farms in these provinces and diagnosis data from the College of Veterinary Science and Medicine in Central Luzon State University, the incidence is 67 % in Pampanga, 79 % in Tarlac, 61 % in Batangas, and 90 to 100 % in Agusan. This is the first report of PEDV S1 gene sequences from the provincial PEDV hotspots of the Philippines, which include Batangas, Pampanga, Tarlac and Agusan. Phylogenetic analysis of the spike (S) gene of the new variants of porcine epidemic diarrhoea virus in Taiwan Molecular characterization of the spike and ORF3 genes of porcine epidemic diarrhea virus in the Philippines cache = ./cache/cord-330825-apfcql4m.txt txt = ./txt/cord-330825-apfcql4m.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-333331-ddcz7zck author = Yang, Jin title = Detection of hepatitis C virus by an improved loop-mediated isothermal amplification assay date = 2011-05-12 pages = extension = .txt mime = text/plain words = 5207 sentences = 245 flesch = 54 summary = An improved, sensitive, specific, and rapid one-step reverse transcription loop-mediated isothermal amplification (LAMP) assay targeting the 5′ untranslated region (UTR) was developed to detect hepatitis C virus (HCV) infection. A variety of molecular diagnostic assays, such as reverse transcriptase PCR [12] , nucleic-acid-sequence-based amplification [13] , transcription-mediated amplification [29] , branched-chain DNA assay [26] , and in-house realtime PCR [8] , have been developed for the detection of HCV RNA. Confirmed cases of HCV infection were verified by a positive result in an enzyme-linked immunosorbent assay (Kehua Bio-engineering, Shanghai, China) for antibodies against HCV or a quantitative real-time PCR for HCV RNA. Given that the sensitivity of the AP-LAMP assay for detecting HCV is higher than that of the pre-LAMP method, the pathway of AP-based amplification was investigated. Reverse transcription-loop-mediated isothermal amplification assay for rapid detection of hepatitis E virus cache = ./cache/cord-333331-ddcz7zck.txt txt = ./txt/cord-333331-ddcz7zck.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 === === 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-338607-22f04uqe author = Verbeek, A. title = Genomic relationship between turkey and bovine enteric coronaviruses identified by hybridization with BCV or TCV specific cDNA probes date = 1991 pages = extension = .txt mime = text/plain words = 4120 sentences = 192 flesch = 47 summary = title: Genomic relationship between turkey and bovine enteric coronaviruses identified by hybridization with BCV or TCV specific cDNA probes Genomic relationships between turkey and bovine coronavirus (TCV and BCV), which are currently placed in distinct antigenic groups, were demonstrated by hybridization using specific cDNA probes. BCV-specific recombinant plasmids p 52, p 27, and p 247, which served previously for the optimization of hybridization conditions for BCV-RNA detection [33] , and probes pN 17 and pN 9, holding respectively the BCV N and M gene ( Fig. 1) , were used in the detection of several coronaviruses in order to establish the presence of potential genomic homologies. Clinical diagnosis of TCV was assayed with a pool of six 32p-labelled BCV specific recombinant plasmids (pBCV-pool), holding non-overlapping eDNA sequences, in order to amplify the detection signal. Detection signals were absent when testing spotted supernatant fluids of non-infected HRT-18 cells (Fig. 2) and when probing identical blots with 32p-labelled pUC-DNA (not shown), confirming the specificity of the hybridization signals obtained. cache = ./cache/cord-338607-22f04uqe.txt txt = ./txt/cord-338607-22f04uqe.txt === reduce.pl bib === id = cord-338641-s006a7m0 author = Black, W. D. title = Reverse transcriptase-polymerase chain reaction for the detection equine rhinitis B viruses and cell culture isolation of the virus date = 2006-08-24 pages = extension = .txt mime = text/plain words = 4042 sentences = 214 flesch = 56 summary = title: Reverse transcriptase-polymerase chain reaction for the detection equine rhinitis B viruses and cell culture isolation of the virus The RT-PCR was used to detect viral RNA in six of 17 nasopharyngeal swab samples from horses that had clinical signs of acute febrile respiratory disease but from which ERBV was not initially isolated in cell culture. Virus isolation in cell culture had been attempted for all 17 nasopharyngeal swab samples, but no CPE was visible during three passages on RK13, Vero and EFK cells. The conclusive determination of ERBV as the cause of equine respiratory disease by detection of virus in nasopharyngeal samples by nested RT-PCR is, however, also made difficult by the long-term persistent infection of horses with these viruses without causing apparent disease, as reported after the repeated isolation of ERBV1 over 2 years after two yearling colts were experimentally infected [3] . cache = ./cache/cord-338641-s006a7m0.txt txt = ./txt/cord-338641-s006a7m0.txt === reduce.pl bib === === reduce.pl bib === id = cord-339178-d6f6a5ds author = Pensaert, M. B. title = A new coronavirus-like particle associated with diarrhea in swine date = 1978 pages = extension = .txt mime = text/plain words = 1749 sentences = 109 flesch = 58 summary = Coronavirus-like particles were detected by electron microscopy in the intestinal contents of pigs during a diarrheal outbreak on 4 swine breeding farms. Coronavirus-like particles were detected by electron microscopy in the intestinal contents of pigs during a diarrheal outbreak on 4 swine breeding farms. Diarrhea was reproduced in experimental pigs with one of the isolates, designated CV777, which was found to be distinct from the 2 known porcine coronaviruses, transmissible gastroenteritis virus and hemagglutinating encephalomyelitis virus. Diarrhea was reproduced in experimental pigs with one of the isolates, designated CV777, which was found to be distinct from the 2 known porcine coronaviruses, transmissible gastroenteritis virus and hemagglutinating encephalomyelitis virus. In a search for rotaviruses on Belgian swine breeding farms with diarrheal problems, a new coronavirus-like particle was detected b y electron microscopic examination of intestinal or fecal samples from sick pigs. cache = ./cache/cord-339178-d6f6a5ds.txt txt = ./txt/cord-339178-d6f6a5ds.txt === reduce.pl bib === id = cord-334810-hw1aijwf author = Banyard, Ashley C. title = Repeated detection of European bat lyssavirus type 2 in dead bats found at a single roost site in the UK date = 2009-10-20 pages = extension = .txt mime = text/plain words = 1962 sentences = 101 flesch = 56 summary = In August 2007, European bat lyssavirus type 2 (EBLV-2) was isolated from a Daubenton's bat found at Stokesay Castle. However, studies with EBLV-1 infection in the natural host, Eptesicus serotinus, showed no substantial pattern of virus distribution in different non-neuronal organs in bats that developed disease [7] . Whilst this is widely documented for larger species, low levels of viable virus or viral RNA detected in saliva swabs tested during experimental studies with different bat lyssaviruses highlight the difficulty in determining the importance of this route of transmission for virus dissemination within a roost [5, 11, 14] . Detection of high levels of European bat lyssavirus type-1 viral RNA in the thyroid gland of experimentally infected Eptesicus fuscus bats Experimental infection of Serotine bats (Eptesicus serotinus) with European bat lyssavirus type 1a (EBLV-1a) Experimental study of European bat lyssavirus type-2 infection in Daubenton's bats (Myotis daubentonii) cache = ./cache/cord-334810-hw1aijwf.txt txt = ./txt/cord-334810-hw1aijwf.txt === reduce.pl bib === id = cord-332811-kjgah8ts author = Lee, Do Hyun title = Immunoprophylactic effect of chicken egg yolk antibody (IgY) against a recombinant S1 domain of the porcine epidemic diarrhea virus spike protein in piglets date = 2015-06-23 pages = extension = .txt mime = text/plain words = 5898 sentences = 237 flesch = 43 summary = title: Immunoprophylactic effect of chicken egg yolk antibody (IgY) against a recombinant S1 domain of the porcine epidemic diarrhea virus spike protein in piglets A codon-optimized PEDV S1 gene consisting of amino acid residues 25–749 was synthesized and used to establish a stable porcine cell line constitutively expressing a recombinant PEDV S1 protein containing the chicken immunoglobulin Fc fragment at its C-terminus. Moreover, oral passive immunization using chicken IgY raised against the PEDV S1 protein was found to control and prevent PED post-challenge in suckling piglets. All neonatal piglets except for animals in the control group were inoculated orally with 1 ml of the small-intestine homogenate containing 10 4 TCID 50 /ml PEDV field virus determined using real-time RT-PCR as described previously [10] . Immunoprophylactic effect of chicken egg yolk immunoglobulin (IgY) against porcine epidemic diarrhea virus (PEDV) in piglets cache = ./cache/cord-332811-kjgah8ts.txt txt = ./txt/cord-332811-kjgah8ts.txt === reduce.pl bib === id = cord-334090-66d8c75g author = Seger, Waleed title = Genotyping of infectious bronchitis viruses from broiler farms in Iraq during 2014-2015 date = 2016-02-18 pages = extension = .txt mime = text/plain words = 3613 sentences = 178 flesch = 54 summary = Thus, the spread of viral respiratory diseases has become the most commonly reported condition in commercial broiler flocks in Iraq; however, there have been no studies on the detection and genotyping of these viruses using molecular techniques and sequencing. Phylogenetic analysis of the 32 strains (Fig. 2) revealed that Iraqi IBV strains could be classified into four genetic groups or genotypes: group I, variant 2 IS/1494-like viruses, including 15 field isolates (46.87 %); group II, 793/Blike viruses, including 13 field strains (40.62 %); group III, QX-like viruses, including three field strains (9.37); and caused by bacteria and mycoplasmas have already been detected on broiler farms located in the central and southern parts of Iraq. Our result were in line with those of Mahmood et al., who conducted the first study of identification and genotyping of IBV isolates and indicated that the 4/91-like virus is circulating on vaccinated broiler farms of the Kurdistan region of Iraq [21] . cache = ./cache/cord-334090-66d8c75g.txt txt = ./txt/cord-334090-66d8c75g.txt === reduce.pl bib === id = cord-340905-8nyew5i5 author = Chen, Yi-Ning title = Genotyping of turkey coronavirus field isolates from various geographic locations in the Unites States based on the spike gene date = 2015-08-08 pages = extension = .txt mime = text/plain words = 3189 sentences = 152 flesch = 53 summary = The objective of the present study was to elucidate the relationship between the genotypes and geographic distribution of TCoV isolates from turkey farms in multiple states in the United States by using sequence analysis and comparing the full-length S gene. Three genetic groups, referred to as groups I, II, and III, were observed in North American TCoV isolates ( Fig. 2A) Because of the high degree of variation, most phylogenetic groupings based on the S1a deduced amino acid sequences did not have a bootstrap value over 50 % (Fig. 2B) . Nevertheless, the Texas TCoV isolates of group II and all three TCoV isolates of group III shown in the phylogenetic tree based on the full-length S nucleotide sequences still clustered according to their S1a amino acid sequences containing their HVR. In the present study, similar to previous findings with IBV strains, most of the variations in the S protein sequences among TCoV isolates were observed in the amino-terminal half. cache = ./cache/cord-340905-8nyew5i5.txt txt = ./txt/cord-340905-8nyew5i5.txt === reduce.pl bib === id = cord-339991-k8z6v2vx author = Rong, Q. title = Multiple mechanisms for HSV-1 induction of interferon α production by peripheral blood mononuclear cells date = 2003 pages = extension = .txt mime = text/plain words = 5571 sentences = 273 flesch = 48 summary = UV-inactivated, infectious, and other forms of herpes simplex virus 1 (HSV-1) induced interferon (IFN) production by different routes in myeloid origin mononuclear cells (MOMC) (consisting predominantly of monocytes). Comparison of the activities of different strains of infectious HSV, UV-inactivated HSV, and a mutant HSV incapable of penetration (K T) [9] and results of treatment with a mannose receptor antagonist indicate that there are more than one mechanism for HSV induction of interferon in the MOMC origin cell populations. The greater response to UV-inactivated virus suggests that non-infectious virions and possibly HSV infected cell debris are the more potent activators of IFN α production and that replicating virus can limit the induction of interferon production as a means of escaping host protection. Interferons and the colony-stimulating factors IL-3 and GM-CSF enhance the ifn-alpha response in human blood leucocytes induced by herpes simplex virus cache = ./cache/cord-339991-k8z6v2vx.txt txt = ./txt/cord-339991-k8z6v2vx.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-341278-klv9jdm8 author = Smith, Abigail L. title = The role of gamma interferon in infection of susceptible mice with murine coronavirus, MHV-JHM date = 1991 pages = extension = .txt mime = text/plain words = 3861 sentences = 182 flesch = 45 summary = Infection of BALB/c mice with mouse hepatitis virus, strain JHM (MHV-JHM), at any of several intervals relative to ovalbumin (OVA) administration resulted in elevated OVA-specific IgG 2 a titers. Serum IFN-γ was not detected, but treatment of MHV-JHM-infected mice with monoclonal anti-IFN-γ antibody resulted in high mortality with decreased survival times, enhanced virus titers in liver and spleen, and more severe virus-associated pathology, compared to mock-treated, infected mice. Sera from mice infected with MHV-JHM one day prior to OVA administration contained substantially elevated levels of antigen-specific IgG2 a on day 7 (Table 1 ) with geometric mean titers that were 17 times control (OVA only) values at that interval. The elevated IgG 2 a OVA-specific response of most groups of MHV-infected mice and the preferential production of this isotype by mice infected one day prior to antigen administration suggested that these mice were producing IFNy. However, using the WEHI 279 B cell lymphoma bioassay [24] , attempts to detect the cytokine in sera of infected mice failed, as had earlier attempts to 27] . cache = ./cache/cord-341278-klv9jdm8.txt txt = ./txt/cord-341278-klv9jdm8.txt === reduce.pl bib === id = cord-343349-ftzjdvfj author = Bhatt, P. N. title = Experimental infection of adult axenic rats with Parker's Rat Coronavirus date = 1977 pages = extension = .txt mime = text/plain words = 2128 sentences = 131 flesch = 51 summary = Virus was recovered from the nasopharynx and trachea after twenty-four hours and from the lung by day three but was not detected in respiratory tract after seven days. Viral antigen was detected by indirect immunofluorescence in the mucosal epithelium of upper respiratory tract and in pulmonary alveolar septae from day two to six postinoculation. Dacryoadenitis did not occur, sialoadenitis was detected in only three rats and virus was recovered from only one submaxillary salivary gland. Coronavirus infection is common in laboratory rats and two antigenically related viruses, sialodacryoadenitis virus (SDAV) and Parker's rat coronavirus (PRCV), have been isolated from naturally-infected rats (2, 7) . Virus in lungs, tracheas, nasal washings, salivary glands and lacrimal glands was quantitated for individual rats. Virus was not detected in nasopharynx, trachea and lung a~ter day six and in other tissues after day seven except in ~he submaxillary salivary gland of one rat. cache = ./cache/cord-343349-ftzjdvfj.txt txt = ./txt/cord-343349-ftzjdvfj.txt === reduce.pl bib === id = cord-335690-66t5fjld author = Khromykh, A. A. title = RNA binding properties of core protein of the flavivirus Kunjin date = 1996 pages = extension = .txt mime = text/plain words = 5858 sentences = 250 flesch = 58 summary = For this study we exploited the use of glutathione-S-transferase (GST)-core fusion proteins attached to an insoluble matrix (Glutathione Sepharose 4B) for rapid RNAprotein binding assays, and extended some of these results by mobility shift assays [17] which were possible because of the relatively small size of the RNA probes, KUN UTR probes bound strongly to fusion proteins incorporating full length or mature C, and to the isolated amino-terminal or carboxy-terminal domains of mature C. In attempts to define which regions of the mature form of C were binding to RNA, three regions enriched in basic amino acids were chosen arbitrarily for All these deleted fusion proteins bound to 3' UTR and 5' core probes on beads as efficiently as C107 (Fig. 3a) . cache = ./cache/cord-335690-66t5fjld.txt txt = ./txt/cord-335690-66t5fjld.txt === reduce.pl bib === id = cord-343131-tu6g977q author = Cheung, Andrew K. title = A divergent clade of circular single-stranded DNA viruses from pig feces date = 2013-04-24 pages = extension = .txt mime = text/plain words = 1856 sentences = 108 flesch = 56 summary = Using metagenomics and molecular cloning methods, we characterized five novel small, circular viral genomes from pig feces that are distantly related to chimpanzee and porcine stool-associated circular viruses, (ChiSCV and PoSCV1). This new clade of viruses, provisionally named porcine stool-associated circular virus 2 and 3 (PoSCV2 and PoSCV3), encodes a stem–loop structure (presumably the origin of DNA replication) in the small intergenic region and a replication initiator protein commonly found in other biological systems that replicate their genomes via the rolling–circle mechanism. The viral genomes can be divided into four regions: two large ORFs with deduced amino acid sequences exhibiting homology to the Rep and Cap of ChiSCV, a LIR that encodes multiple overlapping ORFs, and an SIR that contains a palindromic sequence capable of forming a stem-loop structure. cache = ./cache/cord-343131-tu6g977q.txt txt = ./txt/cord-343131-tu6g977q.txt === reduce.pl bib === id = cord-341469-7guojyay author = Park, Seong-Jun title = Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field isolates in Korea date = 2011-01-06 pages = extension = .txt mime = text/plain words = 3718 sentences = 165 flesch = 53 summary = Especially, ORF3 gene analysis can be used for discrimination between vaccine and wild-type PEDVs. Sequence and phylogenetic analysis showed that recent, prevalent Korean PEDV field isolates have close relationships to Chinese field strains and differ genetically from European strains and vaccine strains used in Korea. Sequence analysis of the complete ORF3 genes showed that all PEDVs, including the Korean field isolates, fell into three groups, and group 3 had two subgroups (3-1 and 3-2), as can be seen in the phylogenetic tree (Fig. 2) . Genetic analysis based on complete M and ORF3 genes showed that each PEDV group had several unique characteristics, and these results indicated that specific groups of PEDVs may be differentiated from other PEDVs, including Korean field isolates, by specific nucleotide differences, but more PEDVs need to be analyzed for more accurate analysis. cache = ./cache/cord-341469-7guojyay.txt txt = ./txt/cord-341469-7guojyay.txt === reduce.pl bib === id = cord-343780-084lq92r author = Hsu, Tien-Huan title = Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan date = 2018-07-26 pages = extension = .txt mime = text/plain words = 2083 sentences = 109 flesch = 60 summary = title: Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan To investigate if PDCoV is also present in Taiwan, three swine coronaviruses—PDCoV, porcine epidemic diarrhea virus (PEDV), and transmissible gastroenteritis coronavirus (TGEV)—were tested using real-time reverse transcription polymerase chain reaction (rRT-PCR) in 172 rectal swab samples from piglets exhibiting diarrhea between January 2016 and May 2017 on 68 pig farms in Taiwan. Currently, there are at least three members of the family Coronaviridae that can cause diarrhea in pigs: transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), and porcine deltacoronavirus (PDCoV) [8] . Based on the real-time RT-PCR (rRT-PCR) detection results, the percentage of pig farms that were positive for at least of one of the coronaviruses was 25% for PDCoV (17/68), 22.1% for PEDV (15/68), and 2.9% for TGEV (2/68). Phylogeny analysis of PDCoV-N genes showed that PDCoVs found in Taiwan were highly similar in their nucleotide sequences to isolates from the United States, mainland China, and other countries (Fig. 1) . cache = ./cache/cord-343780-084lq92r.txt txt = ./txt/cord-343780-084lq92r.txt === reduce.pl bib === id = cord-341342-kyavg4vu author = Masters, P. S. title = Localization of an RNA-binding domain in the nucleocapsid protein of the coronavirus mouse hepatitis virus date = 1992 pages = extension = .txt mime = text/plain words = 5901 sentences = 279 flesch = 57 summary = The RNase sensitivity of the ability of N protein to migrate into nondenaturing gels was not due to possible contaminating protease activity in the RNase preparations, since the same RNase-treated samples of translated N 148 P.S. Masters protein showed no degradation when analyzed by SDS-PAGE (Fig. 3, lanes an, lower) . Since the N mRNAs synthesized from the transcription vectors shown in Fig. 1 contained this portion of the leader sequence, it seemed possible that the N-RNA complex observed in nondenaturing PAGE was that of translated N protein binding to its own mRNA. That the observed complex was not due to translated N protein binding to the leader portion of its own mRNA was also supported by the observation that full-length N protein translated from a construct in which the MHV leader sequence was entirely deleted was also able to migrate into nondenaturing gels (data not shown). cache = ./cache/cord-341342-kyavg4vu.txt txt = ./txt/cord-341342-kyavg4vu.txt === reduce.pl bib === id = cord-341383-e2jrhycj author = Dong, Wei title = Epidemiological and clinical characteristics of respiratory viral infections in children in Shanghai, China date = 2016-05-02 pages = extension = .txt mime = text/plain words = 3347 sentences = 178 flesch = 52 summary = In this study, we investigated the prevalence and clinical characteristics of children with virus-related ARTIs and determined the spectrum of respiratory viruses and their correlation with meteorological variables in Jiading District, Shanghai, China. Investigations of the prevalence of ARTIs and its correlation with viral pathogens are critical for improving the prevention and treatment of ARTIs. There are more than 200 respiratory viruses that can cause ARTIs. Respiratory syncytial virus (RSV), human rhinovirus (HRV), human metapneumovirus (HMPV), human parainfluenza virus (PIV), human enterovirus (EV), influenza virus (IFV), human coronavirus (CoV), adenovirus (ADV), and human bocavirus (BoV) are the most common viral agents associated with ARTIs, accounting for around 70 % of ARTIs [3, 4] . Seventeen respiratory viruses, including IFV (IFV-A/B/C), PIV 1-4, EV, RSV, CoV (229E, HKU1, OC43, NL63), ADV, HMPV, BoV, and HRV were detected among 691 of 2819 children with ARTIs in Nanxiang District of Shanghai (Table 3) . cache = ./cache/cord-341383-e2jrhycj.txt txt = ./txt/cord-341383-e2jrhycj.txt === reduce.pl bib === id = cord-346629-770qyee8 author = Mase, M. title = Phylogenetic analysis of avian infectious bronchitis virus strains isolated in Japan date = 2004-07-15 pages = extension = .txt mime = text/plain words = 2367 sentences = 137 flesch = 50 summary = title: Phylogenetic analysis of avian infectious bronchitis virus strains isolated in Japan To define the origin and evolution of recent avian infectious bronchitis virus (IBV) in Japan, a genetic analysis was performed. By phylogenetic analysis based on the S1 gene including the sequence of the hypervariable regions, IBV isolates in Japan were classified into five genetic groups, which included two already-known groups (Mass and Gray). In this study, to define the origin and evolution of recent IBV in Japan, we determined the nucleotide sequences of IBV isolated in Japan using the reverse transcriptase-polymerase chain reaction (RT-PCR) method coupled with direct sequencing, and analyzed the sequences phylogenetically with viruses isolated in other countries. By phylogenetic analysis, the IBV isolates in Japan used in this study were divided into five genetic groups (Fig. 1 ). Typing of field isolates of infectious bronchitis virus based on the sequence of the hypervariable region in the S1 gene cache = ./cache/cord-346629-770qyee8.txt txt = ./txt/cord-346629-770qyee8.txt === reduce.pl bib === id = cord-344464-if6js43s author = Cowley, J. A. title = The complete genome sequence of gill-associated virus of Penaeus monodon prawns indicates a gene organisation unique among nidoviruses(*): Brief Report date = 2002 pages = extension = .txt mime = text/plain words = 3523 sentences = 183 flesch = 54 summary = title: The complete genome sequence of gill-associated virus of Penaeus monodon prawns indicates a gene organisation unique among nidoviruses(*): Brief Report We report here a 5596 nt sequence comprising the 3′-end of the (+) ssRNA genome of gill-associated virus (GAV), an invertebrate nidovirus of Penaeus monodon prawns. The sequence extends from a subgenomic RNA start site 35 nt upstream of the 4923 nt ORF3 gene to a 3′-poly(A) tail of the 26235 nt genome of GAV. Completion of the genome sequence of GAV has revealed a gene organisation unique among nidoviruses in there is no discrete membrane protein gene and that the putative ORF3 spike glycoprotein gene resides downstream of a gene (ORF2) encoding a structural protein associated with nucleocapsids. A contig of a 5596 nt sequence from the GAV genomic 3 -poly(A) tail to an intergenic 5 -sgRNA start site 35 nt upstream of the ORF3 start codon [10] was deduced from overlapping cDNA clones (Figs. cache = ./cache/cord-344464-if6js43s.txt txt = ./txt/cord-344464-if6js43s.txt === reduce.pl bib === id = cord-343256-n593kh7u author = Percy, D. H. title = A comparison of the sensitivity and specificity of sialodacryoadenitis virus, Parker's rat coronavirus, and mouse hepatitis virus-infected cells as a source of antigen for the detection of antibody to rat coronaviruses date = 1991 pages = extension = .txt mime = text/plain words = 1738 sentences = 107 flesch = 55 summary = title: A comparison of the sensitivity and specificity of sialodacryoadenitis virus, Parker's rat coronavirus, and mouse hepatitis virus-infected cells as a source of antigen for the detection of antibody to rat coronaviruses Using SDAVand PRC-infected L-2 cells as the source of antigen, and sera from rats collected post inoculation with either of these viral strains, the indirect fluorescent antibody (IFA) procedure was used to determine whether antibody titers could be used to differentiate infections from the homologous and heterologous virus. However, using MHV or SDAV-infected cells as the source of antigen, there was a significant difference in antibody titers to the homologous virus detected using the immunoenzyme technique. Using the I F A procedure and MHV-, SDAV-, or PRC-infected cells as a source of antigen and sera from rats exposed to S D A virus, antibody titers to all three antigens were similar (Table 1 ). cache = ./cache/cord-343256-n593kh7u.txt txt = ./txt/cord-343256-n593kh7u.txt === reduce.pl bib === id = cord-345552-h6fwi0qn author = Li, Q.-G. title = Hydropathic characteristics of adenovirus hexons date = 1997-07-01 pages = extension = .txt mime = text/plain words = 3522 sentences = 206 flesch = 53 summary = The strength of the surface charge accumulated on the hydrophilic and hydrophobic regions correlated to the tissue tropism of the different adenovirus types. The sequence of the predicted protein, consisting of 937 amino acids, was obtained with the LaserGene software program EditSeq. The hydropathy data of hexon proteins from human adenovirus types 2, 3, 4, 5, 7, 12, 16, 40, 41, and 48, bovine adenovirus type 3, murine adenovirus type 1, and avian adenovirus types 1 and 10 were derived using the prediction method of Kyte-Doolittle in the LaserGene computer program Protean. The nucleotide and amino acid sequence pair distances and the phylogenetic tree of 14 hexon proteins showed serotypes of subgenera B, D and E to be closely related (Table 3 and Fig. 2) . DNA sequence of the adenovirus type 41 hexon gene and predicted structure of the protein cache = ./cache/cord-345552-h6fwi0qn.txt txt = ./txt/cord-345552-h6fwi0qn.txt === reduce.pl bib === id = cord-345957-wuk2arf9 author = Mohamed, Fakry F. title = Detection and genetic characterization of bovine kobuvirus from calves in Egypt date = 2018-02-08 pages = extension = .txt mime = text/plain words = 4245 sentences = 219 flesch = 61 summary = When compared to the only recorded BKoV genome sequence (BKoV/U-1/AB084788), the studied strain showed 94 amino acid (aa) substitutions through its entire polyprotein (2463 aa), one nucleotide (nt) insertion and one nt deletion in the 2B gene and 4-nt deletions in the UTRs (2 each). Initially, kobuviruses included Aichivirus (AiV), bovine kobuvirus (BKoV), and porcine kobuvirus (PKoV) based on the hosts infected e.g. humans, cattle, 1 3 and swine, respectively. In this study, we report BKoV infections among cattle populations of Egypt, the full-length genome of one Egyptian strain (BKoV/ Egy-1/ KY407744) as well as the phylogenetic analysis of BKoV strains from Cairo and Sharkia provinces. The RNA samples (n = 36) were subjected to RT-PCR for the detection of BKoV using degenerate primers (Univ-Kobu-F and Univ-Kobu-R), which amplify a conserved region in the 3D (RdRp) gene of all kobuviruses [12] ( Table 1 ). cache = ./cache/cord-345957-wuk2arf9.txt txt = ./txt/cord-345957-wuk2arf9.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-347443-0evqo01m author = Litwin, Christine M. title = Seasonality and prevalence of respiratory pathogens detected by multiplex PCR at a tertiary care medical center date = 2013-07-24 pages = extension = .txt mime = text/plain words = 3991 sentences = 218 flesch = 50 summary = Seasonality has been reported for many viruses, including influenza virus, respiratory syncytial virus (RSV), and the recently described human metapneumovirus (hMPV). Major causes of bronchiolitis and lower respiratory tract illnesses in children include respiratory syncytial virus (RSV), parainfluenza viruses, influenza virus, and human metapneumovirus (hMPV). The organism/viruses detected by the FilmArray included adenovirus, influenza A virus (FluA), influenza B virus (FluB), parainfluenza virus 1 (Para 1), parainfluenza virus 2 (Para 2), parainfluenza virus 3 (Para 3), parainfluenza virus 4 (Para 4), respiratory syncytial virus (RSV), coronavirus 229E (CoronaV 229E), CoronaV NL63, CoronaV HKU1, CoronaV OC43, human metapneumovirus (hMPV), Bordetella pertussis, Chlamydophila pneumoniae and Mycoplasma pneumoniae. In our study, 939 specimens were analyzed over the course of a year using a respiratory pathogen multiplex PCR that yielded a positivity rate of 65 % with multiple analytes detected in 12 % of specimens, especially in children. RSV and hMPV PCR-positive cases were statistically much more likely than Rhino/Entero PCR-positive infections to initially present with pneumonia or bronchiolitis in our study. cache = ./cache/cord-347443-0evqo01m.txt txt = ./txt/cord-347443-0evqo01m.txt === reduce.pl bib === id = cord-345940-adg264vb author = Wanitchang, Asawin title = Characterization of influenza A virus pseudotyped with the spike protein of porcine epidemic diarrhea virus date = 2018-08-22 pages = extension = .txt mime = text/plain words = 5030 sentences = 262 flesch = 54 summary = In this study, we constructed scIAV-S, a single-cycle influenza A virus pseudotyped with the spike protein of porcine epidemic diarrhea virus (PEDV), and demonstrated that this virus could infect cultured cells and trigger massive syncytium formation. It should also be noted that control supernatants from HEK293T cells transfected with pCAGGS expressing S AVCT12 alone did not yield detectable syncytium formation in VeroE6-APN cells, suggesting that the detected syncytia were not due to PEDV-S expressed from residual plasmids (data not shown). To further test whether the mCherry expression in infected cells required active influenza A virus polymerase activity, we attempted to construct scIAV-S AVCT12 by omitting the plasmid encoding the PB2 polymerase and examined its infectivity in VeroE6-APN cells. Likewise, VeroE6-APN cells treated with NH 4 Cl (50 mM for 2 h) to neutralize the intracellular pH also displayed strong mCherry expression and extensive syncytium formation when infected with scIAV-S AVCT12 (Fig. 3A) . cache = ./cache/cord-345940-adg264vb.txt txt = ./txt/cord-345940-adg264vb.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-348179-i8w7huke author = Xue, Yong title = Increased risk of hepatitis E virus infection in schizophrenia date = 2012-10-07 pages = extension = .txt mime = text/plain words = 3363 sentences = 190 flesch = 56 summary = Moreover, schizophrenia patients with increased CD4(+)/CD8(+) T-cell ratios (>2.03) had higher anti-HEV IgG detection rates than those with normal ratios (1.05-2.03). Epidemiological studies have already shown that the rates of hepatitis B and hepatitis C virus infection in patients with schizophrenia were five and 11 times higher, respectively, than the estimated general population rates [26] . In the current study, we found that the detection rates for HEV antibodies in schizophrenia patients were much higher than those in healthy controls. In the present study, the detection rate of anti-HEV IgG in schizophrenia patients with increased CD4 ? T-cell levels and the increased risk of HEV infection in schizophrenia patients. Moreover, significant differences of the serum IL-4, IL-10 and IL-12 levels were observed among schizophrenia patients with and without HEV IgG antibodies. Taken together, schizophrenia patients exhibited higher risk of HEV infection than controls in the present study. cache = ./cache/cord-348179-i8w7huke.txt txt = ./txt/cord-348179-i8w7huke.txt === reduce.pl bib === id = cord-349907-dwhyx97y author = Noh, Ji Yeong title = Simultaneous detection of severe acute respiratory syndrome, Middle East respiratory syndrome, and related bat coronaviruses by real-time reverse transcription PCR date = 2017-02-20 pages = extension = .txt mime = text/plain words = 3274 sentences = 138 flesch = 62 summary = Therefore, in this study, a duplex real-time reverse transcription (RT)-PCR method was developed based on primers and probes that target the conserved spike S2 region of SARS-CoV, SARS-like bat CoVs, MERS-CoV, and MERS-related bat CoVs. For the universal detection of SARS-CoV and SARS-like bat CoVs, consensus primers and probes (Fig. 1a) were designed based on the conserved sequences of the spike S2 region by aligning the following reference sequences: human SARS-CoVs Sino1 (GenBank no. The specificity of the real-time RT-PCR method developed in this study was evaluated using RNAs from several RNA viruses, including MERS-CoV (KOR/KNIH/ 002_05_2015), a recombinant plasmid for the bat CoV HKU4 strain, and RNA from a bat fecal sample containing SARS-like bat CoV. The new real-time RT-PCR method also showed positive results for RNA extracted from a fecal sample containing SARS-like bat CoV (B15-21) [7] . cache = ./cache/cord-349907-dwhyx97y.txt txt = ./txt/cord-349907-dwhyx97y.txt === reduce.pl bib === id = cord-349800-s9w2yr08 author = Hohdatsu, T. title = Characterization of monoclonal antibodies against feline infectious peritonitis virus type II and antigenic relationship between feline, porcine, and canine coronaviruses date = 1991 pages = extension = .txt mime = text/plain words = 3073 sentences = 170 flesch = 58 summary = Seven monoclonal antibodies (MAbs) with neutralizing activity against feline infectious peritonitis virus (FIPV) strain 79-1149 (type II) were prepared. The reactivity of these MAbs with 6 viruses classified as FIPV type I (UCD-1, UCD-2, UCD-3, UCD-4, NW-1, and Black), feline enteric coronavirus (FECV) type II strain 79-1683, canine coronavirus (CCV) strain 1-71, and transmissible gastroenteritis virus (TGEV) strains TO-163 and SH was examined by neutralization tests. Feline coronaviruses are divided into FIPV types I and II, and FECV types I and II, on the basis of the disease types, that is, whether it causes feline infectious peritonitis (FIP) or not, the ability of the viruses to proliferate in cell cultures, and the antigenic relationship to TGEV and CCV [17] . These MAbs did not neutralize the 6 FIPV type I viruses, but neutralized FECV strain 79-1683, TGEV strains TO-163 and SH, and CCV strain 1-71, which do not cause feline infectious peritonitis (Table 4) . cache = ./cache/cord-349800-s9w2yr08.txt txt = ./txt/cord-349800-s9w2yr08.txt === reduce.pl bib === id = cord-342568-3sj235rm author = Bald-Blume, Niklas title = Development of a molecular assay for the general detection of tospoviruses and the distinction between tospoviral species date = 2017-02-11 pages = extension = .txt mime = text/plain words = 5364 sentences = 277 flesch = 54 summary = In this study a new method for plant virus diagnosis is described using the Luminex xTAG technology to test for tospoviruses in general and for the four species TSWV, WSMoV, INSV and CaCV. Infected, dried plant material of 12 tospoviral isolates from eight different species was obtained from the DSMZ including single isolates of alstroemeria necrotic streak virus (ANSV), CaCV, GRSV, IYSV, TCSV and WSMoV as well as three isolates each of INSV and TSWV. The generic tospovirus primers Tospo_GENs/as (without tags) allowed the detection of all eight tospoviruses and of all three isolates of INSV and TSWV tested in RT-PCR experiments. A molecular assay for the detection of tospoviruses in general and for viruses from the four species belonging to this genus (TSWV, INSV, CaCV and WSMoV), using the Luminex xTAG technology, was successfully developed. cache = ./cache/cord-342568-3sj235rm.txt txt = ./txt/cord-342568-3sj235rm.txt === reduce.pl bib === id = cord-348147-leni23pa author = Müller, B. title = Genetic diversity and recombination of murine noroviruses in immunocompromised mice date = 2007-05-29 pages = extension = .txt mime = text/plain words = 3482 sentences = 203 flesch = 52 summary = Sequence analysis of the full-length and partial genomes obtained from naturally infected mice yielded valuable data on genetic diversity of murine noroviruses. These specimens were obtained from 28 different mouse lines, including immunocompetent mice, lines with muta(4), b-TCR À=À (2), RAG2=gChain À=À (5), B6 Casp À=À (2), CD36=SRA À=À (2), CCL3 À=À (2), LFA À=À (2), LyZ À=À (2), PSEN tg (2), Bl6 wt (4) a GE genome equivalents; for more than one positive sample the mean was calculated b Includes partial sequences of the ORFs (underlined isolates; ORF1, RNA polymerase gene; ORF2, capsid gene) Ã Contains both regions tions in a number of immune effector molecules, and transgenic mouse lines (Table 1) . Like human noroviruses, the present sequence data indicate that murine norovirus strains are also genetically diverse and can, therefore, be subdivided in genetic clusters. cache = ./cache/cord-348147-leni23pa.txt txt = ./txt/cord-348147-leni23pa.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-346321-drhiqch0 author = Hohdatsu, T. title = The role of IgG subclass of mouse monoclonal antibodies in antibody-dependent enhancement of feline infectious peritonitis virus infection of feline macrophages date = 1994 pages = extension = .txt mime = text/plain words = 3722 sentences = 165 flesch = 53 summary = title: The role of IgG subclass of mouse monoclonal antibodies in antibody-dependent enhancement of feline infectious peritonitis virus infection of feline macrophages Antibody-dependent enhancement (ADE) of feline infectious peritonitis virus (FIPV) infection was studied in feline alveolar macrophages and human monocyte cell line U937 using mouse neutralizing monoclonal antibodies (MAbs) directed to the spike protein of FIPV. It is especially important for development of vaccines to understand the relationship between FIPV neutralizing activity and ADE activity of anti FIPV MAbs. In this study, we determined the relationship between immunoglobulin subclass and ADE activity of FIPV-neutralizing MAbs, and attempted to explore mechanisms of ADE of FIPV infection in in vitro system using mouse MAbs and feline alveolar macrophages or human monocytes. The present study, however, explored ADE of FIPV infection by in vitro experiments in which xenogeneic combination of virus targets and anti-FIPV antibody, i.e., feline alveolar macrophages or human monocyte U937 cells and mouse anti-FIPV S protein MAbs, was used. cache = ./cache/cord-346321-drhiqch0.txt txt = ./txt/cord-346321-drhiqch0.txt === reduce.pl bib === id = cord-345856-ckm0ol20 author = Zhong, Qiong title = Antiviral activity of Arbidol against Coxsackie virus B5 in vitro and in vivo date = 2009-03-17 pages = extension = .txt mime = text/plain words = 3778 sentences = 200 flesch = 58 summary = Arbidol not only prevented the cytopathic effect (CPE) of CVB(5), as demonstrated in an MTT colorimetric assay, when added during or after viral infection, with a 50% inhibitory concentration (IC(50)) from 2.66 to 6.62 μg/ml, but it also decreased the CVB(5)-RNA level in infected host cells, as shown in semi-quantitative RT-PCR. Orally administered Arbidol at 50 mg/kg body weight/day (once a day) significantly reduced mean virus yields in the lungs and heart as well as mortality after infection for 6 days. In our previous study, Arbidol showed broad-spectrum antiviral activity against a number of respiratory viruses, including FLU-A, RSV, HRV 14, and CVB 3 in vitro [20] . The virus titers of lung and heart were significantly lower in mice receiving oral administration of Arbidol daily for 6 days than in the viral control group. We also cocultured HEp-2 cells with different doses of Arbidol after infection to study whether it still had an antiviral effect after virus entry into the host cell. cache = ./cache/cord-345856-ckm0ol20.txt txt = ./txt/cord-345856-ckm0ol20.txt === reduce.pl bib === id = cord-346928-g1dqiki6 author = Costantini, V. title = Respiratory and fecal shedding of Porcine respiratory coronavirus (PRCV) in sentinel weaned pigs and sequence of the partial S-gene of the PRCV isolates date = 2003-11-26 pages = extension = .txt mime = text/plain words = 5893 sentences = 255 flesch = 55 summary = Porcine respiratory coronavirus (PRCV), a spike (S) gene deletion mutant of Transmissible gastroenteritis virus (TGEV), causes mild or subclinical respiratory infections in pigs. In preliminary studies, inoculation of gnotobiotic pigs with each plaque-purified pair of the nasal and fecal PRCV isolates, revealed no clinical disease but different tropisms. Fecal and nasal swabs from the field cases (sentinel pigs), cell culture isolates and fecal and nasal swabs from gnotobiotic pigs were tested by nested-RT-PCR to detect and to differentiate TGEV and PRCV viral RNA as previously described by Kim et al. Fecal and nasal swab supernatant fluids from the sentinel field cases or the cell culture passaged PRCV isolates and nasal and fecal swabs from gnotobiotic pigs were diluted in minimum essential medium (MEM-E) and tested by CCIF to detect infectious virus using previously described procedures [23] . cache = ./cache/cord-346928-g1dqiki6.txt txt = ./txt/cord-346928-g1dqiki6.txt === reduce.pl bib === id = cord-353797-yb355mxk author = Inaba, Y. title = Replication of bovine coronavirus in cell line BEK-1 culture date = 1976 pages = extension = .txt mime = text/plain words = 835 sentences = 51 flesch = 55 summary = Bovine coronavirus readily multiplied and induced marked cytopathic effect in BEK-1 cultures, thus providing a sensitive, practical assay system for viral infectivity and neutralizing antibody and a satisfactory source of the virus. 1V[~iBus and his associates (4--6) have demonstrated an agent with morphologic features of coronavirus by electron microscopy in fractions prepared by density gradient ultracentrifugation from diarrheal feces of calves with natural and experimentally produced neonatal diarrhea. The agent multiplied but failed to induce readily recognizable cytopathic effect in bovine embryonic kidney cell cultures (3) . This paper describes briefly our recent observation that the virus readily replicates and induces a marked cytopathic effect in cultures of a continuous cell line, BEK-1, derived from bovine embryonic kidney (2), thus providing a sensitive, practical assay method and a satisfactory source of the virus. Coverslip cultures of BEK-1 cells inoculated with the virus were examined after 2 or 3 days of incubation at 34 ° C. cache = ./cache/cord-353797-yb355mxk.txt txt = ./txt/cord-353797-yb355mxk.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-349964-38rgcc5h author = Pedersen, N. C. title = Antigenic relationship of the feline infectious peritonitis virus to coronaviruses of other species date = 1978 pages = extension = .txt mime = text/plain words = 3024 sentences = 190 flesch = 54 summary = The first antigenically related group was comprised of mouse hepatitis virus, type 3 (MHV-3), hemeagglutinating encephalomyelitis virus 67N (HEV-67N) of swine, calf diarrhea coronavirus (CDCV), and human coronavirus OC43 (HCV-OC43). Utilizing the direct and indirect fluorescent antibody procedure, the antigenic relationship of the feline infectious peritonitis virus (FIPV) to 7 other human and animal coronaviruses was studied. Utilizing the direct and indirect fluorescent antibody procedure, the antigenic relationship of the feline infectious peritonitis virus (FIPV) to 7 other human and animal coronaviruses was studied. Transmissible gastroenteritis virus and FIPV were in turn antigenically related to human eoronavirus 229E (I-ICV-229E) and canine coronavirus (CCV). A possible antigenic relationship between feline infectious peritonitis virus (FIPV) and the transmissible gastroenteritis virus (TGEV) of swine has been recently reported (13, 19, 25) , which further supports the assumption t h a t F I P V is a coronavirus. cache = ./cache/cord-349964-38rgcc5h.txt txt = ./txt/cord-349964-38rgcc5h.txt === reduce.pl bib === id = cord-355512-tycuoslv author = Storz, J. title = Comparison of hemagglutinating, receptor-destroying, and acetylesterase activities of avirulent and virulent bovine coronavirus strains date = 1992 pages = extension = .txt mime = text/plain words = 3246 sentences = 172 flesch = 57 summary = Hemagglutinating and acetylesterase functions as well as the 124 kDa glycoprotein were present in the highly cell-culture adapted, avirulent bovine coronavirus strain BCV-L9, in the Norden vaccine strain derived from it, and in 5 wild-type, virulent strains that multiplied in HRT-18 cells but were restricted in several types of cultured bovine cells. Purified preparations of the vaccine and the wild-type strains agglutinated chicken erythrocytes at low titers and mouse erythrocytes at 128 to 256 times higher titers whereas receptor destroying enzyme activity was detectable only with chicken erythrocytes. When wild-type strains were propagated in HRT cells at low passage levels, they produced 5×10(5) to 4.5×10(6) plaque forming units per 50 µl which agglutinated erythrocytes from mice but not from chickens. The objective of our investigations was to identify the HE of wild-type BCV strains at low passage levels in H R T cell cultures and to compare it with the HE of prototype BCV-L9 and vaccine strains by relating its functions to the interaction with different erythrocytes, the effects of enzyme inhibitors, and to plaque-forming infectivity. cache = ./cache/cord-355512-tycuoslv.txt txt = ./txt/cord-355512-tycuoslv.txt === reduce.pl bib === id = cord-356192-8b96rgqa author = Xie, Qian title = Two deletion variants of Middle East respiratory syndrome coronavirus found in a patient with characteristic symptoms date = 2017-04-18 pages = extension = .txt mime = text/plain words = 2413 sentences = 131 flesch = 52 summary = title: Two deletion variants of Middle East respiratory syndrome coronavirus found in a patient with characteristic symptoms Significant sequence variation of Middle East respiratory syndrome coronavirus (MERS CoV) has never been detected since it was first reported in 2012. To predict the function of the E protein of MERS CoV, we aligned the E and ORF5-E protein sequences of MERS CoV with those of two other coronaviruses, SARS-CoV and China Rattus coronavirus HKU24, using MEGA software (version 6.0) [11] . The truncated E protein with a deletion of aa 1-30 lacks the N-terminus and a major part of the hydrophobic transmembrane domain in MERS CoV variant 1, which might directly impair virus packaging and replication [24] . Genomic sequencing and analysis of the first imported Middle East Respiratory Syndrome Coronavirus (MERS CoV) in China Middle East respiratory syndrome coronavirus (MERS-CoV) entry inhibitors targeting spike protein cache = ./cache/cord-356192-8b96rgqa.txt txt = ./txt/cord-356192-8b96rgqa.txt ===== Reducing email addresses cord-261749-lq1ah16x cord-254405-yc1q20fz cord-276617-chgjpg0v cord-010900-2ie1v1wy cord-340905-8nyew5i5 cord-283178-4wefykbi cord-355535-01h8yyqj cord-348163-9q1rt8i7 Creating transaction Updating adr table ===== Reducing keywords cord-004680-u3cnsdl8 cord-003050-n25wnmq5 cord-001274-vz0qvp01 cord-004764-tmvebf23 cord-004810-g0y7ied0 cord-004812-ikco4h5k cord-004673-c8qcjve9 cord-004798-5budstbg cord-004778-xrv0qs6n cord-004724-llex3yed cord-004690-q38ogrem cord-004781-ajf9zig0 cord-004719-3stcx0dd cord-004672-0lf5j8lo cord-004681-02wem2u3 cord-048485-b8xb1f12 cord-004755-rmnjs1t6 cord-258374-qht98q0l cord-004840-4rbrzv5o cord-004793-6yh36r0w cord-004790-69lry0ys cord-004774-fvf671jn cord-004831-lu62noak cord-004808-6w9n03fy cord-272955-kkkrkgg1 cord-004717-41ui4lqc cord-258768-bjjfkfgg cord-006674-ywzpwlrb cord-252232-vgq6gjpx cord-004693-1xglujqk cord-264392-he1vekrt cord-011105-or9azf1g cord-006459-9kizif98 cord-004769-hhge62sl cord-256859-7ixegm72 cord-029775-mntcor5d cord-295308-ruwxm4fd cord-004754-5596p4ma cord-004685-qote5nx2 cord-004713-gzts5h0y cord-274780-fmnro0kw cord-004759-jozdnhgy cord-004838-cdas57cx cord-276630-qci7khki cord-012032-zolowuhj cord-004802-rhkrmftn cord-004851-h9ppa064 cord-271831-vekok62k cord-004848-2cfphi88 cord-004743-ido065mh cord-261749-lq1ah16x cord-004728-rjl35dpa cord-004720-r6b34tjm cord-279676-sk9xyd1r cord-004729-nmkilkcx cord-004765-7e4yu2do cord-290546-zu5ns4yq cord-004827-bnf3mvaf cord-265768-hwki5lk2 cord-266716-pghnl980 cord-276617-chgjpg0v cord-254405-yc1q20fz cord-252037-rj61mzqj cord-026518-xv03vpji cord-263193-paeosfiu cord-004694-43yvs52a cord-004738-vnz15x84 cord-260708-l9w5jhsw cord-280905-g2vcy9ea cord-004775-foaf3vyl cord-265201-ab67pnct cord-280781-u3wd27rn cord-265631-b0kg6qpo cord-262505-1ufgwxxg cord-272973-kzaowysv cord-271884-86yl9ren cord-032801-b2ncmkjg cord-004825-cdvnqfjz cord-261036-zdhg4axx cord-004742-5movyeb4 cord-277847-vgf9lz76 cord-010900-2ie1v1wy cord-004732-mgzmzeyr cord-255653-0bj5eh5d cord-006106-u5npu6ng cord-267446-rpv19oy6 cord-285329-62yafd2d cord-004849-d64hnqkh cord-004727-9sniu39j cord-257859-9hmrt96h cord-283178-4wefykbi cord-269948-zfbu9646 cord-259193-ifdjyp5b cord-282062-h9smg0w9 cord-267155-3rhdxzj3 cord-285547-7m3dh8hu cord-283804-dje7qbps cord-004766-gvom0f13 cord-304109-yirs7kjg cord-278388-lzvtgwox cord-004733-i0a3igc7 cord-289926-y1rjgbui cord-270473-5tok4mqk cord-281410-y558a5jf cord-291718-cz1bi0ym cord-287275-vwyny1vt cord-309145-6aqc074e cord-293945-gyb9mjb5 cord-302871-x3mjov5l cord-285892-tp6mlqtw cord-299342-l8ugjou9 cord-294218-v4gjabp3 cord-307408-6wfx0wey cord-299763-ttb7o8lv cord-291530-ffex7dw9 cord-280865-shwxhak9 cord-283710-55m16q7c cord-305859-vt8vwo3y cord-285429-vmnj25b5 cord-294467-kq5wmavt cord-296167-np0b9a7o cord-283525-kvcqayl4 cord-295409-7l0pglef cord-284087-g2jfnxja cord-286794-adbxzgvs cord-310669-6hwq5jfv cord-004749-wyzb8v4a cord-302323-vvo8a4hp cord-321471-gev5xq3a cord-291707-dzmvjh7j cord-294323-mryiqmsw cord-290819-zhywlf6r cord-306380-msk9p1yy cord-302063-ct5rvqtd cord-302798-q0mbngqy cord-298883-uiwg482s cord-294138-h7sfd1wa cord-288948-89cdfhi0 cord-312787-j7ye7ed5 cord-316153-wet0go35 cord-322593-bgm6smuo cord-308950-bl83r4v3 cord-307098-oq7zrnuv cord-325827-492xi3ee cord-312338-r6jqmes3 cord-292286-ygomb3oi cord-328381-bfvdhai8 cord-306725-0vam15pt cord-315811-wpeac0lk cord-324377-br2uorg8 cord-299428-gon6bzat cord-317009-8tqnt1l9 cord-314751-i9rxesrg cord-290695-ubrqy2zf cord-311773-r9c7sx6r cord-314069-8dxzf2ip cord-324495-0pee1i3o cord-322760-tsxniu3j cord-330035-0d6w8xyd cord-316525-uadfehr6 cord-307378-cx1jz7wf cord-317617-snrumw3x cord-333403-imx3990a cord-321195-cndq6aqb cord-316797-sf2lu45f cord-318731-vlszl0i8 cord-333043-fe24ezt6 cord-330825-apfcql4m cord-333636-h2sg6shp cord-329145-424vv8a8 cord-333331-ddcz7zck cord-299345-2i48ld8d cord-294947-g4ntyddb cord-338641-s006a7m0 cord-327855-txryqil7 cord-340422-8f5xe4zc cord-338607-22f04uqe cord-334090-66d8c75g cord-334810-hw1aijwf cord-339991-k8z6v2vx cord-340905-8nyew5i5 cord-339178-d6f6a5ds cord-340065-f4ffvkr9 cord-338916-fqxjzavm cord-343131-tu6g977q cord-335690-66t5fjld cord-343349-ftzjdvfj cord-341469-7guojyay cord-341342-kyavg4vu cord-332811-kjgah8ts cord-343780-084lq92r cord-341278-klv9jdm8 cord-342568-3sj235rm cord-343256-n593kh7u cord-344464-if6js43s cord-346629-770qyee8 cord-345552-h6fwi0qn cord-347443-0evqo01m cord-341383-e2jrhycj cord-348163-9q1rt8i7 cord-345957-wuk2arf9 cord-345940-adg264vb cord-355535-01h8yyqj cord-348147-leni23pa cord-346321-drhiqch0 cord-349907-dwhyx97y cord-348867-c0xpzd4d cord-345856-ckm0ol20 cord-348179-i8w7huke cord-353797-yb355mxk cord-349800-s9w2yr08 cord-355512-tycuoslv cord-346928-g1dqiki6 cord-349964-38rgcc5h cord-356192-8b96rgqa cord-356176-1nwjjgul Creating transaction Updating wrd table ===== Reducing urls cord-001274-vz0qvp01 cord-003050-n25wnmq5 cord-011105-or9azf1g cord-258768-bjjfkfgg cord-012032-zolowuhj cord-280905-g2vcy9ea cord-257859-9hmrt96h cord-004717-41ui4lqc cord-006106-u5npu6ng cord-269948-zfbu9646 cord-285547-7m3dh8hu cord-287275-vwyny1vt cord-286794-adbxzgvs cord-010900-2ie1v1wy cord-285429-vmnj25b5 cord-032801-b2ncmkjg cord-288948-89cdfhi0 cord-302323-vvo8a4hp cord-302798-q0mbngqy cord-295308-ruwxm4fd cord-307408-6wfx0wey cord-302063-ct5rvqtd cord-307378-cx1jz7wf cord-306725-0vam15pt cord-324495-0pee1i3o cord-314069-8dxzf2ip cord-316525-uadfehr6 cord-322760-tsxniu3j cord-330035-0d6w8xyd cord-333331-ddcz7zck cord-329145-424vv8a8 cord-340905-8nyew5i5 cord-341469-7guojyay cord-345957-wuk2arf9 cord-348867-c0xpzd4d cord-349907-dwhyx97y cord-356192-8b96rgqa Creating transaction Updating url table ===== Reducing named entities cord-004764-tmvebf23 cord-004793-6yh36r0w cord-011105-or9azf1g cord-004681-02wem2u3 cord-004781-ajf9zig0 cord-004778-xrv0qs6n cord-004831-lu62noak cord-001274-vz0qvp01 cord-004798-5budstbg cord-004680-u3cnsdl8 cord-004717-41ui4lqc cord-004673-c8qcjve9 cord-004755-rmnjs1t6 cord-004810-g0y7ied0 cord-004790-69lry0ys cord-256859-7ixegm72 cord-004812-ikco4h5k cord-004769-hhge62sl cord-004719-3stcx0dd cord-004724-llex3yed cord-004672-0lf5j8lo cord-003050-n25wnmq5 cord-004774-fvf671jn cord-006459-9kizif98 cord-006674-ywzpwlrb cord-004754-5596p4ma cord-004713-gzts5h0y cord-252232-vgq6gjpx cord-004690-q38ogrem cord-029775-mntcor5d cord-004848-2cfphi88 cord-252037-rj61mzqj cord-261749-lq1ah16x cord-004743-ido065mh cord-274780-fmnro0kw cord-004685-qote5nx2 cord-048485-b8xb1f12 cord-271831-vekok62k cord-004802-rhkrmftn cord-004808-6w9n03fy cord-004851-h9ppa064 cord-276630-qci7khki cord-012032-zolowuhj cord-258768-bjjfkfgg cord-004728-rjl35dpa cord-004759-jozdnhgy cord-004720-r6b34tjm cord-255653-0bj5eh5d cord-263193-paeosfiu cord-004827-bnf3mvaf cord-004729-nmkilkcx cord-291718-cz1bi0ym cord-279676-sk9xyd1r cord-004825-cdvnqfjz cord-276617-chgjpg0v cord-291530-ffex7dw9 cord-254405-yc1q20fz cord-004765-7e4yu2do cord-258374-qht98q0l cord-004840-4rbrzv5o cord-265768-hwki5lk2 cord-277847-vgf9lz76 cord-026518-xv03vpji cord-278388-lzvtgwox cord-004775-foaf3vyl cord-004749-wyzb8v4a cord-299763-ttb7o8lv cord-004732-mgzmzeyr cord-004727-9sniu39j cord-265201-ab67pnct cord-266716-pghnl980 cord-296167-np0b9a7o cord-004738-vnz15x84 cord-280905-g2vcy9ea cord-264392-he1vekrt cord-280865-shwxhak9 cord-283525-kvcqayl4 cord-285547-7m3dh8hu cord-032801-b2ncmkjg cord-010900-2ie1v1wy cord-260708-l9w5jhsw cord-257859-9hmrt96h cord-307408-6wfx0wey cord-004849-d64hnqkh cord-302063-ct5rvqtd cord-004693-1xglujqk cord-272973-kzaowysv cord-262505-1ufgwxxg cord-261036-zdhg4axx cord-271884-86yl9ren cord-283178-4wefykbi cord-259193-ifdjyp5b cord-281410-y558a5jf cord-285429-vmnj25b5 cord-283804-dje7qbps cord-265631-b0kg6qpo cord-004742-5movyeb4 cord-272955-kkkrkgg1 cord-004733-i0a3igc7 cord-287275-vwyny1vt cord-299342-l8ugjou9 cord-293945-gyb9mjb5 cord-267446-rpv19oy6 cord-282062-h9smg0w9 cord-270473-5tok4mqk cord-006106-u5npu6ng cord-004766-gvom0f13 cord-289926-y1rjgbui cord-288948-89cdfhi0 cord-285892-tp6mlqtw cord-284087-g2jfnxja cord-294218-v4gjabp3 cord-302871-x3mjov5l cord-295409-7l0pglef cord-285329-62yafd2d cord-283710-55m16q7c cord-295308-ruwxm4fd cord-302323-vvo8a4hp cord-298883-uiwg482s cord-286794-adbxzgvs cord-305859-vt8vwo3y cord-004694-43yvs52a cord-294947-g4ntyddb cord-269948-zfbu9646 cord-267155-3rhdxzj3 cord-004838-cdas57cx cord-290695-ubrqy2zf cord-290546-zu5ns4yq cord-280781-u3wd27rn cord-302798-q0mbngqy cord-294323-mryiqmsw cord-294467-kq5wmavt cord-311773-r9c7sx6r cord-292286-ygomb3oi cord-308950-bl83r4v3 cord-294138-h7sfd1wa cord-290819-zhywlf6r cord-291707-dzmvjh7j cord-309145-6aqc074e cord-315811-wpeac0lk cord-299428-gon6bzat cord-339991-k8z6v2vx cord-312338-r6jqmes3 cord-340065-f4ffvkr9 cord-307378-cx1jz7wf cord-299345-2i48ld8d cord-304109-yirs7kjg cord-306380-msk9p1yy cord-307098-oq7zrnuv cord-310669-6hwq5jfv cord-316153-wet0go35 cord-317009-8tqnt1l9 cord-324377-br2uorg8 cord-325827-492xi3ee cord-312787-j7ye7ed5 cord-321471-gev5xq3a cord-306725-0vam15pt cord-328381-bfvdhai8 cord-314751-i9rxesrg cord-322593-bgm6smuo cord-324495-0pee1i3o cord-330035-0d6w8xyd cord-314069-8dxzf2ip cord-317617-snrumw3x cord-322760-tsxniu3j cord-316525-uadfehr6 cord-316797-sf2lu45f cord-318731-vlszl0i8 cord-333403-imx3990a cord-330825-apfcql4m cord-333331-ddcz7zck cord-327855-txryqil7 cord-329145-424vv8a8 cord-333636-h2sg6shp cord-321195-cndq6aqb cord-333043-fe24ezt6 cord-338641-s006a7m0 cord-339178-d6f6a5ds cord-338607-22f04uqe cord-334810-hw1aijwf cord-340905-8nyew5i5 cord-334090-66d8c75g cord-332811-kjgah8ts cord-340422-8f5xe4zc cord-343349-ftzjdvfj cord-338916-fqxjzavm cord-335690-66t5fjld cord-341278-klv9jdm8 cord-341469-7guojyay cord-341342-kyavg4vu cord-341383-e2jrhycj cord-346629-770qyee8 cord-344464-if6js43s cord-343131-tu6g977q cord-343780-084lq92r cord-343256-n593kh7u cord-345552-h6fwi0qn cord-348163-9q1rt8i7 cord-345957-wuk2arf9 cord-347443-0evqo01m cord-345940-adg264vb cord-355535-01h8yyqj cord-348179-i8w7huke cord-342568-3sj235rm cord-349800-s9w2yr08 cord-348147-leni23pa cord-348867-c0xpzd4d cord-345856-ckm0ol20 cord-356176-1nwjjgul cord-353797-yb355mxk cord-355512-tycuoslv cord-346928-g1dqiki6 cord-349964-38rgcc5h cord-346321-drhiqch0 cord-356192-8b96rgqa cord-349907-dwhyx97y Creating transaction Updating ent table ===== Reducing parts of speech cord-004680-u3cnsdl8 cord-004774-fvf671jn cord-004812-ikco4h5k cord-004764-tmvebf23 cord-004798-5budstbg cord-004778-xrv0qs6n cord-004724-llex3yed cord-004717-41ui4lqc cord-004681-02wem2u3 cord-004755-rmnjs1t6 cord-006459-9kizif98 cord-011105-or9azf1g cord-004810-g0y7ied0 cord-029775-mntcor5d cord-001274-vz0qvp01 cord-004690-q38ogrem cord-004793-6yh36r0w cord-004790-69lry0ys cord-004754-5596p4ma cord-004781-ajf9zig0 cord-004694-43yvs52a cord-272973-kzaowysv cord-252232-vgq6gjpx cord-004831-lu62noak cord-272955-kkkrkgg1 cord-003050-n25wnmq5 cord-004672-0lf5j8lo cord-004673-c8qcjve9 cord-285547-7m3dh8hu cord-280865-shwxhak9 cord-285429-vmnj25b5 cord-004808-6w9n03fy cord-252037-rj61mzqj cord-004802-rhkrmftn cord-004719-3stcx0dd cord-004685-qote5nx2 cord-271831-vekok62k cord-004848-2cfphi88 cord-004693-1xglujqk cord-004838-cdas57cx cord-274780-fmnro0kw cord-279676-sk9xyd1r cord-004759-jozdnhgy cord-258374-qht98q0l cord-256859-7ixegm72 cord-004713-gzts5h0y cord-261749-lq1ah16x cord-255653-0bj5eh5d cord-266716-pghnl980 cord-254405-yc1q20fz cord-004743-ido065mh cord-004720-r6b34tjm cord-265768-hwki5lk2 cord-276617-chgjpg0v cord-263193-paeosfiu cord-004729-nmkilkcx cord-265631-b0kg6qpo cord-282062-h9smg0w9 cord-258768-bjjfkfgg cord-004728-rjl35dpa cord-004825-cdvnqfjz cord-004840-4rbrzv5o cord-032801-b2ncmkjg cord-004732-mgzmzeyr cord-006674-ywzpwlrb cord-004742-5movyeb4 cord-264392-he1vekrt cord-004749-wyzb8v4a cord-276630-qci7khki cord-004727-9sniu39j cord-004827-bnf3mvaf cord-265201-ab67pnct cord-271884-86yl9ren cord-257859-9hmrt96h cord-328381-bfvdhai8 cord-283178-4wefykbi cord-281410-y558a5jf cord-262505-1ufgwxxg cord-004849-d64hnqkh cord-048485-b8xb1f12 cord-010900-2ie1v1wy cord-260708-l9w5jhsw cord-004733-i0a3igc7 cord-283525-kvcqayl4 cord-004769-hhge62sl cord-004775-foaf3vyl cord-278388-lzvtgwox cord-269948-zfbu9646 cord-277847-vgf9lz76 cord-004765-7e4yu2do cord-004766-gvom0f13 cord-004738-vnz15x84 cord-283804-dje7qbps cord-285892-tp6mlqtw cord-293945-gyb9mjb5 cord-284087-g2jfnxja cord-287275-vwyny1vt cord-285329-62yafd2d cord-294218-v4gjabp3 cord-299342-l8ugjou9 cord-295409-7l0pglef cord-280905-g2vcy9ea cord-267155-3rhdxzj3 cord-280781-u3wd27rn cord-294467-kq5wmavt cord-012032-zolowuhj cord-298883-uiwg482s cord-302871-x3mjov5l cord-026518-xv03vpji cord-004851-h9ppa064 cord-283710-55m16q7c cord-305859-vt8vwo3y cord-294947-g4ntyddb cord-270473-5tok4mqk cord-290546-zu5ns4yq cord-290695-ubrqy2zf cord-296167-np0b9a7o cord-299763-ttb7o8lv cord-267446-rpv19oy6 cord-288948-89cdfhi0 cord-286794-adbxzgvs cord-295308-ruwxm4fd cord-291530-ffex7dw9 cord-291718-cz1bi0ym cord-302323-vvo8a4hp cord-261036-zdhg4axx cord-259193-ifdjyp5b cord-289926-y1rjgbui cord-291707-dzmvjh7j cord-321195-cndq6aqb cord-302798-q0mbngqy cord-311773-r9c7sx6r cord-006106-u5npu6ng cord-294323-mryiqmsw cord-290819-zhywlf6r cord-292286-ygomb3oi cord-294138-h7sfd1wa cord-329145-424vv8a8 cord-304109-yirs7kjg cord-306380-msk9p1yy cord-299345-2i48ld8d cord-307408-6wfx0wey cord-302063-ct5rvqtd cord-310669-6hwq5jfv cord-308950-bl83r4v3 cord-312338-r6jqmes3 cord-309145-6aqc074e cord-299428-gon6bzat cord-316153-wet0go35 cord-324377-br2uorg8 cord-317009-8tqnt1l9 cord-325827-492xi3ee cord-334810-hw1aijwf cord-315811-wpeac0lk cord-307378-cx1jz7wf cord-307098-oq7zrnuv cord-306725-0vam15pt cord-312787-j7ye7ed5 cord-330035-0d6w8xyd cord-322593-bgm6smuo cord-314751-i9rxesrg cord-339991-k8z6v2vx cord-321471-gev5xq3a cord-322760-tsxniu3j cord-317617-snrumw3x cord-316525-uadfehr6 cord-314069-8dxzf2ip cord-330825-apfcql4m cord-324495-0pee1i3o cord-318731-vlszl0i8 cord-333043-fe24ezt6 cord-316797-sf2lu45f cord-333403-imx3990a cord-333331-ddcz7zck cord-338641-s006a7m0 cord-339178-d6f6a5ds cord-334090-66d8c75g cord-327855-txryqil7 cord-338607-22f04uqe cord-333636-h2sg6shp cord-332811-kjgah8ts cord-340905-8nyew5i5 cord-340422-8f5xe4zc cord-340065-f4ffvkr9 cord-341278-klv9jdm8 cord-343349-ftzjdvfj cord-338916-fqxjzavm cord-343131-tu6g977q cord-341469-7guojyay cord-343780-084lq92r cord-341342-kyavg4vu cord-344464-if6js43s cord-342568-3sj235rm cord-341383-e2jrhycj cord-346629-770qyee8 cord-345957-wuk2arf9 cord-335690-66t5fjld cord-343256-n593kh7u cord-345552-h6fwi0qn cord-348163-9q1rt8i7 cord-347443-0evqo01m cord-348179-i8w7huke cord-355535-01h8yyqj cord-345940-adg264vb cord-349800-s9w2yr08 cord-349907-dwhyx97y cord-346321-drhiqch0 cord-348147-leni23pa cord-356176-1nwjjgul cord-353797-yb355mxk cord-348867-c0xpzd4d cord-356192-8b96rgqa cord-346928-g1dqiki6 cord-355512-tycuoslv cord-349964-38rgcc5h cord-345856-ckm0ol20 Creating transaction Updating pos table Building ./etc/reader.txt cord-260708-l9w5jhsw cord-348163-9q1rt8i7 cord-294323-mryiqmsw cord-004719-3stcx0dd cord-327855-txryqil7 cord-006106-u5npu6ng number of items: 216 sum of words: 651,247 average size in words: 3,409 average readability score: 53 nouns: virus; cells; protein; infection; viruses; cell; strains; sequence; °; coronavirus; study; gene; proteins; strain; analysis; samples; sequences; mice; antibody; influenza; replication; isolates; disease; diarrhea; antibodies; activity; results; acid; detection; serum; genome; type; region; ml; assay; studies; mouse; group; culture; pigs; amino; days; data; time; genes; infections; expression; species; coronaviruses; min verbs: used; shows; infected; detected; containing; isolates; found; described; observed; binding; indicated; suggests; following; reported; including; determined; associated; obtained; induced; based; causing; identified; performed; tested; compared; produced; inoculated; neutralized; demonstrated; treated; increased; collected; incubating; expressed; purified; resulted; occurred; inhibit; revealing; strain; known; encoding; related; confirms; provide; involved; added; appeared; see; examined adjectives: viral; respiratory; porcine; human; infectious; different; specific; positive; clinical; similar; anti; infected; present; feline; bovine; genetic; high; molecular; like; new; non; nucleotide; structural; antiviral; phylogenetic; canine; acute; antigenic; several; recombinant; cellular; immune; negative; first; severe; significant; important; major; small; higher; complete; avian; low; fecal; novel; large; dependent; possible; single; common adverbs: also; however; previously; well; respectively; therefore; highly; approximately; nt; significantly; recently; furthermore; first; closely; prior; together; even; still; subsequently; later; moreover; probably; directly; clearly; relatively; genetically; twice; briefly; especially; interestingly; currently; much; experimentally; generally; newly; less; similarly; alone; mainly; least; usually; often; frequently; partially; rather; orally; initially; yet; worldwide; naturally pronouns: it; we; i; their; its; our; they; them; his; us; he; itself; one; themselves; you; her; your; s; pregn; me; hlj-073; him; clustalx; ch/; ~tcttaaaa; ourselves; mrnas; js-2/2014; inhibit/; il-12-r; ibv-212; http://www.picor; hsp70; hsp60; hm175/24a; fapn; em; de072; cq6747; cotl; chil-12; aichi/2004 proper nouns: RNA; Fig; PCR; PEDV; IBV; S; PRRSV; C; RT; A; MHV; China; N; M; SARS; TGEV; CoV; PBS; Table; FIPV; T; HA; MAbs; USA; sera; S1; B; BCV; pH; II; Japan; Virol; IFN; F; ORF; IgG; Vero; Dr.; Korea; MERS; aa; K; p.i; GenBank; D; PRCV; hepatitis; ELISA; TM; Arch keywords: virus; rna; pcr; pedv; cell; ibv; prrsv; fipv; mhv; tgev; protein; sars; mouse; ifn; bcv; sequence; sdav; rsv; mers; h1n1; dvim; dna; canine; vero; thailand; tcv; rotavirus; respiratory; prcv; pid; orf3; orf1; orf; mvc; mcmv; korean; kbsh; jhm; influenza; ictv; ibdv; h9n2; gii; fip; fecv; eav; covid-19; china; ccv; brv one topic; one dimension: virus file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086593/ titles(s): Typing of recent infectious bronchitis virus isolates causing nephritis in chicken three topics; one dimension: virus; virus; virus file(s): https://doi.org/10.1007/s00705-017-3545-4, https://www.ncbi.nlm.nih.gov/pubmed/27664026/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7098428/ titles(s): Cellular cholesterol is required for porcine nidovirus infection | Fatality risks for nosocomial outbreaks of Middle East respiratory syndrome coronavirus in the Middle East and South Korea | Genus Coltivirus (family Reoviridae): genomic and morphologic characterization of Old World and New World viruses five topics; three dimensions: virus cells infection; virus strains gene; virus rna protein; virus pedv influenza; virus bcv protein file(s): https://doi.org/10.1007/s00705-017-3545-4, https://www.ncbi.nlm.nih.gov/pubmed/16397751/, https://www.ncbi.nlm.nih.gov/pubmed/14689278/, https://www.ncbi.nlm.nih.gov/pubmed/27619798/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086705/ titles(s): Cellular cholesterol is required for porcine nidovirus infection | Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between 1995 and 2004 | Mitochondrial HSP70, HSP40, and HSP60 bind to the 3′ untranslated region of the Murine hepatitis virus genome | Experimental infection of gnotobiotic pigs with the cell-culture-adapted porcine deltacoronavirus strain OH-FD22 | Pathogenetic observations on pleural effusion disease in rabbits Type: cord title: journal-archVirol-cord date: 2021-05-30 time: 15:05 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: facet_journal:"Arch Virol" ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-265768-hwki5lk2 author: Abi, Keha-mo title: An emerging novel bovine coronavirus with a 4-amino-acid insertion in the receptor-binding domain of the hemagglutinin-esterase gene date: 2020-10-06 words: 1947.0 sentences: 91.0 pages: flesch: 50.0 cache: ./cache/cord-265768-hwki5lk2.txt txt: ./txt/cord-265768-hwki5lk2.txt summary: title: An emerging novel bovine coronavirus with a 4-amino-acid insertion in the receptor-binding domain of the hemagglutinin-esterase gene We previously reported a novel recombinant bovine coronavirus (BCoV) strain that was circulating in dairy cattle in China, but this virus was not successfully isolated, and the genetic characteristics of BCoV are still largely unknown. A 3D model constructed based on the crystal structure of bovine coronavirus hemagglutinin-esterase (SMTL ID: 3cl4.1) using the online software SWISSMODEL (https ://www.swiss model .expas y.org/inter activ e) showed that the position of the 4-aa insertion in the R3-loop between F 211 and F 212 in HE in the recombinant BCoV strains would alter the spatial conformation of the receptor-binding site relative to that in the HE recombinant strains and prototype strains lacking this insertion ( Fig. 2B and C) . abstract: The hemagglutinin-esterase (HE) protein of betacoronavirus lineage A is a secondary receptor in the infection process and is involved in the emergence of new betacoronavirus genotypes with altered host specificity and tissue tropism. We previously reported a novel recombinant bovine coronavirus (BCoV) strain that was circulating in dairy cattle in China, but this virus was not successfully isolated, and the genetic characteristics of BCoV are still largely unknown. In this study, 20 diarrheic faecal samples were collected from a farm in Liaoning province that had an outbreak of calf diarrhea (≤ 3 months of age) in November 2018, and all of the samples tested positive for BCoV by RT-PCR. In addition, a BCoV strain with a recombinant HE (designated as SWUN/A1/2018) and another BCoV strain with a recombinant HE containing an insertion (designated as SWUN/A10/2018) were successfully isolated in cell culture (TCID50: 10(4.25)/mL and 10(4.73)/mL, respectively). Unexpectedly, we identified the emergence of a novel BCoV variant characterized by a 12-nt bovine gene insertion in the receptor-binding domain in a natural recombinant HE gene, suggesting a novel evolutionary pattern in BCoV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-020-04840-y) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/33025200/ doi: 10.1007/s00705-020-04840-y id: cord-317009-8tqnt1l9 author: Aita, Tsunehiko title: Characterization of epidemic diarrhea outbreaks associated with bovine torovirus in adult cows date: 2011-12-14 words: 3922.0 sentences: 191.0 pages: flesch: 57.0 cache: ./cache/cord-317009-8tqnt1l9.txt txt: ./txt/cord-317009-8tqnt1l9.txt summary: However, other viruses, including bovine torovirus (BToV), are also suspected to be etiologic agents of diarrhea [14, 15, 21] , although the epidemiological situation of infections caused by these viruses in adult cattle remains unclear. In the present study, we report the epidemiological features of three outbreaks of epidemic diarrhea in adult cows between May 2007 and February 2008 at three dairy farms in Niigata Prefecture, Japan, in which BToV was detected as the only pathogen. Further, we describe the isolation of a cytopathogenic BToV strain from diarrheic feces using HRT-18 cells, as well as the molecular characterization of the detected BToVs. Three epidemic outbreaks of adult cattle diarrhea occurred between May 2007 and February 2008 in Niigata Prefecture, Japan. Here, we examined the etiological agents and conducted detailed serological tests with samples from three outbreaks of adult cattle diarrhea in Niigata, Japan, and found that BToV was the only causative pathogen. abstract: Bovine torovirus (BToV) is recognized as an enteric pathogen of calves, but its etiological role in diarrhea and epidemiological characterization in adult cows remain unclear. In 2007-2008, three outbreaks of epidemic diarrhea occurred in adult cows at three dairy farms in Niigata Prefecture, Japan. BToV was the only enteric pathogen detected in these outbreaks, as determined by electron microscopy, reverse transcription-PCR, bacteria and parasite tests of fecal samples, and antibody tests with paired sera. The epidemiological features of the three outbreaks were similar to those of bovine coronavirus infection, except for the absence of bloody diarrhea, with diarrhea spreading among most adult cows, but not in calves, within several days and diarrhea lasting for 3-5 days with anorexia. Decreased milk production and mild respiratory symptoms were also observed in two of the outbreaks. Nucleotide sequence analysis of the BToV nucleocapsid, spike, and hemagglutinin-esterase (HE) genes revealed a close relatedness among the detected BToV strains from each outbreak and those of Japanese BToV strain Aichi/2004. Furthermore, we isolated a BToV strain, designated Niigata (TC), from a fecal sample using a human rectal tumor cell line. Sequence analysis of this isolate and Aichi/2004 indicated that both strains have truncated HE genes with deletions in the 3′ region that occurred through cell culture-adaptation. The short projections that are believed to be formed by the HE protein on virus particles were not observed in these cultured strains by electron microscopy. Taken together, these results suggest that BToV causes epidemic diarrhea in adult cows and should be included in the differential diagnosis of diarrhea in adult cows. In addition, our findings indicate that the HE protein of BToV may not be necessary for viral replication. url: https://www.ncbi.nlm.nih.gov/pubmed/22167249/ doi: 10.1007/s00705-011-1183-9 id: cord-281410-y558a5jf author: Akashi, H. title: Propagation of the Kakegawa strain of bovine coronavirus in suckling mice, rats and hamsters date: 1981 words: 1120.0 sentences: 85.0 pages: flesch: 63.0 cache: ./cache/cord-281410-y558a5jf.txt txt: ./txt/cord-281410-y558a5jf.txt summary: title: Propagation of the Kakegawa strain of bovine coronavirus in suckling mice, rats and hamsters Infected animals died with nervous symptoms, and serial passage was readily accomplished by intracerebral inoculation with brain emulsions. Infected animals died with nervous symptoms, and serial passage was readily accomplished by intraeerebral inoculation with brain emulsions. The present paper describes briefly our recent observation that the Kakegawa strain of BCV readily propagates in suckling mice, rats and hamsters. Four-day-old mouse 3 days after intraeerebral inoculation with the 3rd mouse brain passaged Kakegawa strain (left) and an uninoeulated 4-day-old mouse (right) Four litters (10 to 12/litter) of suckling mice were inoculated intracerebrally with infected tissue culture fluid containing 106-5 TCID50/ml. These findings showed that the viruses recovered from the brains of affected animals were antigenieally the same as the cell culture passaged virus and could be clearly differentiated from the MttV strain 2. abstract: The Kakegawa strain of bovine coronavirus was easily propagated in suckling mice. Infected animals died with nervous symptoms, and serial passage was readily accomplished by intracerebral inoculation with brain emulsions. The 3rd passage viral material from infected mice evoked the same disease in suckling mice, rats and hamsters inoculated by the intracerebral or by the subcutaneous route. Viruses recovered from mice, rats and hamsters could be clearly differentiated from mouse hepatitis virus strain 2 by the neutralization test. url: https://www.ncbi.nlm.nih.gov/pubmed/6263232/ doi: 10.1007/bf01314841 id: cord-312338-r6jqmes3 author: Althani, Asma title: Characterisation of winter respiratory viral infections in patients with asthma and COPD in Qatar date: 2012-12-14 words: 2420.0 sentences: 140.0 pages: flesch: 53.0 cache: ./cache/cord-312338-r6jqmes3.txt txt: ./txt/cord-312338-r6jqmes3.txt summary: This study aimed to identify the most common viral strains responsible for respiratory tract infections in asthma/COPD patients (without exacerbations) in Qatar during the winter season (2008) (2009) . This study aimed to identify the most common viral strains responsible for respiratory tract infections in asthma/COPD patients (without exacerbations) in Qatar during the winter season (2008) (2009) . carried out a study in the UK to investigate the role of viral infections in acute exacerbations of asthma in schoolchildren, and they reported that the most commonly identified virus type in this population was rhinovirus [3] . During October 2008-March 2009, adults with COPD or asthma, seeking care at the Chest clinic of the Hamad Medical Corporation, Qatar, with symptoms of upper respiratory tract infection were eligible for participation. Our study is the first in Qatar to analyse the clinical aetiology of respiratory tract viral infections in adult patients from all age groups with asthma or COPD. abstract: Respiratory viruses in patients with chronic obstructive pulmonary disease (COPD) or asthma have not been characterised in Qatar. This study aimed to identify the most common viral strains responsible for respiratory tract infections in asthma/COPD patients (without exacerbations) in Qatar during the winter season (2008-2009). Nasal swabs from patients with asthma/COPD and respiratory symptoms were evaluated for 15 common viruses. 200 adult patients (190 with asthma and 10 with COPD) were enrolled. Viral infections were present in 36 out of 200 patients (18 %). Cough and wheezing were the most common symptoms. Rhinovirus was the most common causative agent, followed by coronaviruses. Our findings confirm previous reports of rhinovirus prevalence in respiratory tract infections in asthma/COPD. A countrywide survey to confirm our findings is warranted. url: https://doi.org/10.1007/s00705-012-1576-4 doi: 10.1007/s00705-012-1576-4 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: 5703.0 sentences: 298.0 pages: flesch: 59.0 cache: ./cache/cord-004672-0lf5j8lo.txt txt: ./txt/cord-004672-0lf5j8lo.txt summary: In this communication, the structurM proteins of the wfld-ty]pe and mutant, viruses were compared by SDS-PAGE, peptide mapping, and twodimensional gel electrophoresis to determine which of the mutant structural proteins differed from that of wild-type and the extent of homology among analogous proteins. To determine whether the arrangement of the structural proteins on the surface of mutants 205 and 280 was similar to that of wild-type, purified virions were labeled with r25I and analyzed by SDS-PAGE (Fig. 2) . Eight virus-specified intracellular proteins were resolved in wild-type and mutant strain-infected cells: A (1-2 A), B (1), C (3), D (3 CD), 1 ABC, D 2 (1 CD), alpha (1 D), and gamma (1 C). To further examine these viruses for structural differences, surface labeling of intact wild-type and mutant virus particles was done to compare the arrangement of the structural proteins which form the xdral capsids. 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-338916-fqxjzavm author: Anindita, Paulina Duhita title: Detection of coronavirus genomes in Moluccan naked-backed fruit bats in Indonesia date: 2015-02-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Bats have been shown to serve as natural reservoirs for numerous emerging viruses including severe acute respiratory syndrome coronavirus (SARS-CoV). In the present study, we report the discovery of bat CoV genes in Indonesian Moluccan naked-backed fruit bats (Dobsonia moluccensis). A partial RNA-dependent RNA polymerase gene sequence was detected in feces and tissues samples from the fruit bats, and the region between the RdRp and helicase genes could also be amplified from fecal samples. Phylogenetic analysis suggested that these bat CoVs are related to members of the genus Betacoronavirus. url: https://doi.org/10.1007/s00705-015-2342-1 doi: 10.1007/s00705-015-2342-1 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-006106-u5npu6ng author: Attoui, H. title: Genus Coltivirus (family Reoviridae): genomic and morphologic characterization of Old World and New World viruses date: 2002 words: nan sentences: nan pages: flesch: nan cache: txt: summary: 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-342568-3sj235rm author: Bald-Blume, Niklas title: Development of a molecular assay for the general detection of tospoviruses and the distinction between tospoviral species date: 2017-02-11 words: 5364.0 sentences: 277.0 pages: flesch: 54.0 cache: ./cache/cord-342568-3sj235rm.txt txt: ./txt/cord-342568-3sj235rm.txt summary: In this study a new method for plant virus diagnosis is described using the Luminex xTAG technology to test for tospoviruses in general and for the four species TSWV, WSMoV, INSV and CaCV. Infected, dried plant material of 12 tospoviral isolates from eight different species was obtained from the DSMZ including single isolates of alstroemeria necrotic streak virus (ANSV), CaCV, GRSV, IYSV, TCSV and WSMoV as well as three isolates each of INSV and TSWV. The generic tospovirus primers Tospo_GENs/as (without tags) allowed the detection of all eight tospoviruses and of all three isolates of INSV and TSWV tested in RT-PCR experiments. A molecular assay for the detection of tospoviruses in general and for viruses from the four species belonging to this genus (TSWV, INSV, CaCV and WSMoV), using the Luminex xTAG technology, was successfully developed. abstract: A Luminex xTAG-based assay for plant-infecting tospoviruses was developed. The test enables the detection of tospoviruses in general and the differentiation of the four important member species of this genus: Tomato spotted wilt virus, Impatiens necrotic spot virus, the proposed ‘Capsicum chlorosis virus’ and Watermelon silver mottle virus. The generic tospovirus primers used in this method are also applicable for detection of tospoviruses by basic RT-PCR. We also describe an economic alternative method for the distinction of the four tospoviruses mentioned and of additional member viruses, based on a restriction fragment length polymorphism (RFLP). The sophisticated Luminex xTAG technology allows the simultaneous detection of various targets. This study is part of a project that aims to develop a method for the simultaneous detection of various plant pathogens (viral, bacterial and fungal) in plant material. url: https://www.ncbi.nlm.nih.gov/pubmed/28190200/ doi: 10.1007/s00705-017-3256-x id: cord-334810-hw1aijwf author: Banyard, Ashley C. title: Repeated detection of European bat lyssavirus type 2 in dead bats found at a single roost site in the UK date: 2009-10-20 words: 1962.0 sentences: 101.0 pages: flesch: 56.0 cache: ./cache/cord-334810-hw1aijwf.txt txt: ./txt/cord-334810-hw1aijwf.txt summary: In August 2007, European bat lyssavirus type 2 (EBLV-2) was isolated from a Daubenton''s bat found at Stokesay Castle. However, studies with EBLV-1 infection in the natural host, Eptesicus serotinus, showed no substantial pattern of virus distribution in different non-neuronal organs in bats that developed disease [7] . Whilst this is widely documented for larger species, low levels of viable virus or viral RNA detected in saliva swabs tested during experimental studies with different bat lyssaviruses highlight the difficulty in determining the importance of this route of transmission for virus dissemination within a roost [5, 11, 14] . Detection of high levels of European bat lyssavirus type-1 viral RNA in the thyroid gland of experimentally infected Eptesicus fuscus bats Experimental infection of Serotine bats (Eptesicus serotinus) with European bat lyssavirus type 1a (EBLV-1a) Experimental study of European bat lyssavirus type-2 infection in Daubenton''s bats (Myotis daubentonii) abstract: In August 2007, European bat lyssavirus type 2 (EBLV-2) was isolated from a Daubenton’s bat found at Stokesay Castle. In September 2008, another bat from the same vicinity of Stokesay Castle also tested positive for EBLV-2. This is the first occurrence of repeated detection of EBLV-2 from a single site. Here, we report the detection of low levels of viral RNA in various bat organs by qRT-PCR and detection of viral antigen by immunohistochemistry. We also report sequence data from both cases and compare data with those derived from other EBLV-2 isolations in the UK. url: https://doi.org/10.1007/s00705-009-0504-8 doi: 10.1007/s00705-009-0504-8 id: cord-004690-q38ogrem author: Barthold, S. W. title: Viremic dissemination of mouse hepatitis virus-JHM following intranasal inoculation of mice date: 1992 words: 3308.0 sentences: 154.0 pages: flesch: 50.0 cache: ./cache/cord-004690-q38ogrem.txt txt: ./txt/cord-004690-q38ogrem.txt summary: Using a sensitive infant mouse bioassay to detect infectious virus, the pattern of mouse hepatitis virus (MHV) JHM dissemination in blood and other tissues was examined during the first 5 days following intranasal inoculation. Previous studies have shown that both of these mouse strains develop disseminated infections between days 3 and 5 after i.n. inoculation, but virus titers and disease are significantly greater in BALB mice compared to SJL mice [5] . The association of interferon-a/~ with viremia was explored initially by analyzing pooled samples of nasal turbinate, blood, liver, brain, or spleen obtained from 3 mice of each genotype on days 0 (controls), 1, 2, 3, and 4 after i.n. inoculation. In the current study, interferon was found in spleen and serum of MHV-JHM-infected BALB mice, but not nose, liver or brain and was not detectable in any tissue of SJL mice. abstract: Using a sensitive infant mouse bioassay to detect infectious virus, the pattern of mouse hepatitis virus (MHV) JHM dissemination in blood and other tissues was examined during the first 5 days following intranasal inoculation. MHV replicated in nasal turbinates of both susceptible BALB and resistant SJL mice from days 1 through 5, but BALB mice had higher titers on days 1 and 2. Viremia was detectable on days 1 through 5 in BALB mice, but only on days 3 and 5 in SJL mice. Transient virus replication occurred in the lungs of both mouse genotypes at 1 and 2 days, then ceased. This correlated with more consistently demonstrable virus in blood collected from the left atrium of the heart, compared to jugular vein, portal vein and right atrial blood. Virus was associated equally with the plasma and cellular fractions of blood on day 3, but was primarily in the buffy coat of the cellular fraction on day 5. Interferon-α/β was detected in serum and spleen, but not liver or brain of BALB mice or in any tissue of SJL mice. BALB serum and spleen interferon was first detected at 36h, peaked between 48 and 72h, and was undetectable by 108h. The distribution of virus in nose, cervical, axillary and mesenteric lymph nodes, spleen, Peyer's patch, thymus, bone marrow and liver was examined at 1, 2, and 3 days. The resulting pattern suggested lymphatic spread of virus to cervical lymph node and mesenteric lymph node as pathways of dissemination in addition to viremia. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086624/ doi: 10.1007/bf01321116 id: cord-272955-kkkrkgg1 author: Belsy, Acosta title: Molecular characterization of adenoviral infections in Cuba: report of an unusual association of species D adenoviruses with different clinical syndromes date: 2009-03-12 words: 4219.0 sentences: 233.0 pages: flesch: 39.0 cache: ./cache/cord-272955-kkkrkgg1.txt txt: ./txt/cord-272955-kkkrkgg1.txt summary: title: Molecular characterization of adenoviral infections in Cuba: report of an unusual association of species D adenoviruses with different clinical syndromes The objectives of this study were to identify and characterize members of different adenovirus species at the molecular level and to describe the correlation between viruses and clinical syndromes during a period of 4 years. Four isolates from clinical materials obtained from patients with encephalitis, acute flaccid paralysis and meningoencephalitis were identified as belonging to the species Human adenovirus D. In the present report, the nested PCR method used was able to detect different HAdVs in clinical samples and supernatant culture with a sensitive internal control system to assure the quality of reaction conditions in each individual tube. Human adenovirus DNA was detected in the supernatant of a cell culture infected with viruses obtained from fecal specimens taken from a patient with acute flaccid paralysis (AFP), as well as in two cases of meningoencephalitis. abstract: Adenoviruses are common pathogens that are responsible for a wide variety of infectious syndromes. The objectives of this study were to identify and characterize members of different adenovirus species at the molecular level and to describe the correlation between viruses and clinical syndromes during a period of 4 years. Between 2002 and 2006, 45 of 512 respiratory specimens (8%) from patients with acute respiratory tract infection tested positive for adenovirus. Four adenovirus isolates from samples sent for enterovirus isolation were also analyzed. This research identified 49 confirmed cases of human adenovirus infection by PCR and/or viral culture. The most common diagnosis was upper respiratory infection (44%). Human adenovirus D was the major species found (59%), followed by Human adenovirus C (36%) and Human adenovirus B (4%). Human adenovirus 5 was the major serotype found producing bronchiolitis, followed by human adenovirus 6. In patients with upper respiratory infection, the major serotype found was human adenovirus 17. Viruses of the species Human adenovirus D were identified in seven (77%) cases of acute febrile syndrome. Four isolates from clinical materials obtained from patients with encephalitis, acute flaccid paralysis and meningoencephalitis were identified as belonging to the species Human adenovirus D. Our data demonstrate a surprising result about the identification of an unusual association of viruses of the species Human adenovirus D with different clinical syndromes. This observation could be evaluated as a possible indicator of the emergence of a novel strain but further studies are required. url: https://www.ncbi.nlm.nih.gov/pubmed/19280320/ doi: 10.1007/s00705-009-0338-4 id: cord-343349-ftzjdvfj author: Bhatt, P. N. title: Experimental infection of adult axenic rats with Parker''s Rat Coronavirus date: 1977 words: 2128.0 sentences: 131.0 pages: flesch: 51.0 cache: ./cache/cord-343349-ftzjdvfj.txt txt: ./txt/cord-343349-ftzjdvfj.txt summary: Virus was recovered from the nasopharynx and trachea after twenty-four hours and from the lung by day three but was not detected in respiratory tract after seven days. Viral antigen was detected by indirect immunofluorescence in the mucosal epithelium of upper respiratory tract and in pulmonary alveolar septae from day two to six postinoculation. Dacryoadenitis did not occur, sialoadenitis was detected in only three rats and virus was recovered from only one submaxillary salivary gland. Coronavirus infection is common in laboratory rats and two antigenically related viruses, sialodacryoadenitis virus (SDAV) and Parker''s rat coronavirus (PRCV), have been isolated from naturally-infected rats (2, 7) . Virus in lungs, tracheas, nasal washings, salivary glands and lacrimal glands was quantitated for individual rats. Virus was not detected in nasopharynx, trachea and lung a~ter day six and in other tissues after day seven except in ~he submaxillary salivary gland of one rat. abstract: The pathogenesis of Parker's Rat Coronavirus (PRCV) was studied in axenic CD rats. Three to four 9 to 10 week old rats were euthanized daily for eight days after intranasal inoculation. Rats remained free of clinical disease. Virus was recovered from the nasopharynx and trachea after twenty-four hours and from the lung by day three but was not detected in respiratory tract after seven days. Viral antigen was detected by indirect immunofluorescence in the mucosal epithelium of upper respiratory tract and in pulmonary alveolar septae from day two to six postinoculation. Acute rhinitis developed by day two and was associated with mild focal necrosis of respiratory mucosal epithelium. Mild nonsuppurative tracheitis and multifocal interstitial pneumonia appeared by day five and persisted through day eight. Dacryoadenitis did not occur, sialoadenitis was detected in only three rats and virus was recovered from only one submaxillary salivary gland. This experiment indicates that PRCV can be a primary pathogen for the respiratory system of adult rats. In contrast to sialodacryoadenitis (SDA) virus the tropism of PRCV for salivary and lacrimal glands is low. url: https://www.ncbi.nlm.nih.gov/pubmed/907478/ doi: 10.1007/bf01314779 id: cord-338641-s006a7m0 author: Black, W. D. title: Reverse transcriptase-polymerase chain reaction for the detection equine rhinitis B viruses and cell culture isolation of the virus date: 2006-08-24 words: 4042.0 sentences: 214.0 pages: flesch: 56.0 cache: ./cache/cord-338641-s006a7m0.txt txt: ./txt/cord-338641-s006a7m0.txt summary: title: Reverse transcriptase-polymerase chain reaction for the detection equine rhinitis B viruses and cell culture isolation of the virus The RT-PCR was used to detect viral RNA in six of 17 nasopharyngeal swab samples from horses that had clinical signs of acute febrile respiratory disease but from which ERBV was not initially isolated in cell culture. Virus isolation in cell culture had been attempted for all 17 nasopharyngeal swab samples, but no CPE was visible during three passages on RK13, Vero and EFK cells. The conclusive determination of ERBV as the cause of equine respiratory disease by detection of virus in nasopharyngeal samples by nested RT-PCR is, however, also made difficult by the long-term persistent infection of horses with these viruses without causing apparent disease, as reported after the repeated isolation of ERBV1 over 2 years after two yearling colts were experimentally infected [3] . abstract: Equine rhinitis B virus (ERBV), genus Erbovirus, family Picornaviridae occurs as two serotypes, ERBV1 and ERBV2. An ERBV-specific nested reverse transcriptase-polymerase chain reaction (RT-PCR) that amplified a product within the 3D(pol) and 3′ non-translated region of the viral genome was developed. The RT-PCR detected all 24 available ERBV1 isolates and one available ERBV2 isolate. The limit of detection for the prototype strain ERBV1.1436/71 was 0.1 50% tissue culture infectious doses. The RT-PCR was used to detect viral RNA in six of 17 nasopharyngeal swab samples from horses that had clinical signs of acute febrile respiratory disease but from which ERBV was not initially isolated in cell culture. The sequences of these six ERBV RT-PCR positive samples had 93–96% nucleotide identity with six other partially sequenced ERBV1 isolates and one ERBV2. ERBV was isolated from one of the six samples at fourth cell culture passage when it was shown that the addition of 20 mg/mL MgCl(2) to the cell culture medium enhanced the growth of the virus. This isolated virus was antigenically similar to ERBV2.313/75. Determination of the nucleotide sequence of the P1 region of the genome also indicated that the isolate was ERBV2, and it was therefore designated ERBV2.1576/99. This is the first reported isolation of ERBV in Australia. The study highlights the utility of PCR for the identification of viruses in clinical samples that may initially be considered negative by conventional cell culture isolation. url: https://www.ncbi.nlm.nih.gov/pubmed/16932985/ doi: 10.1007/s00705-006-0810-3 id: cord-288948-89cdfhi0 author: Campalto, M. title: Divergent minute virus of canines strains identified in illegally imported puppies in Italy date: 2020-10-08 words: 1924.0 sentences: 98.0 pages: flesch: 59.0 cache: ./cache/cord-288948-89cdfhi0.txt txt: ./txt/cord-288948-89cdfhi0.txt summary: This study reports the characterization of four divergent MVC strains detected between 2012 and 2018, three of which were from dogs illegally imported into Italy, most probably from Eastern Europe, that cluster together phylogenetically but share low genetic similarity with the fourth MVC from an autochthonous dog and other available MVC sequences. In detail: the complete ORF1, encoding the NS1 protein, of three of the four MVC isolates (Italy/4033/2012, BIO-CRIME/2018 and Italy/59116/2017, which had a gap of 17 nt) was sequenced and was 2325 bases in length, corresponding to 774 aa (Fig. 1a) . The phylogenetic tree based on the ORF2 nt sequences encoding the VP1/VP2 proteins (Fig. 2c) , was constructed using all 124 MVC sequences available in the GenBank database and included the only Italian MVC sequence available, Italy/285_11/2011 (JQ612703_Canine_ minute_virus_strain_285_11_Italy_2011), for which only the partial VP1/VP2 sequence is present [9] . abstract: Minute virus of canines (MVC) belongs to the family Parvoviridae, genus Bocaparvovirus, and has been mainly described during enteritis episodes in young dogs. This study reports the characterization of four divergent MVC strains detected between 2012 and 2018, three of which were from dogs illegally imported into Italy, most probably from Eastern Europe, that cluster together phylogenetically but share low genetic similarity with the fourth MVC from an autochthonous dog and other available MVC sequences. Our data indicate that the introduction of genetically distinct MVC strains occurred through the illegal movement of dogs from a geographic area where a distinct MVC lineage was most likely circulating. Enforced surveillance of MVC in the dog population of Eastern Europe and its neighboring countries may shed light on, and eventually trace back to, illegal animal movements. url: https://doi.org/10.1007/s00705-020-04800-6 doi: 10.1007/s00705-020-04800-6 id: cord-279676-sk9xyd1r author: Carossino, Mariano title: Detection of SARS-CoV-2 by RNAscope(®)in situ hybridization and immunohistochemistry techniques date: 2020-08-05 words: 1643.0 sentences: 94.0 pages: flesch: 45.0 cache: ./cache/cord-279676-sk9xyd1r.txt txt: ./txt/cord-279676-sk9xyd1r.txt summary: In situ hybridization (ISH) and immunohistochemistry (IHC) are essential tools to characterize SARS-CoV-2 infection and tropism in naturally and experimentally infected animals and also for diagnostic purposes. In situ hybridization (ISH) and immunohistochemistry (IHC) techniques allow visualization of viral nucleic acid and protein antigens, respectively, within tissues and cells. For this purpose, the development of SARS-CoV-2-specific ISH and IHC are both critical for the assessment of viral distribution, cell tropism, and cytopathology within tissues, complementing classical histopathology, various molecular tools, and serological assays. Thus, the objective of this study was to develop RNAscope ® ISH and IHC methods for the detection of SARS-CoV-2-specific antigen and RNA in infected cells that can be utilized for both research (e.g., studies involving experimentally and naturally infected animals) and diagnostic purposes. Furthermore, the development of IHC and ISH tools is of utmost significance for understanding the pathogenesis of SARS-CoV-2 by characterizing the viral tissue distribution/cellular tropism in animal models and humans. abstract: In situ hybridization (ISH) and immunohistochemistry (IHC) are essential tools to characterize SARS-CoV-2 infection and tropism in naturally and experimentally infected animals and also for diagnostic purposes. Here, we describe three RNAscope(®)-based ISH assays targeting the ORF1ab, spike, and nucleocapsid genes and IHC assays targeting the spike and nucleocapsid proteins of SARS-CoV-2. url: https://doi.org/10.1007/s00705-020-04737-w doi: 10.1007/s00705-020-04737-w id: cord-280905-g2vcy9ea author: Carstens, E. B. title: Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2008) date: 2009-06-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In accordance with the Statutes of the International Committee of Taxonomy of Viruses (ICTV), the final stage in the process of making changes to the Universal Scheme of Virus Classification is the ratification of taxonomic proposals by ICTV Members. This can occur either at a Plenary meeting of ICTV, held during an International Congress of Virology meeting, or by circulation of proposals by mail followed by a ballot. Therefore, a list of proposals that had been subjected to the full, multi-stage review process was prepared and presented on the ICTVonline web pages in March 2008. This review process involved input from the ICTV Study Groups and Subcommittees, other interested virologists, and the ICTV Executive Committee. For the first time, the ratification process was performed entirely by email. The proposals were sent electronically via email on 18 March 2008 to ICTV Life Members (11), ICTV Subcommittee Members (74), and ICTV National Representatives (53). url: https://www.ncbi.nlm.nih.gov/pubmed/19495937/ doi: 10.1007/s00705-009-0400-2 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-004825-cdvnqfjz author: Castilla, V. title: The entry of Junin virus into Vero cells date: 1994 words: 2668.0 sentences: 141.0 pages: flesch: 50.0 cache: ./cache/cord-004825-cdvnqfjz.txt txt: ./txt/cord-004825-cdvnqfjz.txt summary: The entry mechanism of Junin virus (JV) into Vero cells was studied analyzing the effect of lysosomotropic compounds and acid pH on JV infection. Vero cells grown in coverslips were infected with JV (moi 1) and 15 mM ammonium chloride was added to the culture medium after adsorption. To reinforce that the membrane fusion activity of Junin virus is expressed at low pH, the formation of JV-induced syncytia in infected Vero cells incubated in medium at pH 5.5 or 7.5 was quantitated. In fact, a bypass of the ammonium chloride block of JV infection was achieved when the extracellular medium was at a pH below 6.1 (Fig. 5) , suggesting that the acidic conditions would probably trigger direct fusion of virus envelope with the cell membrane. abstract: The entry mechanism of Junin virus (JV) into Vero cells was studied analyzing the effect of lysosomotropic compounds and acid pH on JV infection. Ammonium chloride, amantadine, chlorpheniramine and procaine inhibited JV production. The action of ammonium chloride was exerted at early times of infection. Virus internalization was inhibited and viral protein expression was not detected. When the extracellular medium was buffered at low pH, the ammonium chloride induced block on JV infection was overcome. Furthermore, JV was able to induce fusion of infected cells at pH 5.5 leading to polykaryoctye formation. Taken together, these results demonstrate that JV entry occurs through an endocytic mechanism requiring a low pH dependent membrane fusion. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087180/ doi: 10.1007/bf01321064 id: cord-293945-gyb9mjb5 author: Chai, Weidong title: Antiviral effects of a probiotic Enterococcus faecium strain against transmissible gastroenteritis coronavirus date: 2012-11-28 words: 4304.0 sentences: 199.0 pages: flesch: 41.0 cache: ./cache/cord-293945-gyb9mjb5.txt txt: ./txt/cord-293945-gyb9mjb5.txt summary: Virus yield reduction assay ST cell monolayers were infected with TGEV with or without probiotic bacteria treatment according to the experimental design. faecium (1.00E?07 CFU/ml) when the probiotic was added to the cells together with the virus during the infection period (competition assay). faecium inactivates TGEV particles by direct physical interaction with virus, a cell-free preincubation assay was performed. faecium together with the virus significantly increases mRNA expression levels of the pro-inflammatory cytokines interleukin 6 (IL-6) and IL-8 (an approximately 3-and 13-fold increase, respectively) when compared with TGEV-infected ST cells that had not been exposed to the probiotic (Fig. 6) . faecium (pretreatment), the viability of TGEV-infected cells was protected, and virus yields were reduced (Figs. In this study, the competition assay in which virus and probiotic bacteria are present in the culture medium side by side, exhibited the most pronounced antiviral activity in terms of cell survival (Figs. abstract: The enteropathogenic coronavirus transmissible gastroenteritis virus (TGEV) causes severe disease in young piglets. We have studied the protective effects of the probiotic Enterococcus faecium NCIMB 10415 (E. faecium), which is approved as a feed additive in the European Union, against TGEV infection. E. faecium was added to swine testicle (ST) cells before, concomitantly with, or after TGEV infection. Viability assays revealed that E. faecium led to a dose-dependent rescue of viability of TGEV-infected cells reaching nearly to complete protection. Virus yields of the E. faecium–treated cultures were reduced by up to three log(10) units. Western blot analysis of purified TGEV revealed that the levels of all viral structural proteins were reduced after E. faecium treatment. Using transmission electron microscopy, we observed attachment of TGEV particles to the surface of E. faecium which might be a means to trap virus and to prevent infection. Increased production of nitric oxide in the cells treated with E. faecium and elevated expression of interleukin 6 and 8 pointed to stimulated cellular defense as a mechanism to fight TGEV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/23188495/ doi: 10.1007/s00705-012-1543-0 id: cord-004693-1xglujqk author: Chasey, D. title: Morphogenesis of avian infectious bronchitis virus in primary chick kidney cells date: 1976 words: 3300.0 sentences: 238.0 pages: flesch: 68.0 cache: ./cache/cord-004693-1xglujqk.txt txt: ./txt/cord-004693-1xglujqk.txt summary: Late in infection large numbers of virus particles were present, mainly in cytoplasmic vacuoles, and the majority were released by cell lysis. Since this mechanism is the reverse of micropinocytosis it was important to establish in which direction the vesicles at the cell surface were moving in order to distinguish outgoing particles from already released progeny virus re-entering the monolayer in a secondary cycle of infection. Virus particles were seen in the process of budding from internal membranes but, unlike strain Beaudette, appeared to form predominantly within pre-existing cytoplasmic vacuoles (Fig. 8) . The method of release of virus particles by fusion of vacuoles with the cell plasma membranes seen in ''T'' strain infected cells appears similar to the process described for coronaviruscs from human respiratory infections (12) . abstract: Primary chick kidney cells were infected with avian infectious bronchitis virus (IBV) and examined by electron microscopy. Virus particles entered the cells by viropexis and distinction could be made between engulfment by cell processes (phagocytosis) and entry by micropinocytosis in coated transport vesicles. Virus maturation occurred by budding into either the cisternae of the endoplasmic reticulum or cytoplasmic vacuoles, and evidence was obtained to suggest that the viral surface projections could be attached during the budding process. Late in infection large numbers of virus particles were present, mainly in cytoplasmic vacuoles, and the majority were released by cell lysis. Release by fusion of vacuoles with the plasma membrane was also observed, and individual virions could be transported from the endoplasmic reticulum to the surface within coated vesicles. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086645/ doi: 10.1007/bf01317869 id: cord-004738-vnz15x84 author: Chen, H. H. title: The rubella virus nonstructural protease recognizes itself via an internal sequence present upstream of the cleavage site for trans-activity date: 2006-03-27 words: 3966.0 sentences: 160.0 pages: flesch: 52.0 cache: ./cache/cord-004738-vnz15x84.txt txt: ./txt/cord-004738-vnz15x84.txt summary: To evaluate the trans-cleavage activity of RV protease on P200-derived substrates, a series of RV P200-related polypeptide expression plasmids that express protein with different N-terminal lengths from the cleavage site (72, 199, 309, and 475 residues) were constructed. To test whether replacement of P200-related sequences C-terminal to the cleavage site by non-rubella sequences affect RV protease trans-activity, the plasmid pRVS-GFP, which contains PCR-amplified RV protease substrate sequences representing polypeptide residues 827-1306 (residues 1302-1306 represent the C-terminal side of the cleavage site), fused at its C-terminus to GFP ORF in-frame, was created (Fig. 1B) . Similarly, to test whether a heterologous sequence on the N-terminal side of the cleavage site affects substrate recognition by the protease trans-activity, GFP ORF was fused in-frame at the N-terminus of the rubella sequence in the plasmid pRVS-1102-1548 to create pRVS-GFP-1102-1548 (Fig. 1B) . In this report, we have shown that RV protease trans-activity demonstrates substrate specificity by requiring an internal sequence within the region that is N-terminal to the cleavage site. abstract: The substrate requirement for rubella virus protease trans-activity is unknown. Here, we analyzed the cleavability of RV P200-derived substrates varying in their N-terminal lengths (72–475 amino acids) from the cleavage site by the RV protease trans-activity. Only substrates with at least 309 amino acid residues N-terminal to the cleavage site were able to undergo cleavage. Further, rubella sequence was found to be necessary in the N-terminal region of the substrate, whereas a heterologous sequence C-terminal to the cleavage site was tolerated. These results demonstrated a requirement for residues located between amino acids 994–1102 of the RV P200 polyprotein, besides its cleavage site for RV protease trans-activity. This region overlaps with the starting site of the essential cis-protease activity of RV P200 polyprotein. This is a novel observation for a viral protease of the family Togaviridae. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086818/ doi: 10.1007/s00705-006-0744-9 id: cord-295308-ruwxm4fd author: Chen, S.-P. title: Identification of a recombinant dengue virus type 1 with 3 recombination regions in natural populations in Guangdong province, China date: 2008-04-30 words: 1499.0 sentences: 78.0 pages: flesch: 47.0 cache: ./cache/cord-295308-ruwxm4fd.txt txt: ./txt/cord-295308-ruwxm4fd.txt summary: title: Identification of a recombinant dengue virus type 1 with 3 recombination regions in natural populations in Guangdong province, China Using recombination analysis, we identified a recombinant dengue virus type 1 strain, namely, GD23/95, with three recombination regions, located within the sequences of the prM/E junction, NS1, and NS3, respectively. This appears to be the first study to confirm the existence of three recombination regions in a single dengue virus isolate and to report recombination between parent virus strains isolated from the same geographic area (Guangdong province, China). Recombination events have been proven to occur in RNA viruses such as polioviruses [3] , feline calicivirus [4] , Western equine encephalitis virus [6] , severe acute respiratory syndrome coronavirus (SARS-CoV) [20, 21, 25] , and hepatitis C virus (HCV) [2, 9, 10, 12, 17] . abstract: Using recombination analysis, we identified a recombinant dengue virus type 1 strain, namely, GD23/95, with three recombination regions, located within the sequences of the prM/E junction, NS1, and NS3, respectively. The recombinant dengue virus was further confirmed by phylogenetic analysis based on its recombination and non-recombination regions. This appears to be the first study to confirm the existence of three recombination regions in a single dengue virus isolate and to report recombination between parent virus strains isolated from the same geographic area (Guangdong province, China). It is also the first to report breakpoints within the NS3 gene of dengue viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/18446424/ doi: 10.1007/s00705-008-0090-1 id: cord-318731-vlszl0i8 author: Chen, Si title: Molecular characterization of HLJ-073, a recombinant canine coronavirus strain from China with an ORF3abc deletion date: 2019-05-31 words: 2215.0 sentences: 137.0 pages: flesch: 57.0 cache: ./cache/cord-318731-vlszl0i8.txt txt: ./txt/cord-318731-vlszl0i8.txt summary: title: Molecular characterization of HLJ-073, a recombinant canine coronavirus strain from China with an ORF3abc deletion Interestingly, sequence analysis suggested that HLJ-073 contained a 350-nt deletion in ORF3abc compared with reference CCoV isolates, resulting in the loss of portions of ORF3a and ORF3c and the complete loss of ORF3b. This is the first report of the isolation of strain HLJ-073 in China, and this virus has biological characteristics that are different from those of other reported CCoVs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-019-04296-9) contains supplementary material, which is available to authorized users. In the present study, we report the emergence and molecular characterization of an, FCoV-like recombinant CCoV-HLJ-073, which was isolated from a fecal sample from a dead dog that exhibited enteritis. We isolated a canine coronavirus with a deletion in the ORF3abc region from a dead dog in China. abstract: Canine enteric coronaviruses (CCoVs) are important enteric pathogens of dogs. CCoVs with different variations are typically pantropic and pathogenic in dogs. In this study, we isolated a CCoV, designated HLJ-073, from a dead 6-week-old male Pekingese with gross lesions and diarrhea. Interestingly, sequence analysis suggested that HLJ-073 contained a 350-nt deletion in ORF3abc compared with reference CCoV isolates, resulting in the loss of portions of ORF3a and ORF3c and the complete loss of ORF3b. Phylogenetic analysis based on the S gene showed that HLJ-073 was more closely related to members of the FCoV II cluster than to members of the CCoV I or CCoV II cluster. Furthermore, recombination analysis suggested that HLJ-073 originated from the recombination of FCoV 79-1683 and CCoV A76, which were both isolated in the United States. Cell tropism experiments suggested that HLJ-073 could effectively replicate in canine macrophages/monocytes and human THP-1 cells. This is the first report of the isolation of strain HLJ-073 in China, and this virus has biological characteristics that are different from those of other reported CCoVs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-019-04296-9) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/31152250/ doi: 10.1007/s00705-019-04296-9 id: cord-340905-8nyew5i5 author: Chen, Yi-Ning title: Genotyping of turkey coronavirus field isolates from various geographic locations in the Unites States based on the spike gene date: 2015-08-08 words: 3189.0 sentences: 152.0 pages: flesch: 53.0 cache: ./cache/cord-340905-8nyew5i5.txt txt: ./txt/cord-340905-8nyew5i5.txt summary: The objective of the present study was to elucidate the relationship between the genotypes and geographic distribution of TCoV isolates from turkey farms in multiple states in the United States by using sequence analysis and comparing the full-length S gene. Three genetic groups, referred to as groups I, II, and III, were observed in North American TCoV isolates ( Fig. 2A) Because of the high degree of variation, most phylogenetic groupings based on the S1a deduced amino acid sequences did not have a bootstrap value over 50 % (Fig. 2B) . Nevertheless, the Texas TCoV isolates of group II and all three TCoV isolates of group III shown in the phylogenetic tree based on the full-length S nucleotide sequences still clustered according to their S1a amino acid sequences containing their HVR. In the present study, similar to previous findings with IBV strains, most of the variations in the S protein sequences among TCoV isolates were observed in the amino-terminal half. abstract: Turkey flocks have experienced turkey coronaviral enteritis sporadically in the United States since the 1990s. Twenty-four field isolates of turkey coronavirus (TCoV) from multiple states in the United States were recovered from 1994 to 2010 to determine the genetic relationships among them. The entire spike (S) gene of each TCoV isolate was amplified and sequenced. Pairwise comparisons were performed using the Clustal W program, revealing 90.0 % to 98.4 % sequence identity in the full-length S protein, 77.6 % to 96.6 % in the amino terminus of the S1 subunit (containing one hypervariable region in S1a), and 92.1 % to 99.3 % in the S2 subunit at the deduced amino acid sequence level. The conserved motifs, including two cleavage recognition sequences of the S protein, two heptad repeats, the transmembrane domain, and the Golgi retention signal were identified in all TCoV isolates. Phylogenetic analysis based on the full-length S gene was used to distinguish North American TCoV isolates from French TCoV isolates. Among the North American TCoV isolates, three distinct genetic groups with 100 % bootstrap support were observed. North Carolina isolates formed group I, Texas isolates formed group II, and Minnesota isolates formed Group III. The S genes of 24 TCoV isolates from the United States remained conserved because they contained predominantly synonymous substitutions. The findings of the present study suggest endemic circulation of distinct TCoV genotypes in different geographic locations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-015-2556-2) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/26254026/ doi: 10.1007/s00705-015-2556-2 id: cord-343131-tu6g977q author: Cheung, Andrew K. title: A divergent clade of circular single-stranded DNA viruses from pig feces date: 2013-04-24 words: 1856.0 sentences: 108.0 pages: flesch: 56.0 cache: ./cache/cord-343131-tu6g977q.txt txt: ./txt/cord-343131-tu6g977q.txt summary: Using metagenomics and molecular cloning methods, we characterized five novel small, circular viral genomes from pig feces that are distantly related to chimpanzee and porcine stool-associated circular viruses, (ChiSCV and PoSCV1). This new clade of viruses, provisionally named porcine stool-associated circular virus 2 and 3 (PoSCV2 and PoSCV3), encodes a stem–loop structure (presumably the origin of DNA replication) in the small intergenic region and a replication initiator protein commonly found in other biological systems that replicate their genomes via the rolling–circle mechanism. The viral genomes can be divided into four regions: two large ORFs with deduced amino acid sequences exhibiting homology to the Rep and Cap of ChiSCV, a LIR that encodes multiple overlapping ORFs, and an SIR that contains a palindromic sequence capable of forming a stem-loop structure. abstract: Using metagenomics and molecular cloning methods, we characterized five novel small, circular viral genomes from pig feces that are distantly related to chimpanzee and porcine stool-associated circular viruses, (ChiSCV and PoSCV1). Phylogenetic analysis placed these viruses into a highly divergent clade of this rapidly growing new viral family. This new clade of viruses, provisionally named porcine stool-associated circular virus 2 and 3 (PoSCV2 and PoSCV3), encodes a stem–loop structure (presumably the origin of DNA replication) in the small intergenic region and a replication initiator protein commonly found in other biological systems that replicate their genomes via the rolling–circle mechanism. Furthermore, these viruses also exhibit three additional overlapping open reading frames in the large intergenic region between the capsid and replication initiator protein genes. url: https://doi.org/10.1007/s00705-013-1701-z doi: 10.1007/s00705-013-1701-z id: cord-001274-vz0qvp01 author: Chitray, M. title: Genetic heterogeneity in the leader and P1-coding regions of foot-and-mouth disease virus serotypes A and O in Africa date: 2013-11-13 words: 6307.0 sentences: 285.0 pages: flesch: 52.0 cache: ./cache/cord-001274-vz0qvp01.txt txt: ./txt/cord-001274-vz0qvp01.txt summary: For this study, the L and P1 coding regions for eight FMDV A and nine FMDV O viruses isolated between 1975 and 2003 were successfully sequenced and analysed using phylogenetic analysis, examination of sequence variability, and identification of highly conserved genomic regions relating to previously identified FMDV functional and structural biological capabilities. The sub-Saharan African isolates included in this study belong to different topotypes of FMDV serotypes A and O as defined by 1D sequencing and represent a broad geographical distribution of viruses within East and West Africa. Characterising sequence variation in the VP1 capsid proteins of foot-and-mouth disease virus (serotype O) with the respect to virion structure Sequence analysis of monoclonal antibody resistant mutants of type O foot and mouth disease virus: evidence for the involvement of the three surface exposed capsid proteins in four antigenic sites abstract: Genetic information regarding the leader (L) and complete capsid-coding (P1) region of FMD serotype A and O viruses prevalent on the African continent is lacking. Here, we present the complete L-P1 sequences for eight serotype A and nine serotype O viruses recovered from FMDV outbreaks in East and West Africa over the last 33 years. Phylogenetic analysis of the P1 and capsid-coding regions revealed that the African isolates grouped according to serotype, and certain clusters were indicative of transboundary as well as intra-regional spread of the virus. However, similar analysis of the L region revealed random groupings of isolates from serotypes O and A. Comparisons between the phylogenetic trees derived from the structural coding regions and the L region pointed to a possibility of genetic recombination. The intertypic nucleotide and amino acid variation of all the isolates in this study supported results from previous studies where the externally located 1D was the most variable whilst the internally located 1A was the most conserved, which likely reflects the selective pressures on these proteins. Amino acids identified previously as important for FMDV structure and functioning were found to be highly conserved. The information gained from this study will contribute to the construction of structurally designed FMDV vaccines in Africa. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-013-1838-9) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4010724/ doi: 10.1007/s00705-013-1838-9 id: cord-004793-6yh36r0w author: Choi, C. S. title: Replication of two porcine parvovirus isolates at non-permissive temperatures date: 1990 words: 3234.0 sentences: 178.0 pages: flesch: 57.0 cache: ./cache/cord-004793-6yh36r0w.txt txt: ./txt/cord-004793-6yh36r0w.txt summary: Previous studies have shown that replication in vitro of the porcine parvovirus (PPV) isolate, KBSH, was restricted at 39°C but not at 37°C. In this study, Kresse and KBSH isolates were passaged up to ten times in swine testicle (ST) cells at non-permissive temperatures, and at subsequent passage viral protein synthesis, viral DNA synthesis, and progeny virus were evaluated. Kresse and KBSH isolates were serially passaged at non-permissive temperatures in an attempt to evaluate the effect of in vitro passages on the pattern of virus replication. KBSH appeared to gain the ability to replicate in swine fetuses following serial cell culture passages at 39 °C evidenced by fetal death and virus detection in fetal tissues. Furthermore, KBSH isolate passaged at 39 °C for 10 times now showed the ability to replicate in swine fetuses, indicating that pathogenicity can be recovered by serial adaptation at the mean body temperature of pigs, 39 °C. abstract: Previous studies have shown that replication in vitro of the porcine parvovirus (PPV) isolate, KBSH, was restricted at 39°C but not at 37°C. In contrast, replication of the Kresse isolate was restricted at 37°C but not at 39°C. In this study, Kresse and KBSH isolates were passaged up to ten times in swine testicle (ST) cells at non-permissive temperatures, and at subsequent passage viral protein synthesis, viral DNA synthesis, and progeny virus were evaluated. KBSH became adapted for replication at 39°C upon serial passages, displaying an appreciable increase in viral progeny, viral polypeptides, and viral DNA concentration. This finding was also observed with Kresse virus isolate continuously passaged at 37°C. Neither isolate became adapted for replication at 32°C. In an attempt to examine the effect of in vitro passage at non-permissive temperatures on pathogenicity in swine, KBSH passaged 10 times either at 37°C or 39°C was inoculated into swine fetuses. Two of four fetuses inoculated with 39°C-passaged KBSH were dead and hemorrhagic or mummified. All four fetuses inoculated with 39°C-KBSH contained viral antigen and viral DNA. In contrast, fetuses inoculated with 37°C-passaged KBSH, or with cell culture fluid were normal in appearance. Viral antigen and viral DNA were not demonstrated in fetuses inoculated with 37°C-KBSH or cell culture fluids. These findings suggest the possibility that the ability to replicate at 39°C is associated with virulence in swine fetuses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087007/ doi: 10.1007/bf01316676 id: cord-004849-d64hnqkh author: Choi, C. S. title: Temperature dependent replication of porcine parvovirus isolates date: 1989 words: 2338.0 sentences: 121.0 pages: flesch: 48.0 cache: ./cache/cord-004849-d64hnqkh.txt txt: ./txt/cord-004849-d64hnqkh.txt summary: The replication of four porcine parvovirus isolates, NADL-8, NADL-2, KBSH, and Kresse, in swine testes cells were compared at temperatures of 32, 37, and 39 °C. Similar patterns of cell associated virus were detected from both NADL-8 and NADL-2 infected ceils at the 3 temperatures (Fig. 2 a, b) , whereas marked differences were again observed for Kresse and KBSH-infected cells (Fig. 2 c, d) . Since marked differences in replication of Kresse and KBSH isolates were observed at 37 and 39°C evidenced by both intracellular and extracellular infectious virus and HA antigen, further characterization of viral polypeptide production was attempted. Temperature dependent differences in the number and quantity of viral polypeptides were observed in cells infected with Kresse and KBSH and propagated at either 32, 37 or 39 °C (Fig. 3 A) . To further examine the mechanism of temperature-dependent replication of PPV isolates, the synthesis of viral D N A was evaluated by nucleic acid hybridization of cell extracts (Fig. 4) . abstract: The replication of four porcine parvovirus isolates, NADL-8, NADL-2, KBSH, and Kresse, in swine testes cells were compared at temperatures of 32, 37, and 39 °C. Replication of the Kresse isolate was restricted at 32 and 37 °C as evidenced by progeny virus, virus polypeptide and viral DNA synthesis, but not at 39 °C. In contrast, replication of KBSH was restricted at 39 °C, but not at 37 or 32 °C. Findings from this study support the contention that replication of KBSH and Kresse isolates are temperature dependent. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087287/ doi: 10.1007/bf01313749 id: cord-299763-ttb7o8lv author: Choi, Jeong-Won title: Molecular characteristics of a novel strain of canine minute virus associated with hepatitis in a dog date: 2016-06-01 words: 2615.0 sentences: 128.0 pages: flesch: 49.0 cache: ./cache/cord-299763-ttb7o8lv.txt txt: ./txt/cord-299763-ttb7o8lv.txt summary: Necropsy performed on the dog revealed that the surgeries were not the cause of death; however, degenerative viral hepatitis, showing intranuclear inclusion bodies in hepatic cells, was observed in histopathologic examination. On analyzing the in situ hybridization images, hepatic cells surrounding the damaged regions and intranuclear inclusion bodies were found positive for MVC nucleic acid (Fig. 1) . However, the NP1 region of the 15D009 strain showed greater nucleotide and amino acid sequence similarity to that of the HM-6 strain (AB158475), which was isolated from a Korean dog in 2004 (99.1 % and 99.4 %, respectively), compared to those of the other MVC strains (mean similarities of 90.9-91.4 % and 93.0 %, respectively) ( Table 1 ). A minute virus of canines (MVC: canine bocavirus) isolated from an elderly dog with severe gastroenteritis, and phylogenetic analysis of MVC strains abstract: A 5-year-old female Yorkshire terrier dog died a few days following hernia and ovariohysterectomy surgeries. Necropsy performed on the dog revealed that the surgeries were not the cause of death; however, degenerative viral hepatitis, showing intranuclear inclusion bodies in hepatic cells, was observed in histopathologic examination. Several diagnostic methods were used to screen for the cause of disease, and minute virus of canines (MVC) was detected in all parenchymal organs, including the liver. Other pathogens that may cause degenerative viral hepatitis were not found. Infection with MVC was confirmed by in situ hybridization, which revealed the presence of MVC nucleic acid in the liver tissue of the dog. Through sequencing and phylogenetic analysis of the nearly complete genome sequence, the strain was found to be distinct from other previously reported MVC strains. These results indicate that this novel MVC strain might be related to degenerative viral hepatitis in dogs. url: https://www.ncbi.nlm.nih.gov/pubmed/27251050/ doi: 10.1007/s00705-016-2895-7 id: cord-004840-4rbrzv5o author: Choudhary, Manohar Lal title: Development of real-time RT-PCR for detection of human metapneumovirus and genetic analysis of circulating strains (2009-2011) in Pune, India date: 2013-08-09 words: 3379.0 sentences: 186.0 pages: flesch: 52.0 cache: ./cache/cord-004840-4rbrzv5o.txt txt: ./txt/cord-004840-4rbrzv5o.txt summary: title: Development of real-time RT-PCR for detection of human metapneumovirus and genetic analysis of circulating strains (2009-2011) in Pune, India This study describes the development of real time RT-PCR assay for the detection of all four HMPV lineages (A1, A2, B1, B2) in respiratory specimens and genotyping of circulating strains from July 2009 to August 2011 in Pune, western India. [24] designed two sets of primers and probes within the nucleoprotein gene to detect all known genetic lineages of HMPV in a one-step real-time RT-PCR. We have designed a primer-probe set using conserved regions of the nucleoprotein gene to detect all known genetic lineages of HMPV in a one-step real-time RT-PCR. Detection of human metapneumovirus RNA sequences in nasopharyngeal aspirates of young French children with acute bronchiolitis by real-time reverse transcriptase PCR and phylogenetic analysis abstract: Human metapneumovirus (HMPV) is an important respiratory virus implicated in respiratory infections. The purpose of this study was to develop a one-step real-time RT-PCR assay that can detect all four lineages of HMPV and to identify the HMPV lineages circulating in Pune, India. Conserved regions of the nucleoprotein gene were used to design real-time primers and a probe. A total of 224 clinical samples that were positive for different respiratory viruses (including 51 samples that were positive for HMPV) were tested using the real time RT-PCR assay, and the specificity of the assay was observed to be 100 %. Using in vitro-synthesized RNA, the sensitivity of the assay was ascertained to be 100 copies of the target gene per reaction. Phylogenetic analysis of the nucleoprotein (N) and attachment glycoprotein (G) genes confirmed that this assay detected all lineages of HMPV. A2, B1 and B2 strains were observed during the study period. Our assay is highly sensitive and specific for all known lineages of HMPV, making it a valuable tool for rapid detection of the virus. A2 and B2 were the predominant subtypes circulating in Pune, Western India. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087245/ doi: 10.1007/s00705-013-1812-6 id: cord-333403-imx3990a author: Christianson, K. K. title: Characterization of a temperature sensitive feline infectious peritonitis coronavirus date: 1989 words: 4008.0 sentences: 223.0 pages: flesch: 56.0 cache: ./cache/cord-333403-imx3990a.txt txt: ./txt/cord-333403-imx3990a.txt summary: The characteristics of a temperature sensitive feline infectious peritonitis virus (TS-FIPV) were examined. Viral structural proteins and RNA were synthesized at 39 °C but some undefined maturational defect prevented the formation of infectious TS-FIPV at its nonpermissive temperature. TS-FIPV proteins in supernatants from cells infected at 31 °C and 39 °C were examined by Western blot. Immune sera from both TS-FIPV vaccinated cats and WT-FIPV challenged cats showed the same differences in the envelope protein of the two viruses as did the monoclonal antibody (data not shown). The culture supernatant from TS-FIPV infected cells was monitored for the appearance of structural proteins at both the permissive and nonpermissive temperatures. All three structural proteins of TS-FIPV were detected in the cells by IFA at both the permissive and nonpermissive temperatures ( Table 2 ). Surface expression of TS-FIPV and WT-FIPV peplomer and envelope proteins but not nucleocapsid at the optimal temperature for each virus resembles the situation in FIPV-infected macrophage-like cells [8] . abstract: The characteristics of a temperature sensitive feline infectious peritonitis virus (TS-FIPV) were examined. TS-FIPV, unlike its parent strain, DF2 wild type FIPV (WT-FIPV), propagated at 31 °C (permissive temperature) but not at 39 °C (nonpermissive temperature). This temperature preference of TS-FIPV was also demonstrated in cats by the ability of the virus to replicate only at the lower temperature in the upper respiratory tract and not at systemic sites where higher temperatures (38–39 °C) prevail. Viral structural proteins and RNA were synthesized at 39 °C but some undefined maturational defect prevented the formation of infectious TS-FIPV at its nonpermissive temperature. TS-FIPV was more thermolabile than WT-FIPV which indicated alterations in the structural proteins of TS-FIPV, and a difference in the envelope protein of the two viruses was revealed by Western blot analysis. Plaque assay characterization showed that TS-FIPV produced small plaques in comparison to the large plaques of WT-FIPV. These unique characteristics possessed by TS-FIPV may account for its nonvirulent nature and ability to stimulate protective immune responses in cats. url: https://www.ncbi.nlm.nih.gov/pubmed/2558634/ doi: 10.1007/bf01311080 id: cord-346928-g1dqiki6 author: Costantini, V. title: Respiratory and fecal shedding of Porcine respiratory coronavirus (PRCV) in sentinel weaned pigs and sequence of the partial S-gene of the PRCV isolates date: 2003-11-26 words: 5893.0 sentences: 255.0 pages: flesch: 55.0 cache: ./cache/cord-346928-g1dqiki6.txt txt: ./txt/cord-346928-g1dqiki6.txt summary: Porcine respiratory coronavirus (PRCV), a spike (S) gene deletion mutant of Transmissible gastroenteritis virus (TGEV), causes mild or subclinical respiratory infections in pigs. In preliminary studies, inoculation of gnotobiotic pigs with each plaque-purified pair of the nasal and fecal PRCV isolates, revealed no clinical disease but different tropisms. Fecal and nasal swabs from the field cases (sentinel pigs), cell culture isolates and fecal and nasal swabs from gnotobiotic pigs were tested by nested-RT-PCR to detect and to differentiate TGEV and PRCV viral RNA as previously described by Kim et al. Fecal and nasal swab supernatant fluids from the sentinel field cases or the cell culture passaged PRCV isolates and nasal and fecal swabs from gnotobiotic pigs were diluted in minimum essential medium (MEM-E) and tested by CCIF to detect infectious virus using previously described procedures [23] . abstract: Porcine respiratory coronavirus (PRCV), a spike (S) gene deletion mutant of Transmissible gastroenteritis virus (TGEV), causes mild or subclinical respiratory infections in pigs. The shedding of PRCV/TGEV was studied at different days post-arrival in fecal and nasal swabs from PRCV/TGEV seronegative sentinel pigs introduced into a PRCV seropositive herd with questionable TGEV serology and diarrhea. Nasal shedding of PRCV was detected in 57% and 63% of samples by nested-RT-PCR and cell culture immunofluorescence (CCIF), respectively. However fecal shedding of PRCV was detected in 37% of the samples by nested-RT-PCR and 19% by CCIF. Four respiratory and 5 fecal PRCV strains were isolated in swine testicle cells including nasal/fecal PRCV pairs (isolated at the same time) from 3 pigs. Comparison of nasal/fecal PRCV pairs from individual pigs revealed different deletions in the spike (S) gene (648 or 681 nt) in 2 pairs and a consistent change in nt 790/791 (aa T to V) for all pairs. In preliminary studies, inoculation of gnotobiotic pigs with each plaque-purified pair of the nasal and fecal PRCV isolates, revealed no clinical disease but different tropisms. The nasal isolate was shed both nasally and in feces, but the fecal isolate was shed only marginally in feces, and not nasally. Our results show that nested-RT-PCR was as sensitive as CCIF for PRCV detection in nasal swabs, but was more sensitive than CCIF for PRCV detection in fecal samples; alternatively PRCV shed in feces was more labile with loss of infectivity. The S-gene sequence differences found between the fecal and respiratory PRCV isolates may influence their tissue tropism. These new PRCV isolates should be useful to understand the molecular basis of coronavirus tropism and evolution in infected swine. url: https://www.ncbi.nlm.nih.gov/pubmed/15098110/ doi: 10.1007/s00705-003-0245-z id: cord-344464-if6js43s author: Cowley, J. A. title: The complete genome sequence of gill-associated virus of Penaeus monodon prawns indicates a gene organisation unique among nidoviruses(*): Brief Report date: 2002 words: 3523.0 sentences: 183.0 pages: flesch: 54.0 cache: ./cache/cord-344464-if6js43s.txt txt: ./txt/cord-344464-if6js43s.txt summary: title: The complete genome sequence of gill-associated virus of Penaeus monodon prawns indicates a gene organisation unique among nidoviruses(*): Brief Report We report here a 5596 nt sequence comprising the 3′-end of the (+) ssRNA genome of gill-associated virus (GAV), an invertebrate nidovirus of Penaeus monodon prawns. The sequence extends from a subgenomic RNA start site 35 nt upstream of the 4923 nt ORF3 gene to a 3′-poly(A) tail of the 26235 nt genome of GAV. Completion of the genome sequence of GAV has revealed a gene organisation unique among nidoviruses in there is no discrete membrane protein gene and that the putative ORF3 spike glycoprotein gene resides downstream of a gene (ORF2) encoding a structural protein associated with nucleocapsids. A contig of a 5596 nt sequence from the GAV genomic 3 -poly(A) tail to an intergenic 5 -sgRNA start site 35 nt upstream of the ORF3 start codon [10] was deduced from overlapping cDNA clones (Figs. abstract: We report here a 5596 nt sequence comprising the 3′-end of the (+) ssRNA genome of gill-associated virus (GAV), an invertebrate nidovirus of Penaeus monodon prawns. The sequence extends from a subgenomic RNA start site 35 nt upstream of the 4923 nt ORF3 gene to a 3′-poly(A) tail of the 26235 nt genome of GAV. The putative 1640 amino acid (aa) ORF3 protein (MW = 182049 Da, pI = 6.62) contains 15 potential N-linked glycosylation sites, 15 potential O-linked glycosylation sites and six highly hydrophobic regions predicted to represent transmembrane (TM) domains. Three of the predicted TM domains occur in the amino-terminal 228 aa, two in the central portion, and one near the carboxy-terminus of ORF3. Only one short (83 aa) open reading frame (ORF4) was identified between ORF3 and the 3′-poly(A) tail. Completion of the genome sequence of GAV has revealed a gene organisation unique among nidoviruses in there is no discrete membrane protein gene and that the putative ORF3 spike glycoprotein gene resides downstream of a gene (ORF2) encoding a structural protein associated with nucleocapsids. url: https://www.ncbi.nlm.nih.gov/pubmed/12376758/ doi: 10.1007/s00705-002-0847-x id: cord-307378-cx1jz7wf author: Dadar, Maryam title: The association between the incidence of COVID-19 and the distance from the virus epicenter in Iran date: 2020-09-02 words: 2337.0 sentences: 112.0 pages: flesch: 49.0 cache: ./cache/cord-307378-cx1jz7wf.txt txt: ./txt/cord-307378-cx1jz7wf.txt summary: Since the first official report of the spread of SARS-CoV-2 infections in the city of Qom in mid-February, Iran has become the country most affected by the COVID-19 epidemic in the Middle East. The aim of the present study was to evaluate whether the distance from the epicenter of the infection (Qom) or demographic factors such as population density and the ratio of the elderly population are associated with the incidence of COVID-19 in different Iranian provinces. Through regression analysis, this study aimed to evaluate whether the distance of different Iranian provinces from the epicenter of the infection (Qom) was associated with the incidence of COVID-19 at the early stages of the epidemic in Iran. COVID-19 has spread to all 31 Iranian provinces, and the city of Tehran, the densely populated capital with over 13 million people located 150 km northeast of Qom, leads the country in COVID-19 cases ( Table 1) . abstract: Since the first official report of the spread of SARS-CoV-2 infections in the city of Qom in mid-February, Iran has become the country most affected by the COVID-19 epidemic in the Middle East. All Iranian provinces are now affected, although to a different extent. The aim of the present study was to evaluate whether the distance from the epicenter of the infection (Qom) or demographic factors such as population density and the ratio of the elderly population are associated with the incidence of COVID-19 in different Iranian provinces. For the purpose of determining whether the distance from the virus epicenter could be associated with the spread of infection, linear regression analysis was performed using STATA 12.0 software. The association of the incidence of COVID-19 with the population density and the ratio of the population over 65 years old in 31 Iranian provinces was also evaluated. According to our results, a strong association was found between the incidence of COVID-19 in Iranian provinces and their respective distance from Qom (p < 0.001; C = -0.68). The incidence of COVID-19 in Iranian provinces was also positively associated with the ratio of the population over 65 years old (p = 0.002; C = 0.53), while no significant association with population density was found (p = 0.39; C = 0.16). These results suggest that the implementation of travel restrictions from highly affected areas to other provinces could considerably reduce the rate of transmission of the disease throughout the country. Also, provinces with a higher proportion of elderly people (over 65) were identified as particularly at risk for the spread of SARS-CoV-2 infections. These results will contribute to better management of the COVID-19 outbreak in Iran, taking into account demographic and geographic characteristics of different provinces. url: https://doi.org/10.1007/s00705-020-04774-5 doi: 10.1007/s00705-020-04774-5 id: cord-294218-v4gjabp3 author: Dea, S. title: Intracellular synthesis and processing of the structural glycoproteins of turkey enteric coronavirus date: 1989 words: 5297.0 sentences: 256.0 pages: flesch: 49.0 cache: ./cache/cord-294218-v4gjabp3.txt txt: ./txt/cord-294218-v4gjabp3.txt summary: Pulse labeling of cells with [(35)S]methionine or [(3)H]glucosamine at different times after infection, followed by SDS-PAGE and Western immunoblotting analysis using rabbit anti-TCV hyperimmune serum, was used to resolve and identify TCV-induced intracellular proteins. In the present study, we have investigated the intracellular synthesis and post-translational modifications of virus-coded polypeptides in cultures of HRT-18 infected with TCV in the presence or the absence of glycosylation inhibitors. Radioim-munoprecipitation experiments using the anti-TCV hyperimmune serum, after [35S]methionine and [3H]glucosamine labeling, confirmed the absence of the peplomeric glycoproteins from TM-treated cells, whereas the relative amount of the unglycosylated high mol.wt, polypeptide species increased (Fig. 4A, lanes 5 and 7) . In this paper, we described the identification of virus-induced intracellular polypeptides in TCV-infected HRT-18 cells, the kinetic of their synthesis, their post-translational processing in the presence of glycosylation inhibitors and their significance with respect to the production of mature virions. abstract: Pulse labeling of cells with [(35)S]methionine or [(3)H]glucosamine at different times after infection, followed by SDS-PAGE and Western immunoblotting analysis using rabbit anti-TCV hyperimmune serum, was used to resolve and identify TCV-induced intracellular proteins. The viral structural proteins (gp200, gp140/gp66, gp100/gp120, p52, and gp24/p20) were detected in radiolabeled cell extracts by 9 to 12 hours post-infection, as well as two possible non-structural proteins with apparent mol.wts. of 36,000 and 32,000. The predominant 52,000 nucleocapsid protein could be detected in cell lysates as soon as 6 to 8 hours after infection; it was initially resolved as a complex of 3 closely migrating species with mol.wts. ranging from 46,000 to 52,000. Pulse-chase and immunoprecipitation experiments indicated that gp200 arose from a putative precursor with mol.wt. of 150,000 to 170,000, that underwent glycosylation. Proteolytic cleavage of gp200, in turn, probably yielded the gp100 and gp120 species. The unique TCV hemagglutinin protein originated from a primary precursor with mol.wt. of 60,000, which underwent rapid dimerization by disulfide bond formation and glycosylation to yield gp140. The peplomeric and matrix proteins were both shown to be N-glycosylated, as indicated by their sensitivity to tunicamycin (TM) and their resistance to sodium monensin (SM). In the presence of TM, proteins with mol.wts. of 90,000, 120–130,000, and 150,000 accumulated in TCV-infected cells rather than peplomeric glycoproteins, and the matrix protein E1 was only detected in its unglycosylated form. The addition of TM to the culture medium interfered with the maturation of progeny viral particles, as suggested by the absence of peplomers at the surface of the intravacuolar and extracellular virions, and the accumulation of amorphous material not found in the absence of the glycosylation inhibitor. High yields of virus replication were obtained, in the presence of SM, even at concentrations which greatly affected the cellular functions. url: https://www.ncbi.nlm.nih.gov/pubmed/2774975/ doi: 10.1007/bf01313956 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-006459-9kizif98 author: Deng, Guangcun title: Acute respiratory distress syndrome induced by H9N2 virus in mice date: 2009-11-28 words: 3874.0 sentences: 217.0 pages: flesch: 52.0 cache: ./cache/cord-006459-9kizif98.txt txt: ./txt/cord-006459-9kizif98.txt summary: Clinical signs, pathological changes and viral replication in lungs, arterial blood gas, and cytokines in bronchoalveolar lavage fluid (BALF) were observed at different time points after infection. Our data show that H9N2 viral infection resulted in ARDS in mice, and this may facilitate studies of the pathogenesis of future potential H9N2 disease in humans. Arterial blood gas, white blood cell counts, tumor necrosis factor (TNF)-a and interleukin (IL)-6 levels in bronchoalveolar lavage fluid (BALF), and viral titers in the lungs were measured at different times. In H9N2-virus-infected mice, we observed that circulating leukocytes dramatically decreased in the blood and that a great number of inflammatory cells infiltrated the lungs. Acute respiratory distress syndrome induced by avian influenza A (H5N1) virus in mice abstract: H9N2 avian influenza viruses have repeatedly caused infections in swine and humans in some countries. The purpose of the present study was to evaluate the pulmonary pathology caused by H9N2 viral infection in mice. Six- to eight-week-old BALB/c mice were infected intranasally with 1 × 10(4) MID(50) of A/Chicken/Hebei/4/2008(H9N2) virus. Clinical signs, pathological changes and viral replication in lungs, arterial blood gas, and cytokines in bronchoalveolar lavage fluid (BALF) were observed at different time points after infection. A control group was infected intranasally with noninfectious allantoic fluid. H9N2-infected mice exhibited severe respiratory syndrome, with a mortality rate of 60%. Gross observations showed that infected lungs were highly edematous. Major histopathological changes in infected lungs included diffuse pneumonia and alveolar damage, with neutrophil-dominant inflammatory cellular infiltration, interstitial and alveolar edema, hemorrhage, and severe bronchiolitis/peribronchiolitis. In addition, H9N2 viral infection resulted in severe progressive hypoxemia, lymphopenia, and a significant increase in neutrophils, tumor necrosis factor-α and interleukin-6 in BALF. The features described above satisfy the criteria for acute respiratory distress syndrome (ARDS). Our data show that H9N2 viral infection resulted in ARDS in mice, and this may facilitate studies of the pathogenesis of future potential H9N2 disease in humans. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101852/ doi: 10.1007/s00705-009-0560-0 id: cord-283178-4wefykbi author: Deng, Xiaoyu title: A multiplex PCR method for the simultaneous detection of three viruses associated with canine viral enteric infections date: 2018-04-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The aim of this study was to establish a multiplex PCR (mPCR) method that can simultaneously detect canine parvovirus (CPV-2), canine coronavirus (CCoV) and canine adenovirus (CAV), thereby eliminating the need to detect these pathogens individually. Based on conserved regions in the genomes of these three viruses, the VP2 gene of CPV-2, the endoribonuclease nsp15 gene of CCoV, and the 52K gene of CAV were selected for primer design. The specificity of the mPCR results showed no amplification of canine distemper virus (CDV), canine parainfluenza virus (CPIV), or pseudorabies virus (PRV), indicating that the method had good specificity. A sensitivity test showed that the detection limit of the mPCR method was 1 × 10(4) viral copies. A total of 63 rectal swabs from dogs with diarrheal symptoms were evaluated using mPCR and routine PCR. The ratio of positive samples to total samples for CPV-2, CCoV, and CAV was 55.6% (35/63) for mPCR and 55.6% (35/63) for routine PCR. Thirty-five positive samples were detected by both methods, for a coincidence ratio of 100%. This mPCR method can simultaneously detect CCoV (CCoV-II), CAV (CAV-1, CAV-2) and CPV-2 (CPV-2a, CPV-2b, CPV-2c), which are associated with viral enteritis, thereby providing an efficient, inexpensive, specific, and accurate new tool for clinical diagnosis and laboratory epidemiological investigations. url: https://www.ncbi.nlm.nih.gov/pubmed/29675651/ doi: 10.1007/s00705-018-3828-4 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-271831-vekok62k author: Dewerchin, H. L. title: Replication of feline coronaviruses in peripheral blood monocytes date: 2005-08-01 words: 4704.0 sentences: 247.0 pages: flesch: 53.0 cache: ./cache/cord-271831-vekok62k.txt txt: ./txt/cord-271831-vekok62k.txt summary: Feline infectious peritonitis virus (FIPV) (Coronaviridae) causes the most lethal viral infection in cats: FIP. In this study, infection kinetics (titres and antigen expression) of FIPV 79-1146, and FECV 79-1683, were determined in peripheral blood monocytes from 3 donor cats and compared to those in Crandell feline kidney (CrFK) cells. Two coronaviruses are described in cats: feline infectious peritonitis virus (FIPV) and feline enteric coronavirus (FECV). Within this population of 19 cats, the monocytes isolated from 9 cats showed a continuous increase in viral antigen positive cells during a 24 hour time span after inoculation with FIPV. Monocytes from 9 cats did not sustain both FIPV and FECV infection since the number of viral antigen positive cells dropped after 6 or 12 hpi (third pattern). In an infection kinetics study where another cell type, feline peritoneal macrophages, was used, different results in the antigen expression kinetics were obtained [29] . abstract: Feline infectious peritonitis virus (FIPV) (Coronaviridae) causes the most lethal viral infection in cats: FIP. The related feline enteric coronavirus (FECV) causes mild enteritis. Why these feline coronaviruses manifest so differently in vivo is not known. In this study, infection kinetics (titres and antigen expression) of FIPV 79-1146, and FECV 79-1683, were determined in peripheral blood monocytes from 3 donor cats and compared to those in Crandell feline kidney (CrFK) cells. The infection kinetics in monocytes were host dependent. Monocytes from 1 cat were resistant to both FIPV- and FECV-infection. Monocytes from the other 2 cats could initially be infected by both FIPV and FECV but FIPV infection was sustained in monocytes of only one cat. FECV-infection was never sustained and viral production was up to 100 times lower than in FIPV-infected monocytes. In CrFK cells, FIPV and FECV infection kinetics did not differ. In monocytes of a larger cat population (n = 19) the 3 infection patterns were also found. Considering all 22 investigated cats, 3/22 were not susceptible for FIPV and FECV. The rest could be infected with FECV and FIPV but 10/22 cats had monocytes that only sustained FIPV infection and 9/22 sustained neither FIPV nor FECV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/16052283/ doi: 10.1007/s00705-005-0598-6 id: cord-257859-9hmrt96h author: Di Martino, Barbara title: Molecular evidence of kobuviruses in free-ranging red foxes (Vulpes vulpes) date: 2014-01-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Red foxes (Vulpes vulpes) are susceptible to viral diseases of domestic carnivores. In this study, by screening rectal swabs collected from 34 red foxes in Italy, we identified kobuvirus RNA in five samples. Based on analysis of partial RdRp and full-length VP1 genes, all of the strains shared the highest identity with canine kobuviruses (CaKVs) recently detected in the US, the UK and Italy. These findings provide the first evidence of the circulation of these novel viruses in foxes. url: https://www.ncbi.nlm.nih.gov/pubmed/24452667/ doi: 10.1007/s00705-014-1975-9 id: cord-341383-e2jrhycj author: Dong, Wei title: Epidemiological and clinical characteristics of respiratory viral infections in children in Shanghai, China date: 2016-05-02 words: 3347.0 sentences: 178.0 pages: flesch: 52.0 cache: ./cache/cord-341383-e2jrhycj.txt txt: ./txt/cord-341383-e2jrhycj.txt summary: In this study, we investigated the prevalence and clinical characteristics of children with virus-related ARTIs and determined the spectrum of respiratory viruses and their correlation with meteorological variables in Jiading District, Shanghai, China. Investigations of the prevalence of ARTIs and its correlation with viral pathogens are critical for improving the prevention and treatment of ARTIs. There are more than 200 respiratory viruses that can cause ARTIs. Respiratory syncytial virus (RSV), human rhinovirus (HRV), human metapneumovirus (HMPV), human parainfluenza virus (PIV), human enterovirus (EV), influenza virus (IFV), human coronavirus (CoV), adenovirus (ADV), and human bocavirus (BoV) are the most common viral agents associated with ARTIs, accounting for around 70 % of ARTIs [3, 4] . Seventeen respiratory viruses, including IFV (IFV-A/B/C), PIV 1-4, EV, RSV, CoV (229E, HKU1, OC43, NL63), ADV, HMPV, BoV, and HRV were detected among 691 of 2819 children with ARTIs in Nanxiang District of Shanghai (Table 3) . abstract: Acute respiratory tract infections (ARTIs) due to various viruses are not only the most common causes of upper and lower respiratory infection but are also major causes of morbidity and mortality in children. In this study, we investigated the prevalence and clinical characteristics of children with virus-related ARTIs and determined the spectrum of respiratory viruses and their correlation with meteorological variables in Jiading District, Shanghai, China. Nasopharyngeal swabs from 2819 children with ARTIs were collected from August 2011 to December 2014, and used for detection of respiratory viruses by multiplex RT-PCR. Seventeen respiratory viruses were detected among 691 (24.5 %) of 2819 patients. The highest prevalence of respiratory viruses was detected in the age group of less than 1 year (29.0 %), and the prevalence decreased with age. This suggests that children less than one year old are the most susceptible to infection. Influenza virus (IFV) was the most frequently detected virus (5.8 %), followed by parainfluenza virus (PIV) (5.7 %), enterovirus (EV) (4.3 %), and respiratory syncytial virus (RSV) (3.6 %). Statistical analysis showed that epidemics of IFV, PIV and EV had distinct seasonal variations. Mean monthly temperature appeared to be the only meteorological factor associated with IFV and PIV infection. These findings will provide valuable information for decision-making, prevention and treatment of ARTIs in children. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-016-2866-z) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/27138548/ doi: 10.1007/s00705-016-2866-z id: cord-314069-8dxzf2ip author: Dongliu, Yuan title: Outbreak of acute febrile respiratory illness caused by human adenovirus B P14H11F14 in a military training camp in Shandong China date: 2016-06-28 words: 4283.0 sentences: 206.0 pages: flesch: 51.0 cache: ./cache/cord-314069-8dxzf2ip.txt txt: ./txt/cord-314069-8dxzf2ip.txt summary: authors: Dongliu, Yuan; Guoliang, Yang; Haocheng, Xu; Shuaijia, Qing; Li, Bing; Yanglei, Jia This study reports an outbreak of acute febrile respiratory illness caused by human adenovirus B [P14H11F14] in a military training center in China between May and June 2014. A HAdV-B [P14H11F14] virus was confirmed as the etiological pathogen of this acute outbreak of febrile respiratory illness based on clinical manifestations, epidemiological characteristics, specific molecular detection results, phylogenetic analysis, and serological assays. In conclusion, the regional CDC officials concluded that a type-55-like human adenovirus B human/CHN/SD77001/ 2014/[P14H11F14] virus was the etiological pathogen responsible for this acute FRI outbreak based on the clinical manifestations in the patients, the epidemiological characteristics of the outbreak, the HAdV-DNA-specific PCR results, isolation of the virus, sequencing and alignment of the PCR amplicons, homology and phylogenetic analyses based on the complete E1A, penton base, hexon, and fiber gene sequences, and serological assays specific for HAdV IgA/IgG. abstract: This study reports an outbreak of acute febrile respiratory illness caused by human adenovirus B [P14H11F14] in a military training center in China between May and June 2014. In total, 164 military personnel were affected, and two patients were admitted into the intensive care unit of the military regional central hospital. A HAdV-B [P14H11F14] virus was confirmed as the etiological pathogen of this acute outbreak of febrile respiratory illness based on clinical manifestations, epidemiological characteristics, specific molecular detection results, phylogenetic analysis, and serological assays. The virus was isolated by the rhabdomyosarcoma cell culture method, and the complete sequences of the E1A, penton base, hexon, and fiber genes were determined and deposited in the GenBank database. Phylogenetic and sequence homology analyses indicated that the isolated strain is most closely related to some HAdV-55 strains from mainland China. However, this strain appeared to be less virulent than former HAdV-55 strains. According to the chest X-ray results of 31 affected patients, there was no radiological evidence of pneumonia. The most frequent symptoms in these patients were sore throat (95.12 %, 156/164) and tonsillitis (93.29 %, 153/164). During the course of the outbreak, incorrect response measures and some potential risk factors, such as fire training and marching training, may have exacerbated the spread of the infection. This outbreak illustrates the urgent need to improve the epidemiological and etiological surveillance of HAdV infections and to improve the ability of doctors and health officials in basic units of the Chinese army to respond effectively to febrile respiratory illness. url: https://doi.org/10.1007/s00705-016-2949-x doi: 10.1007/s00705-016-2949-x id: cord-286794-adbxzgvs author: Du, Juan title: Identification and complete genome characterization of human enterovirus 117 from a child with pneumonia in China date: 2019-03-16 words: 1172.0 sentences: 61.0 pages: flesch: 54.0 cache: ./cache/cord-286794-adbxzgvs.txt txt: ./txt/cord-286794-adbxzgvs.txt summary: title: Identification and complete genome characterization of human enterovirus 117 from a child with pneumonia in China In this study, human enterovirus C117 (EV-C117) was detected in a 3-month-old boy diagnosed with pneumonia in China. Here, we report the identification and complete genomic sequence of EV-117 in a child with pneumonia in China, which may provide more information for understanding EV-C117 infection. Using multiple primers (Table 1) , we determined the full-length viral genome sequence of the strain detected in patient CQ6747 (GenBank accession no. Conversely, all genome regions of CQ6747 showed less similarity to other EV-C strains (including EV-C104, EV-C105, EV-C109, and EV-C118) ( Table 2) . Complete genomic sequencing shows that polioviruses and members of human enterovirus species C are closely related in the noncapsid coding region Complete genome sequence of a novel human enterovirus C (HEV-C117) identified in a child with communityacquired pneumonia Respiratory infection with enterovirus genotype C117, China and Mongolia abstract: In this study, human enterovirus C117 (EV-C117) was detected in a 3-month-old boy diagnosed with pneumonia in China. A phylogenetic analysis showed that this strain was genetically closer to the Lithuanian strain than to the USA strain. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-019-04196-y) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-019-04196-y doi: 10.1007/s00705-019-04196-y id: cord-004754-5596p4ma author: Duan, X. title: Effects of origin and state of differentiation and activation of monocytes/macrophages on their susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) date: 2014-04-06 words: 4875.0 sentences: 252.0 pages: flesch: 50.0 cache: ./cache/cord-004754-5596p4ma.txt txt: ./txt/cord-004754-5596p4ma.txt summary: title: Effects of origin and state of differentiation and activation of monocytes/macrophages on their susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) To evaluate the effect of maturation of monocytes/macrophages on their susceptibility to PRRSV, freshly isolated AMf, PMf and BMo from ®ve donors were seeded in 24-well tissue culture plates at a concentration of 10 6 cells/ml/well and further incubated in RPMI medium plus 5% of foetal bovine serum at 37 C with 5% CO 2 . The virus titres and percentage of viral antigen positive cells in freshly isolated porcine AMf at 24 and 48 h after inoculation were respectively 1 to 2 log 10 TCID 50 and 5 to 10 times lower than those of one day cultivated ones, which is signi®cantly different (P''0.01). Porcine reproductive and respiratory syndrome virus infection of alveolar macrophages can be blocked by monoclonal antibodies against cell surface surface antigens abstract: In this study, the susceptibility of porcine peripheral blood monocytes (BMo), peritoneal macrophages (PMφ) and alveolar macrophages (AMφ) to PRRSV was examined. To test the effect of differentiation and activation on their susceptibility, AMφ and BMo were aged, cultivated in either adhesion or suspension and treated with bacterial lipopolysaccharide (LPS) and phorbol myristate acetate (PMA). It was found that freshly isolated PMφ and BMo were non-permissive to PRRSV. PMφ remained refractory but a few BMo became susceptible after 1 day cultivation. AMφ were permissive with a significant increase of their susceptibility after one day cultivation. In a binding assay, it was demonstrated that the attachment of biotinylated PRRSV to AMf is much more efficient than to PMφ and BMo. Two monoclonal antibodies (Mabs) 41D3 and 41D5 which block PRRSV infection of AMφ and are directed against a candidate receptor for PRRSV only reacted with the cell membrane of AMφ. PMA treatment of AMφ blocked PRRSV replication in the cells in a dose-dependent manner. The blocking effect of PMA decreased after 9 h continuous pre-treatment and diminished after 24 h continuous pre-treatment. PMA treatment did not affect the binding of PRRSV and MAb 41D3 and 41D5 to AMφ. Direct or indirect treatment of AMφ and BMo with LPS or cultivation in suspension did not significantly affect their susceptibility. These results provide clear evidence that PRRSV has a strongly restricted tropism for only some sub-populations of porcine monocytes/macrophages and that some specific states of differentiation and activation of monocytes/macrophages considerably affect their susceptibility. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086874/ doi: 10.1007/s007050050256 id: cord-310669-6hwq5jfv author: Erles, K. title: Investigation into the causes of canine infectious respiratory disease: antibody responses to canine respiratory coronavirus and canine herpesvirus in two kennelled dog populations date: 2005-04-21 words: 4104.0 sentences: 205.0 pages: flesch: 60.0 cache: ./cache/cord-310669-6hwq5jfv.txt txt: ./txt/cord-310669-6hwq5jfv.txt summary: Two training centres for working dogs were monitored for one year to determine the presence of viruses and viral antibodies and their association with canine infectious respiratory disease (CIRD). Canine herpesvirus (CHV) has been detected in dogs with CIRD [3] the importance of this infection in the pathogenesis of the disease however has not yet been determined. From dogs that were not on the study but showed clinical symptoms of CIRD, both a blood sample and a swab were taken at the time of disease as well as four weeks after. In total twelve out of 54 serum samples (22.2%) obtained from dogs on the day they entered Kennel A were positive for antibodies to CRCoV. None of the samples obtained from dogs at Kennel B tested by PCR for CRCoV (n = 28), CPIV (n = 18), CAV (n = 9) or CHV (n = 26) were found positive. abstract: Two training centres for working dogs were monitored for one year to determine the presence of viruses and viral antibodies and their association with canine infectious respiratory disease (CIRD). Tonsillar swabs and serum were obtained from dogs on entry into the kennels and in regular intervals thereafter. Additional samples were collected during outbreaks of CIRD. The swabs were examined by virus culture and PCR for canine parainfluenza virus, canine adenovirus, canine herpesvirus (CHV) and canine respiratory coronavirus (CRCoV). Furthermore the prevalence of antibodies to CHV and CRCoV was determined. During this study CIRD was reported mainly in one of the two kennels investigated. In that kennel antibody responses to CRCoV indicated a seasonal occurrence of the virus, which coincided with two outbreaks of respiratory disease. CHV antibody responses were detected throughout the year. In the other kennel, which reported few cases of CIRD a high prevalence of antibodies to CRCoV was detected on entry but only sporadic seroconversions to CRCoV or CHV. By PCR three dogs were found positive for CRCoV in one kennel whereas all PCR tests for other viruses were negative for both kennels. Virus culture failed to detect any viruses in either kennel. url: https://www.ncbi.nlm.nih.gov/pubmed/15841339/ doi: 10.1007/s00705-005-0533-x id: cord-291530-ffex7dw9 author: Escutenaire, S. title: Characterization of divergent and atypical canine coronaviruses from Sweden date: 2007-05-29 words: 2326.0 sentences: 129.0 pages: flesch: 57.0 cache: ./cache/cord-291530-ffex7dw9.txt txt: ./txt/cord-291530-ffex7dw9.txt summary: Field canine coronaviruses (CCVs) identified during a series of outbreaks of gastroenteritis in Swedish dogs were subjected to genetic analysis involving the open reading frame 1b (ORF1b) and the membrane (M) and spike (S) protein genes. Four field viruses originating from the Stockholm region presented identical sequences and segregated separately from other CCVs characterized so far and from GOT/05, the variant recovered in Western Sweden. In the alignment based on 3 0 S gene sequences, the Swedish field viruses displayed higher ranges of nucleotide and amino acid identity with both CCVs and FCoVs of type II (Table 2 ). Comparable or even higher percentages of nucleotide variation were observed between GOT=05 and the same reference strains, thus suggesting that GOT=05 also constitutes a genetically distinct variant among CCVs. In addition, 5 0 S gene sequences related to CCV type I were identified among the SWE1 viruses and UPPS2=04. abstract: Field canine coronaviruses (CCVs) identified during a series of outbreaks of gastroenteritis in Swedish dogs were subjected to genetic analysis involving the open reading frame 1b (ORF1b) and the membrane (M) and spike (S) protein genes. Four field viruses originating from the Stockholm region presented identical sequences and segregated separately from other CCVs characterized so far and from GOT/05, the variant recovered in Western Sweden. A recombinant origin of the fifth virus identified in the Stockholm region is suggested. In addition, the five viruses originating from the same geographical area displayed atypical 5′ S gene sequences. url: https://www.ncbi.nlm.nih.gov/pubmed/17533554/ doi: 10.1007/s00705-007-0986-1 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-004673-c8qcjve9 author: Faaberg, K. S. title: Membrane association of the C-terminal half of the open reading frame 1a protein of lactate dehydrogenase-elevating virus date: 1996 words: 4647.0 sentences: 220.0 pages: flesch: 55.0 cache: ./cache/cord-004673-c8qcjve9.txt txt: ./txt/cord-004673-c8qcjve9.txt summary: cDNAs encoding ORF 1a protein segments encompassing transmembrane segments 5 to 11 and its amphipathic C-terminal end as well as the N-terminal 80 amino acids of the downstream ORF 1b protein were transcribed and the transcripts in vitro translated in the absence and presence of microsomal membranes. Eisenberg hydrophobic moment analysis of the protein predicted the presence of eleven transmembrane segments in the C-terminal half of the molecule (amino acids 980-1852) that flank the serine protease domain, cDNAs encoding ORF la protein segments encompassing transmembrane segments 5 to 11 and its amphipathic C-terminal end as well as the N-terminal 80 amino acids of the downstream ORF lb protein were transcribed and the transcripts in vitro translated in the absence and presence of microsomal membranes. In the present study we provide strong evidence that the segment of LDV ORF la protein with transmembrane segments 5-11 (see Fig. 1 ) becomes intimately associated with endoplasmic reticulum (ER) membranes during synthesis and that none of its potential N-glycosylation sites becomes glycosylated. abstract: ORF 1a of lactate dehydrogenase-elevating virus, strain P (LDV-P), encodes a protein of 2206 amino acids. Eisenberg hydrophobic moment analysis of the protein predicted the presence of eleven transmembrane segments in the C-terminal half of the molecule (amino acids 980–1852) that flank the serine protease domain. cDNAs encoding ORF 1a protein segments encompassing transmembrane segments 5 to 11 and its amphipathic C-terminal end as well as the N-terminal 80 amino acids of the downstream ORF 1b protein were transcribed and the transcripts in vitro translated in the absence and presence of microsomal membranes. The synthesis of the protein products with putative transmembrane segments was enhanced by the presence of the microsomal membranes and the proteins became membrane associated. When synthesized in the absence of membranes they were recovered in the supernatant upon ultracentrifugation of the translation reaction mixtures, whereas they were recovered in the membrane pellet when synthesized in the presence of membranes. Furthermore, the latter proteins were not released from the membranes by disruption of the membrane vesicles in carbonate buffer, pH 11.5, and large portions of the proteins were resistant to digestion by trypsin, chymotrypsin and proteinase K. No N-glycosylation was observed and only little, if any, processing of the protein by the putative serine protease. The results indicate that the C-terminal half of the ORF 1a protein represents a non-glycosylated integral membrane protein. Potential modes of synthesis and function of the protein are discussed. In addition, the results showed that the synthesis of the ORF 1a protein was generally terminated at its termination codon, but that read-through into the ORF 1b gene occurred with low frequency. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086564/ doi: 10.1007/bf01718835 id: cord-284087-g2jfnxja author: Falcone, Valeria title: Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season date: 2013-02-09 words: 3417.0 sentences: 189.0 pages: flesch: 51.0 cache: ./cache/cord-284087-g2jfnxja.txt txt: ./txt/cord-284087-g2jfnxja.txt summary: In this study, we investigated the molecular evolution of influenza virus A(H1N1)pdm09 in the 2010/11 influenza season in southern Germany by sequence analysis of the influenza virus hemagglutinin gene from 25 patients with mild, moderate, and severe disease. The H275Y mutation in the influenza virus neuraminidase gene, known to confer resistance to the neuraminidase inhibitor oseltamivir, was detected in one patient. Aim of this study was to investigate the molecular evolution of A(H1N1)pdm09 in the 2010/11 influenza season in southern Germany by sequence analysis of the HA gene of mild, moderate, and severe influenza cases. In order to detect molecular changes in the HA gene of influenza virus, 33 A(H1N1)pdm09 HA sequences representing 25 individual patients were analysed. e., C 2 weeks) of influenza virus in the respiratory tract was observed in 6 of the 25 patients (24 %; 3 with severe, 2 with moderate, and 1 with mild disease). abstract: A novel influenza A virus emerged in early 2009 to cause the first influenza pandemic of the 21(st) century. Understanding the evolution of influenza virus is crucial to determine pathogenesis, vaccine efficacy, and resistance to antiviral drugs. In this study, we investigated the molecular evolution of influenza virus A(H1N1)pdm09 in the 2010/11 influenza season in southern Germany by sequence analysis of the influenza virus hemagglutinin gene from 25 patients with mild, moderate, and severe disease. Phylogenetic analysis revealed co-circulation of different genetic groups. The D222G mutation, which had previously been observed in severe cases, was not detected. Immunocompromised patients were not affected more severely than non-immunocompromised patients (p>0.05), although longer shedding was observed in some of them. Interestingly, additional mutations and potential glycosylation sites were detected in samples from the lower respiratory tract in two patients, but not in the corresponding upper respiratory tract specimens. The H275Y mutation in the influenza virus neuraminidase gene, known to confer resistance to the neuraminidase inhibitor oseltamivir, was detected in one patient. url: https://www.ncbi.nlm.nih.gov/pubmed/23397331/ doi: 10.1007/s00705-013-1610-1 id: cord-004713-gzts5h0y author: Fennestad, K. L. title: Pathogenetic observations on pleural effusion disease in rabbits date: 1985 words: 3596.0 sentences: 193.0 pages: flesch: 53.0 cache: ./cache/cord-004713-gzts5h0y.txt txt: ./txt/cord-004713-gzts5h0y.txt summary: A pathogenetic study of pleural effusion disease (PED) in rabbits was made, using the virulent PED agent or virus (PEDV) and an avirulent derivate of this isolate. Support for this contention is the enhancement of virulence of PED virus (PEDV) observed in the "natural" disease and --after its isolation --by continued serial propagation in rabbits at intervals of 3---10 days (Fig. 1) . However, there is also evidence which might suggest that increasing time of persistence of virulent virus in the individual rabbit host may operate in the reverse direction by selecting a population of predominantly avirulent PEDV particles, which appear to be unable to cause disease unless undergoing new rabbit passages at short intervals (t, 6). After infection with the avirulent derivate, the isolates from serum obtained during the entire period of viraemia were demonstrable in serum dilution 10 -1 to 10 -a, but the primary rabbit inoculation of these dilutions never resulted in clinical signs of PED. abstract: A pathogenetic study of pleural effusion disease (PED) in rabbits was made, using the virulent PED agent or virus (PEDV) and an avirulent derivate of this isolate. Independent of infective dose within the range examined, the virulent isolate caused fatal clinical disease, whereas the avirulent isolate caused subclinical infection. The two isolates differed in rapidity of initial spread of infection and in the maximum virus titres in serum, but they both resulted in a similar low level persisting viraemia. Circulating virulent virus gradually became avirulent during the viraemia. Avirulent infection induced protective immunity to virulent challenge during the first week after primary infection, but full clinical protection was not established until after the fourth week. The findings, corrobated with other closely comparable observations, suggest that the emergence of PED as an intercurrent mortality problem during rabbit passage of pathogenicTreponema pallidum is the result of a specific selective pressure on a benign passenger virus. The expression of virulence of PEDV appears to be dependent on length of interval between passages. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086705/ doi: 10.1007/bf01378969 id: cord-004727-9sniu39j author: Fennestad, K. L. title: Pleural effusion disease in rabbits: Observations on viraemia, immunity and transmissibility date: 1981 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Baby rabbits surviving infection with pleural effusion disease virus (PEDV) developed viraemia persisting for at least six months. Only the infectious serum samples collected during the first 2 months of disease could transfer the typical PED. Six months after neonatal infection, virus concentration in serum was 10(2) to 10(4) rabbit-infectious doses per ml, the level of IgG appeared elevated, and serum rendered non-infectious by ether-treatment had a protective effect in passive immunisation experiments. No evidence of glomerulonephritis or deposits of immunoglobulins could be demonstrated in the kidneys. During the nursing period PEDV was transmitted from infected baby rabbits to two out of four dams, but not to control litter-mates. After the nursing period control rabbits, caged together with the viraemic rabbits for 60 to 150 days, remained free from PEDV infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086771/ doi: 10.1007/bf01320789 id: cord-290546-zu5ns4yq author: Fennestad, K. L. title: Pleural effusion disease in rabbits. Properties of the aetiological agent date: 1983 words: 3821.0 sentences: 403.0 pages: flesch: 83.0 cache: ./cache/cord-290546-zu5ns4yq.txt txt: ./txt/cord-290546-zu5ns4yq.txt summary: The size and heat sensitivity of Pleural effusion disease (PED) agent or virus (PEDV) propagated in rabbits were examined. PEDV and the Stockholm agent appeared identical concerning pathogenic and immunogenic properties by infection experiments and protection tests in rabbits. The third isolate, obtained from the laboratory, which several years previously had supplied material for demonstration of the Stockholm agent, differed from PEDV in pathogenic and immunogenic properties. Stock PEDV consisted of pooled rabbit sera obtained 48 hours after subcutaneous inoculation with pleural fluid or infectious serum. Stocks of the Stockholm agent and the three isolates were from the first or second rabbit passage, prepared in the same manner as for PEDV. HCV229E and CV Paris were used as antigens in E L I S A to detect antibody rises to coronaviruses in paired sere from 20 rabbits infected with the 5 isolates. abstract: The size and heat sensitivity of Pleural effusion disease (PED) agent or virus (PEDV) propagated in rabbits were examined. The infectious particles were estimated to be between 25 and 50 nm by filtration. Residual infectivity of infectious serum was 0.1 per cent after heating at 56° C for 4 hours. PEDV and the Stockholm agent appeared identical concerning pathogenic and immunogenic properties by infection experiments and protection tests in rabbits. Two of the three PEDV isolates were less pathogenic but appeared immunogenically identical to PEDV. The third isolate, obtained from the laboratory, which several years previously had supplied material for demonstration of the Stockholm agent, differed from PEDV in pathogenic and immunogenic properties. Serological examinations of paired rabbit sera did not indicate any antigenic relationship between PEDV and representative members of the two mammalian coronavirus antigenic groups. It is concluded that the aetiological agent of PED is a virus not belonging to the coronaviridae. url: https://www.ncbi.nlm.nih.gov/pubmed/6409056/ doi: 10.1007/bf01311102 id: cord-004749-wyzb8v4a author: Forsyth, M. title: Rhinovirus detection using probes from the 5′ and 3′ end of the genome date: 1989 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This study investigated the abilities of cDNA probes from the 5′ and 3′ ends of the genome of human rhinoviruses (HRV-) 14, 9, and 1B to detect RNA from 59 rhinovirus serotypes. The results show that probes from the 5′ end of the genomes of HRV-14, 9, and 1B detected a large number of serotypes but the detection rate was variable and depended on the degree of homology with the particular probe. In contrast, all the 3′ end probes were specific for the homologous virus. However, along HRV-9 probe detected a large number of serotypes. It was concluded that such cDNA probes would not detect all serotypes with equal efficiency. Synthetic oligonucleotides corresponding to short but highly conserved regions in the 5′ non coding region may overcome this problem. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086855/ doi: 10.1007/bf01313878 id: cord-311773-r9c7sx6r author: Gaertner, Diane J. title: Susceptibility of rodent cell lines to rat coronaviruses and differential enhancement by trypsin or DEAE-dextran date: 1991 words: 2675.0 sentences: 150.0 pages: flesch: 57.0 cache: ./cache/cord-311773-r9c7sx6r.txt txt: ./txt/cord-311773-r9c7sx6r.txt summary: Cell lines of rodent origin were tested for susceptibility to infection with rat coronavirus (RCV), including sialodacryoadenitis virus (SDAV) and Parker''s rat coronavirus (PRCV). In a single attempt to isolate SDAV-681 from the lung of an experimentally infected rat, syncytia and viral antigen were first seen after 6 passages in untreated L2 (Percy) cells. Based on this finding, a small study was initiated to ascertain the sensitivity of trypsin-treated L2 (Percy) cells for primary isolation of RCVs. Virus isolations were attempted using tissue homogenates previously tested for SDAV-681 by infant mouse inoculation (Table 4 ). Of the cell lines and treatments tested, L2 (Percy) cells treated with trypsin supported maximal growth of RCVs as evidenced by syncytium formation and viral antigen. RCV growth in L2 (Percy) cells was not enhanced by trypsin treatment of later passages when the enzyme was added at the time of virus inoculation. abstract: Cell lines of rodent origin were tested for susceptibility to infection with rat coronavirus (RCV), including sialodacryoadenitis virus (SDAV) and Parker's rat coronavirus (PRCV). LBC rat mammary adenocarcinoma cells were susceptible only if the cells were treated with diethylaminoethyl-dextran (DEAE-D). A recent report that RCVs grow well in L2 mouse fibroblast cells was confirmed and expanded. RCV infection of L2 cells was substantially enhanced by treatment of cells with trypsin but not by treatment with DEAE-D. Primary isolation of SDAV from experimentally infected rats was accomplished using trypsin-treated L2 cells. One of 13 additional cell lines tested (rat urinary bladder epithelium, RBL-02) supported growth of RCVs, and growth was slightly enhanced by DEAE-D, but not by trypsin. These refinements of in vitro growth conditions for RCVs should facilitate further studies of their basic biology and improve options for primary isolation. url: https://www.ncbi.nlm.nih.gov/pubmed/2048975/ doi: 10.1007/bf01311303 id: cord-004742-5movyeb4 author: García-Luque, I. title: The nucleotide sequence of the coat protein genes and 3′ non-coding regions of two resistance-breaking tobamoviruses in pepper shows that they are different viruses date: 1993 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The nucleotide sequence of the coat protein genes and 3′ non-coding regions of two different resistance-breaking tobamoviruses in pepper have been determined. The deduced coat protein of an Italian isolate of pepper mild mottle virus (PMMV-I) consists of 156 amino acids and its 3′ non-coding region is 198 nucleotides long. They have been found to be very similar in sequence and structure to those previously reported for a Spanish isolate (PMMV-S). In contrast, a Dutch isolate termed P 11 codes for a coat protein of 160 amino acids and its 3′ non-coding region is 291 nucleotides long, which may have arisen by duplication. The nucleotide and the predicted coat protein amino acid sequence analysis show that this isolate should be considered as a new virus within the tobamovirus group. The term paprika mild mottle virus (PaMMV) is proposed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086834/ doi: 10.1007/bf01379081 id: cord-302798-q0mbngqy author: Ge, Junwei title: Genomic characterization of circoviruses associated with acute gastroenteritis in minks in northeastern China date: 2018-06-14 words: 4343.0 sentences: 273.0 pages: flesch: 58.0 cache: ./cache/cord-302798-q0mbngqy.txt txt: ./txt/cord-302798-q0mbngqy.txt summary: In this study, the role of circoviruses (CVs) in mink acute gastroenteritis was investigated, and the MiCV genome was molecularly characterized through sequence analysis. MiCVs and previously characterized CVs shared genome organizational features, including the presence of (i) a potential stem-loop/nonanucleotide motif that is considered to be the origin of virus DNA replication; (ii) two major inversely arranged open reading frames encoding putative replication-associated proteins (Rep) and a capsid protein; (iii) direct and inverse repeated sequences within the putative 5ʹ region; and (iv) motifs in Rep. Pairwise comparisons showed that the capsid proteins of MiCV shared the highest amino acid sequence identity with those of porcine CV (PCV) 2 (45.4%) and bat CV (BatCV) 1 (45.4%). In our study, sequence analysis confirmed that MiCV genomes displayed the characteristics of members of the genus Circovirus, and the common features included their genome organization, the presence of a potential stem-loop and conserved nonanucleotide motif postulated to be the origin of viral DNA replication, and major ORFs and repeats [26, 27] . abstract: Mink circovirus (MiCV), a virus that was newly discovered in 2013, has been associated with enteric disease. However, its etiological role in acute gastroenteritis is unclear, and its genetic characteristics are poorly described. In this study, the role of circoviruses (CVs) in mink acute gastroenteritis was investigated, and the MiCV genome was molecularly characterized through sequence analysis. Detection results demonstrated that MiCV was the only pathogen found in this infection. MiCVs and previously characterized CVs shared genome organizational features, including the presence of (i) a potential stem-loop/nonanucleotide motif that is considered to be the origin of virus DNA replication; (ii) two major inversely arranged open reading frames encoding putative replication-associated proteins (Rep) and a capsid protein; (iii) direct and inverse repeated sequences within the putative 5ʹ region; and (iv) motifs in Rep. Pairwise comparisons showed that the capsid proteins of MiCV shared the highest amino acid sequence identity with those of porcine CV (PCV) 2 (45.4%) and bat CV (BatCV) 1 (45.4%). The amino acid sequence identity levels of Rep shared by MiCV with BatCV 1 (79.7%) and dog CV (dogCV) (54.5%) were broadly similar to those with starling CV (51.1%) and PCVs (46.5%). Phylogenetic analysis indicated that MiCVs were more closely related to mammalian CVs, such as BatCV, PCV, and dogCV, than to other animal CVs. Among mammalian CVs, MiCV and BatCV 1 were the most closely related. This study could contribute to understanding the potential pathogenicity of MiCV and the evolutionary and pathogenic characteristics of mammalian CVs. url: https://www.ncbi.nlm.nih.gov/pubmed/29948383/ doi: 10.1007/s00705-018-3908-5 id: cord-252037-rj61mzqj author: Gerna, G. title: Changing circulation rate of human metapneumovirus strains and types among hospitalized pediatric patients during three consecutive winter-spring seasons date: 2005-06-28 words: 2203.0 sentences: 116.0 pages: flesch: 44.0 cache: ./cache/cord-252037-rj61mzqj.txt txt: ./txt/cord-252037-rj61mzqj.txt summary: In this study, we examined: i) the circulation rate of hMPV among the other respiratory viruses during 3 consecutive winter-spring seasons; ii) the relative circulation of the 2 types and the 4 subtypes of hMPV during the same 3-year period; iii) the relative impact of hMPV as compared to hRSV in determining admission to the hospital of infants with acute respiratory infections. The relative distribution of different respiratory viruses causing severe infections requiring admission to the hospital of infants and young children in three consecutive winter-spring seasons from 2001 through 2004 is reported in Table 2 Within the aliquot of patients found positive for some respiratory virus, no difference in the circulation rate was observed for respiratory virus infections caused by influenzavirus B, hPIVs, hAdVs, hCoVs, and coinfections along the three years studied. abstract: From 2001 through 2004, 808 pediatric patients admitted to hospital because of acute respiratory infections were examined for presence of respiratory viruses by either direct fluorescent staining using monoclonal antibodies or RT-PCR during three consecutive winter-spring seasons. On the whole, 336 (42%) patients were detected as positive for one or more respiratory viruses. The most widely circulating virus was human respiratory syncytial virus (hRSV) infecting 50% of positive patients, followed by human metapneumovirus (hMPV) found in 13% of patients, and then by influenza virus type A, human parainfluenzaviruses and coinfections. Significant variations in the circulation rate of hRSV, hMPV and influenzavirus type A were observed during the individual seasons. In addition, the circulation rates of the different types of hMPV changed yearly. In 2001–2002 and 2002–2003 hMPV circulated at a significant lower proportion than hRSV, while in 2003–2004 the circulation rates of the two viruses were closer. In conclusion, the 4 hMPV subtypes circulated yearly in Northern Italy flanking hRSV as major respiratory pathogens in the infantile patient population. url: https://www.ncbi.nlm.nih.gov/pubmed/15986171/ doi: 10.1007/s00705-005-0581-2 id: cord-004694-43yvs52a author: Han, Tae-Hee title: Detection of human rhinovirus C in children with acute lower respiratory tract infections in South Korea date: 2009-05-05 words: 1987.0 sentences: 103.0 pages: flesch: 57.0 cache: ./cache/cord-004694-43yvs52a.txt txt: ./txt/cord-004694-43yvs52a.txt summary: A total of 54 single HRV-positive specimens from children hospitalized with acute LRTIs were sequenced after performing RT-PCR based on the 5 0 NCR region. Recently, novel HRV species were identified and their members were reported to be associated with acute respiratory tract infections with febrile wheeze, asthmatic exacerbation, influenza-like illness, pneumonia and rhinitis [10, 13, 14, 17] . An association of members of novel HRV species with severe respiratory tract infections [19, 20] and a global distribution of members of novel species in respiratory specimens have Fig. 1 Phylogenetic tree of clinical viral isolates (n = 54) based on analysis of *285 bp from the 5 0 noncoding region (nt 178-462 of HRV16 L24917). In the present study, phylogenetic analysis of the 5 0 NCR region showed that QPM, HRV-C strain026 and HRV X1 were grouped into the HRV-C species, but 9 strains could not be identified. abstract: Recently, HRV-C was identified as a new species of HRV, but its spectrum of clinical disease is still not clear. The purpose of this study was to investigate the molecular epidemiology of HRVs in children with acute lower respiratory tract infections (LRTIs). A total of 54 HRV-positive samples that were negative for other respiratory viruses were sequenced. HRV-A was detected in 33, HRV-B in 4, and HRV-C in 17 of these samples. All HRV-C-positive patients showed favorable clinical outcomes. We confirmed the presence of HRV-C in children with LRTIs, but its association with clinical severity is not clear. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086646/ doi: 10.1007/s00705-009-0383-z id: cord-278388-lzvtgwox author: Hasoksuz, M. title: Antigenic variation among bovine enteric coronaviruses (BECV) and bovine respiratory coronaviruses (BRCV) detected using monoclonal antibodies date: 2014-05-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Bovine coronavirus (BCV) causes neonatal calf diarrhea (CD) and is associated with winter dysentery (WD) in adult dairy cattle. It can also be isolated from the respiratory tracts of cattle entering feedlots. Monoclonal antibodies (MAbs) specific for the hemagglutinin esterase (HE) and spike (S) surface proteins of 2 bovine enteric coronavirus (BECV) strains and two bovine respiratory coronavirus (BRCV) strains were tested against 6 BECV strains and 6 recently isolated BRCV strains, in order to characterize the antigenicity of BCV strains with varied tissue tropisms. All MAbs had high immunofluorescence (IF) titers against BECV and BRCV strains, indicative of conserved cross-reactive epitopes. In hemagglutination inhibition (HI) tests, the S-MAbs were more broadly reactive than HE-MAbs. The BRCV and CD MAbs were more broadly reactive in HI than the WD MAbs. The HA activity of the Mebus vaccine CD strain was not inhibited by any of the MAbs tested. The HI activity of BRCV strain R6 was unique among the 6 BRCV isolates. In virus neutralization assays, MAbs to the BRCV strain R4 neutralized all 6 BECV strains tested. Antigenic variation exists among both BECV and BRCV strains, but it cannot be attributed soley to the clinical origin of the strain. url: https://www.ncbi.nlm.nih.gov/pubmed/10664396/ doi: 10.1007/s007050050656 id: cord-328381-bfvdhai8 author: Hattermann, K. title: Susceptibility of different eukaryotic cell lines to SARS-coronavirus date: 2005-01-13 words: 1829.0 sentences: 103.0 pages: flesch: 60.0 cache: ./cache/cord-328381-bfvdhai8.txt txt: ./txt/cord-328381-bfvdhai8.txt summary: In all susceptible cell lines mRNA of the Angiotensin-converting enzyme 2 (ACE2), the functional receptor for SARS-CoV infection, could be detected by RT-PCR. In contrast, 50% of the Huh-7 cells were positive for viral antigen not until 31 h after infection ( The quantification of SARS-CoV RNA by quantitative real-time PCR revealed a significant increase of intracellular viral RNA in Vero E6, Huh-7, POEK, (Fig. 1/I A-C) and PS cells (data not shown). An increase of SARS-CoV RNA was detected in the supernatant of infected Vero E6, Huh-7, POEK ( Fig. 1/I A-C) and PS cells (data not shown). As expected, the investigation of all SARS-CoV susceptible cell lines (Vero E6, Huh-7, POEK and PS) for mRNA of ACE2 was positive in all cases though we failed to detect ACE2 expression by IFA, Western Blot and FACS analysis using commercially available monoclonal and polyclonal antibodies (ALPHA DIAGNOSTICS, San Antonio, USA) against human ACE2 (data not shown). abstract: In order to define and characterize target cells of SARS-coronavirus (SARS-CoV) we studied the susceptibility of 23 different permanent and primary eukaryotic cell lines to SARS-coronavirus. Beneath Vero E6 cells SARS- Coronavirus infection could also be demonstrated in two pig cell lines (POEK, PS) and one human cell line (Huh-7) using the indirect immunofluorescence assay and a newly established quantitative real-time PCR. In all susceptible cell lines mRNA of the Angiotensin-converting enzyme 2 (ACE2), the functional receptor for SARS-CoV infection, could be detected by RT-PCR. Our results show that there is a correlation between the abundance of ACE2 mRNA and SARS-CoV susceptibility. url: https://www.ncbi.nlm.nih.gov/pubmed/15645376/ doi: 10.1007/s00705-004-0461-1 id: cord-316797-sf2lu45f author: Hirano, N. title: Replication of rat coronavirus in a rat cell line, LBC date: 1985 words: 895.0 sentences: 61.0 pages: flesch: 65.0 cache: ./cache/cord-316797-sf2lu45f.txt txt: ./txt/cord-316797-sf2lu45f.txt summary: Rat coronavirus readily propagated and induced marked cytopathic effect in a rat cell line, LBC cell culture, which provided a sensitive, practical assay system for viral infectivity and neutralizing antibody, and a satisfactory source of the virus. The growth of RCV has been reported on a primary rat kidney cell culture but not on any established cell lines. This brief communication recommends a rat cell line, LBC, providing propagation of RCV and useful tool for infectivity assay. The culture fluid sampled at ¢8 hours p.i. was assayed for infectivity by inoculating into LBC cells prepared in 13 × 100 mm test tubes, showing an infectivity titer of i07.5 50 per cent tissue culture infective doses (TCIDs0)/0.2 ml. The LBC cell culture might be a much more useful tool for RCV propagation and assay. The LBC cells can also support growth of siModaeryoadenitis virus of rat, strain 681 (1), but not of MHV strains (unpublished observation). abstract: Rat coronavirus readily propagated and induced marked cytopathic effect in a rat cell line, LBC cell culture, which provided a sensitive, practical assay system for viral infectivity and neutralizing antibody, and a satisfactory source of the virus. url: https://www.ncbi.nlm.nih.gov/pubmed/3896201/ doi: 10.1007/bf01314238 id: cord-346321-drhiqch0 author: Hohdatsu, T. title: The role of IgG subclass of mouse monoclonal antibodies in antibody-dependent enhancement of feline infectious peritonitis virus infection of feline macrophages date: 1994 words: 3722.0 sentences: 165.0 pages: flesch: 53.0 cache: ./cache/cord-346321-drhiqch0.txt txt: ./txt/cord-346321-drhiqch0.txt summary: title: The role of IgG subclass of mouse monoclonal antibodies in antibody-dependent enhancement of feline infectious peritonitis virus infection of feline macrophages Antibody-dependent enhancement (ADE) of feline infectious peritonitis virus (FIPV) infection was studied in feline alveolar macrophages and human monocyte cell line U937 using mouse neutralizing monoclonal antibodies (MAbs) directed to the spike protein of FIPV. It is especially important for development of vaccines to understand the relationship between FIPV neutralizing activity and ADE activity of anti FIPV MAbs. In this study, we determined the relationship between immunoglobulin subclass and ADE activity of FIPV-neutralizing MAbs, and attempted to explore mechanisms of ADE of FIPV infection in in vitro system using mouse MAbs and feline alveolar macrophages or human monocytes. The present study, however, explored ADE of FIPV infection by in vitro experiments in which xenogeneic combination of virus targets and anti-FIPV antibody, i.e., feline alveolar macrophages or human monocyte U937 cells and mouse anti-FIPV S protein MAbs, was used. abstract: Antibody-dependent enhancement (ADE) of feline infectious peritonitis virus (FIPV) infection was studied in feline alveolar macrophages and human monocyte cell line U937 using mouse neutralizing monoclonal antibodies (MAbs) directed to the spike protein of FIPV. Even among the MAbs that have been shown to recognize the same antigenic site, IgG 2a MAbs enhanced FIPV infection strongly, whereas IgG 1 MAbs did not. These IgG 2a MAbs enhanced the infection even when macrophages pretreated with the MAb were washed and then inoculated with the virus. Immunofluorescence flow cytometric analysis of the macrophages treated with each of the MAbs showed that the IgG 2a MAbs but not the IgG 1 MAbs bound to feline alveolar macrophages. Treatment of the IgG 2a MAb with protein A decreased the binding to the macrophages and, in parallel, diminished the ADE activity. Although no infection was observed by inoculation of FIPV to human monocyte cell line U937 cells, FIPV complexed with either the IgG 2a MAb or the IgG 1 MAb caused infection in U937 cells which are shown to express Fc gamma receptor (Fc γ R) I and II that can bind mouse IgG 2a and IgG 1, respectively. These results suggest that the enhancing activity of MAb is closely correlated with IgG subclass and that the correlation is involved in binding of MAb to Fc γ R on feline macrophage. url: https://www.ncbi.nlm.nih.gov/pubmed/7832635/ doi: 10.1007/bf01310791 id: cord-349800-s9w2yr08 author: Hohdatsu, T. title: Characterization of monoclonal antibodies against feline infectious peritonitis virus type II and antigenic relationship between feline, porcine, and canine coronaviruses date: 1991 words: 3073.0 sentences: 170.0 pages: flesch: 58.0 cache: ./cache/cord-349800-s9w2yr08.txt txt: ./txt/cord-349800-s9w2yr08.txt summary: Seven monoclonal antibodies (MAbs) with neutralizing activity against feline infectious peritonitis virus (FIPV) strain 79-1149 (type II) were prepared. The reactivity of these MAbs with 6 viruses classified as FIPV type I (UCD-1, UCD-2, UCD-3, UCD-4, NW-1, and Black), feline enteric coronavirus (FECV) type II strain 79-1683, canine coronavirus (CCV) strain 1-71, and transmissible gastroenteritis virus (TGEV) strains TO-163 and SH was examined by neutralization tests. Feline coronaviruses are divided into FIPV types I and II, and FECV types I and II, on the basis of the disease types, that is, whether it causes feline infectious peritonitis (FIP) or not, the ability of the viruses to proliferate in cell cultures, and the antigenic relationship to TGEV and CCV [17] . These MAbs did not neutralize the 6 FIPV type I viruses, but neutralized FECV strain 79-1683, TGEV strains TO-163 and SH, and CCV strain 1-71, which do not cause feline infectious peritonitis (Table 4) . abstract: Seven monoclonal antibodies (MAbs) with neutralizing activity against feline infectious peritonitis virus (FIPV) strain 79-1149 (type II) were prepared. When the polypeptide specificity recognized by these monoclonal antibodies (MAbs) was investigated by Western immunoblotting, all of the MAbs reacted with peplomer glycoprotein (S) of the virus. By competitive binding assay these MAbs were found to recognize at least 3 different epitopes. The reactivity of these MAbs with 6 viruses classified as FIPV type I (UCD-1, UCD-2, UCD-3, UCD-4, NW-1, and Black), feline enteric coronavirus (FECV) type II strain 79-1683, canine coronavirus (CCV) strain 1-71, and transmissible gastroenteritis virus (TGEV) strains TO-163 and SH was examined by neutralization tests. All MAbs neutralized FECV strain 79-1683, CCV strain 1-71, and TGEV strains TO-163 and SH, while they did not neutralize the 6 FIPV type I viruses. Moreover, the MAb against TGEV strain TO-163, which has strong neutralizing activity against 7 TGEV viruses, neutralized CCV strain 1-71, FECV strain 79-1683, and FIPV strain 79-1146, but did not neutralize the 6 FIPV type I viruses. These results demonstrated that there are at least 3 epitopes involved in the neutralization of FIPV type II strain 79-1146, and that these epitopes are not present in FIPV type I viruses but are present in FECV strain 79-1683 which does not induce feline infectious peritonitis, TGEV strains TO-163 and SH, and CCV strain 1-71. These results suggest the presence of 2 serotypes of FIPV which can be clearly distinguished by the neutralization test using MAbs. url: https://www.ncbi.nlm.nih.gov/pubmed/1706593/ doi: 10.1007/bf01310494 id: cord-004765-7e4yu2do author: Homberger, F. R. title: Maternally-derived passive immunity to enterotropic mouse hepatitis virus date: 1992 words: 3091.0 sentences: 182.0 pages: flesch: 60.0 cache: ./cache/cord-004765-7e4yu2do.txt txt: ./txt/cord-004765-7e4yu2do.txt summary: Maternally-derived antibody to enterotropic mouse hepatitis virus (MHV) strain Y was transferred to pups by both intrauterine (IgG) and lactogenic (IgA and IgG) routes. MHV-IgG, but not IgA or IgM, could be found in the serum of pups suckling immune dams. Stomach contents of pups suckling immune dams yielded constant IgG titers and gradually declining IgA titers up to the age of 14 days, but neither isotype of MHV antibody was detected at or beyond 21 days (Table 3 ). Pups from three consecutive litters born to immune and naive dams were exsanguated at 2, 4, 6, 8, and 10 weeks of age and sera were tested for MHV-specific IgG. Antibodies persisted for 4 weeks in pups born to dams with low MHV IgG serum titers and then declined to undetectable levels. abstract: Maternally-derived antibody to enterotropic mouse hepatitis virus (MHV) strain Y was transferred to pups by both intrauterine (IgG) and lactogenic (IgA and IgG) routes. Antibody present in the gastric whey of pups suckling immune dams dropped to undetectable levels by weaning age (21 days post partum). MHV-specific IgG was found in the serum of passively immune pups up to 10 weeks of age. Immune dams transferred equal levels of antibody to 3 consecutive litters of pups, without evidence of decline. Immunoblots showed that IgA and IgG in whey and serum were directed against nucleoprotein N and glycoprotein S. MHV-specific IgM was not detected in any sample. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086897/ doi: 10.1007/bf01321123 id: cord-340065-f4ffvkr9 author: Horváth, Trén title: Ultrastructural changes in the small intestinal epithelium of suckling pigs affected with a transmissible gastroenteritis (TGE)-like disease date: 1981 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The small intestine of piglets collected during a sudden outbreak of diarrhoeal disease resembling transmissible gastroenteritis (TGE) was examined by light and electron microscopy. The principal histopathological changes were moderate infiltration by mononuclear cells in the lamina propria of the villi and cytoplasmic vacuolation. These were most pronounced in the epithelial cells covering the villous tips. By scanning electron microscopy, the intestinal villi were swollen and the transverse furrows disappeared. Microvilli were reduced in number leaving denuded areas on the brush border of the villous epithelial cells. The ultrastructural changes were restricted to the cytoplasm of affected villous epithelial cells. The cell organelles were missing in rounded areas leaving cleared areas in the cytoplasm. Parallel fascicles and bundles were seen in these areas. Viral particles with an average diameter of 70 nm were found within the dilated apical tubulo-vesicular system, free in the cytoplasm, among the microvilli or lying free in the intestinal lumen. Viral particles surrounded a non-membrane bound viroplasm in some cases. The negatively stained particles showed a typical coronavirus morphology. These particles were found to be distinct from the known coronaviruses of swine, TGE virus and hemagglutinating encephalomyelitis virus by immune electron microscopy. url: https://www.ncbi.nlm.nih.gov/pubmed/7247729/ doi: 10.1007/bf01314440 id: cord-004802-rhkrmftn author: Hoshino, Y. title: Isolation and characterization of a canine rotavirus date: 1982 words: 2902.0 sentences: 172.0 pages: flesch: 47.0 cache: ./cache/cord-004802-rhkrmftn.txt txt: ./txt/cord-004802-rhkrmftn.txt summary: Replication of the virus in cell culture was found to be less dependent upon trypsin than that of human, bovine and porcine rotaviruses. Reproducible, sharp-edged plaques of various sizes were produced by the canine rotavirus in an established cell line of fetal rhesus monkey kidney, MA104, under overlays of carboxymethyl cellulose or agarose. By plaque reduction neutralization assay, a two-way antigenic relationship was found between the canine (CU-1) and simian (rhesus MMU 18006 and SA-11) rotaviruses. Although canine rotavirus readily replicated and produced CPE in monolayer cultures of MA104 cells in the absence of trypsin, detectable plaques were not formed even 8 D P I under the overlays of CMC or agarose without trypsin. Since both IFT and CFT detect only group-specific antibodies, and rotaviruses from one species can infect another species (5, 8, 34, 36, 46, 50, 51, 52, 55) , it was not clear from these studies whether the antibodies in the dogs resulted from infection with distinctly canine rotavirus or with human or some other rotavirus. abstract: Canine rotavirus particles were visualized by direct electron microscopy in the feces from a clinically normal dog. The virus was subsequently propagated in cell cultures; it was chracterized and compared with rotaviruses from other species. Replication of the virus in cell culture was found to be less dependent upon trypsin than that of human, bovine and porcine rotaviruses. Reproducible, sharp-edged plaques of various sizes were produced by the canine rotavirus in an established cell line of fetal rhesus monkey kidney, MA104, under overlays of carboxymethyl cellulose or agarose. Intracytoplasmic inclusion bodies of different sizes and shapes were produced in infected MA104 cells. By plaque reduction neutralization assay, a two-way antigenic relationship was found between the canine (CU-1) and simian (rhesus MMU 18006 and SA-11) rotaviruses. The canine rotavirus had a one-way antigenic relationship with feline (Taka), bovine (NCDV), and porcine (OSU) rotaviruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087106/ doi: 10.1007/bf01314456 id: cord-274780-fmnro0kw author: Hoshino, Y. title: Detection of astroviruses in feces of a cat with diarrhea date: 1981 words: 1367.0 sentences: 96.0 pages: flesch: 52.0 cache: ./cache/cord-274780-fmnro0kw.txt txt: ./txt/cord-274780-fmnro0kw.txt summary: Astroviruses were detected by electron microscopy in the feces from a 4 month old kitten with diarrhea. Astroviruses were detected by electron microscopy in the feces from a 4 month old kitten with diarrhea. The clinical disease manifested by the cat and the observed morphology of the viral particles are consistent with previous reports on astroviruses of other species. The clinical disease manifested by the cat and the observed morphology of the viral particles are consistent with previous reports on astroviruses of other species. Viral antigen was detected by indirect immunofluorescent staining within the cytoplasm of cultured cells infected with fecal material of human (10, 11) and bovine (23) astroviruses. Studies on the pathogenesis of astrovirus infection in lambs have shown the site of virus multiplication to be the mature villous epithelial cells of the small intestine (21, 22) . abstract: Astroviruses were detected by electron microscopy in the feces from a 4 month old kitten with diarrhea. The mean diameter of the viral particles was 28.7 nm, and they showed characteristic five- or six-pointed star-shaped surface configurations. The clinical disease manifested by the cat and the observed morphology of the viral particles are consistent with previous reports on astroviruses of other species. url: https://www.ncbi.nlm.nih.gov/pubmed/6798953/ doi: 10.1007/bf01320252 id: cord-252232-vgq6gjpx author: Hou, Yuxuan title: Angiotensin-converting enzyme 2 (ACE2) proteins of different bat species confer variable susceptibility to SARS-CoV entry date: 2010-06-22 words: 3208.0 sentences: 159.0 pages: flesch: 57.0 cache: ./cache/cord-252232-vgq6gjpx.txt txt: ./txt/cord-252232-vgq6gjpx.txt summary: Here, we extended our previous study to ACE2 molecules from seven additional bat species and tested their interactions with human SARS-CoV spike protein using both HIV-based pseudotype and live SARS-CoV infection assays. However, although the genetically related SARS-like coronavirus (SL-CoV) has been identified in horseshoe bats of the genus Rhinolophus [5, 8, 12, 18] , its spike protein was not able to use the human ACE2 (hACE2) protein as a receptor [13] . To this end, we have extended our studies to include ACE2 molecules from different bat species and examined their interaction with the human SARS-CoV spike protein. Our results show that there is great genetic diversity among bat ACE2 molecules, especially at the key residues known to be important for interacting with the viral spike protein, and that ACE2s of Myotis daubentoni and Rhinolophus sinicus from Hubei province can support viral entry. abstract: The discovery of SARS-like coronavirus in bats suggests that bats could be the natural reservoir of SARS-CoV. However, previous studies indicated the angiotensin-converting enzyme 2 (ACE2) protein, a known SARS-CoV receptor, from a horseshoe bat was unable to act as a functional receptor for SARS-CoV. Here, we extended our previous study to ACE2 molecules from seven additional bat species and tested their interactions with human SARS-CoV spike protein using both HIV-based pseudotype and live SARS-CoV infection assays. The results show that ACE2s of Myotis daubentoni and Rhinolophus sinicus support viral entry mediated by the SARS-CoV S protein, albeit with different efficiency in comparison to that of the human ACE2. Further, the alteration of several key residues either decreased or enhanced bat ACE2 receptor efficiency, as predicted from a structural modeling study of the different bat ACE2 molecules. These data suggest that M. daubentoni and R. sinicus are likely to be susceptible to SARS-CoV and may be candidates as the natural host of the SARS-CoV progenitor viruses. Furthermore, our current study also demonstrates that the genetic diversity of ACE2 among bats is greater than that observed among known SARS-CoV susceptible mammals, highlighting the possibility that there are many more uncharacterized bat species that can act as a reservoir of SARS-CoV or its progenitor viruses. This calls for continuation and expansion of field surveillance studies among different bat populations to eventually identify the true natural reservoir of SARS-CoV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-010-0729-6) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-010-0729-6 doi: 10.1007/s00705-010-0729-6 id: cord-343780-084lq92r author: Hsu, Tien-Huan title: Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan date: 2018-07-26 words: 2083.0 sentences: 109.0 pages: flesch: 60.0 cache: ./cache/cord-343780-084lq92r.txt txt: ./txt/cord-343780-084lq92r.txt summary: title: Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan To investigate if PDCoV is also present in Taiwan, three swine coronaviruses—PDCoV, porcine epidemic diarrhea virus (PEDV), and transmissible gastroenteritis coronavirus (TGEV)—were tested using real-time reverse transcription polymerase chain reaction (rRT-PCR) in 172 rectal swab samples from piglets exhibiting diarrhea between January 2016 and May 2017 on 68 pig farms in Taiwan. Currently, there are at least three members of the family Coronaviridae that can cause diarrhea in pigs: transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), and porcine deltacoronavirus (PDCoV) [8] . Based on the real-time RT-PCR (rRT-PCR) detection results, the percentage of pig farms that were positive for at least of one of the coronaviruses was 25% for PDCoV (17/68), 22.1% for PEDV (15/68), and 2.9% for TGEV (2/68). Phylogeny analysis of PDCoV-N genes showed that PDCoVs found in Taiwan were highly similar in their nucleotide sequences to isolates from the United States, mainland China, and other countries (Fig. 1) . abstract: Porcine deltacoronavirus (PDCoV) was initially documented in Hong Kong and later in the United States, South Korea, and Thailand. To investigate if PDCoV is also present in Taiwan, three swine coronaviruses—PDCoV, porcine epidemic diarrhea virus (PEDV), and transmissible gastroenteritis coronavirus (TGEV)—were tested using real-time reverse transcription polymerase chain reaction (rRT-PCR) in 172 rectal swab samples from piglets exhibiting diarrhea between January 2016 and May 2017 on 68 pig farms in Taiwan. The rRT-PCR results were positive for PDCoV (29/172, 16.9%), PEDV (36/172, 20.9%), TGEV (2/172, 1.2%), and coinfections (16/172, 9.3%). After cloning and sequencing, PDCoV nucleocapsid genes were analyzed. Phylogeny results indicated that the nucleotide sequences of all isolates were like those reported in other countries. To further trace PDCoV in the period of 2011 to 2015, an enzyme-linked immunosorbent assay (ELISA) was used to detect antibodies against PDCoV. The results showed that 279 of 1,039 (26.9%) sera were positive for the PDCoV nucleocapsid protein, implying that PDCoV might have existed in Taiwan before 2011. url: https://doi.org/10.1007/s00705-018-3964-x doi: 10.1007/s00705-018-3964-x id: cord-315811-wpeac0lk author: Hu, Hui title: Experimental infection of gnotobiotic pigs with the cell-culture-adapted porcine deltacoronavirus strain OH-FD22 date: 2016-09-12 words: 6500.0 sentences: 365.0 pages: flesch: 62.0 cache: ./cache/cord-315811-wpeac0lk.txt txt: ./txt/cord-315811-wpeac0lk.txt summary: The aims of our current study were to investigate i) the pathogenicity of the tissue-culture-grown PDCoV (TC-PDCoV) strain OH-FD22 at passage 5 (P5), P20, and P40 on LLC-PK cells in 14-day-old Gn pigs compared with that of the wild-type parent virus [12] ; ii) Fecal PDCoV shedding, viremia, and pathology tested at post-inoculation day (PID) 1 to 23-24 or PID 28; iii) possible attenuation of TC-PDCoV OH-FD22 P40, the highest passage in cell culture among the passages tested; iv) serum-PDCoV-specific IgG and IgA and virus neutralization (VN) antibody titers and any differences in the titers among OH-FD22 P5, P20, and P40-inoculated pigs; and v) the genetic stability of TC-and Gn-pig-passaged PDCoV OH-FD22 P5, P20, and P40 by analysis of the complete spike (S) and nucleocapsid (N) gene sequences. Regardless of the cell culture passage number of the virus strains used, serum virus neutralization (VN) antibodies were first detected in all of the original and TC-PDCoV OH-FD22-inoculated pigs at PID 7 (64-256), and thereafter, the titers increased gradually and peaked at PID 23/24. abstract: Porcine deltacoronavirus (PDCoV) is a novel enteropathogenic coronavirus in pigs. We have isolated and passaged the PDCoV strain OH-FD22 in an LLC porcine kidney (LLC-PK) cell line. Our study investigated the pathogenicity of the tissue-culture-grown PDCoV (TC-PDCoV) OH-FD22 at cell passages 5, 20 and 40 in LLC-PK cells, in eight 14-day-old gnotobiotic (Gn) pigs. Pigs (n = 3) were euthanized for pathologic examination at post-inoculation day (PID) 3, and the remainder were monitored for clinical signs, virus shedding, and serum antibody responses until PID 28. All inoculated pigs developed watery diarrhea and/or vomiting at PID 1-2 and shed the highest amount of viral RNA in feces at PID 3-5, accompanied by severe atrophic enteritis. They developed high titers of PDCoV-specific IgG/IgA and virus-neutralizing antibodies in serum at PID 23-24. Histologic lesions were limited to the villous epithelium of the jejunum and ileum at PID 3. Two inoculated pigs tested at PID 23-24 had small to moderate numbers of PDCoV antigen-positive cells in the intestinal lamina propria and mesenteric lymph nodes, but not in enterocytes. An analysis of full-length S and N genes of TC- and Gn-pig-passaged OH-FD22 revealed a high genetic stability in cell culture and pigs. TC-PDCoV OH-FD22 (cell passages 5, 20 and 40) was enteropathogenic, and the pathogenicity was similar to that of the original field virus. The TC-PDCoV OH-FD22 will be useful for further pathogenesis studies and for evaluating if higher-level cell-culture passaged virus becomes attenuated for vaccine development. url: https://www.ncbi.nlm.nih.gov/pubmed/27619798/ doi: 10.1007/s00705-016-3056-8 id: cord-011105-or9azf1g author: Huang, Zheng title: Full-genome sequences of GII.13[P21] recombinant norovirus strains from an outbreak in Changsha, China date: 2020-04-30 words: 2436.0 sentences: 165.0 pages: flesch: 58.0 cache: ./cache/cord-011105-or9azf1g.txt txt: ./txt/cord-011105-or9azf1g.txt summary: title: Full-genome sequences of GII.13[P21] recombinant norovirus strains from an outbreak in Changsha, China Further, we determined the full-genome sequences of two strains of GII.13[P21] recombinant noroviruses, which were 7434 nt long. Although those genotypes have not caused severe outbreaks, studying these strains has helped us to obtain more information on the genetic diversity and gene constellation of noroviruses. Hence, we determined the genome sequences of GII.13[P21] recombinant strains isolated in the city of Changsha, China. Although the sporadic norovirus genotypes do not cause serious epidemic worldwide, unlike GII.2[P16] and GII.4[P4], due to these special binding sites, human infections are associated with severe vomiting and diarrhea. Although only a few samples were collected in this outbreak, we obtained the full genome of GII.13[P21] recombinant strains that have rarely been reported in China. Full-genomic analysis of a human norovirus recombinant GII.12/13 novel strain isolated from South Korea Full-genome sequence analysis of an uncommon norovirus genotype, GII.21, from South Korea abstract: On 31 March 2019, 68 school students suffered from vomiting, diarrhea, and abdominal pain after participating in a group activity at a commercial park. In this outbreak, multiple norovirus genotypes were observed, including GII.2[P16], GII.17[P17], and GII.13[P21]. Further, we determined the full-genome sequences of two strains of GII.13[P21] recombinant noroviruses, which were 7434 nt long. Phylogenetic analysis based on open reading frames (ORFs) 1 and 2 revealed that these recombinants were related to stains of different genotypes from different countries. The full genome nucleotide sequences of the two isolates were 97.0% and 98.0% identical to those of strains from London and Thailand, respectively. Simplot analysis revealed the presence of a break point at nt 5059 in the ORF1 region. The histo-blood group antigen binding sites were conserved in both recombinant viruses. Our findings not only provide valuable genetic information about a recombinant norovirus but also contribute to our general understanding of the evolution, genetic diversity, and distribution of noroviruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223583/ doi: 10.1007/s00705-020-04643-1 id: cord-048485-b8xb1f12 author: Hulst, Marcel title: Early transcriptional response in the jejunum of germ-free piglets after oral infection with virulent rotavirus date: 2008-06-04 words: 6269.0 sentences: 313.0 pages: flesch: 45.0 cache: ./cache/cord-048485-b8xb1f12.txt txt: ./txt/cord-048485-b8xb1f12.txt summary: RNA pools prepared from two infected piglets were used to compare whole mucosal gene expression at 12 and 18 hpi to expression in uninfected germ-free piglets (n = 3) using a porcine intestinal cDNA microarray. However, the fluorescence intensity was not higher than the background threshold for any of these probes, indicating that mRNA concentrations of these cytokines (including IFN-c) in infected and uninfected mucosal scrapings were too low to detect by microarray analysis, probably due to the relatively low percentage of cytokine-producing (immune) cells present in intestinal mucosa [6] . Using microarray analysis, we detected a set of genes that are differently expressed in rotavirus-infected jejunal mucosa compared to uninfected mucosa. Perhaps, enhanced expression of a PLA2-inh in our study may be a countermeasure of specific intestinal epithelial cells to normalize and/or inhibit PLA2 enzyme activity in response to extra-and intracellular changes in [Ca 2+ ] evoked by rotavirus replication, either to protect specific cells from extra-and intracellular membrane-damage or to negatively regulate A-acid production. abstract: Germ-free piglets were orally infected with virulent rotavirus to collect jejunal mucosal scrapings at 12 and 18 hours post infection (two piglets per time point). IFN-gamma mRNA expression was stimulated in the mucosa of all four infected piglets, indicating that they all responded to the rotavirus infection. RNA pools prepared from two infected piglets were used to compare whole mucosal gene expression at 12 and 18 hpi to expression in uninfected germ-free piglets (n = 3) using a porcine intestinal cDNA microarray. Microarray analysis identified 13 down-regulated and 17 up-regulated genes. Northern blot analysis of a selected group of genes confirmed the data of the microarray. Genes were functionally clustered in interferon-regulated genes, proliferation/differentiation genes, apoptosis genes, cytoskeleton genes, signal transduction genes, and enterocyte digestive, absorptive, and transport genes. Down-regulation of the transport gene cluster reflected in part the loss of rotavirus-infected enterocytes from the villous tips. Data mining suggested that several genes were regulated in lower- or mid-villus immature enterocytes and goblet cells, probably to support repair of the damaged epithelial cell layer at the villous tips. Furthermore, up-regulation was observed for IFN-γ induced guanylate binding protein 2, a protein that effectively inhibited VSV and EMCV replication in vitro (Arch Virol 150:1213–1220, 2005). This protein may play a role in the small intestine’s innate defense against enteric viruses like rotavirus. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-008-0118-6) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2441536/ doi: 10.1007/s00705-008-0118-6 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-006674-ywzpwlrb author: Ikeda, T. title: Pathogenesis of cytomegalovirus-associated pneumonitis in ICR mice: possible involvement of superoxide radicals date: 1992 words: 3716.0 sentences: 193.0 pages: flesch: 45.0 cache: ./cache/cord-006674-ywzpwlrb.txt txt: ./txt/cord-006674-ywzpwlrb.txt summary: When the activity of xanthine oxidase (XO) in lung tissue homogenates was measured, the activity was found to significantly increase after intranasal infection with MCMV irrespective of CP administration and there was a good correlation between the elevation of XO activity and the degree of pathological changes in the lung. Furthermore, recent studies have shown that the enhanced production of superoxide radicals by xanthine oxidase (XO) plays a key role in the pathogenesis of influenza virus-induced pulmonary infection [1, 193. In this study, we have established a model of murine cytomegalovirus (MCMV) pneumonitis in ICR mice, measured XO activity in tung tissues, and evaluated the effect of superoxide dismutase (SOD) and allopurinol in this model. Although the precise role of superoxide radicals in the pathogenesis of MCMV pneumonitis is still unknown, such a process seems to be involved in the formation of pulmonary lesions in MCMV-infected mice. abstract: We have studied the pathogenesis of murine cytomegalovirus (MCMV) pneumonitis in immunocompetent ICR mice and in mice treated with cyclophosphamide (CP). Intranasal infection of immunocompetent mice with MCMV resulted in transient and self-limited pulmonary lesions. When mice were given 200 mg/kg of CP one day before virus infection, transient splenic atrophy and subsequent splenic hypertrophy were induced, and the lesions in the lung were markedly augmented in their number and size although there was no significant enhancement of the virus growth. The augmentation coincided with the period of splenic hypertrophy. A marked increase in the number of pulmonary lesions was also induced in mice given 100 mg/kg of CP every 4 days following the initial dose of 200 mg/kg. In these mice, however, continuous splenic atrophy and augmented replication of MCMV in the lung were observed. When the activity of xanthine oxidase (XO) in lung tissue homogenates was measured, the activity was found to significantly increase after intranasal infection with MCMV irrespective of CP administration and there was a good correlation between the elevation of XO activity and the degree of pathological changes in the lung. In addition, we found that the administration of allopurinol, a specific inhibitor of XO and superoxide dismutase, a superoxide radical scavenger, reduced the number of the pulmonary lesions. These results suggest that superoxide radicals are involved in the pathogenesis of MCMV-associated pneumonitis in ICR mice. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102218/ doi: 10.1007/bf01309571 id: cord-353797-yb355mxk author: Inaba, Y. title: Replication of bovine coronavirus in cell line BEK-1 culture date: 1976 words: 835.0 sentences: 51.0 pages: flesch: 55.0 cache: ./cache/cord-353797-yb355mxk.txt txt: ./txt/cord-353797-yb355mxk.txt summary: Bovine coronavirus readily multiplied and induced marked cytopathic effect in BEK-1 cultures, thus providing a sensitive, practical assay system for viral infectivity and neutralizing antibody and a satisfactory source of the virus. 1V[~iBus and his associates (4--6) have demonstrated an agent with morphologic features of coronavirus by electron microscopy in fractions prepared by density gradient ultracentrifugation from diarrheal feces of calves with natural and experimentally produced neonatal diarrhea. The agent multiplied but failed to induce readily recognizable cytopathic effect in bovine embryonic kidney cell cultures (3) . This paper describes briefly our recent observation that the virus readily replicates and induces a marked cytopathic effect in cultures of a continuous cell line, BEK-1, derived from bovine embryonic kidney (2), thus providing a sensitive, practical assay method and a satisfactory source of the virus. Coverslip cultures of BEK-1 cells inoculated with the virus were examined after 2 or 3 days of incubation at 34 ° C. abstract: Bovine coronavirus readily multiplied and induced marked cytopathic effect in BEK-1 cultures, thus providing a sensitive, practical assay system for viral infectivity and neutralizing antibody and a satisfactory source of the virus. url: https://www.ncbi.nlm.nih.gov/pubmed/179503/ doi: 10.1007/bf01317959 id: cord-309145-6aqc074e author: Ito, Y. title: Induction of interferon by virus glycoprotein(s) in lymphoid cells through interaction with the cellular receptors via lectin-like action: An alternative interferon induction mechanism date: 1994 words: 4391.0 sentences: 210.0 pages: flesch: 36.0 cache: ./cache/cord-309145-6aqc074e.txt txt: ./txt/cord-309145-6aqc074e.txt summary: The interferon induction system, in which attachment of virus glycoprotein to the cellular receptor on the cell surface triggers interferon induction in lymphoid cells, is similar to a system in which plant lectins such as concanavalin A (Con-A) and phytohemagglutinin (PHA) stimulate lymphocytes and consequently induce interferon. For example, sialyl-oligosaccharides are receptors for parainfluenza and influenza viruses [62] , human membrane cofactor protein (CD46) for measles virus [13, 58] , MHC class I for Semliki Forest virus (SFV) [24] , MHC class II for lactose dehydrogenase virus (LDH virus) [26] , phosphatidylserine and phosphatidylinositol for vesicular stomatitis virus (VSV) [51] , the CD4 for human immunodeficiency virus (HIV) [11, 43] , the C3d receptor CR2 for Epstein-Barr virus [15, 59, 69] , acetylcholin receptor for rabies virus [47] , the intercellular adhesion molecule-1 (ICAM-1) for the major subgroup of human rhinoviruses [23, 67, 69] , another member of the immunoglobulin superfamily for poliovirus [45, 54-1, a basic amino acid transporter for gibbon ape leukemia virus and feline leukemia virus [1, 40, 68, 70, 71] , aminopeptidase N [13, 75-1 or a member of the carcinoembryonic antigen family of proteins for the coronavirus virus [14] , a high-affinity laminin receptor for sindbis virus [72] , ~2 subunit of human VLA-2 for echoviruses 1 and 8 [5] , erythrocyte P antigen for B19 Parvovirus Viral glycoproteins and interferon induction 193 [6] , and CD13 (human aminopeptidase N) for cytomegalovirus [66] . abstract: When animals and cells are infected with a virus, interferon is produced. Viral-nucleic acid is considered to be one of actual components for interferon induction. In addition, viral glycoproteins trigger interferon induction in lymphoid cells by membrane-membrane interaction via a lectin-like activity. A biological significance of lectin-like activity of viral glycoproteins is discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/7527998/ doi: 10.1007/bf01379125 id: cord-330035-0d6w8xyd author: Jeon, Ji Hyun title: Cellular cholesterol is required for porcine nidovirus infection date: 2017-09-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) and porcine epidemic diarrhea virus (PEDV) are porcine nidoviruses that are considered emerging and re-emerging viral pathogens of pigs that pose a significant economic threat to the global pork industry. Although cholesterol is known to affect the replication of a broad range of viruses in vitro, its significance and role in porcine nidovirus infection remains to be elucidated. Therefore, the present study was conducted to determine whether cellular or/and viral cholesterol levels play a role in porcine nidovirus infection. Our results showed that depletion of cellular cholesterol by treating cells with methyl-β-cyclodextrin (MβCD) dose-dependently suppressed the replication of both nidoviruses. Conversely, cholesterol depletion from the viral envelope had no inhibitory effect on porcine nidovirus production. The addition of exogenous cholesterol to MβCD-treated cells moderately restored the infectivity of porcine nidoviruses, indicating that the presence of cholesterol in the target cell membrane is critical for viral replication. The antiviral activity of MβCD on porcine nidovirus infection was found to be predominantly exerted when used as a treatment pre-infection or prior to the viral entry process. Furthermore, pharmacological sequestration of cellular cholesterol efficiently blocked both virus attachment and internalization and, accordingly, markedly affected subsequent post-entry steps of the replication cycle, including viral RNA and protein biosynthesis and progeny virus production. Taken together, our data indicate that cell membrane cholesterol is required for porcine nidovirus entry into cells, and pharmacological drugs that hamper cholesterol-dependent virus entry may have antiviral potential against porcine nidoviruses. url: https://doi.org/10.1007/s00705-017-3545-4 doi: 10.1007/s00705-017-3545-4 id: cord-316153-wet0go35 author: Jia, W. title: A novel variant of avian infectious bronchitis virus resulting from recombination among three different strains date: 1995 words: 3917.0 sentences: 232.0 pages: flesch: 61.0 cache: ./cache/cord-316153-wet0go35.txt txt: ./txt/cord-316153-wet0go35.txt summary: An antigenic variant of avian infectious bronchitis virus (IBV), a coronavirus, was isolated and characterized. Therefore, several recently reported diagnostic and serotyping methods of IBV which are based on dot-blot hybridization, restriction fragment length polymorphism (RFLP), and polymerase chain reaction (PCR), may not reveal the true antigenic and/or genetic nature of IBV isolates, and may in fact yield misleading information. More recently, two American field isolates were found to contain fragments of Mass-like sequences in the S1 gene, which were 94% to 95% homologous to IBV strain Mass41 [38] . Sequence data were obtained from cDNA clones, except for the first 1100 bases of the S gene, the last 200 bases of the N gene, the 3'' end non-coding region of CU-T2, and the partial Gene3 of Ark99 and Ho1152, which were obtained from direct sequencing of IBV genomic RNA. Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus abstract: An antigenic variant of avian infectious bronchitis virus (IBV), a coronavirus, was isolated and characterized. This strain, CU-T2, possesses a number of unusual features, which have not been previously observed in IBV. The S1 glycoprotein of CU-T2 carries virus-neutralizing and serotype-specific epitopes of two IBV serotypes, Arkansas (Ark) and Massachusetts (Mass). Sequence analysis revealed that the virus, originally an Ark serotype, has acquired the Mass-specific epitope by mutation(s). This provides evidence that point mutations may lead to generation of IBV antigenic variants in the field. It was further observed that two independent recombination events involving three different IBV strains had occurred in the S2 glycoprotein gene and N protein gene of CU-T2, indicating that genomic RNA recombination in IBV may occur in multiple genes in nature. It was especially significant that a sequence of Holland 52 (a vaccine strain) had replaced half of the N gene of CU-T2. This proves that recombination among vaccine strains is contributing to the generation of IBV variants in the field. Based on these observations it is predicted that every IBV field isolate could have unique genetic nature. Therefore, several recently reported diagnostic and serotyping methods of IBV which are based on dot-blot hybridization, restriction fragment length polymorphism (RFLP), and polymerase chain reaction (PCR), may not reveal the true antigenic and/or genetic nature of IBV isolates, and may in fact yield misleading information. url: https://www.ncbi.nlm.nih.gov/pubmed/7710354/ doi: 10.1007/bf01309861 id: cord-254405-yc1q20fz author: Jie, Tao title: Preparation and characterization of an attenuated porcine epidemic diarrhea virus strain by serial passaging date: 2018-07-31 words: 3450.0 sentences: 189.0 pages: flesch: 57.0 cache: ./cache/cord-254405-yc1q20fz.txt txt: ./txt/cord-254405-yc1q20fz.txt summary: Furthermore, we cultured the virus and screened for attenuated PEDV strains by analyzing the genovariations that occurred during passaging -confirming the results in animal experiments. [27] analyzed a cell culture-adapted PEDV (passage 100) strain with a smaller ORF3 gene and found it to have lower virulence relative to the wild-type virus. Molecular characterization of the ORF3 and S1 genes of porcine epidemic diarrhea virus non S-INDEL strains in seven regions of China Comparative genomic analysis of classical and variant virulent parental/attenuated strains of porcine epidemic diarrhea virus Isolation and identification of porcine epidemic diarrhea virus strain HBMC2012 and its pathogenicity in piglet Cloning and further sequence analysis of the spike gene of attenuated porcine epidemic diarrhea virus DR13 Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China abstract: Porcine epidemic diarrhea virus (PEDV) is prevalent in most parts of the world. Owing to its antigenic variation, prevention of the diseases caused by this virus is difficult. In this study, two PEDV isolates with similar growth kinetics were successfully propagated in Vero cells. Complete genome sequence analysis showed that they have a 49nt deletion in the ORF3 gene and were classified into Group 1, the same group that includes the classical CV777 strain. Recombination analysis revealed that the event had occurred in the ORF1a gene, at 3596–6819 nt, among the two PEDV isolates and the CV777 and DR13 strains. During their continuous propagation, 14 nonsynonymous mutations occurred in the spike (S) gene of strain JS-2/2014 between generations G5 and G90, but there were no changes between G90 and G100. We assumed that strain JS-2/2014 might be attenuated by the 90th generation. Piglets orally fed with JS-2/2014 G90 showed no clinical symptoms, and no virus was detected in the feces and nasal fluid. In conclusion, JS-2/2014 was successfully identified by screening, was attenuated after propagation in Vero cells, and may serve as a candidate virus for vaccine preparations. url: https://doi.org/10.1007/s00705-018-3968-6 doi: 10.1007/s00705-018-3968-6 id: cord-272973-kzaowysv author: Joshi, Lok R. title: Passive immunity to porcine epidemic diarrhea virus following immunization of pregnant gilts with a recombinant orf virus vector expressing the spike protein date: 2018-05-03 words: 4281.0 sentences: 210.0 pages: flesch: 54.0 cache: ./cache/cord-272973-kzaowysv.txt txt: ./txt/cord-272973-kzaowysv.txt summary: PEDV NA, IgG and IgA were detected in the serum of piglets born to immunized gilts, demonstrating the transfer of antibodies through colostrum and milk. In the present study, we investigated the immunogenicity of ORFV-PEDV-S recombinant virus in pregnant gilts and its ability to induce passive immunity and protection in piglets born to immunized animals. Animals in G1 seroconverted to PEDV, presenting detectable levels of IgG, IgA and NA a week after challenge of the piglets (day 7 post-birth; Fig. 1 ). Notably, passive transfer of antibodies from gilts to piglets was observed in both G2 and G3, as PEDV-specific IgG, IgA and NAs were detected in serum of piglets born to immunized gilts following ingestion of colostrum and milk. Additionally, passive transfer of antibodies from gilts to piglets was observed, as PEDV-specific IgG, IgA and NAs were detected in serum of piglets born to immunized gilts following ingestion of colostrum and milk. abstract: Passive immunity is critical for protection of neonatal piglets against porcine epidemic diarrhea virus (PEDV). Here, we investigated the immunogenicity of an orf virus (ORFV) vector expressing the full-length spike (S) protein of PEDV (ORFV-PEDV-S) in pregnant gilts and its ability to confer passive immunity and protection in piglets. Three doses of ORFV-PEDV-S were given to two groups of PEDV-negative pregnant gilts, with the last dose being administered two weeks prior to farrowing. One of the two groups immunized with the ORFV-PEDV-S recombinant virus was also exposed to live PEDV orally on day 31 post-immunization (pi). Antibody responses were assessed in serum, colostrum and milk of immunized gilts, and passive transfer of antibodies was evaluated in piglet sera. The protective efficacy of ORFV-PEDV-S was evaluated after challenge of the piglets with PEDV. PEDV-specific IgG, IgA and neutralizing antibody (NA) responses were detected in ORFV-PEDV-S-immunized and ORFV-PEDV-S-immunized/PEDV-exposed gilts. PEDV NA, IgG and IgA were detected in the serum of piglets born to immunized gilts, demonstrating the transfer of antibodies through colostrum and milk. Piglets born to immunized gilts showed reduced morbidity and a marked reduction in mortality after PEDV challenge in comparison to control piglets. Piglets born to gilts that received ORFV-PEDV-S and were exposed to live PEDV showed stronger NA responses and lower clinical scores when compared to piglets born to gilts immunized with ORFV-PEDV-S alone. These results demonstrate the potential of ORFV as a vaccine delivery platform capable of eliciting passive immunity against PEDV. url: https://doi.org/10.1007/s00705-018-3855-1 doi: 10.1007/s00705-018-3855-1 id: cord-305859-vt8vwo3y author: Jung, Kwonil title: Calves are susceptible to infection with the newly emerged porcine deltacoronavirus, but not with the swine enteric alphacoronavirus, porcine epidemic diarrhea virus date: 2017-04-03 words: 3232.0 sentences: 167.0 pages: flesch: 56.0 cache: ./cache/cord-305859-vt8vwo3y.txt txt: ./txt/cord-305859-vt8vwo3y.txt summary: Fecal virus shedding, seroconversion and histopathology were evaluated in 3-7-year-old gnotobiotic calves orally inoculated with porcine deltacoronavirus (PDCoV) (9.0-9.6 log(10) genomic equivalents [GE] of OH-FD22-P5; n=4) or porcine epidemic diarrhea virus (PEDV) (10.2-12.5 log(10) GE of PC21A; n=3). In PDCoV-inoculated calves, an acute but persisting fecal viral RNA shedding and PDCoV-specific serum IgG antibody responses were observed, but without lesions or clinical disease. Our study demonstrated that Gn calves orally inoculated with the PDCoV strain OH-FD22 (ICs of cell-culture grown PDCoV from infected Gn pigs) develop an acute infection with persistent fecal PDCoV RNA shedding and PDCoVspecific serum IgG antibody responses, but show no signs of significant intestinal lesions or clinical disease [8] . In our study, there were no detectable fecal viral RNA shedding, virus-specific serum IgG antibody responses, histological lesions, and clinical disease in Gn calves orally inoculated with the PEDV strain PC21A (ICs of wild-type PEDV-infected Gn pigs) [6] . abstract: Fecal virus shedding, seroconversion and histopathology were evaluated in 3-7-year-old gnotobiotic calves orally inoculated with porcine deltacoronavirus (PDCoV) (9.0-9.6 log(10) genomic equivalents [GE] of OH-FD22-P5; n=4) or porcine epidemic diarrhea virus (PEDV) (10.2-12.5 log(10) GE of PC21A; n=3). In PDCoV-inoculated calves, an acute but persisting fecal viral RNA shedding and PDCoV-specific serum IgG antibody responses were observed, but without lesions or clinical disease. However, no fecal shedding, seroconversion, histological lesions, and clinical disease were detected in PEDV-inoculated calves. Our data indicate that calves are susceptible to infection by the newly emerged PDCoV, but not by the swine coronavirus, PEDV. url: https://www.ncbi.nlm.nih.gov/pubmed/28374120/ doi: 10.1007/s00705-017-3351-z id: cord-004720-r6b34tjm author: Kaiser, C. J. title: Inhibition by monensin of human cytomegalovirus DNA replication date: 1987 words: 4357.0 sentences: 246.0 pages: flesch: 50.0 cache: ./cache/cord-004720-r6b34tjm.txt txt: ./txt/cord-004720-r6b34tjm.txt summary: Phosphonoacetic acid (PAA) and monensin were purchased from Sigma, Deisenhofen, Federal Republic of Germany, tunieamycin from Calbiochem, La Jolla, U.S.A. In a typicM experiment for the determination of infected cell DNA synthesis in the presence of monensin, parallel cultures of HFF (5 × 106 cells) were infected by HCMV (MOI of 1) and pulse labelled with att-thymidine (5 ~Ci/ml) during the late phase of the consecutive infectious cycle (28) . To examine whether pretreated cells support, viral replication, confluent serum-starved HFF were exposed to various concentrations of monensin prior to virus infection and subsequently pulse labelled with 3H-thymidine during the interval of expected viral DNA synthesis (28; Fig. 2 A) . This protocol again did not prevent subsequent recovery of viral DNA replication within 48-72 hours after removal, an observation which was based on the comparative anMysis by isopycnie centrifugation in CsC1 of DNA samples from untreated and drug-treated infected cultures labelled during corresponding pulse intervals (Fig. 2 B, w/o and monint) . abstract: Monensin, at concentrations which depended on the multiplicity of infection, was found to prevent DNA replication of human cytomegalovirus (HCMV) as well as production of viral progeny in human foreskin fibroblasts. The drug did not affect DNA replication of herpes simplex virus. Inhibition of consecutive HCMV DNA synthesis was also observed following delayed addition of the drug within 12–24 hours postinfection, but was fully reversible upon its removal. Viral replication proceeded, however, without impairment in cultures treated with monensin prior to infection. Induction of viral DNA polymerase activity was not impeded by the inhibitor. Analysis of protein- and glycoprotein synthesis revealed that monensin interfered with the production of a number of HCMV-specific polypeptides. Furthermore, evidence was obtained that the drug may hinder intracellular transport of a 135 kd glycopolypeptide. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086728/ doi: 10.1007/bf01310716 id: cord-324495-0pee1i3o author: Kang, Hyeonjeong title: Sasa quelpaertensis Nakai extract suppresses porcine reproductive and respiratory syndrome virus replication and modulates virus-induced cytokine production date: 2015-06-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Although Sasa quelpaertensis Nakai, a dwarf bamboo, is known to exert a variety of beneficial effects on health, its antiviral effect remains to be elucidated. Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most devastating viral pathogens of swine and has a substantial economic impact on the global pork industry. Therefore, the present study was conducted to determine whether Sasa quelpaertensis Nakai extract (SQE) inhibits PRRSV infection in cultured porcine alveolar macrophages (PAMs). Our results demonstrated that SQE treatment suppressed the replication of PRRSV in a dose-dependent manner. The antiviral activity of SQE on PRRSV replication was found to be primarily exerted at early times postinfection. Treatment with SQE resulted in marked reduction of viral genomic and subgenomic RNA synthesis, viral protein expression, and progeny virus production. Notably, pro-inflammatory cytokine production in PAM cells infected with PRRSV was shown to be modulated in the presence of SQE. Taken together, our data indicate that SQE has potential as a therapeutic agent against PRRSV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-015-2469-0) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/26047649/ doi: 10.1007/s00705-015-2469-0 id: cord-294467-kq5wmavt author: Kasai, H. title: Characterization of haemagglutinin-esterase protein (HE) of murine corona virus DVIM by monoclonal antibodies date: 2014-04-08 words: 1947.0 sentences: 116.0 pages: flesch: 60.0 cache: ./cache/cord-294467-kq5wmavt.txt txt: ./txt/cord-294467-kq5wmavt.txt summary: title: Characterization of haemagglutinin-esterase protein (HE) of murine corona virus DVIM by monoclonal antibodies We analyzed the characteristics of seven monoclonal antibodies (mAbs) raised against purified HE (hemagglutinin-esterase) glycoprotein of the murine coronavirus DVIM (diarrhea virus of infant mice). Neutralizing activity was shown in group A mAbs exclusively, suggesting that the ratio of HA and/or AE activities may play important roles in the cell fusion activity of DVIM-infected cells. As described in a previous report [8] , by treatment of DVIM with the non-ionic detergent NP-40 we isolated the HE protein, which carries the functional sites for both acetylesterase (AE) and the haemagglutination (HA) activities. We examined the cytopathic effect of mAbs with respect to the formation of syncytia in DVIM-infected cells. The antibodies that had low titers to both activities did not delay the fusion of infected cells. abstract: We analyzed the characteristics of seven monoclonal antibodies (mAbs) raised against purified HE (hemagglutinin-esterase) glycoprotein of the murine coronavirus DVIM (diarrhea virus of infant mice). Immunocrossreaction of these mAbs with JHM and/or MHV-S suggest that antigenic epitopes of HE of DVIM are similar to those of JHM and/or MHV-S. Four mAbs (1b4, 3Aff28, 4c19, 10b7), designated as group A mAbs, strongly inhibited both HA and AE activities. On the other hand, three mAbs (5Aff3, 6Aff6, 13Aff4), referred to as group B, had a comparatively weak HA inhibition activity. These results indicate that the antigenic epitopes of this glycoprotein can be classified into at least two groups and that the functional sites of HA and AE activities are similar but not identical. Neutralizing activity was shown in group A mAbs exclusively, suggesting that the ratio of HA and/or AE activities may play important roles in the cell fusion activity of DVIM-infected cells. url: https://www.ncbi.nlm.nih.gov/pubmed/9856082/ doi: 10.1007/s007050050431 id: cord-004831-lu62noak author: Kempf, C. title: A novel method for the detection of early events in cell-cell fusion of Semliki Forest virus infected cells growing in monolayer cultures date: 1987 words: 1890.0 sentences: 119.0 pages: flesch: 55.0 cache: ./cache/cord-004831-lu62noak.txt txt: ./txt/cord-004831-lu62noak.txt summary: title: A novel method for the detection of early events in cell-cell fusion of Semliki Forest virus infected cells growing in monolayer cultures Furthermore, it was shown that potassium cyanide, a potent inhibitor of polykaryon formation in the described system, inhibits an early step of membrane-membrane fusion of neighbouring cells. Furthermore, we show that potassium cyanide, a potent inhibitor of SFV induced polykaryon formation (4) acts at an early stage in the fusion process. The aim of this investigation was to clarify the early events in cell-cell fusion and the action of potassium cyanide an inhibitor of oxidative phosphorylation-which inhibits SFV-induced polykaryon formation [4] -on the fusion process. That this assumption holds true is depicted in Fig. 1A where a single, SFV infected cell was injected with Lucifer yellow 5 minutes after exposure to pH 6. Therefore, it can be concluded that potassium cyanide inhibits SFV-induced polykaryon formation at the level of membrane-membrane fusion. abstract: Semliki Forest virus infected Aedes albopictus cells were used to investigate virus induced cell-cell fusion. It was shown by a novel method that cell-cell fusion was completed within approximately 5 minutes after triggering the fusion event by low pH. This method consists of fixing fusing cells with glutaraldehyde and microinjecting the highly fluroescent and rapidly diffusing dye Lucifer yellow. In contrast, polykaryon formation, the usually used criterion to measure cell-cell fusion occurred only within 30 minutes. Furthermore, it was shown that potassium cyanide, a potent inhibitor of polykaryon formation in the described system, inhibits an early step of membrane-membrane fusion of neighbouring cells. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087209/ doi: 10.1007/bf01310786 id: cord-335690-66t5fjld author: Khromykh, A. A. title: RNA binding properties of core protein of the flavivirus Kunjin date: 1996 words: 5858.0 sentences: 250.0 pages: flesch: 58.0 cache: ./cache/cord-335690-66t5fjld.txt txt: ./txt/cord-335690-66t5fjld.txt summary: For this study we exploited the use of glutathione-S-transferase (GST)-core fusion proteins attached to an insoluble matrix (Glutathione Sepharose 4B) for rapid RNAprotein binding assays, and extended some of these results by mobility shift assays [17] which were possible because of the relatively small size of the RNA probes, KUN UTR probes bound strongly to fusion proteins incorporating full length or mature C, and to the isolated amino-terminal or carboxy-terminal domains of mature C. In attempts to define which regions of the mature form of C were binding to RNA, three regions enriched in basic amino acids were chosen arbitrarily for All these deleted fusion proteins bound to 3'' UTR and 5'' core probes on beads as efficiently as C107 (Fig. 3a) . abstract: Kunjin virus (KUN) C is a typical flavivirus core protein which is truncated in vivo to a mature form of 105 residues enriched in lysine and arginine. In order to study the possible association of KUN C with RNA in vitro, we prepared several recombinant C proteins with specific deletions, each fused at the amino-terminus to glutathione-S-transferase (GST) and expressed inE. coli. They were reacted with KUN RNA probes transcribed in vitro from cDNA representing the 5′ untranslated region (5′ UTR, 93 of 96 nucleotides), the 3′ UTR (624 nucleotides), and the 5′ UTR plus most of the C coding region (t′ core, 440 nucleotides). Fusion protein C107 (incorporating mature C) bound strongly to all KUN RNA probes with apparent specificity, being completely resistant to inhibition by 800 mM NaCl, and to competition by a large excess of tRNA. In reactions with labelled KUN RNA probes putative binding sites were identified in the isolated amino-terminal (32 residues) and carboxyterminal (26 residues) basic amino acid domains; this binding was strongly competed by unlabelled KUN UTR probes but weakly or not at all by tRNA. These small domains probably acted co-operatively in binding of mature C to KUN RNA probes. The KUN RNA-core protein binding reactions are similar to those reported with other viral coat or capsid proteins and viral RNAs. url: https://www.ncbi.nlm.nih.gov/pubmed/8645104/ doi: 10.1007/bf01718326 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-333636-h2sg6shp author: Kochan, G. title: Characterization of the RNA-binding activity of VP3, a major structural protein of Infectious bursal disease virus date: 2003 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infectious bursal disease virus (IBDV) is the agent of an immune-depressive disease affecting the poultry industry worldwide. Infection of IBDV leads to expression of five mature virus-encoded proteins. Proteolytic processing of the virus-encoded polyprotein generates VP3 which coats the inner surface of the IBDV capsid. In this report, we describe the characterization of the RNA-binding activity of VP3. For these studies, the VP3 coding region was fused to a histidine tag and expressed in insect cells using a recombinant baculovirus. The histidine-tagged VP3 was affinity-purified and used to study its ability to bind RNA molecules using three complementary methods: (i) Northwestern blotting; (ii) binding of VP3 protein-RNA complexes to nitrocellulose membranes; and (iii) electrophoretic mobility shift assays. The results demonstrated that VP3 efficiently bound ssRNA and dsRNA. Under the experimental conditions used in this study, the formation of VP3-RNA complexes did not depend upon the presence of specific RNA sequences. A series of histidine-tagged VP3 deletion mutants spanning the whole VP3 coding region were generated. The use of these mutants revealed that the VP3 RNA-binding domain layed in a highly conserved 69 aa stretch close to the N-terminus of the protein. url: https://www.ncbi.nlm.nih.gov/pubmed/12664296/ doi: 10.1007/s00705-002-0949-5 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-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-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-262505-1ufgwxxg author: Lai, M. M. C. title: Genetic heterogeneity of murine coronaviruses date: 1983 words: 2559.0 sentences: 162.0 pages: flesch: 57.0 cache: ./cache/cord-262505-1ufgwxxg.txt txt: ./txt/cord-262505-1ufgwxxg.txt summary: Several mouse hepatitis viruses (MHV) with different pathogenicity were studied by oligonucleotide fingerprinting. The MHVs isolated from separate cloned neuroblastoma cell lines persistently infected with JHM strain were also found to have diverged more markedly than the corresponding virus maintained under the conditions of lytic infection. The viruses maintained under the latter conditions exhibit much more variability, suggesting that persistent infections may be a mechanism contributing to the genetic heterogeneity of the current MHV strains. To study the genetic relationship of different MHV strains causing various diseases in mice, we first examined the oligonucleotide fingerprints of two of the IKHVs isolated in Japan. To assess the genetic stability and variability of MItV and to study the possible mechanism of viral divergence observed as above, we examined the heterogeneity of viral genomic sequences in viruses isolated from persistently and latently infected cells. abstract: Several mouse hepatitis viruses (MHV) with different pathogenicity were studied by oligonucleotide fingerprinting. Two strains, MHV-K and MHV-D, which were isolated in Japan and, which cause anaplasia and necrosis of bone marrow and diarrhea, respectively, were found to be closely related to MHV-A59, the prototype MHV. Two other MHV strains, isolated from nude mice, were found to have diverged extensively from the known MHV strains. The MHVs isolated from separate cloned neuroblastoma cell lines persistently infected with JHM strain were also found to have diverged more markedly than the corresponding virus maintained under the conditions of lytic infection. Genetic divergence during persistent infection may be one of the mechanisms by which the MHV diverges. url: https://www.ncbi.nlm.nih.gov/pubmed/6318691/ doi: 10.1007/bf01311312 id: cord-264392-he1vekrt author: Lambeth, L. S. title: Complete genome sequence of Nariva virus, a rodent paramyxovirus date: 2008-12-23 words: 4363.0 sentences: 204.0 pages: flesch: 52.0 cache: ./cache/cord-264392-he1vekrt.txt txt: ./txt/cord-264392-he1vekrt.txt summary: This study confirmed the classification of NarPV as a member of the subfamily Paramyxovirinae and established the close genome organization and sequence relationship between the two rodent paramyxoviruses isolated almost a decade apart and from two locations separated by more than 15,000 km. This was then followed by PCR to fill in the ''''gaps'''' using specific primers designed from NarPV Nariva virus genome 201 sequences obtained from the cDNA subtraction or degenerate primers designed using highly conserved consensus sequences of known paramyxoviruses in the subfamily Paramyxovirinae. Overall comparison of deduced sizes and amino acid sequences of all proteins indicated that NarPV is most closely related to MosPV (Table 1) genome is significantly larger (16,650 nt) than that of NarPV due to the longer untranslated regions (UTRs) located at the 3 0 end of most genes ( Fig. 1b and Table 1 ). abstract: Nariva virus (NarPV) was isolated from forest rodents (Zygodontomys b. brevicauda) in eastern Trinidad in the early 1960s. Initial classification within the family Paramyxoviridae was based mainly on morphological observations including the structure of nucleocapsids and virion surface projections. Here, we report the characterization of the complete genome sequence of NarPV. The genome is 15,276 nucleotides in length, conforming to the rule-of-six, and has a genome organization typical of most members of the family, with six transcriptional units in the order 3′-N–P-M-F–H-L-5′. The gene junctions contain highly conserved gene start and stop signals and a tri-nucleotide intergenic sequence present in most members of the subfamily Paramyxovirinae. Sequence comparison studies indicate that NarPV is most closely related to Mossman virus, which was isolated from wild rats (Rattus leucopus) in Queensland, Australia, in 1970. This study confirmed the classification of NarPV as a member of the subfamily Paramyxovirinae and established the close genome organization and sequence relationship between the two rodent paramyxoviruses isolated almost a decade apart and from two locations separated by more than 15,000 km. url: https://doi.org/10.1007/s00705-008-0287-3 doi: 10.1007/s00705-008-0287-3 id: cord-260708-l9w5jhsw author: Lasecka, Lidia title: The molecular biology of nairoviruses, an emerging group of tick-borne arboviruses date: 2013-12-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: 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-004717-41ui4lqc author: Laurin, Marc-André title: Detection and genetic characterization of a novel pig astrovirus: relationship to other astroviruses date: 2011-09-08 words: 2226.0 sentences: 115.0 pages: flesch: 49.0 cache: ./cache/cord-004717-41ui4lqc.txt txt: ./txt/cord-004717-41ui4lqc.txt summary: Phylogenetic analysis of the 3 0 end of this strain suggests that a novel and possibly fifth lineage of AstV exists in swine and heightens concerns about the role of pigs as a potential source of emerging astrovirus infections. However, a group of four related sequences revealed only approximately 70% nucleotide identity to bat and human AstV sequences in the database, suggesting that these sequences were divergent from known PoAstV strains and possibly novel. Phylogenetic analysis of these sequences, in addition to prototypical animal AstV strains, confirmed their relatedness and grouped them in a unique lineage on a divergent branch distantly related to other known mamastroviruses (PoAstV 5 in Fig. 2a) . Phylogenetic analysis of the complete capsid coding region of PoAstV CC12 confirms that this strain forms a distinct lineage in the family Mamastroviridae, including previously identified porcine astroviruses from different continents (Fig. 2b ). abstract: Emerging viruses represent a continuous threat to human health and to farmed animals, as evidenced on multiple occasions by outbreaks of influenza, henipavirus and SARS. Knowledge about the diversity of viromes present in reservoir species can lead to a better understanding of the origin of emerging pathogens. In this study, we extend the knowledge of astrovirus diversity in pigs by reporting the genetic characterization of an unknown astrovirus lineage. Phylogenetic analyses provided evidence that this porcine astrovirus lineage is unique and does not appear to share a recent common ancestor with any known mamastrovirus. The data reported in this study extend the number of porcine astrovirus lineages to a total of five, all of which most likely represent distinct species of different origins. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086720/ doi: 10.1007/s00705-011-1088-7 id: cord-306380-msk9p1yy author: Lee, C.-W. title: Evidence of genetic diversity generated by recombination among avian coronavirus IBV date: 2000 words: 2796.0 sentences: 146.0 pages: flesch: 58.0 cache: ./cache/cord-306380-msk9p1yy.txt txt: ./txt/cord-306380-msk9p1yy.txt summary: Phylogenetic analysis of selected regions of the genome of the DE072 serotype field isolates further support those results and indicate that isolates within the same serotype may have different amounts of nucleotide sequence similarity with each other in individual genes other than the S gene. Further, we conducted sequence analysis of six isolates of the DE072 serotype in order to determine if recombination is frequently occurring in this region in field isolates of IBV. We conducted phylogenetic analysis by dividing 3.8 kb of the 3 end of the genome among five IBV strains at the IG sequences. However, these 6 isolates had a much different level of nucleotide sequence similarity with each other in gene 3 and gene 4, and clustered randomly with other serotypes of IBV (Fig. 3) . Sequence analysis of gene 3, gene 4 and gene 5 of avian infectious bronchitis virus strain CU-T2 Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus abstract: Previously, we demonstrated that the DE072 strain of IBV is a recombinant which has an IBV strain D1466-like sequence in the S gene. Herein, we analyzed the remaining 3.8 kb 3′ end of the genome, which includes Gene 3, Gene 4, Gene 5, Gene 6, and the 3′ non-coding region of the DE072 and D1466 strains. Those two viruses had high nucleotide similarity in Gene 4. However, the other individual genes had a much different level of sequence similarity with the same gene of the other IBV strains. The genome of five IBV strains, of which the complete sequence of the 3′ end of the genome has been determined, were divided at an intergenic (IG) consensus sequence (CTGAACAA or CTTAACAA) and compared phylogenetically. Phylogenetic trees of different topology indicated that the consensus IG sequences and the highly conserved sequence around this regions may serve as recombination ‘hot spots’. Phylogenetic analysis of selected regions of the genome of the DE072 serotype field isolates further support those results and indicate that isolates within the same serotype may have different amounts of nucleotide sequence similarity with each other in individual genes other than the S gene. Presumably this occurs because the consensus IG sequence serves as the template switching site for the viral encoded polymerase. url: https://www.ncbi.nlm.nih.gov/pubmed/11087096/ doi: 10.1007/s007050070044 id: cord-332811-kjgah8ts author: Lee, Do Hyun title: Immunoprophylactic effect of chicken egg yolk antibody (IgY) against a recombinant S1 domain of the porcine epidemic diarrhea virus spike protein in piglets date: 2015-06-23 words: 5898.0 sentences: 237.0 pages: flesch: 43.0 cache: ./cache/cord-332811-kjgah8ts.txt txt: ./txt/cord-332811-kjgah8ts.txt summary: title: Immunoprophylactic effect of chicken egg yolk antibody (IgY) against a recombinant S1 domain of the porcine epidemic diarrhea virus spike protein in piglets A codon-optimized PEDV S1 gene consisting of amino acid residues 25–749 was synthesized and used to establish a stable porcine cell line constitutively expressing a recombinant PEDV S1 protein containing the chicken immunoglobulin Fc fragment at its C-terminus. Moreover, oral passive immunization using chicken IgY raised against the PEDV S1 protein was found to control and prevent PED post-challenge in suckling piglets. All neonatal piglets except for animals in the control group were inoculated orally with 1 ml of the small-intestine homogenate containing 10 4 TCID 50 /ml PEDV field virus determined using real-time RT-PCR as described previously [10] . Immunoprophylactic effect of chicken egg yolk immunoglobulin (IgY) against porcine epidemic diarrhea virus (PEDV) in piglets abstract: Porcine epidemic diarrhea virus (PEDV) is a highly contagious enteric pathogen of swine causing high mortality rates in piglets. PEDV outbreaks have occurred continuously in most swine-producing Asian countries and have recently emerged in the United States, leading to large economic losses for both the Asian and US pig industries. The spike (S) protein of PEDV consists of the S1 and S2 domains, responsible for virus binding and fusion, respectively. The involvement of the S1 domain in specific high-affinity interactions with the cellular receptor and induction of neutralizing antibodies in the natural host makes it a logical target for the development of effective vaccines and therapeutics against PEDV. Passive immunization by oral administration of egg yolk antibodies (IgY) obtained from immunized chickens provides an alternative source of specific antibodies for the prevention and treatment of PEDV in newborn piglets. In this study, we produced an IgY against the PEDV S1 protein and investigated its immunoprophylactic effect in neonatal piglets. A codon-optimized PEDV S1 gene consisting of amino acid residues 25–749 was synthesized and used to establish a stable porcine cell line constitutively expressing a recombinant PEDV S1 protein containing the chicken immunoglobulin Fc fragment at its C-terminus. The purified recombinant S1 protein was found to mediate potent immune responses in immunized hens. We next tested the ability of oral passive immunization with anti-PEDV S1 IgY to protect piglets against PEDV. Specific chicken IgY against the S1 protein was orally administered to neonatal piglets, and their responses subsequent to a virulent PEDV challenge were monitored. The results showed that oral administration of anti-PEDV S1 IgY efficiently protects neonatal piglets against PEDV, suggesting its potential as a prophylactic or therapeutic agent against acute PEDV infection. url: https://doi.org/10.1007/s00705-015-2494-z doi: 10.1007/s00705-015-2494-z id: cord-004810-g0y7ied0 author: Lee, S. K. title: S1 glycoprotein gene analysis of infectious bronchitis viruses isolated in Korea date: 2003-11-13 words: 3750.0 sentences: 190.0 pages: flesch: 59.0 cache: ./cache/cord-004810-g0y7ied0.txt txt: ./txt/cord-004810-g0y7ied0.txt summary: The S1 glycoprotein gene of IBV isolates were amplified by reverse transcriptase – polymerase chain reaction (RT-PCR) and analyzed by restriction fragment length polymorphism (RFLP) analysis. And these IBV isolates showed different patterns from each other and non-Korean IBV isolates in reverse transcriptase-polymerase chain reaction-restriction fragment length polymorphism (RT-PCR-RFLP) analysis [29] . Amplified S1 genes were first classified by RFLP analysis and then the representative strains were cloned, sequenced and compared to other non-Korean published IBV sequences. Phylogenetic trees were constructed from the nucleotide and deduced amino acid sequences of the S1 glycoprotein genes of Korean IBV isolates and non-Korean IBV strains (Fig. 3) . Korean IBV K281-01 and K210-02 isolates formed distinct clusters that were related to non-Korean IBV Ark99, Ark DPI, Gray and JMK strains although K281-01 and K210-02 isolates were classified into the Arkansas type by PCR-RFLP analysis. abstract: Fifteen isolates of Infectious bronchitis virus (IBV) were obtained from the kidney, trachea, and cecal tonsil of IB suspected chickens between 2001 and 2002 years in Korea. The S1 glycoprotein gene of IBV isolates were amplified by reverse transcriptase – polymerase chain reaction (RT-PCR) and analyzed by restriction fragment length polymorphism (RFLP) analysis. Fifteen Korean IBV isolates were classified into 4 groups by their RFLP patterns using restriction enzymes, HaeIII, BstYI, and XcmI. The RFLP patterns for 3, 1, and 1 of 15 isolates corresponded to the patterns of IBV Arkansas, Connecticut, and Massachusetts strains, respectively. Ten of 15 isolates generated unique KM91 RFLP pattern that was observed in the IBV KM 91 strain previously isolated in Korea. To confirm genetic diversity in the S1 genes of IBV isolates, viral RNAs of representative 9 of 15 IBV isolates were amplified, cloned, sequenced and compared with published sequences for non-Korean IBV strains. Korean IBV isolates showed amino acid sequence similarity between 61.8% (K446-01 and K161-02) and 96.1% (K281-01 and K210-02) with each other and they showed amino acid sequence similarity between 42.9% (K161-02 and GA980470) and 96.5% (K203-02 and KB8523) compared to non-Korean IBV strains. By phylogenetic tree analysis, Korean IBV field isolates were branched into five clusters in which 3 clusters were differentiated from non-Korean IBV strains. Especially, Korean IBV isolates K069-01, K507-01, K774-01 and K142-02 formed a separate cluster. It seems that IBVs continue to evolve and IBVs showing various genetic differences may cocirculate in Korea. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087141/ doi: 10.1007/s00705-003-0225-3 id: cord-306725-0vam15pt author: Li, Hao title: First detection and genomic characteristics of bovine torovirus in dairy calves in China date: 2020-05-09 words: 3015.0 sentences: 156.0 pages: flesch: 58.0 cache: ./cache/cord-306725-0vam15pt.txt txt: ./txt/cord-306725-0vam15pt.txt summary: Sequence analysis showed that the two isolates shared 10 identical amino acid mutations in the S protein compared to the complete S sequences of BToV available in the GenBank database. A phylogenetic analysis based on the complete amino acid sequence of the S protein showed that the BToVs could be separated into four groups (Fig. 2) , designated tentatively as group 1 to group 4. The bovine torovirus strains BToV/SC-1/China and BToV /SC-2/China investigated in this study are indicated by black triangles Fig. 2 Phylogenetic tree based on the deduced 1586-aa sequence of the complete S gene. Moreover, the two Chinese strains shared identical unique amino acid changes in the S and HE genes when compared to the other strains with sequences available in the GenBank database, indicating the unique evolution in Chinese BToV strains. Moreover, two complete BToV genome sequences were obtained from the clinical samples, and these two BToV isolates had unique amino acid changes in the S and HE proteins. abstract: Bovine torovirus (BToV) is a diarrhea-causing pathogen. In this study, 92 diarrheic fecal samples from five farms in four provinces in China were collected and tested for BToV using a RT-PCR assay, and 21.73% samples were found to be BToV positive. Moreover, two complete BToV genome sequences (MN073058 and MN073059) were obtained from the clinical samples, which were 28,297 and 28,301 nucleotides in length, respectively. Sequence analysis showed that the two isolates shared 10 identical amino acid mutations in the S protein compared to the complete S sequences of BToV available in the GenBank database. In addition, seven consecutive amino acid mutations were found from aa 1,486 to 1,492 in the S protein of isolate MN073058. Moreover, the two isolates shared one identical amino acid mutation in the receptor binding sites of the HE protein. To the best of our knowledge, this is the first report on the epidemic and genomic characterization of BToV in China, which is helpful for further understanding the genetic evolution of BToV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-020-04657-9) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-020-04657-9 doi: 10.1007/s00705-020-04657-9 id: cord-322593-bgm6smuo author: Li, Lan title: Antiviral activity of recombinant porcine surfactant protein A against porcine reproductive and respiratory syndrome virus in vitro date: 2016-04-21 words: 4702.0 sentences: 235.0 pages: flesch: 54.0 cache: ./cache/cord-322593-bgm6smuo.txt txt: ./txt/cord-322593-bgm6smuo.txt summary: In this present study, we assessed the antiviral properties of recombinant porcine SP-A (RpSP-A) on PRRSV infection in Marc 145 cells and revealed its antiviral mechanism using a plaque assay, real-time qPCR, western blotting analysis and an attachment and penetration assay. Our results showed that RpSP-A could inhibit the infectivity of PRRSV in Marc 145 cells and could reduce the total RNA and protein level. Notably, porcine ficolin is also a collagenous lectin that was established to reduce PRRSV infection in Marc-145 cells in neutralization assays and to inhibit the replication of infectious viral particles in a GlcNAc-dependent manner [30] . Porcine reproductive and respiratory syndrome virus-infected alveolar macrophages contain no detectable levels of viral proteins in their plasma membrane and are protected against antibody-dependent, complement-mediated cell lysis Recombinant porcine lung surfactant protein A inhibits porcine reproductive and respiratory syndrome virus infection into host cells in vitro abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) has caused significant economic losses in the swine industry worldwide. However, there is not an ideal vaccine to provide complete protection against PRRSV. Thus, the need for new antiviral strategies to control PRRSV still remains. Surfactant protein A (SP-A) belongs to the family of C-type lectins, which can exert antiviral activities. In this present study, we assessed the antiviral properties of recombinant porcine SP-A (RpSP-A) on PRRSV infection in Marc 145 cells and revealed its antiviral mechanism using a plaque assay, real-time qPCR, western blotting analysis and an attachment and penetration assay. Our results showed that RpSP-A could inhibit the infectivity of PRRSV in Marc 145 cells and could reduce the total RNA and protein level. The attachment assay indicated that RpSP-A in the presence of Ca(2+) could largely inhibit Marc 145 cell attachment; however, in the penetration assay, it was relatively inactive. Furthermore, our study suggested that virus progeny released from infected Marc145 cells were blocked by RpSP-A from infecting other cells. We conclude that RpSP-A has antiviral activity against PRRSV, most probably by blocking viral attachment and the cell-to-cell transmission pathway, and therefore, RpSP-A holds promise as a novel antiviral agent against PRRSV. url: https://doi.org/10.1007/s00705-016-2838-3 doi: 10.1007/s00705-016-2838-3 id: cord-345552-h6fwi0qn author: Li, Q.-G. title: Hydropathic characteristics of adenovirus hexons date: 1997-07-01 words: 3522.0 sentences: 206.0 pages: flesch: 53.0 cache: ./cache/cord-345552-h6fwi0qn.txt txt: ./txt/cord-345552-h6fwi0qn.txt summary: The strength of the surface charge accumulated on the hydrophilic and hydrophobic regions correlated to the tissue tropism of the different adenovirus types. The sequence of the predicted protein, consisting of 937 amino acids, was obtained with the LaserGene software program EditSeq. The hydropathy data of hexon proteins from human adenovirus types 2, 3, 4, 5, 7, 12, 16, 40, 41, and 48, bovine adenovirus type 3, murine adenovirus type 1, and avian adenovirus types 1 and 10 were derived using the prediction method of Kyte-Doolittle in the LaserGene computer program Protean. The nucleotide and amino acid sequence pair distances and the phylogenetic tree of 14 hexon proteins showed serotypes of subgenera B, D and E to be closely related (Table 3 and Fig. 2) . DNA sequence of the adenovirus type 41 hexon gene and predicted structure of the protein abstract: The complete nucleotide sequence and the predicted amino acid sequence of the adenovirus type 7 hexon gene were determined. The hydro-pathy of the hexon proteins from human adenovirus types 2, 3, 4, 5, 7, 12, 16, 40, 41, and 48, bovine adenovirus type 3, murine adenovirus type 1, and avian adenovirus types 1 and 10 was analysed. The presence of purines and pyrimid-ines in the second position of the codons was correlated to hydrophilicity and hydrophobicity, respectively. Comparison of the hydrophilicity plots of eight hexons showed seven hypervariable regions to be distributed on the surface. A large portion of the hypervariable regions manifests hydrophilicity. The strength of the surface charge accumulated on the hydrophilic and hydrophobic regions correlated to the tissue tropism of the different adenovirus types. Analysis of codon usage for adenovirus hexons showed that among synony-mous codons those with cytidine in the third position were preferably used to a great extent. Analysis of the nucleotide and amino acid sequence pair distances and the phylogenetic tree of 14 hexon proteins showed members of subgenera B, D and E to be closely related, especially Ad4 and Ad16, and subgenus A to be closely related to subgenus F. url: https://www.ncbi.nlm.nih.gov/pubmed/9267445/ doi: 10.1007/s007050050162 id: cord-307408-6wfx0wey author: Li, Renfeng title: Phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in central China based on the ORF3 gene and the main neutralization epitopes date: 2013-11-30 words: 3224.0 sentences: 159.0 pages: flesch: 58.0 cache: ./cache/cord-307408-6wfx0wey.txt txt: ./txt/cord-307408-6wfx0wey.txt summary: title: Phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in central China based on the ORF3 gene and the main neutralization epitopes In this study, we aimed to investigate the molecular epidemiology and antigenic variability of PEDV field strains based on analysis of ORF3 and a portion of the S gene encoding three neutralizing epitopes (aa 499-638, 748-755, and 764-771) of the S protein. To further investigate the molecular epidemiology of this virus, we chose the ORF3 gene and a partial S gene encoding a region including three neutralization epitopes for studying the evolutionary characteristic and antigenic variation of PEDV. Based on the sequence analysis of ORF3 and partial S genes of PEDV, molecular epidemiology was conducted using 14 field strains from central China. Sequence and phylogenetic analysis of nucleocapsid genes of porcine epidemic diarrhea virus (PEDV) strains in China abstract: Since 2010, porcine epidemic diarrhea has re-emerged with devastating impact on the swine-raising industry in central China. To investigate the epidemic characteristics of PEDV, the complete ORF3 genes of 14 PEDV field strains from central China during 2012 to 2013 were cloned, sequenced and compared with reference strains. Phylogenetic analysis based on the complete ORF3 gene showed that the PEDVs in central China and the reference strains could be divided into three groups: G1, G2, and G3. The 14 PEDV isolates were classified as G1 and showed a close relationship to some Chinese strains isolated previously in central China and differed genetically from recent isolates from southern China, Korean strains (SM98 and DB1865, 2012), the Chinese LZC strain (2007), and the vaccine strain (CV777) being used in China. Our findings suggested that the PEDVs circulating between 2012 and 2013 in central China might have evolved from earlier strains in the local region. To determine the reason for recent vaccination failures, we also studied variations in antigenicity of field strains by analyzing the three neutralizing epitope regions in the S gene. The results showed that the neutralizing epitopes at aa 245-252 were highly conserved, but most of the amino acid changes occurred in the epitope regions aa 7-146 and 271-278. We speculate that the amino acid mutations in the neutralizing epitope regions may be associated with changes in the antigenicity of PEDV and consequently result in vaccination failure. Together, these findings may be useful for understanding the epidemiology of PEDV and may be relevant for designing of new and more efficacious vaccines. url: https://doi.org/10.1007/s00705-013-1929-7 doi: 10.1007/s00705-013-1929-7 id: cord-285892-tp6mlqtw author: Li, Yingli title: Isolation of two Chinese bovine enteroviruses and sequence analysis of their complete genomes date: 2012-08-01 words: 2956.0 sentences: 123.0 pages: flesch: 49.0 cache: ./cache/cord-285892-tp6mlqtw.txt txt: ./txt/cord-285892-tp6mlqtw.txt summary: In this study, RNA corresponding to bovine enterovirus (BEV) was detected in 24.6 % of faecal samples (17/69) from diarrheic and healthy cattle in six different areas in China by an RT-PCR screening method. These viruses were characterized molecularly through sequence analysis of complete genomes, and the BHM26 and BJ50 isolates were therefore classified into genotype 2 of the BEV-B cluster. A total of 69 bovine diarrheic and healthy faecal specimens from six different areas were examined by RT-PCR using the primer pair 6424U24 and 7450L24, which cover the highly conserved partial 3D gene and 3 0 UTR of BEVs. The results showed that virus-specific RNA could be detected directly in faecal material in 17 of 69 samples (24.6 %). The results showed that the 3D/3 0 UTR (1026 nt) of BHM26 and BJ50 shared 86 % and 88 % nucleotide sequence identity, respectively, to that of BEV strain Jena38/02 (GenBank accession number: DQ092789), indicating that the two isolates are bovine enterovirus. abstract: In this study, RNA corresponding to bovine enterovirus (BEV) was detected in 24.6 % of faecal samples (17/69) from diarrheic and healthy cattle in six different areas in China by an RT-PCR screening method. Furthermore, two cytopathic agents, designated as BHM26 and BJ50, were isolated from the bovine diarrheic fecal samples. During passage in MA104 cells, ultrathin sections of virus-infected monolayers were examined using a transmission electron microscope, and a large number of symmetrical virus crystals were seen in the cytoplasm, with monomorphic small viral particles of 27-30 nm in diameter. The full-length RNA genomes were 7433 and 7416 nucleotides long, respectively, with a genome organization analogous to that of picornaviruses. Phylogenetic analysis of the VP1 and VP3 capsid protein coding sequences suggested that the viruses BHM26 and BJ50 belong to genotype 2 of the BEV cluster B (BEV-B). In addition, sequence comparisons of the 5′ and 3′ UTRs and P1, P2 and P3 subgenomic regions of the two isolates suggested that there were intergenotypic recombination events occurring during evolution of the BHM26 and BJ50 isolates. url: https://www.ncbi.nlm.nih.gov/pubmed/22851010/ doi: 10.1007/s00705-012-1424-6 id: cord-276630-qci7khki author: Lima, William Gustavo title: The potential of drug repositioning as a short-term strategy for the control and treatment of COVID-19 (SARS-CoV-2): a systematic review date: 2020-06-08 words: 3727.0 sentences: 214.0 pages: flesch: 49.0 cache: ./cache/cord-276630-qci7khki.txt txt: ./txt/cord-276630-qci7khki.txt summary: Due to the evidence of the anti-SARS-CoV-2 activity of various clinically available agents, drug repositioning stands out as a promising strategy for a short-term response in the fight against the novel coronavirus. Only seven drugs (chloroquine, tetrandrine, umifenovir (arbidol), carrimycin, Table 1 Clinical evidence of potential candidates for drug repositioning against COVID-19 (SARS-CoV-2) *Lopinavir (400 mg) + ritonavir (100 mg), q12h, orally; associated with umifenovir (200 mg), q12h, orally. [14] reported that the use of arbidol in combination with lopinavir/ritonavir inhibits the aggravation of pneumonia caused by SARS-CoV-2 and promotes a virus-negative conversion in patients from China. Of these, only six drugs (lopinavir/ritonavir, umifenovir (arbidol), remdesivir, chloroquine, and hydroxychloroquine) have shown promising results in preclinical trials and have clinically lessened the symptoms of COVID-19. Although lopinavir/ ritonavir had low anti-SARS-CoV-2 activity, arbidol, remdesivir, and chloroquine/hydroxychloroquine showed promising effects against this coronavirus. abstract: The novel human coronavirus (SARS-CoV-2), the causative agent of COVID-19, has quickly become a threat to the public health and economy worldwide. Despite the severity of some cases, there are no current pathogen-specific antivirals available to treat the disease. Therefore, many studies have focused on the evaluation of the anti-SARS-CoV-2 activity of clinically available drugs. Here, we conducted a systematic review to describe the drug repositioning strategy against SARS-CoV-2 and to discuss the clinical impact of this approach in the current pandemic context. The systematic review was performed on March 23, 2020, using PubMed/MEDLINE, Scopus, Cochrane Library, and Biblioteca Virtual de Saúde (BVS). The data were summarized in tables and critically analyzed. After the database search, 12 relevant studies were identified as eligible for the review. Among the drugs reported in these studies, 57 showed some evidence of antiviral activity. Antivirals, especially antiretrovirals, are the main class of therapeutic agents evaluated against COVID-19. Moreover, studies have reported the anti-SARS-CoV-2 activity of antitumor (16%; 9/57), antimalarial (7%, 4/57), and antibacterial (5%; 3/57) agents. Additionally, seven pharmacological agents (chloroquine, tetrandrine, umifenovir (arbidol), carrimycin, damageprevir, lopinavir/ritonavir) are in phase IV of clinical trials. Due to the evidence of the anti-SARS-CoV-2 activity of various clinically available agents, drug repositioning stands out as a promising strategy for a short-term response in the fight against the novel coronavirus. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-020-04693-5) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-020-04693-5 doi: 10.1007/s00705-020-04693-5 id: cord-004680-u3cnsdl8 author: Lin, Z. title: Typing of recent infectious bronchitis virus isolates causing nephritis in chicken date: 1991 words: 860.0 sentences: 47.0 pages: flesch: 57.0 cache: ./cache/cord-004680-u3cnsdl8.txt txt: ./txt/cord-004680-u3cnsdl8.txt summary: Four isolates of infectious bronchitis viruses (IBV) from chickens with nephritis, were characterized by polymerase chain reaction (PCR) and restriction enzyme fragment length polymorphism (RFLP), and were found to be genetically different from the other twelve strains which we previously studied. HinfI digested pUC 19 DNA was used as the molecular size markers (3//), and their sizes are indicated in base pairs (bp) on the left In this study, essentially the same procedure was used in an attempt to characterize four IBV isolates F-88, Y-4, M-l, and NI-1 from chickens with nephritis in different endemic areas of Japan between 1988 and 1989. The results of the present study, indicate that the four recently obtained IBV isolates causing nephritis are, by our genetic criteria, similar to each other but different from previous isolates, hence are classified together into a new subtype (group VI). Serological comparisons of strains of infectious bronchitis virus using plaque-purified isolants abstract: Four isolates of infectious bronchitis viruses (IBV) from chickens with nephritis, were characterized by polymerase chain reaction (PCR) and restriction enzyme fragment length polymorphism (RFLP), and were found to be genetically different from the other twelve strains which we previously studied. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086593/ doi: 10.1007/bf01310957 id: cord-347443-0evqo01m author: Litwin, Christine M. title: Seasonality and prevalence of respiratory pathogens detected by multiplex PCR at a tertiary care medical center date: 2013-07-24 words: 3991.0 sentences: 218.0 pages: flesch: 50.0 cache: ./cache/cord-347443-0evqo01m.txt txt: ./txt/cord-347443-0evqo01m.txt summary: Seasonality has been reported for many viruses, including influenza virus, respiratory syncytial virus (RSV), and the recently described human metapneumovirus (hMPV). Major causes of bronchiolitis and lower respiratory tract illnesses in children include respiratory syncytial virus (RSV), parainfluenza viruses, influenza virus, and human metapneumovirus (hMPV). The organism/viruses detected by the FilmArray included adenovirus, influenza A virus (FluA), influenza B virus (FluB), parainfluenza virus 1 (Para 1), parainfluenza virus 2 (Para 2), parainfluenza virus 3 (Para 3), parainfluenza virus 4 (Para 4), respiratory syncytial virus (RSV), coronavirus 229E (CoronaV 229E), CoronaV NL63, CoronaV HKU1, CoronaV OC43, human metapneumovirus (hMPV), Bordetella pertussis, Chlamydophila pneumoniae and Mycoplasma pneumoniae. In our study, 939 specimens were analyzed over the course of a year using a respiratory pathogen multiplex PCR that yielded a positivity rate of 65 % with multiple analytes detected in 12 % of specimens, especially in children. RSV and hMPV PCR-positive cases were statistically much more likely than Rhino/Entero PCR-positive infections to initially present with pneumonia or bronchiolitis in our study. abstract: Respiratory tract infections (RTIs) are a leading cause of mortality and morbidity. Seasonality has been reported for many viruses, including influenza virus, respiratory syncytial virus (RSV), and the recently described human metapneumovirus (hMPV). We hypothesize that the availability of rapid, multiplex PCR diagnostics will provide better clinical care and new insights into the etiology and clinical spectrum of RTIs. We conducted a retrospective analysis of the incidence of respiratory pathogens at a 500-bed adult and 154-bed pediatric hospital tertiary care center. A total of 939 specimens from patients with an age range of 5 days to 91 years (median, 2 years) were tested by a multiplex respiratory pathogen PCR from November 14, 2011 to November 13, 2012. Sixty-five percent of specimens were positive for at least one pathogen. As the age of the patient increased, the positivity rate for the PCR decreased proportionately. Rhinoviruses/enteroviruses (Rhino/Entero) were the most prevalent (34.3 %) followed by RSV (19.2 %) and hMPV (6.2 %). Twelve percent of the positive samples were positive for multiple analytes, with Rhino/Entero and RSV being the most common combination. The peak months were September and May for Rhino/Entero infections, January for RSV and February for coronavirus. hMPV peaked 2 months after RSV, as has been observed recently in other studies. Multiplex PCR provides rapid diagnostic information that can be used to make knowledgeable clinical decisions and potentially reduce the use of antibiotics. Active respiratory PCR surveillance could also predict seasonal respiratory epidemics to allow for adequate planning of additional infection control measures. url: https://www.ncbi.nlm.nih.gov/pubmed/23881085/ doi: 10.1007/s00705-013-1794-4 id: cord-256859-7ixegm72 author: Liu, S. W. title: Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between 1995 and 2004 date: 2006-01-09 words: 5156.0 sentences: 266.0 pages: flesch: 56.0 cache: ./cache/cord-256859-7ixegm72.txt txt: ./txt/cord-256859-7ixegm72.txt summary: Except for isolates in genotype V, which included the Mass-type strains, none of the Chinese IBV isolates examined in this study shared more than 83% amino acid similarity in the S1 protein with the H120 vaccine strain. Furthermore, almost all of the Chinese IBV isolates contained deletions and insertions except for those of the Mass-type IBV, which were included in genotype V in this study, and had amino acid sequences similar to those of the H120 strain ( Table 4 ). The low identities (<83%) of amino acid sequences between Chinese IBV isolates and H120, except for those of the Mass-type IBV, which were included in genotype V in this study, may account for the prevalence of the viruses during the past ten years in spite of the extensive use of Mass-type vaccines in the field in China. abstract: Twenty-six avian infectious bronchitis (IB) viruses (IBV) were isolated from outbreaks in chickens in China between 1995 and 2004. They were characterized by comparison with twenty-six Chinese reference strains and five other IBV strains. Chinese IBVs, which were mainly nephropathogenic, were placed into seven genotypes. Fourteen Chinese IBV isolates were placed in genotype I, having small evolutionary distances from each other. Genotype II included 6 strains that were isolated in the 1990s in China. Genotype III consisted of eight Chinese isolates that showed close relationship with Korean IBV isolates. Another eight IBV isolates clustered in genotype IV and showed larger evolutionary distances. The Massachusetts serotype was present in China in 1990s and was in a separate genotype. Two isolates, HN99 and CK/CH/LHN/00I, which might be a reisolation of vaccine strains, clustered into genotype VI. Four Chinese IBV isolates formed another genotype and showed larger evolutionary distances from other Chinese IBV genotypes (genotype VII). IBVs in same genotypes showed more than 90% amino acid sequence similarities, whereas most of the viruses in different genotypes showed less than 90%. The results showed that IBVs in China came from genetic changes both in IBV populations that existed before the advent of vaccination and in the viruses that were introduced through live vaccines. IBVs showing various genetic differences are cocirculating in China. url: https://www.ncbi.nlm.nih.gov/pubmed/16397751/ doi: 10.1007/s00705-005-0695-6 id: cord-312787-j7ye7ed5 author: Loemba, H. D. title: Kinetics of humoral immune response to the major structural proteins of the porcine reproductive and respiratory syndrome virus date: 1996 words: 3411.0 sentences: 149.0 pages: flesch: 41.0 cache: ./cache/cord-312787-j7ye7ed5.txt txt: ./txt/cord-312787-j7ye7ed5.txt summary: coli-expressed ORFs 5 to 7 gene products, suggested that antibodies directed against the envelope E protein appear by day 7 p.i., whereas antibodies directed against the nucleocapsid N and membrane M proteins can only be detected by the end of the second week p.i. No correlation could be demonstrated between VN and IIF antibody titers, viremia, and viral protein specificities of circulating antibodies at various times p.i. Summary. coli-expressed ORFs 5 to 7 gene products, suggested that antibodies directed against the envelope E protein appear by day 7 p.i., whereas antibodies directed against the nucleocapsid N and membrane M proteins can only be detected by the end of the second week p.i. No correlation could be demonstrated between VN and IIF antibody titers, viremia, and viral protein specificities of circulating antibodies at various times p.i. The porcine reproductive and respiratory syndrome virus (PRRSV) is an enveloped RNA virus which has been found to be responsible for reproductive failure in sows of any parities (late-term abortions, increased numbers of stillborn, mummified and weakborn pigs) and respiratory problems affecting pigs of all ages [8, 20] . abstract: The kinetics of appearance of antibodies directed to the major structural proteins N, M and E of porcine reproductive and respiratory syndrome virus (PRRSV) was followed in pigs naturally- and experimentally-exposed to the virus. Specific IgM antibody titers were first detected by indirect immunofluorescence (IIF) at the end of the first week of PRRSV infection, peaked by day 14 to 21 post-inoculation (p.i.), then rapidly decreased to undetectable levels by day 35 to 42 p.i. On the other hand, specific IgG antibody titers peaked by day 21 to 28 p.i. and remained unchanged to the end of the 6- or 9-week observation period; in addition, a persistent viremia was observed. Virus neutralizing (VN) antibody titers >8 were not detected until 3 to 4 weeks p.i. Taken together, the results obtained by Western blotting analyses using purified virus andE. coli-expressed ORFs 5 to 7 gene products, suggested that antibodies directed against the envelope E protein appear by day 7 p.i., whereas antibodies directed against the nucleocapsid N and membrane M proteins can only be detected by the end of the second week p.i. No correlation could be demonstrated between VN and IIF antibody titers, viremia, and viral protein specificities of circulating antibodies at various times p.i. url: https://www.ncbi.nlm.nih.gov/pubmed/8645111/ doi: 10.1007/bf01718333 id: cord-283804-dje7qbps author: Macnaughton, M. R. title: The polypeptide composition of avian infectious bronchitis virus particles date: 1977 words: 2683.0 sentences: 221.0 pages: flesch: 78.0 cache: ./cache/cord-283804-dje7qbps.txt txt: ./txt/cord-283804-dje7qbps.txt summary: The polypeptides of the different density virus particles from the three IBV strains were analysed on polyacrylamide gels. Other studies on the polypeptide composition of eoronaviruses have shown 6 polypeptides in the virus particles of human coronavirus (HCV) strain OC43 (7) a n d t r a n s m i s s i b l e g a s t r o e n t e r i t i s v i r u s ( T G E V ) (5), a n d 7 p o l y p e p t i d e s in t h e v i r u s p a r t i c l e s of H C V s t r a i n 229 E (8) Virus Polypeptide Analysis Figure 2 shows the polsTeptides of the purified major virus species of the IBV strains Beaudette, Connecticut and Massachusetts, on polyaerylamide gels. abstract: Egg grown avian infectious bronchitis virus (IBV) centrifuged on sucrose density gradients was found to consist of a major virus peak of density 1.17 to 1.18 g/cm(3) and occasionally two minor virus peaks of density 1.21 to 1.22 g/cm(3) and 1.13 g/cm(3). Three different IBV strains were examined and no morphological differences were detected between virus particles of different densities or from different strains. The polypeptides of the different density virus particles from the three IBV strains were analysed on polyacrylamide gels. In all cases 7 polypeptides were observed, although there were differences in the proportions of these polypeptides in particles of different densities and those from the different strains. The polypeptides have been called VP1 (molecular weight 130,000), VP2 (105,000), VP3 (97,000), VP4 (81,000), VP5 (74,000), VP6 (51,000) and VP7 (33,000). Additional polypeptides were produced if slightly harsher treatments were used. url: https://www.ncbi.nlm.nih.gov/pubmed/200202/ doi: 10.1007/bf01314478 id: cord-296167-np0b9a7o author: Mardani, Karim title: Naturally occurring recombination between distant strains of infectious bronchitis virus date: 2010-06-24 words: 2955.0 sentences: 132.0 pages: flesch: 50.0 cache: ./cache/cord-296167-np0b9a7o.txt txt: ./txt/cord-296167-np0b9a7o.txt summary: In the present study, the 3′ terminal 7.2 kb of the genome of a recently isolated variant of IBV (N1/03) was sequenced and compared with the sequences of classical and novel strains of IBV, the two main groups of these viruses in Australia. The 3 0 -terminal 7.2 kb of the genomes of the representative classical and novel Australian IBV strains were aligned with the sequences from the same region of the N1/03 isolate, and the multiple alignment results were introduced into SimPlot version 3.5.1 to identify likely recombination sites [19] . It would be appropriate to sequence and analyse the polymerase genes of classical, novel and new variant strains of IBV to obtain further information about the relationships between the different Australian IBVs. Isolation and characterization of new infectious bronchitis virus variants in Hungary abstract: New variants of infectious bronchitis virus (IBV) have emerged in Australia despite its geographical isolation and intensive vaccination programs. In the present study, the 3′ terminal 7.2 kb of the genome of a recently isolated variant of IBV (N1/03) was sequenced and compared with the sequences of classical and novel strains of IBV, the two main groups of these viruses in Australia. The comparison revealed that recombination between classical and novel IBVs was responsible for the emergence of the new variant. It was concluded that novel IBVs, which have not been detected since 1993, and which are phylogenically more distant from classical IBVs than turkey coronaviruses, might still be circulating and contributing to the evolution of IBV in Australia. url: https://doi.org/10.1007/s00705-010-0731-z doi: 10.1007/s00705-010-0731-z id: cord-346629-770qyee8 author: Mase, M. title: Phylogenetic analysis of avian infectious bronchitis virus strains isolated in Japan date: 2004-07-15 words: 2367.0 sentences: 137.0 pages: flesch: 50.0 cache: ./cache/cord-346629-770qyee8.txt txt: ./txt/cord-346629-770qyee8.txt summary: title: Phylogenetic analysis of avian infectious bronchitis virus strains isolated in Japan To define the origin and evolution of recent avian infectious bronchitis virus (IBV) in Japan, a genetic analysis was performed. By phylogenetic analysis based on the S1 gene including the sequence of the hypervariable regions, IBV isolates in Japan were classified into five genetic groups, which included two already-known groups (Mass and Gray). In this study, to define the origin and evolution of recent IBV in Japan, we determined the nucleotide sequences of IBV isolated in Japan using the reverse transcriptase-polymerase chain reaction (RT-PCR) method coupled with direct sequencing, and analyzed the sequences phylogenetically with viruses isolated in other countries. By phylogenetic analysis, the IBV isolates in Japan used in this study were divided into five genetic groups (Fig. 1 ). Typing of field isolates of infectious bronchitis virus based on the sequence of the hypervariable region in the S1 gene abstract: To define the origin and evolution of recent avian infectious bronchitis virus (IBV) in Japan, a genetic analysis was performed. By phylogenetic analysis based on the S1 gene including the sequence of the hypervariable regions, IBV isolates in Japan were classified into five genetic groups, which included two already-known groups (Mass and Gray). Among them, three major genetic groups were associated with the recent outbreaks of IB in Japan. One group is indigenous to Japan and could not be placed within the known existing groups in other countries. The remaining two groups, which have emerged recently, are related to isolates in China and Taiwan. url: https://www.ncbi.nlm.nih.gov/pubmed/15290359/ doi: 10.1007/s00705-004-0369-9 id: cord-341342-kyavg4vu author: Masters, P. S. title: Localization of an RNA-binding domain in the nucleocapsid protein of the coronavirus mouse hepatitis virus date: 1992 words: 5901.0 sentences: 279.0 pages: flesch: 57.0 cache: ./cache/cord-341342-kyavg4vu.txt txt: ./txt/cord-341342-kyavg4vu.txt summary: The RNase sensitivity of the ability of N protein to migrate into nondenaturing gels was not due to possible contaminating protease activity in the RNase preparations, since the same RNase-treated samples of translated N 148 P.S. Masters protein showed no degradation when analyzed by SDS-PAGE (Fig. 3, lanes an, lower) . Since the N mRNAs synthesized from the transcription vectors shown in Fig. 1 contained this portion of the leader sequence, it seemed possible that the N-RNA complex observed in nondenaturing PAGE was that of translated N protein binding to its own mRNA. That the observed complex was not due to translated N protein binding to the leader portion of its own mRNA was also supported by the observation that full-length N protein translated from a construct in which the MHV leader sequence was entirely deleted was also able to migrate into nondenaturing gels (data not shown). abstract: The interaction between the nucleocapsid (N) protein of mouse hepatitis virus (MHV) and RNA was studied in an effort to define portions of the N molecule that participate in binding to RNA. N mRNAs transcribed from SP6 and T7 vectors were translated in a rabbit reticulocyte lysate. Analysis of synthesized N protein in a nondenaturing gel system showed that it bound in vitro to an endogenous RNA in the reticulocyte lysate but not to its own mRNA. A set of deletion mutants was constructed in order to localize the RNA-binding activity of the N protein. It was found that removal of as much as 135 amino-terminal or 57 carboxy-terminal amino acids from the molecule had little or no effect on RNA binding. Moreover, deletion mutants lacking both termini still retained RNA-binding ability. By contrast, internal deletions or truncations extending beyond these two limits effectively abolished RNA binding by N protein. Thus, the RNA-binding region of N has been mapped to the second (central) of the three structural domains of the molecule. url: https://www.ncbi.nlm.nih.gov/pubmed/1322650/ doi: 10.1007/bf01309634 id: cord-261749-lq1ah16x author: Mayo, M. A. title: Report from the 36(th) and the 37(th) Meetings of the Executive Committee of the International Committee on Taxomony of Viruses date: 2006-03-03 words: 2288.0 sentences: 119.0 pages: flesch: 60.0 cache: ./cache/cord-261749-lq1ah16x.txt txt: ./txt/cord-261749-lq1ah16x.txt summary: At EC36 there were extensive discussions of proposals to revise the statutes under which ICTV operates and to revise the International Code for Virus Classification and Nomenclature (ICVCN). In response to the proposal that ICTV should provide for each approved species a latinized binomial name to link its common name(s), the ''type'' description and the classification, the EC felt that there was little support in the virology community for using latinized names. The changes proposed further stipulated that ICTV should keep an official list of virus names that were used previously but are no longer in current taxonomy. It was pointed out that fixing these lists of criteria was an important task for individual SGs. It was proposed that the category "tentative species" be eliminated from taxonomic usage because a virus can either be a member of a species or it cannot. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/16514500/ doi: 10.1007/s00705-006-0728-9 id: cord-258768-bjjfkfgg author: McElligott, Susan title: Detection and genetic characterization of canine parvoviruses and coronaviruses in southern Ireland date: 2010-11-24 words: 4380.0 sentences: 220.0 pages: flesch: 53.0 cache: ./cache/cord-258768-bjjfkfgg.txt txt: ./txt/cord-258768-bjjfkfgg.txt summary: Two hundred fifty samples were collected in total, Fig. 2 Phylogenetic tree based on partial S gene nucleotide sequences of CCoVs described in this study and reference strains. As a result of RNA recombination, insertions, deletions and a high susceptibility to frequent mutation, coronaviruses can mutate rapidly, leading to new genotypes (CCoV-I), biotypes (pantropic CCoV) and host variants (canine respiratory coronavirus), all of which may present possible difficulties regarding successful vaccination of dogs. As a result of this study, it can be concluded that although it appears that the viral evolution of CPV type 2 is not yet a significant problem for the canine population in Ireland, vaccine efficacy may need to be re-evaluated by the animal healthcare industry, as it is a possibility that the new CPV-2c strain will eventually emerge into the population as a result of importing dogs from other parts of the world. abstract: Canine parvovirus (CPV) and canine coronavirus (CCoV) are considered the main pathogens responsible for acute gastroenteritis in dogs. From a collection of 250 samples, seven CPV strains and three CCoV strains were identified in symptomatic Irish dogs. Samples were screened for the viruses using polymerase chain reaction (PCR) and typed via DNA sequence analysis. Three CPV strains were characterized as CPV-2a, while four others were characterized as CPV-2b. To date, CPV-2c remains unreported in Ireland. Two CCoV strains were characterized as CCoV-II and one as CCoV-I. In the case of one sample, PH4/09/Ire, a mixed infection with CPV and CCoV was detected. url: https://www.ncbi.nlm.nih.gov/pubmed/21107617/ doi: 10.1007/s00705-010-0861-3 id: cord-294138-h7sfd1wa author: McIver, David J. title: Coronavirus surveillance of wildlife in the Lao People’s Democratic Republic detects viral RNA in rodents date: 2020-06-01 words: 2780.0 sentences: 130.0 pages: flesch: 56.0 cache: ./cache/cord-294138-h7sfd1wa.txt txt: ./txt/cord-294138-h7sfd1wa.txt summary: Both countries were involved in the United States Agency for International Development''s (USAID) Emerging Pandemic Threats PREDICT program, and surveillance of bats in wildlife markets in rural areas in Laos using family-level PCR assays revealed the presence of CoV RNA in 41 animals [5] . Considering the significant interactions of wildlife and especially rodents with humans in Laos, we were interested in investigating the presence of CoVs in these animals, which can be primary or intermediate hosts for CoVs with zoonotic potential. Since there are abundant contact opportunities for wildlife pathogens and humans in Laos, and considering that coronavirus-zoonotic events can involve intermediate hosts, as in the cases of SARS and MERS, we focused our screening on non-bat species potentially capable of playing that role. It is worth noting that we targeted rodents most likely to be in contact with humans and transmit virus and found fewer CoV-RNA-positive animals than in other studies of rodents in the region or elsewhere. abstract: Coronaviruses can become zoonotic, as in the case of COVID-19, and hunting, sale, and consumption of wild animals in Southeast Asia increases the risk for such incidents. We sampled and tested rodents (851) and other mammals and found betacoronavirus RNA in 12 rodents. The sequences belong to two separate genetic clusters and are closely related to those of known rodent coronaviruses detected in the region and distantly related to those of human coronaviruses OC43 and HKU1. Considering the close human-wildlife contact with many species in and beyond the region, a better understanding of virus diversity is urgently needed for the mitigation of future risks. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-020-04683-7) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-020-04683-7 doi: 10.1007/s00705-020-04683-7 id: cord-308950-bl83r4v3 author: Miguel, B. title: The role of feline aminopeptidase N as a receptor for infectious bronchitis virus : Brief Review date: 2002 words: 2543.0 sentences: 157.0 pages: flesch: 56.0 cache: ./cache/cord-308950-bl83r4v3.txt txt: ./txt/cord-308950-bl83r4v3.txt summary: Our objective was to determine if fAPN can serve as a receptor for infectious bronchitis virus (IBV). Feline kidney cells that express fAPN and hamster kidney fibroblasts that do not express fAPN were inoculated with IBV and monitored for replication by indirect fluorescent assay and confocal microscopy and in chicken embryonated eggs. To evaluate the permissiveness of cells to IBV, monolayers of transfected (pBK-fAPN and pBK-CMV) BHK-21, non-transfected BHK-21 and FEK on coverslips were infected with a 10 3.2 EID 50 of Ark/IBV virus. To test the hypothesis that the feline APN had a role in permissiveness of FEK cells to Ark/IBV, BHK-21 cells were transfected with pBK-CMV plasmid or pBK-fAPN. The BHK-21 cells transfected with pBK-fAPN were shown to express the fAPN receptor on the cell surface (Fig. 3) , and were permissive to Ark/IBV (Figs. abstract: Feline aminopeptidase N (fAPN) has been shown to serve as a receptor for feline, canine, porcine and human coronaviruses. Our objective was to determine if fAPN can serve as a receptor for infectious bronchitis virus (IBV). Feline kidney cells that express fAPN and hamster kidney fibroblasts that do not express fAPN were inoculated with IBV and monitored for replication by indirect fluorescent assay and confocal microscopy and in chicken embryonated eggs. The results showed that the feline cells were permissive to IBV but the hamster cells were not. The hamster cells became permissive to IBV after transfection with a fAPN cDNA suggesting that the feline APN molecule plays a role in IBV entry. url: https://www.ncbi.nlm.nih.gov/pubmed/12417943/ doi: 10.1007/s00705-002-0888-1 id: cord-302063-ct5rvqtd author: Mohamed, Fakry F. title: Molecular detection of enteric viruses from diarrheic calves in Egypt date: 2016-09-29 words: 3198.0 sentences: 227.0 pages: flesch: 60.0 cache: ./cache/cord-302063-ct5rvqtd.txt txt: ./txt/cord-302063-ct5rvqtd.txt summary: RNA was extracted and tested by reverse transcription polymerase chain reaction (RT-PCR) for the presence of rotavirus, norovirus, astrovirus, torovirus, coronavirus and bovine viral diarrhea virus. Bovine rotavirus and bovine coronavirus (BRV and BCV) are the leading causes of viral diarrhea [2] , although bovine viral diarrhea virus (BVDV), bovine norovirus (BNoV), bovine astrovirus (BAstV) and bovine torovirus (BToV) have also been implicated. The phylogenetic analysis of the BRV-VP7 coding sequences revealed that they clustered with the G6 and G10 genotypes of group A rotaviruses (http://rotac.regatools.be/) [19] (Fig. 2) . One of the study sequences (BNoV-4) grouped differently from the remaining sequences, with 87.5 % and 96.7 % nt and aa identity, respectively, and showed maximum identity to isolates from Italy (BEC195), the UK (Aberystwyth24) and Belgium (Florennes-B242). BNoV was molecularly detected (24 %) either alone or as a co-infection with other enteric viruses (BRV and BAstV). abstract: Neonatal calf diarrhea (NCD) is a major cause of morbidity, mortality and economic losses in the beef and dairy industries. This study was conducted to investigate the existence of enteric viruses in two Egyptian farms with a history of recurrent diarrhea. Fecal samples were collected from 25 diarrheic calves. RNA was extracted and tested by reverse transcription polymerase chain reaction (RT-PCR) for the presence of rotavirus, norovirus, astrovirus, torovirus, coronavirus and bovine viral diarrhea virus. Overall, 76 % (19/25) of samples tested positive for one or more viruses. Rota-, noro- and astroviruses were detected in 48 %, 24 % and 32 % of tested samples, respectively. About 37 % (7/19) of positive samples had two different viruses. One-month-old calves were the group most vulnerable to infections. Based on phylogenetic analysis, bovine rotaviruses were of genotypes G6 and G10, bovine noroviruses were in GIII.2, and bovine astroviruses were in the BAstV lineage 1. Astrovirus sequences showed a high level nucleotide sequence similarity with the Brazilian BAstV sequences available in GenBank. We believe this is the first report of bovine norovirus and bovine astrovirus circulating among calves in Egypt. Further epidemiological studies are recommended to investigate their presence on a wider scale, to predict their association with NCD, and to design appropriate diagnostic and control methods. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-016-3088-0) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/27686074/ doi: 10.1007/s00705-016-3088-0 id: cord-345957-wuk2arf9 author: Mohamed, Fakry F. title: Detection and genetic characterization of bovine kobuvirus from calves in Egypt date: 2018-02-08 words: 4245.0 sentences: 219.0 pages: flesch: 61.0 cache: ./cache/cord-345957-wuk2arf9.txt txt: ./txt/cord-345957-wuk2arf9.txt summary: When compared to the only recorded BKoV genome sequence (BKoV/U-1/AB084788), the studied strain showed 94 amino acid (aa) substitutions through its entire polyprotein (2463 aa), one nucleotide (nt) insertion and one nt deletion in the 2B gene and 4-nt deletions in the UTRs (2 each). Initially, kobuviruses included Aichivirus (AiV), bovine kobuvirus (BKoV), and porcine kobuvirus (PKoV) based on the hosts infected e.g. humans, cattle, 1 3 and swine, respectively. In this study, we report BKoV infections among cattle populations of Egypt, the full-length genome of one Egyptian strain (BKoV/ Egy-1/ KY407744) as well as the phylogenetic analysis of BKoV strains from Cairo and Sharkia provinces. The RNA samples (n = 36) were subjected to RT-PCR for the detection of BKoV using degenerate primers (Univ-Kobu-F and Univ-Kobu-R), which amplify a conserved region in the 3D (RdRp) gene of all kobuviruses [12] ( Table 1 ). abstract: Kobuviruses are small non-enveloped RNA viruses that probably cause diarrhea in cattle and swine. Since its discovery in 2003, few studies have addressed bovine kobuvirus (BKoV; a species of Aichivirus B) infections. BKoV has been reported in Europe, Asia, and South America, suggesting a worldwide distribution. To investigate the presence of BKoV in Egypt, 36 fecal specimens from diarrheic calves in two different Egyptian provinces (Cairo and Sharkia) were screened by RT-PCR and 24 (66.7%) were found positive for BKoV. RNA from one of the positive samples (BKoV/Egy-1/KY407744) was subjected to next-generation sequencing to determine the complete BKoV genome sequence. When compared to the only recorded BKoV genome sequence (BKoV/U-1/AB084788), the studied strain showed 94 amino acid (aa) substitutions through its entire polyprotein (2463 aa), one nucleotide (nt) insertion and one nt deletion in the 2B gene and 4-nt deletions in the UTRs (2 each). Additionally, five VP1 and seven 3D sequences were obtained from other samples by using RT-PCR and Sanger sequencing. A discrepancy in the phylogenetic topography of VP1 and 3D was observed, where the Egyptian VP1 sequences were classified as a distinct cluster within the proposed lineage 1 (genotype A), which also contained strains from the UK, Brazil, and Japan. While, the 3D sequences from Cairo were related to those of Chinese strains unlike Sharkia ones that were more closer to Korean strains. To the best of our knowledge, this is the first detection and genomic characterization of BKoV in Egypt or indeed Africa. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-018-3758-1) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-018-3758-1 doi: 10.1007/s00705-018-3758-1 id: cord-299428-gon6bzat author: Mondal, Shankar title: Sequence analysis of infectious bronchitis virus isolates from the 1960s in the United States date: 2012-10-11 words: 3262.0 sentences: 152.0 pages: flesch: 56.0 cache: ./cache/cord-299428-gon6bzat.txt txt: ./txt/cord-299428-gon6bzat.txt summary: To better understand the molecular epidemiology of infectious bronchitis virus (IBV) in the United States following the introduction of commercial IBV vaccines, we sequenced the S1 and N structural protein genes of thirteen IBV field isolates collected in the 1960s. Analysis of the S1 sequence showed that seven isolates were of the Massachusetts (Mass) genotype, five were SE17, and one was of the Connecticut (Conn) genotype, suggesting that these three IBVs were circulating in commercial poultry raised in different regions in the United States during the 1960s. In addition, the Mass-type isolates had high levels of sequence identity in the S1 gene compared with widely used modified live vaccines (Mass41, Ma5 and H120) and modern field strains from the USA and other countries, suggesting a common ancestor. abstract: To better understand the molecular epidemiology of infectious bronchitis virus (IBV) in the United States following the introduction of commercial IBV vaccines, we sequenced the S1 and N structural protein genes of thirteen IBV field isolates collected in the 1960s. Analysis of the S1 sequence showed that seven isolates were of the Massachusetts (Mass) genotype, five were SE17, and one was of the Connecticut (Conn) genotype, suggesting that these three IBVs were circulating in commercial poultry raised in different regions in the United States during the 1960s. The S1 genes of Mass-type isolates had high levels of sequence variation, representing 81.3-81.9 % nucleotide (nt) and 77.3-78.7 % amino acid (aa) identity when compared to those of the SE17-type isolates. In contrast, the N genes from the same isolates were less variable (>92 % nt and >93 % aa identity) when compared to those of the SE17-type isolates. Phylogenetic analysis based on the S1 gene indicated that one isolate (L748) was more closely related to the Mass type. In contrast, phylogenetic analysis based on the N gene showed that L748 was more closely related to the SE17 type, indicating that there had been exchange of S1 genetic materials between Mass- and SE17-like viruses. In addition, the Mass-type isolates had high levels of sequence identity in the S1 gene compared with widely used modified live vaccines (Mass41, Ma5 and H120) and modern field strains from the USA and other countries, suggesting a common ancestor. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-012-1500-y) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-012-1500-y doi: 10.1007/s00705-012-1500-y id: cord-004812-ikco4h5k author: Moore, K. M. title: Identification of amino acids involved in a serotype and neutralization specific epitope with in the s1 subunit of avian infectious bronchitis virus date: 1997-04-06 words: 2731.0 sentences: 172.0 pages: flesch: 57.0 cache: ./cache/cord-004812-ikco4h5k.txt txt: ./txt/cord-004812-ikco4h5k.txt summary: title: Identification of amino acids involved in a serotype and neutralization specific epitope with in the s1 subunit of avian infectious bronchitis virus We identified amino acids involved in a serotype specific, conformationally dependent epitope by analysis of the S1 gene of 13 monoclonal antibody-neutralization-resistant mutants. However, based on data obtained using monoclonal antibodies (Mab), there appears to be at least three to ®ve neutralizing, conformationally dependent epitopes on the S1 subunit in different IBV strains [13, 15, 20] . Mab-neutralization-resistant (NR) mutants have been used to identify amino acids (AA) involved in conformationally dependent epitopes in the spike protein of IBV [5, 12] . Based on AA substitutions in Mab-NR mutants, the S1 subunit was divided into three regions associated with neutralizing, conformationally dependent epitopes. In previous research, AA substitutions in IBV Mab-NR mutants were divided into three regions associated with neutralizing epitopes. abstract: Localization of neutralizing, serotype specific epitopes of infectious bronchitis virus has been difficult because these epitopes are conformationally dependent. We identified amino acids involved in a serotype specific, conformationally dependent epitope by analysis of the S1 gene of 13 monoclonal antibody-neutralization-resistant mutants. Substitutions in the predicted amino acid sequence of these mutants were located at residues 304 and/or 386. Most of the substitutions at residue 304 were from threonine to isoleucine, whereas the substitutions at residue 386 were from arginine to proline, histidine, cysteine, or tryptophan. Based on this data, it appears that AA residues at 304 and 386 on the S1 glycoprotein are involved in a virus neutralizing serotype specific epitope. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087143/ doi: 10.1007/s007050050239 id: cord-004838-cdas57cx author: Morozov, I. title: Sequence analysis of open reading frames (ORFs) 2 to 4 of a U.S. isolate of porcine reproductive and respiratory syndrome virus date: 1995 words: 2240.0 sentences: 122.0 pages: flesch: 60.0 cache: ./cache/cord-004838-cdas57cx.txt txt: ./txt/cord-004838-cdas57cx.txt summary: title: Sequence analysis of open reading frames (ORFs) 2 to 4 of a U.S. isolate of porcine reproductive and respiratory syndrome virus The sequence of ORFs 2 to 4 of a U.S. isolate of porcine reproductive and respiratory syndrome virus (PRRSV), ATCC VR2385, was determined by analysis of a cDNA λ library. No overlap was found between ORFs 4 and 5, and instead there was a 10 bp sequence which separated these two ORFs. The nucleic acid homology with corresponding ORFs of the European PRRSV isolate Lelystad virus (LV) was 65% for ORF 2, 64% for ORF 3 and 66% for ORF 4. Cloning, expression, and sequence analysis of the ORF 4 gene of porcine reproductive and respiratory syndrome virus MN-lb Molecular cloning and nucleotide sequencing of the 3''-terminal genomic RNA of porcine reproductive and respiratory syndrome virus abstract: The sequence of ORFs 2 to 4 of a U.S. isolate of porcine reproductive and respiratory syndrome virus (PRRSV), ATCC VR2385, was determined by analysis of a cDNA λ library. The cDNA clones containing PRRSV specific sequences were selected using a VR2385 ORF 4 specific PCR probe and sequenced. The ORFs 2, 3 and 4 overlapped each other and encoded polypeptides with predicted M(r) of 29.5 kDa (ORF 2), 28.7 kDa (ORF 3) and 19.5 kDa (ORF 4), respectively. No overlap was found between ORFs 4 and 5, and instead there was a 10 bp sequence which separated these two ORFs. The nucleic acid homology with corresponding ORFs of the European PRRSV isolate Lelystad virus (LV) was 65% for ORF 2, 64% for ORF 3 and 66% for ORF 4. Comparison of the ORF 4 sequences of VR2385 with that of another U.S. isolate MN-1b revealed only 86% amino acid sequence homology and the presence of deletions in the ORF 4 of MN-1b. Our results further strengthen the observation that there is sequence variation between US and European PRRSV isolates. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087238/ doi: 10.1007/bf01322758 id: cord-304109-yirs7kjg author: Mueller, Andreas title: Polyomaviruses KI and WU in children with respiratory tract infection date: 2009-09-12 words: 1935.0 sentences: 109.0 pages: flesch: 54.0 cache: ./cache/cord-304109-yirs7kjg.txt txt: ./txt/cord-304109-yirs7kjg.txt summary: The polyomaviruses KI (KIPyV) and WU (WUPyV) have recently been discovered in specimens from patients with respiratory tract infections. Nasopharyngeal aspirates or bronchoalveolar lavage specimens of 229 children with acute respiratory tract infection were screened for KIPyV and WUPyV using polymerase chain reaction-based methods. Since 2001, an increasing number of ''''new'''' respiratory viruses have been detected in children with respiratory tract infection (RTI), including the human metapneumovirus (hMPV) and the human bocavirus (hBoV) [4, 15] . The authors amplified and cloned the genome of WU Polyomavirus (WUPyV) from NPA of a 3-year-old patient with pneumonia without detection of other respiratory pathogens. The very low prevalence of polyomavirus KI and WU DNA in NPA specimens of 3 out of 229 pediatric patients with acute RTI in this series does not confirm or exclude a pathogenic role of these newly described viruses. Presence of the newly discovered human polyomaviruses KI and WU in Australian patients with acute respiratory tract infection abstract: The polyomaviruses KI (KIPyV) and WU (WUPyV) have recently been discovered in specimens from patients with respiratory tract infections. To analyze the frequency and clinical impact in a cohort of pediatric patients in a German University Children’s Hospital. Nasopharyngeal aspirates or bronchoalveolar lavage specimens of 229 children with acute respiratory tract infection were screened for KIPyV and WUPyV using polymerase chain reaction-based methods. KIPyV was detected in 2 (0.9%) and WUPyV in 1 (0.4%) patients, without co-infections with other respiratory viruses but with co-detection of CMV, EBV and HHV 6 in one immunocompromised patient. Only a very small proportion (1.3%) of positive samples for KIPyV and WUPyV was documented in this study; the clinical relevance of these viruses remains unclear and requires further evaluation. url: https://www.ncbi.nlm.nih.gov/pubmed/19756357/ doi: 10.1007/s00705-009-0498-2 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: 6347.0 sentences: 280.0 pages: flesch: 44.0 cache: ./cache/cord-004719-3stcx0dd.txt txt: ./txt/cord-004719-3stcx0dd.txt summary: 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. 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. 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. With representative sequences of plant virus genomes from many groups available, efforts were made to identify regions of similarity between known movement proteins and to predict movement functions for uncharacterized ORFs. Early observations made by this approach have been reviewed previously (e.g. 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-348147-leni23pa author: Müller, B. title: Genetic diversity and recombination of murine noroviruses in immunocompromised mice date: 2007-05-29 words: 3482.0 sentences: 203.0 pages: flesch: 52.0 cache: ./cache/cord-348147-leni23pa.txt txt: ./txt/cord-348147-leni23pa.txt summary: Sequence analysis of the full-length and partial genomes obtained from naturally infected mice yielded valuable data on genetic diversity of murine noroviruses. These specimens were obtained from 28 different mouse lines, including immunocompetent mice, lines with muta(4), b-TCR À=À (2), RAG2=gChain À=À (5), B6 Casp À=À (2), CD36=SRA À=À (2), CCL3 À=À (2), LFA À=À (2), LyZ À=À (2), PSEN tg (2), Bl6 wt (4) a GE genome equivalents; for more than one positive sample the mean was calculated b Includes partial sequences of the ORFs (underlined isolates; ORF1, RNA polymerase gene; ORF2, capsid gene) Ã Contains both regions tions in a number of immune effector molecules, and transgenic mouse lines (Table 1) . Like human noroviruses, the present sequence data indicate that murine norovirus strains are also genetically diverse and can, therefore, be subdivided in genetic clusters. abstract: Murine noroviruses (MNV) are newly identified pathogens which infect laboratory mice. In this study, we found a high prevalence (64.3%) of MNV in various breeding colonies of immunocompromised, transgenic and wild-type mouse lines. All mice survived infection with no signs of clinical disease. Faeces samples were collected from animals housed in two separate laboratory mouse colonies in Berlin, Germany, and screened using quantitative reverse transcription (RT)-PCR. We have determined the complete nucleotide sequences of 3 novel MNV strains. Furthermore, we sequenced two subgenomic regions within open reading frames (ORFs) 1 and 2 that are suitable for genotyping. Sequence analysis of the full-length and partial genomes obtained from naturally infected mice yielded valuable data on genetic diversity of murine noroviruses. The discordance of genotype affiliation of some MNVs shown in ORF1 and ORF2 suggests intertypic recombination events in vivo. url: https://www.ncbi.nlm.nih.gov/pubmed/17533553/ doi: 10.1007/s00705-007-0989-y id: cord-004733-i0a3igc7 author: Nagata, S. title: Identification of epitopes associated with different biological activities on the glycoprotein of vesicular stomatitis virus by use of monoclonal antibodies date: 1992 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Thirteen monoclonal antibodies (MAbs) to the glycoprotein (G) of vesicular stomatitis virus (VSV) serotype Indiana were prepared and examined for their effects on various biological activities of VSV, including in vitro infection, hemagglutination, adsorption to cells, and mediation of cell fusion. Competitive binding assays with these MAbs revealed the presence of at least seven distinct antigenic determinants (epitopes) on the G protein. In some cases, overlappings among epitopes to various degrees were observed as partial inhibition or binding enhancement. The MAbs to all the epitopes but one (epitopes 1–6) reacted with the denatured G protein in a Western immunoblot analysis. Four of the epitopes (epitopes 2, 4, 5, and 7) were involved in neutralization and two (epitopes 1 and 2) in hemagglutination inhibition. None of the MAbs inhibited the adsorption of radiolabeled VSV to BHK-21 cells; the MAbs to epitope 2 slightly enhanced the virus adsorption. All neutralization epitopes except epitope 2 (epitopes 4, 5, and 7) were associated with inhibition of VSV-mediated cell fusion. These results show a direct spatial relationship between the epitopes recognized by the MAbs and functional sites on G protein and further insights into the structure and function of G protein. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086791/ doi: 10.1007/bf01309581 id: cord-004743-ido065mh author: Nagy, Éva title: Polypeptide patterns of infectious bronchitis virus serotypes fall into two categories date: 1979 words: 1068.0 sentences: 68.0 pages: flesch: 59.0 cache: ./cache/cord-004743-ido065mh.txt txt: ./txt/cord-004743-ido065mh.txt summary: authors: Nagy, Éva; Lomniczi, B. title: Polypeptide patterns of infectious bronchitis virus serotypes fall into two categories Molecular weights of six major polypeptides of infectious bronchitis virus (IBV) are: 1. All IBV strains examined showed one of two protein patterns with polypeptides having apparent molecular weights in the range of 20,000 and 110,000 dalton (Fig. 1) . Pattern M (named after Massachusetts) includes strains from two serotypes, Massachusetts and Georgia (SE 17), and here the "broad" protein has an apparent molecular weight of 28,000 dalton. Pattern C (named after Connecticut) is characterized by a smaller "broad" protein of an apparent molecular weight of 24,000 dalton, and includes the five remaining serotypes studied: Connecticut, Delaware (Gray), Iowa 97, Iowa 609 and Australia T. 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-270473-5tok4mqk author: Nanda, S. K. title: Mitochondrial HSP70, HSP40, and HSP60 bind to the 3′ untranslated region of the Murine hepatitis virus genome date: 2003-09-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We have previously shown that mitochondrial-aconitase binds specifically to the 3′ terminal 42 nucleotides of the Murine hepatitis virus (MHV) RNA along with three additional proteins of 70, 58 and 40 kDa to form a stable RNA-protein complex. Supershift and western blot assays have identified these three proteins as mitochondrial HSP70 (mtHSP70), HSP60, and HSP40. A series of co-immunoprecipitation assays have established that these four MHV RNA binding proteins are associated, even in the absence of MHV RNA. However, the presence of a synthetic RNA containing the sequence bound by these four proteins does increase the amount of co-precipitated protein, in particular the amount of HSP60 which is brought down with antibodies directed against HSP40 and mtHSP70. We have provided evidence for the interaction of these four proteins with the 3′ end region of MHV RNA in infected cells by a series of immunoprecipitation RT-PCR assays. We believe it is likely that MHV RNA interacts with m-aconitase prior to its import into mitochondria in cooperation with extra-mitochondrial mtHSP70, HSP60, and HSP40. url: https://www.ncbi.nlm.nih.gov/pubmed/14689278/ doi: 10.1007/s00705-003-0196-4 id: cord-299345-2i48ld8d author: Nefedeva, Mariia title: Molecular characteristics of a novel recombinant of porcine epidemic diarrhea virus date: 2019-02-06 words: 1535.0 sentences: 114.0 pages: flesch: 49.0 cache: ./cache/cord-299345-2i48ld8d.txt txt: ./txt/cord-299345-2i48ld8d.txt summary: Pairwise identity analysis of the whole genome sequences revealed that PEDV/Belgorod/dom/2008 is an intermediate between PEDV and transmissible gastroenteritis virus (TGEV) strains. Based on the phylogenetic analysis of the M gene, the PEDV/Belgorod/ dom/2008 isolate belongs to the same clade as other virulent Russian PEDV strains, indicating a high degree of sequence homogeneity in the M gene (Fig. 3a) isolate is genetically distinct and does not belong to any group (Fig. 3b ). The identification of recombinant regions in PEDV/Belgorod/dom/2008 can be useful for further analysis of evolutionary variability, epidemiology, and development of a new diagnostic gene-based assay for porcine epidemic diarrhea virus. Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China abstract: Porcine epidemic diarrhea (PED) is a contagious viral disease in pigs, caused by the coronavirus porcine epidemic diarrhea virus (PEDV). PEDV infection results in significant mortality in piglets in unvaccinated herds. Like many others RNA viruses, PEDV has high evolutionary rate and is prone to genetic mutations. In this study, we analyzed the complete genome sequence of the recently sequenced isolate PEDV/Belgorod/dom/2008. A recombination event in S gene of PEDV/Belgorod/dom/2008 was detected. Pairwise identity analysis of the whole genome sequences revealed that PEDV/Belgorod/dom/2008 is an intermediate between PEDV and transmissible gastroenteritis virus (TGEV) strains. These results can be used for further analysis of the evolutionary variability, prevalence, and epidemiology of the porcine epidemic diarrhea virus. url: https://www.ncbi.nlm.nih.gov/pubmed/30725181/ doi: 10.1007/s00705-019-04166-4 id: cord-003050-n25wnmq5 author: Nibert, Max L. title: A barnavirus sequence mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis date: 2018-03-07 words: 3324.0 sentences: 159.0 pages: flesch: 53.0 cache: ./cache/cord-003050-n25wnmq5.txt txt: ./txt/cord-003050-n25wnmq5.txt summary: The 4.2-kb plus-strand sequence of this virus encompasses four main open reading frames (ORFs), as expected for barnaviruses, including ORFs for a protease-containing polyprotein, an RNA-dependent RNA polymerase whose translation appears to rely on − 1 ribosomal frameshifting, and a capsid protein that is likely to be translated from a subgenomic RNA. Based on similar genome sizes, coding organizations, and P2-and P3-region sequence similarities, both MBV and RsBV1 appear to be most closely related to plant viruses in the unassigned genus Sobemovirus [12, 16] . As a result, the consensus sequence for the apparent new barnavirus reported here (GenBank MG686618) is 4206 nt long, appears to be coding complete for ORFs 1-4 ( Fig. 1) , and was newly assembled from a total of 821 individual reads (reads per position: mean, 19; range, 2-35). abstract: Because so few viruses in the family Barnaviridae have been reported, we searched for more of them in public sequence databases. Here, we report the complete coding sequence of Colobanthus quitensis associated barnavirus 1, mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis. The 4.2-kb plus-strand sequence of this virus encompasses four main open reading frames (ORFs), as expected for barnaviruses, including ORFs for a protease-containing polyprotein, an RNA-dependent RNA polymerase whose translation appears to rely on − 1 ribosomal frameshifting, and a capsid protein that is likely to be translated from a subgenomic RNA. The possible derivation of this virus from a fungus associated with C. quitensis is discussed. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-018-3794-x) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5999160/ doi: 10.1007/s00705-018-3794-x id: cord-349907-dwhyx97y author: Noh, Ji Yeong title: Simultaneous detection of severe acute respiratory syndrome, Middle East respiratory syndrome, and related bat coronaviruses by real-time reverse transcription PCR date: 2017-02-20 words: 3274.0 sentences: 138.0 pages: flesch: 62.0 cache: ./cache/cord-349907-dwhyx97y.txt txt: ./txt/cord-349907-dwhyx97y.txt summary: Therefore, in this study, a duplex real-time reverse transcription (RT)-PCR method was developed based on primers and probes that target the conserved spike S2 region of SARS-CoV, SARS-like bat CoVs, MERS-CoV, and MERS-related bat CoVs. For the universal detection of SARS-CoV and SARS-like bat CoVs, consensus primers and probes (Fig. 1a) were designed based on the conserved sequences of the spike S2 region by aligning the following reference sequences: human SARS-CoVs Sino1 (GenBank no. The specificity of the real-time RT-PCR method developed in this study was evaluated using RNAs from several RNA viruses, including MERS-CoV (KOR/KNIH/ 002_05_2015), a recombinant plasmid for the bat CoV HKU4 strain, and RNA from a bat fecal sample containing SARS-like bat CoV. The new real-time RT-PCR method also showed positive results for RNA extracted from a fecal sample containing SARS-like bat CoV (B15-21) [7] . abstract: Since severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses (CoVs) share similar characteristics with respect to clinical signs, etiology, and transmission, methods for a rapid and accurate differential diagnosis are important. Therefore, the aim of this study was to develop a duplex real-time reverse transcription (RT)-PCR method for the simultaneous detection of these viruses. Primers and probes that target the conserved spike S2 region of human SARS-CoV, MERS-CoV, and their related bat CoVs were designed. The results of real-time RT-PCR showed specific reactions for each virus with adequate detection limits of 50–100 copies/mL and 5–100 copies/mL using pUC57-SARS-pS2 (a template for SARS-CoV) and pGEM-MERS-S2 (a template for MERS-CoV), respectively. In addition, this real-time RT-PCR system was able to detect the target viruses SARS-like bat CoV and MERS-CoV in bat fecal samples and sputum of MERS patients, respectively. Therefore, this newly developed real-time RT-PCR method is expected to detect not only SARS-CoV and MERS-CoV in humans but also several bat CoVs that are closely related to these viruses in bats. url: https://doi.org/10.1007/s00705-017-3281-9 doi: 10.1007/s00705-017-3281-9 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-314751-i9rxesrg author: Oh, Jongsuk title: Immunogenicity and protective efficacy of recombinant S1 domain of the porcine epidemic diarrhea virus spike protein date: 2014-07-10 words: 6006.0 sentences: 242.0 pages: flesch: 44.0 cache: ./cache/cord-314751-i9rxesrg.txt txt: ./txt/cord-314751-i9rxesrg.txt summary: In this study, a codon-optimized PEDV S1 gene containing amino acid residues 25–738 was synthesized based on a multiple alignment of the S amino acid sequences of PEDV field isolates and used to establish a stable porcine cell line constitutively expressing the PEDV S1 protein. In the present study, therefore, we first synthesized a full-length, codon-optimized PEDV S1 gene and then generated a stable porcine-origin cell line constitutively expressing the recombinant S1 protein. These results were coincident with the rabbit study described above, since the rabbit antisera generated by immunization with the recombinant S1 protein also contained low levels of neutralizing antibodies to the heterologous PEDV vaccine strain. In the present study, the first aim was to stably express the full-length, codon-optimized S1 gene of PEDV in porcine-origin cells and to evaluate the immunogenicity and efficacy of the recombinant S1 protein. abstract: Porcine epidemic diarrhea virus (PEDV) is a highly contagious enteric pathogen of swine. Acute PEDV outbreaks have continually emerged in most swine-producing Asian countries and, recently, in the United States, causing significant economic losses in the pig industry. The spike (S) protein of PEDV is a type 1 transmembrane envelope glycoprotein and consists of the S1 and S2 domains, which are responsible for virus binding and fusion, respectively. Since the S1 domain is involved in a specific high-affinity interaction with the cellular receptor and induction of neutralizing antibody in the natural host, it is a primary target for the development of effective vaccines against PEDV. In this study, a codon-optimized PEDV S1 gene containing amino acid residues 25–738 was synthesized based on a multiple alignment of the S amino acid sequences of PEDV field isolates and used to establish a stable porcine cell line constitutively expressing the PEDV S1 protein. The purified recombinant S1 protein was found to mediate highly potent antibody responses in immunized rabbits. The antibodies strongly recognized the recombinant S1 protein from cell lysates and supernatants of S1-expressing cells, whereas they bound weakly to the authentic S protein of PEDV vaccine strain SM98-1. Furthermore, a serum neutralization test revealed that the rabbit antisera completely inhibit infection of the PEDV vaccine strain at a serum dilution of 1:16. We then tested the ability of vaccination with the recombinant S1 protein to protect piglets against PEDV. Late-term pregnant sows were inoculated intramuscularly with the purified S1 protein, and the outcome was investigated in passively immunized suckling piglets after a virulent PEDV challenge. The results showed that vaccination with S1 protein efficiently protected neonatal piglets against PEDV. Our data suggest that the recombinant S1 protein shows potential as an effective and safe subunit vaccine for PED prevention. url: https://www.ncbi.nlm.nih.gov/pubmed/25008896/ doi: 10.1007/s00705-014-2163-7 id: cord-029775-mntcor5d author: Oka, Tomoichiro title: Polymerase chain reaction primer sets for the detection of genetically diverse human sapoviruses date: 2020-07-27 words: 1827.0 sentences: 100.0 pages: flesch: 58.0 cache: ./cache/cord-029775-mntcor5d.txt txt: ./txt/cord-029775-mntcor5d.txt summary: For the initial reactivity test, double-stranded DNA fragments (gBlocks® Gene Fragments) including the sequence targeted by the PCR primers (approximately 1700 bp each) of the human sapovirus genotypes GI.1 (GenBank accession number X86560), GI.2 (AB614356), GI.3 (AB623037), GI.4 (AJ606693), GI.5 (DQ366345), GI.6 (AJ606694), GI.7 (AB522390), GII.1 (AJ249939), GII.2 (AY237420), GII.3 (AB630068), GII.4 (AB522397), GII.5 (LC190463), GII.6 (AY646855), GII.7 (AB630067), GII.8 (KX894315), GIV.1 (DQ058829), GV.1 (DQ366344), and GV.2 (AB775659) were synthesized (Integrated DNA Technologies, Coralville, IA), and 1.0 × 10 4 copies of these fragments were used. The target regions of HuSaV-F1, -F2, and -F3 recently designed as forward primers in a broadly reactive real-time PCR for human sapoviruses [11] are similar to those of SV-F13 and SV-F14 (Fig. 2) , and the sapovirus-specific sequence of M13R-HuSaV5498R (5′-CCCCANCCNGCVHACAT-3′) ( [11] are shown in parentheses. The assay including two primers (M13F-HuSaV-5159F and M13R-HuSaV-5498R) generated similar-sized PCR products (approximately 380 bp) for all of the sapovirus genotypes tested (Fig. 1A, right panel, and Fig. 1B) . abstract: Sapoviruses are increasingly being recognized as pathogens associated with gastroenteritis in humans. Human sapoviruses are currently assigned to 18 genotypes (GI.1-7, GII.1-8, GIV.1, and GV.1-2) based on the sequence of the region encoding the major structural protein. In this study, we evaluated 11 polymerase chain reaction (PCR) assays using published and newly designed/modified primers and showed that four PCR assays with different primer combinations amplified all of the tested human sapovirus genotypes using either synthetic DNA or cDNA prepared from human sapovirus-positive fecal specimens. These assays can be used as improved broadly reactive screening tests or as tools for molecular characterization of human sapoviruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7383071/ doi: 10.1007/s00705-020-04746-9 id: cord-004732-mgzmzeyr author: Olofsson, S. title: Populations of herpes simplex virus glycoprotein gC with and without affinity for the N-acetyl-galactosamine specific lectin ofHelix pomatia date: 1983 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Two fractions of herpes simplex virus glycoprotein gC were isolated and characterized by means of immunosorbent-purification with monoclonal antibodies against gC and Helix pomatia lectin (HPA) affinity chromatography. About 25 per cent of the glycoprotein gC population demonstrated affinity for the lectin, compatible with presence of N-acetylgalactosamine as terminal sugar of the oligosaccharide. The HPA-binding populations of gC appeared as two electrophoretic bands with lower molecular weights than the non-binding gC. The gC subfraction without affinity for the HPA was subjected to treatments aiming to desialylize the carbohydrate moiety. Only 5 per cent of the initially non-reactive fraction of gC became reactive to HPA after the treatments, suggesting that masking of penultimate N-acetylgalactosamine by sialic acid was not a main reason for lack of HPA affinity. Results of treatment with alkaline Na BH(4) demonstrated presence of oligosaccharide-peptide linkages sensitive to β-elimination suggesting O-glycosidic type of linkage. The subfraction of gC demonstrating affinity for HPA as well as gC devoid of HPA binding capacity both revealed affinity for Con A. Therefore N-glycosidically as well as O-glycosidically linked oligosaccharides seemed to be present on the one and same glycoprotein. On the basis of the results presented we assume that the glycosylation of HSV glycoprotein gC may lead to, at least, two populations of the glycoprotein gC, one with terminal N-acetylgalactosamine residues of oligosaccharides 0-glycosidically linked to the polypeptide and the other without affinity for HPA. However, both populations of gC contain similar proportions of oligosaccharides of the high mannose or complex types with N-glycosidic carbohydrate-peptide linkages as indicated by their affinity for Con A. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086787/ doi: 10.1007/bf01315701 id: cord-330825-apfcql4m author: Paraguison-Alili, Rubigilda title: Phylogenetic tracking of current porcine epidemic diarrhea virus (PEDV) strains in the Philippines date: 2016-06-28 words: 2175.0 sentences: 116.0 pages: flesch: 54.0 cache: ./cache/cord-330825-apfcql4m.txt txt: ./txt/cord-330825-apfcql4m.txt summary: title: Phylogenetic tracking of current porcine epidemic diarrhea virus (PEDV) strains in the Philippines Since the receptor-binding sites and majority of the neutralization epitopes are located in the S1 portion, this region has been subjected to sequencing and molecular analysis to determine the genetic relatedness of different PEDV viruses [1] [2] [3] . Using data from swine farms in these provinces and diagnosis data from the College of Veterinary Science and Medicine in Central Luzon State University, the incidence is 67 % in Pampanga, 79 % in Tarlac, 61 % in Batangas, and 90 to 100 % in Agusan. This is the first report of PEDV S1 gene sequences from the provincial PEDV hotspots of the Philippines, which include Batangas, Pampanga, Tarlac and Agusan. Phylogenetic analysis of the spike (S) gene of the new variants of porcine epidemic diarrhoea virus in Taiwan Molecular characterization of the spike and ORF3 genes of porcine epidemic diarrhea virus in the Philippines abstract: To trace the possible route of introduction of porcine epidemic diarrhea virus (PEDV), the phylogenetic relationships of PEDV strains in the regions of epidemicity in the Philippines to PEDV strains that are endemic in other countries were investigated. Partial nucleotide sequences of the S1 spike gene was determined from the PEDV-positive samples and compared with S1 sequences from other countries. Phylogenetic analysis indicated that PEDV strains in the Philippines segregate into two groups. Members of group 1 are related to strains from the USA, Taiwan, Japan and Canada, while those in group 2 are related to strains from China and Vietnam. url: https://doi.org/10.1007/s00705-016-2938-0 doi: 10.1007/s00705-016-2938-0 id: cord-267446-rpv19oy6 author: Park, Jung-Eun title: Receptor-bound porcine epidemic diarrhea virus spike protein cleaved by trypsin induces membrane fusion date: 2011-06-12 words: 4075.0 sentences: 186.0 pages: flesch: 47.0 cache: ./cache/cord-267446-rpv19oy6.txt txt: ./txt/cord-267446-rpv19oy6.txt summary: The addition of trypsin was shown to induce fusion of the infected Vero cells, resulting in the formation of multiple syncytia, and produced a significant increase in virus titer after several passages. For example, infection by severe acute respiratory syndrome coronavirus (SARS-CoV) and murine hepatitis virus strain 2 (MHV-2) requires proteolytic cleavage in their target cells, which is mediated by trypsin-like proteases [24, 29, 32] . To investigate the effects of proteolytic cleavage of the surface protein of Vero cells and free virions by trypsin, Vero cells or KPEDV-9 were pre-treated with trypsin prior to infection. These results are consistent with the suggestion that trypsin is not absolutely essential for Vero-cell-adapted PEDV infection, as reported for other group 1 coronaviruses, but the titer increases during infection with trypsin-treated virus. abstract: Porcine epidemic diarrhea virus (PEDV) infection in Vero cells is facilitated by trypsin through an undefined mechanism. The present study describes the mode of action of trypsin in enhancing PEDV infection in Vero cells during different stage of the virus life cycle. During the viral entry stage, trypsin increased the penetration of Vero-cell-attached PEDV by approximately twofold. However, trypsin treatment of viruses before receptor binding did not enhance infectivity, indicating that receptor binding is essentially required for trypsin-mediated entry upon PEDV infection. Trypsin treatment during the budding stage of virus infection induces an obvious cytopathic effect in infected cells. Furthermore, we also show that the PEDV spike (S) glycoprotein is cleaved by trypsin in virions that are bound to the receptor, but not in free virions. These findings indicate that trypsin affects only cell-attached PEDV and increases infectivity and syncytium formation in PEDV-infected Vero cells by cleavage of the PEDV S protein. These findings strongly suggest that the PEDV S protein may undergo a conformational change after receptor binding and cleavage by exogenous trypsin, which induces membrane fusion. url: https://www.ncbi.nlm.nih.gov/pubmed/21667287/ doi: 10.1007/s00705-011-1044-6 id: cord-341469-7guojyay author: Park, Seong-Jun title: Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field isolates in Korea date: 2011-01-06 words: 3718.0 sentences: 165.0 pages: flesch: 53.0 cache: ./cache/cord-341469-7guojyay.txt txt: ./txt/cord-341469-7guojyay.txt summary: Especially, ORF3 gene analysis can be used for discrimination between vaccine and wild-type PEDVs. Sequence and phylogenetic analysis showed that recent, prevalent Korean PEDV field isolates have close relationships to Chinese field strains and differ genetically from European strains and vaccine strains used in Korea. Sequence analysis of the complete ORF3 genes showed that all PEDVs, including the Korean field isolates, fell into three groups, and group 3 had two subgroups (3-1 and 3-2), as can be seen in the phylogenetic tree (Fig. 2) . Genetic analysis based on complete M and ORF3 genes showed that each PEDV group had several unique characteristics, and these results indicated that specific groups of PEDVs may be differentiated from other PEDVs, including Korean field isolates, by specific nucleotide differences, but more PEDVs need to be analyzed for more accurate analysis. abstract: Porcine epidemic diarrhea virus (PEDV) has caused enteric disease with devastating impact since the first identification of PEDV in 1992 in Korea. In this study, we investigated molecular epidemiology, showed genetic diversity, and analyzed phylogenetic relationships of Korean PEDV field isolates with other PEDV reference strains. Genetic analysis of the complete M and ORF3 genes showed that each PEDV group had several unique characteristics, and this indicated that specific groups of PEDVs may be differentiated from the other PEDVs by specific nucleotide differences. Especially, ORF3 gene analysis can be used for discrimination between vaccine and wild-type PEDVs. Sequence and phylogenetic analysis showed that recent, prevalent Korean PEDV field isolates have close relationships to Chinese field strains and differ genetically from European strains and vaccine strains used in Korea. These results raise questions as to whether a new type of PEDV vaccine may be necessary for preventing PEDV infection more effectively in Korea. url: https://doi.org/10.1007/s00705-010-0892-9 doi: 10.1007/s00705-010-0892-9 id: cord-290695-ubrqy2zf author: Payne, H. R. title: Analysis of cell fusion induced by bovine coronavirus infection date: 1988 words: 2078.0 sentences: 109.0 pages: flesch: 50.0 cache: ./cache/cord-290695-ubrqy2zf.txt txt: ./txt/cord-290695-ubrqy2zf.txt summary: Polykaryon formation in bovine fetal spleen (BFS) cells infected with bovine coronavirus L9 occurred only in media supplemented with trypsin. Cell fusion and polykaryon formation in cultures infected with bovine coronavirus (BCV) occur late in the virus replication cycle. We analyzed the trypsin-dependent cell fusion of BCV-infected BFS cells and found that the range of pH 7.5 to 8.0 was optimal for polykaryon formation. The cells were inoculated with BCV at a multiplicity of 2 PFU per cell, incubated in MEM containing trypsin (0.4 ug per ml; Sigma Chemical Company) treated with L-l-tosylamide-2-phenylethyl chloromethyl ketone, an inhibitor of chymotrypsin activity. The ability of anti-BCV IgG to affect polykaryon formation at 37 °C was tested by two procedures: (i) Infected cell monolayers were incubated for 6 h in trypsin-free MEM then exposed to MEM that contained antibody freshly diluted with trypsin containing medium. Trypsin treatments of BCV-infected BFS cells during the time of maximal fusion enhancement were effective only with media of pH levels 7.5 to 8.0. abstract: Polykaryon formation in bovine fetal spleen (BFS) cells infected with bovine coronavirus L9 occurred only in media supplemented with trypsin. A single 1 to 2 h trypsin treatment 10 h and later after infection induced formation of polykaryons. Trypsin treatment at pH 7.5 and 8.0 induced polykaryons while treatments at lower or higher pH levels did not. Cell fusion activity was partially suppressed by the presence of antibody. url: https://www.ncbi.nlm.nih.gov/pubmed/3214271/ doi: 10.1007/bf01319806 id: cord-349964-38rgcc5h author: Pedersen, N. C. title: Antigenic relationship of the feline infectious peritonitis virus to coronaviruses of other species date: 1978 words: 3024.0 sentences: 190.0 pages: flesch: 54.0 cache: ./cache/cord-349964-38rgcc5h.txt txt: ./txt/cord-349964-38rgcc5h.txt summary: The first antigenically related group was comprised of mouse hepatitis virus, type 3 (MHV-3), hemeagglutinating encephalomyelitis virus 67N (HEV-67N) of swine, calf diarrhea coronavirus (CDCV), and human coronavirus OC43 (HCV-OC43). Utilizing the direct and indirect fluorescent antibody procedure, the antigenic relationship of the feline infectious peritonitis virus (FIPV) to 7 other human and animal coronaviruses was studied. Utilizing the direct and indirect fluorescent antibody procedure, the antigenic relationship of the feline infectious peritonitis virus (FIPV) to 7 other human and animal coronaviruses was studied. Transmissible gastroenteritis virus and FIPV were in turn antigenically related to human eoronavirus 229E (I-ICV-229E) and canine coronavirus (CCV). A possible antigenic relationship between feline infectious peritonitis virus (FIPV) and the transmissible gastroenteritis virus (TGEV) of swine has been recently reported (13, 19, 25) , which further supports the assumption t h a t F I P V is a coronavirus. abstract: Utilizing the direct and indirect fluorescent antibody procedure, the antigenic relationship of the feline infectious peritonitis virus (FIPV) to 7 other human and animal coronaviruses was studied. FIPV was found to be closely related to transmissible gastroenteritis virus (TGEV) of swine. Transmissible gastroenteritis virus and FIPV were in turn antigenically related to human coronavirus 229E (HCV-229E) and canine coronavirus (CCV). An interesting finding in the study was that the 8 coronaviruses selected for this study fell into one of two antigenically distinct groups. Viruses in each group were antigenically related to each other to varying degrees, but were antigenically unrelated to coronaviruses of the second group. The first antigenically related group was comprised of mouse hepatitis virus, type 3 (MHV-3), hemeagglutinating encephalomyelitis virus 67N (HEV-67N) of swine, calf diarrhea coronavirus (CDCV), and human coronavirus OC43 (HCV-OC43). The second antigenically related group was comprised of FIPV, TGEV, HCV-229E and CCV. url: https://www.ncbi.nlm.nih.gov/pubmed/81044/ doi: 10.1007/bf01315534 id: cord-255653-0bj5eh5d author: Pensaert, M. B. title: An immunoelectron microscopic and immunofluorescent study on the antigenic relationship between the coronavirus-like agent, CV 777, and several coronaviruses date: 1981 words: 2521.0 sentences: 171.0 pages: flesch: 52.0 cache: ./cache/cord-255653-0bj5eh5d.txt txt: ./txt/cord-255653-0bj5eh5d.txt summary: A possible antigenic relationship between the porcine enteropathogenic coronavirus-like agent (CVLA) and 6 known coronaviruses was examined by immunoelectron microscopy (IEM) and by immunofluorescence (IF). CVLA did not show cross reactivity with infectious bronchitis virus, transmissible gastroenteritis virus (TGEV), canine coronavirus (CCV) hemagglutinating encephalomyelitis virus (HEV), neonatal calf diarrhea coronavirus (NCDCV) or feline infectious peritonitis virus (FIPV). The CVLA was shown by serologic cross protection studies to differ from the two knowm porcine coronaviruses, transmissible gastroenteritis virus (TGEV) and hemagglntinating encephalomyelitis virus (HEV) (4, 14) . The coronaviruses selected for the present study were TGEV, HEV, neonatal calf diarrhea coronavirus (NCDCV), canine coronavirus (CCV), avian infectious bronchitis virus (IBV) and feline infectious peritonitis virus (FIPV). This hyperimmune serum had a virus neutralizing titer of 1:2560 when tested against the cell culture adapted Purdue strain of TGEV. Antiserum to TGEV reacted with CCV, but did not show detectable antigenic cross-reactivity with FIPV. abstract: A possible antigenic relationship between the porcine enteropathogenic coronavirus-like agent (CVLA) and 6 known coronaviruses was examined by immunoelectron microscopy (IEM) and by immunofluorescence (IF). CVLA did not show cross reactivity with infectious bronchitis virus, transmissible gastroenteritis virus (TGEV), canine coronavirus (CCV) hemagglutinating encephalomyelitis virus (HEV), neonatal calf diarrhea coronavirus (NCDCV) or feline infectious peritonitis virus (FIPV). Antigenic relationship was detected by IEM between TGEV and CCV, NCDCV and HEV and by IF between TGEV and CCV, TGEV and FIPV, HEV and NCDCV. url: https://www.ncbi.nlm.nih.gov/pubmed/6166280/ doi: 10.1007/bf01315166 id: cord-339178-d6f6a5ds author: Pensaert, M. B. title: A new coronavirus-like particle associated with diarrhea in swine date: 1978 words: 1749.0 sentences: 109.0 pages: flesch: 58.0 cache: ./cache/cord-339178-d6f6a5ds.txt txt: ./txt/cord-339178-d6f6a5ds.txt summary: Coronavirus-like particles were detected by electron microscopy in the intestinal contents of pigs during a diarrheal outbreak on 4 swine breeding farms. Coronavirus-like particles were detected by electron microscopy in the intestinal contents of pigs during a diarrheal outbreak on 4 swine breeding farms. Diarrhea was reproduced in experimental pigs with one of the isolates, designated CV777, which was found to be distinct from the 2 known porcine coronaviruses, transmissible gastroenteritis virus and hemagglutinating encephalomyelitis virus. Diarrhea was reproduced in experimental pigs with one of the isolates, designated CV777, which was found to be distinct from the 2 known porcine coronaviruses, transmissible gastroenteritis virus and hemagglutinating encephalomyelitis virus. In a search for rotaviruses on Belgian swine breeding farms with diarrheal problems, a new coronavirus-like particle was detected b y electron microscopic examination of intestinal or fecal samples from sick pigs. abstract: Coronavirus-like particles were detected by electron microscopy in the intestinal contents of pigs during a diarrheal outbreak on 4 swine breeding farms. Diarrhea was reproduced in experimental pigs with one of the isolates, designated CV777, which was found to be distinct from the 2 known porcine coronaviruses, transmissible gastroenteritis virus and hemagglutinating encephalomyelitis virus. url: https://www.ncbi.nlm.nih.gov/pubmed/83132/ doi: 10.1007/bf01317606 id: cord-295409-7l0pglef author: Percy, D. title: Replication of sialodacryoadenitis virus in mouse L-2 cells date: 1989 words: 3069.0 sentences: 178.0 pages: flesch: 54.0 cache: ./cache/cord-295409-7l0pglef.txt txt: ./txt/cord-295409-7l0pglef.txt summary: The ability to propagate SDAV to high titers in the widely available L-2 cell line should promote the study of this virus and facilitate its comparison with other murine coronaviruses. In LBC cells inoculated with strain #681 of SDAV, CPE was first detected in infected cultures 48 hours pi, and syncytia were observed by 72 hours pi [11] . Viral antigen and TCIDs0 titers of 107/0.2ml could be detected in inoculated culture fluid at 24 hours pi by the tenth passage of SDAV in LBC cells [11] . Submandibular and parotid salivary glands from animals infected with the eighth pass of SDAV were homogenized to make a 10% (w/v) suspension in PBS, then 0.5 ml was inoculated onto L-2 or L-929 cells, incubated at 37 °C, and observed for evidence of viral antigen and CPE. Following 5-6 serial passages of supernatant fluid from infected cell cultures, viral antigen, infectious virus, and CPE could be readily demonstrated. abstract: Sialodacryoadenitis (SDA) is a naturally-occurring infection of the laboratory rat raused by the coronavirus, sialodacryoadenitis virus (SDAV). The study of SDAV has been limited because there is no widely available continuous cell line for the propagation of high titers of the virus. The purpose of this study, therefore, was to compare the ability of SDAV to replicate in the permanent cell lines, LBC, of rat origin, and the mouse cell lines. L-929 and L-2. Following 2 to 6 repeated passages of SDAV in LBC cells, the virus could be readily propagated in LBC and L-2 cells, but not in L-929 cells. Similarly, SDAV adapted to replicate directly in L-2 cells could be readily propagated in LBC, but not L-929 cells. In LBC and L-2 cells, cytopathic effect (CPE), viral antigen, viral particles, and virus infectivity could be demonstrated. Titers of up to 10(8.0) infectious viral particles/0.25 ml of culture fluid were obtained at 48 hours in L-2 cells. Titers in LBC cells were one to two logs lower. When susceptible rats were inoculated with eighth passage L-2 cell-adapted virus, they developed typical lesions of SDA. Virus could be recovered from infected tissues and propagated in L-2 cells on first passage. The ability to propagate SDAV to high titers in the widely available L-2 cell line should promote the study of this virus and facilitate its comparison with other murine coronaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/2539798/ doi: 10.1007/bf01315553 id: cord-343256-n593kh7u author: Percy, D. H. title: A comparison of the sensitivity and specificity of sialodacryoadenitis virus, Parker''s rat coronavirus, and mouse hepatitis virus-infected cells as a source of antigen for the detection of antibody to rat coronaviruses date: 1991 words: 1738.0 sentences: 107.0 pages: flesch: 55.0 cache: ./cache/cord-343256-n593kh7u.txt txt: ./txt/cord-343256-n593kh7u.txt summary: title: A comparison of the sensitivity and specificity of sialodacryoadenitis virus, Parker''s rat coronavirus, and mouse hepatitis virus-infected cells as a source of antigen for the detection of antibody to rat coronaviruses Using SDAVand PRC-infected L-2 cells as the source of antigen, and sera from rats collected post inoculation with either of these viral strains, the indirect fluorescent antibody (IFA) procedure was used to determine whether antibody titers could be used to differentiate infections from the homologous and heterologous virus. However, using MHV or SDAV-infected cells as the source of antigen, there was a significant difference in antibody titers to the homologous virus detected using the immunoenzyme technique. Using the I F A procedure and MHV-, SDAV-, or PRC-infected cells as a source of antigen and sera from rats exposed to S D A virus, antibody titers to all three antigens were similar (Table 1 ). abstract: Sialodacryoadenitis virus (SDAV) and Parker's rat coronavirus (PRC) are two recognized viral strains which cause spontaneous disease in the laboratory rat. Currently there is no recognized practical procedure which will accurately differentiate infections with these strains. Using SDAV- and PRC-infected L-2 cells as the source of antigen, and sera from rats collected post inoculation with either of these viral strains, the indirect fluorescent antibody (IFA) procedure was used to determine whether antibody titers could be used to differentiate infections from the homologous and heterologous virus. There was no detectable difference in the sensitivity or specificity of these systems in detecting antibody to the homologous or heterologous virus. Thus there was no evidence that SDAV- and PRC-infected cells would serve to differentiate antibody to the homologous virus using the IFA technique. In addition, antibody titers were similar when mouse hepatitis virus (MHV)-infected cells were used as the source of antigen for the IFA technique. However, using MHV or SDAV-infected cells as the source of antigen, there was a significant difference in antibody titers to the homologous virus detected using the immunoenzyme technique. url: https://www.ncbi.nlm.nih.gov/pubmed/1877886/ doi: 10.1007/bf01310668 id: cord-004851-h9ppa064 author: Plagemann, P. G. W. title: Hepatitis C virus date: 1991 words: 6835.0 sentences: 320.0 pages: flesch: 48.0 cache: ./cache/cord-004851-h9ppa064.txt txt: ./txt/cord-004851-h9ppa064.txt summary: The viral proteins have not been identified, but on the basis of the predicted amino acid sequences, hydrophobicity plots, location of potential glycosylation sites and similarities of these properties to those of pestiand flaviviruses, the following genome organization has been predicted. A recent study of stored blood samples from prospective studies of 15 U.S.A. patients with transfusion-associated chronic hepatitis documented by liver biopsies indicated that the time course of changes in plasma ALT activity and of the formation of anti-HepCV antibodies can vary considerably between patients [4] . The putative nucleocapsid protein sequence derived from PCR products of RNA extracted from healthy Japanese carrier plasma exhibited a 97.4% amino acid identity with the sequence determined for the original chimpanzee HepCV isolate (HepCV-1) but only a 90.5 % identity at the nucleotide level [45] [46] [47] . abstract: HepCV is the major cause of NANB PT hepatitis and is also implicated as the cause in a large proportion of sporadic cases of NANBH. Chronic infection with HepCV has also been linked to the development of hepatocellular carcinoma. Chimpanzees and marmosets are the only animals found to be experimentally infectable and the virus has not been propagated in any cell culture system. HepCV is an enveloped virus with a diameter of 30–60 nm and a 10-kb positive-stranded RNA genome. Its genome organization resembles that of the flaviviruses and pestiviruses. A 5′-untranslated segment of 341 nucleotides precedes a continuous ORF of 9030/9033 nucleotides which is followed by a 54 nucleotides long 3′-non-coding segment. Further work is required to resolve the question of whether the genomic RNA possesses a 3′-poly(U) or poly(A) tail. The genome also carries an internal poly(A) segment towards the 5′-end of its ORF. Genomic RNA is probably translated into a single polyprotein of 3010/3011 amino acids which is processed into functional proteins. The viral proteins have not been identified, but on the basis of the predicted amino acid sequences, hydrophobicity plots, location of potential glycosylation sites and similarities of these properties to those of pesti- and flaviviruses, the following genome organization has been predicted. The predicted viral structural proteins, a nucleocapsid protein and two envelope glycoproteins are located at the aminoterminal end of the polyprotein. They are followed by a highly hydrophobic protein and proteins that exhibit proteinase, helicase and replicase domains and thus are probably involved in RNA replication and protein processing. The replicase domain is located close to the carboxy terminus of the polyprotein. Although the overall nucleotide and amino acid homologies between HepCV and pestiviruses are low, a number of similarities exist that point to a closer ancestral relationship to the latter than the flaviviruses. First, the 5′-untranslated segment of the HepCV genome resembles that of the pestivirus genomes in size and presence of several short ORFs and it contains several segments with high nucleotide homology. Second, the two putative envelope glycoproteins of HepCV resemble two of the three putative envelope glycoproteins of the pestiviruses. Because its genome organization and predicted virion structure closely resemble those of the flaviviruses and pestiviruses, HepCV has been proposed to be placed in the familyFlaviviridae. It has been suggested to be classified as a new third genus in this family because it is only remotely related to the pestiviruses and flaviviruses in nucleotide sequence of its genome and the amino acid sequences of the predicted viral proteins. On the basis of genomic sequence information, an immunoprobe has been devised for screening blood supplies and donors for anti-HepCV antibodies to a non-structural protein of HepCV. The immuno-assay exhibits a high efficiency in detecting infected donors, though one caveat is that antibodies to the test antigen develop in infected individuals only between 2 and 8 months post infection. On the other hand, viral RNA can be detected in plasma by reverse transcription and amplification of the cDNA by PCR within a few days post infection. Thus the latter technique may become more important in the detection of HepCV in blood and tissues once the technique becomes more widely established as a diagnostic tool. The untranslated 5′-segment has been found to be highly conserved in the genomes of different HepCV isolates from various parts of the world. The replicase domain is also highly conserved, but considerable amino acid and nucleotide differences exist in other segments of the long ORFs of various HepCV isolates. Divergence among different isolates is particularly great (up to 30%) in the segment encoding the two putative envelope glycoproteins and the upstream hydrophobic protein. The variability in envelope glycoproteins needs to be considered in the development of immuno-probes and of vaccines for HepCV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087296/ doi: 10.1007/bf01310473 id: cord-010900-2ie1v1wy author: Ramírez-Salinas, G. Lizbeth title: Bioinformatics design and experimental validation of influenza A virus multi-epitopes that induce neutralizing antibodies date: 2020-02-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Pandemics caused by influenza A virus (IAV) are responsible for the deaths of millions of humans around the world. One of these pandemics occurred in Mexico in 2009. Despite the impact of IAV on human health, there is no effective vaccine. Gene mutations and translocation of genome segments of different IAV subtypes infecting a single host cell make the development of a universal vaccine difficult. The design of immunogenic peptides using bioinformatics tools could be an interesting strategy to increase the success of vaccines. In this work, we used the predicted amino acid sequences of the neuraminidase (NA) and hemagglutinin (HA) proteins of different IAV subtypes to perform multiple alignments, epitope predictions, molecular dynamics simulations, and experimental validation. Peptide selection was based on the following criteria: promiscuity, protein surface exposure, and the degree of conservation among different medically relevant IAV strains. These peptides were tested using immunological assays to test their ability to induce production of antibodies against IAV. We immunized rabbits and mice and measured the levels of IgG and IgA antibodies in serum samples and nasal washes. Rabbit antibodies against the peptides P11 and P14 (both of which are hybrids of NA and HA) recognized HA from both group 1 (H1, H2, and H5) and group 2 (H3 and H7) IAV and also recognized the purified NA protein from the viral stock (influenza A Puerto Rico/916/34). IgG antibodies from rabbits immunized with P11 and P14 were capable of recognizing viral particles and inhibited virus hemagglutination. Additionally, intranasal immunization of mice with P11 and P14 induced specific IgG and IgA antibodies in serum and nasal mucosa, respectively. Interestingly, the IgG antibodies were found to have neutralizing capability. In conclusion, the peptides designed through in silico studies were validated in experimental assays. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-020-04537-2) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222995/ doi: 10.1007/s00705-020-04537-2 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-004769-hhge62sl author: Remond, M. title: Partial DNA cloning and sequencing of a canine parvovirus vaccine strain: application of nucleic acid hybridization to the diagnosis of canine parvovirus disease date: 1992 words: 3270.0 sentences: 221.0 pages: flesch: 62.0 cache: ./cache/cord-004769-hhge62sl.txt txt: ./txt/cord-004769-hhge62sl.txt summary: title: Partial DNA cloning and sequencing of a canine parvovirus vaccine strain: application of nucleic acid hybridization to the diagnosis of canine parvovirus disease The cloning and sequencing of anEco RI-Pst I fragment derived from the replicative form of a canine parvovirus (CPV) vaccine strain are reported. In order to improve CPV diagnosis, radioactively labelled RNA or DNA and biotin labelled DNA obtained by random priming of the recombinant plasmid were used as probes mainly on gut or stool samples from naturally infected dogs. Results of filter hybridization correlated well with histopathological diagnosis of parvovirus infection and with hemagglutination tests performed on dog faeces. To elucidate whether the deletion observed was originally in the vaccine or was generated by cell culture passages in our laboratory, DNA sequence was determined on CPV-b 108 after PCR amplification of a 1000 bp fragment including the deleted region and the two H i n d I I I restriction sites (Fig. 1) . abstract: The cloning and sequencing of anEco RI-Pst I fragment derived from the replicative form of a canine parvovirus (CPV) vaccine strain are reported. The variability of the 5′ end of NS 1 protein gene in the genome is confirmed by comparison with previously determined DNA sequences. A 15 nucleotide deletion was also observed in this vaccine strain. In order to improve CPV diagnosis, radioactively labelled RNA or DNA and biotin labelled DNA obtained by random priming of the recombinant plasmid were used as probes mainly on gut or stool samples from naturally infected dogs. Results of filter hybridization correlated well with histopathological diagnosis of parvovirus infection and with hemagglutination tests performed on dog faeces. We propose that nucleic acid hybridization may be an alternative diagnostic method to ascertain the presence of CPV, especially in frozen samples. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086918/ doi: 10.1007/bf01309589 id: cord-004729-nmkilkcx author: Reynolds, D. J. title: Virus isolation and serum antibody responses after infection of cats with transmissible gastroenteritis virus date: 1979 words: 1998.0 sentences: 135.0 pages: flesch: 54.0 cache: ./cache/cord-004729-nmkilkcx.txt txt: ./txt/cord-004729-nmkilkcx.txt summary: No clinical disease resulted but infectious virus was isolated from faeces for up to 22 days after infection and serum antibody was detected by neutralisation and immunofluorescence tests. No clinical disease resulted but infectious virus was isolated from faeces for up to 22 days after infection and serum antibody was detected by neutralisation and immunofluorescence tests. Control and infected animals were tested for TGEV excretion by attempted isolation of virus from faeces for up to 35 days after infection; occasionally rectal swabs were used to obtain fresh samples. The medium was changed after 24 hours and 4 days later any viral eytopathic effect was recorded, the medium was removed and passaged in fresh APT/2 cultures and the eoverslips were stained to demonstrate virM antigen by indirect immunofluorescence, using paired sera from a gnotobiotic piglet before and after TGEV infection, followed by FITCconjugated rabbit anti-swine globulin (Nordic Immunological Laboratories, London). abstract: Transmissible gastroenteritis virus was administered orally to cats. No clinical disease resulted but infectious virus was isolated from faeces for up to 22 days after infection and serum antibody was detected by neutralisation and immunofluorescence tests. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086778/ doi: 10.1007/bf01348032 id: cord-302871-x3mjov5l author: Ribeiro, Juliane title: Extra-intestinal detection of canine kobuvirus in a puppy from Southern Brazil date: 2016-11-25 words: 2586.0 sentences: 129.0 pages: flesch: 45.0 cache: ./cache/cord-302871-x3mjov5l.txt txt: ./txt/cord-302871-x3mjov5l.txt summary: This study presents the pathological, immunohistochemical, and molecular findings associated with the extra-intestinal detection of canine kobuvirus (CaKV) in a 5-month-old Chihuahua puppy, that had a clinical history of bloody-tinged feces. There are few descriptions of coinfection due to CaKV and other viral agents: a recent study identified CaKV in association with a several agents including canine herpesvirus type 1 (CaHV-1), canine distemper virus (CDV), canine parvovirus (CPV), and canine adenovirus A types 1 (CAdV-1) and 2 (CAdV-2) in diarrheic and non-diarrheic dogs from Korea [19] . Furthermore, widespread viral dissemination was demonstrated in multiple tissues as CaKV nucleic acids were detected in the liver, lung, brain, and tonsils of this Fig. 2 Phylogenetic analysis of a partial nucleotide sequence (nt 201) of the RdRp gene (a) and partial region of the VP1 protein (nt 303) of canine kobuvirus (CaKV) (b). abstract: This study presents the pathological, immunohistochemical, and molecular findings associated with the extra-intestinal detection of canine kobuvirus (CaKV) in a 5-month-old Chihuahua puppy, that had a clinical history of bloody-tinged feces. Principal pathological findings were interstitial pneumonia, necrotizing bronchitis, and parvovirus-induced enteritis. Molecular diagnostic methods identified CaKV within the cerebellum, cerebrum, lung, tonsil, and liver. CaKV and rotavirus were not identified within the feces and intestine. Immunohistochemistry (IHC) assays detected antigens of CDV and CAdV-1 in the lungs. These results confirmed the extra-intestinal detection of CaKV in this puppy and represent the first extra-intestinal detection of CaKV in a dog. url: https://www.ncbi.nlm.nih.gov/pubmed/27888408/ doi: 10.1007/s00705-016-3164-5 id: cord-339991-k8z6v2vx author: Rong, Q. title: Multiple mechanisms for HSV-1 induction of interferon α production by peripheral blood mononuclear cells date: 2003 words: 5571.0 sentences: 273.0 pages: flesch: 48.0 cache: ./cache/cord-339991-k8z6v2vx.txt txt: ./txt/cord-339991-k8z6v2vx.txt summary: UV-inactivated, infectious, and other forms of herpes simplex virus 1 (HSV-1) induced interferon (IFN) production by different routes in myeloid origin mononuclear cells (MOMC) (consisting predominantly of monocytes). Comparison of the activities of different strains of infectious HSV, UV-inactivated HSV, and a mutant HSV incapable of penetration (K T) [9] and results of treatment with a mannose receptor antagonist indicate that there are more than one mechanism for HSV induction of interferon in the MOMC origin cell populations. The greater response to UV-inactivated virus suggests that non-infectious virions and possibly HSV infected cell debris are the more potent activators of IFN α production and that replicating virus can limit the induction of interferon production as a means of escaping host protection. Interferons and the colony-stimulating factors IL-3 and GM-CSF enhance the ifn-alpha response in human blood leucocytes induced by herpes simplex virus abstract: UV-inactivated, infectious, and other forms of herpes simplex virus 1 (HSV-1) induced interferon (IFN) production by different routes in myeloid origin mononuclear cells (MOMC) (consisting predominantly of monocytes). GM-CSF activated the MOMC (G-MOMC) to produce greater amounts of interferon while differentiation to DC, by the addition of granulocyte macrophage colony stimulating factor (GM-CSF) and calcium ionophore (GA-MOMC), reduced the levels of interferon production upon challenge with some HSV strains. UV-inactivated virus induced more interferon than infectious virus. L-fucose, an antagonist of the mannose receptor, inhibited the induction of IFN-α by UV-inactivated virus and gB(−) virus (defective in penetration) in MOMC and GA-MOMC but not G-MOMC. L-fucose had little effect on interferon induction by infectious HSV-1. The insensitivity of the G-MOMC to fucose inhibition distinguishes these interferon producing cells from the pDC2 cells previously described as natural interferon producing cells. The mannose receptor appears to be involved in the response to non-infectious forms of HSV but infectious virus appears to use a different pathway. These studies suggest that non-infectious virions and HSV infected cell debris effectively stimulate monocytes and pre-dendritic cells to produce IFN-α to initiate host protection against HSV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/12556996/ doi: 10.1007/s00705-002-0912-5 id: cord-340422-8f5xe4zc author: Rowland, R. R. R. title: Inhibition of porcine reproductive and respiratory syndrome virus by interferon-gamma and recovery of virus replication with 2-aminopurine date: 2001 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) belongs to a group of RNA viruses that establish persistent infections. A proposed strategy for evading immunity during persistent PRRSV infection is by preventing the induction of IFN activity in pigs and/or by blocking the activation of antiviral proteins in permissive cells. IFN-γ mRNA expression was observed in the lymph nodes and lungs of pigs infected with wild-type PRRSV strain SDSU-23983. Pretreatment of MARC-145 cells with IFN-γ inhibited wild-type (SDSU-23983 P6) and culture-adapted (SDSU-23983 P136) PRRS viruses in a dose-dependent manner and at relatively low concentrations. The effect of IFN-γ on virus replication included reductions in the number of infected cells, virus yield, and RNA content in single cells. Virus replication was partially restored by the addition of 2-aminopurine (2-AP), an inhibitor of dsRNA inducible protein kinase (PKR). The addition of 2-AP also restored the viral RNA content per cell to near normal levels, suggesting that inhibition of viral RNA synthesis was through PKR. The principal difference between P6 and P136 isolates was the recovery of P136 replication with lower concentrations of 2-AP. Immunostaining with anti-PKR antibody showed a redistribution of PKR from the cytoplasm into nucleoli of infected cells. url: https://www.ncbi.nlm.nih.gov/pubmed/11338389/ doi: 10.1007/s007050170161 id: cord-265631-b0kg6qpo author: Saeng-chuto, Kepalee title: Retrospective investigation and evolutionary analysis of a novel porcine deltacoronavirus strain detected in Thailand from 2008 to 2015 date: 2017-03-23 words: 1601.0 sentences: 87.0 pages: flesch: 52.0 cache: ./cache/cord-265631-b0kg6qpo.txt txt: ./txt/cord-265631-b0kg6qpo.txt summary: title: Retrospective investigation and evolutionary analysis of a novel porcine deltacoronavirus strain detected in Thailand from 2008 to 2015 We performed a retrospective investigation of the presence of PDCoV in intestinal samples collected from piglets with diarrhea in Thailand from 2008 to 2015 using RT-PCR. Positive samples were subjected to full-length genome characterization followed by genetic analyses to compare Thai strains of PDCoV to those from other countries and to investigate the genetic similarity and the evolutionary relationships among them. To investigate its evolutionary relationships to foreign PDCoV strains and estimate the divergence time of PDCoV in Thailand, phylogenetic analysis of the full-length nucleotide sequence of the PDCoV isolate collected in this study, together with 21 other PDCoV isolate sequences (Supplementary Table 1 ), was performed using the Bayesian Markov chain Monte Carlo (BMCMC) method implemented in the program BEAST v1.8.3 [2, 3] . abstract: Porcine deltacoronavirus (PDCoV) in Thailand was first detected in 2015. We performed a retrospective investigation of the presence of PDCoV in intestinal samples collected from piglets with diarrhea in Thailand from 2008 to 2015 using RT-PCR. PDCoV was found to be present as early as February 2013. Phylogenetic analysis demonstrated that all PDCoV variants from Thailand differ from those from other countries and belong to a novel group of PDCoV that is separate from the US and Chinese PDCoV variants. Evolutionary analysis suggested that the Thai PDCoV isolates probably diverged from a different ancestor from that of the Chinese and US PDCoV isolates and that this separation occurred after 1994. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-017-3331-3) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/28337545/ doi: 10.1007/s00705-017-3331-3 id: cord-285429-vmnj25b5 author: Saikruang, Wilaiporn title: Detection of diarrheal viruses circulating in adult patients in Thailand date: 2014-07-31 words: 2186.0 sentences: 113.0 pages: flesch: 51.0 cache: ./cache/cord-285429-vmnj25b5.txt txt: ./txt/cord-285429-vmnj25b5.txt summary: A total of 332 fecal specimens collected during January-December 2008 from adult patients with diarrhea were screened for group A and C rotaviruses, noroviruses GI and GII, sapovirus, Aichi virus, human parechovirus, enterovirus, adenovirus and astrovirus by RT-multiplex PCR. This study provides epidemiological data for a wide variety of diarrheal viruses circulating in adult patients with diarrhea in Chiang Mai, Thailand. Then, the specimens were tested for the presence of SaV, AiV, group A rotavirus (RVA), group C rotavirus (RVC), HPeV, NoV GI and GII, EV, AdV, and AstV by RT-multiplex PCR using the protocol described previously by Khamrin et al. In addition, this study clearly demonstrates that HPeV is an unusual cause of acute gastroenteritis in adults compared to other viruses. The relatively low rate of diarrheal virus detection in adults with diarrhea in this study suggests that acute gastroenteritis in adults in this area may be caused by other pathogens. abstract: A total of 332 fecal specimens collected during January-December 2008 from adult patients with diarrhea were screened for group A and C rotaviruses, noroviruses GI and GII, sapovirus, Aichi virus, human parechovirus, enterovirus, adenovirus and astrovirus by RT-multiplex PCR. The detection rate for diarrheal viruses was 4.2 %. Adenovirus and enterovirus were equally detected as the most predominant viruses, with prevalence of 1.2 %, followed by Aichi virus (0.9 %) and norovirus GII (0.6 %). Mixed infection with norovirus GII and human parechovirus was also detected (0.3 %). This study provides epidemiological data for a wide variety of diarrheal viruses circulating in adult patients with diarrhea in Chiang Mai, Thailand. url: https://www.ncbi.nlm.nih.gov/pubmed/25078389/ doi: 10.1007/s00705-014-2191-3 id: cord-259193-ifdjyp5b author: Sato, K. title: Detection of bovine coronavirus in feces by reversed passive hemagglutination date: 1984 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A reversed passive hemagglutination (RPHA) method was developed for the detection of bovine coronavirus in fecal specimens. Sheep erythrocytes fixed with glutaraldehyde, and then treated with tannic acid were coated with anti-bovine coronavirus rabbit antibodies purified by affinity chromatography using bovine coronavirus linked to Sepharose 4B. The RPHA test was carried out by a microtiter method. Erythrocytes coated with purified specific antibodies were agglutinated by bovine coronavirus, but not by bovine rotavirus or enterovirus. The reaction was inhibited by antiserum to bovine coronavirus, confirming the specificity of the reaction. The RPHA test detected bovine coronavirus in 13 of 22 fecal specimens (59 per cent), from natural cases of diarrhea, while the positive rates were only 14 per cent (3/22) and 22 per cent (5/22) for immunofluorescent staining of primary cultures of calf kidney cells infected with the specimens, and immune electron microscopy respectively. The advantages of the RPHA method are its simplicity, high sensitivity and rapidity. url: https://www.ncbi.nlm.nih.gov/pubmed/6367710/ doi: 10.1007/bf01315291 id: cord-267155-3rhdxzj3 author: Sato, K. title: Serological relation between calf diarrhea coronavirus and hemagglutinating encephalomyelitis virus date: 1980 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Neutralizing (NT) and hemagglutination-inhibiting (HI) antibodies to calf diarrhea coronavirus (CDCV) and hemagglutinating encephalomyelitis virus of swine (HEV) (strain 67 N) were detected in high proportions of normal adult cattle and pigs in Japan. Since comparison of NT and HI titers in the serum samples suggested an antigenic difference between the viruses, cross NT and HI tests of these viruses were carried out with antisera raised in rabbits. The homologous NT titers were markedly higher than the heterologous titers. In HI tests essentially the same results were obtained. These findings indicate the presence of a marked difference in antigenic make-up between CDCV and HEV. NT and HI tests can clearly differentiate the viruses, although there is some cross reaction. url: https://www.ncbi.nlm.nih.gov/pubmed/6159873/ doi: 10.1007/bf01314983 id: cord-334090-66d8c75g author: Seger, Waleed title: Genotyping of infectious bronchitis viruses from broiler farms in Iraq during 2014-2015 date: 2016-02-18 words: 3613.0 sentences: 178.0 pages: flesch: 54.0 cache: ./cache/cord-334090-66d8c75g.txt txt: ./txt/cord-334090-66d8c75g.txt summary: Thus, the spread of viral respiratory diseases has become the most commonly reported condition in commercial broiler flocks in Iraq; however, there have been no studies on the detection and genotyping of these viruses using molecular techniques and sequencing. Phylogenetic analysis of the 32 strains (Fig. 2) revealed that Iraqi IBV strains could be classified into four genetic groups or genotypes: group I, variant 2 IS/1494-like viruses, including 15 field isolates (46.87 %); group II, 793/Blike viruses, including 13 field strains (40.62 %); group III, QX-like viruses, including three field strains (9.37); and caused by bacteria and mycoplasmas have already been detected on broiler farms located in the central and southern parts of Iraq. Our result were in line with those of Mahmood et al., who conducted the first study of identification and genotyping of IBV isolates and indicated that the 4/91-like virus is circulating on vaccinated broiler farms of the Kurdistan region of Iraq [21] . abstract: Infectious bronchitis virus (IBV) is one of the most critical pathogens in the poultry industry, causing serious economic losses in all countries including Iraq. IBV has many genotypes that do not confer any cross-protection. This virus has been genotyped by sequence analysis of the S1 glycoprotein gene. A total of 100 tracheal and kidney tissue specimens from different commercial broiler flocks in the middle and south of Iraq were collected from September 2013 to September 2014. Thirty-two IBV-positive samples were selected from among the total and were further characterized by nested PCR. Phylogenetic analysis revealed that isolates belong to four groups (group I, variant 2 [IS/1494-like]; group II, 793/B-like; group III, QX-like; group IV, DY12-2-like). Sequence analysis revealed nucleotide sequence identities within groups I, II, and III of 99.68 %-100 %, 99.36 %-100 %, and 96.42 %-100 %, respectively. Group I (variant 2) was the dominant IBV genotype. One Chinese-like recombinant virus (DY12-2-like) that had not been reported in the Middle East was detected. In addition, the presence of QX on broiler chicken farms in the area studied was confirmed. This is the first comprehensive study on the genotyping of IBV in Iraq with useful information regarding the molecular epidemiology of IBV. The phylogenetic relationship of the strains with respect to different time sequences and geographical regions displayed complexity and diversity. Further studies are needed and should include the isolation and full-length molecular characterization of IBV in this region. url: https://www.ncbi.nlm.nih.gov/pubmed/26887967/ doi: 10.1007/s00705-016-2790-2 id: cord-004808-6w9n03fy author: Sekiguchi, K. title: Detection of equine arteritis virus (EAV) by polymerase chain reaction (PCR) and differentiation of EAV strains by restriction enzyme analysis of PCR products date: 1995 words: 2056.0 sentences: 116.0 pages: flesch: 59.0 cache: ./cache/cord-004808-6w9n03fy.txt txt: ./txt/cord-004808-6w9n03fy.txt summary: title: Detection of equine arteritis virus (EAV) by polymerase chain reaction (PCR) and differentiation of EAV strains by restriction enzyme analysis of PCR products A polymerase chain reaction (PCR) based assay capable of detecting and differentiating seven strains of equine arteritis virus (EAV) from around the world was developed. A potymerase chain reaction (PCR) based assay capable of detecting and differentiating seven strains of equine arteritis virus (EAV) from around the world was developed. Viral RNA from cell culture fluids infected with each of the seven EAV strains and RNA from the live vaccine, Arvac, was detected by PCR using four sets of primers. The objective of this study was to detect each of the EAV strains using PCR, and to differentiate the strains through restriction enzyme analysis of their PCR products, based on the M protein nucleotide sequence data of the strains, together with those of the Bucyrus [7] and modified Bucyrus strain [251. abstract: A polymerase chain reaction (PCR) based assay capable of detecting and differentiating seven strains of equine arteritis virus (EAV) from around the world was developed. The primers for the PCR were chosen from the ORF 6 gene encoding the unglycosylated membrane protein (M). Viral RNA from cell culture fluids infected with each of the seven EAV strains and RNA from the live vaccine, Arvac, was detected by PCR using four sets of primers. The sensitivity of detection was increased from 100 to 1000 times by performing nested PCR enabling the detection of RNA at a level of 0.5–5 PFU. Differentiation among the virus strains and the live vaccine was achieved by cutting the PCR-amplified products from three sets of primers with six restriction endonucleases. Using this procedure it was possible to distinguish among the seven EAV strains used. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087138/ doi: 10.1007/bf01322675 id: cord-322760-tsxniu3j author: Sha, Jianping title: Fatality risks for nosocomial outbreaks of Middle East respiratory syndrome coronavirus in the Middle East and South Korea date: 2016-09-23 words: 4625.0 sentences: 207.0 pages: flesch: 55.0 cache: ./cache/cord-322760-tsxniu3j.txt txt: ./txt/cord-322760-tsxniu3j.txt summary: Thus, older age, pre-existing concurrent diseases, and delayed confirmation increase the odds of a fatal outcome in nosocomial MERS-CoV outbreaks in the Middle East and South Korea. Information on all laboratory-confirmed MERS cases was obtained from various publicly available sources, including WHO Global Alert and Response updates, documents officially released by the local health bureau, news releases from Middle Eastern and South Korean authorities, the Weekly Epidemiological Record, ProMed posts, and literature published from 1 April 2012 to 29 June 2016 (http:// www.who.int/csr/don/archive/disease/coronavirus_infections/ en/). In this study, we compared the mortality risk factors in two different nosocomial outbreaks, based on 51 nosocomial outbreaks of MERS-CoV infection in the Middle East and one large outbreak identified in South Korea. The severity of nosocomial outbreaks and the risk of fatal infection in HCP were significantly lower than the overall rate in the Middle East and South Korea. Middle East respiratory syndrome coronavirus (MERS-CoV) nosocomial outbreak in South Korea: insights from modeling abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) was first isolated in 2012. The largest known outbreak outside the Middle East occurred in South Korea in 2015. As of 29 June 2016, 1769 laboratory-confirmed cases (630 deaths; 35.6 % case fatality rate [CFR]) had been reported from 26 countries, particularly in the Middle East. However, the CFR for hospital outbreaks was higher than that of family clusters in the Middle East and Korea. Here, we compared the mortality rates for 51 nosocomial outbreaks in the Middle East and one outbreak of MERS-CoV in South Korea. Our findings showed the CFR in the Middle East was much higher than that in South Korea (25.9 % [56/216] vs. 13.8 % [24/174], p = 0.003). Infected individuals who died were, on average, older than those who survived in both the Middle East (64 years [25–98] vs. 46 years [2–85], p = 0.000) and South Korea (68 years [49–82] vs. 53.5 years [16–87], p = 0.000). Similarly, the co-morbidity rates for the fatal cases were statistically higher than for the nonfatal cases in both the Middle East (64.3 % [36/56] vs. 28.1 % [45/160], p = 0.000) and South Korea (45.8 % [11/24] vs. 12.0 % [18/150], p = 0.000). The median number of days from onset to confirmation of infection in the fatal cases was longer than that for survivors from the Middle East (8 days [1–47] vs. 4 days [0–14], p = 0.009). Thus, older age, pre-existing concurrent diseases, and delayed confirmation increase the odds of a fatal outcome in nosocomial MERS-CoV outbreaks in the Middle East and South Korea. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-016-3062-x) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/27664026/ doi: 10.1007/s00705-016-3062-x id: cord-277847-vgf9lz76 author: Sheppard, M. title: Fowl adenovirus recombinant expressing VP2 of infectious bursal disease virus induces protective immunity against bursal disease date: 2014-04-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The right hand end Nde I fragment 3 (90.8–100 map units) of the fowl adenovirus serotype 10 (FAV-10) was characterised so as to allow the location of an insertion site for recombinant vector construction. Infectious bursal disease virus (IBDV) VP2 gene from the Australian classical strain 002/73, under the control of the FAV-10 major late promoter/leader sequence (MLP/LS) was inserted into a unique Not I site that was generated at 99.5 map units. This recombinant virus was produced without deletion of any portion of the FAV-10 genome. When administered to specific pathogen free (SPF) chickens intravenously, intraperitoneally, subcutaneously or intramuscularly, it was shown that the FAV-10/VP2 recombinant induced a serum VP2 antibody response and protected chickens against challenge with IBDV V877, an intermediate virulent classical strain. Birds were not protected when the recombinant was delivered via the conjunctival sac. url: https://www.ncbi.nlm.nih.gov/pubmed/9645198/ doi: 10.1007/s007050050342 id: cord-261036-zdhg4axx author: Shirato, Kazuya title: Enhanced cell fusion activity in porcine epidemic diarrhea virus adapted to suckling mice date: 2010-09-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine epidemic diarrhea virus (PEDV) is the major causative agent of fatal diarrhea in piglets. To study the pathogenic features of PEDV using a mouse model, PEDV with virulence in mice is required. In pursuit of this, we adapted a tissue-culture-passed PEDV MK strain to suckling mouse brains. PEDV obtained after ten passages through the brains (MK-p10) had increased virulence for mice, and its fusion activity in cultured cells exceeded that of the original strain. However, the replication kinetics of MK and MK-p10 did not differ from each other in the brain and in cultured cells. The spike (S) protein of MK-p10 had four amino acid substitutions relative to the original strain. One of these (an H-to-R substitution at residue 1,381) was first detected in PEDV isolated after eight passages, and both this virus (MK-p8) and MK-p10 showed enhanced syncytium formation relative to the original MK strain and viruses isolated after two, four, and six passages, suggesting the possibility that the H-to-R mutation was responsible for this activity. This mutation could be also involved in the increased virulence of PEDV observed for MK-p10. url: https://www.ncbi.nlm.nih.gov/pubmed/20827493/ doi: 10.1007/s00705-010-0790-1 id: cord-004790-69lry0ys author: Smith, A. L. title: Comparative biological characterization of mouse adenovirus strains FL and K 87 and seroprevalence in laboratory rodents date: 1986 words: 4411.0 sentences: 246.0 pages: flesch: 57.0 cache: ./cache/cord-004790-69lry0ys.txt txt: ./txt/cord-004790-69lry0ys.txt summary: The source of these discrepancies is not immediately apparent; however, our results may explain why seroconversion to mouse adenovirus is not observed among mice thought to be infected with the virus. Finally, we provide serologic evidence that an outbreak of disease in a mouse breeding colony which sustained high infant mortality was associated with the introduction of a mouse adenovirus strain closely related to MAd-K 87. Sera from mice housed in two intramural, barrier-maintained facilities were Mso free of antibody to MAd. Only three mouse sera ofl61 which were tested reacted by IFA with MAd bivalent antigen. (19) for growth of MAd-FL in primary mouse kidney cultures, we have found that the majority of infectious progeny virions (between 90 and 99 percent) are released fl~om infected L 929 or CMT-93 cells. We have provided serologic evidence linking an outbreak of clinical disease in a breeding colony of mice to infection with MAd-K 87 or a very closely related virus. abstract: The growth, stability and seroprevalence in laboratory rodents of the two known strains of mouse adenovirus were compared. The FL strain of mouse adenovirus grew in both L 929 murine fibroblasts and in CMT-93 murine rectal carcinoma cells, whereas the K 87 strain grew only in CMT-93 cells. The bulk of the FL progeny virus was released from the host cells. K 87 virus was largely cell-associated. Both virus strains were stable at 37° C in liquid medium. The K 87 strain was completely inactivated after 5–15 minutes at 56° C, whereas FL infectivity was still detected after two hours at this temperature. Both virus strains were stable in the dessicated state for 14 days, although FL viability was more dependent on the presence of protein in the virus diluent. Seroepidemiologic data suggest that viruses antigenically related to mouse adenovirus are more prevalent among laboratory rats than among laboratory mice and that the virus(es) infecting rats differ from those infecting mice. Results of retrospective serologic testing suggest an association between mouse adenovirus and an outbreak of disease in a mouse breeding colony. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086991/ doi: 10.1007/bf01314283 id: cord-341278-klv9jdm8 author: Smith, Abigail L. title: The role of gamma interferon in infection of susceptible mice with murine coronavirus, MHV-JHM date: 1991 words: 3861.0 sentences: 182.0 pages: flesch: 45.0 cache: ./cache/cord-341278-klv9jdm8.txt txt: ./txt/cord-341278-klv9jdm8.txt summary: Infection of BALB/c mice with mouse hepatitis virus, strain JHM (MHV-JHM), at any of several intervals relative to ovalbumin (OVA) administration resulted in elevated OVA-specific IgG 2 a titers. Serum IFN-γ was not detected, but treatment of MHV-JHM-infected mice with monoclonal anti-IFN-γ antibody resulted in high mortality with decreased survival times, enhanced virus titers in liver and spleen, and more severe virus-associated pathology, compared to mock-treated, infected mice. Sera from mice infected with MHV-JHM one day prior to OVA administration contained substantially elevated levels of antigen-specific IgG2 a on day 7 (Table 1 ) with geometric mean titers that were 17 times control (OVA only) values at that interval. The elevated IgG 2 a OVA-specific response of most groups of MHV-infected mice and the preferential production of this isotype by mice infected one day prior to antigen administration suggested that these mice were producing IFNy. However, using the WEHI 279 B cell lymphoma bioassay [24] , attempts to detect the cytokine in sera of infected mice failed, as had earlier attempts to 27] . abstract: Infection of BALB/c mice with mouse hepatitis virus, strain JHM (MHV-JHM), at any of several intervals relative to ovalbumin (OVA) administration resulted in elevated OVA-specific IgG 2 a titers. Since gamma interferon (IFN) has been implicated as an up-regulator of IgG 2 a production, attempts were made to determine whether levels of this cytokine were modified in sera of infected mice. Serum IFN-γ was not detected, but treatment of MHV-JHM-infected mice with monoclonal anti-IFN-γ antibody resulted in high mortality with decreased survival times, enhanced virus titers in liver and spleen, and more severe virus-associated pathology, compared to mock-treated, infected mice. Immunotherapy with recombinant IFN-γ ameliorated disease as reflected by mortality rates and virus titers in target organs. url: https://www.ncbi.nlm.nih.gov/pubmed/1662041/ doi: 10.1007/bf01316746 id: cord-004778-xrv0qs6n author: Smith, C. B. title: Mouse cytomegalovirus is infectious for rats and alters lymphocyte subsets and spleen cell proliferation date: 1986 words: 3373.0 sentences: 172.0 pages: flesch: 52.0 cache: ./cache/cord-004778-xrv0qs6n.txt txt: ./txt/cord-004778-xrv0qs6n.txt summary: The Smith strain of mouse cytomegalovirus (MCMV) was infectious for infant and mature DA strain laboratory rats as judged by development of neutralizing antibodies and specific spleen cell proliferation on stimulation with MCMV antigen. In the following report, we describe a transient, effect of MCMV infections on rat T lymphoc~ helper/suppressor cell ratios and on spleen cell proliferation following stimulation with mitogens and MCMY antigen. Seven days after MCMV infection, a consistently greater proliferation of spleen cells from MCMV infected rats as compared to control animMs was seen with M1 mitogens and also in unstimulated background cultures (Table 2 and Fig. 1 and 2 ). P. route for infants and adults of three strains of laboratory rats as judged by virus isolation, neutralizing antibody response and development of a high level of spleen cell reactivity to MCMV antigen. abstract: The Smith strain of mouse cytomegalovirus (MCMV) was infectious for infant and mature DA strain laboratory rats as judged by development of neutralizing antibodies and specific spleen cell proliferation on stimulation with MCMV antigen. An i. p. inoculum of 10(6) PFU of MCMV was fatal for more than two-thirds of infant mice (1–7 days of age), and disseminated viral infection was documented by isolation of virus from body organs. In contrast, weanling and adult rats did not become ill as a result of infection with a larger inoculum of 10(7) PFU. However, these older MCMV infected rats did show transient reversals of T helper/suppressor cell ratios and alterations of immune cell function as detected byin vitro spleen cell proliferation assays. Seven days after MCMV infection, there was a generalized increase in(3)H-thymidine incorporation by spleen cells in both resting (unstimulated) cultures and cultures exposed to mitogens (Con A, PHA, LPS) and to MCMV antigen. At 14 days, the spleen cell proliferation in the unstimulated cultures returned to normal but was depressed compared to controls in response to Con A. These observations show that laboratory rats are susceptible to MCMV infection and that assymptomatic infection may occur and cause transient alterations in lymphocyte subsets and in their reactivity to mitogens. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086953/ doi: 10.1007/bf01317379 id: cord-004759-jozdnhgy author: Snodgrass, D. R. title: Pathogenesis of diarrhoea caused by astrovirus infections in lambs date: 1979 words: 2304.0 sentences: 139.0 pages: flesch: 53.0 cache: ./cache/cord-004759-jozdnhgy.txt txt: ./txt/cord-004759-jozdnhgy.txt summary: Experimental infection of 2-day-old gnotobiotic lambs with lamb astrovirus produced mild diarrhoea after an incubation period of about 48 hours. Astrovirus was not observed in faeces from the lambs killed t4 and 23 hours p.i., but was first seen in the faeces of all other infected lambs between 38 and 48 hours p.i. At necropsy, astrovirus was detected in intestinal contents of all Iambs except that killed 14 hours p.i. The control lambs remained clinically normal, and passed firm brown faeces throughout the duration of the experiment. Specific immunofluorescent staining was detected only in scattered epithelial and subepithelial cells on small intestinal villi (Fig. 1) . Lactase levels in the 6 control lambs were ¢.5±0.5, 5.14-0.6, and 2.44-1.2 units/g tissue for the proximal, mid, and distal small intestinal sites respectively. In midgut of infected lambs, observations were consistently below those of the controls, fMling to a minimum of 1.2 units/g tissue at 23 hours p.i. abstract: Experimental infection of 2-day-old gnotobiotic lambs with lamb astrovirus produced mild diarrhoea after an incubation period of about 48 hours. No other clinical symptoms developed. Infection was studied by immunofluorescent and histological examination of tissues from the lambs. Astroviruses infected only mature villus epithelial cells and subepithelial macrophages in the small intestine, where they produced partial villus atrophy. Infected enterocytes were replaced with cuboidal cells from the crypts, and the lesion gradually healed by 5 days after infection. No serological relationship was detected by immunofluorescence between lamb astrovirus antigen in gut sections and antisera to either calf or human astrovirus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086881/ doi: 10.1007/bf01317493 id: cord-032801-b2ncmkjg author: Song, Jie title: Transcriptome analysis following enterovirus 71 and coxsackievirus A16 infection in respiratory epithelial cells date: 2020-09-29 words: 4930.0 sentences: 238.0 pages: flesch: 48.0 cache: ./cache/cord-032801-b2ncmkjg.txt txt: ./txt/cord-032801-b2ncmkjg.txt summary: It was discovered that enriched GO terms (such as histone acetylation and positive regulation of phosphorylation) and pathways (such as glycosylphosphatidylinositol (GPI)-anchor biosynthesis and DNA replication) might be closely associated with the pathogenic mechanism of these two viruses, and key genes (such as TBCK and GPC) might be involved in the progression of HFMD. In the current study, we aimed to discover significant differentially expressed genes in EV-A71-and CV-A16-infected respiratory epithelial cells through transcriptome sequencing. For example, transcriptome analysis revealed differentially expressed genes, including SCARB2, miR-3605-5p, and enriched ECM-receptor interaction and circadian rhythm pathways involved in the pathogenesis of HFMD in CV-A16-infected HEK 293T cells [9] . These 111 common differentially expressed genes were used to perform hierarchical cluster analysis, and the heatmap result showed that these genes were mainly clustered into two categories-either significantly upregulated or significantly downregulated, suggesting that EV-A71 and CV-A16 infections result in largely similar transcriptome-level changes. abstract: Enterovirus 71 (EV-A71) and coxsackievirus A16 (CV-A16) are the major pathogens responsible for hand, foot and mouth disease (HFMD), but the mechanism by which these viruses cause disease remains unclear. In this study, we used transcriptome sequencing technology to investigate changes in the transcriptome profiles after infection with EV-A71 and CV-A16 in human bronchial epithelial (16HBE) cells. Using systematic bioinformatics analysis, we then searched for useful clues regarding the pathogenesis of HFMD. As a result, a total of 111 common differentially expressed genes were present in both EV-A71- and CV-A16-infected cells. A trend analysis of these 111 genes showed that 91 of them displayed the same trend in EV-A71 and CV-A16 infection, including 49 upregulated genes and 42 downregulated genes. These 91 genes were further used to conduct GO, pathway, and coexpression network analysis. It was discovered that enriched GO terms (such as histone acetylation and positive regulation of phosphorylation) and pathways (such as glycosylphosphatidylinositol (GPI)-anchor biosynthesis and DNA replication) might be closely associated with the pathogenic mechanism of these two viruses, and key genes (such as TBCK and GPC) might be involved in the progression of HFMD. Finally, we randomly selected 10 differentially expressed genes for qRT-PCR to validate the transcriptome sequencing data. The experimental qRT-PCR results were roughly in agreement with the results of transcriptome sequencing. Collectively, our results provide clues to the mechanism of pathogenesis of HFMD induced by EV-A71 and CV-A16. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-020-04821-1) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7522011/ doi: 10.1007/s00705-020-04821-1 id: cord-004764-tmvebf23 author: Stephenson, J. R. title: A comparative analysis of measles virus RNA by oligonucleotide fingerprinting date: 1982 words: 4851.0 sentences: 374.0 pages: flesch: 70.0 cache: ./cache/cord-004764-tmvebf23.txt txt: ./txt/cord-004764-tmvebf23.txt summary: In addition to this disorder another CNS disease (subaeute selerosing panencephalitis --SSPE) has been associated with measles virus infection (1--3) . As the methods employed in these previous studies could only detect gross differences in virus-specific products, or examined one protein or ~ small p a r t thereof, we have chosen in this study to analyse the oligonncteotides from a T1 digest of the complete genome. purification scheme is hybridized to unlabelled messenger R N A from infected cells (Table 1) , it can be shown t h a t at, least 85 per cent, is protected from subsequent nuclease digestion and is thus assumed to be negative stranded. In order to compare the genomes of various measles isolates: unlabelled, single stranded, negative sense nueleocapsid I~NA was prepared from infected cell cytoplasm and purified in parallel with similar radio-labelled material as described in the previous section. 85 per cent measles-specific negative sense R N A b y hybridization to infected cell messenger I~NA. abstract: Isolates from two cases of acute measles, one case of acute measles encephalitis and three patients with subacute sclerosing panencephalitis were compared. This comparison was based upon the electrophoretic analysis of T(1) oligonucleotides from single-stranded, full-length RNA isolated from cytoplasmic nucleocapsids. Although all viruses have oligonucleotides in common, each isolate generated a unique pattern of oligonucleotides. However, no group of oligonucleotides was observed which would allow a differentiation between viruses isolated from acute infections and those isolated from CNS diseases; indicating that probably all measles viruses differ in their nucleotide sequence, regardless of origin. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086895/ doi: 10.1007/bf01315058 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-355512-tycuoslv author: Storz, J. title: Comparison of hemagglutinating, receptor-destroying, and acetylesterase activities of avirulent and virulent bovine coronavirus strains date: 1992 words: 3246.0 sentences: 172.0 pages: flesch: 57.0 cache: ./cache/cord-355512-tycuoslv.txt txt: ./txt/cord-355512-tycuoslv.txt summary: Hemagglutinating and acetylesterase functions as well as the 124 kDa glycoprotein were present in the highly cell-culture adapted, avirulent bovine coronavirus strain BCV-L9, in the Norden vaccine strain derived from it, and in 5 wild-type, virulent strains that multiplied in HRT-18 cells but were restricted in several types of cultured bovine cells. Purified preparations of the vaccine and the wild-type strains agglutinated chicken erythrocytes at low titers and mouse erythrocytes at 128 to 256 times higher titers whereas receptor destroying enzyme activity was detectable only with chicken erythrocytes. When wild-type strains were propagated in HRT cells at low passage levels, they produced 5×10(5) to 4.5×10(6) plaque forming units per 50 µl which agglutinated erythrocytes from mice but not from chickens. The objective of our investigations was to identify the HE of wild-type BCV strains at low passage levels in H R T cell cultures and to compare it with the HE of prototype BCV-L9 and vaccine strains by relating its functions to the interaction with different erythrocytes, the effects of enzyme inhibitors, and to plaque-forming infectivity. abstract: Hemagglutinating and acetylesterase functions as well as the 124 kDa glycoprotein were present in the highly cell-culture adapted, avirulent bovine coronavirus strain BCV-L9, in the Norden vaccine strain derived from it, and in 5 wild-type, virulent strains that multiplied in HRT-18 cells but were restricted in several types of cultured bovine cells. The BCV-L9 and the wild-type strain BCV-LY-138 agglutinated chicken and mouse erythrocytes. The acetylesterase facilitated break-down of the BCV-erythrocyte complex with chicken but only to a minimal extent with mouse erythrocytes in the receptor-destroying enzyme test. Purified preparations of the vaccine and the wild-type strains agglutinated chicken erythrocytes at low titers and mouse erythrocytes at 128 to 256 times higher titers whereas receptor destroying enzyme activity was detectable only with chicken erythrocytes. When wild-type strains were propagated in HRT cells at low passage levels, they produced 5×10(5) to 4.5×10(6) plaque forming units per 50 µl which agglutinated erythrocytes from mice but not from chickens. Diisopropylfluoro-phosphate moderately increased the hemagglutination titers, but completely inhibited the receptor destroying enzyme of purified virus of all strains. It had virtually no influence on the plaque-forming infectivity of the different BCV strains. The acetylesterase of strain BCV-L9 reacting in the receptor-destroying enzyme test was stable for 3h at 37 and 42°C. It was inactivated within 30 min at 56°C while the hemagglutinin function of this strain was stable for 3 h at 37, 42, and 56°C, but it was inactivated at 65°C within 1 h. url: https://www.ncbi.nlm.nih.gov/pubmed/1642550/ doi: 10.1007/bf01309637 id: cord-265201-ab67pnct author: Sugiyama, K. title: Hemagglutination and structural polypeptides of a new coronavirus associated with diarrhea in infant mice date: 1980 words: 3274.0 sentences: 272.0 pages: flesch: 69.0 cache: ./cache/cord-265201-ab67pnct.txt txt: ./txt/cord-265201-ab67pnct.txt summary: The hemagglutination (HA) and receptor destroying enzyme (RDE) activities of a newly isolated mouse enteric coronavirus (designated as DVIM) are described. H e madsorbed s y n e y t i u m which were i n c u b a t e d at 37 ° C to release I~BCs for 60 minutes, were exposed to freshly p r e p a r e d RBCs a n d p h o t o g r a p h e d Above results strongly suggest that DVIM possesses an enzymatic activity which reacts with surface components of RBCs. However, this enzymatic action appears to differ from the bacterial neuraminidase and that of Influenza-A virions. A densitometer scan of a stained polyacrylamide gel of the polypeptides of virus particles treated with bromelain (1.0 mg/ml at 37°C for 15 minutes) is shown in Fig. 4 . abstract: The hemagglutination (HA) and receptor destroying enzyme (RDE) activities of a newly isolated mouse enteric coronavirus (designated as DVIM) are described. DVIM agglutinates mouse or rat red blood cells (RBC) at 4° C. At 37° C the agglutination was rapidly reversed. The optimal pH for HA and for RDE activities using mouse red cells were shown to be 6.5 and 7.3 respectively. Hemagglutination by DVIM was not inhibited by pretreatment of RBCs withVibrio cholerae filtrate or by pretreatment with Influenza-A neuraminidase. Therefore, the DVIM receptors on RBCs differ from the receptors of Influenza-A, and the RDE activity of DVIM acts specifically on this receptor. In addition, an analysis of the DVIM polypeptides showed that the virions contain five major, VP1 (M.W. 139,000), VP2 (68,000), VP3 (53,000), VP4 (38,000), VP5 (22,000) and two minor, VP1a (110,000), VP1b (100,000) polypeptides. VP1 and VP1b were digested by bromelain, suggesting that they constitute the surface glycoproteins. url: https://www.ncbi.nlm.nih.gov/pubmed/7436741/ doi: 10.1007/bf01314978 id: cord-317617-snrumw3x author: Sugiyama, K. title: Morphological and biological properties of a new coronavirus associated with diarrhea in infant mice date: 1981 words: 2707.0 sentences: 252.0 pages: flesch: 74.0 cache: ./cache/cord-317617-snrumw3x.txt txt: ./txt/cord-317617-snrumw3x.txt summary: Recently, a new viral agent (DVIM) was isolated from an infant mouse with diarrhea, by the utilization of cultured cells. It has also been shown by complement fixation tests that this new isolate is antigenically related to known coronaviruses, avian infectious bronchitis virus (IBV) and mouse hepatitis virus strain-2 (MHV-2). A virus isolated from t h e intestine of a n i n f a n t mouse w i t h clinical signs of diarrhea, d e s i g n a t e d DVIM, was generously p r o v i d e d b y Dr. K o z a b u r o Sato (Central L a b o r a t o r y of Shionogi P h a r m . Mouse hepatitis virus (MHV), a member of coronaviruses, has been described as a common cause of enteric infection in baby mice (8, 21) . Lethal enteritis in infant mice caused by mouse hepatitis virus New strain of mouse hepatitis virus as the cause of lethal enteritis in infant mice abstract: Biological and morphological properties of a virus, isolated from the intestine of infant mice with clinical signs of diarrhea and designated as diarrhea virus of infant mice (DVIM), were examined. The first infective virus was detected on the cells 4 hours post infection, followed by rapid release of the virus into the culture fluids. Virus-induced syncytia in BALB/c-3T3 cell cultures caused hemadsorption at 4° C and viral antigens were shown to be located in the cytoplasm of the syncytia by immunofluorescent techniques. By scanning electron-microscopy, budding virus-like particles were detected on the surface of virus-induced syncytia. Morphologically the virus was shown to be enveloped and approximately 100 nm in diameter. Two types of projections were demonstrated, one type of projection was club-shaped, 20 nm in length and the other type was small, granular, 5 nm in length. The latter type of projection might be the basal part of the clubshaped type and related to the hemagglutinating activity. url: https://www.ncbi.nlm.nih.gov/pubmed/7224861/ doi: 10.1007/bf01318134 id: cord-004728-rjl35dpa author: Taguchi, F. title: Asymptomatic infection of mouse hepatitis virus in the rat date: 1979 words: 954.0 sentences: 70.0 pages: flesch: 59.0 cache: ./cache/cord-004728-rjl35dpa.txt txt: ./txt/cord-004728-rjl35dpa.txt summary: After intranasal inoculation of suckling rats mouse hepatitis virus multiplied mostly in the nasal epithelium; though there were no symptoms, antibodies were produced. Bar represents 0.1 mm Two-, 4-, 6-and t0-week-old rats were also inoculated i.n. with t05 PFU of MHV-S and infectious viruses were assayed in the lung, brain, salivary glands and liver. So far only mice have been considered to be natural hosts of MHV and rat; has been excluded because highly virulent MHV inoculated by various routes did not cause any sy~lptomatic infection like that produced in the mouse (7, 13) . B~tATT and his eoworkers showed that SDAV multiplied in mice producing some histopathological changes in the respiratory system after i.n. inoculation (3) and we demonstrated in the w e s e n t paper that 3{HV infected rats of any ages. Pathogenicity of mouse hepatitis virus for mice depending upon host age and route of infection abstract: After intranasal inoculation of suckling rats mouse hepatitis virus multiplied mostly in the nasal epithelium; though there were no symptoms, antibodies were produced. Antibodies were also demonstrated in adult rats. These findings suggest that the rat may be a natural host for the virus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086774/ doi: 10.1007/bf01317424 id: cord-307098-oq7zrnuv author: Taguchi, F. title: Difference in Bgp-independent fusion activity among mouse hepatitis viruses date: 2014-05-20 words: 2676.0 sentences: 143.0 pages: flesch: 55.0 cache: ./cache/cord-307098-oq7zrnuv.txt txt: ./txt/cord-307098-oq7zrnuv.txt summary: Co-cultivation of MHV-nonpermissive hamster BHK cells devoid of mouse Bgp with mouse DBT cells infected with MHV-A59 or JHMV induces syncytia formation on BHK cells (Bgp-independent fusion). Under a phase contrast microscopy, JHMV (cl-2, sp-4) induced the Bgp-independent syncytia on BHK cells similar to those observed on DBT cells, while such syncytia were not seen with the infection of other MHV strains (MHV-1, MHV-3, MHV-A59, MHV-S, srr7, srr11 and srr18). Interestingly, no syncytia formation was demonstrated on BHK cells with other strains or srr mutants under the phase contrast microscopy, though all of them produced syncytia on Bgp-positive DBT cells [10] . The cl-2 S protein could have a very strong Bgp-independent fusion activity, but its replication in BHK cells could be less efficient than the other MHV strains. Present study showed that JHMV (cl-2 and sp-4) could induce syncytia on BHK cells detectable by microscopy, whereas the other MHVs and srr mutants failed. abstract: Mouse hepatitis virus (MHV) utilizes a mouse biliary glycoprotein (Bgp) as a receptor. Co-cultivation of MHV-nonpermissive hamster BHK cells devoid of mouse Bgp with mouse DBT cells infected with MHV-A59 or JHMV induces syncytia formation on BHK cells (Bgp-independent fusion). This study shows the difference in Bgp-independent fusion activity among various MHV strains. Under a phase contrast microscopy, JHMV (cl-2, sp-4) induced the Bgp-independent syncytia on BHK cells similar to those observed on DBT cells, while such syncytia were not seen with the infection of other MHV strains (MHV-1, MHV-3, MHV-A59, MHV-S, srr7, srr11 and srr18). Tiny syncytia detectable only by immunofluorescence were produced with the latter MHV strains except for srr7 which failed to produce syncytia. MHVs except for srr7 grew in BHK cells after Bgp-independent infection. The Bgp-independent fusion by JHMV was inhibited either by anti-S1 or anti-S2 antibodies. These results showed that the JHMV spike protein had a remarkably high Bgp-independent fusion activity. url: https://www.ncbi.nlm.nih.gov/pubmed/10550676/ doi: 10.1007/s007050050725 id: cord-258374-qht98q0l author: Takano, Tomomi title: Neutrophil survival factors (TNF-alpha, GM-CSF, and G-CSF) produced by macrophages in cats infected with feline infectious peritonitis virus contribute to the pathogenesis of granulomatous lesions date: 2009-04-03 words: 3690.0 sentences: 198.0 pages: flesch: 45.0 cache: ./cache/cord-258374-qht98q0l.txt txt: ./txt/cord-258374-qht98q0l.txt summary: title: Neutrophil survival factors (TNF-alpha, GM-CSF, and G-CSF) produced by macrophages in cats infected with feline infectious peritonitis virus contribute to the pathogenesis of granulomatous lesions Furthermore, it was investigated whether macrophages, one of the target cells of FIPV infection, produce neutrophil survival factors (TNF-alpha, GM-CSF, and G-CSF). The neutrophil survival rates were significantly increased in the presence of the culture supernatant of macrophages infected with the mixture of FIPV and MAb 6-4-2 compared to those in the presence of other supernatants (Fig. 5) . When SPF-cat-derived alveolar macrophages were infected with a mixture of FIPV and MAb 6-4-2, the intracellular TNF-alpha, GM-CSF, and G-CSF mRNA levels increased (Fig. 6 ). These cytokine mRNA levels were also elevated in macrophages infected with FIPV and MAb 6-4-2, clarifying the presence of neutrophil survival factors in the macrophage culture supernatant. It was suggested that: (1) FIPV-infected macrophages release TNF-alpha, GM-CSF, and G-CSF in response to virus replication, and (2) these cytokines act on neutrophils and prolong their survival. abstract: Feline infectious peritonitis (FIP) is a feline coronavirus (FCoV)-induced fatal disease of domestic and wild cats. The infiltration of neutrophils into granulomatous lesions is unusual for a viral disease, but it is a typical finding of FIP. This study aimed to investigate the reason for the lesions containing neutrophils in cats with FIP. Neutrophils of cats with FIP were cultured, and changes in the cell survival rate were assessed. In addition, the presence or absence of neutrophil survival factors was investigated in specimens collected from cats with FIP. Furthermore, it was investigated whether macrophages, one of the target cells of FIPV infection, produce neutrophil survival factors (TNF-alpha, GM-CSF, and G-CSF). We showed that virus-infected macrophages overproduce neutrophil survival factors, and these factors act on neutrophils and up-regulate their survival. These observations suggest that sustained production of neutrophil survival factors by macrophages during FCoV infection is sufficient for neutrophil survival and contributes to development of granulomatous lesions. url: https://doi.org/10.1007/s00705-009-0371-3 doi: 10.1007/s00705-009-0371-3 id: cord-276617-chgjpg0v author: Takano, Tomomi title: B-cell activation in cats with feline infectious peritonitis (FIP) by FIP-virus-induced B-cell differentiation/survival factors date: 2008-11-30 words: 3971.0 sentences: 216.0 pages: flesch: 50.0 cache: ./cache/cord-276617-chgjpg0v.txt txt: ./txt/cord-276617-chgjpg0v.txt summary: The present study shows that: (1) the ratio of peripheral blood sIg(+) CD21(−) B-cells was higher in cats with FIP than in SPF cats, (2) the albumin-to-globulin ratio has negative correlation with the ratio of peripheral blood sIg(+) CD21(−) B-cell, (3) cells strongly expressing mRNA of the plasma cell master gene, B-lymphocyte-induced maturation protein 1 (Blimp-1), were increased in peripheral blood in cats with FIP, (4) mRNA expression of B-cell differentiation/survival factors, IL-6, CD40 ligand, and B-cell-activating factor belonging to the tumor necrosis factor family (BAFF), was enhanced in macrophages in cats with FIP, and (5) mRNAs of these B-cell differentiation/survival factors were overexpressed in antibody-dependent enhancement (ADE)-induced macrophages. We also collected macrophages from FIP cats and measured the expression levels of the viral RNA and mRNA of B-cell differentiation/survival factors: IL-6, CD40 ligand (CD40L), and Bcell-activating factor belonging to the tumor necrosis factor family (BAFF). abstract: It has been suggested that antibody overproduction plays a role in the pathogenesis of feline infectious peritonitis (FIP). However, only a few studies on the B-cell activation mechanism after FIP virus (FIPV) infection have been reported. The present study shows that: (1) the ratio of peripheral blood sIg(+) CD21(−) B-cells was higher in cats with FIP than in SPF cats, (2) the albumin-to-globulin ratio has negative correlation with the ratio of peripheral blood sIg(+) CD21(−) B-cell, (3) cells strongly expressing mRNA of the plasma cell master gene, B-lymphocyte-induced maturation protein 1 (Blimp-1), were increased in peripheral blood in cats with FIP, (4) mRNA expression of B-cell differentiation/survival factors, IL-6, CD40 ligand, and B-cell-activating factor belonging to the tumor necrosis factor family (BAFF), was enhanced in macrophages in cats with FIP, and (5) mRNAs of these B-cell differentiation/survival factors were overexpressed in antibody-dependent enhancement (ADE)-induced macrophages. These data suggest that virus-infected macrophages overproduce B-cell differentiation/survival factors, and these factors act on B-cells and promote B-cell differentiation into plasma cells in FIPV-infected cats. url: https://doi.org/10.1007/s00705-008-0265-9 doi: 10.1007/s00705-008-0265-9 id: cord-282062-h9smg0w9 author: Takano, Tomomi title: Novel single-stranded, circular DNA virus identified in cats in Japan date: 2018-09-14 words: 1942.0 sentences: 124.0 pages: flesch: 56.0 cache: ./cache/cord-282062-h9smg0w9.txt txt: ./txt/cord-282062-h9smg0w9.txt summary: We detected a novel feline stool-associated circular DNA virus (FeSCV) in fecal samples from cats with diarrhea using consensus primers matching those of circovirus and cyclovirus. Feline cyclovirus was identified by next-generation sequencing analysis in which the viral gene was detected in a pooled fecal sample collected from 4-5 healthy cats. In this study, we performed nested PCR using Circoviridae family consensus primers and detected novel CRESS DNA viruses in several cats with diarrhea symptoms. However, we concluded that FeSCV is a circular DNA virus based on the following: 1) No Giardia intestinalis was detected in the fecal test, and 2) the complete genome of FeSCV was amplified using the rolling-circle amplification and inverse PCR assays. We detected a novel CRESS DNA virus, FeSCV, in fecal samples from cats. Although it was detected using consensus primers of circovirus and cyclovirus, FeSCV was phylogenetically positioned in a clade different from that of these viruses. abstract: We detected a novel feline stool-associated circular DNA virus (FeSCV) in fecal samples from cats with diarrhea using consensus primers matching those of circovirus and cyclovirus. FeSCV is a circular DNA virus containing a genome with a total length of 2,046 nt encoding 2 open reading frames. Phylogenetic analyses indicated that FeSCV is classified into a clade different from that of circovirus and cyclovirus. Since the FeSCVs detected in several cats in the same household had genetically similar genomes, these viruses are most likely derived from the same origin. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-018-4020-6) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-018-4020-6 doi: 10.1007/s00705-018-4020-6 id: cord-004798-5budstbg author: Takayama, N. title: An improved method for titration of mouse hepatitis virus type 3 in a mouse cell culture date: 1976 words: 924.0 sentences: 56.0 pages: flesch: 73.0 cache: ./cache/cord-004798-5budstbg.txt txt: ./txt/cord-004798-5budstbg.txt summary: Plaque assay in DBT cells with DEAE-dextran and trypsin presents a titration system for MHV3 as sensitive as the LD(50) assay in mice. In DBT cells overlaid with ME)/I containing 1 per cent Noble agar, 5 per cent CS, 10 per cent TPB, and 1 : 10,000 neutral red, MHV3-plaques of 0.6--1.4 mm (mean value = 0.9 ram) in diameter could be counted at 40 hours p.i. The plaques were clearly-defined and sometimes contained a deeply-stained area at their center. To ira.prove the sensitivity of the plaque assay we examined the effect of diethylaminoethyl-dextran (DEAE-D) on the plaque formation and plaque diameter of MHV3, as BRADBUllNE and TYRREL]5 had reported that DEAE-D added to overlay agar increased the plaque number of human coronavirus (2). 1%eplication and plaque formation of mouse hepatitis virus (MttV-2) in mouse cell line DBT culture abstract: Plaque assay in DBT cells with DEAE-dextran and trypsin presents a titration system for MHV3 as sensitive as the LD(50) assay in mice. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087043/ doi: 10.1007/bf01315624 id: cord-269948-zfbu9646 author: Teo, Jeanette title: VereFlu™: an integrated multiplex RT-PCR and microarray assay for rapid detection and identification of human influenza A and B viruses using lab-on-chip technology date: 2011-04-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Threatening sporadic outbreaks of avian influenza and the H1N1 pandemic of 2009 highlight the need for rapid and accurate detection and typing of influenza viruses. In this paper, we describe the validation of the VereFlu™ Lab-on-Chip Influenza Assay, which is based on the integration of two technologies: multiplex reverse transcription (RT)-PCR followed by microarray amplicon detection. This assay simultaneously detects five influenza virus subtypes, including the 2009 pandemic influenza A (H1N1), seasonal H1N1, H3N2, H5N1 and influenza B virus. The VereFlu™ assay was clinically validated in Singapore and compared against reference methods of real-time PCR, virus detection by immunofluorescence of cell cultures and sequencing. A sensitivity and specificity of 96.8% and 92.8%, respectively, was demonstrated for pandemic H1N1; 95.7% and 100%, respectively, for seasonal H1N1; 91.2% and 97.6%, respectively, for seasonal H3N2; 95.2% and 100%, respectively, for influenza B. Additional evaluations carried out at the World Health Organization (WHO) Collaborating Centre, Melbourne, Australia, confirmed that the test was able to reliably detect H5N1. This portable, fast time-to-answer (3 hours) device is particularly suited for diagnostic applications of detection, differentiation and identification of human influenza virus subtypes. url: https://doi.org/10.1007/s00705-011-0999-7 doi: 10.1007/s00705-011-0999-7 id: cord-004766-gvom0f13 author: Traavik, T. title: Improvement of arbovirus HA antigens by treatment with a colloidal silica gel and sonication date: 1977 words: 2232.0 sentences: 167.0 pages: flesch: 62.0 cache: ./cache/cord-004766-gvom0f13.txt txt: ./txt/cord-004766-gvom0f13.txt summary: A remarkable increase in HA titers for weakly haemagglutinating Norwegian arbovirus strains, Uukuniemi and Runde viruses, was achieved by including treatment with the colloidal silica gel Aerosil in the antigen preparation scheme. Good antigens also were obtained from virus grown in BHK 21/c 13 cell cultures and concentrated by polyethylene glycol 6000/NaCl. Rubella virus HA antigen and HB(s)Ag were adsorbed to the gel, and excluded from a preparation by treatment with Aerosil. For production of arbovirus haemagglutinating (HA) antigens, the classical sucrose-aeeton extraction method (SA) (3) with infected suckling mouse brains has been almost undisputed, although methods based on infected cell culture fluids (2, 12) and infected mouse aseites fluids (8) have also been reported. Infected brain suspensions and PEG treated cell culture concentrates were titrated by intraeerebral inoculation in suckling mice after Aerosil absorption, incubation with shaking in waterbath at 45 ° C and untreated. Simple method for preparation of haemagglutinating arbo-A virus antigens from brains of suckling mice abstract: A remarkable increase in HA titers for weakly haemagglutinating Norwegian arbovirus strains, Uukuniemi and Runde viruses, was achieved by including treatment with the colloidal silica gel Aerosil in the antigen preparation scheme. By combining this procedure with sonication, the titers of sucrose-aceton extracted, infected suckling mouse brains could be increased several hundred times. Good antigens also were obtained from virus grown in BHK 21/c 13 cell cultures and concentrated by polyethylene glycol 6000/NaCl. Rubella virus HA antigen and HB(s)Ag were adsorbed to the gel, and excluded from a preparation by treatment with Aerosil. This indicates a limitation to the universal use of the method, presumably related to the particle size. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086912/ doi: 10.1007/bf01314788 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-298883-uiwg482s author: Truong, C. title: Identification of an immunorelevant ORF2 epitope from porcine circovirus type 2 as a serological marker for experimental and natural infection date: 2001 words: 4158.0 sentences: 216.0 pages: flesch: 51.0 cache: ./cache/cord-298883-uiwg482s.txt txt: ./txt/cord-298883-uiwg482s.txt summary: Post-weaning multisystemic wasting syndrome (PMWS) is a recently identified disease of pigs linked to the emergence of a new porcine circovirus (PCV2). We report here the characterization of immunorelevant linear B-cell epitopes of the Open Reading Frame 2-encoded protein (Orf2) from PCV2 by an enzyme-linked immunosorbent assay (ELISA) using experimental antisera collected from pigs inoculated with a PCV2 isolate. Antibodies to the 117 to 131 epitope (B-133) were detected in 22% and 100% of specific pathogen-free (SPF) pig sera 6 and 11 weeks post inoculation, respectively. Here, we describe the characterization of an Orf2 peptide as an immunorelevant PCV2 specific linear B-cell epitope by ELISA, using sera from pigs experimentally inoculated with a PCV2 isolate, and its potential use as a serological marker to detect PCV2 antibodies following natural infection in swine herds. abstract: Post-weaning multisystemic wasting syndrome (PMWS) is a recently identified disease of pigs linked to the emergence of a new porcine circovirus (PCV2). We report here the characterization of immunorelevant linear B-cell epitopes of the Open Reading Frame 2-encoded protein (Orf2) from PCV2 by an enzyme-linked immunosorbent assay (ELISA) using experimental antisera collected from pigs inoculated with a PCV2 isolate. Two epitopes spanning residues 69 to 83 and 117 to 131 were specific to PCV2. Antibodies to the 117 to 131 epitope (B-133) were detected in 22% and 100% of specific pathogen-free (SPF) pig sera 6 and 11 weeks post inoculation, respectively. Cross-sectional studies performed with field sera collected from PMWS-affected herds showed B-133 antibodies in 5% of 8 to 10 week-old pigs, 38% of 13–14 week-old pigs, 62% of 16 to 19 week-old pigs, 56% of 20 to 25 week-old pigs and 45% of 26 to 31 week-old pigs. All these data suggest that epitope B-133 is a serological marker of PCV2 infection that could be used for the detection of PCV2 antibody response. url: https://www.ncbi.nlm.nih.gov/pubmed/11504425/ doi: 10.1007/s007050170115 id: cord-285329-62yafd2d author: Tsunemitsu, H. title: Antigenic and biological comparisons of bovine coronaviruses derived from neonatal calf diarrhea and winter dysentery of adult cattle date: 1995 words: 2453.0 sentences: 126.0 pages: flesch: 55.0 cache: ./cache/cord-285329-62yafd2d.txt txt: ./txt/cord-285329-62yafd2d.txt summary: The antigenic and biological properties of 6 strains of bovine coronavirus (BCV) derived from neonatal calf diarrhea (CD) and 8 strains of BCV from winter dysentery (WD) of adult cattle, propagated in HRT-18 cells, were compared to determine if CD and WD strains belong to distinct serotypes or subtypes of BCV. However, in virus neutralization tests, antisera to 1 CD and 2 WD strains had 16-fold or lower antibody titers against 3 WD and 1 CD strains than against the homologous strains, and this variation reflected low antigenic relatedness values (R=13–25%), suggesting the presence of different subtypes among BCV. Receptor-destroying enzyme activity with mouse erythrocytes was not UExpressed as the reciprocal of the highest dilution of virus causing complete disappearance of HA patterns at 4 °C after 2 h incubation at 37 °C ° CD Calf diarrhea, WD winter dysentery of adult cattle dM/C Ratio of HA titer with mouse erythrocytes to HA titer with chicken erythrocytes detected for any strain of BCV. abstract: The antigenic and biological properties of 6 strains of bovine coronavirus (BCV) derived from neonatal calf diarrhea (CD) and 8 strains of BCV from winter dysentery (WD) of adult cattle, propagated in HRT-18 cells, were compared to determine if CD and WD strains belong to distinct serotypes or subtypes of BCV. All strains hemagglutinated both mouse and chicken erythrocytes at 4 °C, but the ratios of hemagglutination titers with mouse erythrocytes compared to chicken erythrocytes showed diversity for both CD and WD strains. Some CD and WD strains did not hemagglutinate chicken erythrocytes at 37 °C and showed receptor-destroying enzyme activity against chicken erythrocytes. Hyperimmune antisera were produced in guinea pigs against 3 and 7 strains of BCV from CD and WD, respectively. No significant differences in antibody titers against these strains were observed by indirect immunofluorescence tests. However, in virus neutralization tests, antisera to 1 CD and 2 WD strains had 16-fold or lower antibody titers against 3 WD and 1 CD strains than against the homologous strains, and this variation reflected low antigenic relatedness values (R=13–25%), suggesting the presence of different subtypes among BCV. In hemagglutination inhibition tests, some one-way antigenic variations among strains were also observed. These results suggest that some antigenic and biological diversity exists among BCV strains, but these variations were unrelated to the clinical source of the strains; i.e. CD or WD. url: https://www.ncbi.nlm.nih.gov/pubmed/7646362/ doi: 10.1007/bf01322757 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-004685-qote5nx2 author: Vassão, R. C. title: A genetic analysis of macrophage activation and specific antibodies in relation to the resistance of heterogeneous mouse populations to MHV3 infection date: 1994 words: 2352.0 sentences: 113.0 pages: flesch: 42.0 cache: ./cache/cord-004685-qote5nx2.txt txt: ./txt/cord-004685-qote5nx2.txt summary: The data indicate, among the mechanisms of resistance against the virus infection, a role of IFN gamma macrophage-activation and of antibodies against MHV3 which may delay the mean survival time in susceptible animals. The virus replication in target cells, the antiviral state induced by interferon (IFN) and the expression of a monokine with procoagulant activity (PCA) have been implicated in the resistance/susceptibility of the genetic homogeneous or heterogeneous mouse populations to the MHV3 infection [t, 2, 4, 7, 17, 18, 23, 243 . For the study of the individual correlation between in vivo resistance and in vitro inhibition of virus replication by IFN gamma, peritoneal macrophages from Hm, Lm and F 2 segregants were collected without sacrificing the animals, which were infected with MHV3 a week later. This brings further support to our previous suggestion that one of the main mechanisms involved in the resistance of mice to the MHV3 infection is based on the ability of their macrophages to restrict the virus replication upon IFN gamma activation [10 13, 153 . abstract: The genetically selected high antibody responder mice (H(III)) are susceptible and the low antibody responder mice (L(III)) are resistant to the experimental infection with Mouse Hepatitis Virus 3 (MHV3). The mortality rates of the F(1) hybrids and of the F(2) segregants showed the codominance of the susceptible and resistant characters. The direct individual intrapopulation correlation between the induction of antiviral state in macrophages activated by IFN gamma and the resistance to the virus infection, showed that an antiviral state could be induced in resistant mouse macrophages, whereas in susceptible mouse macrophages no restriction of virus replication could be observed. A direct inter- and intrapopulation correlation of pre-existing antibody titres against MHV3 with the mortality and a direct interpopulation correlation of those titres with the mean survival time of susceptible animals was shown. The data indicate, among the mechanisms of resistance against the virus infection, a role of IFN gamma macrophage-activation and of antibodies against MHV3 which may delay the mean survival time in susceptible animals. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086603/ doi: 10.1007/bf01310802 id: cord-338607-22f04uqe author: Verbeek, A. title: Genomic relationship between turkey and bovine enteric coronaviruses identified by hybridization with BCV or TCV specific cDNA probes date: 1991 words: 4120.0 sentences: 192.0 pages: flesch: 47.0 cache: ./cache/cord-338607-22f04uqe.txt txt: ./txt/cord-338607-22f04uqe.txt summary: title: Genomic relationship between turkey and bovine enteric coronaviruses identified by hybridization with BCV or TCV specific cDNA probes Genomic relationships between turkey and bovine coronavirus (TCV and BCV), which are currently placed in distinct antigenic groups, were demonstrated by hybridization using specific cDNA probes. BCV-specific recombinant plasmids p 52, p 27, and p 247, which served previously for the optimization of hybridization conditions for BCV-RNA detection [33] , and probes pN 17 and pN 9, holding respectively the BCV N and M gene ( Fig. 1) , were used in the detection of several coronaviruses in order to establish the presence of potential genomic homologies. Clinical diagnosis of TCV was assayed with a pool of six 32p-labelled BCV specific recombinant plasmids (pBCV-pool), holding non-overlapping eDNA sequences, in order to amplify the detection signal. Detection signals were absent when testing spotted supernatant fluids of non-infected HRT-18 cells (Fig. 2) and when probing identical blots with 32p-labelled pUC-DNA (not shown), confirming the specificity of the hybridization signals obtained. abstract: Genomic relationships between turkey and bovine coronavirus (TCV and BCV), which are currently placed in distinct antigenic groups, were demonstrated by hybridization using specific cDNA probes. BCV-specific recombinant plasmid probes p 52, p 27, and p 247, holding inserts derived from (probably nonstructural) genes, and plasmids pN 17 and pN 9 holding the N and M gene, respectively, permitted the detection of isolates of both BCV and TCV with similar sensitivities. Similarly, probing supernatants of cell cultures infected with several isolates of TCV, using probes pN 17 and pM 78, respectively holding the N gene of BCV and TCV, resulted in equally intense detection signals. Only a slight detection of MHV-3, which is antigenically related to BCV, was observed, whereas the probes did not allow the detection of IBV, TGEV, and HCV-229E, which are placed in antigenic groups separate from those of BCV and TCV. Detection of TCV was improved by hybridization with BCV-specific single-stranded (ss) probes holding sequences of the N and M genes and synthesized by the polymerase chain reaction. Diagnosis of TCV in 134 clinical samples by hybridization was better with PCR-produced ss BCV-specific probes than with ds PCR-produced probes or a combination of six recombinant plasmid probes holding non-overlapping BCV-specific cDNA sequences. Detection signals were absent when probing clinical samples with(32)P-labelled pUC-DNA. url: https://www.ncbi.nlm.nih.gov/pubmed/1662038/ doi: 10.1007/bf01316754 id: cord-289926-y1rjgbui author: Veretnik, S. title: RNA binding domain of HDV antigen is homologous to the HMG box of SRY date: 2014-05-18 words: 6679.0 sentences: 309.0 pages: flesch: 53.0 cache: ./cache/cord-289926-y1rjgbui.txt txt: ./txt/cord-289926-y1rjgbui.txt summary: Using sequence analysis methods we have discovered significant sequence similarity between this central domain of HDAg and the HMG (High Mobility Group) box of the SRY gene [40] , whose product binds to DNA and is essential for sex determination. The sequence similarity between the central domain of HDAg and the HMG (High Mobility Group) box of the SRY gene suggests that SRY may be a cellular cognate of HDAg. Another candidate for the ''captured'' cellular RNA was recently proposed: a 202 residue cellular protein referred to as DIPA (delta interacting protein A) was identified by co-immunoprecipitation with HDAg and by its in vivo ability to inhibit viral replication [5] . Statistically significant sequence similarities are limited to the functionally essential regions of both genes: in the SRY gene the similarity is confined to the HMG (High Mobility Group) box, a DNA binding motif found in the HMG protein superfamily [24, 31] , in HDAg the similarity is limited to RNA-binding domain. abstract: The delta antigen of hepatitis delta virus exhibits sequence specific binding to its own RNA and is essential for viral replication. Using statistical methods we have detected significant similarity between the RNA-binding domain of the hepatitis delta antigen and the HMG box of SRY. Our analysis suggests that the RNA-binding domain of HDV antigen evolved from the DNA-binding domain of the HMG box. SRY, or a related protein, is a probable cellular cognate of HDV. url: https://www.ncbi.nlm.nih.gov/pubmed/10446649/ doi: 10.1007/s007050050575 id: cord-004681-02wem2u3 author: Wada, R. title: Ultrastructure and immuno-cytochemistry of BHK-21 cells infected with a modified Bucyrus strain of equine arteritis virus date: 1995 words: 2044.0 sentences: 123.0 pages: flesch: 55.0 cache: ./cache/cord-004681-02wem2u3.txt txt: ./txt/cord-004681-02wem2u3.txt summary: title: Ultrastructure and immuno-cytochemistry of BHK-21 cells infected with a modified Bucyrus strain of equine arteritis virus Morphogenesis of a modified Bucyrus strain of equine arteritis virus (EAV) in BHK-21 cells was studied. Bacillary tubules were first detected in the cytoplasm 8 h after infection, and mature virions 79 to 122 nm in diameter, 101 nm on average, were mostly observed in the cisternae of the rough endoplasmic reticulum (RER) at 12 h or later. Equine arteritis virus (EAV) has been classified into the Togaviridae family [22] on the basis of the virion size and morphology [23] . In the present study a mutant virus showing higher growth on BHK-21 cells than the parental Bucyrus strain of EAV [11] was examined for the fine structure, its morphogenesis and intracellular localization of viral antigen. Through cross-sections of the outer layer of the virion, a grape-like structure seemed to be subunits 13 to 20 nm in diameter around the core (Fig. 3c) . abstract: Morphogenesis of a modified Bucyrus strain of equine arteritis virus (EAV) in BHK-21 cells was studied. Bacillary tubules were first detected in the cytoplasm 8 h after infection, and mature virions 79 to 122 nm in diameter, 101 nm on average, were mostly observed in the cisternae of the rough endoplasmic reticulum (RER) at 12 h or later. They had isometrical cores and morphological subunits in the outer layer. Budding occurred from the RER and the outer nuclear membrane, but not from the cell surface. Structural linkage was detected between the tubule and the virus core. Aberrant strands were occasionally demonstrated within the nucleus 12 h after infection, and immunofluorescence and immunogold labeling revealed viral antigen also in the nucleus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086595/ doi: 10.1007/bf01322744 id: cord-266716-pghnl980 author: Wang, Hai-Ming title: Isobavachalcone inhibits post-entry stages of the porcine reproductive and respiratory syndrome virus life cycle date: 2018-02-06 words: 3385.0 sentences: 170.0 pages: flesch: 48.0 cache: ./cache/cord-266716-pghnl980.txt txt: ./txt/cord-266716-pghnl980.txt summary: title: Isobavachalcone inhibits post-entry stages of the porcine reproductive and respiratory syndrome virus life cycle Since the first report of a porcine reproductive and respiratory syndrome (PRRS) outbreak, tremendous efforts to control this disease, including various national policies and plans incorporating the use of multiple modified live-virus vaccines, have been made. Western blot analysis revealed that PRRSV N protein levels decreased markedly, indicating that increasing concentrations of IBC significantly inhibited PRRSV replication (Fig. 1F) . The in vitro study established that IBC efficiently inhibited the replication of both HP-PRRSV and the current Chinese epidemic NADC30-like strains without significant drug toxicity. Role of phosphatidylinositol 3-kinase (PI3K) and Akt1 kinase in porcine reproductive and respiratory syndrome virus (PRRSV) replication Pathogenicity and antigenicity of a novel NADC30-like strain of porcine reproductive and respiratory syndrome virus emerged in China NADC30-like strain of porcine reproductive and respiratory syndrome virus abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) is a pathogen of great economic significance that impacts the swine industry globally. Since the first report of a porcine reproductive and respiratory syndrome (PRRS) outbreak, tremendous efforts to control this disease, including various national policies and plans incorporating the use of multiple modified live-virus vaccines, have been made. However, PRRSV is still a significant threat to the swine industry, and new variants continually emerge as a result of PRRSV evolution. Several studies have shown that pandemic PRRSV strains have enormous genetic diversity and that commercial vaccines can only provide partial protection against these strains. Therefore, effective anti-PRRSV drugs may be more suitable and reliable for PRRSV control. In this study, we observed that isobavachalcone (IBC), which was first isolated from Psoralea corylifolia, had potent anti-PRRSV activity in vitro. Although many biological activities of IBC have been reported, this is the first report describing the antiviral activity of IBC. Furthermore, after a systematic investigation, we demonstrated that IBC inhibits PRRSV replication at the post-entry stage of PRRSV infection. Thus, IBC may be a candidate for further evaluation as a therapeutic agent against PRRSV infection of swine in vivo. url: https://www.ncbi.nlm.nih.gov/pubmed/29411137/ doi: 10.1007/s00705-018-3755-4 id: cord-302323-vvo8a4hp author: Wang, Xiaobo title: Immunogenicity and antigenic relationships among spike proteins of porcine epidemic diarrhea virus subtypes G1 and G2 date: 2015-11-26 words: 4988.0 sentences: 231.0 pages: flesch: 53.0 cache: ./cache/cord-302323-vvo8a4hp.txt txt: ./txt/cord-302323-vvo8a4hp.txt summary: To determine whether these mutations lead to changes in antigenicity, as suggested by the failure of PEDV vaccines in China, we first optimized the codons of typical S genes of the CV777 vaccine strain (G1 subtype) and LNCT2 strain (G2 subtype) and expressed the recombinant full-length sequence of the S protein in a eukaryotic expression system. The findings of this study confirmed that the recombinant S protein was highly immunogenic in Cross serum neutralization (SN) between the S proteins of the two PEDV subtypes and anti-S PAbs. Reciprocals of PEDV neutralizing antibody titers were expressed as the dilution inhibiting PEDV infection by 50 %, which was calculated as follows: Log50 % neutralizing titer = L-d (s-0.5), where L is the log of the lowest dilution factor, d is the difference between the dilution factors, and s is the sum of the ratios of positive wells Variation between porcine epidemic diarrhea virus subtypes 545 mice and could effectively induce production of antibodies, especially neutralizing antibodies. abstract: Porcine epidemic diarrhea virus (PEDV) is a coronavirus that infects cells lining the small intestine of swine, resulting in vomiting, diarrhea, and dehydration. The amino acid sequence of the spike (S) protein, which is the principal target recognized by host immune cells, has multiple mutations that distinguish the two PEDV genotypes, G1 and G2. To determine whether these mutations lead to changes in antigenicity, as suggested by the failure of PEDV vaccines in China, we first optimized the codons of typical S genes of the CV777 vaccine strain (G1 subtype) and LNCT2 strain (G2 subtype) and expressed the recombinant full-length sequence of the S protein in a eukaryotic expression system. The IgG antibody levels of serum from mice immunized with purified S protein were markedly high. Antigenicity was compared by detection of polyclonal antibodies (PAbs) against the virus and S protein using an enzyme-linked immunosorbent assay (ELISA), an indirect immunofluorescence assay (IFA), and a serum cross-neutralization (SN) assay. Reactivity with the PAbs revealed significant cross-reactivity between the two PEDV subtypes, although there was a twofold difference in the antigenic responses based on PAb titers in the ELISA and IFA. Consistent with the variation in the S gene sequences, the SN titer suggested differences in the neutralization activity of the S protein between the two subtypes, which could explain the antigenic variation between the PEDV subtypes G1 and G2. url: https://www.ncbi.nlm.nih.gov/pubmed/26611909/ doi: 10.1007/s00705-015-2694-6 id: cord-345940-adg264vb author: Wanitchang, Asawin title: Characterization of influenza A virus pseudotyped with the spike protein of porcine epidemic diarrhea virus date: 2018-08-22 words: 5030.0 sentences: 262.0 pages: flesch: 54.0 cache: ./cache/cord-345940-adg264vb.txt txt: ./txt/cord-345940-adg264vb.txt summary: In this study, we constructed scIAV-S, a single-cycle influenza A virus pseudotyped with the spike protein of porcine epidemic diarrhea virus (PEDV), and demonstrated that this virus could infect cultured cells and trigger massive syncytium formation. It should also be noted that control supernatants from HEK293T cells transfected with pCAGGS expressing S AVCT12 alone did not yield detectable syncytium formation in VeroE6-APN cells, suggesting that the detected syncytia were not due to PEDV-S expressed from residual plasmids (data not shown). To further test whether the mCherry expression in infected cells required active influenza A virus polymerase activity, we attempted to construct scIAV-S AVCT12 by omitting the plasmid encoding the PB2 polymerase and examined its infectivity in VeroE6-APN cells. Likewise, VeroE6-APN cells treated with NH 4 Cl (50 mM for 2 h) to neutralize the intracellular pH also displayed strong mCherry expression and extensive syncytium formation when infected with scIAV-S AVCT12 (Fig. 3A) . abstract: The coronavirus spike protein and the influenza virus hemagglutinin are class I viral membrane fusion proteins. While the two proteins display strong structural conservation and the mechanisms underlying membrane fusion are similar, they share no sequence similarity. Whether they are functionally interchangeable is currently unknown. In this study, we constructed scIAV-S, a single-cycle influenza A virus pseudotyped with the spike protein of porcine epidemic diarrhea virus (PEDV), and demonstrated that this virus could infect cultured cells and trigger massive syncytium formation. Treatment with endocytosis inhibitors did not affect syncytium formation by infected cells. Moreover, the infectivity of scIAV-S was associated with the degree of cell adaptation of PEDV-S. Intriguingly, scIAV-S lacking functional neuraminidase (NA) exhibited substantially higher infectivity, suggesting a pivotal role of the sialic acid in the binding/entry of PEDV. Together, scIAV-S offers a robust platform for the investigation of the entry mechanism of PEDV or, possibly, of other coronaviruses. url: https://doi.org/10.1007/s00705-018-4001-9 doi: 10.1007/s00705-018-4001-9 id: cord-283525-kvcqayl4 author: Wei, Zhan-Yong title: Nitric oxide inhibits the replication cycle of porcine parvovirus in vitro date: 2009-05-13 words: 2366.0 sentences: 124.0 pages: flesch: 51.0 cache: ./cache/cord-283525-kvcqayl4.txt txt: ./txt/cord-283525-kvcqayl4.txt summary: This study investigated the inhibitory effect and mechanism of nitric oxide (NO) on porcine parvovirus (PPV) replication in PK-15 cells. The results showed that two NO-generating compounds, S-nitroso-l-acetylpenicillamine (SNAP) and l-arginine (LA), at a noncytotoxic concentration could reduce PPV replication in a dose-dependent manner and that this anti-PPV effect could be reversed by the NO synthase (NOS) inhibitor N-nitro-l-arginine methyl ester (l-NAME). As shown in Fig. 1a , SNAP and LA have the ability to inhibit PPV replication in PK-15 cells, and there is a dose-dependent relationship between the inhibitory effect and the SNAP (or LA) concentration. As shown in Fig. 2 , the PFU value increased with later addition of SNAP (or LA), and adding SNAP (or LA) 6 or 3 h prior to viral infection resulted in the highest level of inhibition. Our results demonstrate that NO specially inhibits the PPV replication cycle during the step of viral protein synthesis (Fig. 3b) . abstract: This study investigated the inhibitory effect and mechanism of nitric oxide (NO) on porcine parvovirus (PPV) replication in PK-15 cells. The results showed that two NO-generating compounds, S-nitroso-l-acetylpenicillamine (SNAP) and l-arginine (LA), at a noncytotoxic concentration could reduce PPV replication in a dose-dependent manner and that this anti-PPV effect could be reversed by the NO synthase (NOS) inhibitor N-nitro-l-arginine methyl ester (l-NAME). By assaying the steps of the PPV life cycle, we also show that NO inhibits viral DNA and protein synthesis. This experiment provides a frame of reference for the study of the anti-viral mechanism of NO. url: https://www.ncbi.nlm.nih.gov/pubmed/19437101/ doi: 10.1007/s00705-009-0392-y 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-004755-rmnjs1t6 author: Welch, Siao-Kun Wan title: Monoclonal antibodies to a virulent strain of transmissible gastroenteritis virus: comparison of reactivity with virulent and attenuated virus date: 1988 words: 4962.0 sentences: 283.0 pages: flesch: 56.0 cache: ./cache/cord-004755-rmnjs1t6.txt txt: ./txt/cord-004755-rmnjs1t6.txt summary: Twelve hybridomas secreting monoclonal antibodies (MAbs) against Miller virulent strain of transmissible gastroenteritis virus (TGEV) were generated and characterized. Two E 2-specific MAbs had higher neutralizing antibody titers (782 to 34,117) and showed 4-to 13-fold differences in titers against the attenuated and virulent TGEV strains. Two E 2-specific MAbs had higher neutralizing antibody titers (782 to 34,117) and showed 4-to 13-fold differences in titers against the attenuated and virulent TGEV strains. In two previous studies, monoclonal antibodies (MAbs) to the structural proteins of the attenuated (Purdue) strain of TGEV were described [9, 12] . These MAbs were further characterized in various comparative assays including cell culture immunofluorescence, virus neutralization, and radioimmunoprecipitation for reactivity against the Miller virulent and Purdue attenuated strains of TGEV. Anti-E 1 MAbs prepared against a mixture of virulent Miller 3 and Purdue attenuated strains of TGEV had virus neutralizing antibody titers only in the presence of guinea pig, rabbit or swine complement [22] . abstract: Twelve hybridomas secreting monoclonal antibodies (MAbs) against Miller virulent strain of transmissible gastroenteritis virus (TGEV) were generated and characterized. In a cell culture immunofluorescence (CCIF) assay, three MAbs directed against peplomer protein (E 2) had perinuclear fluorescence and four unclassified MAbs showed cell membrane fluorescence. Six of these seven MAbs neutralized both attenuated and virulent TGEV, and the seventh (an unclassified MAb) neutralized only the latter virus. Two MAbs able to bind the cell membrane of infected cells had low neutralizing antibody titers (8 to 72) but were able to distinguish between virulent and attenuated TGEV (9- to 72-fold differences in neutralizing titers). Two E 2-specific MAbs had higher neutralizing antibody titers (782 to 34,117) and showed 4- to 13-fold differences in titers against the attenuated and virulent TGEV strains. Five MAbs which were specific for nucleocapsid (N) protein had cytoplasmic, particulate fluorescence in CCIF, and did not neutralize TGEV. Comparison of CCIF antibody titers of MAbs to the virulent and attenuated strains of TGEV indicated that differences existed in titers of most E 2 and all N-specific MAbs, with titers consistently higher against virulent TGEV (homologous strain). Hyperimmune antisera prepared in gnotobiotic pigs against the attenuated, virulent and a recent isolate of TGEV immunoprecipitated the 3 major structural proteins of both the attenuated and virulent TGEV strains. Relative mol. wt. differences in the E 1 and E 2 proteins between the two virus strains were revealed using either the hyperimmune pig sera or MAbs. In addition to the 48 K N protein, a 44 K protein was coimmunoprecipitated by the hyperimmune sera and MAbs, but mainly from lysates of attenuated TGEV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086875/ doi: 10.1007/bf01311003 id: cord-283710-55m16q7c author: Wo, Ying title: Epidemical features of HAdV-3 and HAdV-7 in pediatric pneumonia in Chongqing, China date: 2014-12-12 words: 2891.0 sentences: 145.0 pages: flesch: 45.0 cache: ./cache/cord-283710-55m16q7c.txt txt: ./txt/cord-283710-55m16q7c.txt summary: Multivariate analysis showed that single infections with HAdV-7 were associated with a higher prevalence of severe pneumonia. There is therefore a need for continuous surveillance, with extensive molecular characterization, to determine the prevalence and genetic characteristics of the circulating HAdVs. The current study was performed to identify the predominant HAdV types associated with pediatric pneumonia and to trace the new genetic variants that might be derived from recombination of different types. However, HAdV infection was associated with more-severe pneumonia and more frequent transfer to the intensive care unit in comparison with HAdV-negative patients (P \ 0.001 and P = 0.027, respectively) ( Table 1) . These findings have the clinical implication that in patients with severe pneumonia, the contribution of HAdV, especially HAdV-7, should be considered with high priority, regardless of whether another respiratory pathogen has been detected. Identification and typing of adenovirus from acute respiratory infections in pediatric patients in Beijing from abstract: Human adenoviruses (HAdV) of species B, C, and E (HAdV-B, -C, -E) are frequent causative agents of acute respiratory infections worldwide. No specific analysis has been done on the epidemiological and clinical features of HAdV in pediatric pneumonia in China. Nasopharyngeal aspirates were collected from hospitalized children with pneumonia from June 2009 to May 2014. All samples that tested positive for HAdV were typed by sequencing the hexon and fiber genes. From a total of 3089 samples, 208 (6.7 %) were positive for HAdV, identified as belonging to HAdV-B (186, 89.4 %), HAdV-C (9, 4.3 %) and HAdV-E (1, 0.5 %). HAdV-7 (104, 50.0 %) and HAdV-3 (78, 37.5 %) were the two major types, followed by HAdV-1, HAdV-55 and HAdV-14. There were 87 (41.8 %) single HAdV infections, of which 80 % were HAdV-7 infections. Multivariate analysis showed that single infections with HAdV-7 were associated with a higher prevalence of severe pneumonia. Temporal patterns showed that, except for a simultaneous outbreak of HAdV-3 and HAdV-7 during the years 2010–2011, HAdV-7 and HAdV-3 were alternately predominant, and the dominance shifted to HAdV-3 after 2014. Identification of the predominant HAdV genotypes and their epidemical features is useful for determining preventive strategies. HAdV-7 associated severe pneumonia needs to be considered with high priority in clinical practice. url: https://www.ncbi.nlm.nih.gov/pubmed/25504360/ doi: 10.1007/s00705-014-2308-8 id: cord-290819-zhywlf6r author: Wu, Jiaqi title: The antiviral protein viperin interacts with the viral N protein to inhibit proliferation of porcine epidemic diarrhea virus date: 2020-07-27 words: 4550.0 sentences: 249.0 pages: flesch: 44.0 cache: ./cache/cord-290819-zhywlf6r.txt txt: ./txt/cord-290819-zhywlf6r.txt summary: title: The antiviral protein viperin interacts with the viral N protein to inhibit proliferation of porcine epidemic diarrhea virus In the early stage of virus infection, the pattern recognition receptor (PRR) signaling pathway of the host cell is activated to induce interferon production, activating interferon-stimulated genes (ISGs) that encode antiviral proteins that exert antiviral effects. Increased expression of interferon and viperin and decreased replication of PEDV with a clear reduction in the viral load were observed in PEDV-infected IPEC-J2 cells. After virus infection, pattern recognition receptors recognize released viral nucleic acids and activate downstream signaling pathways to promote the production of specific transcription factors and type I interferons [25] . These results indicate that PEDV infection upregulates the expression of interferon and viperin in IPEC-J2 cells. This study showed that the expression of type I interferon increases and that of viperin is also upregulated in IPEC-J2 cells infected with PEDV. abstract: In the early stage of virus infection, the pattern recognition receptor (PRR) signaling pathway of the host cell is activated to induce interferon production, activating interferon-stimulated genes (ISGs) that encode antiviral proteins that exert antiviral effects. Viperin is one of the innate antiviral proteins that exert broad-spectrum antiviral effects by various mechanisms. Porcine epidemic diarrhea virus (PEDV) is a coronavirus that causes huge losses to the pig industry. Research on early antiviral responses in the gastrointestinal tract is essential for developing strategies to prevent the spread of PEDV. In this study, we investigated the mechanisms of viperin in PEDV-infected IPEJ-C2 cells. Increased expression of interferon and viperin and decreased replication of PEDV with a clear reduction in the viral load were observed in PEDV-infected IPEC-J2 cells. Amino acids 1–50 of porcine viperin contain an endoplasmic reticulum signal sequence that allows viperin to be anchored to the endoplasmic reticulum and are necessary for its function in inhibiting PEDV proliferation. The interaction of the viperin S-adenosylmethionine domain with the N protein of PEDV was confirmed via confocal laser scanning microscopy and co-immunoprecipitation. This interaction might interfere with viral replication or assembly to reduce virus proliferation. Our results highlight a potential mechanism whereby viperin is able to inhibit PEDV replication and play an antiviral role in innate immunity. url: https://www.ncbi.nlm.nih.gov/pubmed/32719955/ doi: 10.1007/s00705-020-04747-8 id: cord-026518-xv03vpji author: Xie, Peng title: Immune effect of a Newcastle disease virus DNA vaccine with IL-12 as a molecular adjuvant delivered by electroporation date: 2020-06-09 words: 5771.0 sentences: 280.0 pages: flesch: 52.0 cache: ./cache/cord-026518-xv03vpji.txt txt: ./txt/cord-026518-xv03vpji.txt summary: An additional 52 14-day-old SPF chickens were randomly divided into four equal groups (N = 13) to investigate the effect of chIL-12 used as an adjuvant to the F gene DNA vaccine. Two weeks after booster vaccination, the birds were challenged with NDV and mortality for 14 days was evaluated the two delivery methods might induce different immune responses in chickens. Oladele and colleagues constructed a DNA vaccine based on the HA gene of H5N1 avian influenza virus and found that EP delivery could enhance the antibody response, significantly reduce morbidity, and protect chickens from fatal NDV attack [25] . However, although all of the chickens in the pCAG-F/EP group survived, they did not all have detectable neutralizing antibodies, indicating that antibodies may not be essential for protection and that cell mediated immunity might play an important role in plasmid DNA-induced protection against NDV challenge. abstract: Newcastle disease (ND), caused by virulent Newcastle disease virus (NDV) strains, has been one of the most problematic diseases affecting the poultry industry worldwide. Conventional vaccines provide effective protection for birds to survive ND outbreaks, but they may not completely suppress NDV shedding. NDV strains circulate on farms for a long time after the initial infection and cause potential risks. A new vaccine with fast clearance ability and low viral shedding is needed. In this study, we used interleukin-12 (IL-12) as an adjuvant and electroporation (EP) as an advanced delivery system to improve a DNA vaccine candidate. The fusion (F) protein gene from an NDV strain of the prevalent genotype VII.1.1 was cloned to prepare the vaccine. Chickens immunized with the F gene DNA vaccine co-delivered with an IL-12-expressing plasmid DNA showed higher neutralizing antibody levels and stronger concanavalin-A-induced lymphocyte proliferation than those treated with the F gene DNA vaccine alone. The co-delivered vaccine provided 100% protection, and less viral shedding and a shorter release time were observed in challenged chickens than when the F gene DNA vaccine was administered alone. The use of F gene DNA combined with IL-12 delivered by electroporation is a promising approach for vaccination against ND. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7282469/ doi: 10.1007/s00705-020-04669-5 id: cord-356192-8b96rgqa author: Xie, Qian title: Two deletion variants of Middle East respiratory syndrome coronavirus found in a patient with characteristic symptoms date: 2017-04-18 words: 2413.0 sentences: 131.0 pages: flesch: 52.0 cache: ./cache/cord-356192-8b96rgqa.txt txt: ./txt/cord-356192-8b96rgqa.txt summary: title: Two deletion variants of Middle East respiratory syndrome coronavirus found in a patient with characteristic symptoms Significant sequence variation of Middle East respiratory syndrome coronavirus (MERS CoV) has never been detected since it was first reported in 2012. To predict the function of the E protein of MERS CoV, we aligned the E and ORF5-E protein sequences of MERS CoV with those of two other coronaviruses, SARS-CoV and China Rattus coronavirus HKU24, using MEGA software (version 6.0) [11] . The truncated E protein with a deletion of aa 1-30 lacks the N-terminus and a major part of the hydrophobic transmembrane domain in MERS CoV variant 1, which might directly impair virus packaging and replication [24] . Genomic sequencing and analysis of the first imported Middle East Respiratory Syndrome Coronavirus (MERS CoV) in China Middle East respiratory syndrome coronavirus (MERS-CoV) entry inhibitors targeting spike protein abstract: Significant sequence variation of Middle East respiratory syndrome coronavirus (MERS CoV) has never been detected since it was first reported in 2012. A MERS patient came from Korea to China in late May 2015. The patient was 44 years old and had symptoms including high fever, dry cough with a little phlegm, and shortness of breath, which are roughly consistent with those associated with MERS, and had had close contact with individuals with confirmed cases of MERS.After one month of therapy with antiviral, anti-infection, and immune-enhancing agents, the patient recovered in the hospital and was discharged. A nasopharyngeal swab sample was collected for direct sequencing, which revealed two deletion variants of MERS CoV. Deletions of 414 and 419 nt occurred between ORF5 and the E protein, resulting in a partial protein fusion or truncation of ORF5 and the E protein. Functional analysis by bioinformatics and comparison to previous studies implied that the two variants might be defective in their ability to package MERS CoV. However, the mechanism of how these deletions occurred and what effects they have need to be further investigated. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-017-3361-x) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-017-3361-x doi: 10.1007/s00705-017-3361-x id: cord-321195-cndq6aqb author: Xue, Chunyi title: Chimeric influenza-virus-like particles containing the porcine reproductive and respiratory syndrome virus GP5 protein and the influenza virus HA and M1 proteins date: 2014-07-27 words: 4542.0 sentences: 229.0 pages: flesch: 49.0 cache: ./cache/cord-321195-cndq6aqb.txt txt: ./txt/cord-321195-cndq6aqb.txt summary: In this study, we have developed a chimeric virus-like particle (VLP) vaccine candidate for porcine reproductive and respiratory syndrome virus (PRRSV) and H3N2 influenza virus and investigated its immunogenicity in mice. The HA and M1 proteins from the H3N2 influenza virus and the PRRSV GP5 protein fused to the cytoplasmic and transmembrane domains of the NA protein were both incorporated into the chimeric VLPs. Analysis of the immune responses showed that the chimeric VLPs elicited serum antibodies specific for both PRRSV GP5 and the H3N2 HA protein, and they stimulated cellular immune responses compared to the responses to equivalent amounts of inactivated viruses. Serum samples were collected on the 14th, 28th, and 42nd day after primary immunization of mice (8 per group) vaccinated with chimeric VLPs, inactivated H3N2 virus, or PBS. A trivalent virus-like particle vaccine elicits protective immune responses against seasonal influenza strains in mice and ferrets abstract: Both porcine reproductive and respiratory syndrome and swine influenza are acute, highly contagious swine diseases. These diseases pose severe threats for the swine industry and cause heavy economic losses worldwide. In this study, we have developed a chimeric virus-like particle (VLP) vaccine candidate for porcine reproductive and respiratory syndrome virus (PRRSV) and H3N2 influenza virus and investigated its immunogenicity in mice. The HA and M1 proteins from the H3N2 influenza virus and the PRRSV GP5 protein fused to the cytoplasmic and transmembrane domains of the NA protein were both incorporated into the chimeric VLPs. Analysis of the immune responses showed that the chimeric VLPs elicited serum antibodies specific for both PRRSV GP5 and the H3N2 HA protein, and they stimulated cellular immune responses compared to the responses to equivalent amounts of inactivated viruses. Taken together, the results suggested that the chimeric VLP vaccine represents a potential strategy for the development of a safe and effective vaccine to control PRRSV and H3N2 influenza virus. url: https://doi.org/10.1007/s00705-014-2178-0 doi: 10.1007/s00705-014-2178-0 id: cord-348179-i8w7huke author: Xue, Yong title: Increased risk of hepatitis E virus infection in schizophrenia date: 2012-10-07 words: 3363.0 sentences: 190.0 pages: flesch: 56.0 cache: ./cache/cord-348179-i8w7huke.txt txt: ./txt/cord-348179-i8w7huke.txt summary: Moreover, schizophrenia patients with increased CD4(+)/CD8(+) T-cell ratios (>2.03) had higher anti-HEV IgG detection rates than those with normal ratios (1.05-2.03). Epidemiological studies have already shown that the rates of hepatitis B and hepatitis C virus infection in patients with schizophrenia were five and 11 times higher, respectively, than the estimated general population rates [26] . In the current study, we found that the detection rates for HEV antibodies in schizophrenia patients were much higher than those in healthy controls. In the present study, the detection rate of anti-HEV IgG in schizophrenia patients with increased CD4 ? T-cell levels and the increased risk of HEV infection in schizophrenia patients. Moreover, significant differences of the serum IL-4, IL-10 and IL-12 levels were observed among schizophrenia patients with and without HEV IgG antibodies. Taken together, schizophrenia patients exhibited higher risk of HEV infection than controls in the present study. abstract: Until now, the risk of HEV infection in schizophrenia was unknown. The present results showed that the seroprevalence of anti-HEV IgG and anti-HEV IgM in schizophrenia were significantly higher than that in healthy controls. Anti-HEV IgG positivity increased with age and with the duration of disease in schizophrenia patients. Moreover, schizophrenia patients with increased CD4(+)/CD8(+) T-cell ratios (>2.03) had higher anti-HEV IgG detection rates than those with normal ratios (1.05-2.03). Compared with the schizophrenia patients who tested anti-HEV IgG negative, the levels of interleukin-4 and interleukin-10 (Th2 cytokines) were significantly higher, while the interleukin-12 (Th1 cytokine) level was significantly lower, in those with anti-HEV IgG positivity. Of five schizophrenia patients who were anti-HEV IgM positive, four had elevated CD4(+)/CD8(+) T-cell ratios. HEV RNA was isolated from one of these four patients and classified as genotype 4. Anti-HEV IgM positivity was not detected among healthy controls. Therefore, schizophrenia patients exhibited a higher risk of HEV infection than controls. url: https://doi.org/10.1007/s00705-012-1494-5 doi: 10.1007/s00705-012-1494-5 id: cord-299342-l8ugjou9 author: Yaling, Zhou title: Porcine epidemic diarrhea virus (CV 777) and feline infectious peritonitis virus (FIPV) are antigenically related date: 1988 words: 2974.0 sentences: 148.0 pages: flesch: 50.0 cache: ./cache/cord-299342-l8ugjou9.txt txt: ./txt/cord-299342-l8ugjou9.txt summary: Using gut sections from pigs infected with porcine epidemic diarrhea virus (strain CV 777) and ascitic fluid from cats which had succumbed to feline infectious peritonitis (FIP), a weak cross reaction was found by immunofluorescence. No reaction was found at the nucleocapsid protein position when blots of a mock infected N L F K cell lysate had been incubated with anti-CV 777 antibodies. As shown in figure 3 , results of the RIP confirmed the cross-reaction between pig anti-CV 777 sera and the 43,000 protein of FIPV found in Western blots; the homologous reaction reveals the typical pattern of FIPV structural polypeptides with Mr of 210,000 (peplomer), 45,000 (nucleocapsid) and 25,000 to 32,000 (envelope). We have confirmed the finding of cross reactions within one group, namely between transmissible gastroenteritis virus (TGEV) of swine, FIPV and canine enteric coronavirus, and showed that common determinants are present on all three structural polypeptides [7] . abstract: Using gut sections from pigs infected with porcine epidemic diarrhea virus (strain CV 777) and ascitic fluid from cats which had succumbed to feline infectious peritonitis (FIP), a weak cross reaction was found by immunofluorescence. Its specificity was confirmed when detergent-treated purified CV 777 showed a prominent reaction with FIPV antibodies in ELISA; no reaction was obtained with intact virions, which indicated common determinants on an internal component of the particle. Antigenic cross-reactions at the nucleocapsid level were found in Western blot ELISA performed both ways (CV 777/FIPV antibodies; FIPV/CV 777 antibodies). In immunoprecipitation using [(35)S]methionine labelled FIPV, anti-CV 777 sera recognized exclusively the nucleocapsid protein. The significance of these findings for the classification of coronaviruses is discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/3196169/ doi: 10.1007/bf01315563 id: cord-333331-ddcz7zck author: Yang, Jin title: Detection of hepatitis C virus by an improved loop-mediated isothermal amplification assay date: 2011-05-12 words: 5207.0 sentences: 245.0 pages: flesch: 54.0 cache: ./cache/cord-333331-ddcz7zck.txt txt: ./txt/cord-333331-ddcz7zck.txt summary: An improved, sensitive, specific, and rapid one-step reverse transcription loop-mediated isothermal amplification (LAMP) assay targeting the 5′ untranslated region (UTR) was developed to detect hepatitis C virus (HCV) infection. A variety of molecular diagnostic assays, such as reverse transcriptase PCR [12] , nucleic-acid-sequence-based amplification [13] , transcription-mediated amplification [29] , branched-chain DNA assay [26] , and in-house realtime PCR [8] , have been developed for the detection of HCV RNA. Confirmed cases of HCV infection were verified by a positive result in an enzyme-linked immunosorbent assay (Kehua Bio-engineering, Shanghai, China) for antibodies against HCV or a quantitative real-time PCR for HCV RNA. Given that the sensitivity of the AP-LAMP assay for detecting HCV is higher than that of the pre-LAMP method, the pathway of AP-based amplification was investigated. Reverse transcription-loop-mediated isothermal amplification assay for rapid detection of hepatitis E virus abstract: An improved, sensitive, specific, and rapid one-step reverse transcription loop-mediated isothermal amplification (LAMP) assay targeting the 5′ untranslated region (UTR) was developed to detect hepatitis C virus (HCV) infection. Based on an accelerating primer (AP), the present assay, named AP-LAMP, has the advantages of rapidity and sensitivity over the routine LAMP method. The possible AP-based amplification pathway during the reaction was revealed by restriction enzyme digestion and eletrophoresis. The detection limit of the AP-LAMP assay was approximately 84 IU/ml, and no cross-detection was observed. The assay was evaluated further with 126 clinical specimens, and the results indicated the suitability and simplicity of the test as a rapid diagnostic tool for detection of HCV RNA. url: https://doi.org/10.1007/s00705-011-1001-4 doi: 10.1007/s00705-011-1001-4 id: cord-291718-cz1bi0ym author: Yu, Liping title: The papain-like protease of avian infectious bronchitis virus has deubiquitinating activity date: 2017-03-18 words: 3426.0 sentences: 180.0 pages: flesch: 54.0 cache: ./cache/cord-291718-cz1bi0ym.txt txt: ./txt/cord-291718-cz1bi0ym.txt summary: Furthermore, the IBV replicase-encoded PLP, including the downstream transmembrane (TM) domain, is a DUB enzyme and dramatically reduced the level of Ub-conjugated proteins, while processing both K48and K63-linked polyubiquitin chains. Overall, these results demonstrate that the IBV-encoded PLP-TM functions as a DUB enzyme and suggest that IBV may interfere with the activation of host antiviral signaling pathway by degrading polyubiquitin-associated proteins. Further experiments indicated that the proteinase PLP-TM plays an important role in IBV DUB activity and can process both K48-and K63-linked polyubiquitin chains. Overall, the results of our study show that IBV has DUB activity and confirm that PLP-TM is not only a classic papain-like protease encoded by IBV but is also a multifunctional protein that plays important roles in the regulation of interactions between IBV and host antiviral innate immune response proteins. IBV PLP-TM may prevent the activation of host antiviral signaling pathways by degrading polyubiquitin chains associated with ubiquitin proteins. abstract: Coronavirus papain-like proteases (PLPs) can act as proteases that process virus-encoded large replicase polyproteins and also as deubiquitinating (DUB) enzymes. Like the PLPs of other coronaviruses (CoVs), the avian infectious bronchitis virus (IBV) PLP catalyzes proteolysis of Gly-Gly dipeptide bonds to release mature cleavage products. However, the other functions of the IBV PLP are not well understood. In this study, we found that IBV exhibits strong global DUB activity with significant reductions of the levels of ubiquitin (Ub)-, K48-, and K63-conjugated proteins. The DUB activity exhibited a clear time dependence, with stronger DUB activity in the early stage of viral infection. Furthermore, the IBV replicase-encoded PLP, including the downstream transmembrane (TM) domain, is a DUB enzyme and dramatically reduced the level of Ub-conjugated proteins, while processing both K48- and K63-linked polyubiquitin chains. By contrast, PLP did not cause any reduction of haemagglutinin (HA)-Ub-conjugated proteins. In addition, mutations of the catalytic residues of PLP-TM, Cys1274Ser and His1437Lys, reduced DUB activity against Ub-, K48- and K63- conjugated proteins, indicating that the DUB activity of the PLP-TM wild-type protein is not completely dependent on its catalytic activity. Overall, these results demonstrate that the IBV-encoded PLP-TM functions as a DUB enzyme and suggest that IBV may interfere with the activation of host antiviral signaling pathway by degrading polyubiquitin-associated proteins. url: https://doi.org/10.1007/s00705-017-3328-y doi: 10.1007/s00705-017-3328-y id: cord-012032-zolowuhj author: Yu, Peifa title: 2’-Fluoro-2’-deoxycytidine inhibits murine norovirus replication and synergizes MPA, ribavirin and T705 date: 2020-08-08 words: 3499.0 sentences: 197.0 pages: flesch: 45.0 cache: ./cache/cord-012032-zolowuhj.txt txt: ./txt/cord-012032-zolowuhj.txt summary: To further examine the antiviral effects, another murine macrophage cell line, J774A.1, was used, and a similar inhibitory effect of 2''-FdC on MNV-1 replication was observed, with decreased viral RNA and NS1/2 protein expression ( Supplementary Fig. 1 ). As shown in Fig. 3D and E, the viral NS1/2 protein expression and viral titers were further decreased when the antivirals were used in combination, supporting the synergistic antiviral effects of 2''-FdC with MPA, ribavirin, or T705 against MNV replication. The combined effect of 2''-FdC and ribavirin on viral replication was analyzed using a qRT-PCR assay (n = 2-4) and mathematical modeling using MacSynergy. RAW264.7 cells were infected with MNV-1 at an MOI of 1 for 1 h and then left untreated or treated with 2''-FdC and MPA, ribavirin, or T705 at the indicated concentrations for 20 h, alone or in combination. abstract: Noroviruses are the main causative agents of acute viral gastroenteritis worldwide. However, no vaccine or specific antiviral treatment is available, imposing a heavy global health burden. The nucleoside analogue 2’-fluoro-2’-deoxycytidine (2’-FdC) has been reported to have broad antiviral activity. Here, we report that 2’-FdC significantly inhibits murine norovirus replication in macrophages. This effect was partially reversed by exogenous supplementation of cytidine triphosphate. The combination of 2’-FdC with mycophenolic acid, ribavirin or favipiravir (T705) exerts synergistic antiviral effects. These results indicate that 2’-FdC is a potential candidate for antiviral drug development against norovirus infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-020-04759-4) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7414258/ doi: 10.1007/s00705-020-04759-4 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-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-280865-shwxhak9 author: Zhang, Dan title: Clinical evaluation of a panel of multiplex quantitative real-time reverse transcription polymerase chain reaction assays for the detection of 16 respiratory viruses associated with community-acquired pneumonia date: 2018-06-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We developed a panel of multiplex quantitative real-time reverse transcription polymerase chain reaction (mqRT-PCR) assay consisting of seven internally controlled qRT-PCR assays to detect 16 different respiratory viruses. We compared the new mqRT-PCR with a previously reported two-tube mRT-PCR assay using 363 clinical sputum specimens. The mqRT-PCR assay performed comparably with the two-tube assay for most viruses, offering the advantages of quantitative analysis, easier performance, lower susceptibility to contamination, and shorter turnaround time in laboratories equipped with conventional real-time PCR instrumentation, and it could therefore be a valuable tool for routine surveillance of respiratory virus infections in China. url: https://www.ncbi.nlm.nih.gov/pubmed/29961119/ doi: 10.1007/s00705-018-3921-8 id: cord-287275-vwyny1vt author: Zhang, Meng-Jia title: Genomic characterization and pathogenicity of porcine deltacoronavirus strain CHN-HG-2017 from China date: 2018-10-30 words: 5181.0 sentences: 267.0 pages: flesch: 56.0 cache: ./cache/cord-287275-vwyny1vt.txt txt: ./txt/cord-287275-vwyny1vt.txt summary: In this study, a Chinese PDCoV strain, designated CHN-HG-2017, was isolated from feces of a suckling piglet with severe watery diarrhea on a farm located in central China. Tissues of small intestines from CHN-HG-2017-infected piglets at 4 DPI displayed significant macroscopic and microscopic lesions with clear viral antigen expression. In addition, it has been reported that newborn piglets inoculated with two recent Chinese PDCoV isolates, named CHN-HN-2014 and CHN-GD-2016, developed clear clinical signs, including severe diarrhea, vomiting, and dehydration [21, 22] . Analysis of the genomic sequence suggested that CHN-HG-2017 is a potential recombinant virus derived from Chinese and Vietnam PDCoV strains. To confirm that virus propagation had occurred, the infectivity of the plaque-purified CHN-HG-2017 strain in LLC-PK1 cells was tested by IFA and western blot with an mAb against the PDCoV N protein. Isolation, genomic characterization, and pathogenicity of a Chinese porcine deltacoronavirus strain CHN-HN-2014 abstract: Porcine deltacoronavirus (PDCoV) was first detected in Hong Kong and has recently spread to many countries around the world. PDCoV causes acute diarrhea and vomiting in pigs, resulting in significant economic losses in the global pork industry. In this study, a Chinese PDCoV strain, designated CHN-HG-2017, was isolated from feces of a suckling piglet with severe watery diarrhea on a farm located in central China. Subsequently, the virus was identified by an indirect immunofluorescence assay and electron microscopy. A nucleotide sequence alignment showed that the whole genome of CHN-HG-2017 is 97.6%-99.1% identical to other PDCoV strains. Analysis of potential recombination sites showed that CHN-HG-2017 is a possible recombinant originating from the strains CH/SXD1/2015 and Vietnam/HaNoi6/2015. Furthermore, the pathogenicity of this recombinant PDCoV strain was investigated in 5-day-old piglets by oral inoculation. The challenged piglets developed typical symptoms, such as vomiting, anorexia, diarrhea and lethargy, from 1 to 7 days post-inoculation (DPI). Viral shedding was detected in rectal swabs until 14 DPI in the challenged piglets. Interestingly, high titers of virus-neutralizing antibodies in sera were detected at 21 DPI. Tissues of small intestines from CHN-HG-2017-infected piglets at 4 DPI displayed significant macroscopic and microscopic lesions with clear viral antigen expression. Our analysis of the full genome sequence of a recombinant PDCoV and its virulence in suckling piglets might provide new insights into the pathogenesis of PDCoV and facilitate further investigation of this newly emerged pathogen. url: https://doi.org/10.1007/s00705-018-4081-6 doi: 10.1007/s00705-018-4081-6 id: cord-316525-uadfehr6 author: Zhang, X. W. title: Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus date: 2004-10-11 words: 3023.0 sentences: 152.0 pages: flesch: 52.0 cache: ./cache/cord-316525-uadfehr6.txt txt: ./txt/cord-316525-uadfehr6.txt summary: Surprisingly, we found that 7 putative recombination regions, located in Replicase 1ab and Spike protein, exist between SARS-CoV and other 6 coronaviruses: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), human coronavirus 229E (HCoV), murine hepatitis virus (MHV), and avian infectious bronchitis virus (IBV). After potential recombination events were identified by at least 3 methods above, separate neighbor joining trees were constructed for each putative recombination region to better evaluate the evidence for conflicting evolutionary histories of different sequence regions. Two regions (13151-13299 and 16051-16449, position in alignment) are identified as putative recombination regions and all 6 coronaviruses are potential parents with SARS-CoV as potential daughter. In this study, seven recombination detection methods and phylogenetic analyses were performed on SARS-CoV and the six coronaviruses identified by BLAST (IBV, BCoV, HCoV, MHV, PEDV and TGEV). abstract: The origin of severe acute respiratory syndrome-associated corona-virus (SARS-CoV) is still a matter of speculation, although more than one year has passed since the onset of the SARS outbreak. In this study, we implemented a 3-step strategy to test the intriguing hypothesis that SARS-CoV might have been derived from a recombinant virus. First, we blasted the whole SARS-CoV genome against a virus database to search viruses of interest. Second, we employed 7 recombination detection techniques well documented in successfully detecting recombination events to explore the presence of recombination in SARS-CoV genome. Finally, we conducted phylogenetic analyses to further explore whether recombination has indeed occurred in the course of coronaviruses history predating the emergence of SARS-CoV. Surprisingly, we found that 7 putative recombination regions, located in Replicase 1ab and Spike protein, exist between SARS-CoV and other 6 coronaviruses: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), human coronavirus 229E (HCoV), murine hepatitis virus (MHV), and avian infectious bronchitis virus (IBV). Thus, our analyses substantiate the presence of recombination events in history that led to the SARS-CoV genome. Like the other coronaviruses used in the analysis, SARS-CoV is also a mosaic structure. url: https://www.ncbi.nlm.nih.gov/pubmed/15480857/ doi: 10.1007/s00705-004-0413-9 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-345856-ckm0ol20 author: Zhong, Qiong title: Antiviral activity of Arbidol against Coxsackie virus B5 in vitro and in vivo date: 2009-03-17 words: 3778.0 sentences: 200.0 pages: flesch: 58.0 cache: ./cache/cord-345856-ckm0ol20.txt txt: ./txt/cord-345856-ckm0ol20.txt summary: Arbidol not only prevented the cytopathic effect (CPE) of CVB(5), as demonstrated in an MTT colorimetric assay, when added during or after viral infection, with a 50% inhibitory concentration (IC(50)) from 2.66 to 6.62 μg/ml, but it also decreased the CVB(5)-RNA level in infected host cells, as shown in semi-quantitative RT-PCR. Orally administered Arbidol at 50 mg/kg body weight/day (once a day) significantly reduced mean virus yields in the lungs and heart as well as mortality after infection for 6 days. In our previous study, Arbidol showed broad-spectrum antiviral activity against a number of respiratory viruses, including FLU-A, RSV, HRV 14, and CVB 3 in vitro [20] . The virus titers of lung and heart were significantly lower in mice receiving oral administration of Arbidol daily for 6 days than in the viral control group. We also cocultured HEp-2 cells with different doses of Arbidol after infection to study whether it still had an antiviral effect after virus entry into the host cell. abstract: We investigated the antiviral activity of Arbidol, an antiviral chemical compound, against Coxsackie virus B5 (CVB(5)) in vitro and in vivo. Arbidol not only prevented the cytopathic effect (CPE) of CVB(5), as demonstrated in an MTT colorimetric assay, when added during or after viral infection, with a 50% inhibitory concentration (IC(50)) from 2.66 to 6.62 μg/ml, but it also decreased the CVB(5)-RNA level in infected host cells, as shown in semi-quantitative RT-PCR. BALB/c mice were used as an animal model to test the Arbidol activity in vivo. Orally administered Arbidol at 50 mg/kg body weight/day (once a day) significantly reduced mean virus yields in the lungs and heart as well as mortality after infection for 6 days. Our results demonstrate that in vitro and in vivo infection with CVB(5) can be effectively treated by Arbidol. url: https://doi.org/10.1007/s00705-009-0346-4 doi: 10.1007/s00705-009-0346-4 id: cord-324377-br2uorg8 author: Zhou, Pei title: Antiviral effect of lithium chloride on infection of cells by canine parvovirus date: 2015-08-28 words: 2930.0 sentences: 164.0 pages: flesch: 58.0 cache: ./cache/cord-324377-br2uorg8.txt txt: ./txt/cord-324377-br2uorg8.txt summary: We determined the antiviral effect of Lithium Chloride on canine parvovirus type 2 in feline kidney cells. These results indicated that lithium chloride could be a potential antiviral drug for curing dogs with canine parvovirus infection. The specific steps of canine parvovirus entry into cells that are affected by lithium chloride and its antiviral effect in vivo should be explored in future studies. As a control, cells infected with the same dose of CPV were not treated with LiCl. Subsequently, the antiviral efficacy was evaluated by analysis of viral RNA levels, protein expression level and CPE. These results indicate that treatment of F81 cells with LiCl inhibits CPV infection and reduces the cytopathic effect in a dose-dependent manner. No significant differences in the relative levels of viral VP2 gene DNA or viral titers were observed between drug-treated and mocktreated cells, indicating that LiCl had no effect on CPV attachment and replication in F81 cells ( Fig. 4A and B) . abstract: Canine parvovirus type 2 causes significant viral disease in dogs, with high morbidity, high infectivity, and high mortality. Lithium chloride is a potential antiviral drug for viruses. We determined the antiviral effect of Lithium Chloride on canine parvovirus type 2 in feline kidney cells. The viral DNA and proteins of canine parvovirus were suppressed in a dose-dependent manner by lithium chloride. Further investigation verified that viral entry into cells was inhibited in a dose-dependent manner by lithium chloride. These results indicated that lithium chloride could be a potential antiviral drug for curing dogs with canine parvovirus infection. The specific steps of canine parvovirus entry into cells that are affected by lithium chloride and its antiviral effect in vivo should be explored in future studies. url: https://doi.org/10.1007/s00705-015-2577-x doi: 10.1007/s00705-015-2577-x id: cord-263193-paeosfiu author: Zhu, Jinyan title: Infectious bronchitis virus inhibits activation of the TLR7 pathway, but not the TLR3 pathway date: 2020-06-10 words: 2831.0 sentences: 163.0 pages: flesch: 55.0 cache: ./cache/cord-263193-paeosfiu.txt txt: ./txt/cord-263193-paeosfiu.txt summary: Here, primary chicken embryo kidney (CEK) cells and specific-pathogen-free (SPF) chickens were infected with three pathogenic IBV strains, and it was observed that the TLR7-MYD88 pathway was inhibited but the TLR3-TIRF pathway was activated. To investigate the effect of innate immune molecules, agonists of TLR3, TLR7, and MDA5 and inhibitors of key molecules of the TLR3 pathway were added to CEK cells that had grown to 80-90% as instructed by the reagent manufacturer (InvivoGen, CA, USA) as follows: 5 μg of imiquimod (a TLR7 agonist) per mL for 12 h, 10 μg of low-molecular-weight (LMW) polyinosinic-polycytidylic acid (poly(I:C)) (a TLR3 agonist) per mL for 12 h, 0.5 μg of poly (I:C)-LMW/LyoVec (an MDA5 agonist) per mL for 12 h, 10 μM Pepinh-TRIF (a TRIF inhibitor) for 6 h, 5 μM celastrol (an NF-κB inhibitor) for 1 h, 50 μM chloroquine (an inhibitor of endosomal acidification) for 0.5 h, and 5 μM BX795 (a TBK1 inhibitor) for 6 h. abstract: Various strains of infectious bronchitis virus (IBV) cause different forms of infectious bronchitis with different clinical signs. Here, primary chicken embryo kidney (CEK) cells and specific-pathogen-free (SPF) chickens were infected with three pathogenic IBV strains, and it was observed that the TLR7-MYD88 pathway was inhibited but the TLR3-TIRF pathway was activated. After treatment with poly(I:C)-LMW, poly (I:C)-LMW/LyoVec, and Imiquimod, the replication of IBV was significantly suppressed after 24 h. However, treatment with TLR3 pathway inhibitors such as Pepinh-TRIF, celastrol, chloroquine, and BX795 resulted in increased replication of IBV after 36 h. These results also showed that chloroquine and celastrol were most effective inhibitors of the antiviral response at 48 hpi. url: https://www.ncbi.nlm.nih.gov/pubmed/32524263/ doi: 10.1007/s00705-020-04690-8 id: cord-321471-gev5xq3a author: Zhu, Liqian title: Control of the PI3K/Akt pathway by porcine reproductive and respiratory syndrome virus date: 2013-02-05 words: 3759.0 sentences: 181.0 pages: flesch: 50.0 cache: ./cache/cord-321471-gev5xq3a.txt txt: ./txt/cord-321471-gev5xq3a.txt summary: The activation of PI3K-Akt pathway promotes cell survival by the phosphorylation of numerous substrates such as glycogen synthase kinase-3 (GSK-3), FoxO1, Bad and mTOR [5, 11, 24, 36, 38] . Previous studies have shown that during PRRSV infection of porcine monocyte-derived dendritic cells (Mo-DCs), the PI3K/Akt pathway is activated at 90 min and 4 h postinfection (h p.i.), and it is inhibited at 12 h p.i. A number of studies have shown that the PI3K/Akt signaling pathway is functionally dependent on downstream substrates of Akt such as FoxO1, Bad and mTOR for regulation of cell survival [3, 11, 15, 25] . Since increased phosphorylation of Akt induced by HP-PRRSV was observed at 5 min and 15 min postinfection in virus-infected MARC-145 cells, and at 5, 15 and 30 min postinfection in PAMs, we hypothesized that the virus entry process accounted for this early-stage activation. abstract: Phosphatidylinositol-3-kinase (PI3K)/Akt is an important cellular pathway that has been shown to participate in various replication steps of multiple viruses. In the present study, we compared the phosphorylation status of Akt during infection of MARC-145 cells and porcine alveolar macrophages (PAMs) with highly pathogenic PRRSV (HP-PRRSV) strain HuN4. We observed that biphasic activation of Akt was induced in at both the early stage (5, 15 and 30 min postinfection) and the late stage (12 and 24 h postinfection) of HP-PRRSV infection of MARC-145 cells, while an early-phase activation of Akt was found exclusively in virus-infected PAMs in vitro. Analysis with the PI3K-specific inhibitor LY294002 confirmed that PI3K acted as the upstream activator for the virus-induced activation of Akt. UV-irradiation-inactivated virus still induced the early event in PAMs but not in MARC-145 cells, suggesting that different mechanisms are employed for the early-stage induction of phosphorylated Akt within different cell cultures. We further demonstrated that FoxO1 and Bad, which serve as downstream targets of Akt, were phosphorylated in virus-infected MARC-145 cells. Moreover, the suppression of phosphorylated Akt with LY294002 significantly inhibited the virus-induced cytopathic effect (CPE) on MARC-145 cells, but it had a negligible effect on virus propagation. Collectively, our data provide new evidence of a novel role for the PI3K/Akt pathway in PRRSV infection of MARC-145 cells. url: https://www.ncbi.nlm.nih.gov/pubmed/23381397/ doi: 10.1007/s00705-013-1620-z id: cord-294947-g4ntyddb author: Zhu, Yu title: Establishment of a nanoparticle-assisted RT-PCR assay to distinguish field strains and attenuated strains of porcine epidemic diarrhea virus date: 2016-06-10 words: 2849.0 sentences: 154.0 pages: flesch: 54.0 cache: ./cache/cord-294947-g4ntyddb.txt txt: ./txt/cord-294947-g4ntyddb.txt summary: title: Establishment of a nanoparticle-assisted RT-PCR assay to distinguish field strains and attenuated strains of porcine epidemic diarrhea virus In this study, a nanoparticle-assisted polymerase chain reaction (nanoparticle-assisted RT-PCR) assay targeting the ORF3 of PEDV was developed to distinguish PEDV field strains from attenuated strains by using a specific pair of primers. The nanoparticle-assisted RT-PCR assay we describe here can be used to distinguish field strains from vaccine strains of PEDV, and it shows promise for reducing economic loss due to PEDV infection. The results showed that the nanoparticle-assisted RT-PCR assay could distinguish PEDV field strains from the attenuated strain in samples from infected pigs. The present study demonstrated that an effective nanoparticle-assisted RT-PCR assay targeting the ORF3 gene of PEDV was able to distinguish field strains from attenuated vaccine strains. Development of a nanoparticle-assisted PCR assay for detection of porcine epidemic diarrhea virus abstract: Porcine epidemic diarrhea virus (PEDV) can cause serious disease and even death in neonatal piglets, resulting in serious damage to the swine industry worldwide. Open reading frame 3 (ORF3) is the only accessory gene in the PEDV genome. Previous studies have indicated that PEDV vaccine strains have a partial deletion in ORF3. In this study, a nanoparticle-assisted polymerase chain reaction (nanoparticle-assisted RT-PCR) assay targeting the ORF3 of PEDV was developed to distinguish PEDV field strains from attenuated strains by using a specific pair of primers. The PCR products of field strains and attenuated strains were 264 bp and 215 bp in length, respectively. The sensitivity and specificity of this assay were also assessed. The nanoparticle-assisted RT-PCR assay was 10-100 times more sensitive than the conventional RT-PCR assay, with no cross-reactions when amplifying porcine pseudorabies virus (PRV), porcine circovirus type 2 (PCV2), classical swine fever virus (CSFV), porcine parvovirus (PPV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine rotavirus (RV), and porcine transmissible gastroenteritis virus (TGEV). The nanoparticle-assisted RT-PCR assay we describe here can be used to distinguish field strains from vaccine strains of PEDV, and it shows promise for reducing economic loss due to PEDV infection. url: https://doi.org/10.1007/s00705-016-2918-4 doi: 10.1007/s00705-016-2918-4 ==== 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