Carrel name: journal-virology-cord Creating study carrel named journal-virology-cord /data-disk/reader-compute/reader-cord/bin/initialize-carrel.sh: fork: retry: No child processes Initializing database file: cache/cord-253351-b36g09r0.json key: cord-253351-b36g09r0 authors: Luo, Zongli; Weiss, Susan R. title: Roles in Cell-to-Cell Fusion of Two Conserved Hydrophobic Regions in the Murine Coronavirus Spike Protein date: 1998-05-10 journal: Virology DOI: 10.1006/viro.1998.9121 sha: doc_id: 253351 cord_uid: b36g09r0 file: cache/cord-008407-jbp8bxjz.json key: cord-008407-jbp8bxjz authors: Derdeyn, Cynthia A.; Frey, Teryl K. title: Characterization of defective-interfering RNAs of rubella virusgenerated during serial undiluted passage date: 1995-01-10 journal: Virology DOI: 10.1016/s0042-6822(95)80036-0 sha: doc_id: 8407 cord_uid: jbp8bxjz file: cache/cord-007373-livz5zuu.json key: cord-007373-livz5zuu authors: Gayathri, P.; Satheshkumar, P.S.; Prasad, K.; Nair, Smita; Savithri, H.S.; Murthy, M.R.N. title: Crystal structure of the serine protease domain of Sesbania mosaic virus polyprotein and mutational analysis of residues forming the S1-binding pocket date: 2006-03-15 journal: Virology DOI: 10.1016/j.virol.2005.11.011 sha: doc_id: 7373 cord_uid: livz5zuu parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. file: cache/cord-254558-gvo0gwjf.json key: cord-254558-gvo0gwjf authors: Guo, Yan Xiang; Wei, Ting; Dallmann, Klara; Kwang, Jimmy title: Induction of caspase-dependent apoptosis by betanodaviruses GGNNV and demonstration of protein α as an apoptosis inducer date: 2003-03-30 journal: Virology DOI: 10.1016/s0042-6822(02)00098-3 sha: doc_id: 254558 cord_uid: gvo0gwjf file: cache/cord-254747-vox5xsgd.json key: cord-254747-vox5xsgd authors: Deng, Xufang; Baker, Susan C title: An “Old” Protein with A New Story: Coronavirus Endoribonuclease Is Important for Evading Host Antiviral Defenses date: 2018-04-01 journal: Virology DOI: 10.1016/j.virol.2017.12.024 sha: doc_id: 254747 cord_uid: vox5xsgd file: cache/cord-253894-4u5yt7b7.json key: cord-253894-4u5yt7b7 authors: Senkevich, Tatiana G.; Koonin, Eugene V.; Moss, Bernard title: Vaccinia virus F16 protein, a predicted catalytically inactive member of the prokaryotic serine recombinase superfamily, is targeted to nucleoli date: 2011-09-01 journal: Virology DOI: 10.1016/j.virol.2011.06.017 sha: doc_id: 253894 cord_uid: 4u5yt7b7 file: cache/cord-252615-ajyv95pu.json key: cord-252615-ajyv95pu authors: Lu, Yanfang; Hou, Hongyan; Wang, Feng; Qiao, Long; Wang, Xiong; Yu, Jing; Liu, Weiyong; Sun, Ziyong title: ATP1B3: a virus-induced host factor against EV71 replication by up-regulating the production of type-I interferons date: 2016-05-27 journal: Virology DOI: 10.1016/j.virol.2016.05.013 sha: doc_id: 252615 cord_uid: ajyv95pu file: cache/cord-256036-gd53s4dv.json key: cord-256036-gd53s4dv authors: Sandmann, Lisa; Ploss, Alexander title: Barriers of hepatitis C virus interspecies transmission date: 2013-01-01 journal: Virology DOI: 10.1016/j.virol.2012.09.044 sha: doc_id: 256036 cord_uid: gd53s4dv file: cache/cord-255453-7e40rj1y.json key: cord-255453-7e40rj1y authors: Oliver, S.L.; Asobayire, E.; Dastjerdi, A.M.; Bridger, J.C. title: Genomic characterization of the unclassified bovine enteric virus Newbury agent-1 (Newbury1) endorses a new genus in the family Caliciviridae date: 2006-06-20 journal: Virology DOI: 10.1016/j.virol.2006.02.027 sha: doc_id: 255453 cord_uid: 7e40rj1y file: cache/cord-255738-r8zfdsix.json key: cord-255738-r8zfdsix authors: Ge, Feng; Luo, Yonghu; Liew, Pei Xiong; Hung, Eugene title: Derivation of a novel SARS–coronavirus replicon cell line and its application for anti-SARS drug screening date: 2007-03-30 journal: Virology DOI: 10.1016/j.virol.2006.10.016 sha: doc_id: 255738 cord_uid: r8zfdsix file: cache/cord-258232-br4z3na6.json key: cord-258232-br4z3na6 authors: Maeda, Junko; Maeda, Akihiko; Makino, Shinji title: Release of Coronavirus E Protein in Membrane Vesicles from Virus-Infected Cells and E Protein-Expressing Cells date: 1999-10-25 journal: Virology DOI: 10.1006/viro.1999.9955 sha: doc_id: 258232 cord_uid: br4z3na6 file: cache/cord-252397-qlu7dilh.json key: cord-252397-qlu7dilh authors: Johnson, Reed F.; Via, Laura E.; Kumar, Mia R.; Cornish, Joseph P.; Yellayi, Srikanth; Huzella, Louis; Postnikova, Elena; Oberlander, Nicholas; Bartos, Christopher; Ork, Britini L.; Mazur, Steven; Allan, Cindy; Holbrook, Michael R.; Solomon, Jeffrey; Johnson, Joshua C.; Pickel, James; Hensley, Lisa E.; Jahrling, Peter B. title: Intratracheal exposure of common marmosets to MERS-CoV Jordan-n3/2012 or MERS-CoV EMC/2012 isolates does not result in lethal disease date: 2015-11-01 journal: Virology DOI: 10.1016/j.virol.2015.07.013 sha: doc_id: 252397 cord_uid: qlu7dilh file: cache/cord-256316-1odgm6hm.json key: cord-256316-1odgm6hm authors: Godet, Murielle; L'Haridon, Rene; Vautherot, Jean-Francois; Laude, Hubert title: TGEV corona virus ORF4 encodes a membrane protein that is incorporated into virions date: 1992-06-30 journal: Virology DOI: 10.1016/0042-6822(92)90521-p sha: doc_id: 256316 cord_uid: 1odgm6hm file: cache/cord-255773-b4re5bky.json key: cord-255773-b4re5bky authors: Zhang, Qingzhan; Shi, Kaichuang; Yoo, Dongwan title: Suppression of type I interferon production by porcine epidemic diarrhea virus and degradation of CREB-binding protein by nsp1 date: 2016-01-14 journal: Virology DOI: 10.1016/j.virol.2015.12.010 sha: doc_id: 255773 cord_uid: b4re5bky file: cache/cord-256703-eaj63c2k.json key: cord-256703-eaj63c2k authors: Matsuoka, Yumiko; Ihara, Takeshi; Bishop, David H.L.; Compans, Richard W. title: Intracellular accumulation of punta toro virus glycoproteins expressed from cloned cDNA date: 1988-11-30 journal: Virology DOI: 10.1016/0042-6822(88)90075-x sha: doc_id: 256703 cord_uid: eaj63c2k file: cache/cord-256737-ptjng78b.json key: cord-256737-ptjng78b authors: McBride, Corrin E.; Machamer, Carolyn E. title: Palmitoylation of SARS-CoV S protein is necessary for partitioning into detergent-resistant membranes and cell-cell fusion but not interaction with M protein date: 2010-09-01 journal: Virology DOI: 10.1016/j.virol.2010.05.031 sha: doc_id: 256737 cord_uid: ptjng78b file: cache/cord-258379-v3lceirh.json key: cord-258379-v3lceirh authors: Liu, D. X.; Inglis, S. C. title: Association of the infectious bronchitis virus 3c protein with the virion envelope date: 1991-12-31 journal: Virology DOI: 10.1016/0042-6822(91)90572-s sha: doc_id: 258379 cord_uid: v3lceirh file: cache/cord-262441-slh52nxm.json key: cord-262441-slh52nxm authors: Sakai, Yusuke; Kawachi, Kengo; Terada, Yutaka; Omori, Hiroko; Matsuura, Yoshiharu; Kamitani, Wataru title: Two-amino acids change in the nsp4 of SARS coronavirus abolishes viral replication date: 2017-07-21 journal: Virology DOI: 10.1016/j.virol.2017.07.019 sha: doc_id: 262441 cord_uid: slh52nxm file: cache/cord-255841-3laov764.json key: cord-255841-3laov764 authors: Duquerroy, Stéphane; Vigouroux, Armelle; Rottier, Peter J.M.; Rey, Félix A.; Jan Bosch, Berend title: Central ions and lateral asparagine/glutamine zippers stabilize the post-fusion hairpin conformation of the SARS coronavirus spike glycoprotein() date: 2005-05-10 journal: Virology DOI: 10.1016/j.virol.2005.02.022 sha: doc_id: 255841 cord_uid: 3laov764 file: cache/cord-258327-03vk6enj.json key: cord-258327-03vk6enj authors: Schultze, Beate; Wahn, Kurt; Klenk, Hans-Dieter; Herrler, Georg title: Isolated HE-protein from hemagglutinating encephalomyelitis virus and bovine coronavirus has receptor-destroying and receptor-binding activity date: 1991-01-31 journal: Virology DOI: 10.1016/0042-6822(91)90026-8 sha: doc_id: 258327 cord_uid: 03vk6enj file: cache/cord-258691-cd83w9o6.json key: cord-258691-cd83w9o6 authors: Whitman, Lucia; Zhou, Haixia; Perlman, Stanley; Lane, Thomas E. title: IFN-γ-mediated suppression of coronavirus replication in glial-committed progenitor cells date: 2009-02-01 journal: Virology DOI: 10.1016/j.virol.2008.10.036 sha: doc_id: 258691 cord_uid: cd83w9o6 file: cache/cord-253024-b393ea2u.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-253024-b393ea2u authors: Fu, Kaisong; Baric, Ralph S. title: Evidence for variable rates of recombination in the MHV genome date: 1992-07-31 journal: Virology DOI: 10.1016/0042-6822(92)90684-h sha: doc_id: 253024 cord_uid: b393ea2u file: cache/cord-260177-xu0elmak.json key: cord-260177-xu0elmak authors: Collins, Arlene R.; Knobler, Robert L.; Powell, Harry; Buchmeier, Michael J. title: Monoclonal antibodies to murine hepatitis virus-4 (strain JHM) define the viral glycoprotein responsible for attachment and cell-cell fusion date: 1982-06-30 journal: Virology DOI: 10.1016/0042-6822(82)90095-2 sha: doc_id: 260177 cord_uid: xu0elmak file: cache/cord-262226-7kwkla73.json key: cord-262226-7kwkla73 authors: Fang, Shouguo; Xu, Linghui; Huang, Mei; Qisheng Li, Frank; Liu, D.X. title: Identification of two ATR-dependent phosphorylation sites on coronavirus nucleocapsid protein with nonessential functions in viral replication and infectivity in cultured cells date: 2013-07-09 journal: Virology DOI: 10.1016/j.virol.2013.06.014 sha: doc_id: 262226 cord_uid: 7kwkla73 file: cache/cord-260108-osg8q89i.json key: cord-260108-osg8q89i authors: Park, Yon Mi; Kim, Jeong-Hoon; Gu, Se Hun; Lee, Sook Young; Lee, Min-Goo; Kang, Yoon Kyoo; Kang, Sung-Ho; Kim, Hak Jun; Song, Jin-Won title: Full genome analysis of a novel adenovirus from the South Polar skua (Catharacta maccormicki) in Antarctica date: 2012-01-05 journal: Virology DOI: 10.1016/j.virol.2011.10.008 sha: doc_id: 260108 cord_uid: osg8q89i file: cache/cord-265173-70wyecwj.json key: cord-265173-70wyecwj authors: Trujillo-Uscanga, Adrian; Gutiérrez-Escolano, Ana Lorena title: Host cell p53 associates with the feline calicivirus major viral capsid protein VP1, the protease-polymerase NS6/7, and the double-stranded RNA playing a role in virus replication date: 2020-08-27 journal: Virology DOI: 10.1016/j.virol.2020.08.008 sha: doc_id: 265173 cord_uid: 70wyecwj file: cache/cord-259717-e8ljkv2y.json key: cord-259717-e8ljkv2y authors: Holtz, Lori R.; Cao, Song; Zhao, Guoyan; Bauer, Irma K.; Denno, Donna M.; Klein, Eileen J.; Antonio, Martin; Stine, O. Colin; Snelling, Thomas L.; Kirkwood, Carl D.; Wang, David title: Geographic variation in the eukaryotic virome of human diarrhea date: 2014-11-01 journal: Virology DOI: 10.1016/j.virol.2014.09.012 sha: doc_id: 259717 cord_uid: e8ljkv2y file: cache/cord-008426-ktn8c0zx.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-008426-ktn8c0zx authors: Othman, Yasmin; Hull, Roger title: Nucleotide sequence of the bean strain of southern bean mosaic virus() date: 1995-01-10 journal: Virology DOI: 10.1016/s0042-6822(95)80044-1 sha: doc_id: 8426 cord_uid: ktn8c0zx file: cache/cord-258286-lodjcj8c.json key: cord-258286-lodjcj8c authors: Zhang, Xuming; Hinton, David R.; Cua, Daniel J.; Stohlman, Stephen A.; Lai, Michael M.C. title: Expression of Interferon-γ by a Coronavirus Defective-Interfering RNA Vector and Its Effect on Viral Replication, Spread, and Pathogenicity date: 1997-07-07 journal: Virology DOI: 10.1006/viro.1997.8598 sha: doc_id: 258286 cord_uid: lodjcj8c file: cache/cord-254950-y6kayxie.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-254950-y6kayxie authors: Morse, Stephen S. title: Mouse thymic virus (MTLV; Murid Herpesvirus 3) infection in athymic nude mice: Evidence for a T lymphocyte requirement date: 1988-03-31 journal: Virology DOI: 10.1016/0042-6822(88)90262-0 sha: doc_id: 254950 cord_uid: y6kayxie file: cache/cord-259095-mfptcw8t.json key: cord-259095-mfptcw8t authors: Lu, Yiqi; Denison, Mark R. title: Determinants of Mouse Hepatitis Virus 3C-like Proteinase Activity date: 1997-04-14 journal: Virology DOI: 10.1006/viro.1997.8479 sha: doc_id: 259095 cord_uid: mfptcw8t file: cache/cord-267718-t47i8hui.json key: cord-267718-t47i8hui authors: Bao, Jingyue; Wang, Qinghua; Li, Lin; Liu, Chunju; Zhang, Zhicheng; Li, Jinming; Wang, Shujuan; Wu, Xiaodong; Wang, Zhiliang title: Evolutionary dynamics of recent peste des petits ruminants virus epidemic in China during 2013–2014 date: 2017-07-19 journal: Virology DOI: 10.1016/j.virol.2017.07.018 sha: doc_id: 267718 cord_uid: t47i8hui file: cache/cord-260782-1lm8tzbc.json key: cord-260782-1lm8tzbc authors: Giles, Julia; Perrott, Matthew; Roe, Wendi; Shrestha, Kshitiz; Aberdein, Danielle; Morel, Patrick; Dunowska, Magdalena title: Viral RNA load and histological changes in tissues following experimental infection with an arterivirus of possums (wobbly possum disease virus) date: 2018-07-14 journal: Virology DOI: 10.1016/j.virol.2018.07.003 sha: doc_id: 260782 cord_uid: 1lm8tzbc file: cache/cord-264359-m9j3pcj1.json key: cord-264359-m9j3pcj1 authors: Vrijsen, R.; Wouters, M.; Boeye, A. title: Resolution of the major poliovirus capsid polypeptides into doublets date: 1978-05-15 journal: Virology DOI: 10.1016/0042-6822(78)90093-4 sha: doc_id: 264359 cord_uid: m9j3pcj1 file: cache/cord-259500-ndjbrtrv.json key: cord-259500-ndjbrtrv authors: Satyanarayana, Tatineni; Gowda, Siddarame; Ayllón, María A; Dawson, William O title: Frameshift mutations in infectious cDNA clones of Citrus tristeza virus: a strategy to minimize the toxicity of viral sequences to Escherichia coli date: 2003-09-01 journal: Virology DOI: 10.1016/s0042-6822(03)00387-8 sha: doc_id: 259500 cord_uid: ndjbrtrv file: cache/cord-262574-gu0930s3.json key: cord-262574-gu0930s3 authors: Slagle, Betty L.; Butel, Janet S. title: Identification and characterization of a mouse mammary tumor virus protein uniquely expressed on the surface of BALB/cV mammary tumor cells date: 1985-05-31 journal: Virology DOI: 10.1016/0042-6822(85)90102-3 sha: doc_id: 262574 cord_uid: gu0930s3 file: cache/cord-260376-29ih5c9v.json key: cord-260376-29ih5c9v authors: Guo, Jian-Ping; Petric, Martin; Campbell, William; McGeer, Patrick L title: SARS corona virus peptides recognized by antibodies in the sera of convalescent cases date: 2004-07-01 journal: Virology DOI: 10.1016/j.virol.2004.04.017 sha: doc_id: 260376 cord_uid: 29ih5c9v file: cache/cord-260695-qwepi0we.json key: cord-260695-qwepi0we authors: Postler, Thomas S.; Pantry, Shara N.; Desrosiers, Ronald C.; Ghosh, Sankar title: Identification and characterization of a long non-coding RNA up-regulated during HIV-1 infection date: 2017-11-01 journal: Virology DOI: 10.1016/j.virol.2017.08.006 sha: doc_id: 260695 cord_uid: qwepi0we file: cache/cord-266230-ia04jc9j.json key: cord-266230-ia04jc9j authors: Rott, M. E.; Tremaine, J. H.; Rochon, D. M. title: Comparison of the 5′ and 3′ termini of tomato ringspot virus RNA1 and RNA2: Evidence for RNA recombination date: 1991-11-30 journal: Virology DOI: 10.1016/0042-6822(91)90801-h sha: doc_id: 266230 cord_uid: ia04jc9j file: cache/cord-266585-jfjrk9gy.json key: cord-266585-jfjrk9gy authors: Fang, Shouguo; Chen, Bo; Tay, Felicia P.L.; Ng, Beng Sern; Liu, Ding Xing title: An arginine-to-proline mutation in a domain with undefined functions within the helicase protein (Nsp13) is lethal to the coronavirus infectious bronchitis virus in cultured cells date: 2007-02-05 journal: Virology DOI: 10.1016/j.virol.2006.08.020 sha: doc_id: 266585 cord_uid: jfjrk9gy file: cache/cord-255828-jrqdyfbg.json key: cord-255828-jrqdyfbg authors: Du, Yijun; Pattnaik, Asit K.; Song, Cheng; Yoo, Dongwan; Li, Gang title: Glycosyl-phosphatidylinositol (GPI)-anchored membrane association of the porcine reproductive and respiratory syndrome virus GP4 glycoprotein and its co-localization with CD163 in lipid rafts date: 2012-03-01 journal: Virology DOI: 10.1016/j.virol.2011.12.009 sha: doc_id: 255828 cord_uid: jrqdyfbg file: cache/cord-263302-z5uhrta5.json key: cord-263302-z5uhrta5 authors: Zhang, Xuming; Liu, Runzhong title: Identification of a Noncanonical Signal for Transcription of a Novel Subgenomic mRNA of Mouse Hepatitis Virus: Implication for the Mechanism of Coronavirus RNA Transcription date: 2000-12-05 journal: Virology DOI: 10.1006/viro.2000.0637 sha: doc_id: 263302 cord_uid: z5uhrta5 file: cache/cord-262245-eb7g9p1x.json key: cord-262245-eb7g9p1x authors: Monica, Nicola La; Banner, Lisa R.; Morris, Vincent L.; Lai, Michael M.C. title: Localization of extensive deletions in the structural genes of two neurotropic variants of murine coronavirus JHM date: 1991-06-30 journal: Virology DOI: 10.1016/0042-6822(91)90635-o sha: doc_id: 262245 cord_uid: eb7g9p1x file: cache/cord-266617-z8uecyl6.json key: cord-266617-z8uecyl6 authors: Pavesi, Angelo title: Asymmetric evolution in viral overlapping genes is a source of selective protein adaptation date: 2019-04-03 journal: Virology DOI: 10.1016/j.virol.2019.03.017 sha: doc_id: 266617 cord_uid: z8uecyl6 file: cache/cord-263334-wwkdum94.json key: cord-263334-wwkdum94 authors: Li, Chen; Ge, Ling-ling; Li, Peng-peng; Wang, Yue; Dai, Juan-juan; Sun, Ming-xia; Huang, Li; Shen, Zhi-qiang; Hu, Xiao-chun; Ishag, Hassan; Mao, Xiang title: Cellular DDX3 regulates Japanese encephalitis virus replication by interacting with viral un-translated regions date: 2014-01-20 journal: Virology DOI: 10.1016/j.virol.2013.11.008 sha: doc_id: 263334 cord_uid: wwkdum94 file: cache/cord-267377-wyhsxj6g.json key: cord-267377-wyhsxj6g authors: Edwards, Michael C.; Weiland, John J. title: Coat protein expression strategy of oat blue dwarf virus() date: 2014-01-14 journal: Virology DOI: 10.1016/j.virol.2013.12.018 sha: doc_id: 267377 cord_uid: wyhsxj6g file: cache/cord-265156-u1re7983.json key: cord-265156-u1re7983 authors: de Wilde, Adriaan H.; Zevenhoven-Dobbe, Jessika C.; Beugeling, Corrine; Chatterji, Udayan; de Jong, Danielle; Gallay, Philippe; Szuhai, Karoly; Posthuma, Clara C.; Snijder, Eric J. title: Coronaviruses and arteriviruses display striking differences in their cyclophilin A-dependence during replication in cell culture date: 2017-12-15 journal: Virology DOI: 10.1016/j.virol.2017.11.022 sha: doc_id: 265156 cord_uid: u1re7983 file: cache/cord-262347-ejhz9rra.json key: cord-262347-ejhz9rra authors: Kappes, Matthew A.; Faaberg, Kay S. title: PRRSV structure, replication and recombination: Origin of phenotype and genotype diversity date: 2015-03-07 journal: Virology DOI: 10.1016/j.virol.2015.02.012 sha: doc_id: 262347 cord_uid: ejhz9rra file: cache/cord-264331-uvi8ucz4.json key: cord-264331-uvi8ucz4 authors: Singh, Shailbala; Briles, Worthie E.; Lupiani, Blanca; Collisson, Ellen W. title: Avian influenza viral nucleocapsid and hemagglutinin proteins induce chicken CD8(+) memory T lymphocytes date: 2010-04-10 journal: Virology DOI: 10.1016/j.virol.2009.12.029 sha: doc_id: 264331 cord_uid: uvi8ucz4 file: cache/cord-266018-8bhnlsgy.json key: cord-266018-8bhnlsgy authors: Trifilo, Matthew J.; Lane, Thomas E. title: The CC chemokine ligand 3 regulates CD11c(+)CD11b(+)CD8α(−) dendritic cell maturation and activation following viral infection of the central nervous system: implications for a role in T cell activation date: 2004-09-15 journal: Virology DOI: 10.1016/j.virol.2004.06.027 sha: doc_id: 266018 cord_uid: 8bhnlsgy file: cache/cord-265895-ck7eto16.json key: cord-265895-ck7eto16 authors: Baric, Ralph S.; Shieh, Chien-Kou; Stohlman, Stephen A.; Lai, Michael M.C. title: Analysis of intracellular small RNAs of mouse hepatitis virus: evidence for discontinuous transcription date: 1987-02-28 journal: Virology DOI: 10.1016/0042-6822(87)90414-4 sha: doc_id: 265895 cord_uid: ck7eto16 file: cache/cord-269986-jdcw59r2.json key: cord-269986-jdcw59r2 authors: Regan, Andrew D.; Cohen, Rebecca D.; Whittaker, Gary R. title: Activation of p38 MAPK by feline infectious peritonitis virus regulates pro-inflammatory cytokine production in primary blood-derived feline mononuclear cells date: 2009-02-05 journal: Virology DOI: 10.1016/j.virol.2008.11.006 sha: doc_id: 269986 cord_uid: jdcw59r2 file: cache/cord-267027-diwm1940.json key: cord-267027-diwm1940 authors: Le, Shu-Yun; Chen, Jih-H.; Sonenberg, Nahum; Maizel, Jacob V. title: Conserved tertiary structure elements in the 5′ untranslated region of human enteroviruses and rhinoviruses date: 1992-12-31 journal: Virology DOI: 10.1016/0042-6822(92)90261-m sha: doc_id: 267027 cord_uid: diwm1940 file: cache/cord-272437-gvzfl8c3.json key: cord-272437-gvzfl8c3 authors: Zhao, Jing; Zhang, Keran; Cheng, Jinlong; Jia, Wenfeng; Zhao, Ye; Zhang, Guozhong title: Replicase 1a gene plays a critical role in pathogenesis of avian coronavirus infectious bronchitis virus date: 2020-08-20 journal: Virology DOI: 10.1016/j.virol.2020.08.009 sha: doc_id: 272437 cord_uid: gvzfl8c3 file: cache/cord-267532-5rnqd9mb.json key: cord-267532-5rnqd9mb authors: Zhang, Xuming; Hinton, David R.; Park, Sungmin; Parra, Beatriz; Liao, Ching-Len; Lai, Michael M.C.; Stohlman, Stephen A. title: Expression of Hemagglutinin/Esterase by a Mouse Hepatitis Virus Coronavirus Defective–Interfering RNA Alters Viral Pathogenesis date: 1998-03-01 journal: Virology DOI: 10.1006/viro.1997.8993 sha: doc_id: 267532 cord_uid: 5rnqd9mb file: cache/cord-268341-103xf3dw.json key: cord-268341-103xf3dw authors: Parra, Beatriz; Hinton, David R.; Lin, Mark T.; Cua, Daniel J.; Stohlman, Stephen A. title: Kinetics of Cytokine mRNA Expression in the Central Nervous System Following Lethal and Nonlethal Coronavirus-Induced Acute Encephalomyelitis date: 1997-07-07 journal: Virology DOI: 10.1006/viro.1997.8613 sha: doc_id: 268341 cord_uid: 103xf3dw file: cache/cord-269419-68kja6bg.json key: cord-269419-68kja6bg authors: Hu, Weibin; Chen, Aizhong; Miao, Yi; Xia, Shengli; Ling, Zhiyang; Xu, Ke; Wang, Tongyan; Xu, Ying; Cui, Jun; Wu, Hongqiang; Hu, Guiyu; Tian, Lin; Wang, Lingling; Shu, Yuelong; Ma, Xiaowei; Xu, Bianli; Zhang, Jin; Lin, Xiaojun; Bian, Chao; Sun, Bing title: Fully human broadly neutralizing monoclonal antibodies against influenza A viruses generated from the memory B cells of a 2009 pandemic H1N1 influenza vaccine recipient date: 2013-01-20 journal: Virology DOI: 10.1016/j.virol.2012.09.034 sha: doc_id: 269419 cord_uid: 68kja6bg file: cache/cord-267014-3vi7pgvr.json key: cord-267014-3vi7pgvr authors: Vennema, H.; Rossen, J.W.A.; Wesseling, J.; Horzinek, M. 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Liu, Rongxian; Lu, Mijia; Yang, Yingzhi; Zhou, Duo; Hao, Xiaoqiang; Zhou, Dongming; Wang, Bin; Li, Jianrong; Huang, Yao-Wei; Zhao, Zhengyan title: Enhancement of safety and immunogenicity of the Chinese Hu191 measles virus vaccine by alteration of the S-adenosylmethionine (SAM) binding site in the large polymerase protein date: 2018-05-01 journal: Virology DOI: 10.1016/j.virol.2018.02.022 sha: doc_id: 289248 cord_uid: 6mx4o0eb file: cache/cord-289712-w1y0lc5c.json key: cord-289712-w1y0lc5c authors: Flintoff, Wayne F. title: Replication of murine coronaviruses in somatic cell hybrids between murine fibroblasts and rat Schwannoma cells date: 1984-04-30 journal: Virology DOI: 10.1016/0042-6822(84)90312-x sha: doc_id: 289712 cord_uid: w1y0lc5c file: cache/cord-279924-09uwhxs9.json key: cord-279924-09uwhxs9 authors: Plaisted, Warren C.; Weinger, Jason G.; Walsh, Craig M.; Lane, Thomas E. title: T cell mediated suppression of neurotropic coronavirus replication in neural precursor cells date: 2014-01-01 journal: Virology DOI: 10.1016/j.virol.2013.11.025 sha: doc_id: 279924 cord_uid: 09uwhxs9 file: cache/cord-285869-jwflooop.json key: cord-285869-jwflooop authors: Clementz, Mark A.; Kanjanahaluethai, Amornrat; O’Brien, Timothy E.; Baker, Susan C. title: Mutation in murine coronavirus replication protein nsp4 alters assembly of double membrane vesicles date: 2008-05-01 journal: Virology DOI: 10.1016/j.virol.2008.01.018 sha: doc_id: 285869 cord_uid: jwflooop file: cache/cord-287777-ogs4mq0v.json key: cord-287777-ogs4mq0v authors: Lindner, Holger A. title: Deubiquitination in virus infection date: 2007-06-05 journal: Virology DOI: 10.1016/j.virol.2006.12.035 sha: doc_id: 287777 cord_uid: ogs4mq0v file: cache/cord-281309-c9y7m5do.json key: cord-281309-c9y7m5do authors: Guo, Baoqing; Lager, Kelly M.; Henningson, Jamie N.; Miller, Laura C.; Schlink, Sarah N.; Kappes, Matthew A.; Kehrli, Marcus E.; Brockmeier, Susan L.; Nicholson, Tracy L.; Yang, Han-Chun; Faaberg, Kay S. title: Experimental infection of United States swine with a Chinese highly pathogenic strain of porcine reproductive and respiratory syndrome virus date: 2013-01-20 journal: Virology DOI: 10.1016/j.virol.2012.09.013 sha: doc_id: 281309 cord_uid: c9y7m5do file: cache/cord-275403-g4rohhtt.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-275403-g4rohhtt authors: Bautista, Elida M.; 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Vogel, Leatrice; Roberts, Anjeanette; Fahle, Gary; Fischer, Steven; Shieh, Wun-Ju; Butler, Emily; Zaki, Sherif; St. Claire, Marisa; Murphy, Brian; Subbarao, Kanta title: Replication of SARS coronavirus administered into the respiratory tract of African Green, rhesus and cynomolgus monkeys date: 2004-12-05 journal: Virology DOI: 10.1016/j.virol.2004.09.030 sha: doc_id: 290993 cord_uid: bsnja161 file: cache/cord-289152-w5ynbewh.json key: cord-289152-w5ynbewh authors: Lee, Sang-Myeong; Kleiboeker, Steven B. title: Porcine arterivirus activates the NF-κB pathway through IκB degradation date: 2005-11-10 journal: Virology DOI: 10.1016/j.virol.2005.07.034 sha: doc_id: 289152 cord_uid: w5ynbewh file: cache/cord-289991-wx4rsr4g.json key: cord-289991-wx4rsr4g authors: Bhowmick, Rahul; Banik, George; Chanda, Shampa; Chattopadhyay, Shiladitya; Chawla-Sarkar, Mamta title: Rotavirus infection induces G1 to S phase transition in MA104 cells via Ca(+2)/Calmodulin pathway date: 2014-03-21 journal: Virology DOI: 10.1016/j.virol.2014.03.001 sha: doc_id: 289991 cord_uid: wx4rsr4g file: cache/cord-290640-kh2t0kfz.json key: cord-290640-kh2t0kfz authors: O'Connor, Jennifer Black; 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C.; Petty, I.T.D.; Jackson, A. O. title: RNA recombination in the genome of Barley stripe mosaic virus date: 1992-07-31 journal: Virology DOI: 10.1016/0042-6822(92)90722-2 sha: doc_id: 330847 cord_uid: a84pcc9z file: cache/cord-337976-c2auspti.json key: cord-337976-c2auspti authors: Weiss, Susan R. title: Coronaviruses SD and SK share extensive nucleotide homology with murine coronavirus MHV-A59, more than that shared between human and murine coronaviruses date: 1983-04-30 journal: Virology DOI: 10.1016/s0042-6822(83)80022-1 sha: doc_id: 337976 cord_uid: c2auspti file: cache/cord-351197-xv6ymc4l.json key: cord-351197-xv6ymc4l authors: Cibulski, Samuel; Alves de Lima, Diane; Fernandes dos Santos, Helton; Teixeira, Thais Fumaco; Tochetto, Caroline; Mayer, Fabiana Quoos; Roehe, Paulo Michel title: A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil date: 2020-09-28 journal: Virology DOI: 10.1016/j.virol.2020.09.005 sha: doc_id: 351197 cord_uid: xv6ymc4l file: cache/cord-340983-w219g6qs.json key: cord-340983-w219g6qs authors: Smith, Mary Ellen; Koser, Martin; Xiao, Sa; Siler, Catherine; McGettigan, James P.; Calkins, Catherine; Pomerantz, Roger J.; Dietzschold, Bernhard; Schnell, Matthias J. title: Rabies Virus Glycoprotein as a Carrier for Anthrax Protective Antigen date: 2006-09-01 journal: Virology DOI: 10.1016/j.virol.2006.05.010 sha: doc_id: 340983 cord_uid: w219g6qs file: cache/cord-345088-krb1eidw.json key: cord-345088-krb1eidw authors: Shen, S; Law, Y.C; Liu, D.X title: A single amino acid mutation in the spike protein of coronavirus infectious bronchitis virus hampers its maturation and incorporation into virions at the nonpermissive temperature date: 2004-09-01 journal: Virology DOI: 10.1016/j.virol.2004.06.016 sha: doc_id: 345088 cord_uid: krb1eidw file: cache/cord-346514-vyo8l14p.json key: cord-346514-vyo8l14p authors: Chen, I-Hsuan; Cheng, Jai-Hong; Huang, Ying-Wen; Lin, Na-Sheng; Hsu, Yau-Heiu; Tsai, Ching-Hsiu title: Characterization of the polyadenylation activity in a replicase complex from Bamboo mosaic virus-infected Nicotiana benthamiana plants date: 2013-06-13 journal: Virology DOI: 10.1016/j.virol.2013.05.032 sha: doc_id: 346514 cord_uid: vyo8l14p file: cache/cord-345630-bam3pa70.json key: cord-345630-bam3pa70 authors: Lee, Han-Jung; Shieh, Chien-Kou; Gorbalenya, Alexander E.; Koonin, Eugene V.; La Monica, Nicola; Tuler, Jeremy; Bagdzhadzhyan, Anush; Lai, Michael M.C. title: The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase date: 1991-02-28 journal: Virology DOI: 10.1016/0042-6822(91)90071-i sha: doc_id: 345630 cord_uid: bam3pa70 file: cache/cord-335482-nx7odchj.json key: cord-335482-nx7odchj authors: Makino, Shinji; Taguchi, Fumihiro; Fujiwara, Kosaku title: Defective interfering particles of mouse hepatitis virus date: 1984-02-29 journal: Virology DOI: 10.1016/0042-6822(84)90420-3 sha: doc_id: 335482 cord_uid: nx7odchj file: cache/cord-332356-au7s3dmp.json key: cord-332356-au7s3dmp authors: Strandin, Tomas; Hepojoki, Jussi; Wang, Hao; Vaheri, Antti; Lankinen, Hilkka title: The cytoplasmic tail of hantavirus Gn glycoprotein interacts with RNA date: 2011-09-15 journal: Virology DOI: 10.1016/j.virol.2011.06.030 sha: doc_id: 332356 cord_uid: au7s3dmp file: cache/cord-353467-wbtzvm4i.json key: cord-353467-wbtzvm4i authors: Lambert, Carsten; Thomé, Nicole; Kluck, Christoph J.; Prange, Reinhild title: Functional incorporation of green fluorescent protein into hepatitis B virus envelope particles date: 2004-12-05 journal: Virology DOI: 10.1016/j.virol.2004.09.031 sha: doc_id: 353467 cord_uid: wbtzvm4i file: cache/cord-353748-y1a52z8e.json key: cord-353748-y1a52z8e authors: Bhattacharya, Rajarshi; Gupta, Aayatti Mallick; Mitra, Suranjita; Mandal, Sukhendu; Biswas, Swadesh R. title: A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2 date: 2021-01-02 journal: Virology DOI: 10.1016/j.virol.2020.10.002 sha: doc_id: 353748 cord_uid: y1a52z8e Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named journal-virology-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: 47985 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: 50196 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: 50411 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: 51163 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: 51312 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: 49416 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: 49885 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: 50709 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. 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: 48445 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: 48367 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: 48325 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: 48757 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: 48900 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: 49056 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: 49611 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: 50133 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: 50272 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: 51147 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: 51517 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: 48353 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: 50488 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: 50742 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: 51912 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: 52529 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: 52604 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 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: 52262 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: 52854 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: 52863 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-258691-cd83w9o6 author: Whitman, Lucia title: IFN-γ-mediated suppression of coronavirus replication in glial-committed progenitor cells date: 2009-02-01 pages: extension: .txt txt: ./txt/cord-258691-cd83w9o6.txt cache: ./cache/cord-258691-cd83w9o6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258691-cd83w9o6.txt' === file2bib.sh === id: cord-255738-r8zfdsix author: Ge, Feng title: Derivation of a novel SARS–coronavirus replicon cell line and its application for anti-SARS drug screening date: 2007-03-30 pages: extension: .txt txt: ./txt/cord-255738-r8zfdsix.txt cache: ./cache/cord-255738-r8zfdsix.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255738-r8zfdsix.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 52617 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 52605 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-258232-br4z3na6 author: Maeda, Junko title: Release of Coronavirus E Protein in Membrane Vesicles from Virus-Infected Cells and E Protein-Expressing Cells date: 1999-10-25 pages: extension: .txt txt: ./txt/cord-258232-br4z3na6.txt cache: ./cache/cord-258232-br4z3na6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258232-br4z3na6.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-272437-gvzfl8c3 author: Zhao, Jing title: Replicase 1a gene plays a critical role in pathogenesis of avian coronavirus infectious bronchitis virus date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-272437-gvzfl8c3.txt cache: ./cache/cord-272437-gvzfl8c3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.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-272437-gvzfl8c3.txt' === file2bib.sh === id: cord-266230-ia04jc9j author: Rott, M. E. title: Comparison of the 5′ and 3′ termini of tomato ringspot virus RNA1 and RNA2: Evidence for RNA recombination date: 1991-11-30 pages: extension: .txt txt: ./txt/cord-266230-ia04jc9j.txt cache: ./cache/cord-266230-ia04jc9j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266230-ia04jc9j.txt' === file2bib.sh === id: cord-254950-y6kayxie author: Morse, Stephen S. title: Mouse thymic virus (MTLV; Murid Herpesvirus 3) infection in athymic nude mice: Evidence for a T lymphocyte requirement date: 1988-03-31 pages: extension: .txt txt: ./txt/cord-254950-y6kayxie.txt cache: ./cache/cord-254950-y6kayxie.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254950-y6kayxie.txt' === file2bib.sh === id: cord-254747-vox5xsgd author: Deng, Xufang title: An “Old” Protein with A New Story: Coronavirus Endoribonuclease Is Important for Evading Host Antiviral Defenses date: 2018-04-01 pages: extension: .txt txt: ./txt/cord-254747-vox5xsgd.txt cache: ./cache/cord-254747-vox5xsgd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254747-vox5xsgd.txt' === file2bib.sh === id: cord-260376-29ih5c9v author: Guo, Jian-Ping title: SARS corona virus peptides recognized by antibodies in the sera of convalescent cases date: 2004-07-01 pages: extension: .txt txt: ./txt/cord-260376-29ih5c9v.txt cache: ./cache/cord-260376-29ih5c9v.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260376-29ih5c9v.txt' === file2bib.sh === id: cord-008407-jbp8bxjz author: Derdeyn, Cynthia A. title: Characterization of defective-interfering RNAs of rubella virusgenerated during serial undiluted passage date: 1995-01-10 pages: extension: .txt txt: ./txt/cord-008407-jbp8bxjz.txt cache: ./cache/cord-008407-jbp8bxjz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-008407-jbp8bxjz.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: 59715 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: 59266 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: 58619 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-267014-3vi7pgvr author: Vennema, H. title: Genomic organization and expression of the 3′ end of the canine and feline enteric coronaviruses date: 1992-11-30 pages: extension: .txt txt: ./txt/cord-267014-3vi7pgvr.txt cache: ./cache/cord-267014-3vi7pgvr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267014-3vi7pgvr.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: 59022 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 59615 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: 59155 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: 59382 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-256703-eaj63c2k author: Matsuoka, Yumiko title: Intracellular accumulation of punta toro virus glycoproteins expressed from cloned cDNA date: 1988-11-30 pages: extension: .txt txt: ./txt/cord-256703-eaj63c2k.txt cache: ./cache/cord-256703-eaj63c2k.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256703-eaj63c2k.txt' === file2bib.sh === id: cord-258379-v3lceirh author: Liu, D. X. title: Association of the infectious bronchitis virus 3c protein with the virion envelope date: 1991-12-31 pages: extension: .txt txt: ./txt/cord-258379-v3lceirh.txt cache: ./cache/cord-258379-v3lceirh.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-258379-v3lceirh.txt' === file2bib.sh === id: cord-260108-osg8q89i author: Park, Yon Mi title: Full genome analysis of a novel adenovirus from the South Polar skua (Catharacta maccormicki) in Antarctica date: 2012-01-05 pages: extension: .txt txt: ./txt/cord-260108-osg8q89i.txt cache: ./cache/cord-260108-osg8q89i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260108-osg8q89i.txt' === file2bib.sh === id: cord-269193-a647hwu9 author: Lin, Debby A. title: Evolutionary relatedness of the predicted gene product of RNA segment 2 of the Tick-Borne Dhori virus and the PB1 polymerase gene of influenza viruses date: 1991-05-31 pages: extension: .txt txt: ./txt/cord-269193-a647hwu9.txt cache: ./cache/cord-269193-a647hwu9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269193-a647hwu9.txt' === file2bib.sh === id: cord-262245-eb7g9p1x author: Monica, Nicola La title: Localization of extensive deletions in the structural genes of two neurotropic variants of murine coronavirus JHM date: 1991-06-30 pages: extension: .txt txt: ./txt/cord-262245-eb7g9p1x.txt cache: ./cache/cord-262245-eb7g9p1x.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262245-eb7g9p1x.txt' === file2bib.sh === id: cord-265895-ck7eto16 author: Baric, Ralph S. title: Analysis of intracellular small RNAs of mouse hepatitis virus: evidence for discontinuous transcription date: 1987-02-28 pages: extension: .txt txt: ./txt/cord-265895-ck7eto16.txt cache: ./cache/cord-265895-ck7eto16.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265895-ck7eto16.txt' === file2bib.sh === id: cord-269866-3tpyj04y author: Liu, D. X. title: Identification of two new polypeptides encoded by mRNA5 of the coronavirus infectious bronchitis virus date: 1992-01-31 pages: extension: .txt txt: ./txt/cord-269866-3tpyj04y.txt cache: ./cache/cord-269866-3tpyj04y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269866-3tpyj04y.txt' === file2bib.sh === id: cord-266018-8bhnlsgy author: Trifilo, Matthew J. title: The CC chemokine ligand 3 regulates CD11c(+)CD11b(+)CD8α(−) dendritic cell maturation and activation following viral infection of the central nervous system: implications for a role in T cell activation date: 2004-09-15 pages: extension: .txt txt: ./txt/cord-266018-8bhnlsgy.txt cache: ./cache/cord-266018-8bhnlsgy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266018-8bhnlsgy.txt' === file2bib.sh === id: cord-260177-xu0elmak author: Collins, Arlene R. title: Monoclonal antibodies to murine hepatitis virus-4 (strain JHM) define the viral glycoprotein responsible for attachment and cell-cell fusion date: 1982-06-30 pages: extension: .txt txt: ./txt/cord-260177-xu0elmak.txt cache: ./cache/cord-260177-xu0elmak.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260177-xu0elmak.txt' === file2bib.sh === id: cord-267377-wyhsxj6g author: Edwards, Michael C. title: Coat protein expression strategy of oat blue dwarf virus() date: 2014-01-14 pages: extension: .txt txt: ./txt/cord-267377-wyhsxj6g.txt cache: ./cache/cord-267377-wyhsxj6g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267377-wyhsxj6g.txt' === file2bib.sh === id: cord-272050-0u62j7nj author: Okamoto, Kimiyuki title: cis-Preferential requirement of a − 1 frameshift product p88 for the replication of Red clover necrotic mosaic virus RNA1 date: 2008-05-25 pages: extension: .txt txt: ./txt/cord-272050-0u62j7nj.txt cache: ./cache/cord-272050-0u62j7nj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272050-0u62j7nj.txt' === file2bib.sh === id: cord-264359-m9j3pcj1 author: Vrijsen, R. title: Resolution of the major poliovirus capsid polypeptides into doublets date: 1978-05-15 pages: extension: .txt txt: ./txt/cord-264359-m9j3pcj1.txt cache: ./cache/cord-264359-m9j3pcj1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264359-m9j3pcj1.txt' === file2bib.sh === id: cord-269419-68kja6bg author: Hu, Weibin title: Fully human broadly neutralizing monoclonal antibodies against influenza A viruses generated from the memory B cells of a 2009 pandemic H1N1 influenza vaccine recipient date: 2013-01-20 pages: extension: .txt txt: ./txt/cord-269419-68kja6bg.txt cache: ./cache/cord-269419-68kja6bg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269419-68kja6bg.txt' === file2bib.sh === id: cord-254558-gvo0gwjf author: Guo, Yan Xiang title: Induction of caspase-dependent apoptosis by betanodaviruses GGNNV and demonstration of protein α as an apoptosis inducer date: 2003-03-30 pages: extension: .txt txt: ./txt/cord-254558-gvo0gwjf.txt cache: ./cache/cord-254558-gvo0gwjf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254558-gvo0gwjf.txt' === file2bib.sh === id: cord-258327-03vk6enj author: Schultze, Beate title: Isolated HE-protein from hemagglutinating encephalomyelitis virus and bovine coronavirus has receptor-destroying and receptor-binding activity date: 1991-01-31 pages: extension: .txt txt: ./txt/cord-258327-03vk6enj.txt cache: ./cache/cord-258327-03vk6enj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-258327-03vk6enj.txt' === file2bib.sh === id: cord-273246-4s54jrww author: Niu, Shengniao title: An infectious RNA with a hepta-adenosine stretch responsible for programmed −1 ribosomal frameshift derived from a full-length cDNA clone of Hibiscus latent Singapore virus date: 2014-01-20 pages: extension: .txt txt: ./txt/cord-273246-4s54jrww.txt cache: ./cache/cord-273246-4s54jrww.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 38 resourceName b'cord-273246-4s54jrww.txt' === file2bib.sh === id: cord-273379-w8vy5rl8 author: Mizutani, Tetsuya title: Nascent Synthesis of Leader Sequence-Containing Subgenomic mRNAs in Coronavirus Genome-Length Replicative Intermediate RNA date: 2000-09-30 pages: extension: .txt txt: ./txt/cord-273379-w8vy5rl8.txt cache: ./cache/cord-273379-w8vy5rl8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273379-w8vy5rl8.txt' === file2bib.sh === id: cord-269204-kajws5xo author: Nitschke, Matthias title: Equine arteritis virus is delivered to an acidic compartment of host cells via clathrin-dependent endocytosis date: 2008-08-01 pages: extension: .txt txt: ./txt/cord-269204-kajws5xo.txt cache: ./cache/cord-269204-kajws5xo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269204-kajws5xo.txt' === file2bib.sh === id: cord-252615-ajyv95pu author: Lu, Yanfang title: ATP1B3: a virus-induced host factor against EV71 replication by up-regulating the production of type-I interferons date: 2016-05-27 pages: extension: .txt txt: ./txt/cord-252615-ajyv95pu.txt cache: ./cache/cord-252615-ajyv95pu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252615-ajyv95pu.txt' === file2bib.sh === id: cord-259095-mfptcw8t author: Lu, Yiqi title: Determinants of Mouse Hepatitis Virus 3C-like Proteinase Activity date: 1997-04-14 pages: extension: .txt txt: ./txt/cord-259095-mfptcw8t.txt cache: ./cache/cord-259095-mfptcw8t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-259095-mfptcw8t.txt' === file2bib.sh === id: cord-274673-tjzlssal author: De Groot, Raoul J. title: Stably expressed FIPV peplomer protein induces cell fusion and elicits neutralizing antibodies in mice date: 1989-08-31 pages: extension: .txt txt: ./txt/cord-274673-tjzlssal.txt cache: ./cache/cord-274673-tjzlssal.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274673-tjzlssal.txt' === file2bib.sh === id: cord-268467-btfz6ye8 author: Schreiber, Steven S. title: Sequence analysis of the nucleocapsid protein gene of human coronavirus 229E date: 1989-03-31 pages: extension: .txt txt: ./txt/cord-268467-btfz6ye8.txt cache: ./cache/cord-268467-btfz6ye8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268467-btfz6ye8.txt' === file2bib.sh === id: cord-252397-qlu7dilh author: Johnson, Reed F. title: Intratracheal exposure of common marmosets to MERS-CoV Jordan-n3/2012 or MERS-CoV EMC/2012 isolates does not result in lethal disease date: 2015-11-01 pages: extension: .txt txt: ./txt/cord-252397-qlu7dilh.txt cache: ./cache/cord-252397-qlu7dilh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252397-qlu7dilh.txt' === file2bib.sh === id: cord-267718-t47i8hui author: Bao, Jingyue title: Evolutionary dynamics of recent peste des petits ruminants virus epidemic in China during 2013–2014 date: 2017-07-19 pages: extension: .txt txt: ./txt/cord-267718-t47i8hui.txt cache: ./cache/cord-267718-t47i8hui.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267718-t47i8hui.txt' === file2bib.sh === id: cord-258286-lodjcj8c author: Zhang, Xuming title: Expression of Interferon-γ by a Coronavirus Defective-Interfering RNA Vector and Its Effect on Viral Replication, Spread, and Pathogenicity date: 1997-07-07 pages: extension: .txt txt: ./txt/cord-258286-lodjcj8c.txt cache: ./cache/cord-258286-lodjcj8c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258286-lodjcj8c.txt' === file2bib.sh === id: cord-259500-ndjbrtrv author: Satyanarayana, Tatineni title: Frameshift mutations in infectious cDNA clones of Citrus tristeza virus: a strategy to minimize the toxicity of viral sequences to Escherichia coli date: 2003-09-01 pages: extension: .txt txt: ./txt/cord-259500-ndjbrtrv.txt cache: ./cache/cord-259500-ndjbrtrv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259500-ndjbrtrv.txt' === file2bib.sh === id: cord-262441-slh52nxm author: Sakai, Yusuke title: Two-amino acids change in the nsp4 of SARS coronavirus abolishes viral replication date: 2017-07-21 pages: extension: .txt txt: ./txt/cord-262441-slh52nxm.txt cache: ./cache/cord-262441-slh52nxm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262441-slh52nxm.txt' === file2bib.sh === id: cord-265173-70wyecwj author: Trujillo-Uscanga, Adrian title: Host cell p53 associates with the feline calicivirus major viral capsid protein VP1, the protease-polymerase NS6/7, and the double-stranded RNA playing a role in virus replication date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-265173-70wyecwj.txt cache: ./cache/cord-265173-70wyecwj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265173-70wyecwj.txt' === file2bib.sh === id: cord-268341-103xf3dw author: Parra, Beatriz title: Kinetics of Cytokine mRNA Expression in the Central Nervous System Following Lethal and Nonlethal Coronavirus-Induced Acute Encephalomyelitis date: 1997-07-07 pages: extension: .txt txt: ./txt/cord-268341-103xf3dw.txt cache: ./cache/cord-268341-103xf3dw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268341-103xf3dw.txt' === file2bib.sh === id: cord-268416-8hw80qx8 author: Grunewald, Matthew E. title: The coronavirus nucleocapsid protein is ADP-ribosylated date: 2018-04-01 pages: extension: .txt txt: ./txt/cord-268416-8hw80qx8.txt cache: ./cache/cord-268416-8hw80qx8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268416-8hw80qx8.txt' === file2bib.sh === id: cord-271526-14nfqusv author: Molenkamp, Richard title: Identification of a Specific Interaction between the Coronavirus Mouse Hepatitis Virus A59 Nucleocapsid Protein and Packaging Signal date: 1997-12-08 pages: extension: .txt txt: ./txt/cord-271526-14nfqusv.txt cache: ./cache/cord-271526-14nfqusv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271526-14nfqusv.txt' === file2bib.sh === id: cord-259717-e8ljkv2y author: Holtz, Lori R. title: Geographic variation in the eukaryotic virome of human diarrhea date: 2014-11-01 pages: extension: .txt txt: ./txt/cord-259717-e8ljkv2y.txt cache: ./cache/cord-259717-e8ljkv2y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-259717-e8ljkv2y.txt' === file2bib.sh === id: cord-007373-livz5zuu author: Gayathri, P. title: Crystal structure of the serine protease domain of Sesbania mosaic virus polyprotein and mutational analysis of residues forming the S1-binding pocket date: 2006-03-15 pages: extension: .txt txt: ./txt/cord-007373-livz5zuu.txt cache: ./cache/cord-007373-livz5zuu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007373-livz5zuu.txt' === file2bib.sh === id: cord-253351-b36g09r0 author: Luo, Zongli title: Roles in Cell-to-Cell Fusion of Two Conserved Hydrophobic Regions in the Murine Coronavirus Spike Protein date: 1998-05-10 pages: extension: .txt txt: ./txt/cord-253351-b36g09r0.txt cache: ./cache/cord-253351-b36g09r0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-253351-b36g09r0.txt' === file2bib.sh === id: cord-008426-ktn8c0zx author: Othman, Yasmin title: Nucleotide sequence of the bean strain of southern bean mosaic virus() date: 1995-01-10 pages: extension: .txt txt: ./txt/cord-008426-ktn8c0zx.txt cache: ./cache/cord-008426-ktn8c0zx.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-008426-ktn8c0zx.txt' === file2bib.sh === id: cord-274172-3dctmmfe author: Lucas, Alexandra title: In vivo and in vitro models of demyelinating diseases II. Persistence and host-regulated thermosensitivity in cells of neural derivation infected with mouse hepatitis and measles viruses date: 1978-07-15 pages: extension: .txt txt: ./txt/cord-274172-3dctmmfe.txt cache: ./cache/cord-274172-3dctmmfe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274172-3dctmmfe.txt' === file2bib.sh === id: cord-255841-3laov764 author: Duquerroy, Stéphane title: Central ions and lateral asparagine/glutamine zippers stabilize the post-fusion hairpin conformation of the SARS coronavirus spike glycoprotein() date: 2005-05-10 pages: extension: .txt txt: ./txt/cord-255841-3laov764.txt cache: ./cache/cord-255841-3laov764.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255841-3laov764.txt' === file2bib.sh === id: cord-270534-ebkwv4zo author: Bodmer, Bianca S. title: Live-attenuated bivalent measles virus-derived vaccines targeting Middle East respiratory syndrome coronavirus induce robust and multifunctional T cell responses against both viruses in an appropriate mouse model date: 2018-06-11 pages: extension: .txt txt: ./txt/cord-270534-ebkwv4zo.txt cache: ./cache/cord-270534-ebkwv4zo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270534-ebkwv4zo.txt' === file2bib.sh === id: cord-263302-z5uhrta5 author: Zhang, Xuming title: Identification of a Noncanonical Signal for Transcription of a Novel Subgenomic mRNA of Mouse Hepatitis Virus: Implication for the Mechanism of Coronavirus RNA Transcription date: 2000-12-05 pages: extension: .txt txt: ./txt/cord-263302-z5uhrta5.txt cache: ./cache/cord-263302-z5uhrta5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263302-z5uhrta5.txt' === file2bib.sh === id: cord-264331-uvi8ucz4 author: Singh, Shailbala title: Avian influenza viral nucleocapsid and hemagglutinin proteins induce chicken CD8(+) memory T lymphocytes date: 2010-04-10 pages: extension: .txt txt: ./txt/cord-264331-uvi8ucz4.txt cache: ./cache/cord-264331-uvi8ucz4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264331-uvi8ucz4.txt' === file2bib.sh === id: cord-255453-7e40rj1y author: Oliver, S.L. title: Genomic characterization of the unclassified bovine enteric virus Newbury agent-1 (Newbury1) endorses a new genus in the family Caliciviridae date: 2006-06-20 pages: extension: .txt txt: ./txt/cord-255453-7e40rj1y.txt cache: ./cache/cord-255453-7e40rj1y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255453-7e40rj1y.txt' === file2bib.sh === id: cord-267532-5rnqd9mb author: Zhang, Xuming title: Expression of Hemagglutinin/Esterase by a Mouse Hepatitis Virus Coronavirus Defective–Interfering RNA Alters Viral Pathogenesis date: 1998-03-01 pages: extension: .txt txt: ./txt/cord-267532-5rnqd9mb.txt cache: ./cache/cord-267532-5rnqd9mb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267532-5rnqd9mb.txt' === file2bib.sh === id: cord-262574-gu0930s3 author: Slagle, Betty L. title: Identification and characterization of a mouse mammary tumor virus protein uniquely expressed on the surface of BALB/cV mammary tumor cells date: 1985-05-31 pages: extension: .txt txt: ./txt/cord-262574-gu0930s3.txt cache: ./cache/cord-262574-gu0930s3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262574-gu0930s3.txt' === file2bib.sh === id: cord-266585-jfjrk9gy author: Fang, Shouguo title: An arginine-to-proline mutation in a domain with undefined functions within the helicase protein (Nsp13) is lethal to the coronavirus infectious bronchitis virus in cultured cells date: 2007-02-05 pages: extension: .txt txt: ./txt/cord-266585-jfjrk9gy.txt cache: ./cache/cord-266585-jfjrk9gy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266585-jfjrk9gy.txt' === file2bib.sh === id: cord-263334-wwkdum94 author: Li, Chen title: Cellular DDX3 regulates Japanese encephalitis virus replication by interacting with viral un-translated regions date: 2014-01-20 pages: extension: .txt txt: ./txt/cord-263334-wwkdum94.txt cache: ./cache/cord-263334-wwkdum94.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263334-wwkdum94.txt' === file2bib.sh === id: cord-253894-4u5yt7b7 author: Senkevich, Tatiana G. title: Vaccinia virus F16 protein, a predicted catalytically inactive member of the prokaryotic serine recombinase superfamily, is targeted to nucleoli date: 2011-09-01 pages: extension: .txt txt: ./txt/cord-253894-4u5yt7b7.txt cache: ./cache/cord-253894-4u5yt7b7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253894-4u5yt7b7.txt' === file2bib.sh === id: cord-260695-qwepi0we author: Postler, Thomas S. title: Identification and characterization of a long non-coding RNA up-regulated during HIV-1 infection date: 2017-11-01 pages: extension: .txt txt: ./txt/cord-260695-qwepi0we.txt cache: ./cache/cord-260695-qwepi0we.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260695-qwepi0we.txt' === file2bib.sh === id: cord-260782-1lm8tzbc author: Giles, Julia title: Viral RNA load and histological changes in tissues following experimental infection with an arterivirus of possums (wobbly possum disease virus) date: 2018-07-14 pages: extension: .txt txt: ./txt/cord-260782-1lm8tzbc.txt cache: ./cache/cord-260782-1lm8tzbc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260782-1lm8tzbc.txt' === file2bib.sh === id: cord-265156-u1re7983 author: de Wilde, Adriaan H. title: Coronaviruses and arteriviruses display striking differences in their cyclophilin A-dependence during replication in cell culture date: 2017-12-15 pages: extension: .txt txt: ./txt/cord-265156-u1re7983.txt cache: ./cache/cord-265156-u1re7983.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265156-u1re7983.txt' === file2bib.sh === id: cord-256036-gd53s4dv author: Sandmann, Lisa title: Barriers of hepatitis C virus interspecies transmission date: 2013-01-01 pages: extension: .txt txt: ./txt/cord-256036-gd53s4dv.txt cache: ./cache/cord-256036-gd53s4dv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256036-gd53s4dv.txt' === file2bib.sh === id: cord-279813-mrei5kih author: Temeeyasen, G. title: Differential gene modulation of pattern-recognition receptor TLR and RIG-I-like and downstream mediators on intestinal mucosa of pigs infected with PEDV non S-INDEL and PEDV S-INDEL strains date: 2017-12-14 pages: extension: .txt txt: ./txt/cord-279813-mrei5kih.txt cache: ./cache/cord-279813-mrei5kih.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279813-mrei5kih.txt' === file2bib.sh === id: cord-256737-ptjng78b author: McBride, Corrin E. title: Palmitoylation of SARS-CoV S protein is necessary for partitioning into detergent-resistant membranes and cell-cell fusion but not interaction with M protein date: 2010-09-01 pages: extension: .txt txt: ./txt/cord-256737-ptjng78b.txt cache: ./cache/cord-256737-ptjng78b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256737-ptjng78b.txt' === file2bib.sh === id: cord-266617-z8uecyl6 author: Pavesi, Angelo title: Asymmetric evolution in viral overlapping genes is a source of selective protein adaptation date: 2019-04-03 pages: extension: .txt txt: ./txt/cord-266617-z8uecyl6.txt cache: ./cache/cord-266617-z8uecyl6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266617-z8uecyl6.txt' === file2bib.sh === id: cord-253024-b393ea2u author: Fu, Kaisong title: Evidence for variable rates of recombination in the MHV genome date: 1992-07-31 pages: extension: .txt txt: ./txt/cord-253024-b393ea2u.txt cache: ./cache/cord-253024-b393ea2u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253024-b393ea2u.txt' === file2bib.sh === id: cord-284968-eymvj6k3 author: Namazue, Junko title: Processing of virus-specific glycoproteins of varicella zoster virus date: 1985-05-31 pages: extension: .txt txt: ./txt/cord-284968-eymvj6k3.txt cache: ./cache/cord-284968-eymvj6k3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284968-eymvj6k3.txt' === file2bib.sh === id: cord-286060-92lazxd7 author: Stohlman, Stephen A. title: Synthesis and subcellular localization of the murine coronavirus nucleocapsid protein date: 1983-10-30 pages: extension: .txt txt: ./txt/cord-286060-92lazxd7.txt cache: ./cache/cord-286060-92lazxd7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-286060-92lazxd7.txt' === file2bib.sh === id: cord-284581-fl2nt4ak author: Kleine-Weber, Hannah title: Spike proteins of novel MERS-coronavirus isolates from North- and West-African dromedary camels mediate robust viral entry into human target cells date: 2019-07-19 pages: extension: .txt txt: ./txt/cord-284581-fl2nt4ak.txt cache: ./cache/cord-284581-fl2nt4ak.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284581-fl2nt4ak.txt' === file2bib.sh === id: cord-274480-aywdmj6o author: Song, Wenfei title: Identification of residues on human receptor DPP4 critical for MERS-CoV binding and entry date: 2014-10-21 pages: extension: .txt txt: ./txt/cord-274480-aywdmj6o.txt cache: ./cache/cord-274480-aywdmj6o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274480-aywdmj6o.txt' === file2bib.sh === id: cord-255828-jrqdyfbg author: Du, Yijun title: Glycosyl-phosphatidylinositol (GPI)-anchored membrane association of the porcine reproductive and respiratory syndrome virus GP4 glycoprotein and its co-localization with CD163 in lipid rafts date: 2012-03-01 pages: extension: .txt txt: ./txt/cord-255828-jrqdyfbg.txt cache: ./cache/cord-255828-jrqdyfbg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255828-jrqdyfbg.txt' === file2bib.sh === id: cord-272871-gu9ptt9y author: White, K.Andrew title: Defective RNAs of clover yellow mosaic virus encode nonstructural/coat protein fusion products date: 1991-08-31 pages: extension: .txt txt: ./txt/cord-272871-gu9ptt9y.txt cache: ./cache/cord-272871-gu9ptt9y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-272871-gu9ptt9y.txt' === file2bib.sh === id: cord-281820-oltqsd6n author: Watanabe, Rie title: Heparan sulfate is a binding molecule but not a receptor for CEACAM1-independent infection of murine coronavirus date: 2007-09-15 pages: extension: .txt txt: ./txt/cord-281820-oltqsd6n.txt cache: ./cache/cord-281820-oltqsd6n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281820-oltqsd6n.txt' === file2bib.sh === id: cord-284646-fhruiw23 author: Jaeger, Anna S. title: Spondweni virus causes fetal harm in Ifnar1(-/-) mice and is transmitted by Aedes aegypti mosquitoes date: 2020-05-24 pages: extension: .txt txt: ./txt/cord-284646-fhruiw23.txt cache: ./cache/cord-284646-fhruiw23.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284646-fhruiw23.txt' === file2bib.sh === id: cord-281237-asnpuami author: Garten, Wolfgang title: Inhibition of proteolytic activation of influenza virus hemagglutinin by specific peptidyl chloroalkyl ketones date: 1989-09-30 pages: extension: .txt txt: ./txt/cord-281237-asnpuami.txt cache: ./cache/cord-281237-asnpuami.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281237-asnpuami.txt' === file2bib.sh === id: cord-255773-b4re5bky author: Zhang, Qingzhan title: Suppression of type I interferon production by porcine epidemic diarrhea virus and degradation of CREB-binding protein by nsp1 date: 2016-01-14 pages: extension: .txt txt: ./txt/cord-255773-b4re5bky.txt cache: ./cache/cord-255773-b4re5bky.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255773-b4re5bky.txt' === file2bib.sh === id: cord-279924-09uwhxs9 author: Plaisted, Warren C. title: T cell mediated suppression of neurotropic coronavirus replication in neural precursor cells date: 2014-01-01 pages: extension: .txt txt: ./txt/cord-279924-09uwhxs9.txt cache: ./cache/cord-279924-09uwhxs9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279924-09uwhxs9.txt' === file2bib.sh === id: cord-280795-wtrt13ij author: Han, Yu-Tsung title: Mutational analysis of a helicase motif-based RNA 5′-triphosphatase/NTPase from bamboo mosaic virus date: 2007-10-10 pages: extension: .txt txt: ./txt/cord-280795-wtrt13ij.txt cache: ./cache/cord-280795-wtrt13ij.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280795-wtrt13ij.txt' === file2bib.sh === id: cord-284707-72vx11aq author: Leibowitz, Julian L. title: Synthesis of virus-specific RNA in permeabilized murine coronavirus-infected cells date: 1988-09-30 pages: extension: .txt txt: ./txt/cord-284707-72vx11aq.txt cache: ./cache/cord-284707-72vx11aq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-284707-72vx11aq.txt' === file2bib.sh === id: cord-286121-ltaxmp3u author: Xu, Ke title: Severe acute respiratory syndrome coronavirus accessory protein 9b is a virion-associated protein date: 2009-06-05 pages: extension: .txt txt: ./txt/cord-286121-ltaxmp3u.txt cache: ./cache/cord-286121-ltaxmp3u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286121-ltaxmp3u.txt' === file2bib.sh === id: cord-275348-jna496x7 author: Kapadia, Sagar U. title: SARS vaccine based on a replication-defective recombinant vesicular stomatitis virus is more potent than one based on a replication-competent vector date: 2008-06-20 pages: extension: .txt txt: ./txt/cord-275348-jna496x7.txt cache: ./cache/cord-275348-jna496x7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-275348-jna496x7.txt' === file2bib.sh === id: cord-283998-whwksoxt author: Tannock, Gregory A. title: The RNA of human coronavirus OC-43 date: 1977-12-31 pages: extension: .txt txt: ./txt/cord-283998-whwksoxt.txt cache: ./cache/cord-283998-whwksoxt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-283998-whwksoxt.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: 64264 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: 63900 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: 64407 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-290640-kh2t0kfz author: O'Connor, Jennifer Black title: Downstream Ribosomal Entry for Translation of Coronavirus TGEV Gene 3b date: 2000-03-30 pages: extension: .txt txt: ./txt/cord-290640-kh2t0kfz.txt cache: ./cache/cord-290640-kh2t0kfz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290640-kh2t0kfz.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: 64747 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-289248-6mx4o0eb author: Wang, Yilong title: Enhancement of safety and immunogenicity of the Chinese Hu191 measles virus vaccine by alteration of the S-adenosylmethionine (SAM) binding site in the large polymerase protein date: 2018-05-01 pages: extension: .txt txt: ./txt/cord-289248-6mx4o0eb.txt cache: ./cache/cord-289248-6mx4o0eb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289248-6mx4o0eb.txt' === file2bib.sh === id: cord-280287-t7uozjml author: Favier, Anne-Laure title: Unique physicochemical properties of human enteric Ad41 responsible for its survival and replication in the gastrointestinal tract date: 2004-04-25 pages: extension: .txt txt: ./txt/cord-280287-t7uozjml.txt cache: ./cache/cord-280287-t7uozjml.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280287-t7uozjml.txt' === file2bib.sh === id: cord-294056-7e477y1x author: La Monica, Nicola title: Coronavirus mRNA synthesis: Identification of novel transcription initiation signals which are differentially regulated by different leader sequences date: 1992-05-31 pages: extension: .txt txt: ./txt/cord-294056-7e477y1x.txt cache: ./cache/cord-294056-7e477y1x.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294056-7e477y1x.txt' === file2bib.sh === id: cord-291611-cfe8yujp author: Zhang, Xuming title: Comparison of the nucleotide and deduced amino acid sequences of the S genes specified by virulent and avirulent strains of bovine coronaviruses date: 1991-07-31 pages: extension: .txt txt: ./txt/cord-291611-cfe8yujp.txt cache: ./cache/cord-291611-cfe8yujp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291611-cfe8yujp.txt' === file2bib.sh === id: cord-275403-g4rohhtt author: Bautista, Elida M. title: Functional Properties of the Predicted Helicase of Porcine Reproductive and Respiratory Syndrome Virus date: 2002-07-05 pages: extension: .txt txt: ./txt/cord-275403-g4rohhtt.txt cache: ./cache/cord-275403-g4rohhtt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-275403-g4rohhtt.txt' === file2bib.sh === id: cord-293375-qcy56ui7 author: Strauss, Ellen G. title: Identification of the active site residues in the nsP2 proteinase of sindbis virus date: 1992-12-31 pages: extension: .txt txt: ./txt/cord-293375-qcy56ui7.txt cache: ./cache/cord-293375-qcy56ui7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293375-qcy56ui7.txt' === file2bib.sh === id: cord-291306-g9qmmugg author: Vey, Martin title: Hemagglutinin activation of pathogenic avian influenza viruses of serotype H7 requires the protease recognition motif R-X-K/R-R date: 1992-05-31 pages: extension: .txt txt: ./txt/cord-291306-g9qmmugg.txt cache: ./cache/cord-291306-g9qmmugg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291306-g9qmmugg.txt' === file2bib.sh === id: cord-287620-vuvgi8xx author: Butler, Noah title: Murine encephalitis caused by HCoV-OC43, a human coronavirus with broad species specificity, is partly immune-mediated date: 2006-04-10 pages: extension: .txt txt: ./txt/cord-287620-vuvgi8xx.txt cache: ./cache/cord-287620-vuvgi8xx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287620-vuvgi8xx.txt' === file2bib.sh === id: cord-285869-jwflooop author: Clementz, Mark A. title: Mutation in murine coronavirus replication protein nsp4 alters assembly of double membrane vesicles date: 2008-05-01 pages: extension: .txt txt: ./txt/cord-285869-jwflooop.txt cache: ./cache/cord-285869-jwflooop.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285869-jwflooop.txt' === file2bib.sh === id: cord-296075-8axbkyyz author: Castro, Raymond F. title: Differential Antigen Recognition by T Cells from the Spleen and Central Nervous System of Coronavirus-Infected Mice date: 1996-08-01 pages: extension: .txt txt: ./txt/cord-296075-8axbkyyz.txt cache: ./cache/cord-296075-8axbkyyz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296075-8axbkyyz.txt' === file2bib.sh === id: cord-282947-3hgku2e4 author: Wong, Hui Hui title: Accessory proteins 8b and 8ab of severe acute respiratory syndrome coronavirus suppress the interferon signaling pathway by mediating ubiquitin-dependent rapid degradation of interferon regulatory factor 3 date: 2017-12-30 pages: extension: .txt txt: ./txt/cord-282947-3hgku2e4.txt cache: ./cache/cord-282947-3hgku2e4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282947-3hgku2e4.txt' === file2bib.sh === id: cord-303497-s3zs1oxf author: Breuning, Astrid title: Characterization of a cold-sensitive (cs) recombinant between two influenza a strains date: 1983-10-15 pages: extension: .txt txt: ./txt/cord-303497-s3zs1oxf.txt cache: ./cache/cord-303497-s3zs1oxf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-303497-s3zs1oxf.txt' === file2bib.sh === id: cord-281309-c9y7m5do author: Guo, Baoqing title: Experimental infection of United States swine with a Chinese highly pathogenic strain of porcine reproductive and respiratory syndrome virus date: 2013-01-20 pages: extension: .txt txt: ./txt/cord-281309-c9y7m5do.txt cache: ./cache/cord-281309-c9y7m5do.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281309-c9y7m5do.txt' === file2bib.sh === id: cord-287777-ogs4mq0v author: Lindner, Holger A. title: Deubiquitination in virus infection date: 2007-06-05 pages: extension: .txt txt: ./txt/cord-287777-ogs4mq0v.txt cache: ./cache/cord-287777-ogs4mq0v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287777-ogs4mq0v.txt' === file2bib.sh === id: cord-289991-wx4rsr4g author: Bhowmick, Rahul title: Rotavirus infection induces G1 to S phase transition in MA104 cells via Ca(+2)/Calmodulin pathway date: 2014-03-21 pages: extension: .txt txt: ./txt/cord-289991-wx4rsr4g.txt cache: ./cache/cord-289991-wx4rsr4g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-289991-wx4rsr4g.txt' === file2bib.sh === id: cord-290282-oxyzndsj author: Ortego, Javier title: Transmissible gastroenteritis coronavirus gene 7 is not essential but influences in vivo virus replication and virulence date: 2003-03-30 pages: extension: .txt txt: ./txt/cord-290282-oxyzndsj.txt cache: ./cache/cord-290282-oxyzndsj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290282-oxyzndsj.txt' === file2bib.sh === id: cord-293248-8vtd9e4n author: Day, J. Michael title: Determination and analysis of the full-length chicken parvovirus genome date: 2010-03-30 pages: extension: .txt txt: ./txt/cord-293248-8vtd9e4n.txt cache: ./cache/cord-293248-8vtd9e4n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293248-8vtd9e4n.txt' === file2bib.sh === id: cord-293790-7hyelm88 author: Guévin, Carl title: Autophagy protein ATG5 interacts transiently with the hepatitis C virus RNA polymerase (NS5B) early during infection date: 2010-09-01 pages: extension: .txt txt: ./txt/cord-293790-7hyelm88.txt cache: ./cache/cord-293790-7hyelm88.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293790-7hyelm88.txt' === file2bib.sh === id: cord-289152-w5ynbewh author: Lee, Sang-Myeong title: Porcine arterivirus activates the NF-κB pathway through IκB degradation date: 2005-11-10 pages: extension: .txt txt: ./txt/cord-289152-w5ynbewh.txt cache: ./cache/cord-289152-w5ynbewh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-289152-w5ynbewh.txt' === file2bib.sh === id: cord-302972-imtttzvr author: Feldmann, H. title: Glycosylation and oligomerization of the spike protein of marburg virus date: 1991-05-31 pages: extension: .txt txt: ./txt/cord-302972-imtttzvr.txt cache: ./cache/cord-302972-imtttzvr.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302972-imtttzvr.txt' === file2bib.sh === id: cord-296364-7rp60d2m author: Youn, Soonjeon title: In vitro assembled, recombinant infectious bronchitis viruses demonstrate that the 5a open reading frame is not essential for replication date: 2005-02-05 pages: extension: .txt txt: ./txt/cord-296364-7rp60d2m.txt cache: ./cache/cord-296364-7rp60d2m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296364-7rp60d2m.txt' === file2bib.sh === id: cord-294990-jdjbjkcp author: Thuy, Nguyen Thanh title: A new nidovirus (NamDinh virus NDiV): Its ultrastructural characterization in the C6/36 mosquito cell line date: 2013-07-25 pages: extension: .txt txt: ./txt/cord-294990-jdjbjkcp.txt cache: ./cache/cord-294990-jdjbjkcp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294990-jdjbjkcp.txt' === file2bib.sh === id: cord-310218-fky0cm5e author: Yoo, Dongwan title: The S2 subunit of the spike glycoprotein of bovine coronavirus mediates membrane fusion in insect cells date: 1991-01-31 pages: extension: .txt txt: ./txt/cord-310218-fky0cm5e.txt cache: ./cache/cord-310218-fky0cm5e.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310218-fky0cm5e.txt' === file2bib.sh === id: cord-319179-gqaxf7mz author: Denison, M. title: Identification of putative polymerase gene product in cells infected with murine coronavirus A59 date: 1987-04-30 pages: extension: .txt txt: ./txt/cord-319179-gqaxf7mz.txt cache: ./cache/cord-319179-gqaxf7mz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319179-gqaxf7mz.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-292019-rfu0bkag author: Gómez, N. title: Expression of Immunogenic Glycoprotein S Polypeptides from Transmissible Gastroenteritis Coronavirus in Transgenic Plants date: 1998-09-30 pages: extension: .txt txt: ./txt/cord-292019-rfu0bkag.txt cache: ./cache/cord-292019-rfu0bkag.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292019-rfu0bkag.txt' === file2bib.sh === id: cord-278578-vq5fy8m5 author: Stodola, Jenny K. title: The OC43 human coronavirus envelope protein is critical for infectious virus production and propagation in neuronal cells and is a determinant of neurovirulence and CNS pathology date: 2017-12-26 pages: extension: .txt txt: ./txt/cord-278578-vq5fy8m5.txt cache: ./cache/cord-278578-vq5fy8m5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278578-vq5fy8m5.txt' === file2bib.sh === id: cord-309919-sm5o0g1c author: Eichwald, Catherine title: Mammalian orthoreovirus core protein μ2 reorganizes host microtubule-organizing center components. date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-309919-sm5o0g1c.txt cache: ./cache/cord-309919-sm5o0g1c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309919-sm5o0g1c.txt' === file2bib.sh === id: cord-292751-tk1oggi9 author: Hosseini, Elahe Seyed title: The novel coronavirus Disease-2019 (COVID-19): Mechanism of action, detection and recent therapeutic strategies date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-292751-tk1oggi9.txt cache: ./cache/cord-292751-tk1oggi9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292751-tk1oggi9.txt' === file2bib.sh === id: cord-290231-4m9lj0uq author: Guirakhoo, Farshad title: The Murray Valley encephalitis virus prM protein confers acid resistance to virus particles and alters the expression of epitopes within the R2 domain of E glycoprotein date: 1992-12-31 pages: extension: .txt txt: ./txt/cord-290231-4m9lj0uq.txt cache: ./cache/cord-290231-4m9lj0uq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290231-4m9lj0uq.txt' === file2bib.sh === id: cord-298934-vtrfqozl author: Makino, Shinji title: Primary structure and translation of a defective interfering rna of murine coronavirus date: 1988-10-31 pages: extension: .txt txt: ./txt/cord-298934-vtrfqozl.txt cache: ./cache/cord-298934-vtrfqozl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298934-vtrfqozl.txt' === file2bib.sh === id: cord-312210-3x9s3g8n author: Stoian, Ana title: The use of cells from ANPEP knockout pigs to evaluate the role of aminopeptidase N (APN) as a receptor for porcine deltacoronavirus (PDCoV) date: 2019-12-24 pages: extension: .txt txt: ./txt/cord-312210-3x9s3g8n.txt cache: ./cache/cord-312210-3x9s3g8n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312210-3x9s3g8n.txt' === file2bib.sh === id: cord-296416-q0rsfzgw author: LAVI, EHUD title: Syncytia Formation Induced by Coronavirus Infection Is Associated with Fragmentation and Rearrangement of the Golgi Apparatus date: 1996-07-15 pages: extension: .txt txt: ./txt/cord-296416-q0rsfzgw.txt cache: ./cache/cord-296416-q0rsfzgw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296416-q0rsfzgw.txt' === file2bib.sh === id: cord-297712-yy4g5npi author: Zhu, Xinyu title: Porcine deltacoronavirus nsp5 inhibits interferon-β production through the cleavage of NEMO date: 2016-12-13 pages: extension: .txt txt: ./txt/cord-297712-yy4g5npi.txt cache: ./cache/cord-297712-yy4g5npi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297712-yy4g5npi.txt' === file2bib.sh === id: cord-299122-djfj4262 author: Yu, Hua title: Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice() date: 2007-03-15 pages: extension: .txt txt: ./txt/cord-299122-djfj4262.txt cache: ./cache/cord-299122-djfj4262.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299122-djfj4262.txt' === file2bib.sh === id: cord-290883-r2744fb3 author: TORRES, JUAN M. title: Induction of Antibodies Protecting against Transmissible Gastroenteritis Coronavirus (TGEV) by Recombinant Adenovirus Expressing TGEV Spike Protein date: 1995-11-30 pages: extension: .txt txt: ./txt/cord-290883-r2744fb3.txt cache: ./cache/cord-290883-r2744fb3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290883-r2744fb3.txt' === file2bib.sh === id: cord-286232-jo24ia4s author: Hasebe, Rie title: Infectious entry of equine herpesvirus-1 into host cells through different endocytic pathways date: 2009-10-25 pages: extension: .txt txt: ./txt/cord-286232-jo24ia4s.txt cache: ./cache/cord-286232-jo24ia4s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286232-jo24ia4s.txt' === file2bib.sh === id: cord-298847-szezd2vb author: Jacomy, Hélène title: Vacuolating encephalitis in mice infected by human coronavirus OC43 date: 2003-10-10 pages: extension: .txt txt: ./txt/cord-298847-szezd2vb.txt cache: ./cache/cord-298847-szezd2vb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-298847-szezd2vb.txt' === file2bib.sh === id: cord-301755-fxfsr9bj author: Wang, F.-I. title: Sequence analysis of the spike protein gene of murine coronavirus variants: Study of genetic sites affecting neuropathogenicity date: 1992-02-29 pages: extension: .txt txt: ./txt/cord-301755-fxfsr9bj.txt cache: ./cache/cord-301755-fxfsr9bj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-301755-fxfsr9bj.txt' === file2bib.sh === id: cord-299976-36r794ow author: O’Brien, Amornrat title: Characterizing replication kinetics and plaque production of type I feline infectious peritonitis virus in three feline cell lines date: 2018-12-01 pages: extension: .txt txt: ./txt/cord-299976-36r794ow.txt cache: ./cache/cord-299976-36r794ow.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299976-36r794ow.txt' === file2bib.sh === id: cord-315158-f6msh8od author: Taguchi, Fumihiro title: Comparison of six different murine coronavirus jhm variants by monoclonal antibodies against the e2 glycoprotein date: 1989-03-31 pages: extension: .txt txt: ./txt/cord-315158-f6msh8od.txt cache: ./cache/cord-315158-f6msh8od.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315158-f6msh8od.txt' === file2bib.sh === id: cord-300810-a1skdp67 author: Lafay, F. title: Spread of the CVS strain of rabies virus and of the avirulent mutant AvO1 along the olfactory pathways of the mouse after intranasal inoculation date: 1991-07-31 pages: extension: .txt txt: ./txt/cord-300810-a1skdp67.txt cache: ./cache/cord-300810-a1skdp67.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300810-a1skdp67.txt' === file2bib.sh === id: cord-303238-us3dybue author: Kanjanahaluethai, Amornrat title: Membrane Topology of Murine Coronavirus Replicase Nonstructural Protein 3 date: 2007-05-01 pages: extension: .txt txt: ./txt/cord-303238-us3dybue.txt cache: ./cache/cord-303238-us3dybue.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303238-us3dybue.txt' === file2bib.sh === id: cord-293635-36pmai6s author: Held, Katherine S. title: Differential roles of CCL2 and CCR2 in host defense to coronavirus infection date: 2004-11-24 pages: extension: .txt txt: ./txt/cord-293635-36pmai6s.txt cache: ./cache/cord-293635-36pmai6s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293635-36pmai6s.txt' === file2bib.sh === id: cord-310748-ao29zx1u author: Banner, Lisa R. title: Random nature of coronavirus RNA recombination in the absence of selection pressure date: 1991-11-30 pages: extension: .txt txt: ./txt/cord-310748-ao29zx1u.txt cache: ./cache/cord-310748-ao29zx1u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310748-ao29zx1u.txt' === file2bib.sh === id: cord-289045-vft163v0 author: Thackray, Larissa B. title: Substitutions of conserved amino acids in the receptor-binding domain of the spike glycoprotein affect utilization of murine CEACAM1a by the murine coronavirus MHV-A59 date: 2005-03-30 pages: extension: .txt txt: ./txt/cord-289045-vft163v0.txt cache: ./cache/cord-289045-vft163v0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-289045-vft163v0.txt' === file2bib.sh === id: cord-288669-46tkedw7 author: Lee, Changhee title: The small envelope protein of porcine reproductive and respiratory syndrome virus possesses ion channel protein-like properties date: 2006-11-10 pages: extension: .txt txt: ./txt/cord-288669-46tkedw7.txt cache: ./cache/cord-288669-46tkedw7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288669-46tkedw7.txt' === file2bib.sh === id: cord-313091-ksrxsdpp author: Shirato, Kazuya title: Wild-type human coronaviruses prefer cell-surface TMPRSS2 to endosomal cathepsins for cell entry date: 2017-12-06 pages: extension: .txt txt: ./txt/cord-313091-ksrxsdpp.txt cache: ./cache/cord-313091-ksrxsdpp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313091-ksrxsdpp.txt' === file2bib.sh === id: cord-313906-fh85fzq9 author: Maruyama, Junki title: Characterization of the glycoproteins of bat-derived influenza viruses date: 2016-01-15 pages: extension: .txt txt: ./txt/cord-313906-fh85fzq9.txt cache: ./cache/cord-313906-fh85fzq9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313906-fh85fzq9.txt' === file2bib.sh === id: cord-300470-vgd1ol2z author: Conradie, Andelé M. title: Establishment of different plasmid only-based reverse genetics systems for the recovery of African horse sickness virus date: 2016-09-19 pages: extension: .txt txt: ./txt/cord-300470-vgd1ol2z.txt cache: ./cache/cord-300470-vgd1ol2z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300470-vgd1ol2z.txt' === file2bib.sh === id: cord-309469-2naxn580 author: An, Hongliu title: Identification and formation mechanism of a novel noncoding RNA produced by avian infectious bronchitis virus date: 2019-01-05 pages: extension: .txt txt: ./txt/cord-309469-2naxn580.txt cache: ./cache/cord-309469-2naxn580.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309469-2naxn580.txt' === file2bib.sh === id: cord-300884-rqfxe0x1 author: Zhang, Jianqiang title: Genomic characterization of equine coronavirus date: 2007-12-05 pages: extension: .txt txt: ./txt/cord-300884-rqfxe0x1.txt cache: ./cache/cord-300884-rqfxe0x1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300884-rqfxe0x1.txt' === file2bib.sh === id: cord-331807-ooym5eh3 author: Wu, Tao title: A reverse-transcription recombinase-aided amplification assay for the rapid detection of N gene of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-331807-ooym5eh3.txt cache: ./cache/cord-331807-ooym5eh3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331807-ooym5eh3.txt' === file2bib.sh === id: cord-305564-dj3vj4tk author: DeDiego, Marta L. title: PATHOGENICITY OF SEVERE ACUTE RESPIRATORY CORONAVIRUS DELETION MUTANTS IN hACE-2 TRANSGENIC MICE date: 2008-07-01 pages: extension: .txt txt: ./txt/cord-305564-dj3vj4tk.txt cache: ./cache/cord-305564-dj3vj4tk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305564-dj3vj4tk.txt' === file2bib.sh === id: cord-308835-999kewdw author: Leibowitz, Julian L. title: The virus-specific intracellular RNA species of two murine coronaviruses: MHV-A59 and MHV-JHM date: 1981-10-15 pages: extension: .txt txt: ./txt/cord-308835-999kewdw.txt cache: ./cache/cord-308835-999kewdw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308835-999kewdw.txt' === file2bib.sh === id: cord-318400-l9kwxsq7 author: Chhabra, Rajesh title: Pathogenicity and tissue tropism of infectious bronchitis virus is associated with elevated apoptosis and innate immune responses date: 2016-01-15 pages: extension: .txt txt: ./txt/cord-318400-l9kwxsq7.txt cache: ./cache/cord-318400-l9kwxsq7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-318400-l9kwxsq7.txt' === file2bib.sh === id: cord-326688-a1djgqpa author: Dubois-Dalcq, Monique E. title: Cell tropism and expression of mouse hepatitis viruses (MHV) in mouse spinal cord cultures date: 1982-06-30 pages: extension: .txt txt: ./txt/cord-326688-a1djgqpa.txt cache: ./cache/cord-326688-a1djgqpa.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326688-a1djgqpa.txt' === file2bib.sh === id: cord-309015-t5v2sjus author: York, Joanne title: Genetic analysis of heptad-repeat regions in the G2 fusion subunit of the Junín arenavirus envelope glycoprotein date: 2005-12-20 pages: extension: .txt txt: ./txt/cord-309015-t5v2sjus.txt cache: ./cache/cord-309015-t5v2sjus.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309015-t5v2sjus.txt' === file2bib.sh === id: cord-321162-pgd34ewv author: Holmes, Kathryn V. title: Tunicamycin resistant glycosylation of a coronavirus glycoprotein: Demonstration of a novel type of viral glycoprotein date: 1981-12-31 pages: extension: .txt txt: ./txt/cord-321162-pgd34ewv.txt cache: ./cache/cord-321162-pgd34ewv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321162-pgd34ewv.txt' === file2bib.sh === id: cord-307396-u6v6bxwj author: Liao, Y. title: Biochemical and functional characterization of the membrane association and membrane permeabilizing activity of the severe acute respiratory syndrome coronavirus envelope protein date: 2006-06-05 pages: extension: .txt txt: ./txt/cord-307396-u6v6bxwj.txt cache: ./cache/cord-307396-u6v6bxwj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307396-u6v6bxwj.txt' === file2bib.sh === id: cord-315069-xo4mbxei author: Knorr, D. A. title: De novo generation of defective interfering RNAs of tomato bushy stunt virus by high multiplicity passage date: 1991-03-31 pages: extension: .txt txt: ./txt/cord-315069-xo4mbxei.txt cache: ./cache/cord-315069-xo4mbxei.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315069-xo4mbxei.txt' === file2bib.sh === id: cord-291192-wm2eyaam author: Becares, Martina title: Antigenic structures stably expressed by recombinant TGEV-derived vectors date: 2014-08-09 pages: extension: .txt txt: ./txt/cord-291192-wm2eyaam.txt cache: ./cache/cord-291192-wm2eyaam.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-291192-wm2eyaam.txt' === file2bib.sh === id: cord-324054-d71rj29o author: Zhang, Xuming title: The hemagglutinin/esterase gene of human coronavirus strain OC43: Phylogenetic relationships to bovine and murine coronaviruses and influenza C virus date: 1992-01-31 pages: extension: .txt txt: ./txt/cord-324054-d71rj29o.txt cache: ./cache/cord-324054-d71rj29o.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324054-d71rj29o.txt' === file2bib.sh === id: cord-322062-nnefbeo6 author: Tam, Albert W. title: Hepatitis E virus (HEV): Molecular cloning and sequencing of the full-length viral genome date: 1991-11-30 pages: extension: .txt txt: ./txt/cord-322062-nnefbeo6.txt cache: ./cache/cord-322062-nnefbeo6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322062-nnefbeo6.txt' === file2bib.sh === id: cord-302486-z36hcvrx author: Cobo, Fernando title: Diagnostic approaches for viruses and prions in stem cell banks date: 2006-03-30 pages: extension: .txt txt: ./txt/cord-302486-z36hcvrx.txt cache: ./cache/cord-302486-z36hcvrx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302486-z36hcvrx.txt' === file2bib.sh === id: cord-299994-1ksfo0pr author: Kanitz, Manuel title: Structural basis for catalysis and substrate specificity of a 3C-like cysteine protease from a mosquito mesonivirus date: 2019-05-02 pages: extension: .txt txt: ./txt/cord-299994-1ksfo0pr.txt cache: ./cache/cord-299994-1ksfo0pr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-299994-1ksfo0pr.txt' === file2bib.sh === id: cord-321265-il9vbbgk author: DEN BOON, JOHAN A. title: Equine Arteritis Virus Subgenomic RNA Transcription: UV Inactivation and Translation Inhibition Studies date: 1995-11-30 pages: extension: .txt txt: ./txt/cord-321265-il9vbbgk.txt cache: ./cache/cord-321265-il9vbbgk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321265-il9vbbgk.txt' === file2bib.sh === id: cord-304421-xpj6c0vx author: Piñón, Josefina D. title: Further Requirements for Cleavage by the Murine Coronavirus 3C-like Proteinase: Identification of a Cleavage Site within ORF1b date: 1999-10-25 pages: extension: .txt txt: ./txt/cord-304421-xpj6c0vx.txt cache: ./cache/cord-304421-xpj6c0vx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304421-xpj6c0vx.txt' === file2bib.sh === id: cord-294260-g410mavp author: Sztuba-Solińska, Joanna title: Subgenomic messenger RNAs: Mastering regulation of (+)-strand RNA virus life cycle date: 2011-04-10 pages: extension: .txt txt: ./txt/cord-294260-g410mavp.txt cache: ./cache/cord-294260-g410mavp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294260-g410mavp.txt' === file2bib.sh === id: cord-301293-jqy7lcbk author: Gupta, Vandana title: SARS coronavirus nucleocapsid immunodominant T-cell epitope cluster is common to both exogenous recombinant and endogenous DNA-encoded immunogens date: 2006-03-30 pages: extension: .txt txt: ./txt/cord-301293-jqy7lcbk.txt cache: ./cache/cord-301293-jqy7lcbk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301293-jqy7lcbk.txt' === file2bib.sh === id: cord-300372-h5g4z8ts author: Kelvin, Alyson A. title: Lack of Group X Secreted Phospholipase A(2) Increases Survival Following Pandemic H1N1 Influenza Infection date: 2014-04-01 pages: extension: .txt txt: ./txt/cord-300372-h5g4z8ts.txt cache: ./cache/cord-300372-h5g4z8ts.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-300372-h5g4z8ts.txt' === file2bib.sh === id: cord-311255-zaa8i9vh author: Kim, Youngnam title: Porcine epidemic diarrhea virus induces caspase-independent apoptosis through activation of mitochondrial apoptosis-inducing factor date: 2014-07-31 pages: extension: .txt txt: ./txt/cord-311255-zaa8i9vh.txt cache: ./cache/cord-311255-zaa8i9vh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-311255-zaa8i9vh.txt' === file2bib.sh === id: cord-319403-5qyc0wsz author: Miura, Tanya A. title: Rat coronaviruses infect rat alveolar type I epithelial cells and induce expression of CXC chemokines date: 2007-12-01 pages: extension: .txt txt: ./txt/cord-319403-5qyc0wsz.txt cache: ./cache/cord-319403-5qyc0wsz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319403-5qyc0wsz.txt' === file2bib.sh === id: cord-310967-15mv5yx7 author: Morris, Vincent L. title: Characterization of coronavirus JHM variants isolated from wistar furth rats with a viral-induced demyelinating disease date: 1989-03-31 pages: extension: .txt txt: ./txt/cord-310967-15mv5yx7.txt cache: ./cache/cord-310967-15mv5yx7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310967-15mv5yx7.txt' === file2bib.sh === id: cord-307354-dkwcheu0 author: Abernathy, Emma title: Emerging roles for RNA degradation in viral replication and antiviral defense date: 2015-05-31 pages: extension: .txt txt: ./txt/cord-307354-dkwcheu0.txt cache: ./cache/cord-307354-dkwcheu0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307354-dkwcheu0.txt' === file2bib.sh === id: cord-322084-gkg1059v author: JEONG, YONG SEOK title: Coronavirus Transcription Mediated by Sequences Flanking the Transcription Consensus Sequence date: 1996-03-01 pages: extension: .txt txt: ./txt/cord-322084-gkg1059v.txt cache: ./cache/cord-322084-gkg1059v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322084-gkg1059v.txt' === file2bib.sh === id: cord-305143-mqd4ioj4 author: Zmasek, Christian M. title: Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO) date: 2019-01-06 pages: extension: .txt txt: ./txt/cord-305143-mqd4ioj4.txt cache: ./cache/cord-305143-mqd4ioj4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305143-mqd4ioj4.txt' === file2bib.sh === id: cord-317537-wgu5cd0y author: Lu, Hsiang-Chia title: Cymbidium mosaic potexvirus isolate-dependent host movement systems reveal two movement control determinants and the coat protein is the dominant date: 2009-05-25 pages: extension: .txt txt: ./txt/cord-317537-wgu5cd0y.txt cache: ./cache/cord-317537-wgu5cd0y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317537-wgu5cd0y.txt' === file2bib.sh === id: cord-330847-a84pcc9z author: Edwards, M. C. title: RNA recombination in the genome of Barley stripe mosaic virus date: 1992-07-31 pages: extension: .txt txt: ./txt/cord-330847-a84pcc9z.txt cache: ./cache/cord-330847-a84pcc9z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330847-a84pcc9z.txt' === file2bib.sh === id: cord-325179-gsf8ad65 author: Jarvis, Donald L. title: Modification of simian virus 40 large tumor antigen by glycosylation date: 1985-03-31 pages: extension: .txt txt: ./txt/cord-325179-gsf8ad65.txt cache: ./cache/cord-325179-gsf8ad65.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325179-gsf8ad65.txt' === file2bib.sh === id: cord-351197-xv6ymc4l author: Cibulski, Samuel title: A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-351197-xv6ymc4l.txt cache: ./cache/cord-351197-xv6ymc4l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351197-xv6ymc4l.txt' === file2bib.sh === id: cord-329794-msxrdhb3 author: Lu, Aili title: Attenuation of SARS coronavirus by a short hairpin RNA expression plasmid targeting RNA-dependent RNA polymerase date: 2004-06-20 pages: extension: .txt txt: ./txt/cord-329794-msxrdhb3.txt cache: ./cache/cord-329794-msxrdhb3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-329794-msxrdhb3.txt' === file2bib.sh === id: cord-337976-c2auspti author: Weiss, Susan R. title: Coronaviruses SD and SK share extensive nucleotide homology with murine coronavirus MHV-A59, more than that shared between human and murine coronaviruses date: 1983-04-30 pages: extension: .txt txt: ./txt/cord-337976-c2auspti.txt cache: ./cache/cord-337976-c2auspti.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-337976-c2auspti.txt' === file2bib.sh === id: cord-330907-srb8ac7l author: Leparc-Goffart, Isabelle title: Altered Pathogenesis of a Mutant of the Murine Coronavirus MHV-A59 Is Associated with a Q159L Amino Acid Substitution in the Spike Protein date: 1997-12-08 pages: extension: .txt txt: ./txt/cord-330907-srb8ac7l.txt cache: ./cache/cord-330907-srb8ac7l.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330907-srb8ac7l.txt' === file2bib.sh === id: cord-328046-5us4se5o author: Xu, H. Y. title: Further Identification and Characterization of Novel Intermediate and Mature Cleavage Products Released from the ORF 1b Region of the Avian Coronavirus Infectious Bronchitis Virus 1a/1b Polyprotein date: 2001-09-30 pages: extension: .txt txt: ./txt/cord-328046-5us4se5o.txt cache: ./cache/cord-328046-5us4se5o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328046-5us4se5o.txt' === file2bib.sh === id: cord-307904-lnagg1uw author: Johnson, Jennifer A title: Sequence elements controlling expression of Barley stripe mosaic virus subgenomic RNAs in vivo date: 2003-08-15 pages: extension: .txt txt: ./txt/cord-307904-lnagg1uw.txt cache: ./cache/cord-307904-lnagg1uw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307904-lnagg1uw.txt' === file2bib.sh === id: cord-329245-6tj2k1yn author: Corse, Emily title: The cytoplasmic tails of infectious bronchitis virus E and M proteins mediate their interaction date: 2003-07-20 pages: extension: .txt txt: ./txt/cord-329245-6tj2k1yn.txt cache: ./cache/cord-329245-6tj2k1yn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-329245-6tj2k1yn.txt' === file2bib.sh === id: cord-316460-ibprgdh4 author: Rodríguez-Grille, Javier title: Avian reovirus-triggered apoptosis enhances both virus spread and the processing of the viral nonstructural muNS protein date: 2014-06-17 pages: extension: .txt txt: ./txt/cord-316460-ibprgdh4.txt cache: ./cache/cord-316460-ibprgdh4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-316460-ibprgdh4.txt' === file2bib.sh === id: cord-317333-unrd76bo author: Danesh, Ali title: Early gene expression events in ferrets in response to SARS coronavirus infection versus direct interferon-alpha2b stimulation date: 2011-01-05 pages: extension: .txt txt: ./txt/cord-317333-unrd76bo.txt cache: ./cache/cord-317333-unrd76bo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317333-unrd76bo.txt' === file2bib.sh === id: cord-333525-67bbmo4m author: Yao, Qianqian title: Negatively charged residues in the endodomain are critical for specific assembly of spike protein into murine coronavirus date: 2013-07-01 pages: extension: .txt txt: ./txt/cord-333525-67bbmo4m.txt cache: ./cache/cord-333525-67bbmo4m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333525-67bbmo4m.txt' === file2bib.sh === id: cord-335482-nx7odchj author: Makino, Shinji title: Defective interfering particles of mouse hepatitis virus date: 1984-02-29 pages: extension: .txt txt: ./txt/cord-335482-nx7odchj.txt cache: ./cache/cord-335482-nx7odchj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335482-nx7odchj.txt' === file2bib.sh === id: cord-331916-n744pymd author: Liu, Jue title: Inhibition of porcine circovirus type 2 replication in mice by RNA interference date: 2006-04-10 pages: extension: .txt txt: ./txt/cord-331916-n744pymd.txt cache: ./cache/cord-331916-n744pymd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331916-n744pymd.txt' === file2bib.sh === id: cord-324321-y96x8x3h author: Cai, Yingyun title: Down-regulation of transcription of the proapoptotic gene BNip3 in cultured astrocytes by murine coronavirus infection date: 2003-11-10 pages: extension: .txt txt: ./txt/cord-324321-y96x8x3h.txt cache: ./cache/cord-324321-y96x8x3h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-324321-y96x8x3h.txt' === file2bib.sh === id: cord-316134-lkd2mj27 author: Sungsuwan, Suttipun title: Nucleocapsid proteins from other swine enteric coronaviruses differentially modulate PEDV replication date: 2020-01-15 pages: extension: .txt txt: ./txt/cord-316134-lkd2mj27.txt cache: ./cache/cord-316134-lkd2mj27.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-316134-lkd2mj27.txt' === file2bib.sh === id: cord-325481-uzch2hwd author: Simmons, Graham title: Different host cell proteases activate the SARS-coronavirus spike-protein for cell-cell and virus-cell fusion date: 2011-05-01 pages: extension: .txt txt: ./txt/cord-325481-uzch2hwd.txt cache: ./cache/cord-325481-uzch2hwd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325481-uzch2hwd.txt' === file2bib.sh === id: cord-329625-hx2rsi91 author: You, Jae-Hwan title: A model for the dynamic nuclear/nucleolar/cytoplasmic trafficking of the porcine reproductive and respiratory syndrome virus (PRRSV) nucleocapsid protein based on live cell imaging date: 2008-08-15 pages: extension: .txt txt: ./txt/cord-329625-hx2rsi91.txt cache: ./cache/cord-329625-hx2rsi91.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-329625-hx2rsi91.txt' === file2bib.sh === id: cord-353748-y1a52z8e author: Bhattacharya, Rajarshi title: A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2 date: 2021-01-02 pages: extension: .txt txt: ./txt/cord-353748-y1a52z8e.txt cache: ./cache/cord-353748-y1a52z8e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353748-y1a52z8e.txt' === file2bib.sh === id: cord-326027-58whwspe author: Hernaez, Bruno title: Visualization of the African swine fever virus infection in living cells by incorporation into the virus particle of green fluorescent protein-p54 membrane protein chimera date: 2006-06-20 pages: extension: .txt txt: ./txt/cord-326027-58whwspe.txt cache: ./cache/cord-326027-58whwspe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-326027-58whwspe.txt' === file2bib.sh === id: cord-329819-dpgexphf author: Hu, Weiwei title: Epidermal growth factor receptor is a co-factor for transmissible gastroenteritis virus entry date: 2018-06-04 pages: extension: .txt txt: ./txt/cord-329819-dpgexphf.txt cache: ./cache/cord-329819-dpgexphf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-329819-dpgexphf.txt' === file2bib.sh === id: cord-346514-vyo8l14p author: Chen, I-Hsuan title: Characterization of the polyadenylation activity in a replicase complex from Bamboo mosaic virus-infected Nicotiana benthamiana plants date: 2013-06-13 pages: extension: .txt txt: ./txt/cord-346514-vyo8l14p.txt cache: ./cache/cord-346514-vyo8l14p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346514-vyo8l14p.txt' === file2bib.sh === id: cord-345630-bam3pa70 author: Lee, Han-Jung title: The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase date: 1991-02-28 pages: extension: .txt txt: ./txt/cord-345630-bam3pa70.txt cache: ./cache/cord-345630-bam3pa70.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345630-bam3pa70.txt' === file2bib.sh === id: cord-340983-w219g6qs author: Smith, Mary Ellen title: Rabies Virus Glycoprotein as a Carrier for Anthrax Protective Antigen date: 2006-09-01 pages: extension: .txt txt: ./txt/cord-340983-w219g6qs.txt cache: ./cache/cord-340983-w219g6qs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340983-w219g6qs.txt' === file2bib.sh === id: cord-345088-krb1eidw author: Shen, S title: A single amino acid mutation in the spike protein of coronavirus infectious bronchitis virus hampers its maturation and incorporation into virions at the nonpermissive temperature date: 2004-09-01 pages: extension: .txt txt: ./txt/cord-345088-krb1eidw.txt cache: ./cache/cord-345088-krb1eidw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345088-krb1eidw.txt' === file2bib.sh === id: cord-334133-61om170g author: Hollier, Mark J. title: The C-terminal tail of the gp41 transmembrane envelope glycoprotein of HIV-1 clades A, B, C, and D may exist in two conformations: an analysis of sequence, structure, and function date: 2005-07-05 pages: extension: .txt txt: ./txt/cord-334133-61om170g.txt cache: ./cache/cord-334133-61om170g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334133-61om170g.txt' === file2bib.sh === id: cord-353467-wbtzvm4i author: Lambert, Carsten title: Functional incorporation of green fluorescent protein into hepatitis B virus envelope particles date: 2004-12-05 pages: extension: .txt txt: ./txt/cord-353467-wbtzvm4i.txt cache: ./cache/cord-353467-wbtzvm4i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353467-wbtzvm4i.txt' === file2bib.sh === id: cord-332356-au7s3dmp author: Strandin, Tomas title: The cytoplasmic tail of hantavirus Gn glycoprotein interacts with RNA date: 2011-09-15 pages: extension: .txt txt: ./txt/cord-332356-au7s3dmp.txt cache: ./cache/cord-332356-au7s3dmp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332356-au7s3dmp.txt' === file2bib.sh === id: cord-344515-e0g911le author: Voss, Kelsey title: Inhibition of host extracellular signal-regulated kinase (ERK) activation decreases new world alphavirus multiplication in infected cells date: 2014-11-30 pages: extension: .txt txt: ./txt/cord-344515-e0g911le.txt cache: ./cache/cord-344515-e0g911le.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-344515-e0g911le.txt' === file2bib.sh === id: cord-342901-ca2xxkb2 author: Lloyd, Richard E. title: Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses date: 2015-05-31 pages: extension: .txt txt: ./txt/cord-342901-ca2xxkb2.txt cache: ./cache/cord-342901-ca2xxkb2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342901-ca2xxkb2.txt' Que is empty; done journal-virology-cord === reduce.pl bib === id = cord-253351-b36g09r0 author = Luo, Zongli title = Roles in Cell-to-Cell Fusion of Two Conserved Hydrophobic Regions in the Murine Coronavirus Spike Protein date = 1998-05-10 pages = extension = .txt mime = text/plain words = 6840 sentences = 356 flesch = 57 summary = Similar substitutions within PEP2 result in a fusion-negative phenotype; however, these mutant S proteins also exhibit defects in protein processing and surface expression which likely explain the loss of the ability to induce fusion. To determine the importance of the asymmetric distribution of hydrophobicity in the induction of cell-to-cell fusion, as predicted by the ability to model this peptide as a sided ␣ helix ( Fig. 2A) , nonconservative and conservative amino acid substitutions were introduced in PEP1 to target representative bulky hydrophobic residues (F977K, F977L, L981K, L981I) and polar or charged residues (S975D, N978D, N978L, D986V-D989V). All mutant PEP1 S proteins were assayed for fusion using both in situ and quantitative fusion assays, performed as shown in Fig. 3 , using the vTF7-3-infected and wild-type S gene-transfected cells as positive controls and vTF7-3-infected and mock-transfected cells as negative controls. cache = ./cache/cord-253351-b36g09r0.txt txt = ./txt/cord-253351-b36g09r0.txt === reduce.pl bib === id = cord-256036-gd53s4dv author = Sandmann, Lisa title = Barriers of hepatitis C virus interspecies transmission date = 2013-01-01 pages = extension = .txt mime = text/plain words = 7894 sentences = 373 flesch = 40 summary = In contrast to human hepatocytes, murine cells do not support HCV entry thereby creating a first and important barrier for a broader host tropism of the virus. Utilizing blocking antibodies specific to CD81 or the viral envelope protein E2, expression of entry factor mutants and mice with a targeted disruption of the SCARB1 gene validated uptake of HCV into murine hepatocytes in an HCV glycoprotein-mediated fashion. Taking advantage of the high mutational plasticity of HCV, three adaptive mutations in the viral glycoproteins E1 and E2 were identified that allowed the virus to enter cells expressing human SCARB1, CLDN1, OCLN and mouse CD81. Recently, a genetically humanized mouse model was constructed utilizing cell culture produced recombinant hepatitis C virus to activate a cellular encoded reporter (Dorner et al., 2011, in press ). Human occludin is a hepatitis C virus entry factor required for infection of mouse cells A humanized mouse model to study Hepatitis C virus infection, immune response, and liver disease cache = ./cache/cord-256036-gd53s4dv.txt txt = ./txt/cord-256036-gd53s4dv.txt === reduce.pl bib === id = cord-255738-r8zfdsix author = Ge, Feng title = Derivation of a novel SARS–coronavirus replicon cell line and its application for anti-SARS drug screening date = 2007-03-30 pages = extension = .txt mime = text/plain words = 5103 sentences = 242 flesch = 49 summary = Sequence analysis of the replicon RNA purified from SCR-1 cells soon after selection in blasticidin (passage number 6) found no sequence differences compared with the published sequence of SARS-CoV strain SIN2774 (GenBank Accession Number AY283798). Baric's group constructed a transmissible gastroenteritis virus (TGEV) replicon for the expression of heterologous GFP gene (Curtis et al., 2002) and Thiel's group generated a non-cytopathic, selectable replicon RNA (based on HCoV 229E) for the identification of coronavirus replicase inhibitors (Hertzig et al., 2004) . Compared to anti-viral agent identification systems based on purified proteins or nucleic acids, our SARS-CoV replicon cell line has two advantages: first, if a candidate inhibitor can inhibit replication of our replicon RNA, which occurs intracellularly, it thus demonstrates that this agent can permeate the cell. To obtain the complete sequence of the SARS-CoV replicon persisting in the SCR-1 cells, the total cellular RNAs isolated from SRC-1 cells at passage number 6 and 40 were used as the templates. cache = ./cache/cord-255738-r8zfdsix.txt txt = ./txt/cord-255738-r8zfdsix.txt === reduce.pl bib === id = cord-007373-livz5zuu author = Gayathri, P. title = Crystal structure of the serine protease domain of Sesbania mosaic virus polyprotein and mutational analysis of residues forming the S1-binding pocket date = 2006-03-15 pages = extension = .txt mime = text/plain words = 6204 sentences = 362 flesch = 62 summary = authors: Gayathri, P.; Satheshkumar, P.S.; Prasad, K.; Nair, Smita; Savithri, H.S.; Murthy, M.R.N. title: Crystal structure of the serine protease domain of Sesbania mosaic virus polyprotein and mutational analysis of residues forming the S1-binding pocket In the present study, the crystal structure of SeMV protease domain was determined to a resolution of 2.4 Å by multiple isomorphous replacement coupled with anomalous scattering, with a view to identify the residues involved in substrate binding as well as protease -VPg interactions. The absence of well-defined density for F301 in SeMV protease suggests that its side chain might undergo substantial displacement on binding of the substrate or on conformational changes induced by the interaction of the protease domain with VPg. TEV and equine arteritis virus proteases, in which a serine residue occurs at the position corresponding to F301, are active in trans. cache = ./cache/cord-007373-livz5zuu.txt txt = ./txt/cord-007373-livz5zuu.txt === reduce.pl bib === id = cord-255773-b4re5bky author = Zhang, Qingzhan title = Suppression of type I interferon production by porcine epidemic diarrhea virus and degradation of CREB-binding protein by nsp1 date = 2016-01-14 pages = extension = .txt mime = text/plain words = 9880 sentences = 584 flesch = 52 summary = title: Suppression of type I interferon production by porcine epidemic diarrhea virus and degradation of CREB-binding protein by nsp1 We showed that PEDV suppressed the type I interferon production and ISGs expression in these cells, and identified nsp1, nsp3, nsp7, nsp14, nsp15, nsp16, E, M, N and ORF3 as the viral IFN antagonists. The CBP degradation is a novel mechanism of coronavirus nsp1 for IFN suppression and our study provides a new insight into the immune modulation and evasion strategy of PEDV. MARC-145 cells have been used to study type I IFN signaling of porcine arterivirus (Kim et al., 2010; Overend et al., 2007; Patel et al., 2010) , and thus infection of these cells One μg of each of the cloned genes was transfected to HeLa cells in 12-well plates, and protein expression was determined by immunofluorescence (B) and cache = ./cache/cord-255773-b4re5bky.txt txt = ./txt/cord-255773-b4re5bky.txt === reduce.pl bib === id = cord-253894-4u5yt7b7 author = Senkevich, Tatiana G. title = Vaccinia virus F16 protein, a predicted catalytically inactive member of the prokaryotic serine recombinase superfamily, is targeted to nucleoli date = 2011-09-01 pages = extension = .txt mime = text/plain words = 6253 sentences = 286 flesch = 44 summary = VACV, by far the most intensively studied poxvirus, replicates entirely in the cytoplasm of infected cells and encodes many of the proteins required for its growth as well as numerous proteins modulating virus-host interactions. Here we provide a detailed computational analysis of the F16 protein indicating that it is unlikely to have serine recombinase activity, and experimental data showing that the F16L gene is not required for virus growth in cell culture. F16-3xflag was detected by Western blotting at 2 h after infection, only slightly increased in amount between 4 and 24 h, and accumulated in the presence of cytosine arabinoside (araC), an inhibitor of DNA synthesis that prevents VACV intermediate and late gene expression. Two other VAC proteins, I3 and B1, containing a C-terminal 3xflag tag and expressed from a transfected plasmid under the control of the CMV promoter were analyzed in parallel with F16-3xflag, and no nucleolar or nuclear membrane staining was detected (not shown). cache = ./cache/cord-253894-4u5yt7b7.txt txt = ./txt/cord-253894-4u5yt7b7.txt === reduce.pl bib === id = cord-256703-eaj63c2k author = Matsuoka, Yumiko title = Intracellular accumulation of punta toro virus glycoproteins expressed from cloned cDNA date = 1988-11-30 pages = extension = .txt mime = text/plain words = 4311 sentences = 224 flesch = 56 summary = On the basis of genetic recombination and sequence analysis, it has been concluded that the S RNA encodes the nucleocapsid protein N and a nonstructural protein NS,; the M RNA encodes two glycoproteins Gl and G2 and in some genera a nonstructural protein, NS,; and the L RNA probably contains the information for the viral transcriptase (Bishop et al., 1982; Bouloy et a/., 1984; Cabradilla et al., 1983; Collett et a/., 1985; Eshita and Bishop, 1984; Fuller et al., 1983; lhara et a/., 1985; Lees et al., 1986; Ronnholm and Pettersson, 1987; Schmaljohn et a/., 1987 , 1982, 1984) . To compare the levels of PlV glycoprotein synthesis, monolayers of CV-1 cells were infected with wildtype vaccinia virus, PTV, or the vaccinia recombinants described above which contain the PTV glycoprotein gene with the different sequences in the translation initiation region. We have constructed vaccinia virus recombinants containing a partial cDNA clone of the M genome segment of PTV, which encodes the Gl and G2 glycoproteins. cache = ./cache/cord-256703-eaj63c2k.txt txt = ./txt/cord-256703-eaj63c2k.txt === reduce.pl bib === id = cord-008407-jbp8bxjz author = Derdeyn, Cynthia A. title = Characterization of defective-interfering RNAs of rubella virusgenerated during serial undiluted passage date = 1995-01-10 pages = extension = .txt mime = text/plain words = 6710 sentences = 298 flesch = 56 summary = During serial undiluted passage of rubella virus (RUB) in Vero cells, two species of defective-interfering (DI) RNAs of approximately 7000 and 800 nucleotides (nts) in length were generated (Frey, T. Finally, to determine whether the majority of DI RNAs present in P12 RNA contained a deletion in the SP-ORF, an oligonucleotide probe which is complementary to a sequence located within the E1 protein coding region (nts 8472 to 8488, eligonucleotide 83, Fig. 3E ) that was deleted in all three cDNA clones was hybridized to P12 RNA. Analysis of the 5' terminus of DI RNA generated during serial passage As shown in Figure 3A , oligonucleotide probes complementary to the exact 5' terminal sequences of the RUB genome hybridized to the large DI RNAs. To confirm that these DI RNAs contained the authentic 5' end of the genome, primer extension was performed on intraceilular RNA from standard RUB-infected cells and P12 RNA. cache = ./cache/cord-008407-jbp8bxjz.txt txt = ./txt/cord-008407-jbp8bxjz.txt === reduce.pl bib === id = cord-252615-ajyv95pu author = Lu, Yanfang title = ATP1B3: a virus-induced host factor against EV71 replication by up-regulating the production of type-I interferons date = 2016-05-27 pages = extension = .txt mime = text/plain words = 4186 sentences = 280 flesch = 54 summary = Although 3A protein had no effect on the expression of ATP1B3, EV71 infection resulted in elevated expression of ATP1B3 in RD cell line, both on messenger RNA (mRNA) and protein levels. Our study demonstrated that ATP1B3 inhibit EV71 replication by enhancing the production of type-I interferons, which could act as a potential therapeutic target in EV71 infection. We observed that both the mRNA and protein levels of ATP1B3 in RD cells were positively correlated with the infection doses of EV71 (Fig. 3B) . We infected ATP1B3 overpression cells or vector controls with EV71 at an MOI of 1, cultured cells with anti-human interferon-α1/β antibodies or isotype control IgG, and examined the viral replication using RT-PCR assay. Previous studies have shown that EV71 infection can induce IFN-β production which is dependent on the infectious dose, but the interferon is not cell type specific (Lu et al., 2012) . cache = ./cache/cord-252615-ajyv95pu.txt txt = ./txt/cord-252615-ajyv95pu.txt === reduce.pl bib === id = cord-254558-gvo0gwjf author = Guo, Yan Xiang title = Induction of caspase-dependent apoptosis by betanodaviruses GGNNV and demonstration of protein α as an apoptosis inducer date = 2003-03-30 pages = extension = .txt mime = text/plain words = 5132 sentences = 261 flesch = 52 summary = The infected SB cells underwent DNA fragmentation and stained positive in terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick-end labeling (TUNEL) assay, suggesting that GGNNV infection induced apoptosis in SB cells. To determine if GGNNV induces apoptosis in fish cells through the CD95 apoptotic pathway, infected SB cells were harvested at 24 PI and 48 h PI, and cell lysates were analyzed for IETDase activity, using IETD as the substrate for caspase-8. To determine which protein encoded by betanovirus GGNNV might be responsible for inducing apoptosis, the transient expression of viral proteins A and ␣ in SB and Cos-7 cells was carried out. The results that GGNNV infection induced activation of caspase-3-like proteases and GGNNV-induced apoptosis could be inhibited by DEVD-CHO indicate that fish caspases are important mediators of virus-induced cell death. Here, protein ␣ of GGNNV was demonstrated to be capable of inducing apoptosis by DNA fragmentation and TUNEL staining in transfected SB and Cos-7 cells at 48 h post-transfection. cache = ./cache/cord-254558-gvo0gwjf.txt txt = ./txt/cord-254558-gvo0gwjf.txt === reduce.pl bib === id = cord-258379-v3lceirh author = Liu, D. X. title = Association of the infectious bronchitis virus 3c protein with the virion envelope date = 1991-12-31 pages = extension = .txt mime = text/plain words = 2868 sentences = 121 flesch = 53 summary = There was considerably less evidence of contaminating cellular proteins in this gradient, and the relative proportion of the 12K protein to the other virion proteins appeared similar to that observed at the previous stage in purification, strongly supporting the idea of a specific association between the 12K protein and virus particles. In order to establish the identity of the 12K polypeptide as the product of the 3c gene, and to examine the possibility that IBV virions might contain other new virus polypeptides in amounts too small to detect directly, we next carried out immunoprecipitation experiments using monospecific antisera directed against the predicted products of the 3a, 3b, 3c, 5a, and 5b ORFs (17, 18, 23) . Messenger RNA 4 of mouse hepatitis virus (MHV) is known to encode a 15K polypeptide, the predicted amino acid sequence of which contains a highly hydrophobic region from residues 8 to 41 (9, 22) , although the protein has not so far been found in virions. cache = ./cache/cord-258379-v3lceirh.txt txt = ./txt/cord-258379-v3lceirh.txt === reduce.pl bib === id = cord-254747-vox5xsgd author = Deng, Xufang title = An “Old” Protein with A New Story: Coronavirus Endoribonuclease Is Important for Evading Host Antiviral Defenses date = 2018-04-01 pages = extension = .txt mime = text/plain words = 5730 sentences = 323 flesch = 53 summary = Overall, current evidence indicates that the EndoU activity of CoV nsp15 is dispensable for viral RNA synthesis and virus replication in cell culture. It was first discovered that the EndoU activity of nsp15 mediates the evasion of host recognition of viral dsRNA by infecting primary macrophages with EndoU-deficient CoVs (Deng et al., 2017; Kindler et al., 2017) . Moreover, treatment with the PKR inhibitor did not affect IFN induction or RNase L-mediated ribosomal RNA degradation in the EndoU-deficient CoV infected-macrophages (Deng et al., unpublished data) . Macrophages infected by the EndoU-deficient CoVs exhibited an early, RNase L-mediated degradation of ribosomal RNA, demonstrating that the OAS-RNase L system was activated (Deng et al., 2017; Kindler et al., 2017) . Lack of MDA5 expression or treatment with the PKR inhibitor did not affect virus-induced RNA degradation (Deng et al., 2017; Kindler et al., 2017) , suggesting that the nsp15-mediated blockage of OAS-RNase L activation is independent of the MDA5-IFN and PKR pathways. cache = ./cache/cord-254747-vox5xsgd.txt txt = ./txt/cord-254747-vox5xsgd.txt === reduce.pl bib === id = cord-258691-cd83w9o6 author = Whitman, Lucia title = IFN-γ-mediated suppression of coronavirus replication in glial-committed progenitor cells date = 2009-02-01 pages = extension = .txt mime = text/plain words = 4938 sentences = 257 flesch = 40 summary = IFN-γ-mediated control of JHMV replication is dampened in glial cultures derived from the neural progenitor cells of type I receptor knock-out mice. These data indicate that JHMV is capable of infecting glial cells generated from neural progenitor cells and that IFN-γ-mediated control of viral replication is dependent, in part, on type I IFN secretion. In the present study, we demonstrate that primary cultures of glia derived from neural progenitor cells are susceptible to JHMV infection and support viral replication. Therefore, these findings provide, to our knowledge, the first demonstration that glia-committed cells derived from neural precursors are susceptible to JHMV infection as well as identify a potential mechanism responsible for controlling viral replication. These findings indicate that differentiated cells derived from neural progenitors are susceptible to JHMV infection and are capable of supporting replicating virus which results in extensive cytopathology. cache = ./cache/cord-258691-cd83w9o6.txt txt = ./txt/cord-258691-cd83w9o6.txt === reduce.pl bib === id = cord-253024-b393ea2u author = Fu, Kaisong title = Evidence for variable rates of recombination in the MHV genome date = 1992-07-31 pages = extension = .txt mime = text/plain words = 8420 sentences = 488 flesch = 56 summary = Six RNA+ mutants that reside within a single complementation group mapping within the S glycoprotein gene of MHV-A59 were isolated which did not cause syncytium at the restrictive temperature. Since these mutants do not produce syncytium at the restrictive temperature ( Fig. 1) and sequence analysis of RNA recombinant viruses suggested that the defect in LA7 mapped within the first 1 .l kb of the S glycoprotein gene (Banner et al., 1990; Keck eta/., 1987 Keck eta/., , 1988a Makino eta/., 1986b Makino eta/., , 1987 , these data provided an anchor for mapping the location of the remaining group F RNA+ mutants. Since the distance between the group Fl and F2 mutants would have required sizable deletions (>lOO bp) to result in ts+ virus (Fig. 4) these data suggested that large deletions were rare events in these crosses, and did not contribute to an increase in the recombination frequency within the S glycoprotein gene. cache = ./cache/cord-253024-b393ea2u.txt txt = ./txt/cord-253024-b393ea2u.txt === reduce.pl bib === id = cord-258232-br4z3na6 author = Maeda, Junko title = Release of Coronavirus E Protein in Membrane Vesicles from Virus-Infected Cells and E Protein-Expressing Cells date = 1999-10-25 pages = extension = .txt mime = text/plain words = 4132 sentences = 189 flesch = 51 summary = The present study demonstrated that mouse hepatitis virus (MHV) E protein was released as an integral membrane protein in lipid vesicles from E-protein-expressing mammalian cells, in the absence of other MHV proteins. Complementation studies using two defective interfering (DI) RNAs of a prototypic coronavirus, mouse hepatitis virus (MHV), showed that E and M proteins are both required for the production of MHV particles containing the viral nucleocapsid (5) . To establish the buoyant density of released E protein, culture fluids from E-protein-expressing cells were applied onto a discontinuous sucrose gradient and centrifuged as described above. The release of E-protein-containing membrane vesicles from MHV-infected cells and E-protein-expressing cells further emphasized the pivotal role of E protein in coronavirus assembly. Furthermore, sucrose gradient centrifugation of MHV particles showed two E protein radioactive peaks, whereas N protein had only one peak corresponding to the MHV buoyant density (Fig. 3) , indicating that membrane vesicles containing only E protein do not include nucleocapsid. cache = ./cache/cord-258232-br4z3na6.txt txt = ./txt/cord-258232-br4z3na6.txt === reduce.pl bib === id = cord-260177-xu0elmak author = Collins, Arlene R. title = Monoclonal antibodies to murine hepatitis virus-4 (strain JHM) define the viral glycoprotein responsible for attachment and cell-cell fusion date = 1982-06-30 pages = extension = .txt mime = text/plain words = 4156 sentences = 232 flesch = 46 summary = title: Monoclonal antibodies to murine hepatitis virus-4 (strain JHM) define the viral glycoprotein responsible for attachment and cell-cell fusion Abstract Hybridoma cell lines producing monoclonal antibodies to the JHM strain of mouse hepatitis virus-4 (MHV-4) were established. A third set of monoclonal antibodies reacted both in the cytoplasm and on the surface of infected cells and precipitated the 25,000d viral glycoprotein (GP-5) and its precursor VP-6 (23,000d). MHV-4 polypeptide specificities of monoclonal antibodies were determined by immune precipitation of [35S]methionine-labeled viral proteins from infected L-241 cells. Only incubation with monoclonal antibodies to GP-1 resulted in inhibition in plaque and syncytium number (Fig. 5) , indicating involvement of that polypeptide in cell to cell spread of infection by fusion. When we examined our collection of monoclonal antibodies for the ability to inhibit spread of infection, only anti-GP-1 was effective, suggesting that the virion peplomer contains the active site for cell-cell co % fusion. cache = ./cache/cord-260177-xu0elmak.txt txt = ./txt/cord-260177-xu0elmak.txt === reduce.pl bib === id = cord-256737-ptjng78b author = McBride, Corrin E. title = Palmitoylation of SARS-CoV S protein is necessary for partitioning into detergent-resistant membranes and cell-cell fusion but not interaction with M protein date = 2010-09-01 pages = extension = .txt mime = text/plain words = 8233 sentences = 414 flesch = 58 summary = The SARS-CoV spike (S) protein mediates virus entry by binding cellular receptors and inducing fusion between the viral envelope and the host cell membrane. Importantly, we show that SARS-CoV S palmitoylation is not necessary for efficient interaction with SARS-CoV M, which differs from published experiments for MHV (Thorp et al., 2006) and suggests a significant difference between the two viruses that may have important implications for virus assembly and infectivity. To determine if SARS-CoV S becomes palmitoylated in a pre-medial Golgi compartment, HEK293T cells exogenously expressing SARS-CoV S were labeled for 30 min with 35 S-methionine/ cysteine to measure total protein expression or 3 H-palmitic acid to measure palmitoylated protein. Although both SARS-CoV S and S PN were present at the cell surface, it is possible that there could be a difference in the amount of protein at the plasma membrane at steady state if palmitoylation affects a post-Golgi trafficking step. cache = ./cache/cord-256737-ptjng78b.txt txt = ./txt/cord-256737-ptjng78b.txt === reduce.pl bib === id = cord-259717-e8ljkv2y author = Holtz, Lori R. title = Geographic variation in the eukaryotic virome of human diarrhea date = 2014-11-01 pages = extension = .txt mime = text/plain words = 6748 sentences = 349 flesch = 49 summary = Viromes from Northern Territory children contained more viral families per sample than viromes from Melbourne, which could be attributed largely to an increased number of sequences from the families Adenoviridae and Picornaviridae (genus enterovirus). Viromes from Northern Territory children contained more viral families per sample than viromes from Melbourne, which could be attributed largely to an increased number of sequences from the families Adenoviridae and Picornaviridae (genus enterovirus). Because previous metagenomic studies demonstrated significant virus diversity in patients with diarrhea (Finkbeiner et al., 2008) we focused this study on comparing the eukaryotic virus populations in stools of children with diarrhea collected from two different locations, Melbourne, Australia and the Northern Territory, Australia. In order to independently confirm the sequencing results, we used PCR to define the prevalence of the most frequently detected viruses for which pan-family or pan-genus primers could be used including: adenovirus, astrovirus, enterovirus, norovirus, and rotavirus. cache = ./cache/cord-259717-e8ljkv2y.txt txt = ./txt/cord-259717-e8ljkv2y.txt === reduce.pl bib === id = cord-259500-ndjbrtrv author = Satyanarayana, Tatineni title = Frameshift mutations in infectious cDNA clones of Citrus tristeza virus: a strategy to minimize the toxicity of viral sequences to Escherichia coli date = 2003-09-01 pages = extension = .txt mime = text/plain words = 6465 sentences = 322 flesch = 60 summary = title: Frameshift mutations in infectious cDNA clones of Citrus tristeza virus: a strategy to minimize the toxicity of viral sequences to Escherichia coli These data demonstrate that, when hosts are sufficiently susceptible for infection by transcripts of reduced specific infectivity, introduction of frameshift mutations at "slippery sequences" near toxic regions of viral cDNAs can be used as an additional strategy to clone recalcitrant viral sequences in high-copy-number plasmids for reverse genetics. A similar frameshift mutation was also found in the derivative replicon pCTV-⌬Cla. However, the sequence of the progeny virion RNA of CTV9 from infected protoplasts or citrus plants did not contain the additional nt at position 3732 that occurred in the cDNA clones, suggesting that the frameshift mutation present in the original cDNA clone was repaired either during the in vitro transcription or during replication in the protoplasts. cache = ./cache/cord-259500-ndjbrtrv.txt txt = ./txt/cord-259500-ndjbrtrv.txt === reduce.pl bib === id = cord-260782-1lm8tzbc author = Giles, Julia title = Viral RNA load and histological changes in tissues following experimental infection with an arterivirus of possums (wobbly possum disease virus) date = 2018-07-14 pages = extension = .txt mime = text/plain words = 6575 sentences = 319 flesch = 43 summary = title: Viral RNA load and histological changes in tissues following experimental infection with an arterivirus of possums (wobbly possum disease virus) The aim of the current study was to describe histological lesions and viral RNA levels in tissues from possum experimentally infected with WPDV. Histology of brain, kidney and liver tissue from wobbly possum disease virus (WPDV)-infected possums. Whilst RNA levels in selected tissues (liver, spleen, brain and kidney) from WPD-infected possums have been previously reported (Dunowska et al., 2013) , we have expanded both the number of possums and the tissue types tested to provide a greater understanding of the tissues targeted by the virus in-vivo. Detection of moderate to high levels of viral RNA from the sera of all but one infected possum in this study also supports the use of blood or serum samples for detection of WPDV. cache = ./cache/cord-260782-1lm8tzbc.txt txt = ./txt/cord-260782-1lm8tzbc.txt === reduce.pl bib === id = cord-252397-qlu7dilh author = Johnson, Reed F. title = Intratracheal exposure of common marmosets to MERS-CoV Jordan-n3/2012 or MERS-CoV EMC/2012 isolates does not result in lethal disease date = 2015-11-01 pages = extension = .txt mime = text/plain words = 5024 sentences = 255 flesch = 49 summary = Results from a natural history study of MERS-CoV-infected rhesus monkeys indicated that intratracheal inoculation induced a non-lethal disease with limited pathology observed in recovering animals at 28 days post-inoculation and infectious virus could be recovered from lung but not other tissues assayed (Yao et al., 2014) . One subject in the MERS-EMC inoculated group appeared to develop a secondary infection observed by CT that increased to study end, day 25 post-exposure. With the use of CT, we observed that IT inoculation of common marmosets with MERS-JOR or MERS-EMC isolates resulted in a non-lethal disease characterized by limited clinical signs and moderate consolidative lung pathology that did not completely resolve by study end. In this experiment, we sought to determine if there were virus specific differences in disease progression following intratracheal inoculation of common marmosets with Middle Eastern Respiratory Syndrome Coronavirus, commonly known as MERS-CoV, with two common laboratory viral isolates (MERS-EMC and MERS-Jordan). cache = ./cache/cord-252397-qlu7dilh.txt txt = ./txt/cord-252397-qlu7dilh.txt === reduce.pl bib === id = cord-267718-t47i8hui author = Bao, Jingyue title = Evolutionary dynamics of recent peste des petits ruminants virus epidemic in China during 2013–2014 date = 2017-07-19 pages = extension = .txt mime = text/plain words = 4760 sentences = 240 flesch = 56 summary = An evolutionary rate of 2.61 × 10(−6) nucleotide substitutions per site per day was estimated, dating the most recent common ancestor of PPRV China 2013–2014 strains to early August 2013. Transmission network analysis revealed that all the virus sequences could be grouped into five clusters of infection, suggesting long-distance animal transmission play an important role in the spread of PPRV in China. Here we present the first intra-epidemic analysis of PPRV genome by studying viruses from 25 farms infected during the 2013-2014 PPR outbreaks in China. In this study, we constructed the transmission pathway of the spread of PPR virus basing on the fulllength genome sequences and identified five clusters of infections. Although more than 200 infected farms were reported during 20132014 PPRV epidemic in China, only 25 of them were full-genome sequenced and analyzed in this study. Full genome sequence of a peste des petits ruminants virus (PPRV) from Ghana cache = ./cache/cord-267718-t47i8hui.txt txt = ./txt/cord-267718-t47i8hui.txt === reduce.pl bib === id = cord-258286-lodjcj8c author = Zhang, Xuming title = Expression of Interferon-γ by a Coronavirus Defective-Interfering RNA Vector and Its Effect on Viral Replication, Spread, and Pathogenicity date = 1997-07-07 pages = extension = .txt mime = text/plain words = 5866 sentences = 296 flesch = 54 summary = Previous studies have shown that immunocoma large plaque variant derived from the parental JHM petent mice infected with MHV exhibited increased exstrain (Stohlman et al., 1982) ; the small plaque variant pression of a number of cytokines, including IL-1, IL-6, DS (Stohlman et al., 1982) ; the neutralization-escape mu-TNF-a, and IFN-g, in the CNS at the time of viral cleartant 2.2-V-1 (Fleming et al., 1987; Wang et al., 1992) , and ance (Pearce et al., 1994) . The expressed IFNg exhibited antiviral activity, prevented virus spread in layers of DBT cells grown at approximately 70% confluence in 60-mm petri dishes were infected with MHV at vitro, and altered viral pathogenesis in mice. Expression of IFN-g using an MHV DI RNA vector cell metabolism prior to infection or it may be that interferon acts at an early stage of viral replication. cache = ./cache/cord-258286-lodjcj8c.txt txt = ./txt/cord-258286-lodjcj8c.txt === reduce.pl bib === id = cord-255453-7e40rj1y author = Oliver, S.L. title = Genomic characterization of the unclassified bovine enteric virus Newbury agent-1 (Newbury1) endorses a new genus in the family Caliciviridae date = 2006-06-20 pages = extension = .txt mime = text/plain words = 6227 sentences = 303 flesch = 53 summary = The relationship of Bo/Newbury1/1976/UK with members of the Caliciviridae Although many features of the Newbury1 genome organization were consistent with the Caliciviridae, the Newbury1 genome had low nucleotide (≤47%) and amino acid (≤39%) identities to all representative viruses of the 4 Caliciviridae genera by comparison of complete non-structural genes (2Chelicase, 3C-protease, 3D-polymerase), complete capsids, capsid subdomains and the 3′ terminal ORF genes ( Table 2 ). Newbury1 failed to group phylogenetically with the 4 recognized Caliciviridae genera but formed a separate clade with NB virus by UPGMA, Fitch-Margoliash, parsimony and maximum likelihood analyses of the nucleotide and translated amino acids of ORF1 (excluding the capsid gene), the individual regions that encoded the 2C-helicase, 3C-protease, 3D-polymerase and complete capsid genes (not shown). The distant relationship of Newbury1 to the 4 recognized Caliciviridae genera was confirmed using additional phylogenetic analyses based on amino acid alignments generated from homology models of structurally conserved regions of the partial polymerase and the capsid S-domain (Fig. 3) . cache = ./cache/cord-255453-7e40rj1y.txt txt = ./txt/cord-255453-7e40rj1y.txt === reduce.pl bib === id = cord-254950-y6kayxie author = Morse, Stephen S. title = Mouse thymic virus (MTLV; Murid Herpesvirus 3) infection in athymic nude mice: Evidence for a T lymphocyte requirement date = 1988-03-31 pages = extension = .txt mime = text/plain words = 2123 sentences = 99 flesch = 51 summary = Abstract Mouse thymic virus (MTLV; murid herpesvirus 3) is a lymphotropic herpesvirus that cytolytically infects developing T lineage lymphocytes in the thymus of neonatal mice. In order to determine whether T lineage lymphocytes are required for infection, young adult athymic nude (nulnu) mice and euthymic littermates were infected with MTLV and tested for virus shedding. To determine whether MTLV infection requires thymus-derived lymphocytes, 4-week-old female ICR Swiss athymic nude (nulnu) and euthymic (+lnu) littermate controls (four each; Memorial Sloan-Kettering Cancer Center nude mouse breeding colony) were inoculated intraperitoneally with either 40 or 200 IDS0 of MTLV and virus shedding was tested by mouth swabs beginning 6 days after infection. litters available did not allow every negative sample to be tested, additional litters of normal newborn mice were inoculated with fresh homogenates (1 O-20%, w/v) of randomly selected negative thymuses and salivary glands, representing various test dates up to Day 48, from 14 assay litters that had received swab fluids from nude mice. cache = ./cache/cord-254950-y6kayxie.txt txt = ./txt/cord-254950-y6kayxie.txt === reduce.pl bib === id = cord-265173-70wyecwj author = Trujillo-Uscanga, Adrian title = Host cell p53 associates with the feline calicivirus major viral capsid protein VP1, the protease-polymerase NS6/7, and the double-stranded RNA playing a role in virus replication date = 2020-08-27 pages = extension = .txt mime = text/plain words = 5671 sentences = 282 flesch = 53 summary = title: Host cell p53 associates with the feline calicivirus major viral capsid protein VP1, the protease-polymerase NS6/7, and the double-stranded RNA playing a role in virus replication Viruses modulate p53 functions in different manners: single-stranded RNA viruses such as the human coronavirus NL63 (HCoV-NL63) induces its degradation of p53 (Yuan et al., 2015) to ensure viral growth in infected cells (Ma-Lauer et al., 2016) , Zika (ZIKV) and West Nile (WNV) activate p53 to facilitate their replication (El Ghouzzi et al., 2016) (Teng et al., 2017) (Yang et al., 2008) while Adenovirus Even though p53 is implicated in the induction of apoptosis and in many viral infections, its role during calicivirus infection has not been studied. Here we found that p53 interacts with FCV dsRNA, the protease-polymerase NS6/7, and VP1 in the RC; moreover, knockdown of p53 resulted in a significant reduction of the NS viral protein synthesis and virus production, indicating its role for efficient viral replication. cache = ./cache/cord-265173-70wyecwj.txt txt = ./txt/cord-265173-70wyecwj.txt === reduce.pl bib === id = cord-260376-29ih5c9v author = Guo, Jian-Ping title = SARS corona virus peptides recognized by antibodies in the sera of convalescent cases date = 2004-07-01 pages = extension = .txt mime = text/plain words = 2994 sentences = 168 flesch = 57 summary = title: SARS corona virus peptides recognized by antibodies in the sera of convalescent cases We synthesized on cellulose membranes 4942 ten-amino-acid peptides which included all of the sequences predicted for the severe acute respiratory syndrome (SARS) corona virus. Peptides incorporating all of the sequences predicted in the open reading frames of the SARS-CoV genome were prepared on derivatized cellulose membranes using a robotic peptide synthesizer (Autospot ASP 222, Intavis Bioanalytical Instruments, Lagenfeld, Germany). These data indicate that the four recovered cases developed antibodies with viral neutralizing potency between the time of acute and convalescent serum sampling. Therefore, those peptides strongly recognized on membranes probed with convalescent sera, but not with acute or control sera, should be the most immunodominant and may include SARS-CoV epitopes that are vulnerable to neutralization by antibody. Shown in Table 2 are the 24 overlapping membrane peptides that were recognized exclusively, or much more strongly, in multiple pairs of convalescent compared with the respective acute sera. cache = ./cache/cord-260376-29ih5c9v.txt txt = ./txt/cord-260376-29ih5c9v.txt === reduce.pl bib === id = cord-260695-qwepi0we author = Postler, Thomas S. title = Identification and characterization of a long non-coding RNA up-regulated during HIV-1 infection date = 2017-11-01 pages = extension = .txt mime = text/plain words = 6315 sentences = 377 flesch = 55 summary = Of the host-encoded lncRNAs reported to be differentially expressed upon HIV-1 infection, only nuclear enriched abundant transcript 1 (NEAT1) and noncoding repressor of nuclear factor of activated T cells (NRON) have been functionally characterized (Lazar et al., 2016) . In this report, we describe a meta-analysis of two independent RNA-seq studies of HIV-1-infected cells and show that, unexpectedly, only three lncRNAs are differentially expressed in both of these datasets (Chang et al., 2011; Mohammadi et al., 2013) . To obtain an unbiased understanding of any changes in lncRNA expression during HIV-1 infection, we performed a meta-analysis of two independent RNA-seq studies conducted by two different groups using two different virus strains ( Supplementary Fig. S1 ) (Chang et al., 2011; Mohammadi et al., 2013) . To validate the results of the in silico analysis of lnc173 expression, we isolated RNA from 4 human cell lines and probed for the presence of both transcript variants by quantitative RT-PCR (qRT-PCR; Fig. 3A -D). cache = ./cache/cord-260695-qwepi0we.txt txt = ./txt/cord-260695-qwepi0we.txt === reduce.pl bib === id = cord-267377-wyhsxj6g author = Edwards, Michael C. title = Coat protein expression strategy of oat blue dwarf virus() date = 2014-01-14 pages = extension = .txt mime = text/plain words = 4709 sentences = 231 flesch = 54 summary = The single, large ORF encodes a polyprotein with domains specifying methyltransferase (mtr), protease (pro), helicase/NTpase (hel), and polymerase (pol) activities fused to the sequence encoding the CPs. The major and minor coat proteins map to the same CP sequence and size differences between them are potentially determined by translation initiation at two different start codons (minor, AUG 5581 and major, AUG 5710 ). Oat protoplasts were inoculated with capped transcripts of wild type clone pOBDV, major CP mutants GH1-7 (premature termination mutant) and KL1-3 (initiation codon mutant), and AB15-25 (marafibox mutant) and incubated for 40 h. Accumulation of viral coat proteins (CPs) and RNA in oat protoplasts inoculated with premature termination and initiation codon mutants of the CP gene. Oat protoplasts were inoculated with capped transcripts of wild type clone pOBDV, premature termination mutants GH1-7 and EF2-2, and initiation codon mutants IJ4-7 (minor CP), and KL1-3 and KL2-5 (major CP) and incubated for 24 h. cache = ./cache/cord-267377-wyhsxj6g.txt txt = ./txt/cord-267377-wyhsxj6g.txt === reduce.pl bib === id = cord-263302-z5uhrta5 author = Zhang, Xuming title = Identification of a Noncanonical Signal for Transcription of a Novel Subgenomic mRNA of Mouse Hepatitis Virus: Implication for the Mechanism of Coronavirus RNA Transcription date = 2000-12-05 pages = extension = .txt mime = text/plain words = 7944 sentences = 411 flesch = 58 summary = Transfection of the reporter RNA into MHV-infected cells resulted in synthesis of a CAT-specific subgenomic mRNA detected by reverse transcription-polymerase chain reaction (RT-PCR). Further sequencing on cDNA clones derived from JHM2c mRNAs by reserve transcription-polymerase chain reaction (RT-PCR) has shown that the leader-body joining sites in subgenomic mRNA2-1 are more heterogeneous . When it was placed in front of the chloramphenicol acetyl-transferase (CAT) gene in the defective-interfering (DI) RNA-CAT reporter plasmid, the IG5-1, which is devoid of any known IRES sequence, can direct the synthesis of a subgenomic CAT-containing mRNA and expression of the CAT activity, thus confirming that the IG5-1 serves as a promoter for transcription of a subgenomic mRNA. To identify the minimal sequence required for subgenomic mRNA transcription, three deletions within the 140-nt sequence were made by PCR, and the deletion fragments were cloned into the DI RNA-CAT reporter vector in place of the wild-type, full-length (140-nt) se, and MHV-1 (F), respectively. cache = ./cache/cord-263302-z5uhrta5.txt txt = ./txt/cord-263302-z5uhrta5.txt === reduce.pl bib === id = cord-255828-jrqdyfbg author = Du, Yijun title = Glycosyl-phosphatidylinositol (GPI)-anchored membrane association of the porcine reproductive and respiratory syndrome virus GP4 glycoprotein and its co-localization with CD163 in lipid rafts date = 2012-03-01 pages = extension = .txt mime = text/plain words = 8986 sentences = 444 flesch = 54 summary = title: Glycosyl-phosphatidylinositol (GPI)-anchored membrane association of the porcine reproductive and respiratory syndrome virus GP4 glycoprotein and its co-localization with CD163 in lipid rafts The porcine reproductive and respiratory syndrome virus (PRRSV) glycoprotein 4 (GP4) resembles a typical type I membrane protein in its structure but lacks a hydrophilic tail at the C-terminus, suggesting that GP4 may be a lipid-anchored membrane protein. Mutational studies for residues adjacent to the GPI modification site and characterization of respective mutant viruses generated from infectious cDNA clones show that the ability of GP4 for membrane association corresponded to virus viability and growth characteristics. The depletion of cholesterol from the plasma membrane of cells reduced the virus production, suggesting a role of lipid rafts in PRRSV infection. 7C, D) .These data indicate that the reduction of virus production by MβCD was due to the depletion of cholesterol from the cells and this effect was reversible, suggesting a role of lipid rafts in PRRSV infection. cache = ./cache/cord-255828-jrqdyfbg.txt txt = ./txt/cord-255828-jrqdyfbg.txt === reduce.pl bib === id = cord-262245-eb7g9p1x author = Monica, Nicola La title = Localization of extensive deletions in the structural genes of two neurotropic variants of murine coronavirus JHM date = 1991-06-30 pages = extension = .txt mime = text/plain words = 3512 sentences = 178 flesch = 60 summary = Abstract The intracellular RNA of two neurotropic variants of the JHM strain of mouse hepatitis virus (MHV) independently isolated from the brain and spinal cord of an infected Wistar Furth rat were compared with that of the parental virus. Both the brain and the spinal cord isolates displayed a different pattern of virus-specific mRNAs from the parental JHM virus in the infected cells (26). The size of several of these mRNAs appeared different; most notably, the mRNA 3 of the At1 lf cord isolate was smaller than those of the parental JHM strain and of the brain isolate but similar to that of JHM (2), which has a deletion of 423 nucleotides in the S gene (28). Figure 5A shows that the S protein of the At1 lf cord variant is smaller than that of the JHM parental virus, but similar in size to that of the JHM(2), which has a deletion of 153 amino acids (28). cache = ./cache/cord-262245-eb7g9p1x.txt txt = ./txt/cord-262245-eb7g9p1x.txt === reduce.pl bib === id = cord-264359-m9j3pcj1 author = Vrijsen, R. title = Resolution of the major poliovirus capsid polypeptides into doublets date = 1978-05-15 pages = extension = .txt mime = text/plain words = 3862 sentences = 223 flesch = 57 summary = The VPl-VP3 group of poliovirion polypeptides can be resolved into multiple components by normal polyacrylamide gel electrophoresis (PAGE) in the presence of sodium dodecyl sulfate (SDS) (Vanden Berghe and Boeye, 1972) ; however, resolution into six components is achieved more easily and reproducibly in the presence of a pH gradient. In summary, fine resolution of the poliovirus capsid polypeptides was achieved by pH gradient electrophoresis and the results were independent of (i) the virus purification or (ii) protein extraction procedures, (iii) the state of maturation (procapsid or mature virion), and (iv) the serotype (type 1 or 2). DISCUSSION The improved resolution of poliovirus capsid polypeptides by pH gradient electrophoresis reported by Vrijsen and Boeye (1978) was confirmed and shown to be independent of the serotype and of the methods used for virus purification and protein extraction. cache = ./cache/cord-264359-m9j3pcj1.txt txt = ./txt/cord-264359-m9j3pcj1.txt === reduce.pl bib === id = cord-260108-osg8q89i author = Park, Yon Mi title = Full genome analysis of a novel adenovirus from the South Polar skua (Catharacta maccormicki) in Antarctica date = 2012-01-05 pages = extension = .txt mime = text/plain words = 3039 sentences = 174 flesch = 48 summary = Here, we report the entire 26,340-bp genome of a novel adenovirus, detected by PCR, in tissues of six of nine South Polar skuas (Catharacta maccormicki), collected in Lake King Sejong, King George Island, Antarctica, from 2007 to 2009. The DNA polymerase, penton base, hexon and fiber genes of the South Polar skua adenovirus (SPSAdV) exhibited 68.3%, 75.4%, 74.9% and 48.0% nucleotide sequence similarity with their counterparts in turkey hemorrhagic enteritis virus. Phylogenetic analysis based on the entire genome revealed that SPSAdV belonged to the genus Siadenovirus, family Adenoviridae. Using newly designed primers based on the obtained sequence, the full genome of the novel adenovirus (SPSAdV) was extended from the left-end inverted terminal repeat (ITR) region to the right-end ITR region. At the nucleotide level, the SPSAdV pol, penton base and hexon genes exhibited somewhat higher sequence similarity of 73.8%, 79.2% and 77.5% with RAdV-1 than with THEV (68.3%, 75.4% and 74.9%) ( Table 4 ). cache = ./cache/cord-260108-osg8q89i.txt txt = ./txt/cord-260108-osg8q89i.txt === reduce.pl bib === id = cord-266585-jfjrk9gy author = Fang, Shouguo title = An arginine-to-proline mutation in a domain with undefined functions within the helicase protein (Nsp13) is lethal to the coronavirus infectious bronchitis virus in cultured cells date = 2007-02-05 pages = extension = .txt mime = text/plain words = 7152 sentences = 356 flesch = 56 summary = During construction of an infectious clone from a Vero cell-adapted coronavirus infectious bronchitis virus (IBV), we found that a G–C point mutation at nucleotide position 15526, causing Arg-to-Pro mutation at amino acid position 132 of the helicase protein, is lethal to the infectivity of IBV on Vero cells. Further characterization of the in vitro-synthesized full-length transcripts containing the G15526C mutation demonstrated that this mutation blocks the transcription of subgenomic RNAs. Substitution mutation of the Arg132 residue to a positively charged amino acid (Lys) affected neither the infectivity of the in vitro-synthesized transcripts nor the growth properties of the rescued virus. To further demonstrate that the failure to rescue infectious virus from the G15526C mutant transcripts is due to a defect in subgenomic RNA transcription, the full-length clones with and without the G15526C mutation were used to generate recombinant IBV expressing the enhanced green fluorescent protein (EGFP) by replacing the 5a gene with EGFP. cache = ./cache/cord-266585-jfjrk9gy.txt txt = ./txt/cord-266585-jfjrk9gy.txt === reduce.pl bib === id = cord-259095-mfptcw8t author = Lu, Yiqi title = Determinants of Mouse Hepatitis Virus 3C-like Proteinase Activity date = 1997-04-14 pages = extension = .txt mime = text/plain words = 4488 sentences = 270 flesch = 66 summary = Numbering of amino acid residues within MHV 3CLpro is based The linear schematic of the MHV genome shows the organization of Ser 1 (Lu et al., 1995) Site-directed mutagenesis of pGpro with bovine chymotrypsin (Gorbalenya and Koonin, 1993) , 3Cpro of human rhinovirus 14 (Matthews et al., 1994) , and hepatitis A virus Asp53 and Asp65 were mutagenized by the Chame-3Cpro (Allaire et al., 1994) . The comparison of the were checked for residual expression and processing from the pGpro construct by the addition of [ 35 S]-four coronavirus 3CLpro sequences revealed two potential cleavage sites present only in MHV, QS 3554-5 , and methionine to an aliquot of the unlabeled reaction mixture after treatment with RNase and cycloheximide and QG 3607-8 . Mutation of Asp65 to Pro or Ala (D65P and D65A) MHV-A59, IBV, HCV-229E, and TGEV revealed no completely conserved Asp or Glu residues at positions analo-resulted in a proteinase with activity comparable to that expressed from wild-type pGpro (Fig. 3B, lanes 3 and 4) . cache = ./cache/cord-259095-mfptcw8t.txt txt = ./txt/cord-259095-mfptcw8t.txt === reduce.pl bib === id = cord-262574-gu0930s3 author = Slagle, Betty L. title = Identification and characterization of a mouse mammary tumor virus protein uniquely expressed on the surface of BALB/cV mammary tumor cells date = 1985-05-31 pages = extension = .txt mime = text/plain words = 7912 sentences = 407 flesch = 53 summary = The BALB/cV subline was used to study the molecular basis of potential virus-host interactions involving cell surface-expressed MMTV proteins. Cell surface iodination identified virus-specific proteins expressed on BALB/cv primary mammary tumor cells grown in culture. Adsorption experiments have demonstrated that the anti-gp52/gp36 serum reacts specifically with MMTV glycoproteins and envelope-related precursors and does not react with normal cell proteins of BALB/c mammary tissue (Slagle et aQ, 1985) . Primary cultures of a BALB/cV tumor were analyzed for cell surface expression of viral proteins using the same iodination procedure. Primary cultures of BALB/cV tumor cells were starved for 2 hr in methionine-free media and were then metabolically labeled for 1 hr with r5S]Met. Intact cell monolayers were rinsed with cold TBS, placed on ice, and reacted with specific antisera to detect 35S-labeled MMTV proteins expressed on the cell surface. DISCUSSION This report describes a thorough analysis of the expression of MMTV-specific proteins on the surface of BALB/cV mammary tumor cells. cache = ./cache/cord-262574-gu0930s3.txt txt = ./txt/cord-262574-gu0930s3.txt === reduce.pl bib === id = cord-266617-z8uecyl6 author = Pavesi, Angelo title = Asymmetric evolution in viral overlapping genes is a source of selective protein adaptation date = 2019-04-03 pages = extension = .txt mime = text/plain words = 6677 sentences = 326 flesch = 52 summary = Analysis of nucleotide and amino acid sequences revealed that half of overlaps undergo asymmetric evolution, as the protein from one frame shows a number of substitutions significantly higher than that of the protein from the other frame. I classified a pair of homologous overlaps as a case of symmetric evolution, if the number of amino acid substitutions in the Up1-Up2 alignment did not significantly differ from that in the Down1-Down2 alignment (chi-square < 3.84). In alternative, I classified a pair of homologous overlaps as a case of asymmetric evolution, if the number of amino acid substitutions in the Up1-Up2 alignment was significantly different from that in the Down1-Down2 alignment (chi-square > 3.84). The analysis of the pattern of nucleotide substitutions in the 75 pairs of homologous overlaps revealed 39 and 36 cases of symmetric and asymmetric evolution, respectively (Supplementary Table S2 ). cache = ./cache/cord-266617-z8uecyl6.txt txt = ./txt/cord-266617-z8uecyl6.txt === reduce.pl bib === id = cord-265156-u1re7983 author = de Wilde, Adriaan H. title = Coronaviruses and arteriviruses display striking differences in their cyclophilin A-dependence during replication in cell culture date = 2017-12-15 pages = extension = .txt mime = text/plain words = 6306 sentences = 327 flesch = 53 summary = Here, we investigated the CypA dependence of three distantly related nidoviruses that can all replicate in Huh7 cells: the arterivirus equine arteritis virus (EAV), the alphacoronavirus human coronavirus 229E (HCoV-229E), and the betacoronavirus Middle East respiratory syndrome coronavirus (MERS-CoV). The replication in cell culture of the arterivirus equine arteritis virus (EAV; de Wilde et al., 2013a) and the alphacoronaviruses feline coronavirus (FCoV; Tanaka et al., 2017) , human coronavirus (HCoV) NL63 (Carbajo-Lozoya et al., 2014), and HCoV-229E (von Brunn et al., 2015) was reported to be affected by CypA knockdown (KD) or knockout (KO), although the level of CypA dependence of these viruses, which was not compared directly, appeared to be quite different. Using different cell lines, the replication of two of these viruses, the arterivirus EAV (de Wilde et al., 2013a) and the alphacoronavirus HCoV-229E , was previously concluded to depend on CypA. cache = ./cache/cord-265156-u1re7983.txt txt = ./txt/cord-265156-u1re7983.txt === reduce.pl bib === id = cord-263334-wwkdum94 author = Li, Chen title = Cellular DDX3 regulates Japanese encephalitis virus replication by interacting with viral un-translated regions date = 2014-01-20 pages = extension = .txt mime = text/plain words = 7683 sentences = 423 flesch = 54 summary = BHK-21 cells transfected with the DDX3 shRNA were infected with JEV (MOI¼ 0.01) for 48 h, Viral titers determined by plaque formation assay at 48 hpi. (F) BHK-21 cells transfected with different amounts of DDX3 shRNA plasmid were infected with JEV (MOI ¼0.01), 48 h later, the amount of virus released into the medium was determined by plaque formation assay. In order to determine whether cellular DDX3 is involved in virus assembly or release, the BHK-21 cells were transfected with DDX3 shRNA plasmid before being infected with JEV (MOI ¼0.01). The virus titers were detected 2 days later by plaque formation assay, the results showed that overexpression of DDX3r-K230E, DDX3r-S382L and the control plasmid pcDNA3.1 after DDX3 knockdown resulted in the reduction of JEV replication for 13-fold (p o0.01), 12-fold (p o0.01) and 15-fold (p o0.01). The DEAD-box RNA helicase DDX5 acts as a positive regulator of Japanese encephalitis virus replication by binding to viral 3′ UTR cache = ./cache/cord-263334-wwkdum94.txt txt = ./txt/cord-263334-wwkdum94.txt === reduce.pl bib === === reduce.pl bib === id = cord-008426-ktn8c0zx author = Othman, Yasmin title = Nucleotide sequence of the bean strain of southern bean mosaic virus() date = 1995-01-10 pages = extension = .txt mime = text/plain words = 5393 sentences = 276 flesch = 57 summary = From a comparison of the predicted sequences of the ORFs of these three sobemoviruses and of the noncoding regions, it is suggested that the two SBMV strains differ from one another as much as they do from RYMV and that they should be considered as different viruses. Southern bean mosaic virus (SBMV) is the type member of the sobemovirus group of small icosahedral positive-strand RNA viruses (for reviews see Sehgal, 1981 ; Tremaine and Hamilton, 1983; Hull, 1988) . The recently published nucleotide sequence (4450 nt) of rice yellow mottle virus (RYMV), another sobemovirus (Ngon A Yassi et aL, 1994) , shows that it has a similar genome organization to SBMV-C (Fig. 1) . Amino acid sequence of southern bean mosaic virus coat protein and its relation to the three dimensional structure of the virus cache = ./cache/cord-008426-ktn8c0zx.txt txt = ./txt/cord-008426-ktn8c0zx.txt === reduce.pl bib === id = cord-265895-ck7eto16 author = Baric, Ralph S. title = Analysis of intracellular small RNAs of mouse hepatitis virus: evidence for discontinuous transcription date = 1987-02-28 pages = extension = .txt mime = text/plain words = 4507 sentences = 228 flesch = 60 summary = These data, coupled with the high frequency of RNA recombination during MHV infection, suggest that the viral polymerase may pause in or around regions of secondary structure, thereby generating pools of free leader-containing RNA intermediates which can reassociate with the template, acting as primers for the synthesis of full-length or recombinant RNAs. These data suggest that MHV transcription uses a discontinuous and nonprocessive mechanism in which RNA polymerase allows the partial RNA products to be dissociated from the template temporarily during the process of transcription. These data, coupled with the presence of discrete large leader-containing RNAs which range from 84 to 1000 nucleotides in length in MHV-infected cells (Baric et a/., 1985) suggest that discontinuous RNA intermediates may be dissociated and reassert between viral RNA templates to generate recombinant viruses by a copy-choice mechanism (Makino eta/., 1986a). The leader-containing RNAs larger than 1 10 nucleotides in length detected by the leader-specific cDNA probe were more heterogeneous (Fig. 2) (Baric et al., 1985) suggesting that multiple RNA species in this size range were present. cache = ./cache/cord-265895-ck7eto16.txt txt = ./txt/cord-265895-ck7eto16.txt === reduce.pl bib === id = cord-266018-8bhnlsgy author = Trifilo, Matthew J. title = The CC chemokine ligand 3 regulates CD11c(+)CD11b(+)CD8α(−) dendritic cell maturation and activation following viral infection of the central nervous system: implications for a role in T cell activation date = 2004-09-15 pages = extension = .txt mime = text/plain words = 5101 sentences = 272 flesch = 60 summary = The major findings of this study are (i) MHV infection of the CNS results in the appearance of two distinct populations of CD11c + cells each expressing markers characteristic of lymphoid (CD11c + CD11b À CD8a + DEC205 + ) and myeloid dendritic cells (CD11c + CD11b + CD8a À DEC205 À ), (ii) the accumulation of CD8a À DCs within the draining CLN is reduced in the absence of CCL3 signaling, (iii) expression of co-stimulatory molecules such as CD40 by CD8a À DCs within either the brain and CLN of MHV-infected CCL3 À/À mice is diminished suggesting that CCL3 signaling enhances expression of these molecules, and (iv) absence of CCL3 signaling results in the re-direction of the T cell response to viral antigens as determined by cytokine production. Our studies clearly indicate that CD8a À DCs isolated from the draining CLN of MHV-infected CCL3 +/+ mice secrete IL-12 suggesting that these cells help influence a protective Th1-mediated immune response characterized by the majority of antigen-specific T cells expressing IFN-g rather than IL-10 (Table 1 ). cache = ./cache/cord-266018-8bhnlsgy.txt txt = ./txt/cord-266018-8bhnlsgy.txt === reduce.pl bib === id = cord-262441-slh52nxm author = Sakai, Yusuke title = Two-amino acids change in the nsp4 of SARS coronavirus abolishes viral replication date = 2017-07-21 pages = extension = .txt mime = text/plain words = 6120 sentences = 261 flesch = 52 summary = To determine the crucial amino acid residue(s) in SARS-CoV nsp4 required to induce membrane rearrangements through the interaction with nsp3C, we constructed additional expression plasmids encoding deletion mutants of SARS-CoV nsp4, pCAG nsp4 Δ112-126-HA and pCAG nsp4 Δ126-164-HA, as shown in Fig. 1B . To determine the effect of the two amino acid residues, H120 and F121, in SARS-CoV nsp4 on the membrane rearrangements thorough interaction with nsp3C, 293T cells transfected with pCAG nsp4-HA or pCAG nsp4 H120N/F121L-HA together with pCAG nsp3C-3xFLAG at 30 h posttransfection were subjected to transmission electron microscopy (TEM) analysis. As we expected, expression of renilla luciferase was detected in cells transfected with pBAC-SARS-Rep-wt, but not in those with pBAC-SARS-Rep-H120N/F121L or pBAC-SARSRep-SAD (Fig. 7C) , suggesting that both H120 and F121 in SARS-CoV nsp4 play critical roles in the viral replication by remodeling the membrane through binding with nsp3. cache = ./cache/cord-262441-slh52nxm.txt txt = ./txt/cord-262441-slh52nxm.txt === reduce.pl bib === id = cord-255841-3laov764 author = Duquerroy, Stéphane title = Central ions and lateral asparagine/glutamine zippers stabilize the post-fusion hairpin conformation of the SARS coronavirus spike glycoprotein() date = 2005-05-10 pages = extension = .txt mime = text/plain words = 6758 sentences = 315 flesch = 62 summary = A striking arrangement of conserved asparagine and glutamine residues of HR1 propagates from two central chloride ions, providing hydrogen-bonding "zippers" that strongly constrain the path of the HR2 main chain, forcing it to adopt an extended conformation at either end of a short HR2 α-helix. We and others have previously shown that, analogous to other class I fusion proteins, peptides corresponding to the HR regions of the mouse hepatitis coronavirus (MHV, Bosch et al., 2003) and SARS-CoV (Bosch et al., 2004; Ingallinella et al., 2004; Xu et al., 2004a; Tripet et al., 2004) can fold into a stable rod-like structure, consisting of three HR1 helices in association with three HR2 peptides in antiparallel orientation. As expected, there is essentially one side chain per turn of the HR1 a-helix participating to the central hydrophobic core of the molecule, resulting in 23 amino acids from each chain (labeled to the left of Fig. 2A ) interacting with their symmetry mates at the central 3-fold axis. cache = ./cache/cord-255841-3laov764.txt txt = ./txt/cord-255841-3laov764.txt === reduce.pl bib === id = cord-258327-03vk6enj author = Schultze, Beate title = Isolated HE-protein from hemagglutinating encephalomyelitis virus and bovine coronavirus has receptor-destroying and receptor-binding activity date = 1991-01-31 pages = extension = .txt mime = text/plain words = 4604 sentences = 267 flesch = 52 summary = The purified HE protein retained acetylesterase activity and was able to function as a receptor-destroying enzyme rendering red blood cells resistant against agglutination by both coronaviruses. However, it was found to recognize glycoconjugates containing N-acetyl-9-O-acetylneuraminic acid as indicated by a binding assay with rat serum proteins blotted to nitrocellulose and by its ability to inhibit the hemagglutinating activity of BCV, HEV, and influenza C virus. The virus pellet was resuspended in PBS and used for (i) analysis by polyacrylamide gel electrophoresis ; (ii) determination of the esterase activity ; (iii) hemagglutination and hemagglutination-inhibition assays ; and (iv) purification of the viral glycoproteins . These erythrocytes and control cells, which had been incubated with PBS, were used to determine the HA titer of BCV, HEV, and influenza C virus . As shown in Table 1 , incubation of erythrocytes with purified acetylesterase from either BCV or HEV rendered the cells resistant to agglutination by both coronaviruses as well as by influenza C virus . cache = ./cache/cord-258327-03vk6enj.txt txt = ./txt/cord-258327-03vk6enj.txt === reduce.pl bib === id = cord-272437-gvzfl8c3 author = Zhao, Jing title = Replicase 1a gene plays a critical role in pathogenesis of avian coronavirus infectious bronchitis virus date = 2020-08-20 pages = extension = .txt mime = text/plain words = 565 sentences = 51 flesch = 57 summary = title: Replicase 1a gene plays a critical role in pathogenesis of avian coronavirus infectious bronchitis virus Avian coronavirus infectious bronchitis virus (IBV) is an important pathogen threatening poultry production worldwide. Our findings demonstrate that the replicase 1a gene of avian coronavirus IBV is a determinant of pathogenicity. In this study, we used an IBV reverse genetics system based on virulent strain Fig. 2. Recombinant live attenuated avian coronavirus 431 vaccines with deletions in the accessory genes 3ab and/or 5ab protect against infectious 432 bronchitis in chickens attenuated Chinese QX-like infectious bronchitis virus strain as a candidate vaccine S gene and 5a accessory gene 455 are responsible for the attenuation of virulent infectious bronchitis coronavirus cache = ./cache/cord-272437-gvzfl8c3.txt txt = ./txt/cord-272437-gvzfl8c3.txt === reduce.pl bib === id = cord-269419-68kja6bg author = Hu, Weibin title = Fully human broadly neutralizing monoclonal antibodies against influenza A viruses generated from the memory B cells of a 2009 pandemic H1N1 influenza vaccine recipient date = 2013-01-20 pages = extension = .txt mime = text/plain words = 4330 sentences = 256 flesch = 53 summary = title: Fully human broadly neutralizing monoclonal antibodies against influenza A viruses generated from the memory B cells of a 2009 pandemic H1N1 influenza vaccine recipient In this study, we used the full-length HA protein from the 2009 pandemic H1N1 influenza virus to raise fully human neutralizing mAbs. We obtained 19 monoclonal antibodies from the memory B cells of a 2009 pandemic H1N1 influenza vaccine recipient and confirmed that all 19 of the monoclonal antibodies recognized the lysates of both the pandemic virus and the recently circulating seasonal H1N1 influenza virus. Interestingly, we found that most of the monoclonal antibodies, including the seven neutralizing mAbs, bound to the HA stem region (HA2), which is relatively conserved among different influenza A virus strains. These findings indicate that a broad cross-subtype neutralizing antibody response targeting the HA stem region exists in individuals vaccinated against 2009 pandemic H1N1 influenza and that these broadly reactive memory B cells may be important for protecting humans from infection with different influenza A viruses. cache = ./cache/cord-269419-68kja6bg.txt txt = ./txt/cord-269419-68kja6bg.txt === reduce.pl bib === id = cord-268416-8hw80qx8 author = Grunewald, Matthew E. title = The coronavirus nucleocapsid protein is ADP-ribosylated date = 2018-04-01 pages = extension = .txt mime = text/plain words = 4795 sentences = 263 flesch = 50 summary = While screening for ADP-ribosylated proteins during coronavirus (CoV) infection, we detected a ~55 kDa ADP-ribosylated protein in mouse hepatitis virus (MHV)-infected cells and in virions, which we identified as the viral nucleocapsid (N) protein. To identify potential targets of the CoV macrodomain, we analyzed infected cells for changes in ADP-ribosylation patterns utilizing antibodies specific for ADPr. We focused on cells infected with a murine CoV, mouse hepatitis virus (MHV). If the macrodomain was indeed removing the ADPr from the N protein, we would expect to see increased N protein ADP-ribosylation in cells infected with mutant virus compared to wild-type infected cells. To determine if N protein expressed in the absence of CoV infection could be ADP-ribosylated in cell culture, we transduced Vero cells with VEEV replicon particles (VRPs) encoding the MERS-CoV N protein or control GFP at different MOIs . cache = ./cache/cord-268416-8hw80qx8.txt txt = ./txt/cord-268416-8hw80qx8.txt === reduce.pl bib === id = cord-267014-3vi7pgvr author = Vennema, H. title = Genomic organization and expression of the 3′ end of the canine and feline enteric coronaviruses date = 1992-11-30 pages = extension = .txt mime = text/plain words = 3543 sentences = 210 flesch = 59 summary = Abstract The genomic organization at the 3′ end of canine coronavirus (CCV) and feline enteric coronavirus (FECV) was determined by sequence analysis and compared to that of feline infectious peritonitis virus (FIPV) and transmissible gastroenteritis virus (TGEV) of swine. Amplification of cDNA was performed by the polymerase chain reaction (PCR) as described (Kawasaki and Wang, 1989) , after the addition of synthetic oligonucleotide 178, 5'-GATGACACACAGGlTGAG-3', which is identical to the carboxyl-terminus of the nucleocapsid (N) protein gene of FIPV (nucleotides 1945-l 962; Vennema et a/., 1991) . The nucleotide sequences flanking the ORFs 6a and 6b of FIPV and CCV and ORF 7 of TGEV were aligned to design primers for cDNA synthesis and polymerase chain reaction (PCR) amplification. The recombinant expression products were compared to the proteins produced in CCV-, FECV-, and FIPV-infected cells, which were analyzed similarly (Fig. 6) . cache = ./cache/cord-267014-3vi7pgvr.txt txt = ./txt/cord-267014-3vi7pgvr.txt === reduce.pl bib === id = cord-268341-103xf3dw author = Parra, Beatriz title = Kinetics of Cytokine mRNA Expression in the Central Nervous System Following Lethal and Nonlethal Coronavirus-Induced Acute Encephalomyelitis date = 1997-07-07 pages = extension = .txt mime = text/plain words = 5778 sentences = 316 flesch = 49 summary = the plaque size and pathogenesis similar to the parental During JHMV infection of the CNS there is an abrupt suckling mouse brain pool of JHMV originally described increase in mRNA encoding interleukin-1 (a and b), ILby Weiner (1973) and produces a lethal encephalomyeli-6, tumor necrosis factor (TNF)-a, and interferon (IFN)-g, tis with minimal demyelination apparent at the time of at the time of maximal decrease in virus replication and death. Similar of mice through Day 5 postinfection, consistent with the to the kinetics of IFN-g, TNF-a mRNA increased until rapid accumulation of both NK and T cells in the CNS of death of lethally infected mice. Similarly, the adoptive transfer at the time most lethally infected mice were about to succumb to infection (Day 7), there was no difference in the of virus-specific CD4 / T cells to JHMV-infected mice demonstrates that some clones protect via reducing viral peak levels of IL-10 mRNA between the two groups. cache = ./cache/cord-268341-103xf3dw.txt txt = ./txt/cord-268341-103xf3dw.txt === reduce.pl bib === id = cord-268467-btfz6ye8 author = Schreiber, Steven S. title = Sequence analysis of the nucleocapsid protein gene of human coronavirus 229E date = 1989-03-31 pages = extension = .txt mime = text/plain words = 5035 sentences = 343 flesch = 59 summary = The 3′-noncoding region of the genome contains an 11-nucleotide sequence, which is relatively conserved throughout the Coronavirus family and lends support to the theory that this region is important for the replication of negative-strand RNA. This result suggested that the HCV229E subgenomic mRNAs possess a nested-set structure similar to other coronaviruses and that A34 represented a cDNA clone of either the 3'-end of the genomic RNA or the leader sequence. The 3'-noncoding region contains the sequence TGGAAGAGCCA, 75 nucleotides from the 3'-end (Fig. 4) which is relatively conserved among coronaviruses and is found at approximately the same location in all of these viral genomes (Kapke and Brian, 1986; Skinner and Siddell, 1984; Armstrong et a/., 1983; Lapps et al., 1987; Kamahora et a/., 1988; Boursnell et al., 1985) ( Table 1) . Three intergenic regions of coronavirus mouse hepatitis virus strain A59 genome RNA contain a common nucleotide sequence that is homologous to the 3'end of the viral mRNA leader sequence cache = ./cache/cord-268467-btfz6ye8.txt txt = ./txt/cord-268467-btfz6ye8.txt === reduce.pl bib === === reduce.pl bib === id = cord-269193-a647hwu9 author = Lin, Debby A. title = Evolutionary relatedness of the predicted gene product of RNA segment 2 of the Tick-Borne Dhori virus and the PB1 polymerase gene of influenza viruses date = 1991-05-31 pages = extension = .txt mime = text/plain words = 2946 sentences = 152 flesch = 57 summary = Abstract The complete nucleotide sequence of the second largest RNA segment of Dhori/India/1313/61 virus was determined and the deduced amino acid sequence was compared with the polymerase (P) proteins of influenza A, B, and C viruses. The viral RNAs have been shown to encode information in the negative-sense (Clerx et al., 1983; Fuller et al., 1987; Freedman-Faulstich and Fuller, 1990) and it was previously shown that the Dhori nucleoprotein (encoded by RNA segment 5) shares conserved amino acid sequences with the influenza A, B, and C virus nucleoproteins (Fuller et al., 1987) . The PBl polymerase proteins are the most highly conserved among the proteins of the influenza A, B, and C viruses (Yamashita et a/,, 1989 ) and they are most likely required for nucleotide addition during viral RNA synthesis (Braam et al., 1983) . cache = ./cache/cord-269193-a647hwu9.txt txt = ./txt/cord-269193-a647hwu9.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-264331-uvi8ucz4 author = Singh, Shailbala title = Avian influenza viral nucleocapsid and hemagglutinin proteins induce chicken CD8(+) memory T lymphocytes date = 2010-04-10 pages = extension = .txt mime = text/plain words = 5972 sentences = 295 flesch = 51 summary = Following ex vivo co-culture with MHC matched B19/B19 APCs infected with H5N9 virus, memory responses were detected in T cell preparations obtained from all chickens receiving plasmids expressing either AIV protein by 3 weeks p.i. Since neither supernatants from the T cells cultured with uninfected APCs nor T cells from PBS inoculated birds cultured with infected MHC matched B19/B19 birds produced IFNγ (data not shown), the memory T lymphocyte activity was considered AIV specific. In order to evaluate the memory T lymphocyte responses of chickens inoculated with infectious AIV, chicks with the B19/B19 haplotype were inoculated with the low pathogenic H5N9/Turkey/Wis/68 strain and blood was collected at 5 weeks p.i. The ex vivo activation of T lymphocytes by AIV infected APCs was determined by the indirect IFNγ assay (Fig. 5) . cache = ./cache/cord-264331-uvi8ucz4.txt txt = ./txt/cord-264331-uvi8ucz4.txt === reduce.pl bib === id = cord-267532-5rnqd9mb author = Zhang, Xuming title = Expression of Hemagglutinin/Esterase by a Mouse Hepatitis Virus Coronavirus Defective–Interfering RNA Alters Viral Pathogenesis date = 1998-03-01 pages = extension = .txt mime = text/plain words = 6892 sentences = 357 flesch = 55 summary = HEor CAT-specific subgenomic mRNAs were detected in the brains at days 1 and 2 p.i. but not later, indicating that the genes in the DI vector were expressed only in the early stage of viral infection. In the present study, we used this DI RNA vector system to express the viral HE gene in the CNS of mice in the presence of an HE-deficient helper virus. To determine the basis for the reduction in mortality following A59-DE-HE infection compared to other viruses ( Fig. 2) , virus titers in the brains of mice infected with A59-DE-HE were initially compared to mice infected with the parental A59 or A59-DE-CAT at 6 days p.i. Based on the survival of most mice infected with A59-DE-HE, reduced viral replication in the CNS was anticipated. IL-6 mRNA was also increased in the CNS of mice infected with A59-DE-HE virus (Fig. 5B) ; however, no differences were detected in the liver between the two groups. cache = ./cache/cord-267532-5rnqd9mb.txt txt = ./txt/cord-267532-5rnqd9mb.txt === reduce.pl bib === id = cord-266230-ia04jc9j author = Rott, M. E. title = Comparison of the 5′ and 3′ termini of tomato ringspot virus RNA1 and RNA2: Evidence for RNA recombination date = 1991-11-30 pages = extension = .txt mime = text/plain words = 2003 sentences = 119 flesch = 56 summary = It is possible that the similar sequences at both ends of TomRSV RNA1 and RNA2 are a result of recombination between these two genomic RNA components. Beginning from the first potential in-frame initiation site at AUG,B, the N-terminal regions of the TomRSV RNA1 and RNA2 polyproteins are identical for the first 132 amino acids, and of the next 145 amino acid residues 75.3% of the positions are identical (Fig. 3A ). The fact that these regions of similarity are present only at the N-termini of the TBRV and GCMV RNAl-encoded polyproteins but are present at the N-termini of both TomRSV RNA1 -and RNA2encoded pofyproteins suggests that a large portion of coding and noncoding sequences at the 5' terminus of TomRSV RNA1 have been duplicated and are now present at the 5' terrnini of both RNA1 and RNA2. cache = ./cache/cord-266230-ia04jc9j.txt txt = ./txt/cord-266230-ia04jc9j.txt === reduce.pl bib === === reduce.pl bib === id = cord-269204-kajws5xo author = Nitschke, Matthias title = Equine arteritis virus is delivered to an acidic compartment of host cells via clathrin-dependent endocytosis date = 2008-08-01 pages = extension = .txt mime = text/plain words = 4831 sentences = 274 flesch = 48 summary = To investigate whether EAV cell entry proceeds via endocytic uptake we first studied the involvement of clathrin-coated pits in EAV internalization using a BHK cell line that can be induced to express antisense RNA of the clathrin heavy chain (CHC) causing a selective block in clathrin-dependent endocytosis (Iversen et al., 2001) . In contrast to EAV, neither concanamycin A nor bafilomycin A1 nor monensin treatment of BHK-21 cells did affect SV5 mediated plaque formation (Fig. 3 ) consistent with the fact that infection by Parainfluenza viruses does not require a low pH compartment (Lamb and Kolakofsky, 2001) . To explore whether proteases of the late acidic compartments may play a role in fusion activation of EAV, we measured infection of BHK-21 cells upon incubation with leupeptin and E64d, which have been shown to inhibit acidic proteases in the endosomal compartment. cache = ./cache/cord-269204-kajws5xo.txt txt = ./txt/cord-269204-kajws5xo.txt === reduce.pl bib === id = cord-272050-0u62j7nj author = Okamoto, Kimiyuki title = cis-Preferential requirement of a − 1 frameshift product p88 for the replication of Red clover necrotic mosaic virus RNA1 date = 2008-05-25 pages = extension = .txt mime = text/plain words = 5335 sentences = 262 flesch = 50 summary = In contrast, cis-preferential function of the viral encoded proteins or a coupling between translation and replication has been reported for several viruses, including Alfalfa mosaic virus (AMV) (Neeleman and Bol, 1999; van Rossum et al., 1996) , Clover yellow mosaic virus (CYMV) (White et al., 1992) , Bovine coronavirus (Chang et al., 1994) , Cowpea mosaic virus (van Bokhoven et al., 1993) , Poliovirus (Hagino-Yamagishi and Nomoto, 1989; Johnson and Sarnow, 1991; Novak and Kirkegaard, 1994) , Turnip crinkle virus (TCV) (White et al., 1995) , Tobacco etch virus (Mahajan et al., 1996; Schaad et al., 1996) , Tobacco mosaic virus (TMV) (Lewandowski and Dawson, 2000) , Tomato bushy stunt virus (TBSV) (Oster et al., 1998) , Turnip yellow mosaic virus (TYMV) (Weiland and Dreher, 1993) , and Rubella virus (Liang and Gillam, 2001) . cis-Acting core RNA elements required for negative-strand RNA synthesis and cap-independent translation are separated in the 3¢-untranslated region of Red clover necrotic mosaic virus RNA1 cache = ./cache/cord-272050-0u62j7nj.txt txt = ./txt/cord-272050-0u62j7nj.txt === reduce.pl bib === id = cord-269866-3tpyj04y author = Liu, D. X. title = Identification of two new polypeptides encoded by mRNA5 of the coronavirus infectious bronchitis virus date = 1992-01-31 pages = extension = .txt mime = text/plain words = 3164 sentences = 137 flesch = 50 summary = We report here that two polypeptides with the sizes expected for the 5a and 5b products can be synthesised by in vitro translation of a single artificial mRNA containing both the 5a and 5b ORFs. To establish whether these polypeptides represent genuine virus gene products, both the 5a and 5b coding sequences were expressed as bacterial fusion proteins, and these were used to raise monospecific antisera. We report here that two polypeptides with the sizes expected for the 5a and 5b products can be synthesised by in vitro translation of a single artificial mRNA containing both the 5a and 5b ORFs. To establish whether these polypeptides represent genuine virus gene products, both the 5a and 5b coding sequences were expressed as bacterial fusion proteins, and these were used to raise monospecific antisera. cache = ./cache/cord-269866-3tpyj04y.txt txt = ./txt/cord-269866-3tpyj04y.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-274673-tjzlssal author = De Groot, Raoul J. title = Stably expressed FIPV peplomer protein induces cell fusion and elicits neutralizing antibodies in mice date = 1989-08-31 pages = extension = .txt mime = text/plain words = 5111 sentences = 295 flesch = 57 summary = authors: De Groot, Raoul J.; Van Leen, Robert W.; Dalderup, Mieke J.M.; Vennema, Harry; Horzinek, Marian C.; Spaan, Willy J.M. title: Stably expressed FIPV peplomer protein induces cell fusion and elicits neutralizing antibodies in mice Abstract We have established bovine papilloma virus (BPV)-transformed mouse C127 cell lines that synthesize the peplomer protein of the feline infectious peritonitis virus (FIPV) strain 79-1146. Mice immunized with whole lysates of the transformed cells produced FIPV-neutralizing antibodies as shown by plaque reduction. Mammalian cell lines expressing the FIPV peplomer gene would provide a convenient source of protein to dissect the role of E2 in FIP. It is shown that the expression product induces fusion of FIPV-permissive feline cells and is immunogenic in mice. (b) Glyoxal-denatured RNA extracted from noninduced (lane 2) and heat-shock-induced (lane 3) RM(-)I 7 cells was separated on 0.8% agarose gels, transferred to a nylon membrane, and hybridized to a nick-translated 4.5-kbBamHl fragment containing the complete FIPV E2 gene. cache = ./cache/cord-274673-tjzlssal.txt txt = ./txt/cord-274673-tjzlssal.txt === reduce.pl bib === === reduce.pl bib === id = cord-270534-ebkwv4zo author = Bodmer, Bianca S. title = Live-attenuated bivalent measles virus-derived vaccines targeting Middle East respiratory syndrome coronavirus induce robust and multifunctional T cell responses against both viruses in an appropriate mouse model date = 2018-06-11 pages = extension = .txt mime = text/plain words = 6539 sentences = 362 flesch = 53 summary = title: Live-attenuated bivalent measles virus-derived vaccines targeting Middle East respiratory syndrome coronavirus induce robust and multifunctional T cell responses against both viruses in an appropriate mouse model One of these candidates, MV vac2 -MERS-S(H) (Malczyk et al., 2015) , is based on the measles virus (MV) vaccine platform technology (Mühlebach, 2017) , and encodes the MERS-CoV spike protein (S) as an additional antigen in the backbone of recombinant MV vac2 (del Valle et al., 2007) resembling vaccine strain Moraten that is authorized and in use in the US since 1968. (G) Secretion of IFN-γ after antigen-specific re-stimulation of splenocytes harvested 32 days post prime immunization and after co-culture with JAWSII (left) or DC2.4 (middle) dendritic cells transgenic for MERS-N (black) or untransduced controls (NC, white). To assess the capacity of the different MV vac2 -MERS-S(H) vaccine preparations to induce MERS-CoV S-specific cellular immune responses, splenocytes of mice, which had already been tested for humoral responses ( Fig. 2A) , were isolated and analyzed 49 days after immunization for antigen(Ag)-dependent IFN-γ secretion using ELISpot assay. cache = ./cache/cord-270534-ebkwv4zo.txt txt = ./txt/cord-270534-ebkwv4zo.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-273379-w8vy5rl8 author = Mizutani, Tetsuya title = Nascent Synthesis of Leader Sequence-Containing Subgenomic mRNAs in Coronavirus Genome-Length Replicative Intermediate RNA date = 2000-09-30 pages = extension = .txt mime = text/plain words = 4033 sentences = 184 flesch = 48 summary = RNase protection assays using the purified genome-length RI and two probes, which corresponded to the 5′ 300-nt region of mRNA 6 and to the same region of mRNA 7, showed the presence of nascent leader sequence-containing subgenomic mRNAs in the genome-length RI. We purified genome-length RI without contamination of any detectable level of MHV subgenomic mRNAs. We used RNase protection assays to look for nascent subgenomic mRNAs containing the leader sequence in the genome-length RI. If leader-sequence-containing subgenomic mRNA 6 elongates on the genome-length RI, then the RNase protection assay using probe 1 and purified radiolabeled genome-length RI should produce a radiolabeled 300-nt-long RNA fragment (300-nt fragment) that corresponds to the 5Ј-end 300 nt of nascent mRNA 6 (see Fig. 3A ). RNase A treatment of the gel-purified genome-length RI produced RF 1 (Fig. 2B) , and the RNase protection assay demonstrated the presence of nascent leader-sequence-containing subgenomic mRNAs in the genome-length RI. cache = ./cache/cord-273379-w8vy5rl8.txt txt = ./txt/cord-273379-w8vy5rl8.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-273246-4s54jrww author = Niu, Shengniao title = An infectious RNA with a hepta-adenosine stretch responsible for programmed −1 ribosomal frameshift derived from a full-length cDNA clone of Hibiscus latent Singapore virus date = 2014-01-20 pages = extension = .txt mime = text/plain words = 4213 sentences = 213 flesch = 61 summary = title: An infectious RNA with a hepta-adenosine stretch responsible for programmed −1 ribosomal frameshift derived from a full-length cDNA clone of Hibiscus latent Singapore virus In HLSV, a À 1 PRF product, 108 kDa protein, was still detected using transcripts derived from BspHI digested pHLSV-7A, in which the far downstream HLSV sequence was cut off (Fig. 2C , fourth lane from the right). We report here the construction of HLSV biologically active full-length cDNA clones and the identification of a heptaadenosine stretch in HLSV genome as a slippery sequence responsible for À 1 PRF, independent of its downstream pseudoknot structure and the far downstream RNA sequence in vitro. Since monotonous runs of nucleotides can also cause À 2 or þ 1 PRF (Brierley et al., 1992) , we noticed that in the in vitro translation products using HLSV-8A transcripts, a 78 kDa protein was detected (Fig. 2C , first lane from the right). cache = ./cache/cord-273246-4s54jrww.txt txt = ./txt/cord-273246-4s54jrww.txt === reduce.pl bib === === reduce.pl bib === id = cord-274172-3dctmmfe author = Lucas, Alexandra title = In vivo and in vitro models of demyelinating diseases II. Persistence and host-regulated thermosensitivity in cells of neural derivation infected with mouse hepatitis and measles viruses date = 1978-07-15 pages = extension = .txt mime = text/plain words = 5403 sentences = 247 flesch = 48 summary = To investigate the replication of measles in the other non-neural and neural continuous cell lines, monolayer cultures were inoculated at 32.5" and examined for cytopathology, virus production, and development of infectious centers. Fol-With vaccinia virus, combined cell-associResults from these studies focus attention on three salient findings: (1) The strains of measles and mouse hepatitis viruses used can readily become established in a persistent form of infection in cell lines of neural and non-neural origin; (2) almost invariably when the infection is of the persistent type, virus replication becomes thermosensitive due to unknown factors under host control; the virus progeny from persistent infections are themselves not thermolabile; and (3) among the many cell types tested a rat RN2-2 Schwannoma has the unique ability to discriminate between the prototype MHV, and the neurotropic variant, JHM, supporting the persistence of only the latter. cache = ./cache/cord-274172-3dctmmfe.txt txt = ./txt/cord-274172-3dctmmfe.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-271526-14nfqusv author = Molenkamp, Richard title = Identification of a Specific Interaction between the Coronavirus Mouse Hepatitis Virus A59 Nucleocapsid Protein and Packaging Signal date = 1997-12-08 pages = extension = .txt mime = text/plain words = 5535 sentences = 341 flesch = 56 summary = To determine the specificity of the nucleocapsid pro-RNA-protein complexes (Fig. 3, lanes 8-10 and 12) , tein-Ps180 RNA interaction in UV cross-linking assays, clearly indicating that the observed supershift was not competition experiments were performed. This interaction was studied by gel retardation and UV Lysates were prepared from the virus peak fractions (pcross-linking assays using an RNA probe containing the lysate) and from the gradient bottom fractions (b-lysate; 69-nt Ps and the N protein from MHV-A59 infected cell negative control). A structural model for coronaviruses was flanked by non-MHV sequences could confer specific proposed, in which a spherical core, composed of a combination of N and M proteins, was present in addition to encapsidation to a heterologous RNA in MHV infected INTERACTION BETWEEN NUCLEOCAPSID PROTEIN AND PACKAGING SIGNAL of a murine coronavirus in the absence of helper virus. cache = ./cache/cord-271526-14nfqusv.txt txt = ./txt/cord-271526-14nfqusv.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-279813-mrei5kih author = Temeeyasen, G. title = Differential gene modulation of pattern-recognition receptor TLR and RIG-I-like and downstream mediators on intestinal mucosa of pigs infected with PEDV non S-INDEL and PEDV S-INDEL strains date = 2017-12-14 pages = extension = .txt mime = text/plain words = 6657 sentences = 337 flesch = 49 summary = authors: Temeeyasen, G.; Sinha, A.; Gimenez-Lirola, L.G.; Zhang, J.Q.; Piñeyro, P.E. title: Differential gene modulation of pattern-recognition receptor TLR and RIG-I-like and downstream mediators on intestinal mucosa of pigs infected with PEDV non S-INDEL and PEDV S-INDEL strains The aim of this study was to investigate the differential gene modulation of pattern recognition TLR and RIG-I-like receptors and downstream mediators on the intestinal mucosa of neonatal pigs infected with PEDV non-S-INDEL and PEDV S-INDEL strains. We evaluated whether the differential modulatory effect observed in PRRs and downstream mediators in response to infection with the PEDV S-INDEL versus the non-S-INDEL strain was also translated into a differential modulation in the expression of gene coding for pro-inflammatory cytokines and type I interferons. Changes in TNF receptor associated factor (TRAF) 6 and interferon regulatory factor 7 (IRF7) genes mRNA expression induced by porcine epidemic diarrhea virus (PEDV) non S-INDEL and PEDV S-INDEL strains in intestinal mucosa (A-B). cache = ./cache/cord-279813-mrei5kih.txt txt = ./txt/cord-279813-mrei5kih.txt === reduce.pl bib === id = cord-278578-vq5fy8m5 author = Stodola, Jenny K. title = The OC43 human coronavirus envelope protein is critical for infectious virus production and propagation in neuronal cells and is a determinant of neurovirulence and CNS pathology date = 2017-12-26 pages = extension = .txt mime = text/plain words = 10925 sentences = 469 flesch = 50 summary = In this study, we demonstrate that the fully functional HCoV-OC43 E protein (harboring specific TMD and PBM) is critical in infectious virus production and dissemination in epithelial and neuronal cell cultures and in the murine CNS and that it is a determinant of neurovirulence, a first demonstration for this coronavirus species. However, in these primary cultures, low levels of infected cells were visualized by immunofluorescence (IFA) where we detect the viral S protein, suggesting that infection was possible even for the complemented rOC/E-Stop virus but that production of new infectious progeny and eventual propagation were severely inhibited compared to wild type virus (Fig. 2C ). Infection of human LA-N-5 cells and mixed primary cultures of mouse CNS cells showed a similar virus production kinetic Infectious viral titer differences observed between experiments, revealed, by sequencing (G), the appearance of reversions at the position in the E gene where a stop codon was introduced are indicated by bold and underline. cache = ./cache/cord-278578-vq5fy8m5.txt txt = ./txt/cord-278578-vq5fy8m5.txt === reduce.pl bib === id = cord-274480-aywdmj6o author = Song, Wenfei title = Identification of residues on human receptor DPP4 critical for MERS-CoV binding and entry date = 2014-10-21 pages = extension = .txt mime = text/plain words = 2815 sentences = 147 flesch = 57 summary = Middle East respiratory syndrome coronavirus (MERS-CoV) infects host cells through binding the receptor binding domain (RBD) on its spike glycoprotein to human receptor dipeptidyl peptidase 4 (hDPP4). Previously, we have generated a panel of MERS-CoV mutant RBD proteins at the residues D539, Y499, D510, E513, L506, W553 and V555 to characterize their impacts on binding activity to hDPP4 and the entry efficiency into target cells. To study the impacts of the substitutions of the critical residues on hDPP4 described above on the interaction between MERS-CoV RBD and hDDP4, we determined the binding efficiency between these two proteins by employing SPR technique. To further study the importance of the critical residues on hDPP4 on viral entry, we measured the entry efficiency of pseudovirus into COS7 cells expressing the wide-type and mutant forms of hDPP4. These results are consistent with our findings and suggest these residues play an important role in RBD binding and viral entry, and determining the tropism to MERS-CoV infection. cache = ./cache/cord-274480-aywdmj6o.txt txt = ./txt/cord-274480-aywdmj6o.txt === reduce.pl bib === === reduce.pl bib === id = cord-284968-eymvj6k3 author = Namazue, Junko title = Processing of virus-specific glycoproteins of varicella zoster virus date = 1985-05-31 pages = extension = .txt mime = text/plain words = 2818 sentences = 125 flesch = 56 summary = Immunoprecipitation experiments performed with VZV-infected cells, pulse labeled with [3H]glucosamine in the presence of tunicamycin, suggest that O-linked oligosaccharide is present on the glycoprotein of gp 2. In order to investigate the effect of TM on the synthesis of VZV glycoprotein, infected cell cultures were labeled with rHlglucosamine for 18 hr, and cell extracts were immunoprecipitated with three kinds of monoclonal antibodies (cl 9, cl 8, and cl 12) which react with glycoproteins gp 2, gp 3, and gp 5, respectively (Okuno et a,?., 1983) . Next, when cell extracts were reacted with antibodies of cl 8, a band at 106K was seen at pulse labeling, and additional 116K and 64K (prominent) polypeptides were detected during chase (Fig. 2, lanes e, g) . Finally, when cell extracts in the absence of TM were reacted with antibody from cl 12, 49K (major) and 43K (minor) polypeptides from cell cultures of pulse labeling and 55K (major) and 94K (minor) polypeptides were observed during chase (Fig. 2, lanes i, k) . cache = ./cache/cord-284968-eymvj6k3.txt txt = ./txt/cord-284968-eymvj6k3.txt === reduce.pl bib === id = cord-280287-t7uozjml author = Favier, Anne-Laure title = Unique physicochemical properties of human enteric Ad41 responsible for its survival and replication in the gastrointestinal tract date = 2004-04-25 pages = extension = .txt mime = text/plain words = 6968 sentences = 382 flesch = 52 summary = We show that Ad41 infectivity is not diminished by acid exposure, a condition limiting the infectivity of the respiratory Ad. This feature can be attributed to a large extent to the global basic charge of enteric Ad virions and to the stability of Ad41 fiber, a viral protein mediating virus attachment. During cell attachment, the distal C-terminal globular head domain of the fiber protein interacts with the primary receptor, which for some human Ad serotypes is the coxsackievirus and adenovirus receptor (CAR) (Bergelson et al., 1997; Roelvink et al., 1998) . In the first attempt to understand the survival mechanism of the human enteric Ad41 under acid conditions of the stomach, we compared the predicted pI values of external structural proteins of different Ad serotypes (Table 1) . cache = ./cache/cord-280287-t7uozjml.txt txt = ./txt/cord-280287-t7uozjml.txt === reduce.pl bib === === reduce.pl bib === id = cord-284646-fhruiw23 author = Jaeger, Anna S. title = Spondweni virus causes fetal harm in Ifnar1(-/-) mice and is transmitted by Aedes aegypti mosquitoes date = 2020-05-24 pages = extension = .txt mime = text/plain words = 3948 sentences = 247 flesch = 57 summary = Vector competence experiments showed that Ae. aegypti could transmit SPONV when 70 exposed to bloodmeal titers that approximate physiological titers, while Cx. quinquefasciatus nonpregnant, mixed sex 6-to 11-week-old mice lacking type I interferon signaling (Ifnar1 -/-) Ar94 (this is the only strain used in these studies, so it will be referred to hereafter as 86 SPONV); or 10 2 PFU of the highly pathogenic African-lineage ZIKV strain DAK AR 41524 87 (ZIKV-DAK) (Jaeger et al., 2019) . Despite significantly higher maternal 141 viremia observed at 4 dpi with ZIKV-DAK-infected dams, the fact that resorption rates did 142 not significantly differ between the two groups indicates that both ZIKV-DAK and SPONV 143 have a propensity to harm the developing fetus that is independent of the amount of 144 replication in maternal blood. In contrast, ZIKV-DAK-and SPONV-inoculated dams displayed 221 varying degrees of placental pathology with severe effects predominantly observed in the 222 the labyrinth zone, including vascular injury involving maternal and/or fetal vascular spaces, 223 infarction (obstructed blood flow), necrosis, apoptosis, and hemorrhage (Fig. 4) . cache = ./cache/cord-284646-fhruiw23.txt txt = ./txt/cord-284646-fhruiw23.txt === reduce.pl bib === id = cord-281237-asnpuami author = Garten, Wolfgang title = Inhibition of proteolytic activation of influenza virus hemagglutinin by specific peptidyl chloroalkyl ketones date = 1989-09-30 pages = extension = .txt mime = text/plain words = 4043 sentences = 208 flesch = 47 summary = The effect of peptidyl chloroalkyl ketones on the activation of the fowl plague virus hemagglutinin by the proteases specific for paired basic residues has been investigated. When virions containing uncleaved hemagglutinin were incubated with lysates of uninfected cells, cleavage was completely inhibited by peptidyl chloroalkyl ketones containing paired basic residues at a concentration of 1 mM. When dibasic peptidyl chloroalkyl ketones were added to infected cell cultures, cleavage of hemagglutinin and multiple cycles of virus replication were inhibited at 10 mM. the hemagglutinins of the pathogenic avian influenza viruses have a cleavage site consisting of several basic amino acids which can be cleaved by endoproteases present in many cells (for review see Klenk and Rott, 1988) . Table 2 shows an experiment in which a cell lysate has been first incubated with AKR-CMK as an inhibitor and subsequently with chromogenic substrates containing also two basic residues at the cleavage site. cache = ./cache/cord-281237-asnpuami.txt txt = ./txt/cord-281237-asnpuami.txt === reduce.pl bib === id = cord-272871-gu9ptt9y author = White, K.Andrew title = Defective RNAs of clover yellow mosaic virus encode nonstructural/coat protein fusion products date = 1991-08-31 pages = extension = .txt mime = text/plain words = 4609 sentences = 241 flesch = 60 summary = Abstract A small group of 1.2-kb RNAs present on polyribosoes from clover yellow mosaic virus (CYMV)-infected tissue contains sequences from the genomic RNA (gRNA) of CYMV and is encapsidated by CYMV coat protein. Figure 2 shows Northern blots of polyribosomal RNA extracted from CYMV-infected tissue containing the 1.2-kb RNAs. The 7.0-kb gRNA is identified by all probes (Fig. 2 , lanes a, c, e, g, i, and k; probes 1 to 6), but the 1 .O-kb sgRNA encoding coat protein hybridizes only to probes corresponding to the 3' region of the gRNA (Fig. 2 , lanes i and k; probes 5 and 6). The majority of the sequence of the prototype 1.2-kb RNA (Fig. 4) and of additional 1.2-kb RNAs is identical WHITE, BANCROFT, AND MACKIE with the corresponding region of CYMV gRNA reported by Sit et al. cache = ./cache/cord-272871-gu9ptt9y.txt txt = ./txt/cord-272871-gu9ptt9y.txt === reduce.pl bib === id = cord-280795-wtrt13ij author = Han, Yu-Tsung title = Mutational analysis of a helicase motif-based RNA 5′-triphosphatase/NTPase from bamboo mosaic virus date = 2007-10-10 pages = extension = .txt mime = text/plain words = 5813 sentences = 300 flesch = 52 summary = As a step toward better understanding the relationship between activities and structures of the helicase-like domain of BaMV replicase, we set out to investigate the importance of each signature motif to its NTPase and RNA 5′-triphosphatase activities by mutational and kinetic analyses. The apparent K i value of AMPPNP in inhibiting RNA 5′-triphosphatase activity The enzymatic activity was determined at 20°C by enzyme-coupled assay in 1 ml solution that contained 10 pmol enzyme, 0.1 to 3 mM NTP and other buffer components as described under Materials and methods except that the amounts of pyruvate kinase were increased up to 50, 75 and 300 U for GTPase, UTPase and CTPase assay, respectively, to assure the rate of NTP hydrolysis being the limiting step within the coupling reaction. The helicase-like domain of plant potexvirus replicase participates in formation of RNA 5′ cap structure by exhibiting RNA 5′-triphosphatase activity cache = ./cache/cord-280795-wtrt13ij.txt txt = ./txt/cord-280795-wtrt13ij.txt === reduce.pl bib === id = cord-286060-92lazxd7 author = Stohlman, Stephen A. title = Synthesis and subcellular localization of the murine coronavirus nucleocapsid protein date = 1983-10-30 pages = extension = .txt mime = text/plain words = 2012 sentences = 114 flesch = 55 summary = Studies on the intracellular synthesis of MHV proteins by pulse-chase experiments have shown that the nucleocapsid protein, pp60, is a primary gene product (3, 12) . In addition, two-dimensional nonequilibrium isoelectric focusing of infected cell lysates indicated that the nucleocapsid protein was composed of multiple heterogeneously charged species which are homogeneous in size (1). In examining the kinetics of the appearance of JHMV proteins in infected DBT cells, we noted that the region of the gel which contains the pp60 protein also contained another protein of slightly lower molecular weight (Fig. 1A) . When infected cells were pulse-labeled with [%]methionine for 2 min and then chased with excess unlabeled methionine (20 m&Q for various lengths of time, only ~57 was detected within the pulse interval (Fig. 1B) . cache = ./cache/cord-286060-92lazxd7.txt txt = ./txt/cord-286060-92lazxd7.txt === reduce.pl bib === id = cord-281820-oltqsd6n author = Watanabe, Rie title = Heparan sulfate is a binding molecule but not a receptor for CEACAM1-independent infection of murine coronavirus date = 2007-09-15 pages = extension = .txt mime = text/plain words = 3700 sentences = 183 flesch = 58 summary = A highly neurovirulent mouse hepatitis virus (MHV) JHMV strain (wt) with receptor (MHVR)-independent infection activity and its low-virulent mutant srr7 without such activity were found to attach to MHVR-negative, non-permissive BHK cells. To identify the molecule that interacts with JHMV, we focused on heparan sulfate (HS) since it works as a receptor of a mutant MHV-rec1 that infects in an MHVR-independent fashion. To evaluate the infectivity of the attached virus, 50 nM of soMHVR was added to the culture of BHK cells inoculated with wt JHMV and srr7 and those cells were further incubated for 14 h at 37°C. Binding of JHMV to HS on the cell surface HS is the major glycosaminoglycan (GAG) found on most cells and was recently reported as an entry receptor for MHV-BHK, a strain that has an extended host range and infects MHVR-negative cells (de Haan et al., 2005) . cache = ./cache/cord-281820-oltqsd6n.txt txt = ./txt/cord-281820-oltqsd6n.txt === reduce.pl bib === === reduce.pl bib === id = cord-282947-3hgku2e4 author = Wong, Hui Hui title = Accessory proteins 8b and 8ab of severe acute respiratory syndrome coronavirus suppress the interferon signaling pathway by mediating ubiquitin-dependent rapid degradation of interferon regulatory factor 3 date = 2017-12-30 pages = extension = .txt mime = text/plain words = 8714 sentences = 423 flesch = 46 summary = title: Accessory proteins 8b and 8ab of severe acute respiratory syndrome coronavirus suppress the interferon signaling pathway by mediating ubiquitin-dependent rapid degradation of interferon regulatory factor 3 Through the construction of recombinant IBV expressing proteins 8a, 8b and 8ab encoded by SARS-CoV ORF8, we demonstrate that expression of 8b and 8ab enables the corresponding recombinant viruses to partially overcome the inhibitory actions of IFN activation to achieve higher replication efficiencies in cells. Compared to wild type and rIBV8a/b, however, rIBV8b and rIBV8ab were observed to replicate significantly better and express higher levels of N protein in cells stimulated by poly (I:C) (Fig. 2a) . In view of the central role of IRF3 in regulating IFN activation during virus infection, 8b and 8ab with Flag epitope-tagged to their Ntermini were co-expressed with Myc-tagged IRF3 (Fig. 3a) in Cos-7 cells using the vaccinia/T7 expression system (Anderson et al., 1996; Lim and Liu, 2001) for co-immunoprecipitation assays to determine if there is any physical interaction between the proteins. cache = ./cache/cord-282947-3hgku2e4.txt txt = ./txt/cord-282947-3hgku2e4.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-284581-fl2nt4ak author = Kleine-Weber, Hannah title = Spike proteins of novel MERS-coronavirus isolates from North- and West-African dromedary camels mediate robust viral entry into human target cells date = 2019-07-19 pages = extension = .txt mime = text/plain words = 3195 sentences = 190 flesch = 58 summary = title: Spike proteins of novel MERS-coronavirus isolates from Northand West-African dromedary camels mediate robust viral entry into human target cells A recent study showed that MERS-CoV found in North/West(Morocco) and West-African (Burkina Faso and Nigeria) dromedary camels are genetically distinct from Arabian viruses and have reduced replicative capacity in human cells, potentially due to amino acid changes in one or more viral proteins. Here, we show that the spike (S) proteins of the prototypic Arabian MERS-CoV strain, human betacoronavirus 2c EMC/2012, and the above stated African MERS-CoV variants do not appreciably differ in expression, DPP4 binding and ability to drive entry into target cells. We employed a previously described vesicular stomatitis virus (VSV)-based pseudotyping system to study MERS-S-driven host cell entry (Kleine-Weber et al., 2018 known to adequately model key aspects of the coronavirus entry process. Host cell entry driven by the S proteins of North/West-and West-African MERS-CoV isolates from dromedary camels is robust. cache = ./cache/cord-284581-fl2nt4ak.txt txt = ./txt/cord-284581-fl2nt4ak.txt === reduce.pl bib === id = cord-275348-jna496x7 author = Kapadia, Sagar U. title = SARS vaccine based on a replication-defective recombinant vesicular stomatitis virus is more potent than one based on a replication-competent vector date = 2008-06-20 pages = extension = .txt mime = text/plain words = 5982 sentences = 317 flesch = 53 summary = A SARS vaccine based on a live-attenuated vesicular stomatitis virus (VSV) recombinant expressing the SARS-CoV S protein provides long-term protection of immunized mice from SARS-CoV infection (Kapadia, S.U., Rose, J. We found that the vaccine given intramuscularly induced a neutralizing antibody response to SARS-CoV that was approximately ten-fold greater than that required for the protection from SARS-CoV infection, and significantly greater than that generated by the replication-competent vector expressing SARS-CoV S protein given by the same route. In order to evaluate this vector as a SARS vaccine candidate, we also developed a SARS-CoV neutralization assay using a pseudotyped VSV recombinant expressing a green fluorescent protein. SARS-CoV neutralizing antibody titers of these sera were determined by incubating VSVΔG-EGFP/SΔtail-HA virus with serial dilutions of these sera, and the virusserum mixtures were transferred to a monolayer of Vero E6 cells. cache = ./cache/cord-275348-jna496x7.txt txt = ./txt/cord-275348-jna496x7.txt === reduce.pl bib === id = cord-289248-6mx4o0eb author = Wang, Yilong title = Enhancement of safety and immunogenicity of the Chinese Hu191 measles virus vaccine by alteration of the S-adenosylmethionine (SAM) binding site in the large polymerase protein date = 2018-05-01 pages = extension = .txt mime = text/plain words = 7018 sentences = 388 flesch = 59 summary = These two mutants grew to high titer in Vero cells, were genetically stable, and were significantly more attenuated in vitro and in vivo compared to the parental rMV-Hu191 vaccine strain. We next compared the replication kinetics of the rMV-Hu191 mutants and the parental virus in Vero cells in the time course of 120 h after infection (Fig. 5 ). These data suggest that rMVs carrying mutations in the SAM binding site were more attenuated in Vero cells than the parental MV vaccine strain. In this study, we successfully generated two recombinant measles viruses with amino acid substitutions in the SAM binding site of L protein and examined the effects of these mutations on viral replication, safety, and immunogenicity. We generated two recombinant MV-Hu191 carrying mutations in the SAM binding site, which not only grew to high titer in Vero cells and were genetically stable but also were significantly more attenuated and immunogenic compared to the currently used Chinese MV vaccine strain. cache = ./cache/cord-289248-6mx4o0eb.txt txt = ./txt/cord-289248-6mx4o0eb.txt === reduce.pl bib === id = cord-279924-09uwhxs9 author = Plaisted, Warren C. title = T cell mediated suppression of neurotropic coronavirus replication in neural precursor cells date = 2014-01-01 pages = extension = .txt mime = text/plain words = 5580 sentences = 280 flesch = 48 summary = In this study, we demonstrate that cultured murine NPCs are infected by the neurotropic JHM strain of mouse hepatitis virus (JHMV), which induces acute encephalomyelitis and chronic demyelination when injected intracranially into immunocompetent mice. We co-cultured virus-specific CTLs at diminishing effectorto-target (E:T) ratios with NPCs pulsed with the immunodominant CD8 peptide specific for JHMV spike (S) glycoprotein spanning amino acids 510-518 (S510-518), and treated with IFN-γ to induce MHC class I expression. To confirm the role of IFN-γ as the major cytokine contributing to suppression of JHMV replication in infected NPC cultures, monoclonal antibody blockade against the IFN-γ receptor was performed on NPCs before and during treatment with virusspecific CD4þ T cell enriched media. Impaired expression of MHC class II following IFN-γ-treatment of infected NPCs may be a mechanism employed to subvert detection by infiltrating virus-specific CD4þ T cells. cache = ./cache/cord-279924-09uwhxs9.txt txt = ./txt/cord-279924-09uwhxs9.txt === reduce.pl bib === id = cord-287777-ogs4mq0v author = Lindner, Holger A. title = Deubiquitination in virus infection date = 2007-06-05 pages = extension = .txt mime = text/plain words = 8904 sentences = 424 flesch = 40 summary = They include the potential recruitment of DUBs for the stabilization of β-catenin in Epstein-Barr virus (EBV)-infected B cells (Ovaa et al., 2004; Shackelford et al., 2003) , and the specific targeting of the cellular DUB ubiquitin-specific protease 7 (USP7) by the Epstein-Barr nuclear antigen 1 (EBNA1) and the herpes simplex virus type 1 (HSV-1) regulatory protein ICP0 (Everett et al., 1997; Holowaty and Frappier, 2004) . The possibility that modulation of deubiquitination is, nevertheless, a more common viral strategy has gained support by the recent in vitro demonstration of deubiquitinating activities for three viral enzymes: the adenovirus protease adenain (Balakirev et al., 2002) , the papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus (SARS-CoV) (Barretto et al., 2005; Lindner et al., 2005) , and a protease domain contained in the N-terminal fragment of the large tegument protein UL36 (UL36 USP ) from several herpesviruses, namely, HSV-1, EBV, and mouse and human cytomegalovirus (MCMV and HCMV) Schlieker et al., 2005; Wang et al., 2006) . cache = ./cache/cord-287777-ogs4mq0v.txt txt = ./txt/cord-287777-ogs4mq0v.txt === reduce.pl bib === id = cord-285869-jwflooop author = Clementz, Mark A. title = Mutation in murine coronavirus replication protein nsp4 alters assembly of double membrane vesicles date = 2008-05-01 pages = extension = .txt mime = text/plain words = 6966 sentences = 380 flesch = 56 summary = Here, we studied the role of a putative replicase anchor, nonstructural protein 4 (nsp4), in the assembly of murine coronavirus DMVs. We used reverse genetics to generate infectious clone viruses (icv) with an alanine substitution at nsp4 glycosylation site N176 or N237, or an asparagine to threonine substitution (nsp4-N258T), which is proposed to confer a temperature sensitive phenotype. Coronaviruses, such as mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SARS-CoV) that causes severe respiratory illness in humans (Peiris et al., 2004; Stadler et al., 2003) , generate double membrane vesicles (DMVs), which are the sites of viral RNA synthesis (Baker and Denison, 2008; Goldsmith et al., 2004; Gosert et al., 2002; Snijder et al., 2006) . However, at the non-permissive temperature, DMV assembly and mitochondria morphology are disrupted in Alb ts6 icv-infected cells and viral replicase proteins partially localize with mitochondria. cache = ./cache/cord-285869-jwflooop.txt txt = ./txt/cord-285869-jwflooop.txt === reduce.pl bib === === reduce.pl bib === id = cord-284707-72vx11aq author = Leibowitz, Julian L. title = Synthesis of virus-specific RNA in permeabilized murine coronavirus-infected cells date = 1988-09-30 pages = extension = .txt mime = text/plain words = 5498 sentences = 316 flesch = 53 summary = For mouse hepatitis virus (MHV), one of the most extensively studied coronaviruses, there are seven species of MHV-specific mRNA present in infected cells, the largest of which is indistinguishable from virion RNA (Leibowitz et a/., 1981; Lai et a/., 1981; Spaan et a/., 1981) . In this paper we report the characteristics of a permeabilized cell system and demonstrate that it incorporates ribonucle-otide triphosphates into RNA molecules which appear identical to the virus-specific mRNAs synthesized in MHV-infected cells. Protease inhibitors and RNase inhibitors have both been reported to increase the RNA-dependent RNA polymerase activity present in extracts of West Nile virus-infected cells (Grun and Brinton, 1986) . The kinetics of the development of the MHV-specific RNA polymerase activity over the course of infection was determined in permeabilized cells. In this work we report the development and characterization of a permeabilized cell system for assaying MHV-specific RNA polymerase activity. cache = ./cache/cord-284707-72vx11aq.txt txt = ./txt/cord-284707-72vx11aq.txt === reduce.pl bib === id = cord-281309-c9y7m5do author = Guo, Baoqing title = Experimental infection of United States swine with a Chinese highly pathogenic strain of porcine reproductive and respiratory syndrome virus date = 2013-01-20 pages = extension = .txt mime = text/plain words = 7954 sentences = 344 flesch = 48 summary = We found that this HP-PRRSV strain caused extreme morbidity, as was seen in Asia, but novel to this study, resulted in up to 100x higher abundance of circulating virus when compared to VR-2332, caused extremely exacerbated thymic atrophy such that the thymus was often difficult to discern, and the host response was assessed in comparison to animals infected with strain VR-2332 for the first time by a swine protein array including 5 innate and 5 adaptive cytokines in serum, bronchoalveolar lavage fluid and lymph nodes. It was demonstrated that infection with a highly pathogenic strain of PRRSV elicited a significant elevation of all adaptive immunity cytokines measured in BALF, as well as a majority of these cytokines in serum and TBLN homogenates of the same groups of pigs. cache = ./cache/cord-281309-c9y7m5do.txt txt = ./txt/cord-281309-c9y7m5do.txt === reduce.pl bib === id = cord-275403-g4rohhtt author = Bautista, Elida M. title = Functional Properties of the Predicted Helicase of Porcine Reproductive and Respiratory Syndrome Virus date = 2002-07-05 pages = extension = .txt mime = text/plain words = 7432 sentences = 401 flesch = 48 summary = To examine characteristics of putative nonstructural proteins (nsp) encoded in ORF1b, which have been identified by nucleotide similarity to domains of equine arteritis virus, defined genomic regions were cloned and expressed in the pRSET expression system. As initial proof of helicase-like activity, experiments were performed to test the ability of purified PRRSV-14 nsp10 protein to hydrolyze radiolabeled ribonucleotides in the presence or absence of polyribonucleotides. To further analyze the predicted helicase activity of the PRRSV nsp10 protein, experiments were performed using duplex substrates prepared with synthetic oligonucleotides containing single-strand regions at the 3Ј or 5Ј ends and short duplex regions (21 and 24 bp). The 5Ј-to-3Ј orientation of the unwinding activity of the PRRSV helicase was further confirmed in experiments using substrates prepared with in vitro transcribed RNA that contained singlestrand regions at the 5Ј end of both strands and duplex regions of 67 bp (5Ј5ЈDuplex #1) and 85 bp (5Ј5ЈDuplex #2), as shown in Fig. 9B . cache = ./cache/cord-275403-g4rohhtt.txt txt = ./txt/cord-275403-g4rohhtt.txt === reduce.pl bib === id = cord-286121-ltaxmp3u author = Xu, Ke title = Severe acute respiratory syndrome coronavirus accessory protein 9b is a virion-associated protein date = 2009-06-05 pages = extension = .txt mime = text/plain words = 5289 sentences = 287 flesch = 56 summary = In this study, we demonstrate that 9b protein is translated from bicistronic mRNA9 via leaky ribosome scanning and it is incorporated into both virus-like particles (VLPs) and purified SARS-CoV virions. The expression of 9b protein in SARS-CoV infected cells was confirmed by Western blot analysis with anti-9b monoclonal antibody. To confirm that 9b protein can be translated from an mRNA corresponding to the SARS-CoV subgenomic RNA9, the sequence encoding ORFN which contains ORF9b was cloned into the eukaryotic expression vector pCAGGS and transfected into 293T cells. As 9b protein is present in virions, it is advantageous to characterize the role of other SARS-CoV structural proteins in incorporation of 9b protein into VLPs. Cultures of 293T cells were transfected with the indicated plasmids, and pCAGGS vector was added to adjust the total amount of DNA to equivalent levels. 9b protein was immunoprecipitated by anti-9b polyclonal antibody from SARS infected FRhK-4 cell lysates in RIPA buffer, the mass spectrometry analysis of the corresponding gel slices detected a specific peptide that represents 9b protein. cache = ./cache/cord-286121-ltaxmp3u.txt txt = ./txt/cord-286121-ltaxmp3u.txt === reduce.pl bib === === reduce.pl bib === id = cord-289991-wx4rsr4g author = Bhowmick, Rahul title = Rotavirus infection induces G1 to S phase transition in MA104 cells via Ca(+2)/Calmodulin pathway date = 2014-03-21 pages = extension = .txt mime = text/plain words = 7167 sentences = 362 flesch = 52 summary = To assess whether RV modulates expression of CDK inhibitors to regulate cell cycle, whole cell lysates or total RNA of MA104 cells infected with either SA11 (3 moi) or mock infected were subjected to either immunoblotting or real time PCR with p15, p21, p27 specific antibodies or primers, respectively. This results in its inability to bind to and prevent nuclear translocation of E2F ( Fig. 2A) , since E2F in nucleus can activate transcription of several downstream genes like thymidine kinase, thymidine synthase and dihydrofolate reductase (Fig. 2C) , which promote cell cycle progression and DNA replication, nuclear accumulation of E2F by RV during early infection facilitates G 1 /S restriction point modulation in favor of RV replication. CaMKI has been shown to induce G 1 to S phase transition (Skelding et al., 2011) , concurrently activation of CaMKI (phospho CaMKI) was also observed during early RV infection (2-6 hpi) which correlated with increased CaM expression and accumulation of cells in S phase (Fig. 4A) . cache = ./cache/cord-289991-wx4rsr4g.txt txt = ./txt/cord-289991-wx4rsr4g.txt === reduce.pl bib === id = cord-289152-w5ynbewh author = Lee, Sang-Myeong title = Porcine arterivirus activates the NF-κB pathway through IκB degradation date = 2005-11-10 pages = extension = .txt mime = text/plain words = 8015 sentences = 424 flesch = 46 summary = In porcine reproductive and respiratory syndrome virus (PRRSV)-infected cells, NF-κB activation was characterized by translocation of NF-κB from the cytoplasm to the nucleus, increased DNA binding activity, and NF-κB-regulated gene expression. Taken together, these results demonstrated that PRRSV induces nuclear translocation of NF-nB followed by increased DNA binding activity of NF-nB both in MARC-145 cells and PAM cultures. To determine if NF-nB activation by PRRSV was dependent on InBa degradation in MARC-145 cells, the NF-nB pathway was blocked by using an adenovirus vector expressing a dominant negative form of InBa (Ad-InBaDN) which lacks both constitutive (Barroga et al., 1995) and inducible (Brown et al., 1995) phosphorylation sites. This study showed that PRRSV infection resulted in increased nuclear translocation of NF-nB and increased DNA binding activity both in MARC-145 cells and PAM cultures. cache = ./cache/cord-289152-w5ynbewh.txt txt = ./txt/cord-289152-w5ynbewh.txt === reduce.pl bib === id = cord-290640-kh2t0kfz author = O'Connor, Jennifer Black title = Downstream Ribosomal Entry for Translation of Coronavirus TGEV Gene 3b date = 2000-03-30 pages = extension = .txt mime = text/plain words = 5946 sentences = 283 flesch = 55 summary = Abstract Gene 3b (ORF 3b) in porcine transmissible gastroenteritis coronavirus (TGEV) encodes a putative nonstructural polypeptide of 27.7 kDa with unknown function that during translation in vitro is capable of becoming a glycosylated integral membrane protein of 31 kDa. In the virulent Miller strain of TGEV, ORF 3b is 5′-terminal on mRNA 3–1 and is presumably translated following 5′ cap-dependent ribosomal entry. Here we report that, whereas mRNA 3 has a sequence predicting leaky scanning for the translation of ORF 3b by the model of Kozak (1989) , experimental results with mutant constructs suggested downstream entry of ribosomes might also be used. To test by in vitro translation whether the 27.7-and 20-kDa gene 3b products (O'Connor and Brian, 1999) are synthesized when ORF 3b is positioned downstream of ORF 3a (beginning at base 337) on synthetic transcripts, uncapped transcripts of pORF3a-3b-4 DNA linearized at the BamHI site 50 nt downstream from the stop codon of gene 4 (Fig. 1C) were translated in either wheat germ extract or rabbit reticulocyte lysate. cache = ./cache/cord-290640-kh2t0kfz.txt txt = ./txt/cord-290640-kh2t0kfz.txt === reduce.pl bib === id = cord-287620-vuvgi8xx author = Butler, Noah title = Murine encephalitis caused by HCoV-OC43, a human coronavirus with broad species specificity, is partly immune-mediated date = 2006-04-10 pages = extension = .txt mime = text/plain words = 6665 sentences = 344 flesch = 56 summary = HCoV-OC43, harvested from a patient with an upper respiratory tract infection, was originally isolated after passage in human embryonic tracheal organ cultures; this virus caused neurological disease after only one passage in suckling mice and encephalitis within 2-4 passages (McIntosh et al., 1967) (termed HCoV-OC43 NV ). For example, Talbot and co-workers showed, using the mouse-adapted virus after passage in tissue culture cells (termed HCoV-OC43 QUE herein;) that mice infected intranasally with 10 4 -10 5 TCID 50 developed encephalitis if inoculated 8 days but not 21 days postnatally (Jacomy and Talbot, 2003) . HCoV-OC43 QUE was passaged 5-6 times in tissue culture prior to use in mice (personal communication, Dr. Pierre Talbot, INRS-Institut Armand-Frappier, Laval, Quebec) and consequently may be less virulent than virus isolated directly from infected suckling mouse brains. As shown in Fig. 5 , immunocytochemical staining for viral antigen revealed that the tissue culture-adapted virus infected hamster, pig, human, mouse, monkey and cat cells, but not FRT rat epithelium cells. cache = ./cache/cord-287620-vuvgi8xx.txt txt = ./txt/cord-287620-vuvgi8xx.txt === reduce.pl bib === id = cord-283998-whwksoxt author = Tannock, Gregory A. title = The RNA of human coronavirus OC-43 date = 1977-12-31 pages = extension = .txt mime = text/plain words = 3978 sentences = 213 flesch = 57 summary = Abstract A homogeneous RNA complex with a sedimentation coefficient of 70 S and an apparent molecular weight of approximately 6.1 × 106 was released from purified 32P-labeled, mouse-brain-derived OC-43 virus after treatment with 1% sodium dodecyl sulfate (SDS) for 15 min at 23°. This suggests that (a) extensive nicking of a large RNA molecule has occurred during viral growth, due to ribonucleases which are inactivated during phenol extractions; (b) heterogeneity for OC-43 RNA is not due to internal ribonuclease activity and fragments are held together by noncovalent linkages much weaker than those present in the 70 S retroviral RNA complex, or by small proteins; or, most probably, (c) a combination of extensive nicking and weak noncovalent linkages results in the heterogeneous denaturation products. The RNA of avian infectious bronchitis virus (IBV) was first described by Tannock (1973) , who obtained from purified virions a highly heterogeneous array of RNA fragments using a phenol-sodium dodecyl sulfate (SDS) extraction procedure. cache = ./cache/cord-283998-whwksoxt.txt txt = ./txt/cord-283998-whwksoxt.txt === reduce.pl bib === id = cord-290883-r2744fb3 author = TORRES, JUAN M. title = Induction of Antibodies Protecting against Transmissible Gastroenteritis Coronavirus (TGEV) by Recombinant Adenovirus Expressing TGEV Spike Protein date = 1995-11-30 pages = extension = .txt mime = text/plain words = 7299 sentences = 390 flesch = 54 summary = The antisera induced in swine by the Ad5 recombinants expressing the amino-terminal 26% of the spike protein (containing sites C and B) or the full-length spike protein, when mixed with a lethal dose of virus prior to administration to susceptible piglets, delayed or completely prevented the induction of symptoms of disease, respectively. Alternatively, S gene ces are determined rather than titers since in the first fragments were removed from the original plasmid or procedure virus-antibody mixtures are evaluated in the from pSV2X3-TS vectors without SV-40 Pr signal, or withplaque assay without further dilution of the antibody, proout both Pr and polyadenylation sequences, using the viding highly reproducible results and information about restriction endonucleases indicated in Fig. 1 . Infectious Ad-TS recombinants expressing S protein fragments were generated by cotransfecting 293 cells with pFG144K3-TS or pAB14-TS (which carry S gene sequences from TGEV and pFG173 plasmids). cache = ./cache/cord-290883-r2744fb3.txt txt = ./txt/cord-290883-r2744fb3.txt === reduce.pl bib === id = cord-288669-46tkedw7 author = Lee, Changhee title = The small envelope protein of porcine reproductive and respiratory syndrome virus possesses ion channel protein-like properties date = 2006-11-10 pages = extension = .txt mime = text/plain words = 9258 sentences = 455 flesch = 51 summary = P129-ΔE-transfected cells however produced virion particles in the culture supernatant, and these particles contained viral genomic RNA, demonstrating that the E protein is essential for PRRSV infection but dispensable for virion assembly. Our study suggests that the PRRSV E protein may function as a viroporin in the virion envelope that facilitates uncoating of the virus in order to release the genomic RNA into the cytoplasm for subsequent replication. At 24 h postinoculation, Marc-145 cells were fixed, and virus infection was examined by immunofluorescent staining with N-specific MAb. Marc-145 cells inoculated with a culture fluid from cells cotransfected with P129-ΔE and E gene showed bright N-specific fluorescent signal, indicating that the P129-ΔE replication may be rescued by trans-complementation of the E protein (Fig. 2C ). Strand-specific RT-PCR experiments were carried out and demonstrated that PRRSV-infected Marc-145 cells produced reduced levels of positive-sense genomic RNA at 2 days post-infection in the presence of the drugs chloroquine, amantadine and verapamil (Fig. 5A, upper panel) . cache = ./cache/cord-288669-46tkedw7.txt txt = ./txt/cord-288669-46tkedw7.txt === reduce.pl bib === id = cord-286232-jo24ia4s author = Hasebe, Rie title = Infectious entry of equine herpesvirus-1 into host cells through different endocytic pathways date = 2009-10-25 pages = extension = .txt mime = text/plain words = 6962 sentences = 364 flesch = 51 summary = Derm cells by infectious virus recovery assay after viral internalization, suggesting that EHV-1 enters E. In HeLa and receptor-expressing CHO cells, infectious entry of HSV requires trafficking of the virus to an acidic intracellular compartment, phosphatidylinositol 3-kinase activity, glycoprotein D (gD) receptors, as well as viral gB, gD, and gH-gL (Nicola et al., 2003; Nicola and Straus, 2004) . With the use of ultrastructural analysis, we have previously suggested that EHV-1 enters equine brain microvascular endothelial cells (EBMECs) via endocytosis (Hasebe et al., 2006) . Localization of EHV-1 and caveolae during viral internalization Caveolar endocytosis has emerged as a route of entry for several viruses including simian virus 40 (SV40) (Anderson et al., 1996) , mouse polyomavirus (Richterová et al., 2001; Gilbert et al., 2003; Gilbert and Benjamin, 2004) , echovirus (Marjomäki et al., 2002) , human papillomavirus type 31 (Bousarghin et al., 2003; Smith et al., 2007) , human polyomavirus BK (BKV) (Eash et al., 2004) , and species C human adenovirus (Colin et al., 2005) . cache = ./cache/cord-286232-jo24ia4s.txt txt = ./txt/cord-286232-jo24ia4s.txt === reduce.pl bib === id = cord-290231-4m9lj0uq author = Guirakhoo, Farshad title = The Murray Valley encephalitis virus prM protein confers acid resistance to virus particles and alters the expression of epitopes within the R2 domain of E glycoprotein date = 1992-12-31 pages = extension = .txt mime = text/plain words = 5738 sentences = 261 flesch = 48 summary = Abstract To study the role of the precursor to the membrane protein (prM) in flavivirus maturation, we inhibited the proteolytic processing of the Murray Valley encephalitis (MVE) virus prM to membrane protein in infected cells by adding the acidotropic agent ammonium chloride late in the virus replication cycle. By using monoclonal antibodies (MAbs) and protease maps, we previously demonstrated that the E glycoprotein of tick-borne encephalitis (TBE) virus undergoes an irreversible conformational change, predominantly in the epitopes of domain A, at mildly acidic pH . To understand the role of prM protein in virus maturation and its interaction with the E glycoprotein, we investigated the effect that ammonium chloride had on MVE viruses grown in C6/36 mosquito cells. The reactivities of MAbs defining nine distinct epitopes on the MVE E glycoprotein were compared on M-and prMcontaining viruses using supernatants of ammonium chloride-treated or untreated virus-infected C6/36 cells. cache = ./cache/cord-290231-4m9lj0uq.txt txt = ./txt/cord-290231-4m9lj0uq.txt === reduce.pl bib === id = cord-293375-qcy56ui7 author = Strauss, Ellen G. title = Identification of the active site residues in the nsP2 proteinase of sindbis virus date = 1992-12-31 pages = extension = .txt mime = text/plain words = 5192 sentences = 265 flesch = 56 summary = coma-, nepo-, and potyviruses; coronaviruses; and flaviviruses (and their proposed relatives pestiviruses and hepatitis C virus.) Originally these domains were predicted to have proteolytic activity based on the presence of certain conserved amino acid residues and on the basis of protein-modeling studies (Bazan and Fletterick, 1989; Boege et a/., 1981; Gorbalenya et al., 1989; Hahn eta/., 1985) . Furthermore, we present data to show that none of the asparagine residues in the proteinase domain of Sindbis nsP2 that are conserved among alphaviruses are absolutely required for proteolytic activity, but that Trp-559, adjacent to His-558, is essential for function. We also examined the effect of changing Cys-525, one of the two remaining conserved cysteine residues in the C-terminal half of nsP2, to serine or arginine, as well as changing Ser-535, which is found in a domain of limited similarity to the active site serine of serine proteinases, to threonine. cache = ./cache/cord-293375-qcy56ui7.txt txt = ./txt/cord-293375-qcy56ui7.txt === reduce.pl bib === id = cord-291192-wm2eyaam author = Becares, Martina title = Antigenic structures stably expressed by recombinant TGEV-derived vectors date = 2014-08-09 pages = extension = .txt mime = text/plain words = 9535 sentences = 526 flesch = 49 summary = Transmissible gastroenteritis virus (TGEV) was engineered to express porcine reproductive and respiratory syndrome virus (PRRSV) small protein domains, as a strategy to improve heterologous gene stability. Recombinant TGEV (rTGEV) vectors have been engineered for dicistronic expression of heterologous genes, such as porcine reproductive and respiratory syndrome virus (PRRSV) GP5 and M proteins (Cruz et al., 2010) , or rotavirus VP2 and VP6, in which formation of rotavirus virus like particles (VLPs) in the cytoplasm of rTGEV infected cells was observed (Enjuanes et al., 2007) . Therefore, heterologous gene size reduction is a promising strategy to achieve stable expression in TGEV-derived vectors and in general in CoVs. This effect could be due to a decrease of the probability of non-homologous recombination in shorter sequences, or to the elimination of protein domains toxically affecting the host cell or rTGEV life cycle. cache = ./cache/cord-291192-wm2eyaam.txt txt = ./txt/cord-291192-wm2eyaam.txt === reduce.pl bib === id = cord-289045-vft163v0 author = Thackray, Larissa B. title = Substitutions of conserved amino acids in the receptor-binding domain of the spike glycoprotein affect utilization of murine CEACAM1a by the murine coronavirus MHV-A59 date = 2005-03-30 pages = extension = .txt mime = text/plain words = 7779 sentences = 345 flesch = 56 summary = Cell lines from host species that are normally resistant to MHV, porcine coronavirus [transmissible gastroenteritis virus (TGEV)] or human coronavirus strain 229E (HCoV-229E) are rendered susceptible to infection by transfection with cDNA encoding the specific coronavirus receptors mCEACAM1a, porcine aminopeptidase N (pAPN) (Delmas et al., 1992; Dveksler et al., 1991; Yeager et al., 1992) . Since some of the aa substitutions in the RBD of S were chosen to reflect residues found in S330 of related rat, bovine or human coronaviruses in group II (Fig. 1A) , we examined the ability of the SA59 B, S33R A, S33G C, T62S A, T62A A, L65H C, L65A C, L79M/T82M A, L79A/ T82A B, Y162F A, K183R A and K183G A viruses to infect non-murine cells lines that are normally resistant to MHV-A59 infection. cache = ./cache/cord-289045-vft163v0.txt txt = ./txt/cord-289045-vft163v0.txt === reduce.pl bib === id = cord-290282-oxyzndsj author = Ortego, Javier title = Transmissible gastroenteritis coronavirus gene 7 is not essential but influences in vivo virus replication and virulence date = 2003-03-30 pages = extension = .txt mime = text/plain words = 4287 sentences = 215 flesch = 53 summary = Transmissible gastroenteritis coronavirus (TGEV) contains eight overlapping genes that are expressed from a 3′-coterminal nested set of leader-containing mRNAs. To facilitate the genetic manipulation of the viral genome, genes were separated by duplication of transcription regulating sequences (TRSs) and introduction of unique restriction endonuclease sites at the 5′ end of each gene using an infectious cDNA clone. All the rTGEV viruses conserved the modifications engineered in the cDNAs (data not shown), indicating that the ORF separation and the insertion of unique endonuclease restriction sites between genes were stably maintained in the rTGEV genomes. Interestingly, analysis of viral growth in the gut of infected piglets showed a 100-to 5000-fold reduction of recombinant viruses containing one or more restriction sites in relation to the rTGEV-wt virus ( Fig. 5D and E) . cache = ./cache/cord-290282-oxyzndsj.txt txt = ./txt/cord-290282-oxyzndsj.txt === reduce.pl bib === id = cord-294056-7e477y1x author = La Monica, Nicola title = Coronavirus mRNA synthesis: Identification of novel transcription initiation signals which are differentially regulated by different leader sequences date = 1992-05-31 pages = extension = .txt mime = text/plain words = 3341 sentences = 173 flesch = 58 summary = Previously, we have identified a transcription initiation site (for mRNA 2-1), which is more efficiently transcribed by viruses containing two copies of UCUAA sequence in the leader RNA than by those with three copies. To understand the mechanism of MHV mRNA transcription, we have attempted to determine whether the differential regulation of transcription initiation by leader RNA containing different UCUAA copy numbers is unique to mRNA 2-l. The analysis of several other recombinant viruses with different genome structures suggested that mRNA 3-l was synthesized only by viruses with a leader RNA containing three copies of UCUAA and gene 3 sequence derived from A59 but not JHM (10, 13). Using various primers representing sequences of different regions of gene 1 of the JHM strain of MHV (2) and a second primer representing the 5'-end of the leader RNA, we detected several PCR products which represented mRNAs initiated from various sites. cache = ./cache/cord-294056-7e477y1x.txt txt = ./txt/cord-294056-7e477y1x.txt === reduce.pl bib === id = cord-291611-cfe8yujp author = Zhang, Xuming title = Comparison of the nucleotide and deduced amino acid sequences of the S genes specified by virulent and avirulent strains of bovine coronaviruses date = 1991-07-31 pages = extension = .txt mime = text/plain words = 2769 sentences = 149 flesch = 60 summary = title: Comparison of the nucleotide and deduced amino acid sequences of the S genes specified by virulent and avirulent strains of bovine coronaviruses Abstract The entire nucleotide sequences of the spike glycoprotein (S) genes of the highly virulent bovine coronavirus (BCV) strain BCV-LY138, the avirulent BCV-L9 and related Norden Vaccine (BCV-Vaccine) strains were determined using the polymerase chain reaction (PCR) to amplify cDNAs obtained by reverse transcription of viral RNA, and to produce single strand cDNAs for DNA sequencing. Substitutions of few amino acids in the putative fusogenic domains and two prolines at 507 and 567 in the antigenic domains may cause altered immunogenic and other functional properties of the S proteins specified by the virulent and avirulent BCV strains. cache = ./cache/cord-291611-cfe8yujp.txt txt = ./txt/cord-291611-cfe8yujp.txt === reduce.pl bib === id = cord-293790-7hyelm88 author = Guévin, Carl title = Autophagy protein ATG5 interacts transiently with the hepatitis C virus RNA polymerase (NS5B) early during infection date = 2010-09-01 pages = extension = .txt mime = text/plain words = 5267 sentences = 290 flesch = 54 summary = title: Autophagy protein ATG5 interacts transiently with the hepatitis C virus RNA polymerase (NS5B) early during infection To identify novel cellular factors that may play an essential role in HCV RNA replication, we have previously screened a human liver cDNA library for proteins interacting with the HCV NS5B RNAdependent RNA polymerase (RdRp). Here we report that ATG5, a protein required for the formation of DMV in embryonic stem cell (Mizushima et al., 2001) , specifically interacts with HCV NS5B. As a control, a panel of proteins (RAR-β, RAR-α, HCV core, and nonstructural protein: NS3 prot , NS3 hel , NS4A, and NS4B) cloned in the GAL4 DNA binding domain was tested for interaction with ATG5. A. Soluble yeast extracts containing NS5BΔ21 (N-terminal c-myc tag) and ATG5 (N-terminal HA tag) were incubated with different monoclonal antibodies and the immunoprecipitates were pulled down using protein A/G beads. cache = ./cache/cord-293790-7hyelm88.txt txt = ./txt/cord-293790-7hyelm88.txt === reduce.pl bib === id = cord-294260-g410mavp author = Sztuba-Solińska, Joanna title = Subgenomic messenger RNAs: Mastering regulation of (+)-strand RNA virus life cycle date = 2011-04-10 pages = extension = .txt mime = text/plain words = 9531 sentences = 506 flesch = 54 summary = Arrow, RNA3 start site at nt 2721 (Lindenbach et al., 2002) ; (D) Schematic of the RCNMV genome showing the relative positions of the in trans interacting RNA elements: the loop portion of a stem-loop in RNA2 (termed trans-activator or TA) and a complementary sequence in RNA1 (termed TA binding site or TABS) located just upstream from the initiation site for SG mRNA transcription (Guenther et al., 2004) ; (E) Representation of CLSV genome and the proposed AS2 and RS2 interaction during regulation of SG RNA2 synthesis (Xu and White, 2008) ; (F) Overview of the BYDV genome and the in cisinteraction between genomic 5′-UTR stem-loop (BCL) and the genomic 3′-BTE, and the in trans interaction between the genomic 3′ BTE and the 5′ UTR of SG RNA1 . cache = ./cache/cord-294260-g410mavp.txt txt = ./txt/cord-294260-g410mavp.txt === reduce.pl bib === id = cord-296364-7rp60d2m author = Youn, Soonjeon title = In vitro assembled, recombinant infectious bronchitis viruses demonstrate that the 5a open reading frame is not essential for replication date = 2005-02-05 pages = extension = .txt mime = text/plain words = 5112 sentences = 270 flesch = 56 summary = Molecular clones of infectious bronchitis virus (IBV), derived from the Vero cell adapted Beaudette strain, were constructed, using an in vitro assembly method. Direct sequencing of RT-PCR products derived from cells infected with the plaque-purified virus, which had lost expression of EGFP, confirmed loss of the EGFP ORF. This strategy was further modified to construct an infectious cDNA clone of MHV with their bno see'mQ technology, in which restriction endonuclease sequences were incorporated into amplicons, such that upon enzyme treatment, the endonuclease sites were eliminated prior to in vitro ligation. In the current study, molecular clones of IBV were generated using the in vitro assembly of cDNA fragments as a template for transcription of full-length genomic RNA. Interestingly, the size of plaques with the 5a deletions, including a revertant that had completely lost the EGFP ORF, was comparable to plaques generated by our standard Beaudette cell-adapted Beaudette virus (Fig. 6B ). cache = ./cache/cord-296364-7rp60d2m.txt txt = ./txt/cord-296364-7rp60d2m.txt === reduce.pl bib === id = cord-292751-tk1oggi9 author = Hosseini, Elahe Seyed title = The novel coronavirus Disease-2019 (COVID-19): Mechanism of action, detection and recent therapeutic strategies date = 2020-09-24 pages = extension = .txt mime = text/plain words = 3784 sentences = 222 flesch = 46 summary = Novel coronavirus SARS-CoV-2, designated as COVID-19 by the World Health Organization (WHO) on the February 11, 2020, is one of the highly pathogenic β‐coronaviruses which infects human. The previously reported viral zoonotic pathogens include SARS-CoV (severe acute respiratory syndrome coronavirus) and MERS (Middle East respiratory syndrome coronavirus) [3, 4] , that can cause severe respiratory disease in human [5, 6] . SARS-CoV-2, a novel coronavirus (which causes COVID19) , has fast spread like a pandemic since its outbreak in Wuhan, China, in December 2019 [7] . Nowadays, Griffithsin, as an inhibitor of SARS and MERS spike, Remdesivir, favipiravir and ribavirin (nucleoside analogues), lopinavir/ritonavir (protease enzyme inhibitors) [61] , oseltamivir (neuraminidase inhibitors), anti-inflammatory drugs and EK1 peptide [62] , the clinical potential to be applied against the 2019-nCoV infection [67, 68] . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan cache = ./cache/cord-292751-tk1oggi9.txt txt = ./txt/cord-292751-tk1oggi9.txt === reduce.pl bib === id = cord-296416-q0rsfzgw author = LAVI, EHUD title = Syncytia Formation Induced by Coronavirus Infection Is Associated with Fragmentation and Rearrangement of the Golgi Apparatus date = 1996-07-15 pages = extension = .txt mime = text/plain words = 4766 sentences = 232 flesch = 50 summary = In many 3-5 hr after infection, individual elements of the GA, cells the secretion blocker Brefeldin A (BFA) reversibly which are associated initially with separate microtubuleredistributes membranes and enzymes of the GA back organizing centers in perinuclear areas of fused cells, into the RER, but does not inhibit endocytosis (Doms et congregate in the center of syncytia and form an exal., 1989; Lippincott-Schwartz et al., 1989; Johnston et al., tended network of nondisrupted intact Golgi complexes 1994). In this study, we used organ-Immunohistochemistry elle-specific antibodies, immunohistochemistry, and transmission electron microscopy to examine the fate of Cells, grown on poly-D-lysine-treated coverslips, were the GA during cell fusion and syncytia formation in mouse fixed with 2% paraformaldehyde for 20 min at room tem-L-2 cells infected with MHV-A59 and fusion defective perature, washed three times in PBS, then incubated for mutants. cache = ./cache/cord-296416-q0rsfzgw.txt txt = ./txt/cord-296416-q0rsfzgw.txt === reduce.pl bib === id = cord-298847-szezd2vb author = Jacomy, Hélène title = Vacuolating encephalitis in mice infected by human coronavirus OC43 date = 2003-10-10 pages = extension = .txt mime = text/plain words = 6882 sentences = 338 flesch = 47 summary = Virus inoculation of 21-day postnatal C57BL/6 and BALB/c mice led to a generalized infection of the whole CNS, demonstrating HCoV-OC43 neuroinvasiveness and neurovirulence. Moreover, mice inoculated with supernatants from cell cultures infected with brain tissue from affected mice developed the same disease, demonstrating that the virus was responsible for pathology. Cells positive for viral antigens were first observed at HCoV-OC43-infected mice gained weight normally during the first 5 days after infection, after which they all lost weight during the acute phase of the disease. (A) 100% of brains from C57BL/6 mice inoculated ic with 10 TCID 50 of HCoV-OC43 were positive for viral RNA between 3 and 11 days postinfection. However, RT-PCR analysis revealed that viral RNA could not be detected after the second week postinfection, suggesting a nonpersistent infection of HCoV-OC43 virus in 21 DPN mice. Every 2 days postinfection, five animals from two groups of infected mice of each strain were sacrificed and processed for detection of viral RNA, viral proteins, and infectious virus. cache = ./cache/cord-298847-szezd2vb.txt txt = ./txt/cord-298847-szezd2vb.txt === reduce.pl bib === id = cord-291306-g9qmmugg author = Vey, Martin title = Hemagglutinin activation of pathogenic avian influenza viruses of serotype H7 requires the protease recognition motif R-X-K/R-R date = 1992-05-31 pages = extension = .txt mime = text/plain words = 2436 sentences = 131 flesch = 54 summary = It has long been known that the hemagglutinins activated by these enzymes have multiple lysine and arginine residues at theircleavage sites, and it has been shown that most of these basic amino acids are critical for cleavage activation (7). Comparison of the published hemagglutinin sequences of the pathogenic avian influenza-A-viruses of serotype H7 reveals a number of conserved amino acids upstream of the cleavage site, notably a series of arginine and lysine residues in positions -1 to -6 and two proline residues in positions -7 or -8 and in position -10 (Table 1) . To determine whether these conserved regions are important for the cleavability of the H7 hemagglutinin, we subjected a cDNA clone of the hemagglutinin of influenza virus AIFPV/Rostock/34 to site-directed mutagenesis at the cleavage site and from the panel of mutants obtained, we have selected two groups. In previous work, pathogenic variants with increased hemagglutinin cleavability could be obtained, when apathogenic avian influenza virus strains were adapted to non-permissive host cells (11, 9, 16) . cache = ./cache/cord-291306-g9qmmugg.txt txt = ./txt/cord-291306-g9qmmugg.txt === reduce.pl bib === id = cord-292019-rfu0bkag author = Gómez, N. title = Expression of Immunogenic Glycoprotein S Polypeptides from Transmissible Gastroenteritis Coronavirus in Transgenic Plants date = 1998-09-30 pages = extension = .txt mime = text/plain words = 3586 sentences = 174 flesch = 46 summary = We report on the immunological response elicited by two recombinant versions of the glycoprotein S from the swine-transmissible gastroenteritis coronavirus (TGEV) expressed in transgenic plants. Arabidoposis plants were genetically transformed with cDNAs constructs encoding either the N-terminal domain (amino acid residues 1–750) or the full-length glycoprotein S of TGEV, responsible for the neutralizing antibody induction against the virus, under the control of the cauliflower mosaic virus 35S (CaMV 35S) promoter. Mice immunized with leaf extracts from transgenic plants developed antibodies that reacted specifically with TGEV in ELISA, immunoprecipitated the virus-induced protein, and neutralized the virus infectivity. In this report, we show that full-length or the globular part (N-terminal domain) of TGEV spike protein (glycoprotein S) expressed in transgenic plants retained the antigenic properties and elicited neutralizing antibodies when used to immunize animals. cache = ./cache/cord-292019-rfu0bkag.txt txt = ./txt/cord-292019-rfu0bkag.txt === reduce.pl bib === id = cord-299122-djfj4262 author = Yu, Hua title = Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice() date = 2007-03-15 pages = extension = .txt mime = text/plain words = 5459 sentences = 273 flesch = 52 summary = title: Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice() Using the phage-displayed peptide library screening method and purified Fab fragments of immunoglobulin G (IgG Fab) from normal human sera and convalescent sera from SARS-CoV-infected patients as targets, 11 B cell epitopes of SARS-CoV spike glycoprotein (S protein) and membrane protein (M protein) were screened. Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice ☆ Therefore, in the present study, we screened and identified specific B cell epitopes of SARS-CoV using phagedisplayed peptide library, Fab fragments from anti-SARS-CoV immunoglobulin G (IgG) and normal human IgG as targets, and an improved biopanning procedure. Splenic lymphocytes from mice on day 42 still exhibited significant proliferative responses to specific antigen, demonstrating that the four epitope-based peptides induced long-term immune responses (data not shown). cache = ./cache/cord-299122-djfj4262.txt txt = ./txt/cord-299122-djfj4262.txt === reduce.pl bib === id = cord-299994-1ksfo0pr author = Kanitz, Manuel title = Structural basis for catalysis and substrate specificity of a 3C-like cysteine protease from a mosquito mesonivirus date = 2019-05-02 pages = extension = .txt mime = text/plain words = 8934 sentences = 450 flesch = 59 summary = In CavV and most other members of the genus Alphamesonivirus, the P2 position of putative 3CL pro substrates is predominantly occupied by Asn. The crystal structure of the 3CL pro /inhibitor complex shows that the Asn side chain fits perfectly into the S2 subpocket, with its carboxamide functionality acting as hydrogen bond donor and acceptor in interactions with the main chain carbonyl oxygen of Asp216 and the Oγ atom of Ser52, respectively. In the first crystal structure reported for a coronavirus 3CL pro , this Asp (Asp186 in the TGEV 3CL pro sequence) was found to form a hydrogen bond to a water molecule located in a position that, in chymotrypsin and related serine proteases, is occupied by the side chain of the third member of the catalytic triad (typically Asp) (Anand et al., 2002) . cache = ./cache/cord-299994-1ksfo0pr.txt txt = ./txt/cord-299994-1ksfo0pr.txt === reduce.pl bib === id = cord-293248-8vtd9e4n author = Day, J. Michael title = Determination and analysis of the full-length chicken parvovirus genome date = 2010-03-30 pages = extension = .txt mime = text/plain words = 3045 sentences = 153 flesch = 50 summary = Through the application of a molecular screening method targeting particle-associated nucleic acid (PAN), we recently described the detection and partial characterization of a novel enteric parvovirus in chickens. Initial analysis of this chicken-origin parvovirus (ChPV) revealed that it is a novel member of the Parvovirinae subfamily within the Parvoviridae, and led to the development of a specific molecular diagnostic test targeting the ChPV non-structural (NS) gene (Zsak et al., 2009) . Parvoviruses have been previously described in chickens based upon their morphology via electron microscopy and upon their genome size Kisary et al., 1984) , and enteric disease signs have been attributed to parvovirus-like particles detected in turkey intestinal tracts (Trampel et al., 1983) . The analysis includes comparisons to other members of the Parvovirinae that infect mammals and birds, including two novel turkey-origin parvoviruses (TuPV) recently sequenced using a similar molecular approach. cache = ./cache/cord-293248-8vtd9e4n.txt txt = ./txt/cord-293248-8vtd9e4n.txt === reduce.pl bib === id = cord-298934-vtrfqozl author = Makino, Shinji title = Primary structure and translation of a defective interfering rna of murine coronavirus date = 1988-10-31 pages = extension = .txt mime = text/plain words = 5188 sentences = 298 flesch = 57 summary = The detection of such RNA intermediates in MHV-infected cells (Baric et a/., 1985 (Baric et a/., , 1987 suggests that coronavirus genomic RNA synthesis involves a discontinuous and nonprocessive mechanism, which may account for the high frequency of recombination via a copy choice mechanism. Since previous oligonucleotide fingerprinting analysis suggested that DlssE RNA contains the leader sequence and the 5' end region of genomic sequence (Makino et al., 1985) cDNA clones were screened by colony hybridization using 5' end-labeled, leader-specific 72-mer, and two cDNA clones F82 and C96, which correspond to the 5' end of genomic RNA of MHV-JHM . Possible secondary structure at the DI RNA rearrangment sites Sequence analysis revealed that DlssE RNA consisted of three noncontiguous regions of MHV-JHM genomic RNA. Furthermore, as previously described for the standard MHV-JHM, the sequence surrounding the junction of leader RNA and the remaining 5'-end genomic sequence also contains a stable secondary structure (Soe eta/., 1987) . cache = ./cache/cord-298934-vtrfqozl.txt txt = ./txt/cord-298934-vtrfqozl.txt === reduce.pl bib === id = cord-294990-jdjbjkcp author = Thuy, Nguyen Thanh title = A new nidovirus (NamDinh virus NDiV): Its ultrastructural characterization in the C6/36 mosquito cell line date = 2013-07-25 pages = extension = .txt mime = text/plain words = 3319 sentences = 154 flesch = 50 summary = The viral nucleocapside-like particles detected in the cytoplasm (white arrows) and accumulated in the ER vesicles (Ves) of 48 h NDiV-infected C6/36 cells, appear immunoglod-labeled on ultrathin sections with anti-NDiV polyclonal antibodies, as shown in Fig. 5 . In this study, the nucleocapsid-like particle of NDiV was identified in the host cell cytoplasm as possessing a round shape and an inner core observed in several types of vesicles and in the ER and its viral nature was confirmed by immunogold labeling on thin sections. By EM analyses, we show that replication and assembly of NDiV was only detected in the cytoplasm of the host cells in which viral nucleocapsid-like particles appeared in the cytoplasm and in the endoplasmic compartments such as vacuoles, ER, and vesicles, but not in mitochondria. cache = ./cache/cord-294990-jdjbjkcp.txt txt = ./txt/cord-294990-jdjbjkcp.txt === reduce.pl bib === id = cord-299976-36r794ow author = O’Brien, Amornrat title = Characterizing replication kinetics and plaque production of type I feline infectious peritonitis virus in three feline cell lines date = 2018-12-01 pages = extension = .txt mime = text/plain words = 6070 sentences = 306 flesch = 56 summary = FCoVs are typically grouped into two biotypes (or pathotypes), which have been classified as feline enteric coronavirus (FECV) and feline infectious peritonitis virus (FIPV), based on tissue tropism, disease progression, and genetic markers (reviewed in Kipar and Meli, 2014; Pedersen, 2014 Pedersen, , 2009 , although the range of disease signs and clinical outcomes are likely to extend beyond these two basic definitions. As part of this study, we characterized three feline cell lines-two from the American Type Culture Collection (ATCC) and one from Cornell University-and evaluated the replication kinetics, efficiency of plaque formation, and responsiveness of these cells to interferon (IFN) in order to identify the optimal cell culture conditions for type I FIPV Black. After observing the rapid and uniform development of CPE and release of virus into cell supernatants during infection of AK-D and Fcwf-4 CU cells, we reasoned that these cells would be employable in a standardized plaque assay to consistently determine FIPV Black titer. cache = ./cache/cord-299976-36r794ow.txt txt = ./txt/cord-299976-36r794ow.txt === reduce.pl bib === id = cord-300470-vgd1ol2z author = Conradie, Andelé M. title = Establishment of different plasmid only-based reverse genetics systems for the recovery of African horse sickness virus date = 2016-09-19 pages = extension = .txt mime = text/plain words = 7888 sentences = 366 flesch = 46 summary = In both of the above reverse genetics systems, recovery of infectious AHSV-4 from plasmid DNA relies on the expression of T7 RNA polymerase within cells transfected with the AHSV-4 cDNA plasmids. The initial AHSV-4 reverse genetics system developed here consists of 10 plasmids, each containing a full-length cDNA copy of single AHSV-4 genome segments flanked by T7 RNA polymerase promoter and HDV ribozyme sequences. However, the same reassortant virus was also recovered successfully by combining the four AHSV-4 dual vectors with two single reverse genetics plasmids, which contained cDNA copies of the S5 and S6 genome segments, respectively. To this end, we have cloned a T7 RNA polymerase expression cassette onto the genetic backbone of the pJAD-S2-S6 dual reverse vector and subsequently demonstrated that AHSV-4 could be recovered in BSR and L929 cells following transfection of the cells with the modified 5-plasmid set. cache = ./cache/cord-300470-vgd1ol2z.txt txt = ./txt/cord-300470-vgd1ol2z.txt === reduce.pl bib === id = cord-303497-s3zs1oxf author = Breuning, Astrid title = Characterization of a cold-sensitive (cs) recombinant between two influenza a strains date = 1983-10-15 pages = extension = .txt mime = text/plain words = 3003 sentences = 166 flesch = 60 summary = Recombinants between fowl plague virus (FPV) and these strains were obtained by double infection of chick embryo cells either with specific ts mutants of FPV or FPV wild-type and the other prototype strains, and extended plaque purifications as described by Scholtissek et aL (1976) and Rott et aL (1979) . When plaque tests were performed on chick embryo cells at 37 or 40" with recombinants between FPV and other prototype influenza virus strains it was found that the plaque morphology of most of these recombinants was similar to that of FPV. In a single-cycle multiplication experiment (infection at a multiplicity of lo-50 PFU per cell) at 33", the yield of infectious 113/Ho was very low when compared with the multiplication at 37" or with the adapted strain or FPV (Fig. 2) . These results indicate that a step before virus maturation is impeded at 33' in 113/Ho-infected cells, since labeling of viral proteins is already slowed down at this temperature. cache = ./cache/cord-303497-s3zs1oxf.txt txt = ./txt/cord-303497-s3zs1oxf.txt === reduce.pl bib === id = cord-296075-8axbkyyz author = Castro, Raymond F. title = Differential Antigen Recognition by T Cells from the Spleen and Central Nervous System of Coronavirus-Infected Mice date = 1996-08-01 pages = extension = .txt mime = text/plain words = 1733 sentences = 88 flesch = 53 summary = Abstract CD8+cytotoxic T lymphocytes (CTLs) isolated from the central nervous system (CNS) of C57Bl/6 mice acutely infected with mouse hepatitis virus, strain JHM (MHV-JHM), and analyzed in a directex vivocytotoxicity assay recognize two epitopes (H-2Dband H-2Kb-restricted encompassing amino acids 510–518 and 598–605, respectively) within the surface (S) glycoprotein. In this report, the preferential recognition of the H-2Db-restricted epitope is confirmed using splenocytes stimulatedin vitrowith either MHV-JHM-infected MC57 cells or with a cell line expressing the S protein and analyzed in secondary CTL assays. To determine whether these results represent a difference in epitope recognition between the spleen and CNS, secondary CTL assays were performed using spleen cells coated with peptides encompassing the CTL epitopes as stimulators. These assays using peptide-coated splenocytes as stimulators revealed comparable CTL precursor/effector frequencies for the H-2K b -(average 1/1291, range 1/927-1/1542 spleen cells) and H-2D b -restricted (average 1/987, range 1/380-1/1323 spleen cells) epitopes in these mice. cache = ./cache/cord-296075-8axbkyyz.txt txt = ./txt/cord-296075-8axbkyyz.txt === reduce.pl bib === id = cord-300884-rqfxe0x1 author = Zhang, Jianqiang title = Genomic characterization of equine coronavirus date = 2007-12-05 pages = extension = .txt mime = text/plain words = 6804 sentences = 378 flesch = 56 summary = Analysis of the sequence identified 11 open reading frames which encode two replicase polyproteins, five structural proteins (hemagglutinin esterase, spike, envelope, membrane, and nucleocapsid) and four accessory proteins (NS2, p4.7, p12.7, and I). In contrast to the replicase proteins which are directly translated from the genomic RNA, coronavirus structural and accessory proteins are expressed from a nested set of 3′ coterminal subgenomic (sg) mRNAs that also possess a common 5′ leader sequence derived from the 5′ end of the genome (Pasternak et al., 2006; Sawicki et al., 2007) . Following multiple alignments with the S proteins of other group 2a coronaviruses, a potential cleavage recognition sequence (RRQRR) was identified at residues 764-768 which would predict a cleavage between amino acids 768 and 769, separating the ECoV S protein into S1 and S2 subunits (Fig. 1) . cache = ./cache/cord-300884-rqfxe0x1.txt txt = ./txt/cord-300884-rqfxe0x1.txt === reduce.pl bib === id = cord-300810-a1skdp67 author = Lafay, F. title = Spread of the CVS strain of rabies virus and of the avirulent mutant AvO1 along the olfactory pathways of the mouse after intranasal inoculation date = 1991-07-31 pages = extension = .txt mime = text/plain words = 5731 sentences = 292 flesch = 54 summary = title: Spread of the CVS strain of rabies virus and of the avirulent mutant AvO1 along the olfactory pathways of the mouse after intranasal inoculation Abstract After intranasal instillation in the mouse, rabies virus (CVS strain) selectively infected olfactory receptor cells. On the other hand, other neuronal cells permissive for CVS, such as mitral cells or the anterior olfactory nucleus, are completely free of infection with the mutant, indicating that restriction is related to the ability of AvO1 to penetrate several categories of neurons. The G protein plays a pivotal role in the pathogenicity of the virus because of its interaction with the host cells ' Abbreviations used: AON, anterior olfactory nucleus; CNS, central nervous system; GABA, Gamma aminobutyric acid; HDB, horizontal limb of the diagonal band; HRP, horseradish peroxidase; HSVl, herpes simplex type 1; IPL, internal plexiform layer: LC, locus coeruleus; LD50, lethal dose 50%; LPA. cache = ./cache/cord-300810-a1skdp67.txt txt = ./txt/cord-300810-a1skdp67.txt === reduce.pl bib === id = cord-301755-fxfsr9bj author = Wang, F.-I. title = Sequence analysis of the spike protein gene of murine coronavirus variants: Study of genetic sites affecting neuropathogenicity date = 1992-02-29 pages = extension = .txt mime = text/plain words = 5594 sentences = 290 flesch = 54 summary = authors: Wang, F.-I.; Fleming, John O.; Lai, Michael M.C. title: Sequence analysis of the spike protein gene of murine coronavirus variants: Study of genetic sites affecting neuropathogenicity To understand the molecular basis of MHV neuropathogenesis, we studied the spike protein gene sequences of several neutralization-resistant variants of the JHM strain of MHV, which were selected with monoclonal antibodies (MAbs) specific for the S protein. We found that variant 2.2-V-1, which was selected with MAb J.2.2 and primarily caused demyelination, had a single point mutation at nucleotide (NT) 3340, as compared to the parental JHM virus, which predominantly caused encephalitis. The viruses used in this study included several JHM variants which were selected for their resistance to neutralizing MAbs specific for the S protein (Fleming et a/., 1983) . cache = ./cache/cord-301755-fxfsr9bj.txt txt = ./txt/cord-301755-fxfsr9bj.txt === reduce.pl bib === id = cord-293635-36pmai6s author = Held, Katherine S. title = Differential roles of CCL2 and CCR2 in host defense to coronavirus infection date = 2004-11-24 pages = extension = .txt mime = text/plain words = 6726 sentences = 312 flesch = 55 summary = The data shown in Fig. 2 indicate that CD4 + and CD8 + T cell infiltration into the CNS of infected CCL2 À/À and CCR2 À/À is dramatically reduced as compared to wild-type mice. In contrast to T cell trafficking, there was a similar reduction in the number of macrophages present within the brains in both CCL2 À/À and CCR2 À/À mice, indicating that both ligand and receptor are important in directing these cells into the CNS in response to MHV infection. This is consistent with an earlier study by our laboratory demonstrating that MHV infection of mice lacking CCL3 resulted in the retention of virus-specific cells in the CLN, and this was the result of impaired expression of chemokine receptors, including CXCR3 and CCR5 that greatly aids T cells in their ability to migrate to the brain (Trifilo et al., 2003) . cache = ./cache/cord-293635-36pmai6s.txt txt = ./txt/cord-293635-36pmai6s.txt === reduce.pl bib === id = cord-308835-999kewdw author = Leibowitz, Julian L. title = The virus-specific intracellular RNA species of two murine coronaviruses: MHV-A59 and MHV-JHM date = 1981-10-15 pages = extension = .txt mime = text/plain words = 6447 sentences = 404 flesch = 56 summary = Abstract Seven virus-specific, polyadenylated RNA species have been identified in mouse cells infected with the murine coronaviruses MHV-A59 (A59V) or MHV-JHM (JHMV). MHV-infected 17CL·1 cells were labeled with [32P]orthophosphate in the presence of actinomycin D and the cytoplasmic RNA was extracted and analyzed by agarose gel electrophoresis. The largest intracellular RNA species is identical to RNA isolated from purified virions, as determined by agarose gel electrophoresis and oligonucleotide fingerprint studies of ribonuclease T1 digests. Oligonucleotide fingerprints of the six subgenomic RNAS show that the sequences they contain are present in virion RNA, confirming their virus-specific nature. Identification of MHV-Specific RNA Species A59V, JHMV, and mock-infected cells were labeled with [32P]orthophosphate from 4 to 8 hpi in the presence of actinomycin D. To determine if there is temporal regulation of MHV-specific RNA synthesis, replicate cultures of A59V, JHMV, or mock-infected cells were pulse labeled for 1 hr at hourly intervals and the intracellular RNA was extracted and analyzed by gel electrophoresis. cache = ./cache/cord-308835-999kewdw.txt txt = ./txt/cord-308835-999kewdw.txt === reduce.pl bib === id = cord-301293-jqy7lcbk author = Gupta, Vandana title = SARS coronavirus nucleocapsid immunodominant T-cell epitope cluster is common to both exogenous recombinant and endogenous DNA-encoded immunogens date = 2006-03-30 pages = extension = .txt mime = text/plain words = 7663 sentences = 316 flesch = 47 summary = In the present study, we analyzed the spectrum of immune responses of mice to three different forms of the SARS coronavirus nucleocapsid (N): (1) exogenous recombinant protein (N-GST) with Freund's adjuvant; (2) DNA encoding unmodified N as an endogenous cytoplasmic protein (pN); and (3) DNA encoding N as a LAMP-1 chimera targeted to the lysosomal MHC II compartment (p-LAMP-N). In the present study, we have demonstrated that the dominant T-cell immune responses of mice immunized with the SARS CoV N protein plus adjuvant or with DNA encoding two different cellular trafficking forms of N are directed to the same peptide epitopes of all three immunogens. For example, in this study, the greater response to the LAMP-N chimera could be related to the quantitatively greater delivery of N to the MHC class II compartment of APCs. There can also be major differences in the repertoire or functionality of T cells responding to any given epitope, such as the differences in the IFN-g and IL-4 responses of mice immunized with DNA or with N-GST plus CFA. cache = ./cache/cord-301293-jqy7lcbk.txt txt = ./txt/cord-301293-jqy7lcbk.txt === reduce.pl bib === id = cord-307396-u6v6bxwj author = Liao, Y. title = Biochemical and functional characterization of the membrane association and membrane permeabilizing activity of the severe acute respiratory syndrome coronavirus envelope protein date = 2006-06-05 pages = extension = .txt mime = text/plain words = 6781 sentences = 326 flesch = 51 summary = In a recent study, we demonstrated that the SARS-CoV E protein could obviously enhance the membrane permeability of bacterial cells to onitrophenyl-β-D-galactopyranoside and hygromycin B, suggesting that the protein may function as a viroporin (Liao et al., 2004) . Western blotting analysis of cells expressing wild type and most mutant constructs showed specific detection of three species migrating at the range of molecular masses from 14 to 18 kDa under reducing conditions and representing three isoforms of the E protein (Fig. 3a) . The E protein from coronavirus MHV and IBV was previously shown to undergo modification by palmitoylation HeLa cells expressing the Flag-tagged SARS-CoV and IBV E proteins, respectively, were harvested at 12 h posttransfection, broken by 20 stokes with a Dounce cell homogenizer, and fractionated into cytosol (C) and membrane (M) fractions after removal of cell debris and nuclei. Expression of the untagged SARS-CoV E protein in the same cell type also shows very similar Golgi localization patterns as the Flag-tagged protein (Fig. 8a , panels G-I). cache = ./cache/cord-307396-u6v6bxwj.txt txt = ./txt/cord-307396-u6v6bxwj.txt === reduce.pl bib === id = cord-310218-fky0cm5e author = Yoo, Dongwan title = The S2 subunit of the spike glycoprotein of bovine coronavirus mediates membrane fusion in insect cells date = 1991-01-31 pages = extension = .txt mime = text/plain words = 2384 sentences = 124 flesch = 50 summary = Abstract The hemagglutinin/esterase (HE), spike precursor (S) and the S1 and S2 subunits of the spike precursor protein of bovine coronavirus were expressed in Spodoptera frugiperda (Sf9) cells, and the cell-fusing activity of each recombinant glycoprotein was examined. The hemagglutinin/esterase (HE), spike precursor (S) and the Sl and S2 subunits of the spike precursor protein of bovine coronavirus were expressed in Spodopfera frugperda (Sf9) cells, and the cell-fusing activity of each recombinant glycoprotein was examined. Thus, in order to identify the viral membrane glycoprotein which induces cell fusion by BCV, we expressed the HE, the S, and the Sl and S2 subunits of the S glycoprotein using recombinant baculoviruses, and examined the cell-fusing activity of each recombinant polypeptide. Therefore, it is clear that proteolytic cleavage is required to induce the fusion activity of both the recombinant S polypeptide in insect cells and the authentic S polypeptide produced in BCV-infected cells (14) . cache = ./cache/cord-310218-fky0cm5e.txt txt = ./txt/cord-310218-fky0cm5e.txt === reduce.pl bib === id = cord-305564-dj3vj4tk author = DeDiego, Marta L. title = PATHOGENICITY OF SEVERE ACUTE RESPIRATORY CORONAVIRUS DELETION MUTANTS IN hACE-2 TRANSGENIC MICE date = 2008-07-01 pages = extension = .txt mime = text/plain words = 6065 sentences = 287 flesch = 53 summary = All these viruses were rescued in monkey (Vero E6) cells and were also infectious for human (Huh-7, Huh7.5.1 and CaCo-2) cell lines and for transgenic (Tg) mice expressing the SARS-CoV receptor human angiotensin converting enzyme-2 (hACE-2), indicating that none of these proteins is essential for the viral cycle. These data indicate that E gene might be a virulence factor influencing replication level, tissue tropism and pathogenicity of SARS-CoV, suggesting that ΔE attenuated viruses are promising vaccine candidates. In contrast, rSARS-CoV-Δ[6-9b] virus was detected at high titers in the brains of infected hACE2 Tg mice suggesting that the E protein is important for virus replication and dissemination within this tissue. Discovery of novel human and animal cells infected by the severe acute respiratory syndrome coronavirus by replication-specific multiplex reverse transcription-PCR cache = ./cache/cord-305564-dj3vj4tk.txt txt = ./txt/cord-305564-dj3vj4tk.txt === reduce.pl bib === id = cord-300372-h5g4z8ts author = Kelvin, Alyson A. title = Lack of Group X Secreted Phospholipase A(2) Increases Survival Following Pandemic H1N1 Influenza Infection date = 2014-04-01 pages = extension = .txt mime = text/plain words = 10489 sentences = 533 flesch = 52 summary = Based on the central role of sPLA(2) enzymes as key initiators of inflammatory processes, we propose that activation of GX-sPLA(2) during H1N1pdm infection is an early step of pulmonary inflammation and its (Reviewer 2 Minor Comment 2) inhibition increases adaptive immunity and improves survival. Increased expression of immunoglobulin chain, lymphocyte differentiation, antigen processing genes and presence of CD3 þ T cells in the lungs of mice lacking GX-sPLA 2 after H1N1pdm infection Lack of GX-sPLA 2 resulted in decreased levels of PGD 2 , LTB 4 , cysteinyl leukotrienes, PGE 2 and Lipoxin A 4 and increased adaptive immune responses at 3 but not 6 days following H1N1pdm infection. MPO protein (neutrophil marker), CD45 protein (leukocyte marker) and GAPDH protein (loading control) expression levels were determined by immunoblot analysis from lung tissue homogenates of GX þ / þ and GX À / À mice over a 14 day time course of H1N1pdm influenza infection (Bi). cache = ./cache/cord-300372-h5g4z8ts.txt txt = ./txt/cord-300372-h5g4z8ts.txt === reduce.pl bib === id = cord-312210-3x9s3g8n author = Stoian, Ana title = The use of cells from ANPEP knockout pigs to evaluate the role of aminopeptidase N (APN) as a receptor for porcine deltacoronavirus (PDCoV) date = 2019-12-24 pages = extension = .txt mime = text/plain words = 3444 sentences = 199 flesch = 59 summary = title: The use of cells from ANPEP knockout pigs to evaluate the role of aminopeptidase N (APN) as a receptor for porcine deltacoronavirus (PDCoV) However, lung fibroblast-like cells, derived from the ANPEP KO PAM cultures, supported PDCoV infection to high levels. In this study, we investigated the role of pAPN as a receptor for PDCoV by evaluating the permissiveness of different cell populations derived from the lungs of ANPEP KO and wild-type (WT) pigs. Porcine alveolar macrophages (PAMs) from ANPEP KO and WT pigs were used to evaluate the permissiveness of cells for infection with PDCoV and TGEV. The results showed that PAMs from pigs lacking a functional ANPEP gene are resistant to TGEV and PDCoV infection. The results from this study showed no PDCoV infection of PAMs obtained from ANPEP KO pigs (see Fig. 1A ), which supports the observations of Wang et al. cache = ./cache/cord-312210-3x9s3g8n.txt txt = ./txt/cord-312210-3x9s3g8n.txt === reduce.pl bib === id = cord-297712-yy4g5npi author = Zhu, Xinyu title = Porcine deltacoronavirus nsp5 inhibits interferon-β production through the cleavage of NEMO date = 2016-12-13 pages = extension = .txt mime = text/plain words = 3284 sentences = 190 flesch = 57 summary = Here, we demonstrate that nonstructural protein 5 (nsp5) of PDCoV, the 3C-like protease, significantly inhibits Sendai virus (SEV)-induced IFN-β production by targeting the NF-κB essential modulator (NEMO), confirmed by the diminished function of NEMO cleaved by PDCoV. A study published by our lab also demonstrated that nsp5, the 3C-like protease of porcine epidemic diarrhea virus (PEDV), which is classified into the Alphacoronavirus family, antagonizes IFN-β production by cleavage of NEMO . In this study, we reveal that nsp5 of PDCoV antagonizes the type I IFN signaling pathway through the cleavage of NEMO, a critical constituent of the IKK complex, thus representing a newly identified mechanism by which PDCoV evades the innate immune response. In contrast, TBK1induced activation of the IFN-β promoter was not affected by nsp5 (Fig. 3A) , suggesting that PDCoV nsp5 inhibits RIG-I/MDA5 signaling by targeting NEMO or other upstream proteins. cache = ./cache/cord-297712-yy4g5npi.txt txt = ./txt/cord-297712-yy4g5npi.txt === reduce.pl bib === id = cord-302972-imtttzvr author = Feldmann, H. title = Glycosylation and oligomerization of the spike protein of marburg virus date = 1991-05-31 pages = extension = .txt mime = text/plain words = 1917 sentences = 116 flesch = 56 summary = As shown in Fig. 1 B, the electrophoretic mobility of GP was slightly enhanced after incubation with endoglycosidase H (lane 4), and a distinct further increase was obtained by treatment with endoglycosidase F (lane 3) indicating that GP contains AI-glycans of the oligomannosidic, but mainly of the complex type. Glycohydrolase treatments were performed at 37" overnight after denaturing of the proteins by boiling in buffer containing 0.1% SDS, 0.5% octylglucoside, 0.5% P-mercaptoethanol, 50 mM sodium acetate, pH 7.0, and 5 mM EDTA. Growth of virus, labeling, and cross-linking were performed as described in the legend of Fig. 1 and as in A above. To further analyze the composition of the GP complexes, purified [35S]methionine-labeled virus was subjected to solubilization by nonionic detergent and sedimentation on sucrose density gradients, and the polypeptides present in the fractions obtained from the gradients were assayed by polyacrylamide gel electrophoresis under denaturing and reducing conditions. A. Virus non-cross-linked and treated with @-mercaptoethanol (5%, 10 min, 96") prior to gradient centrifugation. cache = ./cache/cord-302972-imtttzvr.txt txt = ./txt/cord-302972-imtttzvr.txt === reduce.pl bib === id = cord-311255-zaa8i9vh author = Kim, Youngnam title = Porcine epidemic diarrhea virus induces caspase-independent apoptosis through activation of mitochondrial apoptosis-inducing factor date = 2014-07-31 pages = extension = .txt mime = text/plain words = 8040 sentences = 370 flesch = 41 summary = Abstract The present study sought to investigate whether porcine epidemic diarrhea virus (PEDV) induces apoptosis and to elucidate the mechanisms associated with apoptotic cell death after PEDV infection. Interestingly, mitochondrial apoptosis-inducing factor (AIF) was found to translocate to the nucleus during PEDV infection, and AIF relocalization was completely abrogated by the presence of cyclosporin A (CsA), an inhibitor of cyclophilin D (CypD) that is an essential component of the mitochondrial permeabilization transition pore (mPTP) complex. Altogether, our results indicate that a caspase-independent mitochondrial AIF-mediated pathway plays a central role in PEDV-induced apoptosis to facilitate viral replication and pathogenesis. Therefore, in this study, we aimed to determine if PEDV induces apoptosis following infection in vitro and in vivo and to define the specific pathways involved in apoptotic death of virus-infected cells. cache = ./cache/cord-311255-zaa8i9vh.txt txt = ./txt/cord-311255-zaa8i9vh.txt === reduce.pl bib === id = cord-307354-dkwcheu0 author = Abernathy, Emma title = Emerging roles for RNA degradation in viral replication and antiviral defense date = 2015-05-31 pages = extension = .txt mime = text/plain words = 7160 sentences = 359 flesch = 45 summary = Alpha-herpesviruses such as herpes simplex-1 (HSV-1) express a FEN1-like nuclease termed virion host shutoff protein (vhs) that is directed to mRNAs through interactions with the translation Fig. 1 . Quality control decay pathways such as NMD recognize aberrant mRNAs during translation, including the presence of premature termination codons (PTC), and induce endonucleolytic cleavage, whereupon the fragments are degraded by exonucleases. The RNAi pathway restricts gene expression by processing the long double stranded RNAs frequently generated during viral replication into short interfering RNAs (siR-NAs), which guide endonucleolytic cleavage of complementary target mRNAs. Although mammalian cells possess the RNAi machinery, in most cases RNAi does not appear to play a significant antiviral role, and has instead been supplanted by the protein-based interferon response (Cullen, 2014) . Small interfering RNAs that deplete the cellular translation factor eIF4H impede mRNA degradation by the virion host shutoff protein of herpes simplex virus cache = ./cache/cord-307354-dkwcheu0.txt txt = ./txt/cord-307354-dkwcheu0.txt === reduce.pl bib === id = cord-303238-us3dybue author = Kanjanahaluethai, Amornrat title = Membrane Topology of Murine Coronavirus Replicase Nonstructural Protein 3 date = 2007-05-01 pages = extension = .txt mime = text/plain words = 4789 sentences = 247 flesch = 50 summary = The papain-like protease (PLpro) encoded by the coronavirus that causes severe acute respiratory syndrome (SARS-CoV) processes three sites in the replicase polyprotein (Harcourt et al., 2004) , and has recently been shown to have de-ubiquitinating activity (Barretto et al., 2005; Lindner et al., 2005) . To extend these studies of membrane association of coronavirus replicase products, we analyzed the amino acid sequence of MHV-JHM nsp3 (from glycine-833 to glycine-2840) for probability of transmembrane helices using the five different programs designed to search for putative membrane-spanning sequences: Phobius, TMHMM, HMMTOP, SOSUI and TMpred (Fig. 2) . In contrast, when CMMs were added to the mixture, protein products that included all or part of nsp3-TM (PLP2-2485, -2390 and -2258) were detected predominantly in the pelleted fraction, consistent with membrane association (Fig. 3B ). cache = ./cache/cord-303238-us3dybue.txt txt = ./txt/cord-303238-us3dybue.txt === reduce.pl bib === id = cord-318400-l9kwxsq7 author = Chhabra, Rajesh title = Pathogenicity and tissue tropism of infectious bronchitis virus is associated with elevated apoptosis and innate immune responses date = 2016-01-15 pages = extension = .txt mime = text/plain words = 5153 sentences = 287 flesch = 53 summary = To establish a characteristic host response to predict the pathogenicity and tissue tropism of infectious bronchitis viruses (IBV), we investigated innate immune responses (IIR) and apoptosis in chicken embryo kidney cells (CEKC) and tracheal organ cultures (TOC) infected with three IBV strains. In contrast, M41 infection caused greater expression of these genes than 885 or QX in TOCs. In summary, greater levels of apoptosis and elevated levels of TLR3, MDA5 and IFN-β expression are associated with increased pathogenicity of IBV strains in renal and tracheal tissues. In order to establish the characteristic host response to predict the tissue tropism and pathogenicity of IBVs, we investigated apoptosis and innate immune responses in chicken embryo kidney (CEK) cells and tracheal organ cultures (TOCs) following infection with IS/885/00-like, QX-like and M41 IBV strains. Nephropathogenic IBV strains 885 and QX resulted in significantly greater up-regulation of innate immune sensing genes namely TLR3 and MDA5 along with greater IFN-β mRNA levels in CEK cells at 9 h of infection when compared to M41 infection. cache = ./cache/cord-318400-l9kwxsq7.txt txt = ./txt/cord-318400-l9kwxsq7.txt === reduce.pl bib === id = cord-307904-lnagg1uw author = Johnson, Jennifer A title = Sequence elements controlling expression of Barley stripe mosaic virus subgenomic RNAs in vivo date = 2003-08-15 pages = extension = .txt mime = text/plain words = 10666 sentences = 536 flesch = 58 summary = One RNA, ␥KpnI/HpaI, provided a source of the ␥a replicase protein and also contained a 350-nt deletion (from positions 2112 to 2461 on RNA␥) to remove the majority of the ␥b ORF, and a second derivative designed to assess promoter activity contained deletions engineered within the putative sgRNA␥ promoter ( Fig. 2A) . This result implies that competition between the two promoters has a major role in regulating the differential rates of synthesis of the two sgRNAs. To initially define sequences flanking the sgRNA␤2 promoter, two large deletions were generated in the ␤1Ϫ34/ ϩ14 clone that eliminated RNA␤ positions 1705 to 2109 and 2287 to 2434. Analysis of four deletions extending from position Ϫ179 to positions Ϫ110, Ϫ76, Ϫ52, and Ϫ28 relative to the transcription start site revealed that the mutant RNAs were able to replicate in protoplasts, but only mutants containing the deletions Ϫ179/Ϫ110 or Ϫ179/Ϫ76 were able to direct synthesis of sgRNA␤2 (Fig. 4A ). cache = ./cache/cord-307904-lnagg1uw.txt txt = ./txt/cord-307904-lnagg1uw.txt === reduce.pl bib === id = cord-319403-5qyc0wsz author = Miura, Tanya A. title = Rat coronaviruses infect rat alveolar type I epithelial cells and induce expression of CXC chemokines date = 2007-12-01 pages = extension = .txt mime = text/plain words = 6621 sentences = 390 flesch = 52 summary = Type I cells were productively infected with SDAV and RCoV-P, and both live virus and UV-inactivated virus induced mRNA and protein expression of three CXC chemokines: CINC-2, CINC-3, and LIX, which are neutrophil chemoattractants. Bronchial epithelial cells and alveolar type II cells express and secrete proinflammatory cytokines and chemokines in response to infection with respiratory viruses including respiratory syncytial virus, influenza A virus, and the SARS-associated coronavirus (SARS-CoV) Yen et al., 2006; Zhang et al., 2001) . In this study, cultures of rat alveolar type I cells were evaluated for susceptibility to RCoV infection, and for expression and secretion of proinflammatory cytokines and chemokines in response to RCoV inoculation. To determine whether the CXC chemokine response to infectious or UV-inactivated RCoV-P or SDAV was specific for the rat coronaviruses, we inoculated rat alveolar type I cells with a related group 2a coronavirus, mouse hepatitis virus (MHV) strain A59 that had been purified by sucrose density gradient centrifugation. cache = ./cache/cord-319403-5qyc0wsz.txt txt = ./txt/cord-319403-5qyc0wsz.txt === reduce.pl bib === id = cord-304421-xpj6c0vx author = Piñón, Josefina D. title = Further Requirements for Cleavage by the Murine Coronavirus 3C-like Proteinase: Identification of a Cleavage Site within ORF1b date = 1999-10-25 pages = extension = .txt mime = text/plain words = 7343 sentences = 346 flesch = 57 summary = The coronavirus 3C-like proteinase (3CLpro), flanked on either side by hydrophobic, possibly membrane-spanning regions (HD1 and HD2), is believed to be the prinicipal viral proteinase responsible for the processing events leading to the formation of the viral replicase complex, with as many as 11 potential cleavage sites identified throughout pp1ab (Gorbalenya et al., 1989; Lee et al., 1991 ) (see Fig. 1 ). We therefore created several substrates of various lengths, encoding different putative cleavage sites in ORF1b, in order to investigate processing by the recombinant MBP-3CLpro. The effect of these cleavage site mutations on the autocatalytic cis release of the 29-kDa 3CLpro was assayed by the expression of the Radiolabeled, in vitro transcribed, and translated substrate from pET21-NX.3C was incubated with MBP-3CLpro (lane 2) or an equal volume of column buffer/20% glycerol (lane 1) and the processed products were separated on a 15% SDS-PAGE gel. cache = ./cache/cord-304421-xpj6c0vx.txt txt = ./txt/cord-304421-xpj6c0vx.txt === reduce.pl bib === id = cord-317537-wgu5cd0y author = Lu, Hsiang-Chia title = Cymbidium mosaic potexvirus isolate-dependent host movement systems reveal two movement control determinants and the coat protein is the dominant date = 2009-05-25 pages = extension = .txt mime = text/plain words = 8155 sentences = 474 flesch = 57 summary = All constructs were replication competent in protoplasts as assayed by northern blot hybridization (Fig. 4I) , and statistics analysis (ANOVA) of real-time RT-PCR quantification of average relative percentage (from 3 independent experiments) of CymMV RNA from CymMV clone-infected protoplasts at 24 h postinoculation revealed no significant difference in percentage between these clones (P = 0.91). All constructs were replication competent in protoplasts as assayed by northern blot hybridization (Fig. 6J) , and statistics analysis (ANOVA) of realtime RT-PCR quantification of average relative percentage (from 3 independent experiments) of CymMV RNA from CymMV cloneinfected protoplasts at 24 h post-inoculation revealed no significant difference in percentage between these clones (P = 0.83). Our results indicated that the important amino acids of the CP that allowed for the CymMV systemic infection are located within the previously predicted RNA binding domain ( Fig. 7A; 1) . cache = ./cache/cord-317537-wgu5cd0y.txt txt = ./txt/cord-317537-wgu5cd0y.txt === reduce.pl bib === id = cord-309015-t5v2sjus author = York, Joanne title = Genetic analysis of heptad-repeat regions in the G2 fusion subunit of the Junín arenavirus envelope glycoprotein date = 2005-12-20 pages = extension = .txt mime = text/plain words = 5071 sentences = 240 flesch = 46 summary = The G2 fusion subunit of the Junín virus envelope glycoprotein GP-C contains two hydrophobic heptad-repeat regions that are postulated to form a six-helix bundle structure required for the membrane fusion activity of Class I viral fusion proteins. The mature envelope glycoprotein complex of the arenavirus consists of three noncovalently associated subunits derived from the GP-C precursor by proteolytic cleavage events: a stable myristoylated 58 amino-acid signal peptide (SSP), the receptor-binding G1 subunit and the transmembrane G2 fusion protein (Buchmeier, 2002; Eichler et al., 2003; York et al., 2004) . The molecular basis for envelope glycoprotein-mediated membrane fusion in the arenaviruses is largely unknown, however, sequence analysis of the G2 ectodomain of Lassa virus and lymphocytic choriomeningitis virus (LCMV) has revealed two heptad-repeat regions that can be represented to form amphipathic helices (Gallaher et al., 2001) . cache = ./cache/cord-309015-t5v2sjus.txt txt = ./txt/cord-309015-t5v2sjus.txt === reduce.pl bib === id = cord-322062-nnefbeo6 author = Tam, Albert W. title = Hepatitis E virus (HEV): Molecular cloning and sequencing of the full-length viral genome date = 1991-11-30 pages = extension = .txt mime = text/plain words = 5738 sentences = 296 flesch = 49 summary = We now report on the molecular cloning and sequencing of the complete HEV (Burma; B) viral genome together with the deduced amino acid sequences of viral-encoded proteins General perspectives on the genetic organization of the virus, as deduced from sequence and open reading frame analyses, indicate that HEV bears some similarity to the caliciviridae but may represent a new class of nonenveloped RNA virus. Bife was chosen as the RNA source for cDNA synthesis because it contained relatively large numbers of virus particles when HEV cDNA clones were identified from libraries made from randomly primed cyno bile (solid square), or from cyno liver after priming by oligo-dT (solid circle), random sequence hexamers (open circle) and HEV-sequence specific oligonucleotides (open square). The presence of HEV-specific subgenomic RNAs localized to the 3' one-third of the genome suggests that these may be the transcripts from which these 3' end ORFs are expressed and is indicative of a unique expression strategy among nonenveloped positive-sense RNA viruses infecting humans. cache = ./cache/cord-322062-nnefbeo6.txt txt = ./txt/cord-322062-nnefbeo6.txt === reduce.pl bib === id = cord-309469-2naxn580 author = An, Hongliu title = Identification and formation mechanism of a novel noncoding RNA produced by avian infectious bronchitis virus date = 2019-01-05 pages = extension = .txt mime = text/plain words = 3600 sentences = 234 flesch = 54 summary = For example, polyadenylated nuclear (PAN) RNA encoded by Kaposi's sarcoma-associated herpesvirus (Sun et al., 1996; Zhong and Ganem, 1997) , the~2-kb latency-associated transcript (LAT) expressed by Herpes simplex virus (Bloom, 2004 ), a con-served~5-kb intron expressed by Human cytomegalovirus (hCMV) (Kulesza and Shenk, 2004) , and a 7.2-kb RNA expressed by mouse CMV (Kulesza and Shenk, 2006) , U-rich RNAs (HSURs) produced by Herpesvirus saimiri (HVS), (Albrecht and Fleckenstein, 1992; Ensser and Fleckenstein, 2005) ; (3) Subgenomic ncRNAs from single-stranded RNA viruses by incomplete degradation of genomic RNA by the cellular 5-3′ exonuclease XRN1. The results confirmed previous report that IBV can synthesize sgRNA via template switch mediated by a noncanonical core sequence (Bentley et al., 2013) Notably, the mutant virus carrying four mutations (A27100U/A27111U/G27113C/G27114C) was also unable to produce ncRNA (Fig. 4) , suggesting these nucleotides are required for ncRNA production. cache = ./cache/cord-309469-2naxn580.txt txt = ./txt/cord-309469-2naxn580.txt === reduce.pl bib === id = cord-302486-z36hcvrx author = Cobo, Fernando title = Diagnostic approaches for viruses and prions in stem cell banks date = 2006-03-30 pages = extension = .txt mime = text/plain words = 7276 sentences = 347 flesch = 41 summary = Viral and prion contamination of cell cultures and "feeder" cells, which is a common risk in all biotechnological products derived from the cell lines, is the most challenging and potentially serious outcome to address, due to the difficulty involved in virus and prion detection and the potential to cause serious disease in recipients of these cell products. The use of bovine fetal serum in stem cell cultures requires an urgent need for a risk assessment for Transmissible Spongiform Encephalopathies (TSEs) by means of a sensitive and specific test in all products derived from ruminants (U.S. Food and Drugs Administration, 1999; Directive 2004/C 24/ 03). This panel of tests should necessarily include reverse transcriptase detection as a general test for retroviruses, electron microscopy that can detect different kinds of viral particles and characterize many unknown isolates present in cell cultures and molecular techniques like PCR (conventional or real-time) and RT-PCR tests to include all the viruses that we know pose a risk to the product. cache = ./cache/cord-302486-z36hcvrx.txt txt = ./txt/cord-302486-z36hcvrx.txt === reduce.pl bib === id = cord-313906-fh85fzq9 author = Maruyama, Junki title = Characterization of the glycoproteins of bat-derived influenza viruses date = 2016-01-15 pages = extension = .txt mime = text/plain words = 4241 sentences = 232 flesch = 51 summary = We found that VSVs pseudotyped with BatIV HAs and NAs efficiently infected particular bat cell lines but not those derived from primates, and that proteolytic cleavage with a trypsin-like protease was necessary for HA-mediated virus entry. Treatment of the susceptible bat cells with some enzymes and inhibitors revealed that BatIV HAs might recognize some cellular glycoproteins as receptors rather than the sialic acids used for the other known influenza viruses. To obtain information on the biological characteristics of cellular receptors for BatIVs, IndFSPT1 cells were pretreated with tunicamycin, pronase, or neuraminidase (i.e., an N-linked glycosylation inhibitor, mixture of proteases, and sialidase, respectively), and then infected with pseudotyped VSVs (Fig. 4B-D) . IndFSPT1 should also have such molecules since it showed the highest susceptibility to BatIV HA-pseudotyped VSVs. It was noted that VSVΔG*-H17N10 and -H18N11 also infected MDCK cells, although less efficiently than these bat cell lines. cache = ./cache/cord-313906-fh85fzq9.txt txt = ./txt/cord-313906-fh85fzq9.txt === reduce.pl bib === id = cord-315069-xo4mbxei author = Knorr, D. A. title = De novo generation of defective interfering RNAs of tomato bushy stunt virus by high multiplicity passage date = 1991-03-31 pages = extension = .txt mime = text/plain words = 5134 sentences = 250 flesch = 52 summary = Abstract Defective interfering (DI) RNAs were generated de novo in each of 12 independent isolates of tomato bushy stunt virus (TBSV) upon serial passage at high multiplicities of infection (m.o.i.) in plants, but not in any of 4 additional isolates after 11 serial passages at low m.o.i. The DI RNAs were detected in RNA isolated from virus particles and in 2.3 M LiCl-soluble RNA fractions isolated from inoculated leaves. On each host species, six isolates were passed at high m.o.i. and two control isolates were passed at low m.o.i. In these hosts, DI-free TBSV induces lethal necrosis within 7-l 0 days postinoculation (d.p.i.), except in the presence of DI RNAs which are associated with attenuation and the establishment of persistent infections (Hillman et a/., 1987) . The small RNAs which developed in each of the high m.o.i. isolates hybridized to both 5'-and 3'-proximal TBSV genomic sequences, but generally were larger (-600 bases) than the previously characterized DI 1 RNA species (-400 bases). cache = ./cache/cord-315069-xo4mbxei.txt txt = ./txt/cord-315069-xo4mbxei.txt === reduce.pl bib === id = cord-310967-15mv5yx7 author = Morris, Vincent L. title = Characterization of coronavirus JHM variants isolated from wistar furth rats with a viral-induced demyelinating disease date = 1989-03-31 pages = extension = .txt mime = text/plain words = 5838 sentences = 301 flesch = 56 summary = One of these variants, ATIIf cord virus, which induced a chronic demyelinating disease in 2or 10-day-old intracerebrally inoculated Wistar Furth rats, had a deletion in the coding region of the peplomer glycoprotein mRNA. In this report, we investigated viral variants that arose in the CNS of rats with a JHM-induced demyelinating disease and studied the effect of alterations in their mRNAs. When lo-day-old rats were inoculated with ATllf brain virus or ATlIe brain virus, the rats developed a rapid encephalitis instead of the more chronic demyelinating disease that has previously been seen with wild-type parental JHM virus (Sorensen et al., 1980; Jackson et al., 1984) and was observed with ATIIf cord virus-injected rats. In contrast, when 2-day-old rats were inoculated with ATllf cord virus, the more chronic CNS disease resulted instead of the rapid encephalitis that has been reported for wild-type JHM (Sorensen et a/., 1980; Parham et a/., 1986) and was observed with the ATIIf brain virus variant. cache = ./cache/cord-310967-15mv5yx7.txt txt = ./txt/cord-310967-15mv5yx7.txt === reduce.pl bib === === reduce.pl bib === id = cord-310748-ao29zx1u author = Banner, Lisa R. title = Random nature of coronavirus RNA recombination in the absence of selection pressure date = 1991-11-30 pages = extension = .txt mime = text/plain words = 2839 sentences = 155 flesch = 52 summary = Our results showed that within a 1-kb region of the peplomer gene, RNA recombination occurred at almost every potential crossover site. To study RNA recombination in the absence of selection pressure, we developed a polymer-ase chain reaction (PCR) assay using two primers specific for the potential recombinant viruses which have a crossover site between the two primers. Only recombinant RNAs which had a crossover between the two primers and contained A59-specific sequences on the 5'-side and JHM-DL-specific sequences on the 3'-side could be detected by this PCR approach. DNA sequence analysis of 35 cloned PCR products showed that the crossover sites were almost randomly distributed throughout the nearly 1-kb region of the peplomer gene studied ( Fig. 2A) . Analysis of 53 recombinant clones revealed that, similar to the intracellular recombinants, the crossover sites in the viral recombinant RNAs were almost randomly distributed over the 1 -kb region of the peplomer gene (Fig. 2B) . cache = ./cache/cord-310748-ao29zx1u.txt txt = ./txt/cord-310748-ao29zx1u.txt === reduce.pl bib === id = cord-319179-gqaxf7mz author = Denison, M. title = Identification of putative polymerase gene product in cells infected with murine coronavirus A59 date = 1987-04-30 pages = extension = .txt mime = text/plain words = 1638 sentences = 88 flesch = 59 summary = When infected cells and isolated virions were assayed for this protein by two-dimensional gel electrophoresis, p28 could be detected in infected cells labeled at late times after infection, but not at early times or in purified virions. When infected cells and isolated virions were assayed for this protein by twodimensional gel electrophoresis, p28 could be detected in infected cells labeled at late times after infection, but not at early times or in purified virions. To determine if p28 was a minor protein actually present in virions, infected 17CL-1 cells were labeled with [35S] methionine and virus was purified as described in Fig. 4 . A portion of the labeled virus preparation was analyzed directly by two-dimensional gel electrophoresis whereas a second part was mixed with the [35S] methionine-labeled cell-free products prior to analysis (Fig. 4) . cache = ./cache/cord-319179-gqaxf7mz.txt txt = ./txt/cord-319179-gqaxf7mz.txt === reduce.pl bib === id = cord-305143-mqd4ioj4 author = Zmasek, Christian M. title = Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO) date = 2019-01-06 pages = extension = .txt mime = text/plain words = 7266 sentences = 367 flesch = 44 summary = Coupled with their genome complexity and the availability of numerous complete genome sequences, this deep evolutionary history makes herpesviruses a tractable and informative model to study virus genome evolution at the levels of gene duplication and protein domain rearrangement. In addition, the gene tree for human herpesvirus uracil DNA glycosylases ( Fig. 1B ) precisely recapitulates the herpesvirus species tree (Fig. 1A) ; therefore, this protein family can be inferred to have evolved from a single common ancestor and without any gene duplications or domain rearrangements (see Table 2 for virus-specific gene names). Phylogenetic analysis of human herpesvirus DNA polymerase proteins, plus related proteins from selected mammalian herpesviruses, shows that, similar to the glycoprotein B family, DNA polymerases of the Herpesviride evolved without gene duplication. cache = ./cache/cord-305143-mqd4ioj4.txt txt = ./txt/cord-305143-mqd4ioj4.txt === reduce.pl bib === id = cord-309919-sm5o0g1c author = Eichwald, Catherine title = Mammalian orthoreovirus core protein μ2 reorganizes host microtubule-organizing center components. date = 2020-08-04 pages = extension = .txt mime = text/plain words = 1170 sentences = 81 flesch = 46 summary = In infected cells, the MRV μ2 protein forms punctae in the enlarged region of the filamentous VFs that are co-localized with γ-tubulin and resistant to nocodazole treatment, and permitted microtubule (MT)-extension, features common to MT-organizing centers (MTOCs). Using a previously established reconstituted VF model, we addressed the functions of MT-components and MTOCs concerning their roles in the formation of filamentous VFs. Indeed, the MTOC markers γ-tubulin and centrin were redistributed within the VF-like structures (VFLS) in a μ2-dependent manner. Here, specific µ2 punctae observed in filamentous VFs are investigated concerning their 89 ability to co-localize with other reovirus proteins and host elements. Our study shows that µ2 90 punctae in VFs co-localize with γ-tubulin, are resistant to nocodazole, and permit MT 91 emergence, common features for MTOCs. Moreover, using the VFLS model, we found that 92 specific µ2/µNS ratios that support filamentous morphology relocalize γ-tubulin and centrin to 93 foci within the VFLS. cache = ./cache/cord-309919-sm5o0g1c.txt txt = ./txt/cord-309919-sm5o0g1c.txt === reduce.pl bib === id = cord-325179-gsf8ad65 author = Jarvis, Donald L. title = Modification of simian virus 40 large tumor antigen by glycosylation date = 1985-03-31 pages = extension = .txt mime = text/plain words = 7725 sentences = 450 flesch = 51 summary = In some experiments, SV40-infected cells were labeled with pS]methionine or 3H-monosaccharides in the presence of excess unlabeled amino acids, excess unlabeled sugars, or TM. Infected cells were starved in glucose-free E-MEM from 20.5 to 21 hr p.i., then labeled for 3 hr using 25 &i/ml [?S]methionine or 100 &i/ml rH]galactose in E-MEM containing different sugar concentrations. A polypeptide of about 88,000 (88K) in apparent MW was detected by immunoprecipitation of pS]methionine-labeled, SV40-infected cell extracts with HAF (Fig. lA, lane 3) . Coomassie blue staining revealed that both large T-ag -and small t-ag were also immunoprecipitated from galactose-labeled infected cell extracts (data not shown). To determine the effect of TM treatment, SV40-infected cells were treated with E-MEM or various concentrations of TM starting at 15 hr pi., then were glucose-starved and labeled with pS]methionine or THlglucosamine from 21 to 24 hr p.i. After extraction, T-ag was immunoprecipitated and analyzed by SDS-PAGE (Fig. 8A) . cache = ./cache/cord-325179-gsf8ad65.txt txt = ./txt/cord-325179-gsf8ad65.txt === reduce.pl bib === id = cord-321162-pgd34ewv author = Holmes, Kathryn V. title = Tunicamycin resistant glycosylation of a coronavirus glycoprotein: Demonstration of a novel type of viral glycoprotein date = 1981-12-31 pages = extension = .txt mime = text/plain words = 4822 sentences = 239 flesch = 47 summary = Abstract Tunicamycin has different effects on the glycosylation of the two envelope glycoproteins of mouse hepatitis virus (MHV), a coronavirus. The coronavirus envelope envelope glycoprotein E1 appears to be a novel type of viral glycoprotein which is post-translationally glycosylated by a tunicamycin-resistant process that yields oligosaccharide side chains different from those of N-linked glycoproteins. of the synthesis, glycosylation, and intracellular transport of glycoproteins is essential to understanding the structure and function of cell membranes and the role of oligosaccharides in glycoprotein processing and secretion. Labeling with monospecific fluorescent antibody against isolated El or E2 (Sturman et cd, 1980) showed that El remains restricted to the perinuclear area of the cell while E2, like most other viral glycoproteins, migrates rapidly via intracellular membranes to the plasma membrane (Doller and Holmes, 1980) . cache = ./cache/cord-321162-pgd34ewv.txt txt = ./txt/cord-321162-pgd34ewv.txt === reduce.pl bib === === reduce.pl bib === id = cord-316134-lkd2mj27 author = Sungsuwan, Suttipun title = Nucleocapsid proteins from other swine enteric coronaviruses differentially modulate PEDV replication date = 2020-01-15 pages = extension = .txt mime = text/plain words = 9236 sentences = 495 flesch = 52 summary = Investigation of possible molecular interactions between components of PEDV, PDCoV and TGEV and their influence on replication of each virus would provide a crucial insight into comprehensive understanding of these CoVs. Of all viral proteins, we have chosen to start with the N protein, as it is among the most abundant and ubiquitous structural proteins in infected cells. For viral infection in the transient CoV N expression experiment, VeroE6 cells were transfected with 1 or 2 μg of pCAGGS-PEDV N-Myc, pCAGGS-PDCoV N-HA, pCAGGS-TGEV N-FLAG, or the empty pCAGGS vector and were incubated for 24 h to allow for protein expression. To investigate how this protein-protein interaction might affect PEDV replication, we transiently transfected VeroE6 cells with varying amounts of the pCAGGS plasmid expressing N proteins from either PDCoV or TGEV for 24 h before infection with PEDV-mCherry (MOI = 0.0001) and followed the course of viral replication for each condition. cache = ./cache/cord-316134-lkd2mj27.txt txt = ./txt/cord-316134-lkd2mj27.txt === reduce.pl bib === id = cord-322084-gkg1059v author = JEONG, YONG SEOK title = Coronavirus Transcription Mediated by Sequences Flanking the Transcription Consensus Sequence date = 1996-03-01 pages = extension = .txt mime = text/plain words = 6250 sentences = 302 flesch = 52 summary = Abstract In our studies of murine coronavirus transcription, we continue to use defective interfering (DI) RNAs of mouse hepatitis virus (MHV) in which we insert a transcription consensus sequence in order to mimic subgenomic RNA synthesis from the nondefective genome. By using PCR-based sequences flanking the same intergenic region between site-directed mutagenesis, a 12-nucleotide-long segenes 6 and 7 do not affect the efficiency of subgenomic quence, TCTAATCTAAAC, was inserted into DI cDNA DI RNA transcription (Makino and Joo, 1993) . For all of the constructs used in Deletion analysis of those MHV DI RNAs that contain this study we sequenced the inserts that were derived the intergenic sequence from gene 6-7 with its naturally from PCR products to confirm the presence of specific occurring flanking sequences showed that reducing the mutations and the absence of extraneous mutations. cache = ./cache/cord-322084-gkg1059v.txt txt = ./txt/cord-322084-gkg1059v.txt === reduce.pl bib === === reduce.pl bib === id = cord-313091-ksrxsdpp author = Shirato, Kazuya title = Wild-type human coronaviruses prefer cell-surface TMPRSS2 to endosomal cathepsins for cell entry date = 2017-12-06 pages = extension = .txt mime = text/plain words = 4021 sentences = 217 flesch = 58 summary = Studies using the ATCC isolate suggest that HCoV-229E enters cells via the late endosome using cathepsin L to cleave S protein, although it can enter cells via the cell surface or early endosome in the presence of transmembrane protease serine 2 (TMPRSS2) or trypsin (Bertram et al., 2013; Kawase et al., 2009) . In the present study, we found that field isolates of HCoV-OC43 and HCoV-HKU1 could be isolated using HBTE-ALI cell culture, and we then used these clinical isolates to assess whether the mode of virus entry found in HCoV-229E was also in play in other HCoVs. For isolation of HCoVs, nasal swabs were collected from outpatients who showed respiratory infection as a cardinal symptom when assessed at a hospital in Tokyo, Japan. To evaluate the entry routes of clinical isolates of HCoVs, viruses were inoculated onto HBTE-ALI in the presence of EST or camostat (10 μM) and the amounts virus that entered were estimated by detecting subgenomic mRNAs using real-time RT-PCR (Fig. 2) . cache = ./cache/cord-313091-ksrxsdpp.txt txt = ./txt/cord-313091-ksrxsdpp.txt === reduce.pl bib === id = cord-316460-ibprgdh4 author = Rodríguez-Grille, Javier title = Avian reovirus-triggered apoptosis enhances both virus spread and the processing of the viral nonstructural muNS protein date = 2014-06-17 pages = extension = .txt mime = text/plain words = 7493 sentences = 334 flesch = 49 summary = To assess whether muNS cleavage is promoted by avian reovirus proteins and/or by changes induced in the host during infection, we compared muNS-to-muNSC conversion in ARV-infected cells with that in transfected cells and in insect cells infected with a muNSexpressing recombinant baculovirus (Fig. 1A ). To verify that this putative caspase recognition sequence is a bona fide cleavage site we first examined whether the electrophoretic mobility of muNS, muNSC and muNSN matched with that of transiently expressed polypeptides comprising muNS residues 1-635, The resulting extracts were immunoprecipitated with polyclonal anti-muNS serum and the imunoprecipitated proteins were resolved on an electrophoresis gel system (8% tricine-SDS-PAGE gel) specifically designed to resolve small peptides (Schägger, 2006) . In the absence of an established reverse genetics system for ARV that would allow us to generate a recombinant virus that expresses an uncleavable muNS protein, like D154A, we examined the effect of Q-VD-OPh on ARV replication in CEF cells, since this compound had been shown to block both apoptosis and muNS processing. cache = ./cache/cord-316460-ibprgdh4.txt txt = ./txt/cord-316460-ibprgdh4.txt === reduce.pl bib === id = cord-315158-f6msh8od author = Taguchi, Fumihiro title = Comparison of six different murine coronavirus jhm variants by monoclonal antibodies against the e2 glycoprotein date = 1989-03-31 pages = extension = .txt mime = text/plain words = 1620 sentences = 86 flesch = 58 summary = Abstract We have examined six different JHMV variants, sp-4 (recloned wt JHMV), cl-2, CNSV, DL, DS, and JHM-X, in terms of the sizes of the mRNA3 and E2 glycoprotein as well as their reactivity to a panel of monoclonal antibodies to the E2 glycoprotein. Recently, we have shown that the highly virulent variant viruses with larger E2 glycoproteins were preferentially isolated from rat brain (19) and cultured astrocytes (20) after infection by wild-type (wt) JHMV which contains a small mRNA3 and E2 glycoprotein. E2 glycoproteins produced by sp-4 and JHM-X, both of which synthesized a small mRNA3, were shown to be approximately 15,000 Da smaller than those produced by the other variant viruses with larger mRNA3.s. No significant differences were observed in the sizes of N proteins produced by the variants. As shown in Fig. 3 , the monoclonal antibodies uniformly had excellent binding to all the viruses tested, with the exception of sp-4 and JHM-X, the two variants with small mRNA3s and E2 proteins. cache = ./cache/cord-315158-f6msh8od.txt txt = ./txt/cord-315158-f6msh8od.txt === reduce.pl bib === === reduce.pl bib === id = cord-321265-il9vbbgk author = DEN BOON, JOHAN A. title = Equine Arteritis Virus Subgenomic RNA Transcription: UV Inactivation and Translation Inhibition Studies date = 1995-11-30 pages = extension = .txt mime = text/plain words = 3721 sentences = 222 flesch = 56 summary = In general, MHV transcription was extremely sensitive to translation inhibition, whereas EAV genomic RNA synthesis became independent ofde novoprotein synthesis late in infection. The replication of SIN involves the synthesis of a EAV-infected BHK-21 cells were UV-irradiated at 6 1 2 hr single 4.1-kb sg RNA (26S) from a well-defined internal promoter on the genome-sized minus-strand template p.i., when RNA synthesis approaches its maximum (van RNA (Ou et al., 1982; Levis et al., 1990) . The UV transcription mapping data showed that the Third, the overall MHV transcription was significantly EAV sg RNAs were not produced by processing of a more dependent on de novo protein synthesis than that genome-length precursor RNA. Protein synthesis was inhibited by the addition of cycloheximide to EAV-infected BHK-21 cells at fully independent transcription system the slopes of the curves in Fig. 2B , which reflect the UV target sizes, should different time points after infection. cache = ./cache/cord-321265-il9vbbgk.txt txt = ./txt/cord-321265-il9vbbgk.txt === reduce.pl bib === id = cord-324321-y96x8x3h author = Cai, Yingyun title = Down-regulation of transcription of the proapoptotic gene BNip3 in cultured astrocytes by murine coronavirus infection date = 2003-11-10 pages = extension = .txt mime = text/plain words = 8454 sentences = 416 flesch = 49 summary = Furthermore, treatment of cells with chloroquine, which blocks the acidification of endosomes, significantly inhibited the repression of the BNip3 promoter activity induced by the acidic pH-dependent MHV mutant OBLV60, which enters cells via endocytosis, indicating that the down-regulation of BNip3 expression is mediated by fusion between viral envelope and cell membranes during entry. To establish further the specificity of the down-regulation of BNip3 gene expression, we used vesicular stomatitis virus (VSV) in a parallel experiment, because VSV is also an enveloped RNA virus whose infection has a broad host cell range and is mediated by the interaction between the envelope G protein and cell membranes (Riedel et al., 1984) . By extrapolating the data from the mutant virus, we can envision that fusion between viral envelope and plasma/endosomal membranes during wild-type MHV infection is involved in the down-regulation of BNip3 gene expression. cache = ./cache/cord-324321-y96x8x3h.txt txt = ./txt/cord-324321-y96x8x3h.txt === reduce.pl bib === id = cord-329245-6tj2k1yn author = Corse, Emily title = The cytoplasmic tails of infectious bronchitis virus E and M proteins mediate their interaction date = 2003-07-20 pages = extension = .txt mime = text/plain words = 7414 sentences = 327 flesch = 56 summary = Indeed, it has been shown that both the MHV E and the infectious bronchitis virus (IBV) E proteins are sufficient for formation of the virus-like particles (VLPs) described above (Corse and Machamer, 2000; Maeda et al., 1999) , although the efficiency probably varies with cell type and protein expression system. (B) IBV-infected Vero cells were labeled with [ 35 S]methionine-cysteine at 45 h postinfection, treated with DSP as indicated, lysed, and immunoprecipitated with anti-E or anti-M antibodies as described under Materials and methods. The E and M proteins of several coronaviruses are released from cotransfected cells in membrane-bound particles that are morphologically similar to virions (VLPs), suggesting that interactions between these proteins are an integral part of coronavirus assembly (Baudoux et al., 1998; Corse and Machamer, 2000; Godeke et al., 2000; Vennema et al., 1996) . cache = ./cache/cord-329245-6tj2k1yn.txt txt = ./txt/cord-329245-6tj2k1yn.txt === reduce.pl bib === id = cord-326688-a1djgqpa author = Dubois-Dalcq, Monique E. title = Cell tropism and expression of mouse hepatitis viruses (MHV) in mouse spinal cord cultures date = 1982-06-30 pages = extension = .txt mime = text/plain words = 3946 sentences = 230 flesch = 54 summary = The replication of three different MHV strains was studied in mouse dissociated spinal cord cultures containing differentiated neurons and nonneuronal cells (NN) (including astrocytes). Cell tropism and maturation of each virus strain was analyzed by immunolabeling methods using antisera to the virion or to purified membrane glycoproteins (E1 and E2) and by electron microscopy (EM). In conclusion, in primary CNS cultures consisting of neurons and NN cells: (1) wt-JHM replicates in both neurons and NN cells but has different effects on these cells; (2) Ts8-JHM exhibits no productive infection of neurons, and in NN cells appears to be defective in assembly and to stimulate membrane synthesis; (3) A59 also shows tropism restricted to NN cells which produce many viruses and display differential distribution of the two virion glycoproteins. DISCUSSION The present study describes how three different MHV strains interact in vitro with cultured neurons and NN cells, including astrocytes, isolated from mouse spinal cords. cache = ./cache/cord-326688-a1djgqpa.txt txt = ./txt/cord-326688-a1djgqpa.txt === reduce.pl bib === id = cord-324054-d71rj29o author = Zhang, Xuming title = The hemagglutinin/esterase gene of human coronavirus strain OC43: Phylogenetic relationships to bovine and murine coronaviruses and influenza C virus date = 1992-01-31 pages = extension = .txt mime = text/plain words = 2355 sentences = 147 flesch = 64 summary = Abstract The complete nucleotide sequences of the hemagglutinin/esterase (HE) genes of human coronavirus (HCV) strain OC43 and bovine respiratory coronavirus (BRCV) strain G95 were determined from single-stranded cDNA fragments generated by reverse transcription of virus-specific mRNAs and amplified by polymerase chain reaction. Phylogenetic analysis suggests that the HE genes of coronaviruses and influenza C virus have a common ancestral origin, and that bovine coronaviruses and HCV-OC43 are closely related. We report here the complete nucleotide sequence of the HE genes of HCV-OC43 and BRCV-G95, and their phylogenetic relatedness to BCVs, MHV, and ICV. The predicted amino acid sequences of the HE genes from HCV-OC43 and BRCV-G95 (Fig. l) , BCVMost importantly, the putative acetylesterase active site (F-G-D-S) (at amino acids 72 to 75 in Fig. 2) is conserved in all HE proteins of human, bovine, and murine coronaviruses and ICV. cache = ./cache/cord-324054-d71rj29o.txt txt = ./txt/cord-324054-d71rj29o.txt === reduce.pl bib === id = cord-317333-unrd76bo author = Danesh, Ali title = Early gene expression events in ferrets in response to SARS coronavirus infection versus direct interferon-alpha2b stimulation date = 2011-01-05 pages = extension = .txt mime = text/plain words = 5467 sentences = 278 flesch = 48 summary = Evaluation of gene expression patterns in PBMCs and lung necropsies of SARS-CoV-infected ferrets led us to the identification of 7 upregulated IRGs that also were upregulated in response to IFN-α2b injection. Since STAT1 was phosphorylated following SARS-CoV infection and IFN-α2b injection, we investigated select IRG expression by qRT-PCR following in vitro stimulation of ferret peripheral whole blood with IFN-α2b. These gene expression and STAT1 phosphorylation findings suggested that robust IFN responses were activated following SARS-CoV infection 2 days post-infection. The comparison of microarray results between the lung tissue of IFN-α2b and SARS-CoV ferrets at day 1 revealed commonalities in the expression patterns of most IRGs. STAT1, MX1, OAS1, OAS2, ISG15, IFI44, IFI44L and EIF2AK2 were among the overlapping genes (Fig. 3B ). Analysis of the IFN signaling canonical pathway showed the upregulation of STAT1, MX1, OAS1, OAS2, ISG15 and IFI44 in lung necropsies of IFN-α2b injected and SARS-CoV infected ferrets (Fig. 4) . cache = ./cache/cord-317333-unrd76bo.txt txt = ./txt/cord-317333-unrd76bo.txt === reduce.pl bib === id = cord-326027-58whwspe author = Hernaez, Bruno title = Visualization of the African swine fever virus infection in living cells by incorporation into the virus particle of green fluorescent protein-p54 membrane protein chimera date = 2006-06-20 pages = extension = .txt mime = text/plain words = 7885 sentences = 372 flesch = 45 summary = title: Visualization of the African swine fever virus infection in living cells by incorporation into the virus particle of green fluorescent protein-p54 membrane protein chimera To track the behavior of African swine fever virus (ASFV) in the infected cells in real time, we produced an infectious recombinant ASFV (B54GFP-2) that expresses and incorporates into the virus particle a chimera of the p54 envelope protein fused to the enhanced green fluorescent protein (EGFP). To determine that protein p54, a major component of the external envelope of ASFV, fused to EGFP protein remains incorporated to the viral particle, BA71V and B54GFP-2 virions were Percoll purified and analyzed by SDS-PAGE and Western blotting using specific antibodies (Fig. 2a) . This new role for p54 in morphogenesis supports the selection of p54 as viral fusion protein and suggests that studies about p54-EGFP trafficking during infection in live cells would be helpful to analyze the acquisition of ASFV envelopes from ER during virus assembly. cache = ./cache/cord-326027-58whwspe.txt txt = ./txt/cord-326027-58whwspe.txt === reduce.pl bib === id = cord-328046-5us4se5o author = Xu, H. Y. title = Further Identification and Characterization of Novel Intermediate and Mature Cleavage Products Released from the ORF 1b Region of the Avian Coronavirus Infectious Bronchitis Virus 1a/1b Polyprotein date = 2001-09-30 pages = extension = .txt mime = text/plain words = 5643 sentences = 279 flesch = 51 summary = In cells infected with avian coronavirus infectious bronchitis virus (IBV), three proteins of 100, 39, and 35 kDa, respectively, were previously identified as mature cleavage products released from the 1b region of the 1a/1b polyprotein by the 3C-like proteinase. Immunofluorescent staining of IBV-infected cells and cells expressing individual cleavage products showed that the 100-, 68-, and 58-kDa proteins were associated with the membranes of the endoplasmic reticulum, and the 39and 35-kDa proteins displayed diffuse distribution patterns. Taken together with the Q 3928 -S 2929 dipeptide bond (encoded by nucleotides 12310-12315) identified as the N-terminal cleavage site of the 100-kDa protein, cleavage at these positions would result in the release of five mature products with molecular masses of approximately 100, 68, 58, 39, and 35 kDa. Among them, the 100-, 39-, and 35-kDa proteins were specifically identified in IBV-infected cells (Liu et al., 1994 . cache = ./cache/cord-328046-5us4se5o.txt txt = ./txt/cord-328046-5us4se5o.txt === reduce.pl bib === id = cord-331807-ooym5eh3 author = Wu, Tao title = A reverse-transcription recombinase-aided amplification assay for the rapid detection of N gene of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) date = 2020-07-29 pages = extension = .txt mime = text/plain words = 556 sentences = 48 flesch = 51 summary = title: A reverse-transcription recombinase-aided amplification assay for the rapid detection of N gene of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) The current outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China firstly. Here, we established a real-time reverse-transcription recombinase-aided amplification assay (RT-RAA) to detect SARS-CoV-2 rapidly. These results indicated that this real-time RT-RAA assay may be a valuable tool for detecting SARS-CoV-2. The minimum detection limit of real-time RAA assay was 10 copies / reaction. Use of a rapid 207 reverse-transcription recombinase aided amplification assay for respiratory syncytial virus detection Detection of 2019 novel coronavirus (2019-nCoV) by real-time 214 RT-PCR A rapid 235 and sensitive recombinase aided amplification assay to detect hepatitis B virus without DNA 236 extraction Development of a reverse 248 transcription recombinase-aided amplification assay for the detection of coxsackievirus A10 and 249 coxsackievirus A6 RNA cache = ./cache/cord-331807-ooym5eh3.txt txt = ./txt/cord-331807-ooym5eh3.txt === reduce.pl bib === id = cord-325481-uzch2hwd author = Simmons, Graham title = Different host cell proteases activate the SARS-coronavirus spike-protein for cell-cell and virus-cell fusion date = 2011-05-01 pages = extension = .txt mime = text/plain words = 7139 sentences = 315 flesch = 49 summary = For instance, the majority of strains of the murine coronavirus mouse hepatitis virus (MHV) contain Sproteins that are cleaved by furin in infected cells, and these viruses are believed to enter target cells by receptor-dependent, pH-independent fusion with the plasma membrane (de Haan et al., 2004; Nash and Buchmeier, 1997; Qiu et al., 2006) , although some of these findings are controversial (Eifart et al., 2007) . Treatment of cell-bound virus with trypsin was shown to allow infectious SARS-S-driven entry into ammonium chloride-treated cells (Simmons et al., 2005) , indicating that trypsin can functionally replace cathepsin L as a SARS-S-activating protease under these conditions ("trypsin bypass"). The fusion efficiency is then quantified by the addition of virions to leupeptin-treated (to exclude an impact of host cell proteases on SARS-S activation) HeLa cells, which express the EnvA receptor TvA, and which are not susceptible to SARS-S-driven infection (Simmons et al., 2005) . cache = ./cache/cord-325481-uzch2hwd.txt txt = ./txt/cord-325481-uzch2hwd.txt === reduce.pl bib === id = cord-333525-67bbmo4m author = Yao, Qianqian title = Negatively charged residues in the endodomain are critical for specific assembly of spike protein into murine coronavirus date = 2013-07-01 pages = extension = .txt mime = text/plain words = 5251 sentences = 238 flesch = 53 summary = In the current study, we analyzed the effects of the Endo charge-rich motif on virion incorporation of MHV S protein through substitutions of the homologous regions from the alphacoronavirus porcine transmissible gastroenteritis virus (TGEV), the betacoronaviruses bovine coronavirus (BCoV) and SARS-CoV, or the gammacoronavirus avian infectious bronchitis virus (IBV). Although the S2 portions of coronavirus S proteins show some degree of conservation, the Tm and Endo domains are highly divergent, with the exception of a conserved cluster of seven hydrophobic residues (WPWYVWL) at the start of Tm. To evaluate the functionality of different C-terminal sequence motifs in the MHV S protein, we constructed two sets of mutants in which the ectodomain of either S protein or HK protein was fused to the Tm and Endo domains from TGEV (an alphacoronavirus), BCoV (a betacoronavirus), SARS-CoV (a betacoronavirus), or IBV (a gammacoronavirus) ( Fig. 2A) . Reverting mutations in TGEV chimeras improved S assembly by eliminating positively charged residues in the endodomain MHV S protein mutants containing the entire carboxy terminus or just the charge-rich motif of TGEV S (Mut-TGEV and Mut-MMT) produced irregular plaques (Figs. cache = ./cache/cord-333525-67bbmo4m.txt txt = ./txt/cord-333525-67bbmo4m.txt === reduce.pl bib === id = cord-331916-n744pymd author = Liu, Jue title = Inhibition of porcine circovirus type 2 replication in mice by RNA interference date = 2006-04-10 pages = extension = .txt mime = text/plain words = 6657 sentences = 350 flesch = 52 summary = Specific inhibition of endogenous or pathogen mRNA by RNAi can be triggered by the introduction of 21 -23 nucleotide (nt) duplexes of RNA (siRNA) or by transcription of DNA precursor into short hairpin RNAs (shRNA) homologous to target sequences (Brummelkamp et al., 2002; Elbashir et al., 2001a; Paddison et al., 2002) , opening up possibilities for controlling replicative processes of pathogens. To further examine the ability of ORF1 shRNA to suppress viral gene expression in PCV2-infected PK15 cells, single nucleotide mutations were introduced into pSIR3 sequence as shown in Fig. 4A . As shown in Fig. 4B , a mutant with one nucleotide mutation in the 5V-end of the sense strand (pSIR3-m1) still had an effective reduction in the synthesis of ORF1 and ORF2 proteins, whereas with a nucleotide substitution at the center (pSIR3-m2) or 3V-end (pSIR3-m3) of the sense sequence, the resultant shRNAs failed to significantly suppress expression of PCV2 ORF1 and ORF2 in the transfected cells, further verifying the specificity of RNAi as demonstrated (Amarzguioui et al., 2003; Harborth et al., 2003) . cache = ./cache/cord-331916-n744pymd.txt txt = ./txt/cord-331916-n744pymd.txt === reduce.pl bib === id = cord-334133-61om170g author = Hollier, Mark J. title = The C-terminal tail of the gp41 transmembrane envelope glycoprotein of HIV-1 clades A, B, C, and D may exist in two conformations: an analysis of sequence, structure, and function date = 2005-07-05 pages = extension = .txt mime = text/plain words = 8424 sentences = 437 flesch = 57 summary = For example, the GL envelope protein of equine arteritis virus is proposed to have 1 or 3 MSDs (Snijder and Meulenberg, 1998) , the M protein of transmissible gastroenteritis coronavirus and equine arteritis virus, and the S antigen of hepatitis B virus are proposed to have three or four MSDs (Prange and Streeck, 1995; Risco et al., 1995; Snijder and Meulenberg, 1998) , and the herpes simplex virus glycoprotein B (Pellett et al., 1985) , and the Epstein -Barr virus 58 kDa latent protein Hennessy et al., 1984) both have multiple MSDs. Based on an analysis of their sequence and structure, we propose that the gp41 transmembrane region and C-terminal tail of all HIV-1 clades A to D can exist in two conformations, with either 1 MSD (the conventional structure) or with 3 MSDs. We suggest that these are, respectively, the majority and minority forms of intracellular Env. In the 3-MSD form, MSD 1 and MSD 2 are separated by a highly conserved beta turn, while the MSD 2 and MSD 3 support an unstructured hydrophilic loop/minor ectodomain of 41 residues that in clade B strains is highly antibody-reactive and involved in fusion. cache = ./cache/cord-334133-61om170g.txt txt = ./txt/cord-334133-61om170g.txt === reduce.pl bib === id = cord-329819-dpgexphf author = Hu, Weiwei title = Epidermal growth factor receptor is a co-factor for transmissible gastroenteritis virus entry date = 2018-06-04 pages = extension = .txt mime = text/plain words = 6765 sentences = 435 flesch = 56 summary = IPEC-J2 cells were infected with TGEV (MOI = 2) and cultured for 30 min, then stained for fluorescence microscopy using mouse anti-APN pAb, followed by DyLight 488-conjugated goat anti-mouse IgG and rabbit anti-p-EGFR mAb, followed by DyLight 594-conjugated goat anti-rabbit IgG. Plaque formation in ST cells by the intracellular of infected IPEC-J2 cells showed that APN + EGFR-targeting shRNAs inhibited TGEV entry more significantly (Fig. 3G) . To explore the role of caveolin and clathrin in EGFR internalization early in TGEV infection, we reduced clathrin or caveolin down in normal IPEC-J2 cells through targeting shRNAs, and investigated cell membrane EGFR expression levels during TGEV invasion. We can get to the conclusion that in the early infection stage of TGEV, TGEV particles bound with APN and EGFR, the virus-receptors complex are subsequently internalized by clathrin. cache = ./cache/cord-329819-dpgexphf.txt txt = ./txt/cord-329819-dpgexphf.txt === reduce.pl bib === id = cord-329625-hx2rsi91 author = You, Jae-Hwan title = A model for the dynamic nuclear/nucleolar/cytoplasmic trafficking of the porcine reproductive and respiratory syndrome virus (PRRSV) nucleocapsid protein based on live cell imaging date = 2008-08-15 pages = extension = .txt mime = text/plain words = 5645 sentences = 271 flesch = 46 summary = title: A model for the dynamic nuclear/nucleolar/cytoplasmic trafficking of the porcine reproductive and respiratory syndrome virus (PRRSV) nucleocapsid protein based on live cell imaging Porcine reproductive and respiratory syndrome virus (PRRSV), an arterivirus, in common with many other positive strand RNA viruses, encodes a nucleocapsid (N) protein which can localise not only to the cytoplasm but also to the nucleolus in virus-infected cells and cells over-expressing N protein. To investigate whether the trafficking of N protein between the cytoplasm and the nucleus/nucleolus was associated with microtubules or energy dependent, the mobility of EGFP-PRRSV-N protein was compared in 3D4/31 cells incubated at 37°C in the presence and absence of nocodazole (60ng/ml nocodazole (Sigma) for 16h), a microtubule inhibitor, or incubated at 10°C. In approximately 10% of cells expressing EGFP-PRRSV-N protein fluorescence was observed in the cytoplasm, but only if imaging was adjusted so that the fluorescent signal in the nucleus/nucleolus was above the linear range (for example Fig. 8C, lower panels) . cache = ./cache/cord-329625-hx2rsi91.txt txt = ./txt/cord-329625-hx2rsi91.txt === reduce.pl bib === id = cord-330907-srb8ac7l author = Leparc-Goffart, Isabelle title = Altered Pathogenesis of a Mutant of the Murine Coronavirus MHV-A59 Is Associated with a Q159L Amino Acid Substitution in the Spike Protein date = 1997-12-08 pages = extension = .txt mime = text/plain words = 5445 sentences = 288 flesch = 61 summary = We have previously shown that C12 has two amino acid substitutions relative to wild type virus in the spike protein, Q159L (within a region of S1 shown to bind to viral receptor in anin vitroassay) and H716D (in the proteolytic cleavage recognition site). for the altered pathogenic properties of the mutant viruses, we compared the sequence of the spike (S) genes The murine coronavirus, mouse hepatitis virus strain of wild type and mutant viruses isolated from persistently A59 (MHV-A59), produces both hepatitis and neurologiinfected glial cells cultures. We have shown previously that the spike (S) protein from the supernatant of either the ''C'' culture of persisencoded by the C12 mutant has two amino acid substitutently infected glial cells at 1 week (C3), 6 weeks (C5), tions as compared with the wild type S protein. cache = ./cache/cord-330907-srb8ac7l.txt txt = ./txt/cord-330907-srb8ac7l.txt === reduce.pl bib === id = cord-344515-e0g911le author = Voss, Kelsey title = Inhibition of host extracellular signal-regulated kinase (ERK) activation decreases new world alphavirus multiplication in infected cells date = 2014-11-30 pages = extension = .txt mime = text/plain words = 9184 sentences = 499 flesch = 54 summary = title: Inhibition of host extracellular signal-regulated kinase (ERK) activation decreases new world alphavirus multiplication in infected cells Our previous studies have indicated that host kinases including IKK-β and GSK-3β were modulated in VEEV-infected cells and that inhibition of these kinases with small molecule inhibitors resulted in decreased viral multiplication (Amaya et al., 2014; Kehn-Hall et al., 2012) . Cumulatively, the data included in Fig. 1 suggest that infection of U87MGs with the attenuated TC-83 strain of VEEV results in an activation of the ERK signaling cascade and phosphorylation of ERK1/2 at early time points after infection. Therefore, to confirm that Ag-126 treatment indeed resulted in decreased phosphorylation of ERK1/2 in U87MG cells, we investigated the intracellular p-ERK1/2 localization during VEEV infection in the presence or absence of Ag-126 at different time points using confocal microscopy as described previously (Amaya et al., 2014) . cache = ./cache/cord-344515-e0g911le.txt txt = ./txt/cord-344515-e0g911le.txt === reduce.pl bib === id = cord-342901-ca2xxkb2 author = Lloyd, Richard E. title = Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses date = 2015-05-31 pages = extension = .txt mime = text/plain words = 16221 sentences = 823 flesch = 50 summary = Though PTB was the first, a wide spectrum of factors, largely nuclear RBPs, have also been proposed as poliovirus ITAFs, including Lupus autoantigen (La) (Meerovitch et al., 1993 (Meerovitch et al., , 1989 , poly(rC)binding proteins (PCBPs) (Blyn et al., 1996; Gamarnik and Andino, 1997) , upstream of N-ras (UNR) (Anderson et al., 2007; Boussadia et al., 2003; Hunt et al., 1999) , SRp20 (Bedard et al., 2007) and glycyl-tRNA synthetase (GARS) (Andreev et al., 2012) (Table 1 ). In addition, certain ITAFs play crucial roles in regulating the conversion of translation-competent genomic RNAs into replicationcompetent RNAs. PTB was known as a nuclear splicing factor when its role as an ITAF of poliovirus and EMCV was discovered; a classic hijacked nuclear protein pressed into a new role required for the virus. cache = ./cache/cord-342901-ca2xxkb2.txt txt = ./txt/cord-342901-ca2xxkb2.txt === reduce.pl bib === id = cord-329794-msxrdhb3 author = Lu, Aili title = Attenuation of SARS coronavirus by a short hairpin RNA expression plasmid targeting RNA-dependent RNA polymerase date = 2004-06-20 pages = extension = .txt mime = text/plain words = 2679 sentences = 172 flesch = 61 summary = Here, we provide evidences that RNAi targeting at coronavirus RNA-dependent RNA polymerase (RDRP) using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Here, we provide the evidence that RNAi targeting at coronavirus RDRP using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Design of specific shRNA expression plasmids targeting at coronavirus RDRP Coronavirus isolated from SARS patients has a large genomic RNA (approximately 30 kb). After transfecton, about 40-90% of RDRP gene expression was inhibited, depending on the sequence of the shRNA inserts, based on RT-PCR analysis in both HeLa and 293 cells transfected with RDRP (data not shown). shRNA reduced the expression of SARS RDRP mRNA in 293 and HeLa cells As shown in Fig. 1A , based on the RT-PCR analysis, the expression of extraneous RDRP gene was observed peaking at 48 h after the transfection. cache = ./cache/cord-329794-msxrdhb3.txt txt = ./txt/cord-329794-msxrdhb3.txt === reduce.pl bib === id = cord-330847-a84pcc9z author = Edwards, M. C. title = RNA recombination in the genome of Barley stripe mosaic virus date = 1992-07-31 pages = extension = .txt mime = text/plain words = 2344 sentences = 152 flesch = 67 summary = Northern and Southern hybridization with oligonucleotide probes specific for either α or γ leader sequences indicated that CV17 γ cDNA clones are representative of native CV17 γ RNAs. Furthermore, bioassays indicated that in vitro transcripts derived from these γ cDNA clones were infectious when coinoculated with in vitro transcripts of full-length α and β cDNA clones. A "bandaid" cloning strategy, which exploits the conservation of the 3' terminal sequence, as well as the unique nature of the 5' ends of the BSMV RNAs, has been used previously to obtain full-length cDNA clones from which infectious in vitro transcripts can be produced (3, 7). Analysis of the resulting cDNA clones suggested that CV17 RNA y is a naturally occurring chimeric recombinant, composed of a 70nucleotide (nt) a-specific leader sequence preceding a r-specific coding region. 3. ldentrfrcatron of barley stripe mosaic virus strarn CV17 LY and Type strain y-specific leader sequences In 15 putative CV17 y cDNA clones and native RNAs of strains CV17, CV42, and ND1 8. cache = ./cache/cord-330847-a84pcc9z.txt txt = ./txt/cord-330847-a84pcc9z.txt === reduce.pl bib === id = cord-337976-c2auspti author = Weiss, Susan R. title = Coronaviruses SD and SK share extensive nucleotide homology with murine coronavirus MHV-A59, more than that shared between human and murine coronaviruses date = 1983-04-30 pages = extension = .txt mime = text/plain words = 3818 sentences = 267 flesch = 61 summary = A cDNA probe representing the genome of mouse hepatitis virus (MHV) strain A59 (MHV-A59) was used to measure nucleotide sequence homologies among murine and human coronaviruses and the SD and SK coronaviruses isolated by Burks et al. Since SD and SK were isolated by inoculation of multiple sclerosis (MS) central nervous system (CNS) tissue into mice or cultured mouse cells, it is important to determine their relationships to other murine and human coronavirus isolates. Some strains of HCV such as 0C43, are antigenically related to murine coronaviruses such as MHV strain JHM (McIntosh, 1974; Gerdes et al., 1981a, b) and may be grown in the brains of suckling mice (McIntosh et al., 1967) . We have further compared murine and human coronaviruses and SD and SK by using molecular hybridization of virus-specific RNA with cDNA probes. RNA extracted either from brain homogenates of OC43-infected suckling mice or from HRT cells infected with OC43 shows homology with A59 cDNA when assayed by blot hybridization. cache = ./cache/cord-337976-c2auspti.txt txt = ./txt/cord-337976-c2auspti.txt === reduce.pl bib === id = cord-351197-xv6ymc4l author = Cibulski, Samuel title = A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil date = 2020-09-28 pages = extension = .txt mime = text/plain words = 1711 sentences = 124 flesch = 54 summary = From chicken, six distinct gyroviruses (GyV) were detected, including GyV3 and GyV6, which for the first time were detected in samples from avian species, plus a novel smacovirus species and two highly divergent circular Rep-encoding ssDNA (CRESS-DNA) viruses. A detailed taxonomic 136 classification, including the numbers of reads for each Eukarya-related viral contig 137 recovered is this study, is provided in Supplementary gives them the ability to persist and spread in the environment. A detailed taxonomic classification, including the numbers of 245 J o u r n a l P r e -p r o o f sequenced reads of each Eukarya-related viral contig recovered in this study, is 246 provided in Supplementary Table 1 . including numbers of sequenced reads of each Eukarya-related viral contig recovered in 334 this study, is provided in Supplementary Table 1 . Cressdnaviricota: a virus phylum unifying 7 families of Rep-encoding 519 viruses with single-stranded, circular DNA genomes cache = ./cache/cord-351197-xv6ymc4l.txt txt = ./txt/cord-351197-xv6ymc4l.txt === reduce.pl bib === id = cord-340983-w219g6qs author = Smith, Mary Ellen title = Rabies Virus Glycoprotein as a Carrier for Anthrax Protective Antigen date = 2006-09-01 pages = extension = .txt mime = text/plain words = 7400 sentences = 376 flesch = 50 summary = Using the rabies virus (RV) envelope protein as a carrier molecule we show here that inactivated RV particles can be utilized to present Bacillus anthracis protective antigen (PA) domain-4 in the viral membrane. Rabies virus is a promising vaccine vector able to induce humoral and cellular immune responses efficiently to foreign antigens (McGettigan et al., 2001a (McGettigan et al., , 2001b Schnell et al., 2000) . To evaluate the cell surface expression of the recombinant RV G-D4 fusion proteins, BSR cells were infected with recombinant vaccinia virus expressing T7 RNA polymerase for one h, transfected with 5 μg of each of the five plasmids and 24 h later fixed in paraformaldehyde, permeabilized, and immunostained with anti-PA monoclonal antibody. In contrast, PA expressed on the surface of virus particles induced potent humoral responses with either live or killed SPBN-D4-E51 particles stimulating antibody production after only a single dose. cache = ./cache/cord-340983-w219g6qs.txt txt = ./txt/cord-340983-w219g6qs.txt === reduce.pl bib === id = cord-345088-krb1eidw author = Shen, S title = A single amino acid mutation in the spike protein of coronavirus infectious bronchitis virus hampers its maturation and incorporation into virions at the nonpermissive temperature date = 2004-09-01 pages = extension = .txt mime = text/plain words = 6949 sentences = 316 flesch = 56 summary = title: A single amino acid mutation in the spike protein of coronavirus infectious bronchitis virus hampers its maturation and incorporation into virions at the nonpermissive temperature Here, we report the emergence and isolation of two temperature sensitive (ts) mutants and a revertant in the process of cold-adaptation of coronavirus infectious bronchitis virus (IBV) to a monkey kidney cell line. Evidence presented demonstrated that the Q(294)-to-L(294) mutation, located at a highly conserved domain of the S1 subunit, might hamper processing of the S protein to a matured 180-kDa, endo-glycosidase H-resistant glycoprotein and the translocation of the protein to the cell surface. In virus-infected cells, the Endo-H sensitive, 155-kDa form of ts291602 was abundant at the nonpermissive temperature, clearly indicating that the mutant S protein was trimmed in the ER and cis-Golgi but was not transported to the trans-Golgi. cache = ./cache/cord-345088-krb1eidw.txt txt = ./txt/cord-345088-krb1eidw.txt === reduce.pl bib === id = cord-346514-vyo8l14p author = Chen, I-Hsuan title = Characterization of the polyadenylation activity in a replicase complex from Bamboo mosaic virus-infected Nicotiana benthamiana plants date = 2013-06-13 pages = extension = .txt mime = text/plain words = 5141 sentences = 304 flesch = 60 summary = The polyadenylation signal in the 3′ UTR of BaMV was shown to be involved in the synthesis of minus-strand viral RNA and regulating the length of the poly(A) tail (Chen et al., 2005) . To test whether the replicase preparation could polyadenylate exogenous plus-strand RNA templates, 5′ end-labeled radioactive BaMV plus-strand RNA substrate containing the entire 3′-UTR and 7, 15, or 40 adenylates (r138/7A, r138/15A, or r138/40A, respectively), were subjected to the polyadenylation activity assay. BaMV minigenomes were demonstrated to be suitable templates for an in vitro replication assays (Huang et al., 2009) ; therefore, the exogenous plus-strand or minus-strand BaMV minigenome was added to the reaction to help determine whether the poly(A) tail could be added to the 3′ end of preformed or newly transcribed plus-strand RNA, respectively. cache = ./cache/cord-346514-vyo8l14p.txt txt = ./txt/cord-346514-vyo8l14p.txt === reduce.pl bib === id = cord-345630-bam3pa70 author = Lee, Han-Jung title = The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase date = 1991-02-28 pages = extension = .txt mime = text/plain words = 5973 sentences = 418 flesch = 65 summary = authors: Lee, Han-Jung; Shieh, Chien-Kou; Gorbalenya, Alexander E.; Koonin, Eugene V.; La Monica, Nicola; Tuler, Jeremy; Bagdzhadzhyan, Anush; Lai, Michael M.C. title: The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase Third, the 3'-half of the gene 1 sequences of IBV and MHV-A59 contains the sequence motifs for RNA polymerase and helicase, which are the activities expected to be involved in RNA synthesis Gorbalenya et a/., 198913; Bredenbeek et a/., 1990) . The alignment of amino acids in ORF la of MHV-JHM and IBV showed that there are four possible stretches of moderate homology which are separated by highly diverged sequences (Fig. 8) . Although ORF la is highly diverged between MHV-JHM and IBV, common functional domains could be identified in this ORF of both viruses by detailed amino acid sequence analysis (see Materials and Methods) (Fig. 9 ). cache = ./cache/cord-345630-bam3pa70.txt txt = ./txt/cord-345630-bam3pa70.txt === reduce.pl bib === id = cord-335482-nx7odchj author = Makino, Shinji title = Defective interfering particles of mouse hepatitis virus date = 1984-02-29 pages = extension = .txt mime = text/plain words = 3840 sentences = 210 flesch = 60 summary = We have observed marked reduction of infectivity in the course od serial undiluted passages of JHM virus in DBT cell culture. To avoid contamination of the standard virus stock with DI particles, plaque purified MHV (JHM strain) (Hirano et aL, 1981; Makino et al, 1983) was propagated on DBT cells at a multiplicity of infection (m.o.i.) of 0.0002 and at 15 hr postinfection (p.i.) culture fluid was harvested and clarified by low speed centrifugation. Preparation of the Standard JHM Virus for Interference Assay JHM virus was propagated on DBT cells after infection at an m.o.i. of 1.0 and was harvested at 14 hr p.i. The culture fluid was clarified by centrifugation at 8000 rpm for 30 min. To determine if the reduction in the yield of infectious virus was due to the presence of DI particles, a'n interference analysis was performed with several culture fluid samples at different passage levels. cache = ./cache/cord-335482-nx7odchj.txt txt = ./txt/cord-335482-nx7odchj.txt === reduce.pl bib === id = cord-332356-au7s3dmp author = Strandin, Tomas title = The cytoplasmic tail of hantavirus Gn glycoprotein interacts with RNA date = 2011-09-15 pages = extension = .txt mime = text/plain words = 6554 sentences = 329 flesch = 53 summary = The results indicate that the binding ability of Gn-CT towards nucleic acids is rather unspecific since in addition to genomic RNA, also unrelated RNA as well as single-stranded DNA was able to interact with Gn-CTs of PUUV and TULV. Purified, lysed and micrococcal nuclease (MNase)-treated virus preparation and in vitro transcribed and radiolabeled genomic PUUV S segment were allowed to form RNA-protein complexes prior to UV cross-linking. The capability of structural proteins to bind RNA was analyzed by incubating purified, lysed and micrococcal nuclease (MNase)-treated virus preparations with radioactive PUUV S segment RNA in the case of PUUV ( The samples were immunoprecipitated with MAbs or PAbs specific to N, Gn or Gc and retained radioactivity on protein G beads after washing was measured by scintillation counting. The mapping indicated that the same peptides that were previously shown to interact with RNP and N protein (Hepojoki et al., 2010b) were capable of binding also nucleic acids (Fig. 5A ). cache = ./cache/cord-332356-au7s3dmp.txt txt = ./txt/cord-332356-au7s3dmp.txt === reduce.pl bib === id = cord-353467-wbtzvm4i author = Lambert, Carsten title = Functional incorporation of green fluorescent protein into hepatitis B virus envelope particles date = 2004-12-05 pages = extension = .txt mime = text/plain words = 6316 sentences = 307 flesch = 50 summary = In the late stages of an HBV infection, progeny virions are formed by budding of the pre-assembled cytosolic nucleocapsids, enclosing the partially double-stranded DNA genome 3.2 kb in length and the viral polymerase through intracellular membranes accommodating the viral envelope proteins (for review, see Nassal, 1996) . To determine whether the co-secreted GFP.S and SHA proteins resembled authentic subviral HBV envelope particles, the culture supernatant of transfected cells was fractionated by isopycnic CsCl gradient centrifugation and fractions were analyzed by an S-specific ELISA. According to current models for the transmembrane structure of S, its N-terminus and hence the GFP fusion site are located to the lumenal side of intracellular membranes that is topologically equivalent to the virion surface ( Fig. 4A ) (Berting et al., 1995; Stirk et al., 1992) . Here we applied this approach to hepatitis B virus and obtained fluorescent subviral and viral particles by incorporation of the viral S envelope protein, tagged with GFP, in trans, thereby preserving all the functions necessary for the viral life cycle. cache = ./cache/cord-353467-wbtzvm4i.txt txt = ./txt/cord-353467-wbtzvm4i.txt === reduce.pl bib === id = cord-353748-y1a52z8e author = Bhattacharya, Rajarshi title = A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2 date = 2021-01-02 pages = extension = .txt mime = text/plain words = 3308 sentences = 211 flesch = 61 summary = title: A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2 Nisin, a food-grade antimicrobial peptide produced by lactic acid bacteria has been examined for its probable interaction with the human ACE2 (hACE2) receptor, the site where spike protein of SARS-CoV-2 binds. Among the eight nisin variants examined, nisin H, nisin Z, nisin U and nisin A showed a significant binding affinity towards hACE2, higher than that of the RBD (receptor binding domain) of the SARS-CoV-2 spike protein. The present study attempts to investigate the ability of food-grade nisin A and its natural variants to block the interaction between hACE2 and the spike protein of SARS-CoV-2, a key step of COVID-19 disease initiation. The binding affinity of docked structures of all eight variants of nisin in complex with hACE2 was calculated as ΔG derived from analysis with Prodigy for each complex in comparison with the RBD of spike protein of SARS-CoV-2. cache = ./cache/cord-353748-y1a52z8e.txt txt = ./txt/cord-353748-y1a52z8e.txt ===== Reducing email addresses Creating transaction Updating adr table ===== Reducing keywords cord-008407-jbp8bxjz cord-253894-4u5yt7b7 cord-258232-br4z3na6 cord-254558-gvo0gwjf cord-255738-r8zfdsix cord-252615-ajyv95pu cord-007373-livz5zuu cord-256036-gd53s4dv cord-254747-vox5xsgd cord-252397-qlu7dilh cord-253351-b36g09r0 cord-255453-7e40rj1y cord-256316-1odgm6hm cord-256703-eaj63c2k cord-256737-ptjng78b cord-262441-slh52nxm cord-258327-03vk6enj cord-255841-3laov764 cord-258691-cd83w9o6 cord-260177-xu0elmak cord-258379-v3lceirh cord-253024-b393ea2u cord-262226-7kwkla73 cord-255773-b4re5bky cord-260108-osg8q89i cord-008426-ktn8c0zx cord-259095-mfptcw8t cord-265173-70wyecwj 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cord-299122-djfj4262 cord-296416-q0rsfzgw cord-298847-szezd2vb cord-291306-g9qmmugg cord-293248-8vtd9e4n cord-299994-1ksfo0pr cord-298934-vtrfqozl cord-293375-qcy56ui7 cord-275348-jna496x7 cord-289991-wx4rsr4g cord-290640-kh2t0kfz cord-275403-g4rohhtt cord-296364-7rp60d2m cord-286232-jo24ia4s cord-289045-vft163v0 cord-299976-36r794ow cord-287620-vuvgi8xx cord-292019-rfu0bkag cord-294056-7e477y1x cord-288669-46tkedw7 cord-291611-cfe8yujp cord-290231-4m9lj0uq cord-281820-oltqsd6n cord-291192-wm2eyaam cord-294260-g410mavp cord-294990-jdjbjkcp cord-279924-09uwhxs9 cord-287777-ogs4mq0v cord-303497-s3zs1oxf cord-283035-tpqf458q cord-284581-fl2nt4ak cord-296075-8axbkyyz cord-300470-vgd1ol2z cord-300884-rqfxe0x1 cord-301755-fxfsr9bj cord-300810-a1skdp67 cord-308835-999kewdw cord-312210-3x9s3g8n cord-310218-fky0cm5e cord-300372-h5g4z8ts cord-311255-zaa8i9vh cord-293635-36pmai6s cord-307354-dkwcheu0 cord-307396-u6v6bxwj cord-301293-jqy7lcbk cord-305564-dj3vj4tk cord-319403-5qyc0wsz cord-307904-lnagg1uw cord-304421-xpj6c0vx cord-320590-irybhp4j cord-305143-mqd4ioj4 cord-325179-gsf8ad65 cord-309919-sm5o0g1c cord-321162-pgd34ewv cord-322062-nnefbeo6 cord-322904-9mta0aem cord-319179-gqaxf7mz cord-316134-lkd2mj27 cord-310748-ao29zx1u cord-322084-gkg1059v cord-315158-f6msh8od cord-311774-fhdvcvi0 cord-321265-il9vbbgk cord-325423-d212h4bp cord-316460-ibprgdh4 cord-317537-wgu5cd0y cord-313091-ksrxsdpp cord-309469-2naxn580 cord-302972-imtttzvr cord-309015-t5v2sjus cord-310967-15mv5yx7 cord-302486-z36hcvrx cord-329245-6tj2k1yn cord-281237-asnpuami cord-297712-yy4g5npi cord-315069-xo4mbxei cord-326027-58whwspe cord-324321-y96x8x3h cord-326688-a1djgqpa cord-318400-l9kwxsq7 cord-317333-unrd76bo cord-324054-d71rj29o cord-328046-5us4se5o cord-331807-ooym5eh3 cord-303238-us3dybue cord-325481-uzch2hwd cord-313906-fh85fzq9 cord-331916-n744pymd cord-333525-67bbmo4m cord-334133-61om170g cord-329819-dpgexphf cord-330907-srb8ac7l cord-329625-hx2rsi91 cord-342901-ca2xxkb2 cord-330847-a84pcc9z cord-329794-msxrdhb3 cord-337976-c2auspti cord-351197-xv6ymc4l cord-340983-w219g6qs cord-345088-krb1eidw cord-353467-wbtzvm4i cord-332356-au7s3dmp cord-346514-vyo8l14p cord-335482-nx7odchj cord-344515-e0g911le cord-353748-y1a52z8e cord-345630-bam3pa70 Creating transaction Updating wrd table ===== Reducing urls cord-252615-ajyv95pu cord-252397-qlu7dilh cord-255453-7e40rj1y cord-255773-b4re5bky cord-265173-70wyecwj cord-259717-e8ljkv2y cord-260695-qwepi0we cord-266617-z8uecyl6 cord-267718-t47i8hui cord-260376-29ih5c9v cord-255828-jrqdyfbg cord-264331-uvi8ucz4 cord-270534-ebkwv4zo cord-272050-0u62j7nj cord-274122-n9jnu2ah cord-276358-so390gp4 cord-273246-4s54jrww cord-272260-88l9bq4i cord-280287-t7uozjml cord-280795-wtrt13ij cord-265156-u1re7983 cord-283309-ovx5fzsg cord-283035-tpqf458q cord-278578-vq5fy8m5 cord-275348-jna496x7 cord-289991-wx4rsr4g cord-299994-1ksfo0pr cord-300884-rqfxe0x1 cord-300470-vgd1ol2z cord-300372-h5g4z8ts cord-305564-dj3vj4tk cord-317537-wgu5cd0y cord-309469-2naxn580 cord-305143-mqd4ioj4 cord-312210-3x9s3g8n cord-316134-lkd2mj27 cord-334133-61om170g cord-353748-y1a52z8e cord-320590-irybhp4j cord-311255-zaa8i9vh cord-329819-dpgexphf Creating transaction Updating url table ===== Reducing named entities cord-252615-ajyv95pu cord-252397-qlu7dilh cord-253351-b36g09r0 cord-255841-3laov764 cord-008407-jbp8bxjz cord-262226-7kwkla73 cord-258327-03vk6enj cord-258691-cd83w9o6 cord-259717-e8ljkv2y cord-256036-gd53s4dv cord-265173-70wyecwj cord-255738-r8zfdsix cord-254558-gvo0gwjf cord-253894-4u5yt7b7 cord-259095-mfptcw8t cord-255453-7e40rj1y cord-262574-gu0930s3 cord-260695-qwepi0we cord-256703-eaj63c2k cord-260177-xu0elmak cord-262441-slh52nxm cord-253024-b393ea2u cord-260108-osg8q89i cord-256316-1odgm6hm cord-008426-ktn8c0zx cord-254747-vox5xsgd cord-260782-1lm8tzbc cord-007373-livz5zuu cord-255773-b4re5bky cord-256737-ptjng78b cord-260376-29ih5c9v cord-254950-y6kayxie cord-264331-uvi8ucz4 cord-258232-br4z3na6 cord-265895-ck7eto16 cord-266617-z8uecyl6 cord-264359-m9j3pcj1 cord-269986-jdcw59r2 cord-267718-t47i8hui cord-263302-z5uhrta5 cord-267027-diwm1940 cord-272437-gvzfl8c3 cord-267532-5rnqd9mb cord-262245-eb7g9p1x cord-266585-jfjrk9gy cord-258286-lodjcj8c cord-255828-jrqdyfbg cord-259500-ndjbrtrv cord-266018-8bhnlsgy cord-268341-103xf3dw cord-263334-wwkdum94 cord-267377-wyhsxj6g cord-262347-ejhz9rra cord-265156-u1re7983 cord-268416-8hw80qx8 cord-268467-btfz6ye8 cord-269204-kajws5xo cord-269419-68kja6bg cord-266230-ia04jc9j cord-274673-tjzlssal cord-270586-ohs8z91m cord-269193-a647hwu9 cord-270534-ebkwv4zo cord-272925-xag1yaie cord-266861-t5h133lp cord-258379-v3lceirh cord-270814-krw8zmr5 cord-271763-cual2qv4 cord-273487-nfgjz6f9 cord-274172-3dctmmfe cord-272045-v1wt5t7m cord-271359-dpa8zzc3 cord-273246-4s54jrww cord-271526-14nfqusv cord-275993-isff6lp2 cord-270487-m770a1rl cord-276358-so390gp4 cord-273379-w8vy5rl8 cord-272051-arz8r204 cord-275234-t6e7vr9y cord-256769-flfycl7i cord-267014-3vi7pgvr cord-269866-3tpyj04y cord-274424-juj71nc5 cord-269094-6aka052v cord-273745-mwjh5se7 cord-269862-krcu3hfa cord-268139-tgpsu4qz cord-272050-0u62j7nj cord-274122-n9jnu2ah cord-275664-qbafkxtr cord-272260-88l9bq4i cord-279813-mrei5kih cord-279346-7del8d2p cord-274480-aywdmj6o cord-276034-a8pixbuc cord-280287-t7uozjml cord-279432-aik5bo6o cord-278578-vq5fy8m5 cord-284968-eymvj6k3 cord-284646-fhruiw23 cord-280957-cdd6ngf1 cord-283309-ovx5fzsg cord-270929-utn21ce1 cord-281237-asnpuami cord-280795-wtrt13ij cord-281820-oltqsd6n cord-277838-931sco95 cord-272871-gu9ptt9y cord-286060-92lazxd7 cord-283035-tpqf458q cord-289712-w1y0lc5c cord-282947-3hgku2e4 cord-284581-fl2nt4ak cord-275348-jna496x7 cord-289248-6mx4o0eb cord-287777-ogs4mq0v cord-281309-c9y7m5do cord-285869-jwflooop cord-279924-09uwhxs9 cord-284707-72vx11aq cord-275403-g4rohhtt cord-286121-ltaxmp3u cord-290993-bsnja161 cord-289991-wx4rsr4g cord-283998-whwksoxt cord-293375-qcy56ui7 cord-290231-4m9lj0uq cord-287620-vuvgi8xx cord-286232-jo24ia4s cord-291192-wm2eyaam cord-290640-kh2t0kfz cord-294056-7e477y1x cord-291611-cfe8yujp cord-292019-rfu0bkag cord-296364-7rp60d2m cord-293790-7hyelm88 cord-290883-r2744fb3 cord-288669-46tkedw7 cord-289045-vft163v0 cord-290282-oxyzndsj cord-294260-g410mavp cord-292751-tk1oggi9 cord-298847-szezd2vb cord-291306-g9qmmugg cord-299994-1ksfo0pr cord-299976-36r794ow cord-296416-q0rsfzgw cord-293248-8vtd9e4n cord-300470-vgd1ol2z cord-294990-jdjbjkcp cord-300884-rqfxe0x1 cord-296075-8axbkyyz cord-298934-vtrfqozl cord-303497-s3zs1oxf cord-299122-djfj4262 cord-301755-fxfsr9bj cord-300810-a1skdp67 cord-293635-36pmai6s cord-308835-999kewdw cord-300372-h5g4z8ts cord-307396-u6v6bxwj cord-301293-jqy7lcbk cord-305564-dj3vj4tk cord-310218-fky0cm5e cord-297712-yy4g5npi cord-304421-xpj6c0vx cord-302972-imtttzvr cord-317537-wgu5cd0y cord-309469-2naxn580 cord-312210-3x9s3g8n cord-307354-dkwcheu0 cord-319403-5qyc0wsz cord-313906-fh85fzq9 cord-325179-gsf8ad65 cord-310967-15mv5yx7 cord-320590-irybhp4j cord-322904-9mta0aem cord-315069-xo4mbxei cord-313091-ksrxsdpp cord-316134-lkd2mj27 cord-325423-d212h4bp cord-329245-6tj2k1yn cord-311774-fhdvcvi0 cord-309015-t5v2sjus cord-333525-67bbmo4m cord-324054-d71rj29o cord-326027-58whwspe cord-311255-zaa8i9vh cord-329819-dpgexphf cord-317333-unrd76bo cord-326688-a1djgqpa cord-330907-srb8ac7l cord-328046-5us4se5o cord-322062-nnefbeo6 cord-315158-f6msh8od cord-302486-z36hcvrx cord-324321-y96x8x3h cord-321265-il9vbbgk cord-310748-ao29zx1u cord-334133-61om170g cord-305143-mqd4ioj4 cord-321162-pgd34ewv cord-319179-gqaxf7mz cord-309919-sm5o0g1c cord-331807-ooym5eh3 cord-289152-w5ynbewh cord-329625-hx2rsi91 cord-318400-l9kwxsq7 cord-303238-us3dybue cord-330847-a84pcc9z cord-329794-msxrdhb3 cord-325481-uzch2hwd cord-316460-ibprgdh4 cord-345088-krb1eidw cord-351197-xv6ymc4l cord-307904-lnagg1uw cord-322084-gkg1059v cord-335482-nx7odchj cord-340983-w219g6qs cord-331916-n744pymd cord-346514-vyo8l14p cord-353748-y1a52z8e cord-353467-wbtzvm4i cord-337976-c2auspti cord-344515-e0g911le cord-332356-au7s3dmp cord-342901-ca2xxkb2 cord-345630-bam3pa70 Creating transaction Updating ent table ===== Reducing parts of speech cord-253351-b36g09r0 cord-260177-xu0elmak cord-007373-livz5zuu cord-256036-gd53s4dv cord-254558-gvo0gwjf cord-266230-ia04jc9j cord-262441-slh52nxm cord-265173-70wyecwj cord-255841-3laov764 cord-258232-br4z3na6 cord-252397-qlu7dilh cord-256316-1odgm6hm cord-008407-jbp8bxjz cord-256703-eaj63c2k cord-258379-v3lceirh cord-255773-b4re5bky cord-254747-vox5xsgd cord-253024-b393ea2u cord-252615-ajyv95pu cord-262245-eb7g9p1x cord-262226-7kwkla73 cord-260695-qwepi0we cord-255453-7e40rj1y cord-255738-r8zfdsix cord-260108-osg8q89i cord-253894-4u5yt7b7 cord-267718-t47i8hui cord-260376-29ih5c9v cord-258286-lodjcj8c cord-262574-gu0930s3 cord-260782-1lm8tzbc cord-258691-cd83w9o6 cord-256737-ptjng78b cord-254950-y6kayxie cord-259717-e8ljkv2y cord-008426-ktn8c0zx cord-267027-diwm1940 cord-265156-u1re7983 cord-268139-tgpsu4qz cord-265895-ck7eto16 cord-264331-uvi8ucz4 cord-263334-wwkdum94 cord-269986-jdcw59r2 cord-268467-btfz6ye8 cord-269419-68kja6bg cord-268341-103xf3dw cord-266018-8bhnlsgy cord-269193-a647hwu9 cord-263302-z5uhrta5 cord-268416-8hw80qx8 cord-259095-mfptcw8t cord-262347-ejhz9rra cord-267532-5rnqd9mb cord-267014-3vi7pgvr cord-267377-wyhsxj6g cord-266585-jfjrk9gy cord-266617-z8uecyl6 cord-272437-gvzfl8c3 cord-274673-tjzlssal cord-259500-ndjbrtrv cord-255828-jrqdyfbg cord-270534-ebkwv4zo cord-273745-mwjh5se7 cord-258327-03vk6enj cord-271763-cual2qv4 cord-269094-6aka052v cord-269862-krcu3hfa cord-269866-3tpyj04y cord-272051-arz8r204 cord-272925-xag1yaie cord-270586-ohs8z91m cord-270487-m770a1rl cord-269204-kajws5xo cord-264359-m9j3pcj1 cord-273379-w8vy5rl8 cord-271359-dpa8zzc3 cord-273487-nfgjz6f9 cord-270929-utn21ce1 cord-274172-3dctmmfe cord-266861-t5h133lp cord-256769-flfycl7i cord-274424-juj71nc5 cord-275993-isff6lp2 cord-273246-4s54jrww cord-276358-so390gp4 cord-270814-krw8zmr5 cord-272050-0u62j7nj cord-272045-v1wt5t7m cord-275234-t6e7vr9y cord-274122-n9jnu2ah cord-271526-14nfqusv cord-275664-qbafkxtr cord-277838-931sco95 cord-274480-aywdmj6o cord-276034-a8pixbuc cord-279813-mrei5kih cord-272260-88l9bq4i cord-284968-eymvj6k3 cord-278578-vq5fy8m5 cord-279346-7del8d2p cord-279432-aik5bo6o cord-280287-t7uozjml cord-283309-ovx5fzsg cord-284646-fhruiw23 cord-281237-asnpuami cord-280795-wtrt13ij cord-281820-oltqsd6n cord-272871-gu9ptt9y cord-286060-92lazxd7 cord-280957-cdd6ngf1 cord-282947-3hgku2e4 cord-283035-tpqf458q cord-289712-w1y0lc5c cord-275348-jna496x7 cord-284581-fl2nt4ak cord-284707-72vx11aq cord-283998-whwksoxt cord-290640-kh2t0kfz cord-290993-bsnja161 cord-289991-wx4rsr4g cord-287777-ogs4mq0v cord-287620-vuvgi8xx cord-281309-c9y7m5do cord-289152-w5ynbewh cord-286232-jo24ia4s cord-290883-r2744fb3 cord-290231-4m9lj0uq cord-294056-7e477y1x cord-288669-46tkedw7 cord-289045-vft163v0 cord-292019-rfu0bkag cord-294260-g410mavp cord-291611-cfe8yujp cord-293375-qcy56ui7 cord-296364-7rp60d2m cord-296416-q0rsfzgw cord-291192-wm2eyaam cord-291306-g9qmmugg cord-298847-szezd2vb cord-299122-djfj4262 cord-293248-8vtd9e4n cord-290282-oxyzndsj cord-294990-jdjbjkcp cord-299994-1ksfo0pr cord-300884-rqfxe0x1 cord-298934-vtrfqozl cord-303497-s3zs1oxf cord-301755-fxfsr9bj cord-301293-jqy7lcbk cord-307396-u6v6bxwj cord-308835-999kewdw cord-302972-imtttzvr cord-297712-yy4g5npi cord-311255-zaa8i9vh cord-300810-a1skdp67 cord-307354-dkwcheu0 cord-296075-8axbkyyz cord-318400-l9kwxsq7 cord-303238-us3dybue cord-307904-lnagg1uw cord-319403-5qyc0wsz cord-309015-t5v2sjus cord-302486-z36hcvrx cord-322062-nnefbeo6 cord-304421-xpj6c0vx cord-317537-wgu5cd0y cord-309469-2naxn580 cord-310967-15mv5yx7 cord-315069-xo4mbxei cord-320590-irybhp4j cord-319179-gqaxf7mz cord-321162-pgd34ewv cord-305143-mqd4ioj4 cord-325179-gsf8ad65 cord-310218-fky0cm5e cord-300372-h5g4z8ts cord-305564-dj3vj4tk cord-313906-fh85fzq9 cord-293635-36pmai6s cord-310748-ao29zx1u cord-309919-sm5o0g1c cord-286121-ltaxmp3u cord-322904-9mta0aem cord-316134-lkd2mj27 cord-312210-3x9s3g8n cord-322084-gkg1059v cord-329245-6tj2k1yn cord-311774-fhdvcvi0 cord-299976-36r794ow cord-324321-y96x8x3h cord-326688-a1djgqpa cord-300470-vgd1ol2z cord-325423-d212h4bp cord-289248-6mx4o0eb cord-275403-g4rohhtt cord-316460-ibprgdh4 cord-293790-7hyelm88 cord-313091-ksrxsdpp cord-292751-tk1oggi9 cord-321265-il9vbbgk cord-315158-f6msh8od cord-279924-09uwhxs9 cord-285869-jwflooop cord-317333-unrd76bo cord-324054-d71rj29o cord-328046-5us4se5o cord-326027-58whwspe cord-331807-ooym5eh3 cord-325481-uzch2hwd cord-333525-67bbmo4m cord-334133-61om170g cord-331916-n744pymd cord-329819-dpgexphf cord-329625-hx2rsi91 cord-330907-srb8ac7l cord-330847-a84pcc9z cord-335482-nx7odchj cord-329794-msxrdhb3 cord-351197-xv6ymc4l cord-346514-vyo8l14p cord-337976-c2auspti cord-344515-e0g911le cord-345630-bam3pa70 cord-332356-au7s3dmp cord-353748-y1a52z8e cord-340983-w219g6qs cord-353467-wbtzvm4i cord-345088-krb1eidw cord-342901-ca2xxkb2 Creating transaction Updating pos table Building ./etc/reader.txt cord-342901-ca2xxkb2 cord-266861-t5h133lp cord-262347-ejhz9rra cord-262347-ejhz9rra cord-281309-c9y7m5do cord-289152-w5ynbewh number of items: 229 sum of words: 1,051,747 average size in words: 5,594 average readability score: 53 nouns: virus; cells; protein; cell; infection; proteins; coronavirus; replication; sequence; viruses; expression; gene; mice; type; analysis; membrane; genome; data; activity; sequences; results; site; region; fusion; min; host; acid; antibodies; transcription; rnas; amino; domain; antibody; study; role; mouse; receptor; °; dna; residues; glycoprotein; syndrome; synthesis; studies; genes; cleavage; presence; levels; structure; polymerase verbs: used; show; infected; containing; binding; expressed; indicates; suggests; induce; described; detected; determine; followed; observed; encoding; associate; required; found; including; compared; incubated; performed; identified; demonstrated; resulting; mediates; analyzed; obtained; transfected; produced; generated; increasing; involves; purified; reported; based; isolates; treated; inhibited; provide; reveal; derived; reduced; confirm; labeled; washed; caused; forms; known; represent adjectives: viral; specific; human; respiratory; infectious; different; anti; infected; similar; cellular; recombinant; present; murine; structural; porcine; like; high; wild; genomic; acute; severe; molecular; immune; non; dependent; positive; important; several; small; negative; first; nucleotide; large; single; functional; significant; mutant; essential; low; possible; monoclonal; primary; major; multiple; nuclear; intracellular; full; new; novel; independent adverbs: also; however; previously; respectively; well; therefore; significantly; highly; approximately; nt; recently; furthermore; together; directly; first; even; prior; interestingly; specifically; subsequently; less; still; efficiently; likely; probably; similarly; completely; indeed; briefly; finally; rather; alone; partially; moreover; overnight; later; clearly; upstream; least; downstream; much; twice; closely; yet; strongly; relatively; next; initially; currently; newly pronouns: we; it; its; their; our; i; they; them; us; his; he; itself; ha3; nsp15; mrnas; themselves; one; you; nsp1; her; yubfkt1; pcv2; me; atp1b3; y162; p28; u; s; ps]methionine; nsp4; fmhv; oligodt; nsp10; my; mhv)-a59; mg; ag-126; Ϫ0.013; β2.7; ya; veroe6-pedv; us/; theirs; tgbps; stat1; ribv; r132; puc; pr76gag; pkt0-ibvn proper nouns: RNA; Fig; S; SARS; MHV; CoV; PCR; N; M; IFN; C; T; PRRSV; PEDV; TGEV; IBV; mRNA; ORF; DI; JHM; A59; PBS; pH; RT; Vero; MERS; OC43; K; subgenomic; HCV; B; SDS; p.i; A; E; VSV; HIV-1; HCoV; HA; G; CNS; JHMV; hepatitis; II; HE; GX; D; Coronavirus; Golgi; CD4 keywords: rna; cell; mhv; sars; protein; virus; tgev; ibv; ifn; pcr; dna; prrsv; jhm; a59; orf; oc43; vero; pedv; mers; jhmv; hiv-1; hcv; fipv; bcv; trs; mhc; egfp; vsv; sv40; sds; rna2; rna1; rn2; rbd; ptv; pcv2; mouse; irf3; hev; golgi; gene; fecv; erk1/2; eav; dpp4; domain; day; cov; cns; cat one topic; one dimension: virus file(s): https://api.elsevier.com/content/article/pii/S0042682298991218 titles(s): Roles in Cell-to-Cell Fusion of Two Conserved Hydrophobic Regions in the Murine Coronavirus Spike Protein three topics; one dimension: cells; rna; rna file(s): https://www.ncbi.nlm.nih.gov/pubmed/25277499/, https://www.sciencedirect.com/science/article/pii/004268229290684H, https://api.elsevier.com/content/article/pii/S004268220300285X titles(s): Phosphatidylserine receptors: enhancers of enveloped virus entry and infection | Evidence for variable rates of recombination in the MHV genome | Sequence elements controlling expression of Barley stripe mosaic virus subgenomic RNAs in vivo five topics; three dimensions: cells virus protein; rna virus protein; protein virus cells; rna virus replication; genome virus sequence file(s): https://www.sciencedirect.com/science/article/pii/S0042682217304361, https://www.sciencedirect.com/science/article/pii/004268229290684H, https://www.ncbi.nlm.nih.gov/pubmed/25277499/, https://www.ncbi.nlm.nih.gov/pubmed/25818028/, https://www.sciencedirect.com/science/article/pii/S0042682217302362 titles(s): The OC43 human coronavirus envelope protein is critical for infectious virus production and propagation in neuronal cells and is a determinant of neurovirulence and CNS pathology | Evidence for variable rates of recombination in the MHV genome | Phosphatidylserine receptors: enhancers of enveloped virus entry and infection | Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses | Evolutionary dynamics of recent peste des petits ruminants virus epidemic in China during 2013–2014 Type: cord title: journal-virology-cord date: 2021-05-30 time: 16:05 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: facet_journal:"Virology" ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-307354-dkwcheu0 author: Abernathy, Emma title: Emerging roles for RNA degradation in viral replication and antiviral defense date: 2015-05-31 words: 7160.0 sentences: 359.0 pages: flesch: 45.0 cache: ./cache/cord-307354-dkwcheu0.txt txt: ./txt/cord-307354-dkwcheu0.txt summary: Alpha-herpesviruses such as herpes simplex-1 (HSV-1) express a FEN1-like nuclease termed virion host shutoff protein (vhs) that is directed to mRNAs through interactions with the translation Fig. 1 . Quality control decay pathways such as NMD recognize aberrant mRNAs during translation, including the presence of premature termination codons (PTC), and induce endonucleolytic cleavage, whereupon the fragments are degraded by exonucleases. The RNAi pathway restricts gene expression by processing the long double stranded RNAs frequently generated during viral replication into short interfering RNAs (siR-NAs), which guide endonucleolytic cleavage of complementary target mRNAs. Although mammalian cells possess the RNAi machinery, in most cases RNAi does not appear to play a significant antiviral role, and has instead been supplanted by the protein-based interferon response (Cullen, 2014) . Small interfering RNAs that deplete the cellular translation factor eIF4H impede mRNA degradation by the virion host shutoff protein of herpes simplex virus abstract: Abstract Viral replication significantly alters the gene expression landscape of infected cells. Many of these changes are driven by viral manipulation of host transcription or translation machinery. Several mammalian viruses encode factors that broadly dampen gene expression by directly targeting messenger RNA (mRNA). Here, we highlight how these factors promote mRNA degradation to globally regulate both host and viral gene expression. Although these viral factors are not homologous and use distinct mechanisms to target mRNA, many of them display striking parallels in their strategies for executing RNA degradation and invoke key features of cellular RNA quality control pathways. In some cases, there is a lack of selectivity for degradation of host versus viral mRNA, indicating that the purposes of virus-induced mRNA degradation extend beyond redirecting cellular resources towards viral gene expression. In addition, several antiviral pathways use RNA degradation as a viral restriction mechanism, and we will summarize new findings related to how these host-encoded ribonucleases target and destroy viral RNA. url: https://doi.org/10.1016/j.virol.2015.02.007 doi: 10.1016/j.virol.2015.02.007 id: cord-271763-cual2qv4 author: Abraham, Sushma title: Deduced sequence of the bovine coronavirus spike protein and identification of the internal proteolytic cleavage site date: 1990-05-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract The sequence of the spike (also called peplomer or E2) protein gene of the Mebus strain of bovine coronavirus (BCV) was obtained from cDNA clones of genomic RNA. The gene sequence predicts a 150,825 mol wt apoprotein of 1363 amino acids having an N-terminal hydrophobic signal sequence of 17 amino acids, 19 potential N-linked glycosylation sites, a hydrophobic anchor sequence of approximately 17 amino acids near the C terminus, and a hydrophilic cysteinerich C terminus of 35 amino acids. An internal LysArgArgSerArgArg sequence predicts a protease cleavage site between amino acids 768 and 769 that would separate the S apoprotein into S1 and S2 segments of 85690 and 65153 mol wt, respectively. Amino terminal amino acid sequencing of the virion-derived gp100 spike subunit confirmed the location of the predicted cleavage site, and established that gp120 and gp100 are the glycosylated virion forms of the S1 and S2 subunits, respectively. Sequence comparisons between BCV and the antigenically related mouse hepatitis coronavirus revealed more sequence divergence in the putative knob region of the spike protein (S1) than in the stem region (S2). url: https://www.ncbi.nlm.nih.gov/pubmed/2184576/ doi: 10.1016/0042-6822(90)90257-r id: cord-309469-2naxn580 author: An, Hongliu title: Identification and formation mechanism of a novel noncoding RNA produced by avian infectious bronchitis virus date: 2019-01-05 words: 3600.0 sentences: 234.0 pages: flesch: 54.0 cache: ./cache/cord-309469-2naxn580.txt txt: ./txt/cord-309469-2naxn580.txt summary: For example, polyadenylated nuclear (PAN) RNA encoded by Kaposi''s sarcoma-associated herpesvirus (Sun et al., 1996; Zhong and Ganem, 1997) , the~2-kb latency-associated transcript (LAT) expressed by Herpes simplex virus (Bloom, 2004 ), a con-served~5-kb intron expressed by Human cytomegalovirus (hCMV) (Kulesza and Shenk, 2004) , and a 7.2-kb RNA expressed by mouse CMV (Kulesza and Shenk, 2006) , U-rich RNAs (HSURs) produced by Herpesvirus saimiri (HVS), (Albrecht and Fleckenstein, 1992; Ensser and Fleckenstein, 2005) ; (3) Subgenomic ncRNAs from single-stranded RNA viruses by incomplete degradation of genomic RNA by the cellular 5-3′ exonuclease XRN1. The results confirmed previous report that IBV can synthesize sgRNA via template switch mediated by a noncanonical core sequence (Bentley et al., 2013) Notably, the mutant virus carrying four mutations (A27100U/A27111U/G27113C/G27114C) was also unable to produce ncRNA (Fig. 4) , suggesting these nucleotides are required for ncRNA production. abstract: Viral noncoding (nc) RNAs have been shown to play important roles in viral life cycle. Many viruses employ different mechanism to produce ncRNAs. Here, we report that coronavirus infectious bronchitis virus (IBV) produces a novel ncRNA in virus-infected cells. This ncRNA consists of 563 nucleotides excluding a poly(A) tail, is mainly derived from the 3′-untranslated region of IBV genome, and contains a 63-nt-long of terminal leader sequence derived from the 5′ end of the viral genome. Using mutagenesis and reverse genetics, we reveal that this ncRNA is a subgenomic RNA generated by discontinuous transcription mechanism. url: https://doi.org/10.1016/j.virol.2018.12.019 doi: 10.1016/j.virol.2018.12.019 id: cord-270586-ohs8z91m author: Ballesteros, M. L. title: Two Amino Acid Changes at the N-Terminus of Transmissible Gastroenteritis Coronavirus Spike Protein Result in the Loss of Enteric Tropism date: 1997-01-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract To study the molecular basis of TGEV tropism, a collection of recombinants between the PUR46-MAD strain of transmissible gastroenteritis coronavirus (TGEV) infecting the enteric and respiratory tracts and the PTV strain, which only infects the respiratory tract, was generated. The recombinant isolation frequency was about 10−9recombinants per nucleotide and was 3.7-fold higher at the 5′-end of the S gene than in other areas of the genome. Thirty recombinants were plaque purified and characterized phenotypically and genetically. All recombinant viruses had a single crossover and had inherited the 5′- and 3′-halves of their genome from the enteric and respiratory parents, respectively. Recombinant viruses were classified into three groups, named 1 to 3, according to the location of the crossover. Group 1 recombinants had the crossover in the S gene, while in Groups 2 and 3 the crossovers were located in ORF1b and ORF1a, respectively. The tropism of the recombinants was studied. Recombinants of Group 1 had enteric and respiratory tropism, while Group 2 recombinants infected the respiratory, but not the enteric, tract. Viruses of both groups differed by two nucleotide changes at positions 214 and 655. Both changes may be in principle responsible for the loss of enteric tropism but only the change in nucleotide 655 was specifically found in the respiratory isolates and most likely this single nucleotide change, which leads to a substitution in amino acid 219 of the S protein, was responsible for the loss of enteric tropism in the closely related PUR-46 isolates. The available data indicate that in order to infect enteric tract cells with TGEV, two different domains of the S protein, mapping between amino acids 522 and 744 and around amino acid 219, respectively, are involved. The first domain binds to porcine aminopeptidase N, the cellular receptor for TGEV. In the other domain maps a second factor of undefined nature but which may be the binding site for a coreceptor essential for the enteric tropism of TGEV. url: https://www.sciencedirect.com/science/article/pii/S0042682296983440 doi: 10.1006/viro.1996.8344 id: cord-310748-ao29zx1u author: Banner, Lisa R. title: Random nature of coronavirus RNA recombination in the absence of selection pressure date: 1991-11-30 words: 2839.0 sentences: 155.0 pages: flesch: 52.0 cache: ./cache/cord-310748-ao29zx1u.txt txt: ./txt/cord-310748-ao29zx1u.txt summary: Our results showed that within a 1-kb region of the peplomer gene, RNA recombination occurred at almost every potential crossover site. To study RNA recombination in the absence of selection pressure, we developed a polymer-ase chain reaction (PCR) assay using two primers specific for the potential recombinant viruses which have a crossover site between the two primers. Only recombinant RNAs which had a crossover between the two primers and contained A59-specific sequences on the 5''-side and JHM-DL-specific sequences on the 3''-side could be detected by this PCR approach. DNA sequence analysis of 35 cloned PCR products showed that the crossover sites were almost randomly distributed throughout the nearly 1-kb region of the peplomer gene studied ( Fig. 2A) . Analysis of 53 recombinant clones revealed that, similar to the intracellular recombinants, the crossover sites in the viral recombinant RNAs were almost randomly distributed over the 1 -kb region of the peplomer gene (Fig. 2B) . abstract: Abstract RNA-RNA recombination is thought to occur preferentially at certain selected sites and in only a few RNA viruses; the mechanism for these restrictions is unknown. In this paper we report the development of a recombination assay for coronavirus, using polymerase chain reaction, in the absence of selection pressure. Our results showed that within a 1-kb region of the peplomer gene, RNA recombination occurred at almost every potential crossover site. Thus, coronavirus RNA recombination appears to be more random than previously realized. However, after serial passages of the recombinant viruses in tissue culture, the recombination sites among the progeny viruses became clustered in the region which contains the previously reported “hot spot” for coronavirus recombination. These results suggest that RNA recombination is common and random in nature, but only certain recombinants can be selected. Thus, the presence of recombinational “hot spots” for coronavirus or other RNA viruses most likely resulted from selection of certain recombinant viruses and not restriction on the occurrence of RNA recombination. The failure to detect recombinants in other RNA viruses may therefore be due to unfavorable properties of recombinant viruses. This approach can be used to detect recombinants in these viruses. url: https://www.sciencedirect.com/science/article/pii/004268229190795D doi: 10.1016/0042-6822(91)90795-d id: cord-267718-t47i8hui author: Bao, Jingyue title: Evolutionary dynamics of recent peste des petits ruminants virus epidemic in China during 2013–2014 date: 2017-07-19 words: 4760.0 sentences: 240.0 pages: flesch: 56.0 cache: ./cache/cord-267718-t47i8hui.txt txt: ./txt/cord-267718-t47i8hui.txt summary: An evolutionary rate of 2.61 × 10(−6) nucleotide substitutions per site per day was estimated, dating the most recent common ancestor of PPRV China 2013–2014 strains to early August 2013. Transmission network analysis revealed that all the virus sequences could be grouped into five clusters of infection, suggesting long-distance animal transmission play an important role in the spread of PPRV in China. Here we present the first intra-epidemic analysis of PPRV genome by studying viruses from 25 farms infected during the 2013-2014 PPR outbreaks in China. In this study, we constructed the transmission pathway of the spread of PPR virus basing on the fulllength genome sequences and identified five clusters of infections. Although more than 200 infected farms were reported during 20132014 PPRV epidemic in China, only 25 of them were full-genome sequenced and analyzed in this study. Full genome sequence of a peste des petits ruminants virus (PPRV) from Ghana abstract: Peste des petits ruminants virus (PPRV) causes a highly contagious disease, peste des petits ruminants (PPR), in sheep and goats which has been considered as a serious threat to the local economy in Africa and Asia. However, the in-depth evolutionary dynamics of PPRV during an epidemic is not well understood. We conducted phylogenetic analysis on genomic sequences of 25 PPRV strains from China 2013–2014 outbreaks. All these strains clustered into a novel clade in lineage 4. An evolutionary rate of 2.61 × 10(−6) nucleotide substitutions per site per day was estimated, dating the most recent common ancestor of PPRV China 2013–2014 strains to early August 2013. Transmission network analysis revealed that all the virus sequences could be grouped into five clusters of infection, suggesting long-distance animal transmission play an important role in the spread of PPRV in China. These results expanded our knowledge for PPRV evolution to achieve effective control measures. url: https://www.sciencedirect.com/science/article/pii/S0042682217302362 doi: 10.1016/j.virol.2017.07.018 id: cord-265895-ck7eto16 author: Baric, Ralph S. title: Analysis of intracellular small RNAs of mouse hepatitis virus: evidence for discontinuous transcription date: 1987-02-28 words: 4507.0 sentences: 228.0 pages: flesch: 60.0 cache: ./cache/cord-265895-ck7eto16.txt txt: ./txt/cord-265895-ck7eto16.txt summary: These data, coupled with the high frequency of RNA recombination during MHV infection, suggest that the viral polymerase may pause in or around regions of secondary structure, thereby generating pools of free leader-containing RNA intermediates which can reassociate with the template, acting as primers for the synthesis of full-length or recombinant RNAs. These data suggest that MHV transcription uses a discontinuous and nonprocessive mechanism in which RNA polymerase allows the partial RNA products to be dissociated from the template temporarily during the process of transcription. These data, coupled with the presence of discrete large leader-containing RNAs which range from 84 to 1000 nucleotides in length in MHV-infected cells (Baric et a/., 1985) suggest that discontinuous RNA intermediates may be dissociated and reassert between viral RNA templates to generate recombinant viruses by a copy-choice mechanism (Makino eta/., 1986a). The leader-containing RNAs larger than 1 10 nucleotides in length detected by the leader-specific cDNA probe were more heterogeneous (Fig. 2) (Baric et al., 1985) suggesting that multiple RNA species in this size range were present. abstract: Abstract We have previously shown the presence of multiple small leader-containing RNA species in mouse hepatitis virus (MHV)-infected cells. In this paper, we have analyzed the origin, structure, and mechanism of synthesis of these small RNAs. Using cDNA probes specific for leader RNA and genes A, D, and F, we demonstrate that subsets of these small RNAs were derived from the various viral genes. These subsets have discrete and reproducible sizes, varying with the gene from which they are derived. The size of each subset correlates with regions of secondary structure, whose free energy ranges from −1.6 to −77.1 kcal/mol, in each of the mRNAs examined. In addition, identical subsets were detected on the replicative intermediate (RI) RNA, suggesting that they represent functional transcriptional intermediates. The biological significance of these small RNAs is further supported by the detection of leader-containing RNAs of 47, 50, and 57 nucleotides in length, which correspond to the crossover sites in two MHV recombinant viruses. These data, coupled with the high frequency of RNA recombination during MHV infection, suggest that the viral polymerase may pause in or around regions of secondary structure, thereby generating pools of free leader-containing RNA intermediates which can reassociate with the template, acting as primers for the synthesis of full-length or recombinant RNAs. These data suggest that MHV transcription uses a discontinuous and nonprocessive mechanism in which RNA polymerase allows the partial RNA products to be dissociated from the template temporarily during the process of transcription. url: https://api.elsevier.com/content/article/pii/0042682287904144 doi: 10.1016/0042-6822(87)90414-4 id: cord-275403-g4rohhtt author: Bautista, Elida M. title: Functional Properties of the Predicted Helicase of Porcine Reproductive and Respiratory Syndrome Virus date: 2002-07-05 words: 7432.0 sentences: 401.0 pages: flesch: 48.0 cache: ./cache/cord-275403-g4rohhtt.txt txt: ./txt/cord-275403-g4rohhtt.txt summary: To examine characteristics of putative nonstructural proteins (nsp) encoded in ORF1b, which have been identified by nucleotide similarity to domains of equine arteritis virus, defined genomic regions were cloned and expressed in the pRSET expression system. As initial proof of helicase-like activity, experiments were performed to test the ability of purified PRRSV-14 nsp10 protein to hydrolyze radiolabeled ribonucleotides in the presence or absence of polyribonucleotides. To further analyze the predicted helicase activity of the PRRSV nsp10 protein, experiments were performed using duplex substrates prepared with synthetic oligonucleotides containing single-strand regions at the 3Ј or 5Ј ends and short duplex regions (21 and 24 bp). The 5Ј-to-3Ј orientation of the unwinding activity of the PRRSV helicase was further confirmed in experiments using substrates prepared with in vitro transcribed RNA that contained singlestrand regions at the 5Ј end of both strands and duplex regions of 67 bp (5Ј5ЈDuplex #1) and 85 bp (5Ј5ЈDuplex #2), as shown in Fig. 9B . abstract: Abstract Porcine reproductive and respiratory syndrome virus (PRRSV) is a member of the positive-strand RNA virus family Arteriviridae. Although considerable research has focused on this important pathogen, little is known about the function of most PRRSV proteins. To examine characteristics of putative nonstructural proteins (nsp) encoded in ORF1b, which have been identified by nucleotide similarity to domains of equine arteritis virus, defined genomic regions were cloned and expressed in the pRSET expression system. One region, nsp10, encoded a protein with a putative helicase domain and was further examined for functional helicase-like activities. PRRSV nsp10 was found to possess a thermolabile and pH-sensitive NTPase activity that was modulated by polynucleotides and to unwind dsRNA in a 5′ to 3′ polarity. These results provide the first evidence of the functional properties of PRRSV helicase and further support the finding that nidovirus helicases possess properties that distinguish them from other viral helicases. url: https://www.ncbi.nlm.nih.gov/pubmed/12127789/ doi: 10.1006/viro.2002.1495 id: cord-291192-wm2eyaam author: Becares, Martina title: Antigenic structures stably expressed by recombinant TGEV-derived vectors date: 2014-08-09 words: 9535.0 sentences: 526.0 pages: flesch: 49.0 cache: ./cache/cord-291192-wm2eyaam.txt txt: ./txt/cord-291192-wm2eyaam.txt summary: Transmissible gastroenteritis virus (TGEV) was engineered to express porcine reproductive and respiratory syndrome virus (PRRSV) small protein domains, as a strategy to improve heterologous gene stability. Recombinant TGEV (rTGEV) vectors have been engineered for dicistronic expression of heterologous genes, such as porcine reproductive and respiratory syndrome virus (PRRSV) GP5 and M proteins (Cruz et al., 2010) , or rotavirus VP2 and VP6, in which formation of rotavirus virus like particles (VLPs) in the cytoplasm of rTGEV infected cells was observed (Enjuanes et al., 2007) . Therefore, heterologous gene size reduction is a promising strategy to achieve stable expression in TGEV-derived vectors and in general in CoVs. This effect could be due to a decrease of the probability of non-homologous recombination in shorter sequences, or to the elimination of protein domains toxically affecting the host cell or rTGEV life cycle. abstract: Coronaviruses (CoVs) are positive-stranded RNA viruses with potential as immunization vectors, expressing high levels of heterologous genes and eliciting both secretory and systemic immune responses. Nevertheless, its high recombination rate may result in the loss of the full-length foreign gene, limiting their use as vectors. Transmissible gastroenteritis virus (TGEV) was engineered to express porcine reproductive and respiratory syndrome virus (PRRSV) small protein domains, as a strategy to improve heterologous gene stability. After serial passage in tissue cultures, stable expression of small PRRSV protein antigenic domains was achieved. Therefore, size reduction of the heterologous genes inserted in CoV-derived vectors led to the stable expression of antigenic domains. Immunization of piglets with these TGEV vectors led to partial protection against a challenge with a virulent PRRSV strain, as immunized animals showed reduced clinical signs and lung damage. Further improvement of TGEV-derived vectors will require the engineering of vectors with decreased recombination rate. url: https://api.elsevier.com/content/article/pii/S0042682214003353 doi: 10.1016/j.virol.2014.07.027 id: cord-353748-y1a52z8e author: Bhattacharya, Rajarshi title: A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2 date: 2021-01-02 words: 3308.0 sentences: 211.0 pages: flesch: 61.0 cache: ./cache/cord-353748-y1a52z8e.txt txt: ./txt/cord-353748-y1a52z8e.txt summary: title: A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2 Nisin, a food-grade antimicrobial peptide produced by lactic acid bacteria has been examined for its probable interaction with the human ACE2 (hACE2) receptor, the site where spike protein of SARS-CoV-2 binds. Among the eight nisin variants examined, nisin H, nisin Z, nisin U and nisin A showed a significant binding affinity towards hACE2, higher than that of the RBD (receptor binding domain) of the SARS-CoV-2 spike protein. The present study attempts to investigate the ability of food-grade nisin A and its natural variants to block the interaction between hACE2 and the spike protein of SARS-CoV-2, a key step of COVID-19 disease initiation. The binding affinity of docked structures of all eight variants of nisin in complex with hACE2 was calculated as ΔG derived from analysis with Prodigy for each complex in comparison with the RBD of spike protein of SARS-CoV-2. abstract: Nisin, a food-grade antimicrobial peptide produced by lactic acid bacteria has been examined for its probable interaction with the human ACE2 (hACE2) receptor, the site where spike protein of SARS-CoV-2 binds. Among the eight nisin variants examined, nisin H, nisin Z, nisin U and nisin A showed a significant binding affinity towards hACE2, higher than that of the RBD (receptor binding domain) of the SARS-CoV-2 spike protein. The molecular interaction of nisin with hACE2 was investigated by homology modeling and docking studies. Further, binding efficiency of the most potent nisin H was evaluated through the interaction of hACE2:nisin H complex with RBD (receptor-binding domain) of SARS-CoV-2 and that of hACE2:RBD complex with nisin H. Here, nisin H acted as a potential competitor of RBD to access the hACE2 receptor. The study unravels for the first time that a globally used food preservative, nisin has the potential to bind to hACE2. url: https://www.sciencedirect.com/science/article/pii/S004268222030204X doi: 10.1016/j.virol.2020.10.002 id: cord-289991-wx4rsr4g author: Bhowmick, Rahul title: Rotavirus infection induces G1 to S phase transition in MA104 cells via Ca(+2)/Calmodulin pathway date: 2014-03-21 words: 7167.0 sentences: 362.0 pages: flesch: 52.0 cache: ./cache/cord-289991-wx4rsr4g.txt txt: ./txt/cord-289991-wx4rsr4g.txt summary: To assess whether RV modulates expression of CDK inhibitors to regulate cell cycle, whole cell lysates or total RNA of MA104 cells infected with either SA11 (3 moi) or mock infected were subjected to either immunoblotting or real time PCR with p15, p21, p27 specific antibodies or primers, respectively. This results in its inability to bind to and prevent nuclear translocation of E2F ( Fig. 2A) , since E2F in nucleus can activate transcription of several downstream genes like thymidine kinase, thymidine synthase and dihydrofolate reductase (Fig. 2C) , which promote cell cycle progression and DNA replication, nuclear accumulation of E2F by RV during early infection facilitates G 1 /S restriction point modulation in favor of RV replication. CaMKI has been shown to induce G 1 to S phase transition (Skelding et al., 2011) , concurrently activation of CaMKI (phospho CaMKI) was also observed during early RV infection (2-6 hpi) which correlated with increased CaM expression and accumulation of cells in S phase (Fig. 4A) . abstract: Viruses, obligate cellular parasites rely on host cellular functions and target the host cell cycle for their own benefit. In this study, effect of rotavirus infection on cell cycle machinery was explored. We found that rotavirus (RV) infection in MA104 cells induces the expression of cyclins and cyclin dependent kinases and down-regulates expression of CDK inhibitors, resulting in G1 to S phase transition. The rotavirus induced S phase accumulation was found to be concurrent with induction in expression of calmodulin and activation of CaMKI which is reported as inducer of G1–S phase transition. This cell cycle manipulation was found to be Ca(+2)/Calmodulin pathway dependent. The physiological relevance of G1 to S phase transition was established when viral gene expressions as well as viral titers were found to be increased in S phase synchronized cells and decreased in G0/G1 phase synchronized cells compared to unsynchronized cells during rotavirus infection. url: https://api.elsevier.com/content/article/pii/S004268221400083X doi: 10.1016/j.virol.2014.03.001 id: cord-270534-ebkwv4zo author: Bodmer, Bianca S. title: Live-attenuated bivalent measles virus-derived vaccines targeting Middle East respiratory syndrome coronavirus induce robust and multifunctional T cell responses against both viruses in an appropriate mouse model date: 2018-06-11 words: 6539.0 sentences: 362.0 pages: flesch: 53.0 cache: ./cache/cord-270534-ebkwv4zo.txt txt: ./txt/cord-270534-ebkwv4zo.txt summary: title: Live-attenuated bivalent measles virus-derived vaccines targeting Middle East respiratory syndrome coronavirus induce robust and multifunctional T cell responses against both viruses in an appropriate mouse model One of these candidates, MV vac2 -MERS-S(H) (Malczyk et al., 2015) , is based on the measles virus (MV) vaccine platform technology (Mühlebach, 2017) , and encodes the MERS-CoV spike protein (S) as an additional antigen in the backbone of recombinant MV vac2 (del Valle et al., 2007) resembling vaccine strain Moraten that is authorized and in use in the US since 1968. (G) Secretion of IFN-γ after antigen-specific re-stimulation of splenocytes harvested 32 days post prime immunization and after co-culture with JAWSII (left) or DC2.4 (middle) dendritic cells transgenic for MERS-N (black) or untransduced controls (NC, white). To assess the capacity of the different MV vac2 -MERS-S(H) vaccine preparations to induce MERS-CoV S-specific cellular immune responses, splenocytes of mice, which had already been tested for humoral responses ( Fig. 2A) , were isolated and analyzed 49 days after immunization for antigen(Ag)-dependent IFN-γ secretion using ELISpot assay. abstract: Cases of Middle East respiratory syndrome coronavirus (MERS-CoV) continue to occur, making it one of the WHO´s targets for accelerated vaccine development. One vaccine candidate is based on live-attenuated measles virus (MV) vaccine encoding the MERS-CoV spike glycoprotein (MERS-S). MV(vac2)-MERS-S(H) induces robust humoral and cellular immunity against MERS-S mediating protection. Here, the induction and nature of immunity after vaccination with MV(vac2)-MERS-S(H) or novel MV(vac2)-MERS-N were further characterized. We focused on the necessity for vector replication and the nature of induced T cells, since functional CD8(+) T cells contribute importantly to clearance of MERS-CoV. While no immunity against MERS-CoV or MV was detected in MV-susceptible mice after immunization with UV-inactivated virus, replication-competent MV(vac2)-MERS-S(H) triggered robust neutralizing antibody titers also in adult mice. Furthermore, a significant fraction of MERS CoV-specific CD8(+) T cells and MV-specific CD4(+) T cells simultaneously expressing IFN-γ and TNF-α were induced, revealing that MV(vac2)-MERS-S(H) induces multifunctional cellular immunity. url: https://www.sciencedirect.com/science/article/pii/S0042682218301697 doi: 10.1016/j.virol.2018.05.028 id: cord-303497-s3zs1oxf author: Breuning, Astrid title: Characterization of a cold-sensitive (cs) recombinant between two influenza a strains date: 1983-10-15 words: 3003.0 sentences: 166.0 pages: flesch: 60.0 cache: ./cache/cord-303497-s3zs1oxf.txt txt: ./txt/cord-303497-s3zs1oxf.txt summary: Recombinants between fowl plague virus (FPV) and these strains were obtained by double infection of chick embryo cells either with specific ts mutants of FPV or FPV wild-type and the other prototype strains, and extended plaque purifications as described by Scholtissek et aL (1976) and Rott et aL (1979) . When plaque tests were performed on chick embryo cells at 37 or 40" with recombinants between FPV and other prototype influenza virus strains it was found that the plaque morphology of most of these recombinants was similar to that of FPV. In a single-cycle multiplication experiment (infection at a multiplicity of lo-50 PFU per cell) at 33", the yield of infectious 113/Ho was very low when compared with the multiplication at 37" or with the adapted strain or FPV (Fig. 2) . These results indicate that a step before virus maturation is impeded at 33'' in 113/Ho-infected cells, since labeling of viral proteins is already slowed down at this temperature. abstract: Abstract Recombinants between fowl plague virus (FPV, H7N1) and the Hong Kong (H3N2) or Singapore (H2N2) influenza virus strains carrying the hemagglutinin of FPV and the neuraminidase of the human strains form only very tiny plaques at 33°, but normal plaques at 37°. One recombinant (113/Ho) has been studied in more detail. It multiplies only very slowly at 33°, the nonpermissive temperature. Adsorption and penetration are normal at 33°, but synthesis of protein is impeded. Temperature-shift experiments suggest that the synthesis of viral mRNA is slowed at 33°. 113/Ho does not agglutinate chicken erythrocytes at 40°, as the parent viruses do. 113/Ho can be adapted to grow normally at 33°. The frequency of adaptation is comparable to reversion of a single point mutation (ca. 10−5). Recombinants which grow well at 37° but not at 33° are called cold-sensitive (cs) recombinants. url: https://www.sciencedirect.com/science/article/pii/0042682283901174 doi: 10.1016/0042-6822(83)90117-4 id: cord-268139-tgpsu4qz author: Brockway, Sarah M. title: Mutagenesis of the murine hepatitis virus nsp1-coding region identifies residues important for protein processing, viral RNA synthesis, and viral replication date: 2005-09-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Despite ongoing research investigating mechanisms of coronavirus replication, functions of many viral nonstructural proteins (nsps) remain unknown. In the current study, a reverse genetic approach was used to define the role of the 28-kDa amino-terminal product (nsp1) of the gene 1 polyprotein during replication of the coronavirus murine hepatitis virus (MHV) in cell culture. To determine whether nsp1 is required for MHV replication and to identify residues critical for protein function, mutant viruses that contained deletions or point mutations within the nsp1-coding region were generated and assayed for defects in viral replication, viral protein expression, protein localization, and RNA synthesis. The results demonstrated that the carboxy-terminal half of nsp1 (residues K(124) through L(241)) was dispensable for virus replication in culture but was required for efficient proteolytic cleavage of nsp1 from the gene 1 polyprotein and for optimal viral replication. Furthermore, whereas deletion of nsp1 residues amino-terminal to K(124) failed to produce infectious virus, point mutagenesis of the nsp1 amino-terminus allowed recovery of several mutants with altered replication and RNA synthesis. This study identifies nsp1 residues important for protein processing, viral RNA synthesis, and viral replication. url: https://api.elsevier.com/content/article/pii/S0042682205003776 doi: 10.1016/j.virol.2005.06.035 id: cord-287620-vuvgi8xx author: Butler, Noah title: Murine encephalitis caused by HCoV-OC43, a human coronavirus with broad species specificity, is partly immune-mediated date: 2006-04-10 words: 6665.0 sentences: 344.0 pages: flesch: 56.0 cache: ./cache/cord-287620-vuvgi8xx.txt txt: ./txt/cord-287620-vuvgi8xx.txt summary: HCoV-OC43, harvested from a patient with an upper respiratory tract infection, was originally isolated after passage in human embryonic tracheal organ cultures; this virus caused neurological disease after only one passage in suckling mice and encephalitis within 2-4 passages (McIntosh et al., 1967) (termed HCoV-OC43 NV ). For example, Talbot and co-workers showed, using the mouse-adapted virus after passage in tissue culture cells (termed HCoV-OC43 QUE herein;) that mice infected intranasally with 10 4 -10 5 TCID 50 developed encephalitis if inoculated 8 days but not 21 days postnatally (Jacomy and Talbot, 2003) . HCoV-OC43 QUE was passaged 5-6 times in tissue culture prior to use in mice (personal communication, Dr. Pierre Talbot, INRS-Institut Armand-Frappier, Laval, Quebec) and consequently may be less virulent than virus isolated directly from infected suckling mouse brains. As shown in Fig. 5 , immunocytochemical staining for viral antigen revealed that the tissue culture-adapted virus infected hamster, pig, human, mouse, monkey and cat cells, but not FRT rat epithelium cells. abstract: The human coronavirus HCoV-OC43 causes a significant fraction of upper respiratory tract infections. Most coronaviruses show a strong species specificity, although the SARS-Coronavirus crossed species from palm civet cats to infect humans. Similarly, HCoV-OC43, likely a member of the same coronavirus group as SARS-CoV, readily crossed the species barrier as evidenced by its rapid adaptation to the murine brain [McIntosh, K., Becker, W.B., Chanock, R.M., 1967. Growth in suckling-mouse brain of “IBV-like” viruses from patients with upper respiratory tract disease. Proc Natl Acad Sci U.S.A. 58, 2268–73]. Herein, we investigated two consequences of this plasticity in species tropism. First, we showed that HCoV-OC43 was able to infect cells from a large number of mammalian species. Second, we showed that virus that was passed exclusively in suckling mouse brains was highly virulent and caused a uniformly fatal encephalitis in adult mice. The surface glycoprotein is a major virulence factor in most coronavirus infections. We identified three changes in the HCoV-OC43 surface glycoprotein that correlated with enhanced neurovirulence in mice; these were located in the domain of the protein responsible for binding to host cells. These data suggest that some coronaviruses, including HCoV-OC43 and SARS-CoV, readily adapt to growth in cells from heterologous species. This adaptability has facilitated the isolation of HCoV-OC43 viral variants with markedly differing abilities to infect animals and tissue culture cells. url: https://www.ncbi.nlm.nih.gov/pubmed/16413043/ doi: 10.1016/j.virol.2005.11.044 id: cord-324321-y96x8x3h author: Cai, Yingyun title: Down-regulation of transcription of the proapoptotic gene BNip3 in cultured astrocytes by murine coronavirus infection date: 2003-11-10 words: 8454.0 sentences: 416.0 pages: flesch: 49.0 cache: ./cache/cord-324321-y96x8x3h.txt txt: ./txt/cord-324321-y96x8x3h.txt summary: Furthermore, treatment of cells with chloroquine, which blocks the acidification of endosomes, significantly inhibited the repression of the BNip3 promoter activity induced by the acidic pH-dependent MHV mutant OBLV60, which enters cells via endocytosis, indicating that the down-regulation of BNip3 expression is mediated by fusion between viral envelope and cell membranes during entry. To establish further the specificity of the down-regulation of BNip3 gene expression, we used vesicular stomatitis virus (VSV) in a parallel experiment, because VSV is also an enveloped RNA virus whose infection has a broad host cell range and is mediated by the interaction between the envelope G protein and cell membranes (Riedel et al., 1984) . By extrapolating the data from the mutant virus, we can envision that fusion between viral envelope and plasma/endosomal membranes during wild-type MHV infection is involved in the down-regulation of BNip3 gene expression. abstract: Murine coronavirus mouse hepatitis virus (MHV) causes encephalitis and demyelination in the central nervous system of susceptible rodents. Astrocytes are the major target for MHV persistence. However, the mechanisms by which astrocytes survive MHV infection and permit viral persistence are not known. Here we performed DNA microarray analysis on differential gene expression in astrocyte DBT cells by MHV infection and found that the mRNA of the proapoptotic gene BNip3 was significantly decreased following MHV infection. This finding was further confirmed by quantitative reverse transcription–polymerase chain reaction, Western blot analysis, and BNip3-promoter-luciferase reporter system. Interestingly, infection with live and ultraviolet light-inactivated viruses equally repressed BNip3 expression, indicating that the down-regulation of BNip3 expression does not require virus replication and is mediated during cell entry. Furthermore, treatment of cells with chloroquine, which blocks the acidification of endosomes, significantly inhibited the repression of the BNip3 promoter activity induced by the acidic pH-dependent MHV mutant OBLV60, which enters cells via endocytosis, indicating that the down-regulation of BNip3 expression is mediated by fusion between viral envelope and cell membranes during entry. Deletion analysis showed that the sequence between nucleotides 262 and 550 of the 588-base-pair BNip3 promoter is necessary and sufficient for driving the BNip3 expression and that it contains signals that are responsible for MHV-induced down-regulation of BNip3 expression in DBT cells. These results may provide insights into the mechanisms by which MHV evades host antiviral defense and promotes cell survival, thereby allowing its persistence in the host astrocytes. url: https://www.ncbi.nlm.nih.gov/pubmed/14599795/ doi: 10.1016/j.virol.2003.07.007 id: cord-279346-7del8d2p author: Callendret, Benoît title: Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS date: 2007-07-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The SARS-CoV spike glycoprotein (S) is the main target of the protective immune response in humans and animal models of SARS. Here, we demonstrated that efficient expression of S from the wild-type spike gene in cultured cells required the use of improved plasmid vectors containing donor and acceptor splice sites, as well as heterologous viral RNA export elements, such as the CTE of Mazon-Pfizer monkey virus or the PRE of Woodchuck hepatitis virus (WPRE). The presence of both splice sites and WPRE markedly improved the immunogenicity of S-based DNA vaccines against SARS. Upon immunization of mice with low doses (2 μg) of naked DNA, only intron and WPRE-containing vectors could induce neutralizing anti-S antibodies and provide protection against challenge with SARS-CoV. Our observations are likely to be useful for the construction of plasmid and viral vectors designed for optimal expression of intronless genes derived from cytoplasmic RNA viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/17331558/ doi: 10.1016/j.virol.2007.01.012 id: cord-325423-d212h4bp author: Carrion, Ricardo title: A small nonhuman primate model for filovirus-induced disease date: 2011-11-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Ebolavirus and Marburgvirus are members of the filovirus family and induce a fatal hemorrhagic disease in humans and nonhuman primates with 90% case fatality. To develop a small nonhuman primate model for filovirus disease, common marmosets (Callithrix jacchus) were intramuscularly inoculated with wild type Marburgvirus Musoke or Ebolavirus Zaire. The infection resulted in a systemic fatal disease with clinical and morphological features closely resembling human infection. Animals experienced weight loss, fever, high virus titers in tissue, thrombocytopenia, neutrophilia, high liver transaminases and phosphatases and disseminated intravascular coagulation. Evidence of a severe disseminated viral infection characterized principally by multifocal to coalescing hepatic necrosis was seen in EBOV animals. MARV-infected animals displayed only moderate fibrin deposition in the spleen. Lymphoid necrosis and lymphocytic depletion observed in spleen. These findings provide support for the use of the common marmoset as a small nonhuman primate model for filovirus induced hemorrhagic fever. url: https://www.sciencedirect.com/science/article/pii/S0042682211003965 doi: 10.1016/j.virol.2011.08.022 id: cord-272925-xag1yaie author: Carter, Gemma C. title: HIV entry in macrophages is dependent on intact lipid rafts date: 2009-03-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Macrophages are an important natural target cell for HIV-1, but previous studies of virus entry into these cells are limited, and the involvement of membrane cholesterol and lipid rafts is unknown. Cholesterol disruption of macrophage membranes using four pharmacological agents acting by different mechanisms: methyl-β cyclodextrin, nystatin, filipin complex and Lovastatin, all significantly inhibited productive HIV entry and reverse transcription. The inhibitory effects of these drugs resulted in decreased virus release from infected cells, and could be substantially reversed by the addition of water-soluble cholesterol. The virus bound equally to cholesterol-disrupted cells even though HIV receptor expression levels were significantly reduced. Macrophage CD4 and CCR5 were found to partition with the detergent-resistant membranes with a typical raft-associating protein flotillin-1. HIV particles were observed co-localising with a marker of lipid rafts (CTB-FITC) early post infection. These data suggest that macrophage membrane cholesterol is essential for HIV entry, and implicate lipid raft involvement. url: https://www.sciencedirect.com/science/article/pii/S0042682208008556 doi: 10.1016/j.virol.2008.12.031 id: cord-296075-8axbkyyz author: Castro, Raymond F. title: Differential Antigen Recognition by T Cells from the Spleen and Central Nervous System of Coronavirus-Infected Mice date: 1996-08-01 words: 1733.0 sentences: 88.0 pages: flesch: 53.0 cache: ./cache/cord-296075-8axbkyyz.txt txt: ./txt/cord-296075-8axbkyyz.txt summary: Abstract CD8+cytotoxic T lymphocytes (CTLs) isolated from the central nervous system (CNS) of C57Bl/6 mice acutely infected with mouse hepatitis virus, strain JHM (MHV-JHM), and analyzed in a directex vivocytotoxicity assay recognize two epitopes (H-2Dband H-2Kb-restricted encompassing amino acids 510–518 and 598–605, respectively) within the surface (S) glycoprotein. In this report, the preferential recognition of the H-2Db-restricted epitope is confirmed using splenocytes stimulatedin vitrowith either MHV-JHM-infected MC57 cells or with a cell line expressing the S protein and analyzed in secondary CTL assays. To determine whether these results represent a difference in epitope recognition between the spleen and CNS, secondary CTL assays were performed using spleen cells coated with peptides encompassing the CTL epitopes as stimulators. These assays using peptide-coated splenocytes as stimulators revealed comparable CTL precursor/effector frequencies for the H-2K b -(average 1/1291, range 1/927-1/1542 spleen cells) and H-2D b -restricted (average 1/987, range 1/380-1/1323 spleen cells) epitopes in these mice. abstract: Abstract CD8+cytotoxic T lymphocytes (CTLs) isolated from the central nervous system (CNS) of C57Bl/6 mice acutely infected with mouse hepatitis virus, strain JHM (MHV-JHM), and analyzed in a directex vivocytotoxicity assay recognize two epitopes (H-2Db- and H-2Kb-restricted encompassing amino acids 510–518 and 598–605, respectively) within the surface (S) glycoprotein. In contrast, CD8+T cells isolated from the spleens of mice inoculated intraperitoneally with MHV-JHM and restimulatedin vitroonly respond to the H-2Db-restricted epitope. In this report, the preferential recognition of the H-2Db-restricted epitope is confirmed using splenocytes stimulatedin vitrowith either MHV-JHM-infected MC57 cells or with a cell line expressing the S protein and analyzed in secondary CTL assays. To determine whether these results represent a difference in epitope recognition between the spleen and CNS, secondary CTL assays were performed using spleen cells coated with peptides encompassing the CTL epitopes as stimulators. Under these conditions, both epitopes sensitized cells for lysis by spleen-derived CTLs, suggesting that both epitopes were recognized by splenic CD8+T cells after infectionin vivo.Furthermore, limiting dilution analysis indicated that the precursor frequency of splenic CD8+T cells specific for both the H-2Kb- and H-2Db-restricted epitopes were not significantly different. Thus, the results suggest thatin vitrostimulation of splenocytes specific for the H-2Kb-restricted epitope is inefficient after endogenous processing but that this inefficiency can be corrected if peptide is provided exogenously at sufficiently high concentrations. As a consequence, the results also show that cells responsive to both of the previously identified CNS-derived CD8+T cell epitopes are present in the infected spleen at nearly the same frequency. url: https://www.sciencedirect.com/science/article/pii/S0042682296904158 doi: 10.1006/viro.1996.0415 id: cord-346514-vyo8l14p author: Chen, I-Hsuan title: Characterization of the polyadenylation activity in a replicase complex from Bamboo mosaic virus-infected Nicotiana benthamiana plants date: 2013-06-13 words: 5141.0 sentences: 304.0 pages: flesch: 60.0 cache: ./cache/cord-346514-vyo8l14p.txt txt: ./txt/cord-346514-vyo8l14p.txt summary: The polyadenylation signal in the 3′ UTR of BaMV was shown to be involved in the synthesis of minus-strand viral RNA and regulating the length of the poly(A) tail (Chen et al., 2005) . To test whether the replicase preparation could polyadenylate exogenous plus-strand RNA templates, 5′ end-labeled radioactive BaMV plus-strand RNA substrate containing the entire 3′-UTR and 7, 15, or 40 adenylates (r138/7A, r138/15A, or r138/40A, respectively), were subjected to the polyadenylation activity assay. BaMV minigenomes were demonstrated to be suitable templates for an in vitro replication assays (Huang et al., 2009) ; therefore, the exogenous plus-strand or minus-strand BaMV minigenome was added to the reaction to help determine whether the poly(A) tail could be added to the 3′ end of preformed or newly transcribed plus-strand RNA, respectively. abstract: Bamboo mosaic virus (BaMV) has a positive-sense single-stranded RNA genome with a 5′ cap and a 3′ poly(A) tail. To characterize polyadenylation activity in the BaMV replicase complex, we performed the in vitro polyadenylation with various BaMV templates. We conducted a polyadenylation activity assay for BaMV RNA by using a partially purified BaMV replicase complex. The results showed that approximately 200 adenylates at the 3′ end of the RNA were generated on the endogenous RNA templates. Specific fractions derived from uninfected Nicotiana benthamiana plants enhanced the polyadenylation activity, implying that host factors are involved in polyadenylation. Furthermore, polyadenylation can be detected in newly synthesized plus-strand RNA in vitro when using the exogenous BaMV minus-strand minigenome. For polyadenylation on the exogenous plus-strand minigenome, the 3′ end requires at least 4A to reach 22% polyadenylation activity. The results indicate that the BaMV replicase complex recognizes the 3′ end of BaMV for polyadenylation. url: https://www.sciencedirect.com/science/article/pii/S0042682213003139 doi: 10.1016/j.virol.2013.05.032 id: cord-318400-l9kwxsq7 author: Chhabra, Rajesh title: Pathogenicity and tissue tropism of infectious bronchitis virus is associated with elevated apoptosis and innate immune responses date: 2016-01-15 words: 5153.0 sentences: 287.0 pages: flesch: 53.0 cache: ./cache/cord-318400-l9kwxsq7.txt txt: ./txt/cord-318400-l9kwxsq7.txt summary: To establish a characteristic host response to predict the pathogenicity and tissue tropism of infectious bronchitis viruses (IBV), we investigated innate immune responses (IIR) and apoptosis in chicken embryo kidney cells (CEKC) and tracheal organ cultures (TOC) infected with three IBV strains. In contrast, M41 infection caused greater expression of these genes than 885 or QX in TOCs. In summary, greater levels of apoptosis and elevated levels of TLR3, MDA5 and IFN-β expression are associated with increased pathogenicity of IBV strains in renal and tracheal tissues. In order to establish the characteristic host response to predict the tissue tropism and pathogenicity of IBVs, we investigated apoptosis and innate immune responses in chicken embryo kidney (CEK) cells and tracheal organ cultures (TOCs) following infection with IS/885/00-like, QX-like and M41 IBV strains. Nephropathogenic IBV strains 885 and QX resulted in significantly greater up-regulation of innate immune sensing genes namely TLR3 and MDA5 along with greater IFN-β mRNA levels in CEK cells at 9 h of infection when compared to M41 infection. abstract: To establish a characteristic host response to predict the pathogenicity and tissue tropism of infectious bronchitis viruses (IBV), we investigated innate immune responses (IIR) and apoptosis in chicken embryo kidney cells (CEKC) and tracheal organ cultures (TOC) infected with three IBV strains. Results showed nephropathogenic IBV strains 885 and QX induced greater apoptosis in CEKC than M41, which induced greater apoptosis in TOCs compared to 885 and QX. Elevated IIR is associated with tissue tropism of different IBV strains. Compared to M41, 885 and QX caused greater induction of toll like receptor 3 (TLR3), melanoma differentiation associated protein 5 (MDA5) and interferon beta (IFN-β) in CEKC. In contrast, M41 infection caused greater expression of these genes than 885 or QX in TOCs. In summary, greater levels of apoptosis and elevated levels of TLR3, MDA5 and IFN-β expression are associated with increased pathogenicity of IBV strains in renal and tracheal tissues. url: https://www.ncbi.nlm.nih.gov/pubmed/26655241/ doi: 10.1016/j.virol.2015.11.011 id: cord-351197-xv6ymc4l author: Cibulski, Samuel title: A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil date: 2020-09-28 words: 1711.0 sentences: 124.0 pages: flesch: 54.0 cache: ./cache/cord-351197-xv6ymc4l.txt txt: ./txt/cord-351197-xv6ymc4l.txt summary: From chicken, six distinct gyroviruses (GyV) were detected, including GyV3 and GyV6, which for the first time were detected in samples from avian species, plus a novel smacovirus species and two highly divergent circular Rep-encoding ssDNA (CRESS-DNA) viruses. A detailed taxonomic 136 classification, including the numbers of reads for each Eukarya-related viral contig 137 recovered is this study, is provided in Supplementary gives them the ability to persist and spread in the environment. A detailed taxonomic classification, including the numbers of 245 J o u r n a l P r e -p r o o f sequenced reads of each Eukarya-related viral contig recovered in this study, is 246 provided in Supplementary Table 1 . including numbers of sequenced reads of each Eukarya-related viral contig recovered in 334 this study, is provided in Supplementary Table 1 . Cressdnaviricota: a virus phylum unifying 7 families of Rep-encoding 519 viruses with single-stranded, circular DNA genomes abstract: A viral metagenomics study was conducted in beef, pork, and chicken sold in supermarkets from Southern Brazil. From chicken, six distinct gyroviruses (GyV) were detected, including GyV3 and GyV6, which for the first time were detected in samples from avian species, plus a novel smacovirus species and two highly divergent circular Rep-encoding ssDNA (CRESS-DNA) viruses. From pork, genomes of numerous anelloviruses, porcine parvovirus 5 (PPV5) and 6 (PPV6), two new genomoviruses and two new CRESS-DNA viruses were found. Finally, two new CRESS-DNA genomes were recovered from beef. Although none of these viruses have history of transmission to humans, the findings reported here reveal that such agents are inevitably consumed in diets that include these types of meat. url: https://www.ncbi.nlm.nih.gov/pubmed/33032031/ doi: 10.1016/j.virol.2020.09.005 id: cord-285869-jwflooop author: Clementz, Mark A. title: Mutation in murine coronavirus replication protein nsp4 alters assembly of double membrane vesicles date: 2008-05-01 words: 6966.0 sentences: 380.0 pages: flesch: 56.0 cache: ./cache/cord-285869-jwflooop.txt txt: ./txt/cord-285869-jwflooop.txt summary: Here, we studied the role of a putative replicase anchor, nonstructural protein 4 (nsp4), in the assembly of murine coronavirus DMVs. We used reverse genetics to generate infectious clone viruses (icv) with an alanine substitution at nsp4 glycosylation site N176 or N237, or an asparagine to threonine substitution (nsp4-N258T), which is proposed to confer a temperature sensitive phenotype. Coronaviruses, such as mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SARS-CoV) that causes severe respiratory illness in humans (Peiris et al., 2004; Stadler et al., 2003) , generate double membrane vesicles (DMVs), which are the sites of viral RNA synthesis (Baker and Denison, 2008; Goldsmith et al., 2004; Gosert et al., 2002; Snijder et al., 2006) . However, at the non-permissive temperature, DMV assembly and mitochondria morphology are disrupted in Alb ts6 icv-infected cells and viral replicase proteins partially localize with mitochondria. abstract: Coronaviruses are positive-strand RNA viruses that replicate in the cytoplasm of infected cells by generating a membrane-associated replicase complex. The replicase complex assembles on double membrane vesicles (DMVs). Here, we studied the role of a putative replicase anchor, nonstructural protein 4 (nsp4), in the assembly of murine coronavirus DMVs. We used reverse genetics to generate infectious clone viruses (icv) with an alanine substitution at nsp4 glycosylation site N176 or N237, or an asparagine to threonine substitution (nsp4-N258T), which is proposed to confer a temperature sensitive phenotype. We found that nsp4-N237A is lethal and nsp4-N258T generated a virus (designated Alb ts6 icv) that is temperature sensitive for viral replication. Analysis of Alb ts6 icv-infected cells revealed that there was a dramatic reduction in DMVs and that both nsp4 and nsp3 partially localized to mitochondria when cells were incubated at the non-permissive temperature. These results reveal a critical role of nsp4 in directing coronavirus DMV assembly. url: https://api.elsevier.com/content/article/pii/S0042682208000378 doi: 10.1016/j.virol.2008.01.018 id: cord-302486-z36hcvrx author: Cobo, Fernando title: Diagnostic approaches for viruses and prions in stem cell banks date: 2006-03-30 words: 7276.0 sentences: 347.0 pages: flesch: 41.0 cache: ./cache/cord-302486-z36hcvrx.txt txt: ./txt/cord-302486-z36hcvrx.txt summary: Viral and prion contamination of cell cultures and "feeder" cells, which is a common risk in all biotechnological products derived from the cell lines, is the most challenging and potentially serious outcome to address, due to the difficulty involved in virus and prion detection and the potential to cause serious disease in recipients of these cell products. The use of bovine fetal serum in stem cell cultures requires an urgent need for a risk assessment for Transmissible Spongiform Encephalopathies (TSEs) by means of a sensitive and specific test in all products derived from ruminants (U.S. Food and Drugs Administration, 1999; Directive 2004/C 24/ 03). This panel of tests should necessarily include reverse transcriptase detection as a general test for retroviruses, electron microscopy that can detect different kinds of viral particles and characterize many unknown isolates present in cell cultures and molecular techniques like PCR (conventional or real-time) and RT-PCR tests to include all the viruses that we know pose a risk to the product. abstract: Some stem cell lines may contain an endogenous virus or can be contaminated with exogenous viruses (even of animal origin) and may secrete viral particles or express viral antigens on their surface. Moreover, certain biotechnological products (e.g. bovine fetal serum, murine feeder cells) may contain prion particles. Viral and prion contamination of cell cultures and “feeder” cells, which is a common risk in all biotechnological products derived from the cell lines, is the most challenging and potentially serious outcome to address, due to the difficulty involved in virus and prion detection and the potential to cause serious disease in recipients of these cell products. Stem cell banks should introduce adequate quality assurance programs like the microbiological control program and can provide researchers with valuable support in the standardization and safety of procedures and protocols used for the viral and prion testing and in validation programs to assure the quality and safety of the cells. url: https://api.elsevier.com/content/article/pii/S0042682205007725 doi: 10.1016/j.virol.2005.11.026 id: cord-260177-xu0elmak author: Collins, Arlene R. title: Monoclonal antibodies to murine hepatitis virus-4 (strain JHM) define the viral glycoprotein responsible for attachment and cell-cell fusion date: 1982-06-30 words: 4156.0 sentences: 232.0 pages: flesch: 46.0 cache: ./cache/cord-260177-xu0elmak.txt txt: ./txt/cord-260177-xu0elmak.txt summary: title: Monoclonal antibodies to murine hepatitis virus-4 (strain JHM) define the viral glycoprotein responsible for attachment and cell-cell fusion Abstract Hybridoma cell lines producing monoclonal antibodies to the JHM strain of mouse hepatitis virus-4 (MHV-4) were established. A third set of monoclonal antibodies reacted both in the cytoplasm and on the surface of infected cells and precipitated the 25,000d viral glycoprotein (GP-5) and its precursor VP-6 (23,000d). MHV-4 polypeptide specificities of monoclonal antibodies were determined by immune precipitation of [35S]methionine-labeled viral proteins from infected L-241 cells. Only incubation with monoclonal antibodies to GP-1 resulted in inhibition in plaque and syncytium number (Fig. 5) , indicating involvement of that polypeptide in cell to cell spread of infection by fusion. When we examined our collection of monoclonal antibodies for the ability to inhibit spread of infection, only anti-GP-1 was effective, suggesting that the virion peplomer contains the active site for cell-cell co % fusion. abstract: Abstract Hybridoma cell lines producing monoclonal antibodies to the JHM strain of mouse hepatitis virus-4 (MHV-4) were established. By indirect immunofluorescence and immune precipitation, monoclonal antibodies of three viral polypeptide specificities were characterized. Monoclonal antibodies to nucleocapsid reacted in the cytoplasm of infected cells and precipitated the 60,000d nucleocapsid polypeptide (VP-4) of MHV-4. Other monoclonal antibodies reacted both in the cytoplasm and on the surface of infected cells and were found to precipitate the 170,000d viral glycoprotein (GP-1). A third set of monoclonal antibodies reacted both in the cytoplasm and on the surface of infected cells and precipitated the 25,000d viral glycoprotein (GP-5) and its precursor VP-6 (23,000d). AntiGP-1 alone had direct neutralizing activity for MHV-4 virus, while in the presence of complement both anti-GP-1 and anti-GP-5 neutralized virus. Only anti-GP-1 had the ability to inhibit the spread of infection due to fusion in L241 cells. Thus, the viral glycoprotein GP-1 likely contains both the attachment and fusion activities of MHV-4. url: https://api.elsevier.com/content/article/pii/0042682282900952 doi: 10.1016/0042-6822(82)90095-2 id: cord-300470-vgd1ol2z author: Conradie, Andelé M. title: Establishment of different plasmid only-based reverse genetics systems for the recovery of African horse sickness virus date: 2016-09-19 words: 7888.0 sentences: 366.0 pages: flesch: 46.0 cache: ./cache/cord-300470-vgd1ol2z.txt txt: ./txt/cord-300470-vgd1ol2z.txt summary: In both of the above reverse genetics systems, recovery of infectious AHSV-4 from plasmid DNA relies on the expression of T7 RNA polymerase within cells transfected with the AHSV-4 cDNA plasmids. The initial AHSV-4 reverse genetics system developed here consists of 10 plasmids, each containing a full-length cDNA copy of single AHSV-4 genome segments flanked by T7 RNA polymerase promoter and HDV ribozyme sequences. However, the same reassortant virus was also recovered successfully by combining the four AHSV-4 dual vectors with two single reverse genetics plasmids, which contained cDNA copies of the S5 and S6 genome segments, respectively. To this end, we have cloned a T7 RNA polymerase expression cassette onto the genetic backbone of the pJAD-S2-S6 dual reverse vector and subsequently demonstrated that AHSV-4 could be recovered in BSR and L929 cells following transfection of the cells with the modified 5-plasmid set. abstract: In an effort to simplify and expand the utility of African horse sickness virus (AHSV) reverse genetics, different plasmid-based reverse genetics systems were developed. Plasmids containing cDNAs corresponding to each of the full-length double-stranded RNA genome segments of AHSV-4 under control of a T7 RNA polymerase promoter were co-transfected in cells expressing T7 RNA polymerase, and infectious AHSV-4 was recovered. This reverse genetics system was improved by reducing the required plasmids from 10 to five and resulted in enhanced virus recovery. Subsequently, a T7 RNA polymerase expression cassette was incorporated into one of the AHSV-4 rescue plasmids. This modified 5-plasmid set enabled virus recovery in BSR or L929 cells, thus offering the possibility to generate AHSV-4 in any cell line. Moreover, mutant and cross-serotype reassortant viruses were recovered. These plasmid DNA-based reverse genetics systems thus offer new possibilities for investigating AHSV biology and development of designer AHSV vaccine strains. url: https://doi.org/10.1016/j.virol.2016.07.010 doi: 10.1016/j.virol.2016.07.010 id: cord-329245-6tj2k1yn author: Corse, Emily title: The cytoplasmic tails of infectious bronchitis virus E and M proteins mediate their interaction date: 2003-07-20 words: 7414.0 sentences: 327.0 pages: flesch: 56.0 cache: ./cache/cord-329245-6tj2k1yn.txt txt: ./txt/cord-329245-6tj2k1yn.txt summary: Indeed, it has been shown that both the MHV E and the infectious bronchitis virus (IBV) E proteins are sufficient for formation of the virus-like particles (VLPs) described above (Corse and Machamer, 2000; Maeda et al., 1999) , although the efficiency probably varies with cell type and protein expression system. (B) IBV-infected Vero cells were labeled with [ 35 S]methionine-cysteine at 45 h postinfection, treated with DSP as indicated, lysed, and immunoprecipitated with anti-E or anti-M antibodies as described under Materials and methods. The E and M proteins of several coronaviruses are released from cotransfected cells in membrane-bound particles that are morphologically similar to virions (VLPs), suggesting that interactions between these proteins are an integral part of coronavirus assembly (Baudoux et al., 1998; Corse and Machamer, 2000; Godeke et al., 2000; Vennema et al., 1996) . abstract: Abstract Virus-like particle (VLP) formation by the coronavirus E and M proteins suggests that interactions between these proteins play a critical role in coronavirus assembly. We studied interactions between the infectious bronchitis virus (IBV) E and M proteins using in vivo crosslinking and VLP assembly assays. We show that IBV E and M can be crosslinked to each other in IBV-infected and transfected cells, indicating that they interact. The cytoplasmic tails of both proteins are important for this interaction. We also examined the ability of the mutant and chimeric E and M proteins to form VLPs. IBV M proteins that are missing portions of their cytoplasmic tails or transmembrane regions were not able to support VLP formation, regardless of their ability to be crosslinked to IBV E. Interactions between the E and M proteins and the membrane bilayer are likely to play an important role in VLP formation and virus budding. url: https://www.sciencedirect.com/science/article/pii/S0042682203001752 doi: 10.1016/s0042-6822(03)00175-2 id: cord-321265-il9vbbgk author: DEN BOON, JOHAN A. title: Equine Arteritis Virus Subgenomic RNA Transcription: UV Inactivation and Translation Inhibition Studies date: 1995-11-30 words: 3721.0 sentences: 222.0 pages: flesch: 56.0 cache: ./cache/cord-321265-il9vbbgk.txt txt: ./txt/cord-321265-il9vbbgk.txt summary: In general, MHV transcription was extremely sensitive to translation inhibition, whereas EAV genomic RNA synthesis became independent ofde novoprotein synthesis late in infection. The replication of SIN involves the synthesis of a EAV-infected BHK-21 cells were UV-irradiated at 6 1 2 hr single 4.1-kb sg RNA (26S) from a well-defined internal promoter on the genome-sized minus-strand template p.i., when RNA synthesis approaches its maximum (van RNA (Ou et al., 1982; Levis et al., 1990) . The UV transcription mapping data showed that the Third, the overall MHV transcription was significantly EAV sg RNAs were not produced by processing of a more dependent on de novo protein synthesis than that genome-length precursor RNA. Protein synthesis was inhibited by the addition of cycloheximide to EAV-infected BHK-21 cells at fully independent transcription system the slopes of the curves in Fig. 2B , which reflect the UV target sizes, should different time points after infection. abstract: Abstract The expression of the genetic information of equine arteritis virus (EAV), an arterivirus, involves the synthesis of six subgenomic (sg) mRNAs. These are 5′ and 3′ coterminal since they are composed of a leader and a body sequence, which are identical to the 5′ and 3′ ends of the genome, respectively. Previously, it has been suggested thatcis-splicing of a genome-length precursor RNA is involved in their synthesis. This was reevaluated in a comparative analysis of the sg RNA synthesis of EAV, the coronavirus mouse hepatitis virus (MHV), and the alphavirus Sindbis virus. UV transcription mapping showed that the majority of the EAV sg RNAs made at later stages of infection is not derived from a genome-length precursor. However, complete independence of sg RNA synthesis from that of genomic RNA was never observed during the course of infection. The possibility that this resulted from UV irradiation-induced effects on the synthesis of the viral replicase was investigated by inhibiting translation using cycloheximide. For EAV, ongoing protein synthesis was found to be more important for the synthesis of sg RNA than for that of genomic RNA. In general, MHV transcription was extremely sensitive to translation inhibition, whereas EAV genomic RNA synthesis became independent ofde novoprotein synthesis late in infection. url: https://api.elsevier.com/content/article/pii/S0042682285700098 doi: 10.1006/viro.1995.0009 id: cord-317333-unrd76bo author: Danesh, Ali title: Early gene expression events in ferrets in response to SARS coronavirus infection versus direct interferon-alpha2b stimulation date: 2011-01-05 words: 5467.0 sentences: 278.0 pages: flesch: 48.0 cache: ./cache/cord-317333-unrd76bo.txt txt: ./txt/cord-317333-unrd76bo.txt summary: Evaluation of gene expression patterns in PBMCs and lung necropsies of SARS-CoV-infected ferrets led us to the identification of 7 upregulated IRGs that also were upregulated in response to IFN-α2b injection. Since STAT1 was phosphorylated following SARS-CoV infection and IFN-α2b injection, we investigated select IRG expression by qRT-PCR following in vitro stimulation of ferret peripheral whole blood with IFN-α2b. These gene expression and STAT1 phosphorylation findings suggested that robust IFN responses were activated following SARS-CoV infection 2 days post-infection. The comparison of microarray results between the lung tissue of IFN-α2b and SARS-CoV ferrets at day 1 revealed commonalities in the expression patterns of most IRGs. STAT1, MX1, OAS1, OAS2, ISG15, IFI44, IFI44L and EIF2AK2 were among the overlapping genes (Fig. 3B ). Analysis of the IFN signaling canonical pathway showed the upregulation of STAT1, MX1, OAS1, OAS2, ISG15 and IFI44 in lung necropsies of IFN-α2b injected and SARS-CoV infected ferrets (Fig. 4) . abstract: Type I interferons (IFNs) are essential to the clearance of viral diseases, however, a clear distinction between genes upregulated by direct virus–cell interactions and genes upregulated by secondary IFN production has not been made. Here, we investigated differential gene regulation in ferrets upon subcutaneous administration of IFN-α2b and during SARS-CoV infection. In vivo experiments revealed that IFN-α2b causes STAT1 phosphorylation and upregulation of abundant IFN response genes (IRGs), chemokine receptors, and other genes that participate in phagocytosis and leukocyte transendothelial migration. During infection with SARS-CoV not only a variety of IRGs were upregulated, but also a significantly broader range of genes involved in cell migration and inflammation. This work allowed dissection of several molecular signatures present during SARS-CoV which are part of a robust IFN antiviral response. These signatures can be useful markers to evaluate the status of IFN responses during a viral infection and specific features of different viruses. url: https://www.sciencedirect.com/science/article/pii/S0042682210006380 doi: 10.1016/j.virol.2010.10.002 id: cord-293248-8vtd9e4n author: Day, J. Michael title: Determination and analysis of the full-length chicken parvovirus genome date: 2010-03-30 words: 3045.0 sentences: 153.0 pages: flesch: 50.0 cache: ./cache/cord-293248-8vtd9e4n.txt txt: ./txt/cord-293248-8vtd9e4n.txt summary: Through the application of a molecular screening method targeting particle-associated nucleic acid (PAN), we recently described the detection and partial characterization of a novel enteric parvovirus in chickens. Initial analysis of this chicken-origin parvovirus (ChPV) revealed that it is a novel member of the Parvovirinae subfamily within the Parvoviridae, and led to the development of a specific molecular diagnostic test targeting the ChPV non-structural (NS) gene (Zsak et al., 2009) . Parvoviruses have been previously described in chickens based upon their morphology via electron microscopy and upon their genome size Kisary et al., 1984) , and enteric disease signs have been attributed to parvovirus-like particles detected in turkey intestinal tracts (Trampel et al., 1983) . The analysis includes comparisons to other members of the Parvovirinae that infect mammals and birds, including two novel turkey-origin parvoviruses (TuPV) recently sequenced using a similar molecular approach. abstract: Viral enteric disease in poultry is an ongoing problem in many parts of the world. Many enteric viruses have been identified in turkeys and chickens, including avian astroviruses, rotaviruses, reoviruses, and coronaviruses. Through the application of a molecular screening method targeting particle-associated nucleic acid (PAN), we recently described the detection and partial characterization of a novel enteric parvovirus in chickens. Subsequent surveys of intestinal homogenates from turkeys and chickens in the United States revealed widespread occurrence of parvovirus in poultry. Here we report the first full genome sequence of a novel chicken parvovirus, ChPV ABU-P1. ChPV ABU-P1 genome organization, predicted amino acid sequence, and phylogenetic relationships with other described parvoviruses are discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/20097398/ doi: 10.1016/j.virol.2009.12.027 id: cord-274673-tjzlssal author: De Groot, Raoul J. title: Stably expressed FIPV peplomer protein induces cell fusion and elicits neutralizing antibodies in mice date: 1989-08-31 words: 5111.0 sentences: 295.0 pages: flesch: 57.0 cache: ./cache/cord-274673-tjzlssal.txt txt: ./txt/cord-274673-tjzlssal.txt summary: authors: De Groot, Raoul J.; Van Leen, Robert W.; Dalderup, Mieke J.M.; Vennema, Harry; Horzinek, Marian C.; Spaan, Willy J.M. title: Stably expressed FIPV peplomer protein induces cell fusion and elicits neutralizing antibodies in mice Abstract We have established bovine papilloma virus (BPV)-transformed mouse C127 cell lines that synthesize the peplomer protein of the feline infectious peritonitis virus (FIPV) strain 79-1146. Mice immunized with whole lysates of the transformed cells produced FIPV-neutralizing antibodies as shown by plaque reduction. Mammalian cell lines expressing the FIPV peplomer gene would provide a convenient source of protein to dissect the role of E2 in FIP. It is shown that the expression product induces fusion of FIPV-permissive feline cells and is immunogenic in mice. (b) Glyoxal-denatured RNA extracted from noninduced (lane 2) and heat-shock-induced (lane 3) RM(-)I 7 cells was separated on 0.8% agarose gels, transferred to a nylon membrane, and hybridized to a nick-translated 4.5-kbBamHl fragment containing the complete FIPV E2 gene. abstract: Abstract We have established bovine papilloma virus (BPV)-transformed mouse C127 cell lines that synthesize the peplomer protein of the feline infectious peritonitis virus (FIPV) strain 79-1146. For this purpose, a new cassette expression vector pHSL, which carries the Drosophila HSp70 promotor and the polyadenylation signal of the Moloney murine leukemia virus long terminal repeat, was constructed. Cocultivation of the BPV-transformed cell lines with FIPV-permissive feline fcwf-D cells resulted in polykaryocyte formation. Since it depended on the presence of fcwf-D cells, binding of E2 to the cell receptor may be required for membrane fusion. E2 was synthesized as a core-glycosylated protein of 180K which was only slowly transported from the endoplasmic reticulum to the medial Golgi: of the E2-molecules labeled during a 1-hr pulse about half was still completely sensitive to endoglycosidase H after a 2-hr chase, while the remaining E2 had been chased into multiple, partially endoglycosidase H-resistant forms. Immunofluorescence studies also indicated that most E2 was retained intracellularly. Mice immunized with whole lysates of the transformed cells produced FIPV-neutralizing antibodies as shown by plaque reduction. url: https://www.ncbi.nlm.nih.gov/pubmed/2548329/ doi: 10.1016/0042-6822(89)90619-3 id: cord-305564-dj3vj4tk author: DeDiego, Marta L. title: PATHOGENICITY OF SEVERE ACUTE RESPIRATORY CORONAVIRUS DELETION MUTANTS IN hACE-2 TRANSGENIC MICE date: 2008-07-01 words: 6065.0 sentences: 287.0 pages: flesch: 53.0 cache: ./cache/cord-305564-dj3vj4tk.txt txt: ./txt/cord-305564-dj3vj4tk.txt summary: All these viruses were rescued in monkey (Vero E6) cells and were also infectious for human (Huh-7, Huh7.5.1 and CaCo-2) cell lines and for transgenic (Tg) mice expressing the SARS-CoV receptor human angiotensin converting enzyme-2 (hACE-2), indicating that none of these proteins is essential for the viral cycle. These data indicate that E gene might be a virulence factor influencing replication level, tissue tropism and pathogenicity of SARS-CoV, suggesting that ΔE attenuated viruses are promising vaccine candidates. In contrast, rSARS-CoV-Δ[6-9b] virus was detected at high titers in the brains of infected hACE2 Tg mice suggesting that the E protein is important for virus replication and dissemination within this tissue. Discovery of novel human and animal cells infected by the severe acute respiratory syndrome coronavirus by replication-specific multiplex reverse transcription-PCR abstract: Recombinant severe acute respiratory virus (SARS-CoV) variants lacking the group specific genes 6, 7a, 7b, 8a, 8b and 9b (rSARS-CoV-Δ[6-9b]), the structural gene E (rSARS-CoV-ΔE), and a combination of both sets of genes (rSARS-CoV-Δ[E,6-9b]) have been generated. All these viruses were rescued in monkey (Vero E6) cells and were also infectious for human (Huh-7, Huh7.5.1 and CaCo-2) cell lines and for transgenic (Tg) mice expressing the SARS-CoV receptor human angiotensin converting enzyme-2 (hACE-2), indicating that none of these proteins is essential for the viral cycle. Furthermore, in Vero E6 cells, all the viruses showed the formation of particles with the same morphology as the wt virus, indicating that these proteins do not have a high impact in the final morphology of the virions. Nevertheless, in the absence of E protein, release of virus particles efficacy was reduced. Viruses lacking E protein grew about 100-fold lower than the wt virus in lungs of Tg infected mice but did not grow in the brains of the same animals, in contrast to the rSARS-CoV-Δ[6-9b] virus, which grew almost as well as the wt in both tissues. Viruses lacking E protein were highly attenuated in the highly sensitive hACE-2 Tg mice, in contrast to the minimal rSARS-CoV-Δ[6-9b] and wt viruses. These data indicate that E gene might be a virulence factor influencing replication level, tissue tropism and pathogenicity of SARS-CoV, suggesting that ΔE attenuated viruses are promising vaccine candidates. url: https://doi.org/10.1016/j.virol.2008.03.005 doi: 10.1016/j.virol.2008.03.005 id: cord-254747-vox5xsgd author: Deng, Xufang title: An “Old” Protein with A New Story: Coronavirus Endoribonuclease Is Important for Evading Host Antiviral Defenses date: 2018-04-01 words: 5730.0 sentences: 323.0 pages: flesch: 53.0 cache: ./cache/cord-254747-vox5xsgd.txt txt: ./txt/cord-254747-vox5xsgd.txt summary: Overall, current evidence indicates that the EndoU activity of CoV nsp15 is dispensable for viral RNA synthesis and virus replication in cell culture. It was first discovered that the EndoU activity of nsp15 mediates the evasion of host recognition of viral dsRNA by infecting primary macrophages with EndoU-deficient CoVs (Deng et al., 2017; Kindler et al., 2017) . Moreover, treatment with the PKR inhibitor did not affect IFN induction or RNase L-mediated ribosomal RNA degradation in the EndoU-deficient CoV infected-macrophages (Deng et al., unpublished data) . Macrophages infected by the EndoU-deficient CoVs exhibited an early, RNase L-mediated degradation of ribosomal RNA, demonstrating that the OAS-RNase L system was activated (Deng et al., 2017; Kindler et al., 2017) . Lack of MDA5 expression or treatment with the PKR inhibitor did not affect virus-induced RNA degradation (Deng et al., 2017; Kindler et al., 2017) , suggesting that the nsp15-mediated blockage of OAS-RNase L activation is independent of the MDA5-IFN and PKR pathways. abstract: Here we review the evolving story of the coronavirus endoribonuclease (EndoU). Coronavirus EndoU is encoded within the sequence of nonstructural protein (nsp) 15, which was initially identified as a component of the viral replication complex. Biochemical and structural studies revealed the enzymatic nature of nsp15/EndoU, which was postulated to be essential for the unique replication cycle of viruses in the order Nidovirales. However, the role of nsp15 in coronavirus replication was enigmatic as EndoU-deficient coronaviruses were viable and replicated to near wild-type virus levels in fibroblast cells. A breakthrough in our understanding of the role of EndoU was revealed in recent studies, which showed that EndoU mediates the evasion of viral double-stranded RNA recognition by host sensors in macrophages. This new discovery of nsp15/EndoU function leads to new opportunities for investigating how a viral EndoU contributes to pathogenesis and exploiting this enzyme for therapeutics and vaccine design against pathogenic coronaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/29307596/ doi: 10.1016/j.virol.2017.12.024 id: cord-319179-gqaxf7mz author: Denison, M. title: Identification of putative polymerase gene product in cells infected with murine coronavirus A59 date: 1987-04-30 words: 1638.0 sentences: 88.0 pages: flesch: 59.0 cache: ./cache/cord-319179-gqaxf7mz.txt txt: ./txt/cord-319179-gqaxf7mz.txt summary: When infected cells and isolated virions were assayed for this protein by two-dimensional gel electrophoresis, p28 could be detected in infected cells labeled at late times after infection, but not at early times or in purified virions. When infected cells and isolated virions were assayed for this protein by twodimensional gel electrophoresis, p28 could be detected in infected cells labeled at late times after infection, but not at early times or in purified virions. To determine if p28 was a minor protein actually present in virions, infected 17CL-1 cells were labeled with [35S] methionine and virus was purified as described in Fig. 4 . A portion of the labeled virus preparation was analyzed directly by two-dimensional gel electrophoresis whereas a second part was mixed with the [35S] methionine-labeled cell-free products prior to analysis (Fig. 4) . abstract: Abstract The virion RNA of mouse hepatitis virus, strain A59 (MHV-A59) is believed to be the mRNA for the viral RNA-dependent RNA polymerase. The cell-free translation of virion RNA results in the synthesis of two predominant products p220 and p28 (M. R. Denison and S. Perlman, 1986, J. Virol. 60, 12–18). p28 is a basic protein and is readily detected by two-dimensional gel electrophoresis. When infected cells and isolated virions were assayed for this protein by two-dimensional gel electrophoresis, p28 could be detected in infected cells labeled at late times after infection, but not at early times or in purified virions. p28 represents the first protein product of the putative coronavirus polymerase gene to be identified in infected cells. url: https://www.ncbi.nlm.nih.gov/pubmed/3029990/ doi: 10.1016/0042-6822(87)90303-5 id: cord-008407-jbp8bxjz author: Derdeyn, Cynthia A. title: Characterization of defective-interfering RNAs of rubella virusgenerated during serial undiluted passage date: 1995-01-10 words: 6710.0 sentences: 298.0 pages: flesch: 56.0 cache: ./cache/cord-008407-jbp8bxjz.txt txt: ./txt/cord-008407-jbp8bxjz.txt summary: During serial undiluted passage of rubella virus (RUB) in Vero cells, two species of defective-interfering (DI) RNAs of approximately 7000 and 800 nucleotides (nts) in length were generated (Frey, T. Finally, to determine whether the majority of DI RNAs present in P12 RNA contained a deletion in the SP-ORF, an oligonucleotide probe which is complementary to a sequence located within the E1 protein coding region (nts 8472 to 8488, eligonucleotide 83, Fig. 3E ) that was deleted in all three cDNA clones was hybridized to P12 RNA. Analysis of the 5'' terminus of DI RNA generated during serial passage As shown in Figure 3A , oligonucleotide probes complementary to the exact 5'' terminal sequences of the RUB genome hybridized to the large DI RNAs. To confirm that these DI RNAs contained the authentic 5'' end of the genome, primer extension was performed on intraceilular RNA from standard RUB-infected cells and P12 RNA. abstract: During serial undiluted passage of rubella virus (RUB) in Vero cells, two species of defective-interfering (DI) RNAs of approximately 7000 and 800 nucleotides (nts) in length were generated (Frey, T. K., and Hemphill, M. L., Virology 164, 22–29, 1988). In this study, these DI RNAs were characterized by molecular cloning, hybridization with probes of defined sequence, and primer extension. The 7000-nt DI RNA species were found to be authentic DI RNAs which contain a single 2500- to 2700-nt deletion in the structural protein open reading frame (ORF) region of the genome. The 800-nt RNAs were found to be subgenomic DI RNAs synthesized from the large DI RNA templates. Analysis of the extent of the deletions using a reverse-transcription-PCR protocol revealed that the 3′ end of the deletions did not extend beyond the 3′ terminal 244 nts of the genome. The 5′ end of the deletions did not extend into the nonstructural protein ORF; however, DI RNAs in which the subgenomic start site was deleted were present. Following serial undiluted passage of seven independent stocks of RUB, this was the only pattern of DI RNAs generated. DI RNAs of 2000 to 3000 nt in length were the majority DI RNA species in a persistently infected line of Vero cells, showing that other types of RUB DI RNAs can be generated and selected. However, when supernatant from the persistently infected cells was passaged, the only DI RNAs present after two passages were 7000 nts in length, indicating that this species has a selective advantage over other types of DI RNAs during serial passage. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7130850/ doi: 10.1016/s0042-6822(95)80036-0 id: cord-279432-aik5bo6o author: Digard, Paul title: Complex formation between influenza virus polymerase proteins expressed in Xenopus oocytes date: 1989-07-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract All three influenza virus polymerase (P) proteins were expressed in Xenopus oocytes from microinjected in vitro transcribed mRNA analogs, with yields of up to 100 ng per oocyte. To examine the functional state of the Xenopus-expressed P proteins, the polypeptides were tested for their ability to form stable complexes with each other. As seen in virus-infected cells, all three P proteins associated into an immunoprecipitable complex, suggesting that the system has considerable promise for the reconstruction of an active influenza RNA polymerase. Examination of the ability of paired combinations of the P proteins to associate indicated that PB1 contained independent binding sites for PB2 and PA, and so probably formed the backbone of the complex. Sedimentation analysis of free and complexed P proteins indicated that PB1 and PB2 did not exist as free monomers, and that similarly, complexes of all three P proteins did not simply consist of one copy of each protein. The heterodisperse sedimentation rate seen for complexes of all three P proteins did not appear to result from their binding to RNA, suggesting the incorporation of additional polypeptides polymerase complex. url: https://www.ncbi.nlm.nih.gov/pubmed/2741339/ doi: 10.1016/0042-6822(89)90523-0 id: cord-255828-jrqdyfbg author: Du, Yijun title: Glycosyl-phosphatidylinositol (GPI)-anchored membrane association of the porcine reproductive and respiratory syndrome virus GP4 glycoprotein and its co-localization with CD163 in lipid rafts date: 2012-03-01 words: 8986.0 sentences: 444.0 pages: flesch: 54.0 cache: ./cache/cord-255828-jrqdyfbg.txt txt: ./txt/cord-255828-jrqdyfbg.txt summary: title: Glycosyl-phosphatidylinositol (GPI)-anchored membrane association of the porcine reproductive and respiratory syndrome virus GP4 glycoprotein and its co-localization with CD163 in lipid rafts The porcine reproductive and respiratory syndrome virus (PRRSV) glycoprotein 4 (GP4) resembles a typical type I membrane protein in its structure but lacks a hydrophilic tail at the C-terminus, suggesting that GP4 may be a lipid-anchored membrane protein. Mutational studies for residues adjacent to the GPI modification site and characterization of respective mutant viruses generated from infectious cDNA clones show that the ability of GP4 for membrane association corresponded to virus viability and growth characteristics. The depletion of cholesterol from the plasma membrane of cells reduced the virus production, suggesting a role of lipid rafts in PRRSV infection. 7C, D) .These data indicate that the reduction of virus production by MβCD was due to the depletion of cholesterol from the cells and this effect was reversible, suggesting a role of lipid rafts in PRRSV infection. abstract: The porcine reproductive and respiratory syndrome virus (PRRSV) glycoprotein 4 (GP4) resembles a typical type I membrane protein in its structure but lacks a hydrophilic tail at the C-terminus, suggesting that GP4 may be a lipid-anchored membrane protein. Using the human decay-accelerating factor (DAF; CD55), a known glycosyl-phosphatidylinositol (GPI) lipid-anchored protein, chimeric constructs were made to substitute the GPI-anchor domain of DAF with the putative lipid-anchor domain of GP4, and their membrane association and lipase cleavage were determined in cells. The DAF-GP4 fusion protein was transported to the plasma membrane and was cleaved by phosphatidylinositol-specific phospholipase C (PI-PLC), indicating that the C-terminal domain of GP4 functions as a GPI anchor. Mutational studies for residues adjacent to the GPI modification site and characterization of respective mutant viruses generated from infectious cDNA clones show that the ability of GP4 for membrane association corresponded to virus viability and growth characteristics. The residues T158 (ω − 2, where ω is the GPI moiety at E160), P159 (ω − 1), and M162 (ω + 2) of GP4 were determined to be important for virus replication, with M162 being of particular importance for virus infectivity. The complete removal of the peptide–anchor domain in GP4 resulted in a complete loss of virus infectivity. The depletion of cholesterol from the plasma membrane of cells reduced the virus production, suggesting a role of lipid rafts in PRRSV infection. Remarkably, GP4 was found to co-localize with CD163 in the lipid rafts on the plasma membrane. Since CD163 has been reported as a cellular receptor for PRRSV and GP4 has been shown to interact with this receptor, our data implicates an important role of lipid rafts during entry of the virus. url: https://api.elsevier.com/content/article/pii/S0042682211005691 doi: 10.1016/j.virol.2011.12.009 id: cord-326688-a1djgqpa author: Dubois-Dalcq, Monique E. title: Cell tropism and expression of mouse hepatitis viruses (MHV) in mouse spinal cord cultures date: 1982-06-30 words: 3946.0 sentences: 230.0 pages: flesch: 54.0 cache: ./cache/cord-326688-a1djgqpa.txt txt: ./txt/cord-326688-a1djgqpa.txt summary: The replication of three different MHV strains was studied in mouse dissociated spinal cord cultures containing differentiated neurons and nonneuronal cells (NN) (including astrocytes). Cell tropism and maturation of each virus strain was analyzed by immunolabeling methods using antisera to the virion or to purified membrane glycoproteins (E1 and E2) and by electron microscopy (EM). In conclusion, in primary CNS cultures consisting of neurons and NN cells: (1) wt-JHM replicates in both neurons and NN cells but has different effects on these cells; (2) Ts8-JHM exhibits no productive infection of neurons, and in NN cells appears to be defective in assembly and to stimulate membrane synthesis; (3) A59 also shows tropism restricted to NN cells which produce many viruses and display differential distribution of the two virion glycoproteins. DISCUSSION The present study describes how three different MHV strains interact in vitro with cultured neurons and NN cells, including astrocytes, isolated from mouse spinal cords. abstract: Abstract Mouse hepatitis viruses (MHV) are coronaviruses which cause various infections in mice affecting lung, intestine, liver, and other organs as well as the central nervous system. The replication of three different MHV strains was studied in mouse dissociated spinal cord cultures containing differentiated neurons and nonneuronal cells (NN) (including astrocytes). Cell tropism and maturation of each virus strain was analyzed by immunolabeling methods using antisera to the virion or to purified membrane glycoproteins (E1 and E2) and by electron microscopy (EM). Wt-JHM, which causes acute encephalitis in mice, produces acute cytopathic changes in both neurons and NN cells. In neurons, virions mature in smooth ER cisternae closely associated to the Golgi apparatus. As judged by EM, fewer virions are produced by neurons than NN cells and neurons do not fuse or stain for E2 as do NN cells. NN cells contain large inclusions made of nucleocapsid strands. A temperature-sensitive mutant of JHM, Ts8-JHM, which causes demyelination in mice, infects NN cells but not neurons. Infected NN cells synthesize E1 and E2, and contain large inclusions but few mature virions, even at permissive temperatures. These inclusions appear granular and rarely contain nucleocapsid strands in contrast to wt-JHM infection. NN cells infected with this mutant also display numerous membrane whorls. The hepatotropic strain A59 lacks tropism for neurons and primarily infects NN cells, thus resembling ts8-JHM. Infected NN cells become loaded with intracytoplasmic virions which are secreted from the cells. E1 can only be detected in the perinuclear area of these cells while E2 rapidly spreads throughout the cytoplasm. The cytoplasm of A59 infected NN cells frequently contains large tubular structures often in the lumen of the RER. In conclusion, in primary CNS cultures consisting of neurons and NN cells: (1) wt-JHM replicates in both neurons and NN cells but has different effects on these cells; (2) Ts8-JHM exhibits no productive infection of neurons, and in NN cells appears to be defective in assembly and to stimulate membrane synthesis; (3) A59 also shows tropism restricted to NN cells which produce many viruses and display differential distribution of the two virion glycoproteins. Thus, in the absence of the immune system, the MHV strains assayed exhibit differences in viral tropism, cytopathic changes, and viral assembly in CNS cells, and these differences may account for the different disease patterns. url: https://www.ncbi.nlm.nih.gov/pubmed/6281976/ doi: 10.1016/0042-6822(82)90092-7 id: cord-255841-3laov764 author: Duquerroy, Stéphane title: Central ions and lateral asparagine/glutamine zippers stabilize the post-fusion hairpin conformation of the SARS coronavirus spike glycoprotein() date: 2005-05-10 words: 6758.0 sentences: 315.0 pages: flesch: 62.0 cache: ./cache/cord-255841-3laov764.txt txt: ./txt/cord-255841-3laov764.txt summary: A striking arrangement of conserved asparagine and glutamine residues of HR1 propagates from two central chloride ions, providing hydrogen-bonding "zippers" that strongly constrain the path of the HR2 main chain, forcing it to adopt an extended conformation at either end of a short HR2 α-helix. We and others have previously shown that, analogous to other class I fusion proteins, peptides corresponding to the HR regions of the mouse hepatitis coronavirus (MHV, Bosch et al., 2003) and SARS-CoV (Bosch et al., 2004; Ingallinella et al., 2004; Xu et al., 2004a; Tripet et al., 2004) can fold into a stable rod-like structure, consisting of three HR1 helices in association with three HR2 peptides in antiparallel orientation. As expected, there is essentially one side chain per turn of the HR1 a-helix participating to the central hydrophobic core of the molecule, resulting in 23 amino acids from each chain (labeled to the left of Fig. 2A ) interacting with their symmetry mates at the central 3-fold axis. abstract: The coronavirus spike glycoprotein is a class I membrane fusion protein with two characteristic heptad repeat regions (HR1 and HR2) in its ectodomain. Here, we report the X-ray structure of a previously characterized HR1/HR2 complex of the severe acute respiratory syndrome coronavirus spike protein. As expected, the HR1 and HR2 segments are organized in antiparallel orientations within a rod-like molecule. The HR1 helices form an exceptionally long (120 Å) internal coiled coil stabilized by hydrophobic and polar interactions. A striking arrangement of conserved asparagine and glutamine residues of HR1 propagates from two central chloride ions, providing hydrogen-bonding “zippers” that strongly constrain the path of the HR2 main chain, forcing it to adopt an extended conformation at either end of a short HR2 α-helix. url: https://www.ncbi.nlm.nih.gov/pubmed/15840526/ doi: 10.1016/j.virol.2005.02.022 id: cord-330847-a84pcc9z author: Edwards, M. C. title: RNA recombination in the genome of Barley stripe mosaic virus date: 1992-07-31 words: 2344.0 sentences: 152.0 pages: flesch: 67.0 cache: ./cache/cord-330847-a84pcc9z.txt txt: ./txt/cord-330847-a84pcc9z.txt summary: Northern and Southern hybridization with oligonucleotide probes specific for either α or γ leader sequences indicated that CV17 γ cDNA clones are representative of native CV17 γ RNAs. Furthermore, bioassays indicated that in vitro transcripts derived from these γ cDNA clones were infectious when coinoculated with in vitro transcripts of full-length α and β cDNA clones. A "bandaid" cloning strategy, which exploits the conservation of the 3'' terminal sequence, as well as the unique nature of the 5'' ends of the BSMV RNAs, has been used previously to obtain full-length cDNA clones from which infectious in vitro transcripts can be produced (3, 7). Analysis of the resulting cDNA clones suggested that CV17 RNA y is a naturally occurring chimeric recombinant, composed of a 70nucleotide (nt) a-specific leader sequence preceding a r-specific coding region. 3. ldentrfrcatron of barley stripe mosaic virus strarn CV17 LY and Type strain y-specific leader sequences In 15 putative CV17 y cDNA clones and native RNAs of strains CV17, CV42, and ND1 8. abstract: Abstract Barley stripe mosaic Hordeivirus (BSMV) is a positive-strand RNA virus requiring three single-stranded RNAs (α, β, and γ) for infectivity. A terminal-sequence-dependent cloning strategy was used to clone the entire genome of the CV17 strain. Full-length γ cDNA clones were obtained when oligonucleotides specific for the 5′-terminal sequence of RNA α were used in the cloning procedure, but not when RNA γ-specific oligonucleotides were used. Sequence analysis of six putative γ cDNA clones revealed that nucleotides 1–70 possess 89% homology with the first 70 nucleotides of RNA α. This leader region is separated from the γ-specific coding region by an eight-base intervening sequence common to both CV17 RNAs α and γ. Northern and Southern hybridization with oligonucleotide probes specific for either α or γ leader sequences indicated that CV17 γ cDNA clones are representative of native CV17 γ RNAs. Furthermore, bioassays indicated that in vitro transcripts derived from these γ cDNA clones were infectious when coinoculated with in vitro transcripts of full-length α and β cDNA clones. Thus, the evidence suggests that RNA γ of BSMV strain CV17 is a recombinant molecule which may have arisen as a result of natural recombination between RNAs α and γ. url: https://www.ncbi.nlm.nih.gov/pubmed/1604824/ doi: 10.1016/0042-6822(92)90722-2 id: cord-267377-wyhsxj6g author: Edwards, Michael C. title: Coat protein expression strategy of oat blue dwarf virus() date: 2014-01-14 words: 4709.0 sentences: 231.0 pages: flesch: 54.0 cache: ./cache/cord-267377-wyhsxj6g.txt txt: ./txt/cord-267377-wyhsxj6g.txt summary: The single, large ORF encodes a polyprotein with domains specifying methyltransferase (mtr), protease (pro), helicase/NTpase (hel), and polymerase (pol) activities fused to the sequence encoding the CPs. The major and minor coat proteins map to the same CP sequence and size differences between them are potentially determined by translation initiation at two different start codons (minor, AUG 5581 and major, AUG 5710 ). Oat protoplasts were inoculated with capped transcripts of wild type clone pOBDV, major CP mutants GH1-7 (premature termination mutant) and KL1-3 (initiation codon mutant), and AB15-25 (marafibox mutant) and incubated for 40 h. Accumulation of viral coat proteins (CPs) and RNA in oat protoplasts inoculated with premature termination and initiation codon mutants of the CP gene. Oat protoplasts were inoculated with capped transcripts of wild type clone pOBDV, premature termination mutants GH1-7 and EF2-2, and initiation codon mutants IJ4-7 (minor CP), and KL1-3 and KL2-5 (major CP) and incubated for 24 h. abstract: Oat blue dwarf virus (OBDV) is a member of the genus Marafivirus whose genome encodes a 227 kDa polyprotein (p227) ostensibly processed post-translationally into its functional components. Encoded near the 3' terminus and coterminal with the p227 ORF are ORFs specifying major and minor capsid proteins (CP). Since the CP expression strategy of marafiviruses has not been thoroughly investigated, we produced a series of point mutants in the OBDV CP encoding gene and examined expression in protoplasts. Results support a model in which the 21 kDa major CP is the product of direct translation of a sgRNA, while the 24 kDa minor CP is a cleavage product derived from both the polyprotein and a larger ~26 kDa precursor translated directly from the sgRNA. Cleavage occurs at an LXG[G/A] motif conserved in many viruses that use papain-like proteases for polyprotein processing and protection against degradation via the ubiquitin-proteasome system. url: https://doi.org/10.1016/j.virol.2013.12.018 doi: 10.1016/j.virol.2013.12.018 id: cord-309919-sm5o0g1c author: Eichwald, Catherine title: Mammalian orthoreovirus core protein μ2 reorganizes host microtubule-organizing center components. date: 2020-08-04 words: 1170.0 sentences: 81.0 pages: flesch: 46.0 cache: ./cache/cord-309919-sm5o0g1c.txt txt: ./txt/cord-309919-sm5o0g1c.txt summary: In infected cells, the MRV μ2 protein forms punctae in the enlarged region of the filamentous VFs that are co-localized with γ-tubulin and resistant to nocodazole treatment, and permitted microtubule (MT)-extension, features common to MT-organizing centers (MTOCs). Using a previously established reconstituted VF model, we addressed the functions of MT-components and MTOCs concerning their roles in the formation of filamentous VFs. Indeed, the MTOC markers γ-tubulin and centrin were redistributed within the VF-like structures (VFLS) in a μ2-dependent manner. Here, specific µ2 punctae observed in filamentous VFs are investigated concerning their 89 ability to co-localize with other reovirus proteins and host elements. Our study shows that µ2 90 punctae in VFs co-localize with γ-tubulin, are resistant to nocodazole, and permit MT 91 emergence, common features for MTOCs. Moreover, using the VFLS model, we found that 92 specific µ2/µNS ratios that support filamentous morphology relocalize γ-tubulin and centrin to 93 foci within the VFLS. abstract: Filamentous mammalian orthoreovirus (MRV) viral factories (VFs) are membrane-less cytosolic inclusions in which virus transcription, replication of dsRNA genome segments, and packaging of virus progeny into newly synthesized virus cores take place. In infected cells, the MRV μ2 protein forms punctae in the enlarged region of the filamentous VFs that are co-localized with γ-tubulin and resistant to nocodazole treatment, and permitted microtubule (MT)-extension, features common to MT-organizing centers (MTOCs). Using a previously established reconstituted VF model, we addressed the functions of MT-components and MTOCs concerning their roles in the formation of filamentous VFs. Indeed, the MTOC markers γ-tubulin and centrin were redistributed within the VF-like structures (VFLS) in a μ2-dependent manner. Moreover, the MT-nucleation centers significantly increased in numbers, and γ-tubulin was pulled-down in a binding assay when co-expressed with histidine-tagged-μ2 and μNS. Thus, μ2, by interaction with γ-tubulin, can modulate MTOCs localization and function according to viral needs. url: https://www.sciencedirect.com/science/article/pii/S0042682220301355?v=s5 doi: 10.1016/j.virol.2020.07.008 id: cord-277838-931sco95 author: Erles, Kerstin title: Detection of a group 2 coronavirus in dogs with canine infectious respiratory disease date: 2003-06-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: An investigation into the causes of canine infectious respiratory disease was carried out in a large rehoming kennel. Tissue samples taken from the respiratory tract of diseased dogs were tested for the presence of coronaviruses using RT–PCR with conserved primers for the polymerase gene. Sequence analysis of four positive samples showed the presence of a coronavirus with high similarity to both bovine and human coronavirus (strain OC43) in their polymerase and spike genes, whereas there was a low similarity to comparable genes in the enteric canine coronavirus. This canine respiratory coronavirus (CRCV) was detected by RT–PCR in 32/119 tracheal and 20/119 lung samples, with the highest prevalence being detected in dogs with mild clinical symptoms. Serological analysis showed that the presence of antibodies against CRCV on the day of entry into the kennel decreased the risk of developing respiratory disease. url: https://api.elsevier.com/content/article/pii/S0042682203001600 doi: 10.1016/s0042-6822(03)00160-0 id: cord-262226-7kwkla73 author: Fang, Shouguo title: Identification of two ATR-dependent phosphorylation sites on coronavirus nucleocapsid protein with nonessential functions in viral replication and infectivity in cultured cells date: 2013-07-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Coronavirus encodes an extensively phosphorylated and highly basic nucleocapsid (N) protein. Previous studies have identified Ser190, Ser192, Thr378 and Ser379 as the phosphorylation sites for coronavirus infectious bronchitis virus (IBV) N protein. In this study, we show that phosphorylation at Thr378 and Ser379 sites is dependent on the ataxia-telangiectasia mutated (ATM) and Rad3-related (ATR), a kinase activated during IBV replication. Introduction of Ala substitutions at these two sites individually, in combination of the two and together with other two sites (Ser190 and Ser192) into an infectious IBV clone did not affect recovery of the recombinant viruses containing the mutations. A mutant virus (rIBV-Nm4) carrying the four Ala substitutions grew at a similar, if not better, growth rate as wild type virus. This study reveals a cellular kinase responsible for phosphorylation of a coronavirus N protein at two positions and the functional consequence of this modification on coronavirus replication. url: https://api.elsevier.com/content/article/pii/S0042682213003632 doi: 10.1016/j.virol.2013.06.014 id: cord-266585-jfjrk9gy author: Fang, Shouguo title: An arginine-to-proline mutation in a domain with undefined functions within the helicase protein (Nsp13) is lethal to the coronavirus infectious bronchitis virus in cultured cells date: 2007-02-05 words: 7152.0 sentences: 356.0 pages: flesch: 56.0 cache: ./cache/cord-266585-jfjrk9gy.txt txt: ./txt/cord-266585-jfjrk9gy.txt summary: During construction of an infectious clone from a Vero cell-adapted coronavirus infectious bronchitis virus (IBV), we found that a G–C point mutation at nucleotide position 15526, causing Arg-to-Pro mutation at amino acid position 132 of the helicase protein, is lethal to the infectivity of IBV on Vero cells. Further characterization of the in vitro-synthesized full-length transcripts containing the G15526C mutation demonstrated that this mutation blocks the transcription of subgenomic RNAs. Substitution mutation of the Arg132 residue to a positively charged amino acid (Lys) affected neither the infectivity of the in vitro-synthesized transcripts nor the growth properties of the rescued virus. To further demonstrate that the failure to rescue infectious virus from the G15526C mutant transcripts is due to a defect in subgenomic RNA transcription, the full-length clones with and without the G15526C mutation were used to generate recombinant IBV expressing the enhanced green fluorescent protein (EGFP) by replacing the 5a gene with EGFP. abstract: Genetic manipulation of the RNA genomes by reverse genetics is a powerful tool to study the molecular biology and pathogenesis of RNA viruses. During construction of an infectious clone from a Vero cell-adapted coronavirus infectious bronchitis virus (IBV), we found that a G–C point mutation at nucleotide position 15526, causing Arg-to-Pro mutation at amino acid position 132 of the helicase protein, is lethal to the infectivity of IBV on Vero cells. When the in vitro-synthesized full-length transcripts containing this mutation were introduced into Vero cells, no infectious virus was rescued. Upon correction of the mutation, infectious virus was recovered. Further characterization of the in vitro-synthesized full-length transcripts containing the G15526C mutation demonstrated that this mutation may block the transcription of subgenomic RNAs. Substitution mutation of the Arg132 residue to a positively charged amino acid Lys affected neither the infectivity of the in vitro-synthesized transcripts nor the growth properties of the rescued virus. However, mutation of the Arg132 residue to Leu, a conserved residue in other coronaviruses at the same position, reduced the recovery rate of the in vitro-synthesized transcripts. The recovered mutant virus showed much smaller-sized plaques. On the contrary, a G–C and a G–A point mutations at nucleotide positions 4330 and 9230, respectively, causing Glu–Gln and Gly–Glu mutations in or near the catalytic centers of the papain-like (Nsp3) and 3C-like (Nsp5) proteinases, did not show detectable detrimental effect on the rescue of infectious viruses and the infectivity of the rescued viruses. url: https://api.elsevier.com/content/article/pii/S0042682206005745 doi: 10.1016/j.virol.2006.08.020 id: cord-280287-t7uozjml author: Favier, Anne-Laure title: Unique physicochemical properties of human enteric Ad41 responsible for its survival and replication in the gastrointestinal tract date: 2004-04-25 words: 6968.0 sentences: 382.0 pages: flesch: 52.0 cache: ./cache/cord-280287-t7uozjml.txt txt: ./txt/cord-280287-t7uozjml.txt summary: We show that Ad41 infectivity is not diminished by acid exposure, a condition limiting the infectivity of the respiratory Ad. This feature can be attributed to a large extent to the global basic charge of enteric Ad virions and to the stability of Ad41 fiber, a viral protein mediating virus attachment. During cell attachment, the distal C-terminal globular head domain of the fiber protein interacts with the primary receptor, which for some human Ad serotypes is the coxsackievirus and adenovirus receptor (CAR) (Bergelson et al., 1997; Roelvink et al., 1998) . In the first attempt to understand the survival mechanism of the human enteric Ad41 under acid conditions of the stomach, we compared the predicted pI values of external structural proteins of different Ad serotypes (Table 1) . abstract: Human enteric adenovirus Ad41 is associated with children gastroenteritis. To infect gastrointestinal cells, the invading virus must be acid-stable and resistant to inactivation by bile salts and proteases. In addition, it has to cross the mucus barrier before it infects mucosa cells. We show that Ad41 infectivity is not diminished by acid exposure, a condition limiting the infectivity of the respiratory Ad. This feature can be attributed to a large extent to the global basic charge of enteric Ad virions and to the stability of Ad41 fiber, a viral protein mediating virus attachment. Upon exposure to pH shock, the respiratory Ad2 loses its ability to interact with lipids while enteric Ad41 still binds to the major phospholipids of gastric and intestine mucus. In addition, contrary to respiratory Ad, enteric Ad41 interacts with several sphingolipid components of plasma membranes. These results show that the molecular bases of the Ad41 enteric tropism stem from its particular physicochemical properties. url: https://www.ncbi.nlm.nih.gov/pubmed/15063120/ doi: 10.1016/j.virol.2004.01.020 id: cord-272051-arz8r204 author: Federico, Maurizio title: HIV-protease inhibitors block the replication of both vesicular stomatitis and influenza viruses at an early post-entry replication step date: 2011-08-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The inhibitors of HIV-1 protease (PIs) have been designed to block the activity of the viral aspartyl-protease. However, it is now accepted that this family of inhibitors can also affect the activity of cell proteases. Since the replication of many virus species requires the activity of host cell proteases, investigating the effects of PIs on the life cycle of viruses other than HIV would be of interest. Here, the potent inhibition induced by saquinavir and nelfinavir on the replication of both vesicular stomatitis and influenza viruses is described. These are unrelated enveloped RNA viruses infecting target cells upon endocytosis and intracellular fusion. The PI-induced inhibition was apparently a consequence of a block at the level of the fusion between viral envelope and endosomal membranes. These findings would open the way towards the therapeutic use of PIs against enveloped RNA viruses other than HIV. url: https://www.sciencedirect.com/science/article/pii/S0042682211002157 doi: 10.1016/j.virol.2011.05.002 id: cord-302972-imtttzvr author: Feldmann, H. title: Glycosylation and oligomerization of the spike protein of marburg virus date: 1991-05-31 words: 1917.0 sentences: 116.0 pages: flesch: 56.0 cache: ./cache/cord-302972-imtttzvr.txt txt: ./txt/cord-302972-imtttzvr.txt summary: As shown in Fig. 1 B, the electrophoretic mobility of GP was slightly enhanced after incubation with endoglycosidase H (lane 4), and a distinct further increase was obtained by treatment with endoglycosidase F (lane 3) indicating that GP contains AI-glycans of the oligomannosidic, but mainly of the complex type. Glycohydrolase treatments were performed at 37" overnight after denaturing of the proteins by boiling in buffer containing 0.1% SDS, 0.5% octylglucoside, 0.5% P-mercaptoethanol, 50 mM sodium acetate, pH 7.0, and 5 mM EDTA. Growth of virus, labeling, and cross-linking were performed as described in the legend of Fig. 1 and as in A above. To further analyze the composition of the GP complexes, purified [35S]methionine-labeled virus was subjected to solubilization by nonionic detergent and sedimentation on sucrose density gradients, and the polypeptides present in the fractions obtained from the gradients were assayed by polyacrylamide gel electrophoresis under denaturing and reducing conditions. A. Virus non-cross-linked and treated with @-mercaptoethanol (5%, 10 min, 96") prior to gradient centrifugation. abstract: Abstract The oligosaccharide side chains of the glycoprotein of Marburg virus (MW 170,000) have been analyzed by determining their sensitivity to enzymatic degradation and their reactivity with lectins. It was found that they consist of N- and O-glycans. Studies employing chemical cross-linking showed that the glycoprotein is present as a homotrimer in the viral envelope. url: https://www.ncbi.nlm.nih.gov/pubmed/2024471/ doi: 10.1016/0042-6822(91)90680-a id: cord-289712-w1y0lc5c author: Flintoff, Wayne F. title: Replication of murine coronaviruses in somatic cell hybrids between murine fibroblasts and rat Schwannoma cells date: 1984-04-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract The replication of the murine coronaviruses MHV3 and JHM has been studied in somatic cell hybrids formed between murine fibroblast L2 cells which support lytic infections with both these agents, and rat RN2 Schwannoma cells which support the replication of JHM in a temperature-sensitive, persistent manner but are restrictive to the replication of MHV3. The results described in this report indicate that the totally permissive state is dominant over the persistent or restricted state since the hybrid cells permit the replication of both these viral agents in a lytic manner. url: https://api.elsevier.com/content/article/pii/004268228490312X doi: 10.1016/0042-6822(84)90312-x id: cord-253024-b393ea2u author: Fu, Kaisong title: Evidence for variable rates of recombination in the MHV genome date: 1992-07-31 words: 8420.0 sentences: 488.0 pages: flesch: 56.0 cache: ./cache/cord-253024-b393ea2u.txt txt: ./txt/cord-253024-b393ea2u.txt summary: Six RNA+ mutants that reside within a single complementation group mapping within the S glycoprotein gene of MHV-A59 were isolated which did not cause syncytium at the restrictive temperature. Since these mutants do not produce syncytium at the restrictive temperature ( Fig. 1) and sequence analysis of RNA recombinant viruses suggested that the defect in LA7 mapped within the first 1 .l kb of the S glycoprotein gene (Banner et al., 1990; Keck eta/., 1987 Keck eta/., , 1988a Makino eta/., 1986b Makino eta/., , 1987 , these data provided an anchor for mapping the location of the remaining group F RNA+ mutants. Since the distance between the group Fl and F2 mutants would have required sizable deletions (>lOO bp) to result in ts+ virus (Fig. 4) these data suggested that large deletions were rare events in these crosses, and did not contribute to an increase in the recombination frequency within the S glycoprotein gene. abstract: Abstract Mouse hepatitis virus has been shown to undergo RNA recombination at high frequency during mixed infection. Temperature-sensitive mutants were isolated using 5-fluorouracil and 5-azacytidine as mutagen. Six RNA+ mutants that reside within a single complementation group mapping within the S glycoprotein gene of MHV-A59 were isolated which did not cause syncytium at the restrictive temperature. Using standard genetic techniques, a recombination map was established that indicated that these mutants mapped into two distinct domains designated F1 and F2. These genetic domains may correspond to mutations mapping within the S1 and S2 glycoproteins, respectively, and suggest that both the S1 and S2 domains are important in eliciting the fusogenic activity of the S glycoprotein gene. In addition, assuming that most distal is alleles map roughly 4.0 kb apart, a recombination frequency of 1 % per 575–676 by was predicted through the S glycoprotein gene. Interestingly, this represents a threefold increase in the recombination frequency as compared to rates predicted through the polymerase region. The increase in the recombination rate was probably not due to recombination events resulting in large deletions or insertions (>50 bp), but rather was probably due to a combination of homologous and nonhomologous recombination. A variety of explanations could account for the increased rates of recombination in the S gene. url: https://www.sciencedirect.com/science/article/pii/004268229290684H doi: 10.1016/0042-6822(92)90684-h id: cord-281237-asnpuami author: Garten, Wolfgang title: Inhibition of proteolytic activation of influenza virus hemagglutinin by specific peptidyl chloroalkyl ketones date: 1989-09-30 words: 4043.0 sentences: 208.0 pages: flesch: 47.0 cache: ./cache/cord-281237-asnpuami.txt txt: ./txt/cord-281237-asnpuami.txt summary: The effect of peptidyl chloroalkyl ketones on the activation of the fowl plague virus hemagglutinin by the proteases specific for paired basic residues has been investigated. When virions containing uncleaved hemagglutinin were incubated with lysates of uninfected cells, cleavage was completely inhibited by peptidyl chloroalkyl ketones containing paired basic residues at a concentration of 1 mM. When dibasic peptidyl chloroalkyl ketones were added to infected cell cultures, cleavage of hemagglutinin and multiple cycles of virus replication were inhibited at 10 mM. the hemagglutinins of the pathogenic avian influenza viruses have a cleavage site consisting of several basic amino acids which can be cleaved by endoproteases present in many cells (for review see Klenk and Rott, 1988) . Table 2 shows an experiment in which a cell lysate has been first incubated with AKR-CMK as an inhibitor and subsequently with chromogenic substrates containing also two basic residues at the cleavage site. abstract: Abstract Lysates of cultured cells have been analyzed for arginine-specific endoproteases using peptidyl-p-n itroanil ides as chromogenic substrates. The enzymes present in MDBK, MDCK, VERO, BHK, and chick embryo cells required lysinearginine or arginine-arginine pairs as cleavage sites, whereas chorioallantoic membrane cells contained, in addition, an activity that could cleave at a single arginine. The effect of peptidyl chloroalkyl ketones on the activation of the fowl plague virus hemagglutinin by the proteases specific for paired basic residues has been investigated. When virions containing uncleaved hemagglutinin were incubated with lysates of uninfected cells, cleavage was completely inhibited by peptidyl chloroalkyl ketones containing paired basic residues at a concentration of 1 mM. In contrast a compound containing a single arginine had no inhibitory activity. When dibasic peptidyl chloroalkyl ketones were added to infected cell cultures, cleavage of hemagglutinin and multiple cycles of virus replication were inhibited at 10 mM. However, a 100-to 200-fold increase of the inhibitory activity in intact cells could be achieved by N-terminal acylation. These studies suggest a potential role of peptidyl chloroalkyl ketones as antiviral agents url: https://api.elsevier.com/content/article/pii/0042682289901037 doi: 10.1016/0042-6822(89)90103-7 id: cord-007373-livz5zuu author: Gayathri, P. title: Crystal structure of the serine protease domain of Sesbania mosaic virus polyprotein and mutational analysis of residues forming the S1-binding pocket date: 2006-03-15 words: 6204.0 sentences: 362.0 pages: flesch: 62.0 cache: ./cache/cord-007373-livz5zuu.txt txt: ./txt/cord-007373-livz5zuu.txt summary: authors: Gayathri, P.; Satheshkumar, P.S.; Prasad, K.; Nair, Smita; Savithri, H.S.; Murthy, M.R.N. title: Crystal structure of the serine protease domain of Sesbania mosaic virus polyprotein and mutational analysis of residues forming the S1-binding pocket In the present study, the crystal structure of SeMV protease domain was determined to a resolution of 2.4 Å by multiple isomorphous replacement coupled with anomalous scattering, with a view to identify the residues involved in substrate binding as well as protease -VPg interactions. The absence of well-defined density for F301 in SeMV protease suggests that its side chain might undergo substantial displacement on binding of the substrate or on conformational changes induced by the interaction of the protease domain with VPg. TEV and equine arteritis virus proteases, in which a serine residue occurs at the position corresponding to F301, are active in trans. abstract: Sesbania mosaic virus (SeMV) polyprotein is processed by its N-terminal serine protease domain. The crystal structure of the protease domain was determined to a resolution of 2.4 Å using multiple isomorphous replacement and anomalous scattering. The SeMV protease domain exhibited the characteristic trypsin fold and was found to be closer to cellular serine proteases than to other viral proteases. The residues of the S1-binding pocket, H298, T279 and N308 were mutated to alanine in the ΔN70-Protease–VPg polyprotein, and the cis-cleavage activity was examined. The H298A and T279A mutants were inactive, while the N308A mutant was partially active, suggesting that the interactions of H298 and T279 with P1-glutamate are crucial for the E–T/S cleavage. A region of exposed aromatic amino acids, probably essential for interaction with VPg, was identified on the protease domain, and this interaction could play a major role in modulating the function of the protease. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7111806/ doi: 10.1016/j.virol.2005.11.011 id: cord-255738-r8zfdsix author: Ge, Feng title: Derivation of a novel SARS–coronavirus replicon cell line and its application for anti-SARS drug screening date: 2007-03-30 words: 5103.0 sentences: 242.0 pages: flesch: 49.0 cache: ./cache/cord-255738-r8zfdsix.txt txt: ./txt/cord-255738-r8zfdsix.txt summary: Sequence analysis of the replicon RNA purified from SCR-1 cells soon after selection in blasticidin (passage number 6) found no sequence differences compared with the published sequence of SARS-CoV strain SIN2774 (GenBank Accession Number AY283798). Baric''s group constructed a transmissible gastroenteritis virus (TGEV) replicon for the expression of heterologous GFP gene (Curtis et al., 2002) and Thiel''s group generated a non-cytopathic, selectable replicon RNA (based on HCoV 229E) for the identification of coronavirus replicase inhibitors (Hertzig et al., 2004) . Compared to anti-viral agent identification systems based on purified proteins or nucleic acids, our SARS-CoV replicon cell line has two advantages: first, if a candidate inhibitor can inhibit replication of our replicon RNA, which occurs intracellularly, it thus demonstrates that this agent can permeate the cell. To obtain the complete sequence of the SARS-CoV replicon persisting in the SCR-1 cells, the total cellular RNAs isolated from SRC-1 cells at passage number 6 and 40 were used as the templates. abstract: The severe acute respiratory syndrome (SARS) outbreak in 2002, which had a high morbidity rate and caused worldwide alarm, remains untreated today even though SARS was eventually isolated and controlled. Development and high-throughput screening of efficacious drugs is therefore critical. However, currently there remains a lack of such a safe system. Here, the generation and characterization of the first selectable, SARS–coronavirus (SARS–CoV)-based replicon cell line which can be used for screening is described. Partial SARS–CoV cDNAs and antibiotic resistance/reporter gene DNA were generated and assembled in vitro to produce the replicon transcription template, which was then transcribed in vitro to generate the replicon RNA. The latter was introduced into a mammalian cell line and the transfected cells were selected for by antibiotic application. For the antibiotic-resistant cell lines thus generated, the expression of reporter gene was ensured by continued monitoring using fluorescent microscopy and flow cytometry. The suitability of this replicon cell line in drug screening was demonstrated by testing the inhibitory effect of several existing drugs and the results demonstrate that the SARS–CoV replicon cell lines provide a safe tool for the identification of SARS–CoV replicase inhibitors. The replicon cell lines thus developed can be applied to high-throughput screening for anti-SARS drugs without the need to grow infectious SARS–CoV. url: https://api.elsevier.com/content/article/pii/S0042682206007410 doi: 10.1016/j.virol.2006.10.016 id: cord-260782-1lm8tzbc author: Giles, Julia title: Viral RNA load and histological changes in tissues following experimental infection with an arterivirus of possums (wobbly possum disease virus) date: 2018-07-14 words: 6575.0 sentences: 319.0 pages: flesch: 43.0 cache: ./cache/cord-260782-1lm8tzbc.txt txt: ./txt/cord-260782-1lm8tzbc.txt summary: title: Viral RNA load and histological changes in tissues following experimental infection with an arterivirus of possums (wobbly possum disease virus) The aim of the current study was to describe histological lesions and viral RNA levels in tissues from possum experimentally infected with WPDV. Histology of brain, kidney and liver tissue from wobbly possum disease virus (WPDV)-infected possums. Whilst RNA levels in selected tissues (liver, spleen, brain and kidney) from WPD-infected possums have been previously reported (Dunowska et al., 2013) , we have expanded both the number of possums and the tissue types tested to provide a greater understanding of the tissues targeted by the virus in-vivo. Detection of moderate to high levels of viral RNA from the sera of all but one infected possum in this study also supports the use of blood or serum samples for detection of WPDV. abstract: Tissues from Australian brushtail possums (Trichosurus vulpecula) that had been experimentally infected with wobbly possum disease (WPD) virus (WPDV) were examined to elucidate pathogenesis of WPDV infection. Mononuclear inflammatory cell infiltrates were present in livers, kidneys, salivary glands and brains of WPD-affected possums. Specific staining was detected by immunohistochemistry within macrophages in the livers and kidneys, and undefined cell types in the brains. The highest viral RNA load was found in macrophage-rich tissues. The detection of viral RNA in the salivary gland, serum, kidney, bladder and urine is compatible with transmission via close physical contact during encounters such as fighting or grooming, or by contact with an environment that has been contaminated with saliva or urine. Levels of viral RNA remained high in all tissues tested throughout the study, suggesting that on-going virus replication and evasion of the immune responses may be important in the pathogenesis of disease. url: https://www.ncbi.nlm.nih.gov/pubmed/30014860/ doi: 10.1016/j.virol.2018.07.003 id: cord-256316-1odgm6hm author: Godet, Murielle title: TGEV corona virus ORF4 encodes a membrane protein that is incorporated into virions date: 1992-06-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract The coding potential of the open reading frame ORF4 (82 amino acids) of transmissible gastroenteritis virus (TGEV) has been confirmed by expression using a baculovirus vector. Five monoclonal antibodies (MAbs) raised against the 10K recombinant product immunoprecipitated a polypeptide of a similar size in TGEV-infected cells. Immunofluorescence assays performed both on insect and mammalian cells revealed that ORF4 was a membrane-associated protein, a finding consistent with the prediction of a membrane-spanning segment in ORF4 sequence. Two epitopes were localized within the last 21 C-terminal residues of the sequence through peptide scanning and analysis of the reactivity of a truncated ORF4 recombinant protein. Since the relevant MAbs were found to induce a cell surface fluorescence, these data suggest that ORF4 may be an integral membrane protein having a Cexo-Nendo orientation. Anti-ORF4 MAbs were also used to show that ORF4 polypeptide may be detected in TGEV virion preparations, with an estimated number of 20 molecules incorporated per particle. Comparison of amino acid sequence data provided strong evidence that other coronaviruses encode a polypeptide homologous to TGEV ORF4. Our results led us to propose that ORF4 represents a novel minor structural polypeptide, tentatively designated SM (small membrane protein). url: https://www.ncbi.nlm.nih.gov/pubmed/1316677/ doi: 10.1016/0042-6822(92)90521-p id: cord-268416-8hw80qx8 author: Grunewald, Matthew E. title: The coronavirus nucleocapsid protein is ADP-ribosylated date: 2018-04-01 words: 4795.0 sentences: 263.0 pages: flesch: 50.0 cache: ./cache/cord-268416-8hw80qx8.txt txt: ./txt/cord-268416-8hw80qx8.txt summary: While screening for ADP-ribosylated proteins during coronavirus (CoV) infection, we detected a ~55 kDa ADP-ribosylated protein in mouse hepatitis virus (MHV)-infected cells and in virions, which we identified as the viral nucleocapsid (N) protein. To identify potential targets of the CoV macrodomain, we analyzed infected cells for changes in ADP-ribosylation patterns utilizing antibodies specific for ADPr. We focused on cells infected with a murine CoV, mouse hepatitis virus (MHV). If the macrodomain was indeed removing the ADPr from the N protein, we would expect to see increased N protein ADP-ribosylation in cells infected with mutant virus compared to wild-type infected cells. To determine if N protein expressed in the absence of CoV infection could be ADP-ribosylated in cell culture, we transduced Vero cells with VEEV replicon particles (VRPs) encoding the MERS-CoV N protein or control GFP at different MOIs . abstract: ADP-ribosylation is a common post-translational modification, although how it modulates RNA virus infection is not well understood. While screening for ADP-ribosylated proteins during coronavirus (CoV) infection, we detected a ~55 kDa ADP-ribosylated protein in mouse hepatitis virus (MHV)-infected cells and in virions, which we identified as the viral nucleocapsid (N) protein. The N proteins of porcine epidemic diarrhea virus (PEDV), severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV were also ADP-ribosylated. ADP-ribosylation of N protein was also observed in cells exogenously expressing N protein by transduction using Venezuelan equine encephalitis virus replicon particles (VRPs). However, plasmid-derived N protein was not ADP-ribosylated following transient transfection but was ADP-ribosylated after MHV infection, indicating that this modification requires virus infection. In conclusion, we have identified a novel post-translation modification of the CoV N protein that may play a regulatory role for this important structural protein. url: https://doi.org/10.1016/j.virol.2017.11.020 doi: 10.1016/j.virol.2017.11.020 id: cord-290231-4m9lj0uq author: Guirakhoo, Farshad title: The Murray Valley encephalitis virus prM protein confers acid resistance to virus particles and alters the expression of epitopes within the R2 domain of E glycoprotein date: 1992-12-31 words: 5738.0 sentences: 261.0 pages: flesch: 48.0 cache: ./cache/cord-290231-4m9lj0uq.txt txt: ./txt/cord-290231-4m9lj0uq.txt summary: Abstract To study the role of the precursor to the membrane protein (prM) in flavivirus maturation, we inhibited the proteolytic processing of the Murray Valley encephalitis (MVE) virus prM to membrane protein in infected cells by adding the acidotropic agent ammonium chloride late in the virus replication cycle. By using monoclonal antibodies (MAbs) and protease maps, we previously demonstrated that the E glycoprotein of tick-borne encephalitis (TBE) virus undergoes an irreversible conformational change, predominantly in the epitopes of domain A, at mildly acidic pH . To understand the role of prM protein in virus maturation and its interaction with the E glycoprotein, we investigated the effect that ammonium chloride had on MVE viruses grown in C6/36 mosquito cells. The reactivities of MAbs defining nine distinct epitopes on the MVE E glycoprotein were compared on M-and prMcontaining viruses using supernatants of ammonium chloride-treated or untreated virus-infected C6/36 cells. abstract: Abstract To study the role of the precursor to the membrane protein (prM) in flavivirus maturation, we inhibited the proteolytic processing of the Murray Valley encephalitis (MVE) virus prM to membrane protein in infected cells by adding the acidotropic agent ammonium chloride late in the virus replication cycle. Viruses purified from supernatants of ammonium chloride-treated cells contained prM protein and were unable to fuse C6/36 mosquito cells from without. When ammonium chloride was removed from the cells, both the processing of prM and the fusion activity of the purified viruses were partially restored. By using monoclonal antibodies (MAbs) specific for the envelope (E) glycoprotein of MVE virus, we found that at least three epitopes were less accessible to their corresponding antibodies in the prM-containing MVE virus particles. Amino-terminal sequencing of proteolytic fragments of the E protein which were reactive with sequence-specific peptide antisera or MAb enabled us to estimate the site of the E protein interacting with the prM to be within amino acids 200 to 327. Since prM-containing viruses were up to 400-fold more resistant to a low pH environment, we conclude that the E-prM interaction might be necessary to protect the E protein from irreversible conformational changes caused by maturation into the acidic vesicles of the exocytic pathway. url: https://www.ncbi.nlm.nih.gov/pubmed/1280384/ doi: 10.1016/0042-6822(92)90267-s id: cord-281309-c9y7m5do author: Guo, Baoqing title: Experimental infection of United States swine with a Chinese highly pathogenic strain of porcine reproductive and respiratory syndrome virus date: 2013-01-20 words: 7954.0 sentences: 344.0 pages: flesch: 48.0 cache: ./cache/cord-281309-c9y7m5do.txt txt: ./txt/cord-281309-c9y7m5do.txt summary: We found that this HP-PRRSV strain caused extreme morbidity, as was seen in Asia, but novel to this study, resulted in up to 100x higher abundance of circulating virus when compared to VR-2332, caused extremely exacerbated thymic atrophy such that the thymus was often difficult to discern, and the host response was assessed in comparison to animals infected with strain VR-2332 for the first time by a swine protein array including 5 innate and 5 adaptive cytokines in serum, bronchoalveolar lavage fluid and lymph nodes. It was demonstrated that infection with a highly pathogenic strain of PRRSV elicited a significant elevation of all adaptive immunity cytokines measured in BALF, as well as a majority of these cytokines in serum and TBLN homogenates of the same groups of pigs. abstract: The pathogenesis of Type 2 highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) in 10-week old swine in the United States was investigated. rJXwn06, rescued from an infectious clone of Chinese HP-PRRSV, replicated in swine with at least 100-fold increased kinetics over U.S. strain VR-2332. rJXwn06 caused significant weight loss, exacerbated disease due to bacterial sepsis and more severe histopathological lung lesions in pigs exposed to HP-PRRSV than to those infected with VR-2332. Novel findings include identification of bacterial species present, the degree of thymic atrophy seen, and the inclusion of contact animals that highlighted the ability of HP-PRRSV to rapidly transmit between animals. Furthermore, comprehensive detailed cytokine analysis of serum, bronchoalveolar lavage fluid, and tracheobronchial lymph node tissue homogenate revealed a striking elevation in levels of cytokines associated with both innate and adaptive immunity in HP-PRRSV infected swine, and showed that contact swine differed in the degree of cytokine response. url: https://www.sciencedirect.com/science/article/pii/S0042682212004540 doi: 10.1016/j.virol.2012.09.013 id: cord-260376-29ih5c9v author: Guo, Jian-Ping title: SARS corona virus peptides recognized by antibodies in the sera of convalescent cases date: 2004-07-01 words: 2994.0 sentences: 168.0 pages: flesch: 57.0 cache: ./cache/cord-260376-29ih5c9v.txt txt: ./txt/cord-260376-29ih5c9v.txt summary: title: SARS corona virus peptides recognized by antibodies in the sera of convalescent cases We synthesized on cellulose membranes 4942 ten-amino-acid peptides which included all of the sequences predicted for the severe acute respiratory syndrome (SARS) corona virus. Peptides incorporating all of the sequences predicted in the open reading frames of the SARS-CoV genome were prepared on derivatized cellulose membranes using a robotic peptide synthesizer (Autospot ASP 222, Intavis Bioanalytical Instruments, Lagenfeld, Germany). These data indicate that the four recovered cases developed antibodies with viral neutralizing potency between the time of acute and convalescent serum sampling. Therefore, those peptides strongly recognized on membranes probed with convalescent sera, but not with acute or control sera, should be the most immunodominant and may include SARS-CoV epitopes that are vulnerable to neutralization by antibody. Shown in Table 2 are the 24 overlapping membrane peptides that were recognized exclusively, or much more strongly, in multiple pairs of convalescent compared with the respective acute sera. abstract: We synthesized on cellulose membranes 4942 ten-amino-acid peptides which included all of the sequences predicted for the severe acute respiratory syndrome (SARS) corona virus. We probed these membranes with four pairs of acute and convalescent sera from recovered SARS cases. We correlated positively reacting peptides with the in vitro SARS-CoV neutralizing activity of the samples. We found that convalescent sera with high neutralizing activity recognized exclusively only a limited number of peptides on the membranes. This suggests that antibodies against the epitopes represented by these peptides could be responsible for much of the SARS-CoV neutralizing activity. The findings have implications for monitoring humoral responses to SARS-CoV as well as for developing a successful SARS vaccine. url: https://www.ncbi.nlm.nih.gov/pubmed/15207612/ doi: 10.1016/j.virol.2004.04.017 id: cord-254558-gvo0gwjf author: Guo, Yan Xiang title: Induction of caspase-dependent apoptosis by betanodaviruses GGNNV and demonstration of protein α as an apoptosis inducer date: 2003-03-30 words: 5132.0 sentences: 261.0 pages: flesch: 52.0 cache: ./cache/cord-254558-gvo0gwjf.txt txt: ./txt/cord-254558-gvo0gwjf.txt summary: The infected SB cells underwent DNA fragmentation and stained positive in terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick-end labeling (TUNEL) assay, suggesting that GGNNV infection induced apoptosis in SB cells. To determine if GGNNV induces apoptosis in fish cells through the CD95 apoptotic pathway, infected SB cells were harvested at 24 PI and 48 h PI, and cell lysates were analyzed for IETDase activity, using IETD as the substrate for caspase-8. To determine which protein encoded by betanovirus GGNNV might be responsible for inducing apoptosis, the transient expression of viral proteins A and ␣ in SB and Cos-7 cells was carried out. The results that GGNNV infection induced activation of caspase-3-like proteases and GGNNV-induced apoptosis could be inhibited by DEVD-CHO indicate that fish caspases are important mediators of virus-induced cell death. Here, protein ␣ of GGNNV was demonstrated to be capable of inducing apoptosis by DNA fragmentation and TUNEL staining in transfected SB and Cos-7 cells at 48 h post-transfection. abstract: Betanodaviruses, members of the Nodaviridae family, are the causative agents of viral nervous necrosis in fish and infection by which cause high mortality in larvae and juveniles in a wide range of marine fish species in Asia, Europe, Australia, Martinique, and Tahit. Greasy grouper (Epinephelus tauvina) nervous necrosis viruses (GGNNV) were investigated for their apoptotic activity in culture cells. GGNNV infection of sea bass (SB) cells appeared to induce a typical cytopathic effect (CPE), i.e., cytoplasmic vacuolation, thinning, rounding up, detachment of infected cells from the cultured dish, and eventually cell lysis and death. The infected SB cells underwent DNA fragmentation and stained positive in terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick-end labeling (TUNEL) assay, suggesting that GGNNV infection induced apoptosis in SB cells. In addition, GGNNV-infected SB cells showed an increased activity of caspase-8-like proteases (IETDase) and caspase-3-like proteases (IETDase), whereas inhibitor of caspase-8 and caspase-3 reduced GGNNV-induced apoptosis. This suggests that GGNNV may promote apoptosis via the extrinsic pathway in SB cells. Protein α, the precursor of GGNNV capsid proteins, was transiently expressed in SB and Cos-7 cells. The DNA fragmentation and TUNEL positive signal were apparent in SB and Cos-7 cells expressing protein α, suggesting that protein α may serve as an apoptotic inducer in these cells. Moreover, expression of protein α resulted in the activation of caspase-3-like proteases in both cells, which could be inhibited by a caspase-3-like protease specific inhibitor DEVD-CHO peptide. These results suggest that fish caspases are important elements in GGNNV-meditated apoptosis. url: https://www.sciencedirect.com/science/article/pii/S0042682202000983 doi: 10.1016/s0042-6822(02)00098-3 id: cord-301293-jqy7lcbk author: Gupta, Vandana title: SARS coronavirus nucleocapsid immunodominant T-cell epitope cluster is common to both exogenous recombinant and endogenous DNA-encoded immunogens date: 2006-03-30 words: 7663.0 sentences: 316.0 pages: flesch: 47.0 cache: ./cache/cord-301293-jqy7lcbk.txt txt: ./txt/cord-301293-jqy7lcbk.txt summary: In the present study, we analyzed the spectrum of immune responses of mice to three different forms of the SARS coronavirus nucleocapsid (N): (1) exogenous recombinant protein (N-GST) with Freund''s adjuvant; (2) DNA encoding unmodified N as an endogenous cytoplasmic protein (pN); and (3) DNA encoding N as a LAMP-1 chimera targeted to the lysosomal MHC II compartment (p-LAMP-N). In the present study, we have demonstrated that the dominant T-cell immune responses of mice immunized with the SARS CoV N protein plus adjuvant or with DNA encoding two different cellular trafficking forms of N are directed to the same peptide epitopes of all three immunogens. For example, in this study, the greater response to the LAMP-N chimera could be related to the quantitatively greater delivery of N to the MHC class II compartment of APCs. There can also be major differences in the repertoire or functionality of T cells responding to any given epitope, such as the differences in the IFN-g and IL-4 responses of mice immunized with DNA or with N-GST plus CFA. abstract: Correspondence between the T-cell epitope responses of vaccine immunogens and those of pathogen antigens is critical to vaccine efficacy. In the present study, we analyzed the spectrum of immune responses of mice to three different forms of the SARS coronavirus nucleocapsid (N): (1) exogenous recombinant protein (N-GST) with Freund's adjuvant; (2) DNA encoding unmodified N as an endogenous cytoplasmic protein (pN); and (3) DNA encoding N as a LAMP-1 chimera targeted to the lysosomal MHC II compartment (p-LAMP-N). Lysosomal trafficking of the LAMP/N chimera in transfected cells was documented by both confocal and immunoelectron microscopy. The responses of the immunized mice differed markedly. The strongest T-cell IFN-γ and CTL responses were to the LAMP-N chimera followed by the pN immunogen. In contrast, N-GST elicited strong T cell IL-4 but minimal IFN-γ responses and a much greater antibody response. Despite these differences, however, the immunodominant T-cell ELISpot responses to each of the three immunogens were elicited by the same N peptides, with the greatest responses being generated by a cluster of five overlapping peptides, N(76–114), each of which contained nonameric H2(d) binding domains with high binding scores for both class I and, except for N(76–93), class II alleles. These results demonstrate that processing and presentation of N, whether exogenously or endogenously derived, resulted in common immunodominant epitopes, supporting the usefulness of modified antigen delivery and trafficking forms and, in particular, LAMP chimeras as vaccine candidates. Nevertheless, the profiles of T-cell responses were distinctly different. The pronounced Th-2 and humoral response to N protein plus adjuvant are in contrast to the balanced IFN-γ and IL-4 responses and strong memory CTL responses to the LAMP-N chimera. url: https://www.sciencedirect.com/science/article/pii/S004268220500783X doi: 10.1016/j.virol.2005.11.042 id: cord-293790-7hyelm88 author: Guévin, Carl title: Autophagy protein ATG5 interacts transiently with the hepatitis C virus RNA polymerase (NS5B) early during infection date: 2010-09-01 words: 5267.0 sentences: 290.0 pages: flesch: 54.0 cache: ./cache/cord-293790-7hyelm88.txt txt: ./txt/cord-293790-7hyelm88.txt summary: title: Autophagy protein ATG5 interacts transiently with the hepatitis C virus RNA polymerase (NS5B) early during infection To identify novel cellular factors that may play an essential role in HCV RNA replication, we have previously screened a human liver cDNA library for proteins interacting with the HCV NS5B RNAdependent RNA polymerase (RdRp). Here we report that ATG5, a protein required for the formation of DMV in embryonic stem cell (Mizushima et al., 2001) , specifically interacts with HCV NS5B. As a control, a panel of proteins (RAR-β, RAR-α, HCV core, and nonstructural protein: NS3 prot , NS3 hel , NS4A, and NS4B) cloned in the GAL4 DNA binding domain was tested for interaction with ATG5. A. Soluble yeast extracts containing NS5BΔ21 (N-terminal c-myc tag) and ATG5 (N-terminal HA tag) were incubated with different monoclonal antibodies and the immunoprecipitates were pulled down using protein A/G beads. abstract: Autophagy is an important cellular process by which ATG5 initiates the formation of double membrane vesicles (DMVs). Upon infection, DMVs have been shown to harbor the replicase complex of positive-strand RNA viruses such as MHV, poliovirus, and equine arteritis virus. Recently, it has been shown that autophagy proteins are proviral factors that favor initiation of hepatitis C virus (HCV) infection. Here, we identified ATG5 as an interacting protein for the HCV NS5B. ATG5/NS5B interaction was confirmed by co-IP and metabolic labeling studies. Furthermore, ATG5 protein colocalizes with NS4B, a constituent of the membranous web. Importantly, immunofluorescence staining demonstrated a strong colocalization of ATG5 and NS5B within perinuclear regions of infected cells at 2 days postinfection. However, colocalization was completely lacking at 5 DPI, suggesting that HCV utilizes ATG5 as a proviral factor during the onset of viral infection. Finally, inhibition of autophagy through ATG5 silencing blocks HCV replication. url: https://www.sciencedirect.com/science/article/pii/S0042682210003764 doi: 10.1016/j.virol.2010.05.032 id: cord-292019-rfu0bkag author: Gómez, N. title: Expression of Immunogenic Glycoprotein S Polypeptides from Transmissible Gastroenteritis Coronavirus in Transgenic Plants date: 1998-09-30 words: 3586.0 sentences: 174.0 pages: flesch: 46.0 cache: ./cache/cord-292019-rfu0bkag.txt txt: ./txt/cord-292019-rfu0bkag.txt summary: We report on the immunological response elicited by two recombinant versions of the glycoprotein S from the swine-transmissible gastroenteritis coronavirus (TGEV) expressed in transgenic plants. Arabidoposis plants were genetically transformed with cDNAs constructs encoding either the N-terminal domain (amino acid residues 1–750) or the full-length glycoprotein S of TGEV, responsible for the neutralizing antibody induction against the virus, under the control of the cauliflower mosaic virus 35S (CaMV 35S) promoter. Mice immunized with leaf extracts from transgenic plants developed antibodies that reacted specifically with TGEV in ELISA, immunoprecipitated the virus-induced protein, and neutralized the virus infectivity. In this report, we show that full-length or the globular part (N-terminal domain) of TGEV spike protein (glycoprotein S) expressed in transgenic plants retained the antigenic properties and elicited neutralizing antibodies when used to immunize animals. abstract: Abstract The use of transgenic plants as vaccine production systems was described recently. We report on the immunological response elicited by two recombinant versions of the glycoprotein S from the swine-transmissible gastroenteritis coronavirus (TGEV) expressed in transgenic plants. Arabidoposis plants were genetically transformed with cDNAs constructs encoding either the N-terminal domain (amino acid residues 1–750) or the full-length glycoprotein S of TGEV, responsible for the neutralizing antibody induction against the virus, under the control of the cauliflower mosaic virus 35S (CaMV 35S) promoter. Genomic DNA and mRNA analyses of leaf extracts from transformed plants demonstrated the incorporation of the foreign cDNA into the arabidopsis genome, as well as their transcription. Expression of recombinant polypeptides were observed in most transgenic plants by ELISA using specific antibodies. Mice immunized with leaf extracts from transgenic plants developed antibodies that reacted specifically with TGEV in ELISA, immunoprecipitated the virus-induced protein, and neutralized the virus infectivity. From these results, we conclude that transgenic plants expressing glycoprotein S polypeptides may possibly be used as a source of recombinant antigen for vaccine production. url: https://www.ncbi.nlm.nih.gov/pubmed/9791026/ doi: 10.1006/viro.1998.9315 id: cord-275993-isff6lp2 author: Han, Dong P title: Development of a safe neutralization assay for SARS-CoV and characterization of S-glycoprotein date: 2004-08-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The etiological agent of severe acute respiratory syndrome (SARS) has been identified as a novel coronavirus SARS-CoV. Similar to other coronaviruses, spike (S)-glycoprotein of the virus interacts with a cellular receptor and mediates membrane fusion to allow viral entry into susceptible target cells. Accordingly, S-protein plays an important role in virus infection cycle and is the primary target of neutralizing antibodies. To begin to understand its biochemical and immunological properties, we expressed both full-length and ectodomain of the protein in various primate cells. Our results show that the protein has an electrophoretic mobility of about 160–170 kDa. The protein is glycosylated with high mannose and/or hybrid oligosaccharides, which account for approximately 30 kDa of the apparent protein mass. The detection of S-protein by immunoassays was difficult using human convalescent sera, suggesting that the protein may not elicit strong humoral immune response in virus-infected patients. We were able to pseudotype murine leukemia virus particles with S-protein and produce SARS pseudoviruses. Pseudoviruses infected Vero E6 cells in a pH-independent manner and the infection could be specifically inhibited by convalescent sera. Consistent with low levels of antibodies against S-protein, neutralizing activity was weak with 50% neutralization titers ranging between 1:15 to 1:25. To facilitate quantifying pseudovirus-infected cells, which are stained blue with X-Gal, we devised an automated procedure using an ELISPOT analyzer. The high-throughput capacity of this procedure and the safety of using SARS pseudoviruses should make possible large-scale analyses of neutralizing antibody responses against SARS-CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/15262502/ doi: 10.1016/j.virol.2004.05.017 id: cord-272260-88l9bq4i author: Han, L.Y. title: Prediction of functional class of novel viral proteins by a statistical learning method irrespective of sequence similarity date: 2005-01-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The function of a substantial percentage of the putative protein-coding open reading frames (ORFs) in viral genomes is unknown. As their sequence is not similar to that of proteins of known function, the function of these ORFs cannot be assigned on the basis of sequence similarity. Methods complement or in combination with sequence similarity-based approaches are being explored. The web-based software SVMProt (http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi) to some extent assigns protein functional family irrespective of sequence similarity and has been found to be useful for studying distantly related proteins [Cai, C.Z., Han, L.Y., Ji, Z.L., Chen, X., Chen, Y.Z., 2003. SVM-Prot: web-based support vector machine software for functional classification of a protein from its primary sequence. Nucleic Acids Res. 31(13): 3692–3697]. Here 25 novel viral proteins are selected to test the capability of SVMProt for functional family assignment of viral proteins whose function cannot be confidently predicted on by sequence similarity methods at present. These proteins are without a sequence homolog in the Swissprot database, with its precise function provided in the literature, and not included in the training sets of SVMProt. The predicted functional classes of 72% of these proteins match the literature-described function, which is compared to the overall accuracy of 87% for SVMProt functional class assignment of 34 582 proteins. This suggests that SVMProt to some extent is capable of functional class assignment irrespective of sequence similarity and it is potentially useful for facilitating functional study of novel viral proteins. url: https://api.elsevier.com/content/article/pii/S0042682204006907 doi: 10.1016/j.virol.2004.10.020 id: cord-280795-wtrt13ij author: Han, Yu-Tsung title: Mutational analysis of a helicase motif-based RNA 5′-triphosphatase/NTPase from bamboo mosaic virus date: 2007-10-10 words: 5813.0 sentences: 300.0 pages: flesch: 52.0 cache: ./cache/cord-280795-wtrt13ij.txt txt: ./txt/cord-280795-wtrt13ij.txt summary: As a step toward better understanding the relationship between activities and structures of the helicase-like domain of BaMV replicase, we set out to investigate the importance of each signature motif to its NTPase and RNA 5′-triphosphatase activities by mutational and kinetic analyses. The apparent K i value of AMPPNP in inhibiting RNA 5′-triphosphatase activity The enzymatic activity was determined at 20°C by enzyme-coupled assay in 1 ml solution that contained 10 pmol enzyme, 0.1 to 3 mM NTP and other buffer components as described under Materials and methods except that the amounts of pyruvate kinase were increased up to 50, 75 and 300 U for GTPase, UTPase and CTPase assay, respectively, to assure the rate of NTP hydrolysis being the limiting step within the coupling reaction. The helicase-like domain of plant potexvirus replicase participates in formation of RNA 5′ cap structure by exhibiting RNA 5′-triphosphatase activity abstract: The helicase-like domain of BaMV replicase possesses NTPase and RNA 5′-triphosphatase activities. In this study, mutational effects of the helicase signature motifs and residue L543 on the two activities were investigated. Either activity was inactivated by K643A-S644A, D702A, D730A, R855A, or L543P mutations. On the other hand, Q826A, D858A and L543A had activities, in terms of k(cat)/K(m), reduced by 5- to 15-fold. AMPPNP, a nonhydrolyzable ATP analogue, competitively inhibited RNA 5′-triphosphatase activity. Analogies of mutational effects on the two activities and approximation of K(i(AMPPNP)) and K(m(ATP)) suggest that the catalytic sites of the activities are overlapped. Mutational effects on the viral accumulation in Chenopodium quinoa indicated that the activities manifested by the domain are required for BaMV survival. Results also suggest that Q826 in motif V plays an additional role in preventing tight binding to ATP, which would otherwise decrease further RNA 5′-triphosphatase, leading to demise of the virus in plant. url: https://api.elsevier.com/content/article/pii/S0042682207003492 doi: 10.1016/j.virol.2007.05.013 id: cord-286232-jo24ia4s author: Hasebe, Rie title: Infectious entry of equine herpesvirus-1 into host cells through different endocytic pathways date: 2009-10-25 words: 6962.0 sentences: 364.0 pages: flesch: 51.0 cache: ./cache/cord-286232-jo24ia4s.txt txt: ./txt/cord-286232-jo24ia4s.txt summary: Derm cells by infectious virus recovery assay after viral internalization, suggesting that EHV-1 enters E. In HeLa and receptor-expressing CHO cells, infectious entry of HSV requires trafficking of the virus to an acidic intracellular compartment, phosphatidylinositol 3-kinase activity, glycoprotein D (gD) receptors, as well as viral gB, gD, and gH-gL (Nicola et al., 2003; Nicola and Straus, 2004) . With the use of ultrastructural analysis, we have previously suggested that EHV-1 enters equine brain microvascular endothelial cells (EBMECs) via endocytosis (Hasebe et al., 2006) . Localization of EHV-1 and caveolae during viral internalization Caveolar endocytosis has emerged as a route of entry for several viruses including simian virus 40 (SV40) (Anderson et al., 1996) , mouse polyomavirus (Richterová et al., 2001; Gilbert et al., 2003; Gilbert and Benjamin, 2004) , echovirus (Marjomäki et al., 2002) , human papillomavirus type 31 (Bousarghin et al., 2003; Smith et al., 2007) , human polyomavirus BK (BKV) (Eash et al., 2004) , and species C human adenovirus (Colin et al., 2005) . abstract: We investigated the mechanism by which equine herpesvirus-1 (EHV-1) enters primary cultured equine brain microvascular endothelial cells (EBMECs) and equine dermis (E. Derm) cells. EHV-1 colocalized with caveolin in EBMECs and the infection was greatly reduced by the expression of a dominant negative form of equine caveolin-1 (ecavY14F), suggesting that EHV-1 enters EBMECs via caveolar endocytosis. EHV-1 entry into E. Derm cells was significantly reduced by ATP depletion and treatments with lysosomotropic agents. Enveloped virions were detected from E. Derm cells by infectious virus recovery assay after viral internalization, suggesting that EHV-1 enters E. Derm cells via energy- and pH-dependent endocytosis. These results suggest that EHV-1 utilizes multiple endocytic pathways in different cell types to establish productive infection. url: https://www.sciencedirect.com/science/article/pii/S004268220900470X doi: 10.1016/j.virol.2009.07.032 id: cord-293635-36pmai6s author: Held, Katherine S. title: Differential roles of CCL2 and CCR2 in host defense to coronavirus infection date: 2004-11-24 words: 6726.0 sentences: 312.0 pages: flesch: 55.0 cache: ./cache/cord-293635-36pmai6s.txt txt: ./txt/cord-293635-36pmai6s.txt summary: The data shown in Fig. 2 indicate that CD4 + and CD8 + T cell infiltration into the CNS of infected CCL2 À/À and CCR2 À/À is dramatically reduced as compared to wild-type mice. In contrast to T cell trafficking, there was a similar reduction in the number of macrophages present within the brains in both CCL2 À/À and CCR2 À/À mice, indicating that both ligand and receptor are important in directing these cells into the CNS in response to MHV infection. This is consistent with an earlier study by our laboratory demonstrating that MHV infection of mice lacking CCL3 resulted in the retention of virus-specific cells in the CLN, and this was the result of impaired expression of chemokine receptors, including CXCR3 and CCR5 that greatly aids T cells in their ability to migrate to the brain (Trifilo et al., 2003) . abstract: The CC chemokine ligand 2 (CCL2, monocyte chemoattractant protein-1) is important in coordinating the immune response following microbial infection by regulating T cell polarization as well as leukocyte migration and accumulation within infected tissues. The present study examines the consequences of mouse hepatitis virus (MHV) infection in mice lacking CCL2 (CCL2(−/−)) in order to determine if signaling by this chemokine is relevant in host defense. Intracerebral infection of CCL2(−/−) mice with MHV did not result in increased morbidity or mortality as compared to either wild type or CCR2(−/−) mice and CCL2(−/−) mice cleared replicating virus from the brain. In contrast, CCR2(−/−) mice displayed an impaired ability to clear virus from the brain that was accompanied by a reduction in the numbers of antigen-specific T cells as compared to both CCL2(−/−) and wild-type mice. The paucity in T cell accumulation within the central nervous system (CNS) of MHV-infected CCR2(−/−) mice was not the result of either a deficiency in antigen-presenting cell (APC) accumulation within draining cervical lymph nodes (CLN) or the generation of virus-specific T cells within this compartment. A similar reduction in macrophage infiltration into the CNS was observed in both CCL2(−/−) and CCR2(−/−) mice when compared to wild-type mice, indicating that both CCL2 and CC chemokine receptor 2 (CCR2) contribute to macrophage migration and accumulation within the CNS following MHV infection. Together, these data demonstrate that CCR2, but not CCL2, is important in host defense following viral infection of the CNS, and CCR2 ligand(s), other than CCL2, participates in generating a protective response. url: https://www.ncbi.nlm.nih.gov/pubmed/15518805/ doi: 10.1016/j.virol.2004.09.006 id: cord-326027-58whwspe author: Hernaez, Bruno title: Visualization of the African swine fever virus infection in living cells by incorporation into the virus particle of green fluorescent protein-p54 membrane protein chimera date: 2006-06-20 words: 7885.0 sentences: 372.0 pages: flesch: 45.0 cache: ./cache/cord-326027-58whwspe.txt txt: ./txt/cord-326027-58whwspe.txt summary: title: Visualization of the African swine fever virus infection in living cells by incorporation into the virus particle of green fluorescent protein-p54 membrane protein chimera To track the behavior of African swine fever virus (ASFV) in the infected cells in real time, we produced an infectious recombinant ASFV (B54GFP-2) that expresses and incorporates into the virus particle a chimera of the p54 envelope protein fused to the enhanced green fluorescent protein (EGFP). To determine that protein p54, a major component of the external envelope of ASFV, fused to EGFP protein remains incorporated to the viral particle, BA71V and B54GFP-2 virions were Percoll purified and analyzed by SDS-PAGE and Western blotting using specific antibodies (Fig. 2a) . This new role for p54 in morphogenesis supports the selection of p54 as viral fusion protein and suggests that studies about p54-EGFP trafficking during infection in live cells would be helpful to analyze the acquisition of ASFV envelopes from ER during virus assembly. abstract: Many stages of African swine fever virus infection have not yet been studied in detail. To track the behavior of African swine fever virus (ASFV) in the infected cells in real time, we produced an infectious recombinant ASFV (B54GFP-2) that expresses and incorporates into the virus particle a chimera of the p54 envelope protein fused to the enhanced green fluorescent protein (EGFP). The incorporation of the fusion protein into the virus particle was confirmed immunologically and it was determined that p54-EGFP was fully functional by confirmation that the recombinant virus made normal-sized plaques and presented similar growth curves to the wild-type virus. The tagged virus was visualized as individual fluorescent particles during the first stages of infection and allowed to visualize the infection progression in living cells through the viral life cycle by confocal microscopy. In this work, diverse potential applications of B54GFP-2 to study different aspects of ASFV infection are shown. By using this recombinant virus it was possible to determine the trajectory and speed of intracellular virus movement. Additionally, we have been able to visualize for first time the ASFV factory formation dynamics and the cytophatic effect of the virus in live infected cells. Finally, we have analyzed virus progression along the infection cycle and infected cell death as time-lapse animations. url: https://api.elsevier.com/content/article/pii/S0042682206000353 doi: 10.1016/j.virol.2006.01.021 id: cord-334133-61om170g author: Hollier, Mark J. title: The C-terminal tail of the gp41 transmembrane envelope glycoprotein of HIV-1 clades A, B, C, and D may exist in two conformations: an analysis of sequence, structure, and function date: 2005-07-05 words: 8424.0 sentences: 437.0 pages: flesch: 57.0 cache: ./cache/cord-334133-61om170g.txt txt: ./txt/cord-334133-61om170g.txt summary: For example, the GL envelope protein of equine arteritis virus is proposed to have 1 or 3 MSDs (Snijder and Meulenberg, 1998) , the M protein of transmissible gastroenteritis coronavirus and equine arteritis virus, and the S antigen of hepatitis B virus are proposed to have three or four MSDs (Prange and Streeck, 1995; Risco et al., 1995; Snijder and Meulenberg, 1998) , and the herpes simplex virus glycoprotein B (Pellett et al., 1985) , and the Epstein -Barr virus 58 kDa latent protein Hennessy et al., 1984) both have multiple MSDs. Based on an analysis of their sequence and structure, we propose that the gp41 transmembrane region and C-terminal tail of all HIV-1 clades A to D can exist in two conformations, with either 1 MSD (the conventional structure) or with 3 MSDs. We suggest that these are, respectively, the majority and minority forms of intracellular Env. In the 3-MSD form, MSD 1 and MSD 2 are separated by a highly conserved beta turn, while the MSD 2 and MSD 3 support an unstructured hydrophilic loop/minor ectodomain of 41 residues that in clade B strains is highly antibody-reactive and involved in fusion. abstract: In addition to the major ectodomain, the gp41 transmembrane glycoprotein of HIV-1 is now known to have a minor ectodomain that is part of the long C-terminal tail. Both ectodomains are highly antigenic, carry neutralizing and non-neutralizing epitopes, and are involved in virus-mediated fusion activity. However, data have so far been biologically based, and derived solely from T cell line-adapted (TCLA), B clade viruses. Here we have carried out sequence and theoretically based structural analyses of 357 gp41 C-terminal sequences of mainly primary isolates of HIV-1 clades A, B, C, and D. Data show that all these viruses have the potential to form a tail loop structure (the minor ectodomain) supported by three, β-sheet, membrane-spanning domains (MSDs). This means that the first (N-terminal) tyrosine-based sorting signal of the gp41 tail is situated outside the cell membrane and is non-functional, and that gp41 that reaches the cell surface may be recycled back into the cytoplasm through the activity of the second tyrosine-sorting signal. However, we suggest that only a minority of cell-associated gp41 molecules – those destined for incorporation into virions – has 3 MSDs and the minor ectodomain. Most intracellular gp41 has the conventional single MSD, no minor ectodomain, a functional first tyrosine-based sorting signal, and in line with current thinking is degraded intracellularly. The gp41 structural diversity suggested here can be viewed as an evolutionary strategy to minimize HIV-1 envelope glycoprotein expression on the cell surface, and hence possible cytotoxicity and immune attack on the infected cell. url: https://www.ncbi.nlm.nih.gov/pubmed/15913700/ doi: 10.1016/j.virol.2005.04.015 id: cord-321162-pgd34ewv author: Holmes, Kathryn V. title: Tunicamycin resistant glycosylation of a coronavirus glycoprotein: Demonstration of a novel type of viral glycoprotein date: 1981-12-31 words: 4822.0 sentences: 239.0 pages: flesch: 47.0 cache: ./cache/cord-321162-pgd34ewv.txt txt: ./txt/cord-321162-pgd34ewv.txt summary: Abstract Tunicamycin has different effects on the glycosylation of the two envelope glycoproteins of mouse hepatitis virus (MHV), a coronavirus. The coronavirus envelope envelope glycoprotein E1 appears to be a novel type of viral glycoprotein which is post-translationally glycosylated by a tunicamycin-resistant process that yields oligosaccharide side chains different from those of N-linked glycoproteins. of the synthesis, glycosylation, and intracellular transport of glycoproteins is essential to understanding the structure and function of cell membranes and the role of oligosaccharides in glycoprotein processing and secretion. Labeling with monospecific fluorescent antibody against isolated El or E2 (Sturman et cd, 1980) showed that El remains restricted to the perinuclear area of the cell while E2, like most other viral glycoproteins, migrates rapidly via intracellular membranes to the plasma membrane (Doller and Holmes, 1980) . abstract: Abstract Tunicamycin has different effects on the glycosylation of the two envelope glycoproteins of mouse hepatitis virus (MHV), a coronavirus. Unlike envelope glycoproteins of other viruses, the transmembrane glycoprotein El is glycosylated normally in the presence of tunicamycin. This suggests that glycosylation of El does not involve transfer of core oligosaccharides from dolichol pyrophosphate intermediates to asparagine residues, but may occur by 0-linked glycosylation of serine or threonine residues. Synthesis of the peplomeric glycoprotein E2 is not readily detectable in the presence of tunicamycin. Inhibition of N-linked glycosylation of E2 by tunicamycin either prevents synthesis or facilitates degradation of the protein moiety of E2. Radiolabeling with carbohydrate precursors and borate gel electrophoresis of glycopeptides show that different oligcsaccharide side chains are attached to El and E2. The two coronavirus envelope glycoproteins thus appear to be glycosylated by different mechanisms. In tunicamycin-treated cells, noninfectious virions lacking peplomers are formed at intracytoplasmic membranes and released from the cells. These virions contain normal amounts of nucleocapsid protein and glycosylated El, but lack E2. Thus the transmembrane glycoprotein El is the only viral glycoprotein required for the formation of the viral envelope or for virus maturation and release. The peplomeric glycoprotein E2 appears to be required for attachment to virus receptors on the plasma membrane. The coronavirus envelope envelope glycoprotein E1 appears to be a novel type of viral glycoprotein which is post-translationally glycosylated by a tunicamycin-resistant process that yields oligosaccharide side chains different from those of N-linked glycoproteins. These findings suggest that El may be particularly useful as a model for studying the biosynthesis, glycosylation, and intracellular transport of 0-linked glycoproteins. url: https://www.ncbi.nlm.nih.gov/pubmed/7314449/ doi: 10.1016/0042-6822(81)90115-x id: cord-259717-e8ljkv2y author: Holtz, Lori R. title: Geographic variation in the eukaryotic virome of human diarrhea date: 2014-11-01 words: 6748.0 sentences: 349.0 pages: flesch: 49.0 cache: ./cache/cord-259717-e8ljkv2y.txt txt: ./txt/cord-259717-e8ljkv2y.txt summary: Viromes from Northern Territory children contained more viral families per sample than viromes from Melbourne, which could be attributed largely to an increased number of sequences from the families Adenoviridae and Picornaviridae (genus enterovirus). Viromes from Northern Territory children contained more viral families per sample than viromes from Melbourne, which could be attributed largely to an increased number of sequences from the families Adenoviridae and Picornaviridae (genus enterovirus). Because previous metagenomic studies demonstrated significant virus diversity in patients with diarrhea (Finkbeiner et al., 2008) we focused this study on comparing the eukaryotic virus populations in stools of children with diarrhea collected from two different locations, Melbourne, Australia and the Northern Territory, Australia. In order to independently confirm the sequencing results, we used PCR to define the prevalence of the most frequently detected viruses for which pan-family or pan-genus primers could be used including: adenovirus, astrovirus, enterovirus, norovirus, and rotavirus. abstract: Little is known about the population of eukaryotic viruses in the human gut (“virome”) or the potential role it may play in disease. We used a metagenomic approach to define and compare the eukaryotic viromes in pediatric diarrhea cohorts from two locations (Melbourne and Northern Territory, Australia). We detected viruses known to cause diarrhea, non-pathogenic enteric viruses, viruses not associated with an enteric reservoir, viruses of plants, and novel viruses. Viromes from Northern Territory children contained more viral families per sample than viromes from Melbourne, which could be attributed largely to an increased number of sequences from the families Adenoviridae and Picornaviridae (genus enterovirus). qRT-PCR/PCR confirmed the increased prevalence of adenoviruses and enteroviruses. Testing of additional diarrhea cohorts by qRT-PCR/PCR demonstrated statistically different prevalences in different geographic sites. These findings raise the question of whether the virome plays a role in enteric diseases and conditions that vary with geography. url: https://www.ncbi.nlm.nih.gov/pubmed/25262473/ doi: 10.1016/j.virol.2014.09.012 id: cord-292751-tk1oggi9 author: Hosseini, Elahe Seyed title: The novel coronavirus Disease-2019 (COVID-19): Mechanism of action, detection and recent therapeutic strategies date: 2020-09-24 words: 3784.0 sentences: 222.0 pages: flesch: 46.0 cache: ./cache/cord-292751-tk1oggi9.txt txt: ./txt/cord-292751-tk1oggi9.txt summary: Novel coronavirus SARS-CoV-2, designated as COVID-19 by the World Health Organization (WHO) on the February 11, 2020, is one of the highly pathogenic β‐coronaviruses which infects human. The previously reported viral zoonotic pathogens include SARS-CoV (severe acute respiratory syndrome coronavirus) and MERS (Middle East respiratory syndrome coronavirus) [3, 4] , that can cause severe respiratory disease in human [5, 6] . SARS-CoV-2, a novel coronavirus (which causes COVID19) , has fast spread like a pandemic since its outbreak in Wuhan, China, in December 2019 [7] . Nowadays, Griffithsin, as an inhibitor of SARS and MERS spike, Remdesivir, favipiravir and ribavirin (nucleoside analogues), lopinavir/ritonavir (protease enzyme inhibitors) [61] , oseltamivir (neuraminidase inhibitors), anti-inflammatory drugs and EK1 peptide [62] , the clinical potential to be applied against the 2019-nCoV infection [67, 68] . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan abstract: Novel coronavirus SARS-CoV-2, designated as COVID-19 by the World Health Organization (WHO) on the February 11, 2020, is one of the highly pathogenic β‐coronaviruses which infects human. Early diagnosis of COVID-19 is the most critical step to treat infection. The diagnostic tools are generally molecular methods, serology and viral culture. Recently CRISPR-based method has been investigated to diagnose and treat coronavirus infection. The emergence of 2019-nCoV during the influenza season, has led to the extensive use of antibiotics and neuraminidase enzyme inhibitors, taken orally and intravenously. Currently, antiviral inhibitors of SARS and MERS spike proteins, neuraminidase inhibitors, anti-inflammatory drugs and EK1 peptide are the available therapeutic options for SARS-CoV-2 infected individuals. In addition, Chloroquine, which was previously used for malarial and autoimmune disease, has shown efficacy in the 2019-nCoV infection treatment. In severe hypoxaemia, a combination of antibiotics, α-interferon, lopinavir and mechanical ventilation can effectively mitigate the symptoms. Comprehensive knowledge on the innate and adaptive immune responses, will make it possible to propose potent antiviral drugs with their effective therapeutic measures for the prevention of viral infection. This therapeutic strategy will help patients worldwide to protect themselves against severe and fatal viral infections, that potentially can evolve and develop drug resistance, and to reduce mortality rates. url: https://doi.org/10.1016/j.virol.2020.08.011 doi: 10.1016/j.virol.2020.08.011 id: cord-269419-68kja6bg author: Hu, Weibin title: Fully human broadly neutralizing monoclonal antibodies against influenza A viruses generated from the memory B cells of a 2009 pandemic H1N1 influenza vaccine recipient date: 2013-01-20 words: 4330.0 sentences: 256.0 pages: flesch: 53.0 cache: ./cache/cord-269419-68kja6bg.txt txt: ./txt/cord-269419-68kja6bg.txt summary: title: Fully human broadly neutralizing monoclonal antibodies against influenza A viruses generated from the memory B cells of a 2009 pandemic H1N1 influenza vaccine recipient In this study, we used the full-length HA protein from the 2009 pandemic H1N1 influenza virus to raise fully human neutralizing mAbs. We obtained 19 monoclonal antibodies from the memory B cells of a 2009 pandemic H1N1 influenza vaccine recipient and confirmed that all 19 of the monoclonal antibodies recognized the lysates of both the pandemic virus and the recently circulating seasonal H1N1 influenza virus. Interestingly, we found that most of the monoclonal antibodies, including the seven neutralizing mAbs, bound to the HA stem region (HA2), which is relatively conserved among different influenza A virus strains. These findings indicate that a broad cross-subtype neutralizing antibody response targeting the HA stem region exists in individuals vaccinated against 2009 pandemic H1N1 influenza and that these broadly reactive memory B cells may be important for protecting humans from infection with different influenza A viruses. abstract: Whether the 2009 pandemic H1N1 influenza vaccine can induce heterosubtypic cross-protective anti-hemagglutinin (HA) neutralizing antibodies is an important issue. We obtained a panel of fully human monoclonal antibodies from the memory B cells of a 2009 pandemic H1N1 influenza vaccine recipient. Most of the monoclonal antibodies targeted the HA protein but not the HA1 fragment. Among the analyzed antibodies, seven mAbs exhibited neutralizing activity against several influenza A viruses of different subtypes. The conserved linear epitope targeted by the neutralizing mAbs (FIEGGWTGMVDGWYGYHH) is part of the fusion peptide on HA2. Our work suggests that a heterosubtypic neutralizing antibody response primarily targeting the HA stem region exists in recipients of the 2009 pandemic H1N1 influenza vaccine. The HA stem region contains various conserved neutralizing epitopes with the fusion peptide as an important one. This work may aid in the design of a universal influenza A virus vaccine. url: https://www.ncbi.nlm.nih.gov/pubmed/23084424/ doi: 10.1016/j.virol.2012.09.034 id: cord-329819-dpgexphf author: Hu, Weiwei title: Epidermal growth factor receptor is a co-factor for transmissible gastroenteritis virus entry date: 2018-06-04 words: 6765.0 sentences: 435.0 pages: flesch: 56.0 cache: ./cache/cord-329819-dpgexphf.txt txt: ./txt/cord-329819-dpgexphf.txt summary: IPEC-J2 cells were infected with TGEV (MOI = 2) and cultured for 30 min, then stained for fluorescence microscopy using mouse anti-APN pAb, followed by DyLight 488-conjugated goat anti-mouse IgG and rabbit anti-p-EGFR mAb, followed by DyLight 594-conjugated goat anti-rabbit IgG. Plaque formation in ST cells by the intracellular of infected IPEC-J2 cells showed that APN + EGFR-targeting shRNAs inhibited TGEV entry more significantly (Fig. 3G) . To explore the role of caveolin and clathrin in EGFR internalization early in TGEV infection, we reduced clathrin or caveolin down in normal IPEC-J2 cells through targeting shRNAs, and investigated cell membrane EGFR expression levels during TGEV invasion. We can get to the conclusion that in the early infection stage of TGEV, TGEV particles bound with APN and EGFR, the virus-receptors complex are subsequently internalized by clathrin. abstract: Transmissible gastroenteritis virus (TGEV) causes severe diarrhea and high mortality in newborn piglets. It is well established that porcine intestinal epithelium is the target of the TGEV infection, however the mechanism that TGEV invades the host epithelium remains largely unknown. Aminopeptidase N (APN) is a known receptor of TGEV. This study discovered that the extracellular receptor binding domain 1 pertaining to epidermal growth receptor (EGFR) interact with TGEV spike protein. APN and EGFR synergistically promote TGEV invasion. TGEV promotes APN and EGFR clustering early in infection. Furthermore APN and EGFR synergistically stimulate PI3K/AKT as well as MEK/ERK1/2 endocytosis signaling pathways. TGEV entry is via clathrin and caveolin mediated endocytosis in IPEC-J2 cells. TGEV binds with EGFR, and subsequently promotes EGFR internalization by a clathrin-mediated endocytosis pathway. These results show that EGFR is a co-factor of TGEV, and that it plays a synergistic role with APN early in TGEV infection. url: https://api.elsevier.com/content/article/pii/S0042682218301508 doi: 10.1016/j.virol.2018.05.009 id: cord-322084-gkg1059v author: JEONG, YONG SEOK title: Coronavirus Transcription Mediated by Sequences Flanking the Transcription Consensus Sequence date: 1996-03-01 words: 6250.0 sentences: 302.0 pages: flesch: 52.0 cache: ./cache/cord-322084-gkg1059v.txt txt: ./txt/cord-322084-gkg1059v.txt summary: Abstract In our studies of murine coronavirus transcription, we continue to use defective interfering (DI) RNAs of mouse hepatitis virus (MHV) in which we insert a transcription consensus sequence in order to mimic subgenomic RNA synthesis from the nondefective genome. By using PCR-based sequences flanking the same intergenic region between site-directed mutagenesis, a 12-nucleotide-long segenes 6 and 7 do not affect the efficiency of subgenomic quence, TCTAATCTAAAC, was inserted into DI cDNA DI RNA transcription (Makino and Joo, 1993) . For all of the constructs used in Deletion analysis of those MHV DI RNAs that contain this study we sequenced the inserts that were derived the intergenic sequence from gene 6-7 with its naturally from PCR products to confirm the presence of specific occurring flanking sequences showed that reducing the mutations and the absence of extraneous mutations. abstract: Abstract In our studies of murine coronavirus transcription, we continue to use defective interfering (DI) RNAs of mouse hepatitis virus (MHV) in which we insert a transcription consensus sequence in order to mimic subgenomic RNA synthesis from the nondefective genome. Using our subgenomic DI system, we have studied the effects of sequences flanking the MHV transcription consensus sequence on subgenomic RNA transcription. We obtained the following results. (i) Insertion of a 12-nucleotide-long sequence including the UCUAAAC transcription consensus sequence at different locations of the DI RNA resulted in different efficiencies of subgenomic DI RNA synthesis. (ii) Differences in the amount of subgenomic DI RNA were defined by the sequences that flanked the 12-nucleotide-long sequence and were not affected by the location of the 12-nucleotide-long sequence on the DI RNA. (iii) Naturally occurring flanking sequences of intergenic sequences at gene 6–7, but not at genes 1–2 and 2–3, contained a transcription suppressive element(s). (iv) Each of three naturally occurring flanking sequences of an MHV genomic cryptic transcription consensus sequence from MHV gene 1 also contained a transcription suppressive element(s). These data showed that sequences flanking the transcription consensus sequence affected MHV transcription. url: https://www.sciencedirect.com/science/article/pii/S004268229690118X doi: 10.1006/viro.1996.0118 id: cord-298847-szezd2vb author: Jacomy, Hélène title: Vacuolating encephalitis in mice infected by human coronavirus OC43 date: 2003-10-10 words: 6882.0 sentences: 338.0 pages: flesch: 47.0 cache: ./cache/cord-298847-szezd2vb.txt txt: ./txt/cord-298847-szezd2vb.txt summary: Virus inoculation of 21-day postnatal C57BL/6 and BALB/c mice led to a generalized infection of the whole CNS, demonstrating HCoV-OC43 neuroinvasiveness and neurovirulence. Moreover, mice inoculated with supernatants from cell cultures infected with brain tissue from affected mice developed the same disease, demonstrating that the virus was responsible for pathology. Cells positive for viral antigens were first observed at HCoV-OC43-infected mice gained weight normally during the first 5 days after infection, after which they all lost weight during the acute phase of the disease. (A) 100% of brains from C57BL/6 mice inoculated ic with 10 TCID 50 of HCoV-OC43 were positive for viral RNA between 3 and 11 days postinfection. However, RT-PCR analysis revealed that viral RNA could not be detected after the second week postinfection, suggesting a nonpersistent infection of HCoV-OC43 virus in 21 DPN mice. Every 2 days postinfection, five animals from two groups of infected mice of each strain were sacrificed and processed for detection of viral RNA, viral proteins, and infectious virus. abstract: Involvement of viruses in human neurodegenerative diseases and the underlying pathologic mechanisms remain generally unclear. Human respiratory coronaviruses (HCoV) can infect neural cells, persist in human brain, and activate myelin-reactive T cells. As a means of understanding the human infection, we characterized in vivo the neurotropic and neuroinvasive properties of HCoV-OC43 through the development of an experimental animal model. Virus inoculation of 21-day postnatal C57BL/6 and BALB/c mice led to a generalized infection of the whole CNS, demonstrating HCoV-OC43 neuroinvasiveness and neurovirulence. This acute infection targeted neurons, which underwent vacuolation and degeneration while infected regions presented strong microglial reactivity and inflammatory reactions. Damage to the CNS was not immunologically mediated and microglial reactivity was instead a consequence of direct virus-mediated neuronal injury. Although this acute encephalitis appears generally similar to that induced by murine coronaviruses, an important difference rests in the prominent spongiform-like degeneration that could trigger neuropathology in surviving animals. url: https://www.ncbi.nlm.nih.gov/pubmed/14592756/ doi: 10.1016/s0042-6822(03)00323-4 id: cord-284646-fhruiw23 author: Jaeger, Anna S. title: Spondweni virus causes fetal harm in Ifnar1(-/-) mice and is transmitted by Aedes aegypti mosquitoes date: 2020-05-24 words: 3948.0 sentences: 247.0 pages: flesch: 57.0 cache: ./cache/cord-284646-fhruiw23.txt txt: ./txt/cord-284646-fhruiw23.txt summary: Vector competence experiments showed that Ae. aegypti could transmit SPONV when 70 exposed to bloodmeal titers that approximate physiological titers, while Cx. quinquefasciatus nonpregnant, mixed sex 6-to 11-week-old mice lacking type I interferon signaling (Ifnar1 -/-) Ar94 (this is the only strain used in these studies, so it will be referred to hereafter as 86 SPONV); or 10 2 PFU of the highly pathogenic African-lineage ZIKV strain DAK AR 41524 87 (ZIKV-DAK) (Jaeger et al., 2019) . Despite significantly higher maternal 141 viremia observed at 4 dpi with ZIKV-DAK-infected dams, the fact that resorption rates did 142 not significantly differ between the two groups indicates that both ZIKV-DAK and SPONV 143 have a propensity to harm the developing fetus that is independent of the amount of 144 replication in maternal blood. In contrast, ZIKV-DAK-and SPONV-inoculated dams displayed 221 varying degrees of placental pathology with severe effects predominantly observed in the 222 the labyrinth zone, including vascular injury involving maternal and/or fetal vascular spaces, 223 infarction (obstructed blood flow), necrosis, apoptosis, and hemorrhage (Fig. 4) . abstract: Spondweni virus (SPONV) is the most closely related known flavivirus to Zika virus (ZIKV). Its pathogenic potential and vector specificity have not been well defined. SPONV has been found predominantly in Africa, but was recently detected in a pool of Culex quinquefasciatus mosquitoes in Haiti. Here we show that SPONV can cause significant fetal harm, including demise, comparable to ZIKV, in a mouse model of vertical transmission. Following maternal inoculation, we detected infectious SPONV in placentas and fetuses, along with significant fetal and placental histopathology, together suggesting vertical transmission. To test vector competence, we exposed Aedes aegypti and Culex quinquefasciatus mosquitoes to SPONV-infected bloodmeals. Aedes aegypti could efficiently transmit SPONV, whereas Culex quinquefasciatus could not. Our results suggest that SPONV has the same features that made ZIKV a public health risk. url: https://api.elsevier.com/content/article/pii/S0042682220300921 doi: 10.1016/j.virol.2020.05.005 id: cord-325179-gsf8ad65 author: Jarvis, Donald L. title: Modification of simian virus 40 large tumor antigen by glycosylation date: 1985-03-31 words: 7725.0 sentences: 450.0 pages: flesch: 51.0 cache: ./cache/cord-325179-gsf8ad65.txt txt: ./txt/cord-325179-gsf8ad65.txt summary: In some experiments, SV40-infected cells were labeled with pS]methionine or 3H-monosaccharides in the presence of excess unlabeled amino acids, excess unlabeled sugars, or TM. Infected cells were starved in glucose-free E-MEM from 20.5 to 21 hr p.i., then labeled for 3 hr using 25 &i/ml [?S]methionine or 100 &i/ml rH]galactose in E-MEM containing different sugar concentrations. A polypeptide of about 88,000 (88K) in apparent MW was detected by immunoprecipitation of pS]methionine-labeled, SV40-infected cell extracts with HAF (Fig. lA, lane 3) . Coomassie blue staining revealed that both large T-ag -and small t-ag were also immunoprecipitated from galactose-labeled infected cell extracts (data not shown). To determine the effect of TM treatment, SV40-infected cells were treated with E-MEM or various concentrations of TM starting at 15 hr pi., then were glucose-starved and labeled with pS]methionine or THlglucosamine from 21 to 24 hr p.i. After extraction, T-ag was immunoprecipitated and analyzed by SDS-PAGE (Fig. 8A) . abstract: Abstract The SV40-encoded transforming protein, large tumor antigen (T-ag), is multifunctional. Chemical modifications of the T-ag polypeptide may be important for its multifunctional capacity. T-ag is additionally modified by glycosylation. T-ag was metabolically labeled in SV40-infected cells with tritiated galactose or glucosamine, but not with mannose or fucose. The identity of glycosylated T-ag was established by immunoprecipitation with a variety of T-ag-specific antisera, including monoclonal antibodies. Incorporation of labeled sugar into T-ag was inhibited in the presence of excess unlabeled sugars, but not in the presence of excess unlabeled amino acids. Labeled monosaccharides could be preferentially removed from T-ag with a mixture of glycosidic enzymes. In addition, galactose was removed from purified T-ag by acid hydrolysis and identified as such by thin-layer chromatography. T-ag oligosaccharides were resistant to treatment with EndoH, and glycosylation was not inhibited by tunicamycin. Together, these data strongly suggest that T-ag is glycosylated. Several characteristics, including lack of mannose labeling, EndoH resistance, and tunicamycin resistance, suggest that T-ag is not an N-linked glycoprotein. Rather, these properties are more consistent with the identification of T-ag as an O-linked glycoprotein. url: https://www.sciencedirect.com/science/article/pii/0042682285902508 doi: 10.1016/0042-6822(85)90250-8 id: cord-307904-lnagg1uw author: Johnson, Jennifer A title: Sequence elements controlling expression of Barley stripe mosaic virus subgenomic RNAs in vivo date: 2003-08-15 words: 10666.0 sentences: 536.0 pages: flesch: 58.0 cache: ./cache/cord-307904-lnagg1uw.txt txt: ./txt/cord-307904-lnagg1uw.txt summary: One RNA, ␥KpnI/HpaI, provided a source of the ␥a replicase protein and also contained a 350-nt deletion (from positions 2112 to 2461 on RNA␥) to remove the majority of the ␥b ORF, and a second derivative designed to assess promoter activity contained deletions engineered within the putative sgRNA␥ promoter ( Fig. 2A) . This result implies that competition between the two promoters has a major role in regulating the differential rates of synthesis of the two sgRNAs. To initially define sequences flanking the sgRNA␤2 promoter, two large deletions were generated in the ␤1Ϫ34/ ϩ14 clone that eliminated RNA␤ positions 1705 to 2109 and 2287 to 2434. Analysis of four deletions extending from position Ϫ179 to positions Ϫ110, Ϫ76, Ϫ52, and Ϫ28 relative to the transcription start site revealed that the mutant RNAs were able to replicate in protoplasts, but only mutants containing the deletions Ϫ179/Ϫ110 or Ϫ179/Ϫ76 were able to direct synthesis of sgRNA␤2 (Fig. 4A ). abstract: Barley stripe mosaic virus (BSMV) contains three positive-sense, single-stranded genomic RNAs, designated α, β, and γ, that encode seven major proteins and one minor translational readthrough protein. Three proteins (αa, βa, and γa) are translated directly from the genomic RNAs and the remaining proteins encoded on RNAβ and RNAγ are expressed via three subgenomic messenger RNAs (sgRNAs). sgRNAβ1 directs synthesis of the triple gene block 1 (TGB1) protein. The TGB2 protein, the TGB2′ minor translational readthrough protein, and the TGB3 protein are expressed from sgRNAβ2, which is present in considerably lower abundance than sgRNAβ1. A third sgRNA, sgRNAγ, is required for expression of the γb protein. We have used deletion analyses and site-specific mutations to define the boundaries of promoter regions that are critical for expression of the BSMV sgRNAs in infected protoplasts. The results reveal that the sgRNAβ1 promoter encompasses positions −29 to −2 relative to its transcription start site and is adjacent to a cis-acting element required for RNAβ replication that maps from −107 to −74 relative to the sgRNAβ1 start site. The core sgRNAβ2 promoter includes residues −32 to −17 relative to the sgRNAβ2 transcriptional start site, although maximal activity requires an upstream hexanucleotide sequence residing from positions −64 to −59. The sgRNAγ promoter maps from −21 to +2 relative to its transcription start site and therefore partially overlaps the γa gene. The sgRNAβ1, β2, and γ promoters also differ substantially in sequence, but have similarities to the putative homologous promoters of other Hordeiviruses. These differences are postulated to affect competition for the viral polymerase, coordination of the temporal expression and abundance of the TGB proteins, and constitutive expression of the γb protein. url: https://api.elsevier.com/content/article/pii/S004268220300285X doi: 10.1016/s0042-6822(03)00285-x id: cord-252397-qlu7dilh author: Johnson, Reed F. title: Intratracheal exposure of common marmosets to MERS-CoV Jordan-n3/2012 or MERS-CoV EMC/2012 isolates does not result in lethal disease date: 2015-11-01 words: 5024.0 sentences: 255.0 pages: flesch: 49.0 cache: ./cache/cord-252397-qlu7dilh.txt txt: ./txt/cord-252397-qlu7dilh.txt summary: Results from a natural history study of MERS-CoV-infected rhesus monkeys indicated that intratracheal inoculation induced a non-lethal disease with limited pathology observed in recovering animals at 28 days post-inoculation and infectious virus could be recovered from lung but not other tissues assayed (Yao et al., 2014) . One subject in the MERS-EMC inoculated group appeared to develop a secondary infection observed by CT that increased to study end, day 25 post-exposure. With the use of CT, we observed that IT inoculation of common marmosets with MERS-JOR or MERS-EMC isolates resulted in a non-lethal disease characterized by limited clinical signs and moderate consolidative lung pathology that did not completely resolve by study end. In this experiment, we sought to determine if there were virus specific differences in disease progression following intratracheal inoculation of common marmosets with Middle Eastern Respiratory Syndrome Coronavirus, commonly known as MERS-CoV, with two common laboratory viral isolates (MERS-EMC and MERS-Jordan). abstract: Middle East Respiratory Syndrome Coronavirus (MERS-CoV) continues to be a threat to human health in the Middle East. Development of countermeasures is ongoing; however, an animal model that faithfully recapitulates human disease has yet to be defined. A recent study indicated that inoculation of common marmosets resulted in inconsistent lethality. Based on these data we sought to compare two isolates of MERS-CoV. We followed disease progression in common marmosets after intratracheal exposure with: MERS-CoV-EMC/2012, MERS-CoV-Jordan-n3/2012, media, or inactivated virus. Our data suggest that common marmosets developed a mild to moderate non-lethal respiratory disease, which was quantifiable by computed tomography (CT), with limited other clinical signs. Based on CT data, clinical data, and virological data, MERS-CoV inoculation of common marmosets results in mild to moderate clinical signs of disease that are likely due to manipulations of the marmoset rather than as a result of robust viral replication. url: https://www.sciencedirect.com/science/article/pii/S0042682215003323 doi: 10.1016/j.virol.2015.07.013 id: cord-299994-1ksfo0pr author: Kanitz, Manuel title: Structural basis for catalysis and substrate specificity of a 3C-like cysteine protease from a mosquito mesonivirus date: 2019-05-02 words: 8934.0 sentences: 450.0 pages: flesch: 59.0 cache: ./cache/cord-299994-1ksfo0pr.txt txt: ./txt/cord-299994-1ksfo0pr.txt summary: In CavV and most other members of the genus Alphamesonivirus, the P2 position of putative 3CL pro substrates is predominantly occupied by Asn. The crystal structure of the 3CL pro /inhibitor complex shows that the Asn side chain fits perfectly into the S2 subpocket, with its carboxamide functionality acting as hydrogen bond donor and acceptor in interactions with the main chain carbonyl oxygen of Asp216 and the Oγ atom of Ser52, respectively. In the first crystal structure reported for a coronavirus 3CL pro , this Asp (Asp186 in the TGEV 3CL pro sequence) was found to form a hydrogen bond to a water molecule located in a position that, in chymotrypsin and related serine proteases, is occupied by the side chain of the third member of the catalytic triad (typically Asp) (Anand et al., 2002) . abstract: Cavally virus (CavV) is a mosquito-borne plus-strand RNA virus in the family Mesoniviridae (order Nidovirales). We present X-ray structures for the CavV 3C-like protease (3CL(pro)), as a free enzyme and in complex with a peptide aldehyde inhibitor mimicking the P4-to-P1 residues of a natural substrate. The 3CL(pro) structure (refined to 1.94 Å) shows that the protein forms dimers. The monomers are comprised of N-terminal domains I and II, which adopt a chymotrypsin-like fold, and a C-terminal α-helical domain III. The catalytic Cys-His dyad is assisted by a complex network of interactions involving a water molecule that mediates polar contacts between the catalytic His and a conserved Asp located in the domain II-III junction and is suitably positioned to stabilize the developing positive charge of the catalytic His in the transition state during catalysis. The study also reveals the structural basis for the distinct P2 Asn-specific substrate-binding pocket of mesonivirus 3CL(pro)s. url: https://www.sciencedirect.com/science/article/pii/S0042682219301151 doi: 10.1016/j.virol.2019.05.001 id: cord-303238-us3dybue author: Kanjanahaluethai, Amornrat title: Membrane Topology of Murine Coronavirus Replicase Nonstructural Protein 3 date: 2007-05-01 words: 4789.0 sentences: 247.0 pages: flesch: 50.0 cache: ./cache/cord-303238-us3dybue.txt txt: ./txt/cord-303238-us3dybue.txt summary: The papain-like protease (PLpro) encoded by the coronavirus that causes severe acute respiratory syndrome (SARS-CoV) processes three sites in the replicase polyprotein (Harcourt et al., 2004) , and has recently been shown to have de-ubiquitinating activity (Barretto et al., 2005; Lindner et al., 2005) . To extend these studies of membrane association of coronavirus replicase products, we analyzed the amino acid sequence of MHV-JHM nsp3 (from glycine-833 to glycine-2840) for probability of transmembrane helices using the five different programs designed to search for putative membrane-spanning sequences: Phobius, TMHMM, HMMTOP, SOSUI and TMpred (Fig. 2) . In contrast, when CMMs were added to the mixture, protein products that included all or part of nsp3-TM (PLP2-2485, -2390 and -2258) were detected predominantly in the pelleted fraction, consistent with membrane association (Fig. 3B ). abstract: Mouse hepatitis virus (MHV) is a member of the family Coronaviridae. These positive strand RNA viruses encode a replicase polyprotein that is processed into 16 nonstructural proteins (nsps). The nsps assemble with membranes to generate double membrane vesicles, which are the sites of viral RNA synthesis. MHV nsp3 contains multiple domains including two papain-like protease domains, PLP1 and PLP2, and a predicted transmembrane (TM) domain. In this study, we determined the membrane topology of nsp3-TM and showed that TM-mediated tethering of PLP2 is important for processing at cleavage site 3. Biochemical analysis revealed that nsp3 is an integral membrane protein that is inserted into endoplasmic reticulum (ER) membranes co-translationally and glycosylated at asparagine-2357. Proteinase K digestion experiments indicate that the TM domain of nsp3 has 4 membrane-spanning helices. We show that nsp3-TM is sufficient to mediate ER membrane association of a cytosolic protein. This study is the first detailed analysis of the topology and function of the coronavirus nsp3 TM domain. url: https://www.ncbi.nlm.nih.gov/pubmed/17222884/ doi: 10.1016/j.virol.2006.12.009 id: cord-275348-jna496x7 author: Kapadia, Sagar U. title: SARS vaccine based on a replication-defective recombinant vesicular stomatitis virus is more potent than one based on a replication-competent vector date: 2008-06-20 words: 5982.0 sentences: 317.0 pages: flesch: 53.0 cache: ./cache/cord-275348-jna496x7.txt txt: ./txt/cord-275348-jna496x7.txt summary: A SARS vaccine based on a live-attenuated vesicular stomatitis virus (VSV) recombinant expressing the SARS-CoV S protein provides long-term protection of immunized mice from SARS-CoV infection (Kapadia, S.U., Rose, J. We found that the vaccine given intramuscularly induced a neutralizing antibody response to SARS-CoV that was approximately ten-fold greater than that required for the protection from SARS-CoV infection, and significantly greater than that generated by the replication-competent vector expressing SARS-CoV S protein given by the same route. In order to evaluate this vector as a SARS vaccine candidate, we also developed a SARS-CoV neutralization assay using a pseudotyped VSV recombinant expressing a green fluorescent protein. SARS-CoV neutralizing antibody titers of these sera were determined by incubating VSVΔG-EGFP/SΔtail-HA virus with serial dilutions of these sera, and the virusserum mixtures were transferred to a monolayer of Vero E6 cells. abstract: A SARS vaccine based on a live-attenuated vesicular stomatitis virus (VSV) recombinant expressing the SARS-CoV S protein provides long-term protection of immunized mice from SARS-CoV infection (Kapadia, S.U., Rose, J. K., Lamirande, E., Vogel, L., Subbarao, K., Roberts, A., 2005. Long-term protection from SARS coronavirus infection conferred by a single immunization with an attenuated VSV-based vaccine. Virology 340(2), 174–82.). Because it is difficult to obtain regulatory approval of vaccine based on live viruses, we constructed a replication-defective single-cycle VSV vector in which we replaced the VSV glycoprotein (G) gene with the SARS-CoV S gene. The virus was only able to infect cells when pseudotyped with the VSV G protein. We measured the effectiveness of immunization with the single-cycle vaccine in mice. We found that the vaccine given intramuscularly induced a neutralizing antibody response to SARS-CoV that was approximately ten-fold greater than that required for the protection from SARS-CoV infection, and significantly greater than that generated by the replication-competent vector expressing SARS-CoV S protein given by the same route. Our results, along with earlier studies showing potent induction of T-cell responses by single-cycle vectors, indicate that these vectors are excellent alternatives to live-attenuated VSV. url: https://api.elsevier.com/content/article/pii/S0042682208001736 doi: 10.1016/j.virol.2008.03.002 id: cord-262347-ejhz9rra author: Kappes, Matthew A. title: PRRSV structure, replication and recombination: Origin of phenotype and genotype diversity date: 2015-03-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine reproductive and respiratory disease virus (PRRSV) has the intrinsic ability to adapt and evolve. After 25 years of study, this persistent pathogen has continued to frustrate efforts to eliminate infection of herds through vaccination or other elimination strategies. The purpose of this review is to summarize the research on the virion structure, replication and recombination properties of PRRSV that have led to the extraordinary phenotype and genotype diversity that exists worldwide. url: https://doi.org/10.1016/j.virol.2015.02.012 doi: 10.1016/j.virol.2015.02.012 id: cord-300372-h5g4z8ts author: Kelvin, Alyson A. title: Lack of Group X Secreted Phospholipase A(2) Increases Survival Following Pandemic H1N1 Influenza Infection date: 2014-04-01 words: 10489.0 sentences: 533.0 pages: flesch: 52.0 cache: ./cache/cord-300372-h5g4z8ts.txt txt: ./txt/cord-300372-h5g4z8ts.txt summary: Based on the central role of sPLA(2) enzymes as key initiators of inflammatory processes, we propose that activation of GX-sPLA(2) during H1N1pdm infection is an early step of pulmonary inflammation and its (Reviewer 2 Minor Comment 2) inhibition increases adaptive immunity and improves survival. Increased expression of immunoglobulin chain, lymphocyte differentiation, antigen processing genes and presence of CD3 þ T cells in the lungs of mice lacking GX-sPLA 2 after H1N1pdm infection Lack of GX-sPLA 2 resulted in decreased levels of PGD 2 , LTB 4 , cysteinyl leukotrienes, PGE 2 and Lipoxin A 4 and increased adaptive immune responses at 3 but not 6 days following H1N1pdm infection. MPO protein (neutrophil marker), CD45 protein (leukocyte marker) and GAPDH protein (loading control) expression levels were determined by immunoblot analysis from lung tissue homogenates of GX þ / þ and GX À / À mice over a 14 day time course of H1N1pdm influenza infection (Bi). abstract: The role of Group X secreted phospholipase A(2) (GX-sPLA(2)) during influenza infection has not been previously investigated. We examined the role of (Reviewer 2 Minor Comment 2) GX-sPLA(2) during H1N1 pandemic influenza infection in a GX-sPLA(2) gene targeted mouse (GX(−/−)) model and found that survival after infection was significantly greater in GX(−/−) mice than in GX(+/+) mice. Downstream products of GX-sPLA(2) activity, PGD(2), PGE(2), LTB(4), cysteinyl leukotrienes and Lipoxin A(4) were significantly lower in GX(−/−) mice BAL fluid. Lung microarray analysis identified an earlier and more robust induction of T and B cell associated genes in GX(−/−) mice. Based on the central role of sPLA(2) enzymes as key initiators of inflammatory processes, we propose that activation of GX-sPLA(2) during H1N1pdm infection is an early step of pulmonary inflammation and its (Reviewer 2 Minor Comment 2) inhibition increases adaptive immunity and improves survival. Our findings suggest that GX-sPLA(2) may be a potential therapeutic target during influenza. url: https://www.sciencedirect.com/science/article/pii/S0042682214000439 doi: 10.1016/j.virol.2014.01.030 id: cord-311255-zaa8i9vh author: Kim, Youngnam title: Porcine epidemic diarrhea virus induces caspase-independent apoptosis through activation of mitochondrial apoptosis-inducing factor date: 2014-07-31 words: 8040.0 sentences: 370.0 pages: flesch: 41.0 cache: ./cache/cord-311255-zaa8i9vh.txt txt: ./txt/cord-311255-zaa8i9vh.txt summary: Abstract The present study sought to investigate whether porcine epidemic diarrhea virus (PEDV) induces apoptosis and to elucidate the mechanisms associated with apoptotic cell death after PEDV infection. Interestingly, mitochondrial apoptosis-inducing factor (AIF) was found to translocate to the nucleus during PEDV infection, and AIF relocalization was completely abrogated by the presence of cyclosporin A (CsA), an inhibitor of cyclophilin D (CypD) that is an essential component of the mitochondrial permeabilization transition pore (mPTP) complex. Altogether, our results indicate that a caspase-independent mitochondrial AIF-mediated pathway plays a central role in PEDV-induced apoptosis to facilitate viral replication and pathogenesis. Therefore, in this study, we aimed to determine if PEDV induces apoptosis following infection in vitro and in vivo and to define the specific pathways involved in apoptotic death of virus-infected cells. abstract: Abstract The present study sought to investigate whether porcine epidemic diarrhea virus (PEDV) induces apoptosis and to elucidate the mechanisms associated with apoptotic cell death after PEDV infection. PEDV-infected cells showed evidence of apoptosis in vitro and in vivo. However, experimental data indicated that the caspase cascade is not involved in PEDV-induced apoptotic cell death. Interestingly, mitochondrial apoptosis-inducing factor (AIF) was found to translocate to the nucleus during PEDV infection, and AIF relocalization was completely abrogated by the presence of cyclosporin A (CsA), an inhibitor of cyclophilin D (CypD) that is an essential component of the mitochondrial permeabilization transition pore (mPTP) complex. CsA treatment resulted in significant inhibition of PEDV-triggered apoptosis and suppressed PEDV replication. Furthermore, direct inhibition of AIF strongly impaired PEDV infection and virus-induced apoptosis. Altogether, our results indicate that a caspase-independent mitochondrial AIF-mediated pathway plays a central role in PEDV-induced apoptosis to facilitate viral replication and pathogenesis. url: https://doi.org/10.1016/j.virol.2014.04.040 doi: 10.1016/j.virol.2014.04.040 id: cord-284581-fl2nt4ak author: Kleine-Weber, Hannah title: Spike proteins of novel MERS-coronavirus isolates from North- and West-African dromedary camels mediate robust viral entry into human target cells date: 2019-07-19 words: 3195.0 sentences: 190.0 pages: flesch: 58.0 cache: ./cache/cord-284581-fl2nt4ak.txt txt: ./txt/cord-284581-fl2nt4ak.txt summary: title: Spike proteins of novel MERS-coronavirus isolates from Northand West-African dromedary camels mediate robust viral entry into human target cells A recent study showed that MERS-CoV found in North/West(Morocco) and West-African (Burkina Faso and Nigeria) dromedary camels are genetically distinct from Arabian viruses and have reduced replicative capacity in human cells, potentially due to amino acid changes in one or more viral proteins. Here, we show that the spike (S) proteins of the prototypic Arabian MERS-CoV strain, human betacoronavirus 2c EMC/2012, and the above stated African MERS-CoV variants do not appreciably differ in expression, DPP4 binding and ability to drive entry into target cells. We employed a previously described vesicular stomatitis virus (VSV)-based pseudotyping system to study MERS-S-driven host cell entry (Kleine-Weber et al., 2018 known to adequately model key aspects of the coronavirus entry process. Host cell entry driven by the S proteins of North/West-and West-African MERS-CoV isolates from dromedary camels is robust. abstract: The highly pathogenic Middle East respiratory syndrome (MERS)-related coronavirus (CoV) is transmitted from dromedary camels, the natural reservoir, to humans. For at present unclear reasons, MERS cases have so far only been observed in the Arabian Peninsula, although MERS-CoV also circulates in African dromedary camels. A recent study showed that MERS-CoV found in North/West- (Morocco) and West-African (Burkina Faso and Nigeria) dromedary camels are genetically distinct from Arabian viruses and have reduced replicative capacity in human cells, potentially due to amino acid changes in one or more viral proteins. Here, we show that the spike (S) proteins of the prototypic Arabian MERS-CoV strain, human betacoronavirus 2c EMC/2012, and the above stated African MERS-CoV variants do not appreciably differ in expression, DPP4 binding and ability to drive entry into target cells. Thus, virus-host-interactions at the entry stage may not limit spread of North- and West-African MERS-CoV in human cells. url: https://www.sciencedirect.com/science/article/pii/S0042682219301916 doi: 10.1016/j.virol.2019.07.016 id: cord-315069-xo4mbxei author: Knorr, D. A. title: De novo generation of defective interfering RNAs of tomato bushy stunt virus by high multiplicity passage date: 1991-03-31 words: 5134.0 sentences: 250.0 pages: flesch: 52.0 cache: ./cache/cord-315069-xo4mbxei.txt txt: ./txt/cord-315069-xo4mbxei.txt summary: Abstract Defective interfering (DI) RNAs were generated de novo in each of 12 independent isolates of tomato bushy stunt virus (TBSV) upon serial passage at high multiplicities of infection (m.o.i.) in plants, but not in any of 4 additional isolates after 11 serial passages at low m.o.i. The DI RNAs were detected in RNA isolated from virus particles and in 2.3 M LiCl-soluble RNA fractions isolated from inoculated leaves. On each host species, six isolates were passed at high m.o.i. and two control isolates were passed at low m.o.i. In these hosts, DI-free TBSV induces lethal necrosis within 7-l 0 days postinoculation (d.p.i.), except in the presence of DI RNAs which are associated with attenuation and the establishment of persistent infections (Hillman et a/., 1987) . The small RNAs which developed in each of the high m.o.i. isolates hybridized to both 5''-and 3''-proximal TBSV genomic sequences, but generally were larger (-600 bases) than the previously characterized DI 1 RNA species (-400 bases). abstract: Abstract Defective interfering (DI) RNAs were generated de novo in each of 12 independent isolates of tomato bushy stunt virus (TBSV) upon serial passage at high multiplicities of infection (m.o.i.) in plants, but not in any of 4 additional isolates after 11 serial passages at low m.o.i. The DI RNAs were detected in RNA isolated from virus particles and in 2.3 M LiCl-soluble RNA fractions isolated from inoculated leaves. Symptom attenuation leading to persistent infections was closely correlated with the passage in which DIs first developed. Comparisons of nucleotide sequences of 10 cDNA clones from 2 DI RNA populations and with a previously characterized TBSV DI RNA revealed the same four regions of sequence from the TBSV genome were strictly conserved in each of the DI RNAs: the virus 5′ leader sequence of 168 bases; a region of approximately 200–250 bases from the viral polymerase gene; approximately 70 bases from the 3′ terminus of the viral pl9 and p22 genes; and approximately 130 bases from the 3′terminal noncoding region. Conservation of the sequence motif present in all of the DIs suggests that there might be a common mechanism of DI formation as well as selection pressure to maintain sequences essential for replication and encapsidation. url: https://api.elsevier.com/content/article/pii/004268229190484S doi: 10.1016/0042-6822(91)90484-s id: cord-296416-q0rsfzgw author: LAVI, EHUD title: Syncytia Formation Induced by Coronavirus Infection Is Associated with Fragmentation and Rearrangement of the Golgi Apparatus date: 1996-07-15 words: 4766.0 sentences: 232.0 pages: flesch: 50.0 cache: ./cache/cord-296416-q0rsfzgw.txt txt: ./txt/cord-296416-q0rsfzgw.txt summary: In many 3-5 hr after infection, individual elements of the GA, cells the secretion blocker Brefeldin A (BFA) reversibly which are associated initially with separate microtubuleredistributes membranes and enzymes of the GA back organizing centers in perinuclear areas of fused cells, into the RER, but does not inhibit endocytosis (Doms et congregate in the center of syncytia and form an exal., 1989; Lippincott-Schwartz et al., 1989; Johnston et al., tended network of nondisrupted intact Golgi complexes 1994). In this study, we used organ-Immunohistochemistry elle-specific antibodies, immunohistochemistry, and transmission electron microscopy to examine the fate of Cells, grown on poly-D-lysine-treated coverslips, were the GA during cell fusion and syncytia formation in mouse fixed with 2% paraformaldehyde for 20 min at room tem-L-2 cells infected with MHV-A59 and fusion defective perature, washed three times in PBS, then incubated for mutants. abstract: Abstract Coronavirus mouse hepatitis virus (MHV) possesses a membrane glycoprotein (M) which is targeted to the Golgi apparatus (GA). We used immunocytochemistry with an organelle-specific antiserum to investigate the morphologic changes of the GA during infection of L2 murine fibroblasts with MHV-A59. Twenty-four hours after infection the GA was fragmented and translocated in the center of syncytia, while the microtubular network was also rearranged displaying radiating elements toward the center of syncytia. Two fusion-defective mutants, which contain an identical amino acid substitution in the cleavage signal sequence of the spike glycoprotein (S), induced fragmentation of the GA. However, the GA migrated only partially to the centers of syncytia during infection with these mutants. Revertant viruses, in which the above mutation was corrected, had fusion properties and GA staining similar to wtMHV-A59. Experiments with brefeldin A (BFA), which induces redistribution of the GA into the rough endoplasmic reticulum (RER), revealed that an intact GA for a period of 4–16 hr postinfection, is required for coronavirus replication and syncytia formation. Thus, during MHV infection, syncytia formation is associated with fragmentation of the GA, followed by a previously undescribed phenomenon of migration of the organelle into the centers of syncytia. The fragmentation of the GA, however, may occur without the formation of syncytia. Therefore, two distinct mechanisms may be responsible for the fragmentation of the GA and its subsequent migration to the center of syncytia. url: https://www.ncbi.nlm.nih.gov/pubmed/8661443/ doi: 10.1006/viro.1996.0382 id: cord-294056-7e477y1x author: La Monica, Nicola title: Coronavirus mRNA synthesis: Identification of novel transcription initiation signals which are differentially regulated by different leader sequences date: 1992-05-31 words: 3341.0 sentences: 173.0 pages: flesch: 58.0 cache: ./cache/cord-294056-7e477y1x.txt txt: ./txt/cord-294056-7e477y1x.txt summary: Previously, we have identified a transcription initiation site (for mRNA 2-1), which is more efficiently transcribed by viruses containing two copies of UCUAA sequence in the leader RNA than by those with three copies. To understand the mechanism of MHV mRNA transcription, we have attempted to determine whether the differential regulation of transcription initiation by leader RNA containing different UCUAA copy numbers is unique to mRNA 2-l. The analysis of several other recombinant viruses with different genome structures suggested that mRNA 3-l was synthesized only by viruses with a leader RNA containing three copies of UCUAA and gene 3 sequence derived from A59 but not JHM (10, 13). Using various primers representing sequences of different regions of gene 1 of the JHM strain of MHV (2) and a second primer representing the 5''-end of the leader RNA, we detected several PCR products which represented mRNAs initiated from various sites. abstract: Abstract The mRNA synthesis of mouse hepatitis virus (MHV) has been proposed to be the result of interaction between the leader RNA and the intergenic sites. Previously, we have identified a transcription initiation site (for mRNA 2-1), which is more efficiently transcribed by viruses containing two copies of UCUAA sequence in the leader RNA than by those with three copies. In this study, we have identified several sites which are regulated in the opposite way, namely, they are efficiently transcribed by the leader RNA with three UCUAA copies but not by those with two copies. These sites were characterized by primer extension and amplification by polymerase chain reaction. One of these sites is in the gene 3 region of a recombinant virus between A59 and JHM strains of MHV. Another is in the gene 2 region of MHV-1 strain. Both of these sites have a sequence similar to but different from the consensus transcription initiation signal (UCUAAUCUAUC and UUUAAUCUU, as opposed to UCUAAAC). These two novel intergenic sequences are not present in the genome of the JHM strain, consistent with the absence of these mRNAs in the JHM-infected cells. The discovery of this type of transcription initiation site provides additional evidence for the importance of the leader RNA in the transcription initiation of MHV mRNAs. url: https://www.ncbi.nlm.nih.gov/pubmed/1566582/ doi: 10.1016/0042-6822(92)90774-j id: cord-300810-a1skdp67 author: Lafay, F. title: Spread of the CVS strain of rabies virus and of the avirulent mutant AvO1 along the olfactory pathways of the mouse after intranasal inoculation date: 1991-07-31 words: 5731.0 sentences: 292.0 pages: flesch: 54.0 cache: ./cache/cord-300810-a1skdp67.txt txt: ./txt/cord-300810-a1skdp67.txt summary: title: Spread of the CVS strain of rabies virus and of the avirulent mutant AvO1 along the olfactory pathways of the mouse after intranasal inoculation Abstract After intranasal instillation in the mouse, rabies virus (CVS strain) selectively infected olfactory receptor cells. On the other hand, other neuronal cells permissive for CVS, such as mitral cells or the anterior olfactory nucleus, are completely free of infection with the mutant, indicating that restriction is related to the ability of AvO1 to penetrate several categories of neurons. The G protein plays a pivotal role in the pathogenicity of the virus because of its interaction with the host cells '' Abbreviations used: AON, anterior olfactory nucleus; CNS, central nervous system; GABA, Gamma aminobutyric acid; HDB, horizontal limb of the diagonal band; HRP, horseradish peroxidase; HSVl, herpes simplex type 1; IPL, internal plexiform layer: LC, locus coeruleus; LD50, lethal dose 50%; LPA. abstract: Abstract After intranasal instillation in the mouse, rabies virus (CVS strain) selectively infected olfactory receptor cells. In the main olfactory bulb (MOB), infection was observed in periglomerular, tufted, and mitral cells and in interneurons located in the internal plexiform layer. Beyond the MOB, CVS spread into the brain along the olfactory pathways. This infection is specific to chains of functionally related neurons but at the death of the animal some nuclei remain uninfected. CVS also penetrated the trigeminal system. The avirulent mutant AvOl, carrying a mutation in position 333 of the glycoprotein, infected the olfactory epithelium and the trigeminal nerve as efficiently as CVS. During the second cycle of infection, the mutant was able to infect efficiently periglomerular cells in the MOB and neurons of the horizontal limb of the diagonal band, which indicates that maturation of infective particles is not affected in primarily infected neuronal cells. On the other hand, other neuronal cells permissive for CVS, such as mitral cells or the anterior olfactory nucleus, are completely free of infection with the mutant, indicating that restriction is related to the ability of AvO1 to penetrate several categories of neurons. From these observations, we concluded that CVS should be able to bind several different receptors to penetrate neurons, while the mutant would be unable to recognize some of them. url: https://api.elsevier.com/content/article/pii/0042682291901452 doi: 10.1016/0042-6822(91)90145-2 id: cord-353467-wbtzvm4i author: Lambert, Carsten title: Functional incorporation of green fluorescent protein into hepatitis B virus envelope particles date: 2004-12-05 words: 6316.0 sentences: 307.0 pages: flesch: 50.0 cache: ./cache/cord-353467-wbtzvm4i.txt txt: ./txt/cord-353467-wbtzvm4i.txt summary: In the late stages of an HBV infection, progeny virions are formed by budding of the pre-assembled cytosolic nucleocapsids, enclosing the partially double-stranded DNA genome 3.2 kb in length and the viral polymerase through intracellular membranes accommodating the viral envelope proteins (for review, see Nassal, 1996) . To determine whether the co-secreted GFP.S and SHA proteins resembled authentic subviral HBV envelope particles, the culture supernatant of transfected cells was fractionated by isopycnic CsCl gradient centrifugation and fractions were analyzed by an S-specific ELISA. According to current models for the transmembrane structure of S, its N-terminus and hence the GFP fusion site are located to the lumenal side of intracellular membranes that is topologically equivalent to the virion surface ( Fig. 4A ) (Berting et al., 1995; Stirk et al., 1992) . Here we applied this approach to hepatitis B virus and obtained fluorescent subviral and viral particles by incorporation of the viral S envelope protein, tagged with GFP, in trans, thereby preserving all the functions necessary for the viral life cycle. abstract: The envelope of hepatitis B virus (HBV), containing the L, M, and S proteins, is essential for virus entry and maturation. For direct visualization of HBV, we determined whether envelope assembly could accommodate the green fluorescent protein (GFP). While the C-terminal addition of GFP to S trans-dominant negatively inhibited empty envelope particle secretion, the N-terminal GFP fusion to S (GFP.S) was co-integrated into the envelope, giving rise to fluorescent particles. Microscopy and topogenesis analyses demonstrated that the proper intracellular distribution and folding of GFP.S, required for particle export were rescued by interprotein interactions with wild-type S. Thereby, a dual location of GFP, inside and outside the envelope, was observed. GFP.S was also efficiently packaged into the viral envelope, and these GFP-tagged virions retained the capacity for attachment to HBV receptor-positive cells in vitro. Together, GFP-tagged virions should be suitable to monitor HBV uptake and egress in live hepatocytes. url: https://www.ncbi.nlm.nih.gov/pubmed/15527842/ doi: 10.1016/j.virol.2004.09.031 id: cord-267027-diwm1940 author: Le, Shu-Yun title: Conserved tertiary structure elements in the 5′ untranslated region of human enteroviruses and rhinoviruses date: 1992-12-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract A combination of comparative sequence analysis and thermodynamic methods reveals the conservation of tertiary structure elements in the 5′ untranslated region (UTR) of human enteroviruses and rhinoviruses. The predicted common structural elements occur in the 3′ end of a segment that is critical for internal ribosome binding, termed “ribosome landing pad” (RLP), of polioviruses. Base pairings between highly conserved 17-nucleotide (nt) and 21-nt sequences in the 5′ UTR of human enteroviruses and rhinoviruses constitute a predicted pseudoknot that is significantly more stable than those that can be formed from a large set of randomly shuffled sequences. A conserved single-stranded polypyrimidine tract is located between two conserved tertiary elements. R. Nicholson, J. Pelletier, S.-Y. Le, and N. Sonenberg (1991, J. Virol. 65, 5886–5894) demonstrated that the point mutations of 3-nt UUU out of an essential 4-nt pyrimidine stretch sequence UUUC abolished translation. Structural analysis of the mutant sequence indicates that small point mutations within the short polypyrimidine sequence would destroy the tertiary interaction in the predicted, highly ordered structure. The proposed common tertiary structure can offer experimentalists a model upon which to extend the interpretations for currently available data. Based on these structural features possible base-pairing models between human enteroviruses and 18 S rRNA and between human rhinoviruses and 18 S rRNA are proposed. The proposed common structure implicates a biological function for these sequences in translational initiation. url: https://www.sciencedirect.com/science/article/pii/004268229290261M doi: 10.1016/0042-6822(92)90261-m id: cord-288669-46tkedw7 author: Lee, Changhee title: The small envelope protein of porcine reproductive and respiratory syndrome virus possesses ion channel protein-like properties date: 2006-11-10 words: 9258.0 sentences: 455.0 pages: flesch: 51.0 cache: ./cache/cord-288669-46tkedw7.txt txt: ./txt/cord-288669-46tkedw7.txt summary: P129-ΔE-transfected cells however produced virion particles in the culture supernatant, and these particles contained viral genomic RNA, demonstrating that the E protein is essential for PRRSV infection but dispensable for virion assembly. Our study suggests that the PRRSV E protein may function as a viroporin in the virion envelope that facilitates uncoating of the virus in order to release the genomic RNA into the cytoplasm for subsequent replication. At 24 h postinoculation, Marc-145 cells were fixed, and virus infection was examined by immunofluorescent staining with N-specific MAb. Marc-145 cells inoculated with a culture fluid from cells cotransfected with P129-ΔE and E gene showed bright N-specific fluorescent signal, indicating that the P129-ΔE replication may be rescued by trans-complementation of the E protein (Fig. 2C ). Strand-specific RT-PCR experiments were carried out and demonstrated that PRRSV-infected Marc-145 cells produced reduced levels of positive-sense genomic RNA at 2 days post-infection in the presence of the drugs chloroquine, amantadine and verapamil (Fig. 5A, upper panel) . abstract: The small envelope (E) protein of porcine reproductive and respiratory syndrome virus (PRRSV) is a hydrophobic 73 amino acid protein encoded in the internal open reading frame (ORF) of the bicistronic mRNA2. As a first step towards understanding the biological role of E protein during PRRSV replication, E gene expression was blocked in a full-length infectious clone by mutating the ATG translational initiation to GTG, such that the full-length mutant genomic clone was unable to synthesize the E protein. DNA transfection of PRRSV-susceptible cells with the E gene knocked-out genomic clone showed the absence of virus infectivity. P129-ΔE-transfected cells however produced virion particles in the culture supernatant, and these particles contained viral genomic RNA, demonstrating that the E protein is essential for PRRSV infection but dispensable for virion assembly. Electron microscopy suggests that the P129-ΔE virions assembled in the absence of E had a similar appearance to the wild-type particles. Strand-specific RT-PCR demonstrated that the E protein-negative, non-infectious P129-ΔE virus particles were able to enter cells but further steps of replication were interrupted. The entry of PRRSV has been suggested to be via receptor-mediated endocytosis, and lysomotropic basic compounds and known ion-channel blocking agents both inhibited PRRSV replication effectively during the uncoating process. The expression of E protein in Escherichia coli-mediated cell growth arrests and increased the membrane permeability. Cross-linking experiments in cells infected with PRRSV or transfected with E gene showed that the E protein was able to form homo-oligomers. Taken together, our data suggest that the PRRSV E protein is likely an ion-channel protein embedded in the viral envelope and facilitates uncoating of virus and release of the genome in the cytoplasm. url: https://api.elsevier.com/content/article/pii/S0042682206004521 doi: 10.1016/j.virol.2006.07.013 id: cord-345630-bam3pa70 author: Lee, Han-Jung title: The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase date: 1991-02-28 words: 5973.0 sentences: 418.0 pages: flesch: 65.0 cache: ./cache/cord-345630-bam3pa70.txt txt: ./txt/cord-345630-bam3pa70.txt summary: authors: Lee, Han-Jung; Shieh, Chien-Kou; Gorbalenya, Alexander E.; Koonin, Eugene V.; La Monica, Nicola; Tuler, Jeremy; Bagdzhadzhyan, Anush; Lai, Michael M.C. title: The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase Third, the 3''-half of the gene 1 sequences of IBV and MHV-A59 contains the sequence motifs for RNA polymerase and helicase, which are the activities expected to be involved in RNA synthesis Gorbalenya et a/., 198913; Bredenbeek et a/., 1990) . The alignment of amino acids in ORF la of MHV-JHM and IBV showed that there are four possible stretches of moderate homology which are separated by highly diverged sequences (Fig. 8) . Although ORF la is highly diverged between MHV-JHM and IBV, common functional domains could be identified in this ORF of both viruses by detailed amino acid sequence analysis (see Materials and Methods) (Fig. 9 ). abstract: Abstract The 5′-most gene, gene 1, of the genome of murine coronavirus, mouse hepatitis virus (MHV), is presumed to encode the viral RNA-dependent RNA polymerase. We have determined the complete sequence of this gene of the JHM strain by cDNA cloning and sequencing. The total length of this gene is 21,798 nucleotides long, which includes two overlapping, large open reading frames. The first open reading frame, ORF 1 a, is 4488 amino acids long. The second open reading frame, ORF 1 b, overlaps ORF 1 a for 75 nucleotides, and is 2731 amino acids long. The overlapping region may fold into a pseudoknot RNA structure, similar to the corresponding region of the RNA of avian coronavirus, infectious bronchitis virus (IBV). The in vitro transcription and translation studies of this region indicated that these two ORFs were most likely translated into one polyprotein by a ribosomal frameshifting mechanism. Thus, the predicted molecular weight of the gene 1 product is more than 800,000 Da. The sequence of ORF 1 b is very similar to the corresponding ORF of IBV. In contrast, the ORF 1 a of these two viruses differ in size and have a high degree of divergence. The amino acid sequence analysis suggested that ORF 1 a contains several functional domains, including two hydrophobic, membrane-anchoring domains, and three cysteine-rich domains. It also contains a picornaviral 3C-like protease domain and two papain-like protease domains. The presence of these protease domains suggests that the polyprotein is most likely processed into multiple protein products. In contrast, the ORF 1b contains polymerase, helicase, and zinc-finger motifs. These sequence studies suggested that the MHV gene 1 product is involved in RNA synthesis, and that this product is processed autoproteolytically after translation. This study completes the sequence of the MHV genome, which is 31 kb long, and constitutes the largest viral RNA known. url: https://api.elsevier.com/content/article/pii/004268229190071I doi: 10.1016/0042-6822(91)90071-i id: cord-289152-w5ynbewh author: Lee, Sang-Myeong title: Porcine arterivirus activates the NF-κB pathway through IκB degradation date: 2005-11-10 words: 8015.0 sentences: 424.0 pages: flesch: 46.0 cache: ./cache/cord-289152-w5ynbewh.txt txt: ./txt/cord-289152-w5ynbewh.txt summary: In porcine reproductive and respiratory syndrome virus (PRRSV)-infected cells, NF-κB activation was characterized by translocation of NF-κB from the cytoplasm to the nucleus, increased DNA binding activity, and NF-κB-regulated gene expression. Taken together, these results demonstrated that PRRSV induces nuclear translocation of NF-nB followed by increased DNA binding activity of NF-nB both in MARC-145 cells and PAM cultures. To determine if NF-nB activation by PRRSV was dependent on InBa degradation in MARC-145 cells, the NF-nB pathway was blocked by using an adenovirus vector expressing a dominant negative form of InBa (Ad-InBaDN) which lacks both constitutive (Barroga et al., 1995) and inducible (Brown et al., 1995) phosphorylation sites. This study showed that PRRSV infection resulted in increased nuclear translocation of NF-nB and increased DNA binding activity both in MARC-145 cells and PAM cultures. abstract: Nuclear factor-kappaB (NF-κB) is a critical regulator of innate and adaptive immune function as well as cell proliferation and survival. The present study demonstrated for the first time that a virus belonging to the Arteriviridae family activates NF-κB in MARC-145 cells and alveolar macrophages. In porcine reproductive and respiratory syndrome virus (PRRSV)-infected cells, NF-κB activation was characterized by translocation of NF-κB from the cytoplasm to the nucleus, increased DNA binding activity, and NF-κB-regulated gene expression. NF-κB activation was increased as PRRSV infection progressed and in a viral dose-dependent manner. UV-inactivation of PRRSV significantly reduced the level of NF-κB activation. Degradation of IκB protein was detected late in PRRSV infection, and overexpression of the dominant negative form of IκBα (IκBαDN) significantly suppressed NF-κB activation induced by PRRSV. However, IκBαDN did not affect viral replication and viral cytopathic effect. PRRSV infection induced oxidative stress in cells by generating reactive oxygen species (ROS), and antioxidants inhibited NF-κB DNA binding activity in PRRSV-infected cells, suggesting ROS as a mechanism by which NF-κB was activated by PRRSV infection. Moreover, NF-κB-dependent expression of matrix metalloproteinase (MMP)-2 and MMP-9 was observed in PRRSV-infected cells, an observation which implies that NF-κB activation is a biologically significant aspect of PRRSV pathogenesis. The results presented here provide a basis for understanding molecular pathways of pathology and immune evasion associated with disease caused by PRRSV. url: https://www.ncbi.nlm.nih.gov/pubmed/16129468/ doi: 10.1016/j.virol.2005.07.034 id: cord-284707-72vx11aq author: Leibowitz, Julian L. title: Synthesis of virus-specific RNA in permeabilized murine coronavirus-infected cells date: 1988-09-30 words: 5498.0 sentences: 316.0 pages: flesch: 53.0 cache: ./cache/cord-284707-72vx11aq.txt txt: ./txt/cord-284707-72vx11aq.txt summary: For mouse hepatitis virus (MHV), one of the most extensively studied coronaviruses, there are seven species of MHV-specific mRNA present in infected cells, the largest of which is indistinguishable from virion RNA (Leibowitz et a/., 1981; Lai et a/., 1981; Spaan et a/., 1981) . In this paper we report the characteristics of a permeabilized cell system and demonstrate that it incorporates ribonucle-otide triphosphates into RNA molecules which appear identical to the virus-specific mRNAs synthesized in MHV-infected cells. Protease inhibitors and RNase inhibitors have both been reported to increase the RNA-dependent RNA polymerase activity present in extracts of West Nile virus-infected cells (Grun and Brinton, 1986) . The kinetics of the development of the MHV-specific RNA polymerase activity over the course of infection was determined in permeabilized cells. In this work we report the development and characterization of a permeabilized cell system for assaying MHV-specific RNA polymerase activity. abstract: Abstract We have developed a permeabilized cell system for assaying mouse hepatitis virus-specific RNA polymerase activity. This activity was characterized as to its requirements for mono- and divalent cations, requirements for an exogenous energy source, and pH optimum. This system faithfully reflects MHV-specific RNA synthesis in the intact cell, with regard to both its time of appearance during the course of infection and the products synthesized. The system is efficient and the RNA products were identical to those observed in intact MHV-infected cells as judged by agarose gel electrophoresis and hybridization. Permeabilized cells appear to be an ideal system for studying coronavirus RNA synthesis since they closely mimic in vivo conditions while allowing much of the experimental flexibility of truly cell-free systems. url: https://api.elsevier.com/content/article/pii/004268228890147X doi: 10.1016/0042-6822(88)90147-x id: cord-308835-999kewdw author: Leibowitz, Julian L. title: The virus-specific intracellular RNA species of two murine coronaviruses: MHV-A59 and MHV-JHM date: 1981-10-15 words: 6447.0 sentences: 404.0 pages: flesch: 56.0 cache: ./cache/cord-308835-999kewdw.txt txt: ./txt/cord-308835-999kewdw.txt summary: Abstract Seven virus-specific, polyadenylated RNA species have been identified in mouse cells infected with the murine coronaviruses MHV-A59 (A59V) or MHV-JHM (JHMV). MHV-infected 17CL·1 cells were labeled with [32P]orthophosphate in the presence of actinomycin D and the cytoplasmic RNA was extracted and analyzed by agarose gel electrophoresis. The largest intracellular RNA species is identical to RNA isolated from purified virions, as determined by agarose gel electrophoresis and oligonucleotide fingerprint studies of ribonuclease T1 digests. Oligonucleotide fingerprints of the six subgenomic RNAS show that the sequences they contain are present in virion RNA, confirming their virus-specific nature. Identification of MHV-Specific RNA Species A59V, JHMV, and mock-infected cells were labeled with [32P]orthophosphate from 4 to 8 hpi in the presence of actinomycin D. To determine if there is temporal regulation of MHV-specific RNA synthesis, replicate cultures of A59V, JHMV, or mock-infected cells were pulse labeled for 1 hr at hourly intervals and the intracellular RNA was extracted and analyzed by gel electrophoresis. abstract: Abstract Seven virus-specific, polyadenylated RNA species have been identified in mouse cells infected with the murine coronaviruses MHV-A59 (A59V) or MHV-JHM (JHMV). MHV-infected 17CL·1 cells were labeled with [32P]orthophosphate in the presence of actinomycin D and the cytoplasmic RNA was extracted and analyzed by agarose gel electrophoresis. These RNA species range in size from 6.3 × 105 to 6.1 × 106 daltons. The A59V and JHMV-specific RNAs have identical molecular weights and comigrate in agarose gels. The largest intracellular RNA species is identical to RNA isolated from purified virions, as determined by agarose gel electrophoresis and oligonucleotide fingerprint studies of ribonuclease T1 digests. Oligonucleotide fingerprints of the six subgenomic RNAS show that the sequences they contain are present in virion RNA, confirming their virus-specific nature. The fingerprinting studies also demonstrate that the six subgenomic RNA species make up a nested set. The sequences present in each RNA species are also present in all larger RNA species. These larger RNAs also contain additional sequences consistent with their greater size. The subgenomic RNAs fulfull many of the criteria for mRNAs. Possible mechanisms for generating these RNAs are discussed. url: https://www.sciencedirect.com/science/article/pii/0042682281902506 doi: 10.1016/0042-6822(81)90250-6 id: cord-275234-t6e7vr9y author: Leone, Gustavo title: The N-terminal heptad repeat region of reovirus cell attachment protein σ1 is responsible for σ1 oligomer stability and possesses intrinsic oligomerization function date: 1991-05-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract The oligomerization domain of the reovirus cell attachment protein (σ1) was probed using the type 3 reovirus of synthesized in vitro. Trypsin cleaved the α1 protein (49K molecular weight) approximately in the middle and yielded a 26K N-terminal fragment and a 23K C-terminal fragment. Under conditions which allowed for the identification of intact σ1 in the oligomeric form (∼200K) by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the N-terminal 26K fragment was found to exist as stable trimers (80K) and, to a less extent, as dimers (54K), whereas the C-terminal fragment remained in the monomeric form. A polypeptide (161 amino acids) containing the N-terminal heptad repeat region synthesized in vitro was capable of forming stable dimers and trimers. Using various criteria, we demonstrated that the stability of the intact σ1 oligomer is conferred mainly by the N-terminal heptad repeat region. Our results are summarized in a model in which individual heptad repeats are held together in a three-stranded α-helical coiled-coil structure via both hydrophobic and electrostatic interactions. url: https://api.elsevier.com/content/article/pii/0042682291906774 doi: 10.1016/0042-6822(91)90677-4 id: cord-330907-srb8ac7l author: Leparc-Goffart, Isabelle title: Altered Pathogenesis of a Mutant of the Murine Coronavirus MHV-A59 Is Associated with a Q159L Amino Acid Substitution in the Spike Protein date: 1997-12-08 words: 5445.0 sentences: 288.0 pages: flesch: 61.0 cache: ./cache/cord-330907-srb8ac7l.txt txt: ./txt/cord-330907-srb8ac7l.txt summary: We have previously shown that C12 has two amino acid substitutions relative to wild type virus in the spike protein, Q159L (within a region of S1 shown to bind to viral receptor in anin vitroassay) and H716D (in the proteolytic cleavage recognition site). for the altered pathogenic properties of the mutant viruses, we compared the sequence of the spike (S) genes The murine coronavirus, mouse hepatitis virus strain of wild type and mutant viruses isolated from persistently A59 (MHV-A59), produces both hepatitis and neurologiinfected glial cells cultures. We have shown previously that the spike (S) protein from the supernatant of either the ''''C'''' culture of persisencoded by the C12 mutant has two amino acid substitutently infected glial cells at 1 week (C3), 6 weeks (C5), tions as compared with the wild type S protein. abstract: Abstract C12, an attenuated, fusion delayed, very weakly hepatotropic mutant of mouse hepatitis virus strain A59 (MHV-A59) has been further characterized. We have previously shown that C12 has two amino acid substitutions relative to wild type virus in the spike protein, Q159L (within a region of S1 shown to bind to viral receptor in anin vitroassay) and H716D (in the proteolytic cleavage recognition site). We have sequenced the rest of the 31-kb genome of C12 and compared it to wild type virus. Only three additional amino acids substitutions were found, all encoded within the replicase gene. Analysis of C12in vivoin C57Bl/6 mice has shown that despite the fact that this virus replicates in the brain to titers at least as high as wild type and causes acute encephalitis similar to wild type, this virus causes a minimal level of demyelination and only at very high levels of virus inoculation. Thus acute encephalitis is not sufficient for the induction of demyelination by MHV-A59. Analysis of mutants isolated at earlier times from the same persistently infected glial cell culture as C12, as well as mutants isolated from a second independent culture of persistently infected glial cells, suggests that both the weakly demyelinating and the weakly hepatotropic phenotypes of C12 are associated with the Q159L amino acid substitution. url: https://www.ncbi.nlm.nih.gov/pubmed/9426441/ doi: 10.1006/viro.1997.8877 id: cord-263334-wwkdum94 author: Li, Chen title: Cellular DDX3 regulates Japanese encephalitis virus replication by interacting with viral un-translated regions date: 2014-01-20 words: 7683.0 sentences: 423.0 pages: flesch: 54.0 cache: ./cache/cord-263334-wwkdum94.txt txt: ./txt/cord-263334-wwkdum94.txt summary: BHK-21 cells transfected with the DDX3 shRNA were infected with JEV (MOI¼ 0.01) for 48 h, Viral titers determined by plaque formation assay at 48 hpi. (F) BHK-21 cells transfected with different amounts of DDX3 shRNA plasmid were infected with JEV (MOI ¼0.01), 48 h later, the amount of virus released into the medium was determined by plaque formation assay. In order to determine whether cellular DDX3 is involved in virus assembly or release, the BHK-21 cells were transfected with DDX3 shRNA plasmid before being infected with JEV (MOI ¼0.01). The virus titers were detected 2 days later by plaque formation assay, the results showed that overexpression of DDX3r-K230E, DDX3r-S382L and the control plasmid pcDNA3.1 after DDX3 knockdown resulted in the reduction of JEV replication for 13-fold (p o0.01), 12-fold (p o0.01) and 15-fold (p o0.01). The DEAD-box RNA helicase DDX5 acts as a positive regulator of Japanese encephalitis virus replication by binding to viral 3′ UTR abstract: Japanese encephalitis virus is one of the most common causes for epidemic viral encephalitis in humans and animals. Herein we demonstrated that cellular helicase DDX3 is involved in JEV replication. DDX3 knockdown inhibits JEV replication. The helicase activity of DDX3 is crucial for JEV replication. GST-pulldown and co-immunoprecipitation experiments demonstrated that DDX3 could interact with JEV non-structural proteins 3 and 5. Co-immunoprecipitation and confocal microscopy analysis confirmed that DDX3 interacts and colocalizes with these viral proteins and viral RNA during the infection. We determined that DDX3 binds to JEV 5′ and 3′ un-translated regions. We used a JEV-replicon system to demonstrate that DDX3 positively regulates viral RNA translation, which might affect viral RNA replication at the late stage of virus infection. Collectively, we identified that DDX3 is necessary for JEV infection, suggesting that DDX3 might be a novel target to design new antiviral agents against JEV or other flavivirus infections. url: https://doi.org/10.1016/j.virol.2013.11.008 doi: 10.1016/j.virol.2013.11.008 id: cord-307396-u6v6bxwj author: Liao, Y. title: Biochemical and functional characterization of the membrane association and membrane permeabilizing activity of the severe acute respiratory syndrome coronavirus envelope protein date: 2006-06-05 words: 6781.0 sentences: 326.0 pages: flesch: 51.0 cache: ./cache/cord-307396-u6v6bxwj.txt txt: ./txt/cord-307396-u6v6bxwj.txt summary: In a recent study, we demonstrated that the SARS-CoV E protein could obviously enhance the membrane permeability of bacterial cells to onitrophenyl-β-D-galactopyranoside and hygromycin B, suggesting that the protein may function as a viroporin (Liao et al., 2004) . Western blotting analysis of cells expressing wild type and most mutant constructs showed specific detection of three species migrating at the range of molecular masses from 14 to 18 kDa under reducing conditions and representing three isoforms of the E protein (Fig. 3a) . The E protein from coronavirus MHV and IBV was previously shown to undergo modification by palmitoylation HeLa cells expressing the Flag-tagged SARS-CoV and IBV E proteins, respectively, were harvested at 12 h posttransfection, broken by 20 stokes with a Dounce cell homogenizer, and fractionated into cytosol (C) and membrane (M) fractions after removal of cell debris and nuclei. Expression of the untagged SARS-CoV E protein in the same cell type also shows very similar Golgi localization patterns as the Flag-tagged protein (Fig. 8a , panels G-I). abstract: A diverse group of cytolytic animal viruses encodes small, hydrophobic proteins to modify host cell membrane permeability to ions and small molecules during their infection cycles. In this study, we show that expression of the SARS-CoV E protein in mammalian cells alters the membrane permeability of these cells. Immunofluorescent staining and cell fractionation studies demonstrate that this protein is an integral membrane protein. It is mainly localized to the ER and the Golgi apparatus. The protein can be translocated to the cell surface and is partially associated with lipid rafts. Further biochemical characterization of the protein reveals that it is posttranslationally modified by palmitoylation on all three cysteine residues. Systematic mutagenesis studies confirm that the membrane permeabilizing activity of the SARS-CoV E protein is associated with its transmembrane domain. url: https://www.ncbi.nlm.nih.gov/pubmed/16507314/ doi: 10.1016/j.virol.2006.01.028 id: cord-269193-a647hwu9 author: Lin, Debby A. title: Evolutionary relatedness of the predicted gene product of RNA segment 2 of the Tick-Borne Dhori virus and the PB1 polymerase gene of influenza viruses date: 1991-05-31 words: 2946.0 sentences: 152.0 pages: flesch: 57.0 cache: ./cache/cord-269193-a647hwu9.txt txt: ./txt/cord-269193-a647hwu9.txt summary: Abstract The complete nucleotide sequence of the second largest RNA segment of Dhori/India/1313/61 virus was determined and the deduced amino acid sequence was compared with the polymerase (P) proteins of influenza A, B, and C viruses. The viral RNAs have been shown to encode information in the negative-sense (Clerx et al., 1983; Fuller et al., 1987; Freedman-Faulstich and Fuller, 1990) and it was previously shown that the Dhori nucleoprotein (encoded by RNA segment 5) shares conserved amino acid sequences with the influenza A, B, and C virus nucleoproteins (Fuller et al., 1987) . The PBl polymerase proteins are the most highly conserved among the proteins of the influenza A, B, and C viruses (Yamashita et a/,, 1989 ) and they are most likely required for nucleotide addition during viral RNA synthesis (Braam et al., 1983) . abstract: Abstract The complete nucleotide sequence of the second largest RNA segment of Dhori/India/1313/61 virus was determined and the deduced amino acid sequence was compared with the polymerase (P) proteins of influenza A, B, and C viruses. RNA segment 2 (2224 nucleotides) of Dhori virus contains a single long open reading frame that can encode a 716-amino amid polypeptide (81.3 kDa). The predicted polypeptide shares between 27 and 31% sequence identities with the PB1 polypeptides of influenza A, B, and C viruses. Among the regions most highly conserved are the sequences around the Asp-Asp motif common to many RNA polymerases. In spite of the high level of sequence identity between the Dhori RNA segment 2 gene product and the influenza A, B, and C virus PB1 proteins the amino acid composition of the Dhori protein indicates an acidic charge feature at pH 7.0 in contrast to the basic nature of the PB1 proteins of the influenza viruses. We suggest that the Dhori PB1-like protein be designated the Pα protein of this virus. url: https://www.ncbi.nlm.nih.gov/pubmed/2024457/ doi: 10.1016/0042-6822(91)90641-n id: cord-287777-ogs4mq0v author: Lindner, Holger A. title: Deubiquitination in virus infection date: 2007-06-05 words: 8904.0 sentences: 424.0 pages: flesch: 40.0 cache: ./cache/cord-287777-ogs4mq0v.txt txt: ./txt/cord-287777-ogs4mq0v.txt summary: They include the potential recruitment of DUBs for the stabilization of β-catenin in Epstein-Barr virus (EBV)-infected B cells (Ovaa et al., 2004; Shackelford et al., 2003) , and the specific targeting of the cellular DUB ubiquitin-specific protease 7 (USP7) by the Epstein-Barr nuclear antigen 1 (EBNA1) and the herpes simplex virus type 1 (HSV-1) regulatory protein ICP0 (Everett et al., 1997; Holowaty and Frappier, 2004) . The possibility that modulation of deubiquitination is, nevertheless, a more common viral strategy has gained support by the recent in vitro demonstration of deubiquitinating activities for three viral enzymes: the adenovirus protease adenain (Balakirev et al., 2002) , the papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus (SARS-CoV) (Barretto et al., 2005; Lindner et al., 2005) , and a protease domain contained in the N-terminal fragment of the large tegument protein UL36 (UL36 USP ) from several herpesviruses, namely, HSV-1, EBV, and mouse and human cytomegalovirus (MCMV and HCMV) Schlieker et al., 2005; Wang et al., 2006) . abstract: Post-translational modification of proteins and peptides by ubiquitin, a highly evolutionarily conserved 76 residue protein, and ubiquitin-like modifiers has emerged as a major regulatory mechanism in various cellular activities. Eukaryotic viruses are known to modulate protein ubiquitination to their advantage in various ways. At the same time, the evidence for the importance of deubiquitination as a viral target also is growing. This review centers on known viral interactions with protein deubiquitination, on viral enzymes for which deubiquitinating activities were recently demonstrated, and on the roles of viral ubiquitin-like sequences. url: https://www.ncbi.nlm.nih.gov/pubmed/17291557/ doi: 10.1016/j.virol.2006.12.035 id: cord-258379-v3lceirh author: Liu, D. X. title: Association of the infectious bronchitis virus 3c protein with the virion envelope date: 1991-12-31 words: 2868.0 sentences: 121.0 pages: flesch: 53.0 cache: ./cache/cord-258379-v3lceirh.txt txt: ./txt/cord-258379-v3lceirh.txt summary: There was considerably less evidence of contaminating cellular proteins in this gradient, and the relative proportion of the 12K protein to the other virion proteins appeared similar to that observed at the previous stage in purification, strongly supporting the idea of a specific association between the 12K protein and virus particles. In order to establish the identity of the 12K polypeptide as the product of the 3c gene, and to examine the possibility that IBV virions might contain other new virus polypeptides in amounts too small to detect directly, we next carried out immunoprecipitation experiments using monospecific antisera directed against the predicted products of the 3a, 3b, 3c, 5a, and 5b ORFs (17, 18, 23) . Messenger RNA 4 of mouse hepatitis virus (MHV) is known to encode a 15K polypeptide, the predicted amino acid sequence of which contains a highly hydrophobic region from residues 8 to 41 (9, 22) , although the protein has not so far been found in virions. abstract: Abstract A highly purified radiolabeled preparation of the coronavirus infectious bronchitis virus (IBV) was analyzed, by immunoprecipitation with monospecific antisera, for the presence of a series of small virus proteins recently identified as the products of I BV mRNAs 3 and 5. One of these, 3c, a 12.4K protein encoded by the third open reading frame of the tricistronic mRNA3 was clearly detectable and was found to cofractionate with virion envelope proteins on detergent disruption of virus particles. These results, together with the hydrophobic nature of 3c and its previously demonstrated association with the membranes of infected cells, suggest strongly that 3c represents a new virion envelope protein, which may have counterparts in other coronaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/1962461/ doi: 10.1016/0042-6822(91)90572-s id: cord-269866-3tpyj04y author: Liu, D. X. title: Identification of two new polypeptides encoded by mRNA5 of the coronavirus infectious bronchitis virus date: 1992-01-31 words: 3164.0 sentences: 137.0 pages: flesch: 50.0 cache: ./cache/cord-269866-3tpyj04y.txt txt: ./txt/cord-269866-3tpyj04y.txt summary: We report here that two polypeptides with the sizes expected for the 5a and 5b products can be synthesised by in vitro translation of a single artificial mRNA containing both the 5a and 5b ORFs. To establish whether these polypeptides represent genuine virus gene products, both the 5a and 5b coding sequences were expressed as bacterial fusion proteins, and these were used to raise monospecific antisera. We report here that two polypeptides with the sizes expected for the 5a and 5b products can be synthesised by in vitro translation of a single artificial mRNA containing both the 5a and 5b ORFs. To establish whether these polypeptides represent genuine virus gene products, both the 5a and 5b coding sequences were expressed as bacterial fusion proteins, and these were used to raise monospecific antisera. abstract: Abstract The second smallest subgenomic messenger RNA, mRNA5, of the coronavirus infectious bronchitis virus includes in its “5′ unique region” two separate open reading frames (5a and 5b), whose coding function has not so far been established, and thus it may represent a dicistronic messenger RNA. We report here that two polypeptides with the sizes expected for the 5a and 5b products can be synthesised by in vitro translation of a single artificial mRNA containing both the 5a and 5b ORFs. To establish whether these polypeptides represent genuine virus gene products, both the 5a and 5b coding sequences were expressed as bacterial fusion proteins, and these were used to raise monospecific antisera. Antisera raised against both the 5a and 5b-specific sequences recognized specifically proteins of the expected size in infectious bronchitis virus-infected chicken kidney and Vero cells, indicating that 5a and 5b do represent genuine virus genes, and suggesting that mRNA5 is indeed functionally dicistronic. url: https://www.sciencedirect.com/science/article/pii/0042682292900946 doi: 10.1016/0042-6822(92)90094-6 id: cord-331916-n744pymd author: Liu, Jue title: Inhibition of porcine circovirus type 2 replication in mice by RNA interference date: 2006-04-10 words: 6657.0 sentences: 350.0 pages: flesch: 52.0 cache: ./cache/cord-331916-n744pymd.txt txt: ./txt/cord-331916-n744pymd.txt summary: Specific inhibition of endogenous or pathogen mRNA by RNAi can be triggered by the introduction of 21 -23 nucleotide (nt) duplexes of RNA (siRNA) or by transcription of DNA precursor into short hairpin RNAs (shRNA) homologous to target sequences (Brummelkamp et al., 2002; Elbashir et al., 2001a; Paddison et al., 2002) , opening up possibilities for controlling replicative processes of pathogens. To further examine the ability of ORF1 shRNA to suppress viral gene expression in PCV2-infected PK15 cells, single nucleotide mutations were introduced into pSIR3 sequence as shown in Fig. 4A . As shown in Fig. 4B , a mutant with one nucleotide mutation in the 5V-end of the sense strand (pSIR3-m1) still had an effective reduction in the synthesis of ORF1 and ORF2 proteins, whereas with a nucleotide substitution at the center (pSIR3-m2) or 3V-end (pSIR3-m3) of the sense sequence, the resultant shRNAs failed to significantly suppress expression of PCV2 ORF1 and ORF2 in the transfected cells, further verifying the specificity of RNAi as demonstrated (Amarzguioui et al., 2003; Harborth et al., 2003) . abstract: Porcine circovirus type 2 (PCV2) is the primary causative agent of an emerging swine disease, postweaning multisystemic wasting syndrome (PMWS) for which no antiviral treatment is available. To exploit the possibility of using RNA interference (RNAi) as a therapeutic approach against the disease, plasmid-borne short hairpin RNAs (shRNAs) were generated to target the PCV2 genome. Transfection of these shRNAs into cultured PK15 cells caused a significant reduction in viral RNA production that was accompanied by inhibiting viral DNA replication and protein synthesis in infected cells. The effect was further tested in vivo in a mouse model that has been developed for PCV2 infection. Mice injected with shRNA before PCV2 infection showed substantially decreased microscopic lesions in inguinal lymph nodes compared to controls. In situ hybridization and immunohistochemical analyses showed that shRNA caused a significant inhibition in the level of viral DNA and protein synthesis detected in the lymph nodes of the treated mice relative to the controls. Taken together, these results indicate that shRNAs are capable of inhibiting PCV2 infection in vitro as well as in vivo and thus may constitute an effective therapeutic strategy for PCV2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/16427679/ doi: 10.1016/j.virol.2005.12.006 id: cord-342901-ca2xxkb2 author: Lloyd, Richard E. title: Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses date: 2015-05-31 words: 16221.0 sentences: 823.0 pages: flesch: 50.0 cache: ./cache/cord-342901-ca2xxkb2.txt txt: ./txt/cord-342901-ca2xxkb2.txt summary: Though PTB was the first, a wide spectrum of factors, largely nuclear RBPs, have also been proposed as poliovirus ITAFs, including Lupus autoantigen (La) (Meerovitch et al., 1993 (Meerovitch et al., , 1989 , poly(rC)binding proteins (PCBPs) (Blyn et al., 1996; Gamarnik and Andino, 1997) , upstream of N-ras (UNR) (Anderson et al., 2007; Boussadia et al., 2003; Hunt et al., 1999) , SRp20 (Bedard et al., 2007) and glycyl-tRNA synthetase (GARS) (Andreev et al., 2012) (Table 1 ). In addition, certain ITAFs play crucial roles in regulating the conversion of translation-competent genomic RNAs into replicationcompetent RNAs. PTB was known as a nuclear splicing factor when its role as an ITAF of poliovirus and EMCV was discovered; a classic hijacked nuclear protein pressed into a new role required for the virus. abstract: Abstract Plus strand RNA viruses that replicate in the cytoplasm face challenges in supporting the numerous biosynthetic functions required for replication and propagation. Most of these viruses are genetically simple and rely heavily on co-opting cellular proteins, particularly cellular RNA-binding proteins, into new roles for support of virus infection at the level of virus-specific translation, and building RNA replication complexes. In the course of infectious cycles many nuclear-cytoplasmic shuttling proteins of mostly nuclear distribution are detained in the cytoplasm by viruses and re-purposed for their own gain. Many mammalian viruses hijack a common group of the same factors. This review summarizes recent gains in our knowledge of how cytoplasmic RNA viruses use these co-opted host nuclear factors in new functional roles supporting virus translation and virus RNA replication and common themes employed between different virus groups. url: https://www.ncbi.nlm.nih.gov/pubmed/25818028/ doi: 10.1016/j.virol.2015.03.001 id: cord-329794-msxrdhb3 author: Lu, Aili title: Attenuation of SARS coronavirus by a short hairpin RNA expression plasmid targeting RNA-dependent RNA polymerase date: 2004-06-20 words: 2679.0 sentences: 172.0 pages: flesch: 61.0 cache: ./cache/cord-329794-msxrdhb3.txt txt: ./txt/cord-329794-msxrdhb3.txt summary: Here, we provide evidences that RNAi targeting at coronavirus RNA-dependent RNA polymerase (RDRP) using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Here, we provide the evidence that RNAi targeting at coronavirus RDRP using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Design of specific shRNA expression plasmids targeting at coronavirus RDRP Coronavirus isolated from SARS patients has a large genomic RNA (approximately 30 kb). After transfecton, about 40-90% of RDRP gene expression was inhibited, depending on the sequence of the shRNA inserts, based on RT-PCR analysis in both HeLa and 293 cells transfected with RDRP (data not shown). shRNA reduced the expression of SARS RDRP mRNA in 293 and HeLa cells As shown in Fig. 1A , based on the RT-PCR analysis, the expression of extraneous RDRP gene was observed peaking at 48 h after the transfection. abstract: Abstract Severe acute respiratory syndrome (SARS) is a highly contagious and sometimes a lethal disease, which spread over five continents in 2002–2003. Laboratory analysis showed that the etiologic agent for SARS is a new type of coronavirus. Currently, there is no specific treatment for this disease. RNA interference (RNAi) is a recently discovered antiviral mechanism in plant and animal cells that induces a specific degradation of double-stranded RNA. Here, we provide evidences that RNAi targeting at coronavirus RNA-dependent RNA polymerase (RDRP) using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Moreover, this construct significantly reduced the plaque formation of SARS coronaviruses in Vero-E6 cells. The data may suggest a new approach for treatment of SARS patients. url: https://www.sciencedirect.com/science/article/pii/S0042682204002181 doi: 10.1016/j.virol.2004.03.031 id: cord-317537-wgu5cd0y author: Lu, Hsiang-Chia title: Cymbidium mosaic potexvirus isolate-dependent host movement systems reveal two movement control determinants and the coat protein is the dominant date: 2009-05-25 words: 8155.0 sentences: 474.0 pages: flesch: 57.0 cache: ./cache/cord-317537-wgu5cd0y.txt txt: ./txt/cord-317537-wgu5cd0y.txt summary: All constructs were replication competent in protoplasts as assayed by northern blot hybridization (Fig. 4I) , and statistics analysis (ANOVA) of real-time RT-PCR quantification of average relative percentage (from 3 independent experiments) of CymMV RNA from CymMV clone-infected protoplasts at 24 h postinoculation revealed no significant difference in percentage between these clones (P = 0.91). All constructs were replication competent in protoplasts as assayed by northern blot hybridization (Fig. 6J) , and statistics analysis (ANOVA) of realtime RT-PCR quantification of average relative percentage (from 3 independent experiments) of CymMV RNA from CymMV cloneinfected protoplasts at 24 h post-inoculation revealed no significant difference in percentage between these clones (P = 0.83). Our results indicated that the important amino acids of the CP that allowed for the CymMV systemic infection are located within the previously predicted RNA binding domain ( Fig. 7A; 1) . abstract: Little is known about how plant viruses of a single species exhibit different movement behavior in different host species. Two Cymbidium mosaic potexvirus (CymMV) isolates, M1 and M2, were studied. Both can infect Phalaenopsis orchids, but only M1 can systemically infect Nicotiana benthamiana plants. Protoplast inoculation and whole-mount in situ hybridization revealed that both isolates can replicate in N. benthamiana; however, M2 was restricted to the initially infected cells. Genome shuffling between M1 and M2 revealed that two control modes are involved in CymMV host dependent movement. The M1 coat protein (CP) plays a dominant role in controlling CymMV movement between cells, because all chimeric CymMV viruses containing the M1 CP systemically infected N. benthamiana plants. Without the M1 CP, one chimeric virus containing the combination of the M1 triple gene block proteins (TGBps), the M2 5′ RNA (1–4333), and the M2 CP effectively moved in N. benthamiana plants. Further complementation analysis revealed that M1 TGBp1 and TGBp3 are co-required to complement the movement of the chimeric viruses in N. benthamiana. The amino acids within the CP, TGBp1 and TGBp3 which are required or important for CymMV M2 movement in N. benthamiana plants were mapped. The required amino acids within the CP map to the predicted RNA binding domain. RNA–protein binding assays revealed that M1 CP has higher RNA binding affinity than does M2 CP. Yeast two-hybrid assays to detect all possible interactions of M1 TGBps and CP, and only TGBp1 and CP self-interactions were observed. url: https://api.elsevier.com/content/article/pii/S004268220900172X doi: 10.1016/j.virol.2009.02.049 id: cord-252615-ajyv95pu author: Lu, Yanfang title: ATP1B3: a virus-induced host factor against EV71 replication by up-regulating the production of type-I interferons date: 2016-05-27 words: 4186.0 sentences: 280.0 pages: flesch: 54.0 cache: ./cache/cord-252615-ajyv95pu.txt txt: ./txt/cord-252615-ajyv95pu.txt summary: Although 3A protein had no effect on the expression of ATP1B3, EV71 infection resulted in elevated expression of ATP1B3 in RD cell line, both on messenger RNA (mRNA) and protein levels. Our study demonstrated that ATP1B3 inhibit EV71 replication by enhancing the production of type-I interferons, which could act as a potential therapeutic target in EV71 infection. We observed that both the mRNA and protein levels of ATP1B3 in RD cells were positively correlated with the infection doses of EV71 (Fig. 3B) . We infected ATP1B3 overpression cells or vector controls with EV71 at an MOI of 1, cultured cells with anti-human interferon-α1/β antibodies or isotype control IgG, and examined the viral replication using RT-PCR assay. Previous studies have shown that EV71 infection can induce IFN-β production which is dependent on the infectious dose, but the interferon is not cell type specific (Lu et al., 2012) . abstract: Enterovirus 71 (EV71) infection can cause severe diseases, and is becoming increasingly common in children. In the current study, we carried out yeast two-hybrid assays to screen human proteins that could interact with 3A protein of EV71. Human β3 subunit of Na(+)/K(+)-ATPase (ATP1B3) protein was demonstrated to interact with the 3A protein of EV71. Although 3A protein had no effect on the expression of ATP1B3, EV71 infection resulted in elevated expression of ATP1B3 in RD cell line, both on messenger RNA (mRNA) and protein levels. Interestingly, knockdown of ATP1B3 could significantly increase the replication of EV71, whereas overexpression of ATP1B3 significantly suppressed the replication of EV71 in RD cells. Furthermore, we demonstrated that the expression of ATP1B3 could induce the production of type-I interferons. Our study demonstrated that ATP1B3 inhibit EV71 replication by enhancing the production of type-I interferons, which could act as a potential therapeutic target in EV71 infection. url: https://doi.org/10.1016/j.virol.2016.05.013 doi: 10.1016/j.virol.2016.05.013 id: cord-259095-mfptcw8t author: Lu, Yiqi title: Determinants of Mouse Hepatitis Virus 3C-like Proteinase Activity date: 1997-04-14 words: 4488.0 sentences: 270.0 pages: flesch: 66.0 cache: ./cache/cord-259095-mfptcw8t.txt txt: ./txt/cord-259095-mfptcw8t.txt summary: Numbering of amino acid residues within MHV 3CLpro is based The linear schematic of the MHV genome shows the organization of Ser 1 (Lu et al., 1995) Site-directed mutagenesis of pGpro with bovine chymotrypsin (Gorbalenya and Koonin, 1993) , 3Cpro of human rhinovirus 14 (Matthews et al., 1994) , and hepatitis A virus Asp53 and Asp65 were mutagenized by the Chame-3Cpro (Allaire et al., 1994) . The comparison of the were checked for residual expression and processing from the pGpro construct by the addition of [ 35 S]-four coronavirus 3CLpro sequences revealed two potential cleavage sites present only in MHV, QS 3554-5 , and methionine to an aliquot of the unlabeled reaction mixture after treatment with RNase and cycloheximide and QG 3607-8 . Mutation of Asp65 to Pro or Ala (D65P and D65A) MHV-A59, IBV, HCV-229E, and TGEV revealed no completely conserved Asp or Glu residues at positions analo-resulted in a proteinase with activity comparable to that expressed from wild-type pGpro (Fig. 3B, lanes 3 and 4) . abstract: Abstract The coronavirus, mouse hepatitis virus strain A59 (MHV), expresses a chymotrypsin-like cysteine proteinase (3CLpro) within the gene 1 polyprotein. The MHV 3CLpro is similar to the picornavirus 3C proteinases in the relative location of confirmed catalytic histidine and cysteine residues and in the predicted use of Q/(S, A, G) dipeptide cleavage sites. However, less is known concerning the participation of aspartic acid or glutamic acid residues in catalysis by the coronavirus 3C-like proteinases or of the precise coding sequence of 3CLpro within the gene 1 polyprotein. In this study, aspartic acid residues in MHV 3CLpro were mutated and the mutant proteinases were tested for activity in anin vitro transcleavage assay. MHV 3CLpro was not inactivated by substitutions at Asp3386(D53) or Asp3398(D65), demonstrating that they were not catalytic residues. MHV 3CLpro was able to cleave at a glutamine–glycine (QG3607-8) dipeptide within the 3CLpro domain upstream from the predicted carboxy-terminal QS3635-6cleavage site of 3CLpro. The predicted full-length 3CLpro (S3334to Q3635) had an apparent mass of 27 kDa, identical to the p27 3CLpro in cells, whereas the truncated proteinase (S3334to Q3607) had an apparent mass of 24 kDa. This 28-amino-acid carboxy-terminal truncation of 3CLpro rendered it inactive in atranscleavage assay. Thus, MHV 3CLpro was able to cleave at a site within the putative full-length proteinase, but the entire predicted 3CLpro domain was required for activity. These studies suggest that the coronavirus 3CL-proteinases may have a substantially different structure and catalytic mechanism than other 3C-like proteinases. url: https://www.ncbi.nlm.nih.gov/pubmed/9143289/ doi: 10.1006/viro.1997.8479 id: cord-274172-3dctmmfe author: Lucas, Alexandra title: In vivo and in vitro models of demyelinating diseases II. Persistence and host-regulated thermosensitivity in cells of neural derivation infected with mouse hepatitis and measles viruses date: 1978-07-15 words: 5403.0 sentences: 247.0 pages: flesch: 48.0 cache: ./cache/cord-274172-3dctmmfe.txt txt: ./txt/cord-274172-3dctmmfe.txt summary: To investigate the replication of measles in the other non-neural and neural continuous cell lines, monolayer cultures were inoculated at 32.5" and examined for cytopathology, virus production, and development of infectious centers. Fol-With vaccinia virus, combined cell-associResults from these studies focus attention on three salient findings: (1) The strains of measles and mouse hepatitis viruses used can readily become established in a persistent form of infection in cell lines of neural and non-neural origin; (2) almost invariably when the infection is of the persistent type, virus replication becomes thermosensitive due to unknown factors under host control; the virus progeny from persistent infections are themselves not thermolabile; and (3) among the many cell types tested a rat RN2-2 Schwannoma has the unique ability to discriminate between the prototype MHV, and the neurotropic variant, JHM, supporting the persistence of only the latter. abstract: Abstract Following inoculation of continuous cell lines of neural and other derivations, persistent infections are established with facility by mouse hepatitis and measles viruses. This occurs equally with the prototype MHV3 and its neurotropic variant JHM as well as with the Edmonston vaccine and SSPE Hallé measles variants. In almost every instance that the infection becomes persistent at 32.5°, virus replication is found to be thermosensitive at 39.5°; however, progeny virus derived from such infections at 32.5° is itself thermostable when replicating in the indicator, fully permissive cell lines. The new data, therefore, reveal the existence of a host-conferred interrelationship between persistence and virus restriction at elevated temperature. They indicate that the two agents with neurotropic potential, when they become established as pathogens in the nervous system, could be under close host cell regulation involving as yet unknown mechanisms. url: https://api.elsevier.com/content/article/pii/0042682278902891 doi: 10.1016/0042-6822(78)90289-1 id: cord-253351-b36g09r0 author: Luo, Zongli title: Roles in Cell-to-Cell Fusion of Two Conserved Hydrophobic Regions in the Murine Coronavirus Spike Protein date: 1998-05-10 words: 6840.0 sentences: 356.0 pages: flesch: 57.0 cache: ./cache/cord-253351-b36g09r0.txt txt: ./txt/cord-253351-b36g09r0.txt summary: Similar substitutions within PEP2 result in a fusion-negative phenotype; however, these mutant S proteins also exhibit defects in protein processing and surface expression which likely explain the loss of the ability to induce fusion. To determine the importance of the asymmetric distribution of hydrophobicity in the induction of cell-to-cell fusion, as predicted by the ability to model this peptide as a sided ␣ helix ( Fig. 2A) , nonconservative and conservative amino acid substitutions were introduced in PEP1 to target representative bulky hydrophobic residues (F977K, F977L, L981K, L981I) and polar or charged residues (S975D, N978D, N978L, D986V-D989V). All mutant PEP1 S proteins were assayed for fusion using both in situ and quantitative fusion assays, performed as shown in Fig. 3 , using the vTF7-3-infected and wild-type S gene-transfected cells as positive controls and vTF7-3-infected and mock-transfected cells as negative controls. abstract: Abstract The spike (S) protein of coronavirus, mouse hepatitis virus (MHV), mediates attachment and fusion during viral entry and cell-to-cell fusion later in infection. By analogy with other viral proteins that induce cell fusion the MHV S protein would be expected to have a hydrophobic stretch of amino acids that serves as a fusion peptide. Sequence analysis suggests that the S protein falls within the group of fusion proteins having internal rather than N-terminal fusion peptides. Based on the features of known viral fusion peptides, we identified two regions (PEP1 and PEP2) of MHV-A59 S2 as possible fusion peptides. Site-directed mutagenesis and anin vitrocell-to-cell fusion assay were used to evaluate the roles of PEP1 and PEP2, as well as a third previously identified putative fusion domain (PEP3) in membrane fusion. Substitution of bulky hydrophobic residues with charged residues within PEP1 affects the fusion activity of the S protein without affecting processing and surface expression. Similar substitutions within PEP2 result in a fusion-negative phenotype; however, these mutant S proteins also exhibit defects in protein processing and surface expression which likely explain the loss of the ability to induce fusion. Thus PEP1 remains a candidate fusion peptide, while PEP2 may play a significant role in the overall structure or oligomerization of the S protein. PEP3 is an unlikely putative fusion peptide since it is not conserved among coronaviruses and nonconservative amino acid substitutions in PEP3 have minimal effects on cell-to-cell fusion. url: https://api.elsevier.com/content/article/pii/S0042682298991218 doi: 10.1006/viro.1998.9121 id: cord-258232-br4z3na6 author: Maeda, Junko title: Release of Coronavirus E Protein in Membrane Vesicles from Virus-Infected Cells and E Protein-Expressing Cells date: 1999-10-25 words: 4132.0 sentences: 189.0 pages: flesch: 51.0 cache: ./cache/cord-258232-br4z3na6.txt txt: ./txt/cord-258232-br4z3na6.txt summary: The present study demonstrated that mouse hepatitis virus (MHV) E protein was released as an integral membrane protein in lipid vesicles from E-protein-expressing mammalian cells, in the absence of other MHV proteins. Complementation studies using two defective interfering (DI) RNAs of a prototypic coronavirus, mouse hepatitis virus (MHV), showed that E and M proteins are both required for the production of MHV particles containing the viral nucleocapsid (5) . To establish the buoyant density of released E protein, culture fluids from E-protein-expressing cells were applied onto a discontinuous sucrose gradient and centrifuged as described above. The release of E-protein-containing membrane vesicles from MHV-infected cells and E-protein-expressing cells further emphasized the pivotal role of E protein in coronavirus assembly. Furthermore, sucrose gradient centrifugation of MHV particles showed two E protein radioactive peaks, whereas N protein had only one peak corresponding to the MHV buoyant density (Fig. 3) , indicating that membrane vesicles containing only E protein do not include nucleocapsid. abstract: Abstract Coronavirus E protein is a small viral envelope protein that plays an essential role in coronavirus assembly; coexpression of coronavirus M and E proteins results in the production of virus-like particles. The present study demonstrated that mouse hepatitis virus (MHV) E protein was released as an integral membrane protein in lipid vesicles from E-protein-expressing mammalian cells, in the absence of other MHV proteins. Furthermore, our data indicated that the E-protein-containing vesicles, which had a slightly lighter buoyant density than that of MHV, were released from MHV-infected cells. These data implied that E protein alone can drive the production and release of coronavirus envelope in the absence of M protein. url: https://api.elsevier.com/content/article/pii/S0042682299999555 doi: 10.1006/viro.1999.9955 id: cord-298934-vtrfqozl author: Makino, Shinji title: Primary structure and translation of a defective interfering rna of murine coronavirus date: 1988-10-31 words: 5188.0 sentences: 298.0 pages: flesch: 57.0 cache: ./cache/cord-298934-vtrfqozl.txt txt: ./txt/cord-298934-vtrfqozl.txt summary: The detection of such RNA intermediates in MHV-infected cells (Baric et a/., 1985 (Baric et a/., , 1987 suggests that coronavirus genomic RNA synthesis involves a discontinuous and nonprocessive mechanism, which may account for the high frequency of recombination via a copy choice mechanism. Since previous oligonucleotide fingerprinting analysis suggested that DlssE RNA contains the leader sequence and the 5'' end region of genomic sequence (Makino et al., 1985) cDNA clones were screened by colony hybridization using 5'' end-labeled, leader-specific 72-mer, and two cDNA clones F82 and C96, which correspond to the 5'' end of genomic RNA of MHV-JHM . Possible secondary structure at the DI RNA rearrangment sites Sequence analysis revealed that DlssE RNA consisted of three noncontiguous regions of MHV-JHM genomic RNA. Furthermore, as previously described for the standard MHV-JHM, the sequence surrounding the junction of leader RNA and the remaining 5''-end genomic sequence also contains a stable secondary structure (Soe eta/., 1987) . abstract: Abstract An intracellular defective-interfering (DI) RNA, DIssE, of mouse hepatitis virus (MHV) obtained after serial high multiplicity passage of the virus was cloned and sequenced. DIssE RNA is composed of three noncontiguous genomic regions, representing the first 864 nucleotides of the Fend, an internal 748 nucleotides of the polymerase gene, and 601 nucleotides from the 3′ end of the parental MHV genome. The DIssE sequence contains one large continuous open reading frame. Two protein products from this open reading frame were identified both by in vitro translation and in DI-infected cells. Sequence comparison of DIssE and the corresponding parts of the parental virus genome revealed that DIssE had three base substitutions within the leader sequence and also a deletion of nine nucleotides located at the junction of the leader and the remaining genomic sequence. The 5′ end of DIssE RNA was heterogeneous with respect to the number of UCUAA repeats within the leader sequence. The parental MHV genomic RNA appears to have extensive and stable secondary structures at the regions where DI RNA rearrangements occurred. These data suggest that MHV DI RNA may have been generated as a result of the discontinuous and nonprocessive manner of MHV RNA synthesis. url: https://api.elsevier.com/content/article/pii/0042682288905260 doi: 10.1016/0042-6822(88)90526-0 id: cord-335482-nx7odchj author: Makino, Shinji title: Defective interfering particles of mouse hepatitis virus date: 1984-02-29 words: 3840.0 sentences: 210.0 pages: flesch: 60.0 cache: ./cache/cord-335482-nx7odchj.txt txt: ./txt/cord-335482-nx7odchj.txt summary: We have observed marked reduction of infectivity in the course od serial undiluted passages of JHM virus in DBT cell culture. To avoid contamination of the standard virus stock with DI particles, plaque purified MHV (JHM strain) (Hirano et aL, 1981; Makino et al, 1983) was propagated on DBT cells at a multiplicity of infection (m.o.i.) of 0.0002 and at 15 hr postinfection (p.i.) culture fluid was harvested and clarified by low speed centrifugation. Preparation of the Standard JHM Virus for Interference Assay JHM virus was propagated on DBT cells after infection at an m.o.i. of 1.0 and was harvested at 14 hr p.i. The culture fluid was clarified by centrifugation at 8000 rpm for 30 min. To determine if the reduction in the yield of infectious virus was due to the presence of DI particles, a''n interference analysis was performed with several culture fluid samples at different passage levels. abstract: Abstract After six to eight serial undiluted passages of mouse hepatitis virus (JHM strain) in DBT cell culture, a decrease in the yield of infectious virus occurred, and with further passages fluctuating yields of infectious virus were observed. The serially passaged virus interfered with the multiplication of the standard JHM virus, but not with vesicular stomatitis virus. After sucrose equilibrium centrifugation of high passage virus, a single peak contained both infectious virus and interfering activity. This virus population resembled the original JHM virus in its structural proteins, but it contained an increased proportion of a protein with a molecular weight of 65 × 103. Genomic RNA from standard JHM virus contained a single species of RNA with a molecular weight of 5.4 × 106. After five undiluted passages, however, the virion population contained two RNA species with molecular weights of 5.4 × 106 and 5.2 × 106. RNase T1 resistant oligonucleotide finger-printing of these RNAs showed that the lower molecular weight RNA had lost several oligonucleotide spots that were present in the genomic RNA of the standard JHM virus. After several serial diluted passages of passage 10 virus, a single virus population was obtained which again had only standard virus RNA with a molecular weight of 5.4 × 106 and lacked interfering activity. These results indicated that defective interfering particles were generated by serial undiluted passages of JHM virus. url: https://www.ncbi.nlm.nih.gov/pubmed/6322437/ doi: 10.1016/0042-6822(84)90420-3 id: cord-313906-fh85fzq9 author: Maruyama, Junki title: Characterization of the glycoproteins of bat-derived influenza viruses date: 2016-01-15 words: 4241.0 sentences: 232.0 pages: flesch: 51.0 cache: ./cache/cord-313906-fh85fzq9.txt txt: ./txt/cord-313906-fh85fzq9.txt summary: We found that VSVs pseudotyped with BatIV HAs and NAs efficiently infected particular bat cell lines but not those derived from primates, and that proteolytic cleavage with a trypsin-like protease was necessary for HA-mediated virus entry. Treatment of the susceptible bat cells with some enzymes and inhibitors revealed that BatIV HAs might recognize some cellular glycoproteins as receptors rather than the sialic acids used for the other known influenza viruses. To obtain information on the biological characteristics of cellular receptors for BatIVs, IndFSPT1 cells were pretreated with tunicamycin, pronase, or neuraminidase (i.e., an N-linked glycosylation inhibitor, mixture of proteases, and sialidase, respectively), and then infected with pseudotyped VSVs (Fig. 4B-D) . IndFSPT1 should also have such molecules since it showed the highest susceptibility to BatIV HA-pseudotyped VSVs. It was noted that VSVΔG*-H17N10 and -H18N11 also infected MDCK cells, although less efficiently than these bat cell lines. abstract: Recently found bat-derived influenza viruses (BatIVs) have hemagglutinin (HA) and neuraminidase (NA) gene segments distinct from those of previously known influenza A viruses. However, pathogenicities of these BatIVs remain unknown since infectious virus strains have not been isolated yet. To gain insight into the biological properties of BatIVs, we generated vesicular stomatitis viruses (VSVs) pseudotyped with the BatIV HA and NA. We found that VSVs pseudotyped with BatIV HAs and NAs efficiently infected particular bat cell lines but not those derived from primates, and that proteolytic cleavage with a trypsin-like protease was necessary for HA-mediated virus entry. Treatment of the susceptible bat cells with some enzymes and inhibitors revealed that BatIV HAs might recognize some cellular glycoproteins as receptors rather than the sialic acids used for the other known influenza viruses. These data provide fundamental information on the mechanisms underlying the cellular entry and host restriction of BatIVs. url: https://www.ncbi.nlm.nih.gov/pubmed/26605499/ doi: 10.1016/j.virol.2015.11.002 id: cord-256703-eaj63c2k author: Matsuoka, Yumiko title: Intracellular accumulation of punta toro virus glycoproteins expressed from cloned cDNA date: 1988-11-30 words: 4311.0 sentences: 224.0 pages: flesch: 56.0 cache: ./cache/cord-256703-eaj63c2k.txt txt: ./txt/cord-256703-eaj63c2k.txt summary: On the basis of genetic recombination and sequence analysis, it has been concluded that the S RNA encodes the nucleocapsid protein N and a nonstructural protein NS,; the M RNA encodes two glycoproteins Gl and G2 and in some genera a nonstructural protein, NS,; and the L RNA probably contains the information for the viral transcriptase (Bishop et al., 1982; Bouloy et a/., 1984; Cabradilla et al., 1983; Collett et a/., 1985; Eshita and Bishop, 1984; Fuller et al., 1983; lhara et a/., 1985; Lees et al., 1986; Ronnholm and Pettersson, 1987; Schmaljohn et a/., 1987 , 1982, 1984) . To compare the levels of PlV glycoprotein synthesis, monolayers of CV-1 cells were infected with wildtype vaccinia virus, PTV, or the vaccinia recombinants described above which contain the PTV glycoprotein gene with the different sequences in the translation initiation region. We have constructed vaccinia virus recombinants containing a partial cDNA clone of the M genome segment of PTV, which encodes the Gl and G2 glycoproteins. abstract: Abstract The Punta Toro virus (PTV) middle size (M) RNA encodes two glycoproteins, G1 and G2, and possibly a nonstructural protein, NSM. A partial cDNA clone of the M segment which contains G1 and G2 glycoprotein coding sequences but lacks most of the NSM sequences was inserted into the genome of vaccinia virus under the control of an early vaccinia promoter. Cells infected with the recombinant virus were found to synthesize two polypeptides with molecular weights of 65,000 (G1) and 55,000 (G2) that reacted specifically with antibody against PTV. Studies using indirect immunofluorescence microscopy revealed that these proteins accumulated intracellularly in the perinuclear region. The results of endoglycosidase H digestion of these glycoproteins suggested that both G1 and G2 glycoproteins were transported from the RER to the Golgi complex. These proteins were not chased out from the Golgi region during a 6-hr incubation in the presence of cycloheximide. Surface immune precipitation and 125I-protein A binding assays also demonstrated that the majority of the G1 and G2 glycoproteins are retained intracellularly. These results indicate that the PTV glycoproteins contain the necessary information for retention in the Golgi apparatus. url: https://www.ncbi.nlm.nih.gov/pubmed/3142146/ doi: 10.1016/0042-6822(88)90075-x id: cord-290993-bsnja161 author: McAuliffe, Josephine title: Replication of SARS coronavirus administered into the respiratory tract of African Green, rhesus and cynomolgus monkeys date: 2004-12-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: SARS coronavirus (SARS-CoV) administered intranasally and intratracheally to rhesus, cynomolgus and African Green monkeys (AGM) replicated in the respiratory tract but did not induce illness. The titer of serum neutralizing antibodies correlated with the level of virus replication in the respiratory tract (AGM>cynomolgus>rhesus). Moderate to high titers of SARS-CoV with associated interstitial pneumonitis were detected in the lungs of AGMs on day 2 and were resolving by day 4 post-infection. Following challenge of AGMs 2 months later, virus replication was highly restricted and there was no evidence of enhanced disease. These species will be useful for the evaluation of the immunogenicity of candidate vaccines, but the lack of apparent clinical illness in all three species, variability from animal to animal in level of viral replication, and rapid clearance of virus and pneumonitis in AGMs must be taken into account by investigators considering the use of these species in efficacy and challenge studies. url: https://www.ncbi.nlm.nih.gov/pubmed/15527829/ doi: 10.1016/j.virol.2004.09.030 id: cord-256737-ptjng78b author: McBride, Corrin E. title: Palmitoylation of SARS-CoV S protein is necessary for partitioning into detergent-resistant membranes and cell-cell fusion but not interaction with M protein date: 2010-09-01 words: 8233.0 sentences: 414.0 pages: flesch: 58.0 cache: ./cache/cord-256737-ptjng78b.txt txt: ./txt/cord-256737-ptjng78b.txt summary: The SARS-CoV spike (S) protein mediates virus entry by binding cellular receptors and inducing fusion between the viral envelope and the host cell membrane. Importantly, we show that SARS-CoV S palmitoylation is not necessary for efficient interaction with SARS-CoV M, which differs from published experiments for MHV (Thorp et al., 2006) and suggests a significant difference between the two viruses that may have important implications for virus assembly and infectivity. To determine if SARS-CoV S becomes palmitoylated in a pre-medial Golgi compartment, HEK293T cells exogenously expressing SARS-CoV S were labeled for 30 min with 35 S-methionine/ cysteine to measure total protein expression or 3 H-palmitic acid to measure palmitoylated protein. Although both SARS-CoV S and S PN were present at the cell surface, it is possible that there could be a difference in the amount of protein at the plasma membrane at steady state if palmitoylation affects a post-Golgi trafficking step. abstract: Coronaviruses are enveloped RNA viruses that generally cause mild disease in humans. However, the recently emerged coronavirus that caused severe acute respiratory syndrome (SARS-CoV) is the most pathogenic human coronavirus discovered to date. The SARS-CoV spike (S) protein mediates virus entry by binding cellular receptors and inducing fusion between the viral envelope and the host cell membrane. Coronavirus S proteins are palmitoylated, which may affect function. Here, we created a non-palmitoylated SARS-CoV S protein by mutating all nine cytoplasmic cysteine residues. Palmitoylation of SARS-CoV S was required for partitioning into detergent-resistant membranes and for cell-cell fusion. Surprisingly, however, palmitoylation of S was not required for interaction with SARS-CoV M protein. This contrasts with the requirement for palmitoylation of mouse hepatitis virus S protein for interaction with M protein, and may point to important differences in assembly and infectivity of these two coronaviruses. url: https://doi.org/10.1016/j.virol.2010.05.031 doi: 10.1016/j.virol.2010.05.031 id: cord-273745-mwjh5se7 author: Meng, Fandan title: A phage-displayed peptide recognizing porcine aminopeptidase N is a potent small molecule inhibitor of PEDV entry date: 2014-03-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Three phage-displayed peptides designated H, S and F that recognize porcine aminopeptidase N (pAPN), the cellular receptor of porcine transmissible gastroenteritis virus (TGEV) were able to inhibit cell infection by TGEV. These same peptides had no inhibitory effects on infection of Vero cells by porcine epidemic diarrhea virus (PEDV). However, when PEDV, TGEV and porcine pseudorabies virus were incubated with peptide H (HVTTTFAPPPPR), only infection of Vero cells by PEDV was inhibited. Immunofluoresence assays indicated that inhibition of PEDV infection by peptide H was independent of pAPN. Western blots demonstrated that peptide H interacted with PEDV spike protein and that pre-treatment of PEDV with peptide H led to a higher inhibition than synchronous incubation with cells. These results indicate direct interaction with the virus is necessary to inhibit infectivity. Temperature shift assays demonstrated that peptide H inhibited pre-attachment of the virus to the cells. url: https://www.sciencedirect.com/science/article/pii/S0042682214000130 doi: 10.1016/j.virol.2014.01.010 id: cord-274122-n9jnu2ah author: Mielech, Anna M. title: MERS-CoV papain-like protease has deISGylating and deubiquitinating activities date: 2014-02-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Coronaviruses encode papain-like proteases (PLpro) that are often multifunctional enzymes with protease activity to process the viral replicase polyprotein and deubiquitinating (DUB)/deISGylating activity, which is hypothesized to modify the innate immune response to infection. Here, we investigate the predicted DUB activity of the PLpro domain of the recently described Middle East Respiratory Syndrome Coronavirus (MERS-CoV). We found that expression of MERS-CoV PLpro reduces the levels of ubiquitinated and ISGylated host cell proteins; consistent with multifunctional PLpro activity. Further, we compared the ability of MERS-CoV PLpro and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) PLpro to block innate immune signaling of proinflammatory cytokines. We show that expression of SARS-CoV and MERS-CoV PLpros blocks upregulation of cytokines CCL5, IFN-β and CXCL10 in stimulated cells. Overall these results indicate that the PLpro domains of MERS-CoV and SARS-CoV have the potential to modify the innate immune response to viral infection and contribute to viral pathogenesis. url: https://www.sciencedirect.com/science/article/pii/S0042682213006624 doi: 10.1016/j.virol.2013.11.040 id: cord-319403-5qyc0wsz author: Miura, Tanya A. title: Rat coronaviruses infect rat alveolar type I epithelial cells and induce expression of CXC chemokines date: 2007-12-01 words: 6621.0 sentences: 390.0 pages: flesch: 52.0 cache: ./cache/cord-319403-5qyc0wsz.txt txt: ./txt/cord-319403-5qyc0wsz.txt summary: Type I cells were productively infected with SDAV and RCoV-P, and both live virus and UV-inactivated virus induced mRNA and protein expression of three CXC chemokines: CINC-2, CINC-3, and LIX, which are neutrophil chemoattractants. Bronchial epithelial cells and alveolar type II cells express and secrete proinflammatory cytokines and chemokines in response to infection with respiratory viruses including respiratory syncytial virus, influenza A virus, and the SARS-associated coronavirus (SARS-CoV) Yen et al., 2006; Zhang et al., 2001) . In this study, cultures of rat alveolar type I cells were evaluated for susceptibility to RCoV infection, and for expression and secretion of proinflammatory cytokines and chemokines in response to RCoV inoculation. To determine whether the CXC chemokine response to infectious or UV-inactivated RCoV-P or SDAV was specific for the rat coronaviruses, we inoculated rat alveolar type I cells with a related group 2a coronavirus, mouse hepatitis virus (MHV) strain A59 that had been purified by sucrose density gradient centrifugation. abstract: We analyzed the ability of two rat coronavirus (RCoV) strains, sialodacryoadenitis virus (SDAV) and Parker’s RCoV (RCoV-P), to infect rat alveolar type I cells and induce chemokine expression. Primary rat alveolar type II cells were transdifferentiated into the type I cell phenotype. Type I cells were productively infected with SDAV and RCoV-P, and both live virus and UV-inactivated virus induced mRNA and protein expression of three CXC chemokines: CINC-2, CINC-3, and LIX, which are neutrophil chemoattractants. Dual immunolabeling of type I cells for viral antigen and CXC chemokines showed that chemokines were expressed primarily by uninfected cells. Virus-induced chemokine expression was reduced by the IL-1 receptor antagonist, suggesting that IL-1 produced by infected cells induces uninfected cells to express chemokines. Primary cultures of alveolar epithelial cells are an important model for the early events in viral infection that lead to pulmonary inflammation. url: https://www.ncbi.nlm.nih.gov/pubmed/17804032/ doi: 10.1016/j.virol.2007.07.030 id: cord-273379-w8vy5rl8 author: Mizutani, Tetsuya title: Nascent Synthesis of Leader Sequence-Containing Subgenomic mRNAs in Coronavirus Genome-Length Replicative Intermediate RNA date: 2000-09-30 words: 4033.0 sentences: 184.0 pages: flesch: 48.0 cache: ./cache/cord-273379-w8vy5rl8.txt txt: ./txt/cord-273379-w8vy5rl8.txt summary: RNase protection assays using the purified genome-length RI and two probes, which corresponded to the 5′ 300-nt region of mRNA 6 and to the same region of mRNA 7, showed the presence of nascent leader sequence-containing subgenomic mRNAs in the genome-length RI. We purified genome-length RI without contamination of any detectable level of MHV subgenomic mRNAs. We used RNase protection assays to look for nascent subgenomic mRNAs containing the leader sequence in the genome-length RI. If leader-sequence-containing subgenomic mRNA 6 elongates on the genome-length RI, then the RNase protection assay using probe 1 and purified radiolabeled genome-length RI should produce a radiolabeled 300-nt-long RNA fragment (300-nt fragment) that corresponds to the 5Ј-end 300 nt of nascent mRNA 6 (see Fig. 3A ). RNase A treatment of the gel-purified genome-length RI produced RF 1 (Fig. 2B) , and the RNase protection assay demonstrated the presence of nascent leader-sequence-containing subgenomic mRNAs in the genome-length RI. abstract: Abstract Infection with coronavirus results in the accumulation of genomic-sized mRNA and six to eight subgenomic mRNAs that make up a 3′ coterminal nested-set structure. Genome-length negative-strand RNA and subgenomic-length negative-strand RNAs, each of which corresponds to each of the subgenomic mRNAs, also accumulate in infected cells. The present study examined whether the genome-length negative-strand RNA serves as a template for subgenomic mRNA synthesis. Genome-length replicative intermediate (RI) RNA was purified by two-dimensional gel electrophoresis of intracellular RNAs from cells infected with mouse hepatitis virus. RNase A treatment of the purified genome-length RI resulted in the production of the genome-length replicative form RNA, indicating that the genome-length RI included genome-length template RNA. RNase protection assays using the purified genome-length RI and two probes, which corresponded to the 5′ 300-nt region of mRNA 6 and to the same region of mRNA 7, showed the presence of nascent leader sequence-containing subgenomic mRNAs in the genome-length RI. These data demonstrated that the genome-length negative-strand RNA serves as a template for subgenomic mRNA synthesis. url: https://www.ncbi.nlm.nih.gov/pubmed/10998322/ doi: 10.1006/viro.2000.0489 id: cord-271526-14nfqusv author: Molenkamp, Richard title: Identification of a Specific Interaction between the Coronavirus Mouse Hepatitis Virus A59 Nucleocapsid Protein and Packaging Signal date: 1997-12-08 words: 5535.0 sentences: 341.0 pages: flesch: 56.0 cache: ./cache/cord-271526-14nfqusv.txt txt: ./txt/cord-271526-14nfqusv.txt summary: To determine the specificity of the nucleocapsid pro-RNA-protein complexes (Fig. 3, lanes 8-10 and 12) , tein-Ps180 RNA interaction in UV cross-linking assays, clearly indicating that the observed supershift was not competition experiments were performed. This interaction was studied by gel retardation and UV Lysates were prepared from the virus peak fractions (pcross-linking assays using an RNA probe containing the lysate) and from the gradient bottom fractions (b-lysate; 69-nt Ps and the N protein from MHV-A59 infected cell negative control). A structural model for coronaviruses was flanked by non-MHV sequences could confer specific proposed, in which a spherical core, composed of a combination of N and M proteins, was present in addition to encapsidation to a heterologous RNA in MHV infected INTERACTION BETWEEN NUCLEOCAPSID PROTEIN AND PACKAGING SIGNAL of a murine coronavirus in the absence of helper virus. abstract: Abstract The coronavirus mouse hepatitis virus (MHV) is an enveloped positive stranded RNA virus. In infected cells MHV produces a 3′ coterminal nested set of subgenomic messenger RNAs. Only the genomic RNA, however, is encapsidated by the nucleocapsid protein and incorporated in infectious MHV virions. It is believed that an RNA packaging signal (Ps), present only in the genomic RNA, is responsible for this selectivity. Earlier studies mapped this signal to a 69-nt stem–loop structure positioned in the 3′ end of ORF1b. The selective encapsidation mechanism probably initiates by specific interaction of the packaging signal with the nucleocapsid protein. In this study we demonstrate thein vitrointeraction of the MHV-A59 nucleocapsid protein with the packaging signal of MHV using gel retardation and UV cross-linking assays. This interaction was observed not only with the nucleocapsid protein from infected cells but also with that from purified virions and from cells expressing a recombinant nucleocapsid protein. The specificity of the interaction was demonstrated by competition experiments with nonlabeled Ps containing RNAs, tRNA, and total cytoplasmic RNA. The results indicated that no virus specific modification of the N-protein or the presence of other viral proteins are required for thisin vitrointeraction. The assays described in this report provide us with a powerful tool for studying encapsidation (initiation) in more detail. url: https://api.elsevier.com/content/article/pii/S004268229798867X doi: 10.1006/viro.1997.8867 id: cord-266861-t5h133lp author: Moller-Tank, Sven title: Phosphatidylserine receptors: enhancers of enveloped virus entry and infection date: 2014-11-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A variety of both RNA and DNA viruses envelop their capsids in a lipid bilayer. One of the more recently appreciated benefits this envelope is incorporation of phosphatidylserine (PtdSer). Surface exposure of PtdSer disguises viruses as apoptotic bodies; tricking cells into engulfing virions. This mechanism is termed apoptotic mimicry. Several PtdSer receptors have been identified to enhance virus entry and we have termed this group of proteins PtdSer-mediated virus entry enhancing receptors or PVEERs. These receptors enhance entry of a broad range of enveloped viruses. Internalization of virions by PVEERs provides a broad mechanism of entry with little investment by the virus itself and may allow some viruses to attach to cells, thereby making viral glycoprotein/cellular receptor interactions more probable. Alternatively, other viruses may rely entirely on PVEERs for internalization into endosomes. This review provides an overview of PtdSer receptors that serve as PVEERs and the biology behind virion/PVEER interaction. url: https://www.ncbi.nlm.nih.gov/pubmed/25277499/ doi: 10.1016/j.virol.2014.09.009 id: cord-262245-eb7g9p1x author: Monica, Nicola La title: Localization of extensive deletions in the structural genes of two neurotropic variants of murine coronavirus JHM date: 1991-06-30 words: 3512.0 sentences: 178.0 pages: flesch: 60.0 cache: ./cache/cord-262245-eb7g9p1x.txt txt: ./txt/cord-262245-eb7g9p1x.txt summary: Abstract The intracellular RNA of two neurotropic variants of the JHM strain of mouse hepatitis virus (MHV) independently isolated from the brain and spinal cord of an infected Wistar Furth rat were compared with that of the parental virus. Both the brain and the spinal cord isolates displayed a different pattern of virus-specific mRNAs from the parental JHM virus in the infected cells (26). The size of several of these mRNAs appeared different; most notably, the mRNA 3 of the At1 lf cord isolate was smaller than those of the parental JHM strain and of the brain isolate but similar to that of JHM (2), which has a deletion of 423 nucleotides in the S gene (28). Figure 5A shows that the S protein of the At1 lf cord variant is smaller than that of the JHM parental virus, but similar in size to that of the JHM(2), which has a deletion of 153 amino acids (28). abstract: Abstract The intracellular RNA of two neurotropic variants of the JHM strain of mouse hepatitis virus (MHV) independently isolated from the brain and spinal cord of an infected Wistar Furth rat were compared with that of the parental virus. The mRNAs corresponding to the genes encoding the peplomer (S) and the hemagglutinin-esterase (HE) proteins of the variant viruses were found to be smaller in size. The possible sequence changes were studied by oligonucleotide fingerprinting and direct RNA sequencing. Both variants have a large deletion of 246 amino acids in the carboxy-terminal end of the HE protein. However, this truncated protein was not detected in the infected cells, suggesting either a translational regulation or rapid degradation of the truncated protein in these cells. The variant virus isolated from the spinal cord has a second deletion of 147 amino acids in the amino-terminal half of the S protein. This deletion site corresponds to a hypervariable region where deletions have been frequently noted among MHV variants with different biological properties. These findings suggest that the changes in pathogenic properties of the two neural isolates are associated with drastic alterations of the viral structural glycoproteins. url: https://api.elsevier.com/content/article/pii/004268229190635O doi: 10.1016/0042-6822(91)90635-o id: cord-310967-15mv5yx7 author: Morris, Vincent L. title: Characterization of coronavirus JHM variants isolated from wistar furth rats with a viral-induced demyelinating disease date: 1989-03-31 words: 5838.0 sentences: 301.0 pages: flesch: 56.0 cache: ./cache/cord-310967-15mv5yx7.txt txt: ./txt/cord-310967-15mv5yx7.txt summary: One of these variants, ATIIf cord virus, which induced a chronic demyelinating disease in 2or 10-day-old intracerebrally inoculated Wistar Furth rats, had a deletion in the coding region of the peplomer glycoprotein mRNA. In this report, we investigated viral variants that arose in the CNS of rats with a JHM-induced demyelinating disease and studied the effect of alterations in their mRNAs. When lo-day-old rats were inoculated with ATllf brain virus or ATlIe brain virus, the rats developed a rapid encephalitis instead of the more chronic demyelinating disease that has previously been seen with wild-type parental JHM virus (Sorensen et al., 1980; Jackson et al., 1984) and was observed with ATIIf cord virus-injected rats. In contrast, when 2-day-old rats were inoculated with ATllf cord virus, the more chronic CNS disease resulted instead of the rapid encephalitis that has been reported for wild-type JHM (Sorensen et a/., 1980; Parham et a/., 1986) and was observed with the ATIIf brain virus variant. abstract: Abstract Murine hepatitis virus (MHV) can cause neurological disease when inoculated intracerebrally (ic) into mice and rats. Specifically the JHM strain of MHV (MHV-JHM) generally causes an acute encephalitis when inoculated is into 2-day-old Wistar Furth rats. In contrast, JHM generally produces a chronic demyelinating disease with resulting posterior paralysis when inoculated is into 10-day-old Wistar Furth rats. In addition, while JHM readily produces a productive infection in a mouse fibroblast cell line (L-2), it does not form syncytia or replicate well in a tissue cell line of glial origin (G26-24). We have isolated and characterized three MHV-JHM viral variants from the central nervous system of two Wistar Furth rats with a MHV-JHM-induced demyelinating disease. The pattern of viral-specific mRNA for all three of these variants differed from what was observed for the wild-type parental MHV-JHM that had been passaged only in tissue culture. One of these variants, ATIIf cord virus, which induced a chronic demyelinating disease in 2- or 10-day-old intracerebrally inoculated Wistar Furth rats, had a deletion in the coding region of the peplomer glycoprotein mRNA. In addition, this variant formed massive syncytia and replicated well in G26-24 cells. We have not detected this deletion in the other two JHM variants, ATIIf brain virus and ATIIe brain virus. ATIIf brain virus and ATIIe brain virus primarily produced an acute encephalitis when reinoculated into 2-or 10-day-old Wistar Furth rats. In addition, these two variants did not form syncytia and had a reduced ability to replicate in G26-24 cells. url: https://www.ncbi.nlm.nih.gov/pubmed/2538027/ doi: 10.1016/0042-6822(89)90048-2 id: cord-254950-y6kayxie author: Morse, Stephen S. title: Mouse thymic virus (MTLV; Murid Herpesvirus 3) infection in athymic nude mice: Evidence for a T lymphocyte requirement date: 1988-03-31 words: 2123.0 sentences: 99.0 pages: flesch: 51.0 cache: ./cache/cord-254950-y6kayxie.txt txt: ./txt/cord-254950-y6kayxie.txt summary: Abstract Mouse thymic virus (MTLV; murid herpesvirus 3) is a lymphotropic herpesvirus that cytolytically infects developing T lineage lymphocytes in the thymus of neonatal mice. In order to determine whether T lineage lymphocytes are required for infection, young adult athymic nude (nulnu) mice and euthymic littermates were infected with MTLV and tested for virus shedding. To determine whether MTLV infection requires thymus-derived lymphocytes, 4-week-old female ICR Swiss athymic nude (nulnu) and euthymic (+lnu) littermate controls (four each; Memorial Sloan-Kettering Cancer Center nude mouse breeding colony) were inoculated intraperitoneally with either 40 or 200 IDS0 of MTLV and virus shedding was tested by mouth swabs beginning 6 days after infection. litters available did not allow every negative sample to be tested, additional litters of normal newborn mice were inoculated with fresh homogenates (1 O-20%, w/v) of randomly selected negative thymuses and salivary glands, representing various test dates up to Day 48, from 14 assay litters that had received swab fluids from nude mice. abstract: Abstract Mouse thymic virus (MTLV; murid herpesvirus 3) is a lymphotropic herpesvirus that cytolytically infects developing T lineage lymphocytes in the thymus of neonatal mice. MTLV establishes a persistent infection and can be recovered indefinitely from infected mice, but nothing is known about requirements for this persistent infection. In order to determine whether T lineage lymphocytes are required for infection, young adult athymic nude (nulnu) mice and euthymic littermates were infected with MTLV and tested for virus shedding. Although euthymic littermates regularly shed virus, in the nude mice only about 20% of isolation attempts up to 100 days postinfection were positive. Blind passage yielded an additional three isolations out of 14 samples (21 %). In addition, unlike many other herpesviruses, the virus did not replicate in a number of epithelial and fibroblastic cell lines that were tested. These data confirm that the virus is preferentially T lymphotropic and suggest that infection may require T lineage lymphocytes. url: https://api.elsevier.com/content/article/pii/0042682288902620 doi: 10.1016/0042-6822(88)90262-0 id: cord-284968-eymvj6k3 author: Namazue, Junko title: Processing of virus-specific glycoproteins of varicella zoster virus date: 1985-05-31 words: 2818.0 sentences: 125.0 pages: flesch: 56.0 cache: ./cache/cord-284968-eymvj6k3.txt txt: ./txt/cord-284968-eymvj6k3.txt summary: Immunoprecipitation experiments performed with VZV-infected cells, pulse labeled with [3H]glucosamine in the presence of tunicamycin, suggest that O-linked oligosaccharide is present on the glycoprotein of gp 2. In order to investigate the effect of TM on the synthesis of VZV glycoprotein, infected cell cultures were labeled with rHlglucosamine for 18 hr, and cell extracts were immunoprecipitated with three kinds of monoclonal antibodies (cl 9, cl 8, and cl 12) which react with glycoproteins gp 2, gp 3, and gp 5, respectively (Okuno et a,?., 1983) . Next, when cell extracts were reacted with antibodies of cl 8, a band at 106K was seen at pulse labeling, and additional 116K and 64K (prominent) polypeptides were detected during chase (Fig. 2, lanes e, g) . Finally, when cell extracts in the absence of TM were reacted with antibody from cl 12, 49K (major) and 43K (minor) polypeptides from cell cultures of pulse labeling and 55K (major) and 94K (minor) polypeptides were observed during chase (Fig. 2, lanes i, k) . abstract: Abstract Monoclonal antibodies to varicella zoster virus (VZV) glycoproteins were used to study the processing of three glycoproteins with molecular weights of 83K–94K (gp 2), 64K (gp 3), and 55K (gp 5). Immunoprecipitation experiments performed with VZV-infected cells, pulse labeled with [3H]glucosamine in the presence of tunicamycin, suggest that O-linked oligosaccharide is present on the glycoprotein of gp 2. Use of the enzyme endo-β-N-acetylglucosaminidase H revealed that the fully processed form of gp 3 had high-mannose type and that of gp 5 had only complex type of N-linked oligosaccharides. Experiments with monensin suggest that the precursor form (116K) of gp 3 is cleaved during the processing from Golgi apparatus to cell surface membrane. The extension of O-linked oligosaccharide chain and the complex type of N-linked oligosaccharide chains also occurs during this processing. url: https://www.sciencedirect.com/science/article/pii/0042682285901126 doi: 10.1016/0042-6822(85)90112-6 id: cord-280957-cdd6ngf1 author: Narkpuk, Jaraspim title: The avian influenza virus PA segment mediates strain-specific antagonism of BST-2/tetherin date: 2018-10-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BST-2 is an antiviral protein described as a powerful cross-species transmission barrier for simian immunodeficiency viruses. Influenza viruses appear to interact with BST-2, raising the possibility that BST-2 may be a barrier for cross-species transmission. An MDCK-based cell line expressing human BST-2 was generated to study human-derived A/Puerto Rico/8/36 (H1N1; PR8) as well as two low pathogenic avian influenza viruses (subtypes H4N6 and H6N1). The H4N6 and H6N1 viruses were less affected by BST-2 expression than PR8, due to their ability to decrease BST-2 levels, a function localized to the PA segment of both avian viruses. Experiments with PA-mutant and -chimeric viruses confirmed that the avian PA segment conferred BST-2 downregulation and antagonism. These results indicate a species-specific ability of PA from low pathogenic avian viruses to mitigate human BST-2 antiviral activity, suggesting that BST-2 is unlikely to be a general cross-species barrier to transmission of such viruses to humans. url: https://doi.org/10.1016/j.virol.2018.09.016 doi: 10.1016/j.virol.2018.09.016 id: cord-322904-9mta0aem author: Neu, Ursula title: The Polyomaviridae: Contributions of virus structure to our understanding of virus receptors and infectious entry date: 2009-02-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This review summarizes the fields major findings related to the characterization of polyomavirus structures and to the characterization of virus receptors and mechanisms of host cell invasion. Four members of the family that have received the most attention in this regard are the mouse polyomavirus (mPyV), the monkey polyomavirus SV40, and the two human polyomaviruses, JCV and BKV. The structures of both the mPyV and SV40 alone and in complex with receptor fragments have been solved to high resolution. The majority of polyomaviruses recognize terminal sialic acid in either an α 2,3 linkage or an α 2,6 linkage to the underlying galactose. Studies on virus structure, receptor utilization and mechanisms of entry have led to new insights into how these viruses interact in an active way with cells to ensure the nuclear delivery and expression of their genomes. Critical work on virus entry has led to the discovery of a pH neutral endocytic compartment that accepts cargo from caveolae and to novel roles for endoplasmic reticulum (ER) associated factors in virus uncoating and penetration of ER membranes. This review will summarize the major findings and compare and contrast the mechanisms used by these viruses to infect cells. url: https://doi.org/10.1016/j.virol.2008.12.021 doi: 10.1016/j.virol.2008.12.021 id: cord-276358-so390gp4 author: Nieto-Torres, Jose L. title: Severe acute respiratory syndrome coronavirus E protein transports calcium ions and activates the NLRP3 inflammasome date: 2015-11-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Severe acute respiratory syndrome coronavirus (SARS-CoV) envelope (E) protein is a viroporin involved in virulence. E protein ion channel (IC) activity is specifically correlated with enhanced pulmonary damage, edema accumulation and death. IL-1β driven proinflammation is associated with those pathological signatures, however its link to IC activity remains unknown. In this report, we demonstrate that SARS-CoV E protein forms protein–lipid channels in ERGIC/Golgi membranes that are permeable to calcium ions, a highly relevant feature never reported before. Calcium ions together with pH modulated E protein pore charge and selectivity. Interestingly, E protein IC activity boosted the activation of the NLRP3 inflammasome, leading to IL-1β overproduction. Calcium transport through the E protein IC was the main trigger of this process. These findings strikingly link SARS-CoV E protein IC induced ionic disturbances at the cell level to immunopathological consequences and disease worsening in the infected organism. url: https://doi.org/10.1016/j.virol.2015.08.010 doi: 10.1016/j.virol.2015.08.010 id: cord-269204-kajws5xo author: Nitschke, Matthias title: Equine arteritis virus is delivered to an acidic compartment of host cells via clathrin-dependent endocytosis date: 2008-08-01 words: 4831.0 sentences: 274.0 pages: flesch: 48.0 cache: ./cache/cord-269204-kajws5xo.txt txt: ./txt/cord-269204-kajws5xo.txt summary: To investigate whether EAV cell entry proceeds via endocytic uptake we first studied the involvement of clathrin-coated pits in EAV internalization using a BHK cell line that can be induced to express antisense RNA of the clathrin heavy chain (CHC) causing a selective block in clathrin-dependent endocytosis (Iversen et al., 2001) . In contrast to EAV, neither concanamycin A nor bafilomycin A1 nor monensin treatment of BHK-21 cells did affect SV5 mediated plaque formation (Fig. 3 ) consistent with the fact that infection by Parainfluenza viruses does not require a low pH compartment (Lamb and Kolakofsky, 2001) . To explore whether proteases of the late acidic compartments may play a role in fusion activation of EAV, we measured infection of BHK-21 cells upon incubation with leupeptin and E64d, which have been shown to inhibit acidic proteases in the endosomal compartment. abstract: Equine arteritis virus (EAV) is an enveloped, positive-stranded RNA virus belonging to the family Arteriviridae. Infection by EAV requires the release of the viral genome by fusion with the respective target membrane of the host cell. We have investigated the entry pathway of EAV into Baby Hamster Kindey cells (BHK). Infection of cells assessed by the plaque reduction assay was strongly inhibited by substances which interfere with clathrin-dependent endocytosis and by lysosomotropic compounds. Furthermore, infection of BHK cells was suppressed when clathrin-dependent endocytosis was inhibited by expression of antisense RNA of the clathrin-heavy chain before infection. These results strongly suggest that EAV is taken up via clathrin-dependent endocytosis and is delivered to acidic endosomal compartments. url: https://doi.org/10.1016/j.virol.2008.04.041 doi: 10.1016/j.virol.2008.04.041 id: cord-273246-4s54jrww author: Niu, Shengniao title: An infectious RNA with a hepta-adenosine stretch responsible for programmed −1 ribosomal frameshift derived from a full-length cDNA clone of Hibiscus latent Singapore virus date: 2014-01-20 words: 4213.0 sentences: 213.0 pages: flesch: 61.0 cache: ./cache/cord-273246-4s54jrww.txt txt: ./txt/cord-273246-4s54jrww.txt summary: title: An infectious RNA with a hepta-adenosine stretch responsible for programmed −1 ribosomal frameshift derived from a full-length cDNA clone of Hibiscus latent Singapore virus In HLSV, a À 1 PRF product, 108 kDa protein, was still detected using transcripts derived from BspHI digested pHLSV-7A, in which the far downstream HLSV sequence was cut off (Fig. 2C , fourth lane from the right). We report here the construction of HLSV biologically active full-length cDNA clones and the identification of a heptaadenosine stretch in HLSV genome as a slippery sequence responsible for À 1 PRF, independent of its downstream pseudoknot structure and the far downstream RNA sequence in vitro. Since monotonous runs of nucleotides can also cause À 2 or þ 1 PRF (Brierley et al., 1992) , we noticed that in the in vitro translation products using HLSV-8A transcripts, a 78 kDa protein was detected (Fig. 2C , first lane from the right). abstract: Hibiscus latent Singapore virus (HLSV) is a member of Tobamovirus and its full-length cDNA clones were constructed. The in vitro transcripts from two HLSV full-length cDNA clones, which contain a hepta-adenosine stretch (pHLSV-7A) and an octo-adenosine stretch (pHLSV-8A), are both infectious. The replication level of HLSV-7A in Nicotiana benthamiana protoplasts was 5-fold lower, as compared to that of HLSV-8A. The replicase proteins of HLSV-7A were produced through programmed −1 ribosomal frameshift (−1 PRF) and the 7A stretch was a slippery sequence for −1 PRF. Mutations to the downstream pseudoknot of 7A stretch showed that the pseudoknot was not required for the frameshift in vitro. The stretch was found to be extended to 8A after subsequent replication cycles in vivo. It is envisaged that HLSV employs the monotonous runs of A and −1 PRF to convert its 7A to 8A to reach higher replication for its survival in plants. url: https://www.ncbi.nlm.nih.gov/pubmed/24418557/ doi: 10.1016/j.virol.2013.11.021 id: cord-290640-kh2t0kfz author: O''Connor, Jennifer Black title: Downstream Ribosomal Entry for Translation of Coronavirus TGEV Gene 3b date: 2000-03-30 words: 5946.0 sentences: 283.0 pages: flesch: 55.0 cache: ./cache/cord-290640-kh2t0kfz.txt txt: ./txt/cord-290640-kh2t0kfz.txt summary: Abstract Gene 3b (ORF 3b) in porcine transmissible gastroenteritis coronavirus (TGEV) encodes a putative nonstructural polypeptide of 27.7 kDa with unknown function that during translation in vitro is capable of becoming a glycosylated integral membrane protein of 31 kDa. In the virulent Miller strain of TGEV, ORF 3b is 5′-terminal on mRNA 3–1 and is presumably translated following 5′ cap-dependent ribosomal entry. Here we report that, whereas mRNA 3 has a sequence predicting leaky scanning for the translation of ORF 3b by the model of Kozak (1989) , experimental results with mutant constructs suggested downstream entry of ribosomes might also be used. To test by in vitro translation whether the 27.7-and 20-kDa gene 3b products (O''Connor and Brian, 1999) are synthesized when ORF 3b is positioned downstream of ORF 3a (beginning at base 337) on synthetic transcripts, uncapped transcripts of pORF3a-3b-4 DNA linearized at the BamHI site 50 nt downstream from the stop codon of gene 4 (Fig. 1C) were translated in either wheat germ extract or rabbit reticulocyte lysate. abstract: Abstract Gene 3b (ORF 3b) in porcine transmissible gastroenteritis coronavirus (TGEV) encodes a putative nonstructural polypeptide of 27.7 kDa with unknown function that during translation in vitro is capable of becoming a glycosylated integral membrane protein of 31 kDa. In the virulent Miller strain of TGEV, ORF 3b is 5′-terminal on mRNA 3–1 and is presumably translated following 5′ cap-dependent ribosomal entry. For three other strains of TGEV, the virulent British FS772/70 and Taiwanese TFI and avirulent Purdue-116, mRNA species 3–1 is not made and ORF 3b is present as a non-overlapping second ORF on mRNA 3. ORF 3b begins at base 432 on mRNA 3 in Purdue strain. In vitro expression of ORF 3b from Purdue mRNA 3-like transcripts did not fully conform to a predicted leaky scanning pattern, suggesting ribosomes might also be entering internally. With mRNA 3-like transcripts modified to carry large ORFs upstream of ORF 3a, it was demonstrated that ribosomes can reach ORF 3b by entering at a distant downstream site in a manner resembling ribosomal shunting. Deletion analysis failed to identify a postulated internal ribosomal entry structure (IRES) within ORF 3a. The results indicate that an internal entry mechanism, possibly in conjunction with leaky scanning, is used for the expression of ORF 3b from TGEV mRNA 3. One possible consequence of this feature is that ORF 3b might also be expressed from mRNAs 1 and 2. url: https://api.elsevier.com/content/article/pii/S0042682200902186 doi: 10.1006/viro.2000.0218 id: cord-311774-fhdvcvi0 author: O'Donnell, Vivian title: Foot-and-mouth disease virus utilizes an autophagic pathway during viral replication date: 2011-02-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Foot-and-mouth disease virus (FMDV) is the type species of the Aphthovirus genus within the Picornaviridae family. Infection of cells with positive-strand RNA viruses results in a rearrangement of intracellular membranes into viral replication complexes. The origin of these membranes remains unknown; however induction of the cellular process of autophagy is beneficial for the replication of poliovirus, suggesting that it might be advantageous for other picornaviruses. By using confocal microscopy we showed in FMDV-infected cells co-localization of non-structural viral proteins 2B, 2C and 3A with LC3 (an autophagosome marker) and viral structural protein VP1 with Atg5 (autophagy-related protein), and LC3 with LAMP-1. Importantly, treatment of FMDV-infected cell with autophagy inducer rapamycin, increased viral yield, and inhibition of autophagosomal pathway by 3-methyladenine or small-interfering RNAs, decreased viral replication. Altogether, these studies strongly suggest that autophagy may play an important role during the replication of FMDV. url: https://api.elsevier.com/content/article/pii/S004268221000704X doi: 10.1016/j.virol.2010.10.042 id: cord-272050-0u62j7nj author: Okamoto, Kimiyuki title: cis-Preferential requirement of a − 1 frameshift product p88 for the replication of Red clover necrotic mosaic virus RNA1 date: 2008-05-25 words: 5335.0 sentences: 262.0 pages: flesch: 50.0 cache: ./cache/cord-272050-0u62j7nj.txt txt: ./txt/cord-272050-0u62j7nj.txt summary: In contrast, cis-preferential function of the viral encoded proteins or a coupling between translation and replication has been reported for several viruses, including Alfalfa mosaic virus (AMV) (Neeleman and Bol, 1999; van Rossum et al., 1996) , Clover yellow mosaic virus (CYMV) (White et al., 1992) , Bovine coronavirus (Chang et al., 1994) , Cowpea mosaic virus (van Bokhoven et al., 1993) , Poliovirus (Hagino-Yamagishi and Nomoto, 1989; Johnson and Sarnow, 1991; Novak and Kirkegaard, 1994) , Turnip crinkle virus (TCV) (White et al., 1995) , Tobacco etch virus (Mahajan et al., 1996; Schaad et al., 1996) , Tobacco mosaic virus (TMV) (Lewandowski and Dawson, 2000) , Tomato bushy stunt virus (TBSV) (Oster et al., 1998) , Turnip yellow mosaic virus (TYMV) (Weiland and Dreher, 1993) , and Rubella virus (Liang and Gillam, 2001) . cis-Acting core RNA elements required for negative-strand RNA synthesis and cap-independent translation are separated in the 3¢-untranslated region of Red clover necrotic mosaic virus RNA1 abstract: The genome of Red clover necrotic mosaic virus (RCNMV) consists of RNA1 and RNA2. RNA1 encodes N-terminally overlapping replication proteins, p27 and p88, which are translated in a cap-independent manner. The 3′ untranslated region of RNA1 contains RNA elements essential for cap-independent translation and negative-strand RNA synthesis. In this study, we investigated how p27 and p88 were engaged in the replication of RCNMV genomic RNAs by using DNA vectors or in vitro transcribed RNAs in protoplasts and in a cell-free extract of evacuolated BY-2 protoplasts. Our results show a cis-preferential requirement of p88, but not of p27, for the replication of RNA1. This mechanism might help to facilitate a switch in the role of RNA1 from mRNA to a replication template. url: https://doi.org/10.1016/j.virol.2008.02.004 doi: 10.1016/j.virol.2008.02.004 id: cord-255453-7e40rj1y author: Oliver, S.L. title: Genomic characterization of the unclassified bovine enteric virus Newbury agent-1 (Newbury1) endorses a new genus in the family Caliciviridae date: 2006-06-20 words: 6227.0 sentences: 303.0 pages: flesch: 53.0 cache: ./cache/cord-255453-7e40rj1y.txt txt: ./txt/cord-255453-7e40rj1y.txt summary: The relationship of Bo/Newbury1/1976/UK with members of the Caliciviridae Although many features of the Newbury1 genome organization were consistent with the Caliciviridae, the Newbury1 genome had low nucleotide (≤47%) and amino acid (≤39%) identities to all representative viruses of the 4 Caliciviridae genera by comparison of complete non-structural genes (2Chelicase, 3C-protease, 3D-polymerase), complete capsids, capsid subdomains and the 3′ terminal ORF genes ( Table 2 ). Newbury1 failed to group phylogenetically with the 4 recognized Caliciviridae genera but formed a separate clade with NB virus by UPGMA, Fitch-Margoliash, parsimony and maximum likelihood analyses of the nucleotide and translated amino acids of ORF1 (excluding the capsid gene), the individual regions that encoded the 2C-helicase, 3C-protease, 3D-polymerase and complete capsid genes (not shown). The distant relationship of Newbury1 to the 4 recognized Caliciviridae genera was confirmed using additional phylogenetic analyses based on amino acid alignments generated from homology models of structurally conserved regions of the partial polymerase and the capsid S-domain (Fig. 3) . abstract: The pathogenic bovine enteric virus, Newbury agent-1 (Bo//Newbury1/1976/UK), first identified in 1976, was characterized as a possible calicivirus by morphology, buoyant density in CsCl and the presence of a single capsid protein but genomic sequence could not be obtained. In the present study, the complete genome sequence of Newbury1 was determined and classified Newbury1 in a new genus of the Caliciviridae. The Newbury1 genome, of 7454 nucleotides, had two predicted open reading frames (ORFs). ORF1 encoded the non-structural and contiguous capsid proteins. ORF2 encoded a basic protein characteristic of the family Caliciviridae. Compared to the 4 recognized Caliciviridae genera, Norovirus, Sapovirus, Lagovirus and Vesivirus, Newbury1 had less than 39% amino acid (47% nucleotide) identity in the complete 2C-helicase, 3C-protease, 3D-polymerase and capsid regions but had 89% to 98% amino acid (78% to 92% nucleotide) identity to the recently characterized NB virus in these regions. By phylogenetic analyses, Newbury1 and NB viruses formed a distinct clade independent of the 4 recognized genera. However, amino acid identities showed that Newbury1 and the NB virus were distinct polymerase types (90% amino acid identity), but their complete capsid proteins were almost identical (98% amino acid identity). Analyses of contemporary viruses showed that the two polymerase genotypes, Newbury1 and NB, were circulating in UK cattle and antibody to Newbury1-like viruses was common in cattle sera. The present study defined the existence of a new genus in the Caliciviridae that we propose be named Becovirus or Nabovirus to distinguish the new clade from bovine noroviruses. url: https://www.sciencedirect.com/science/article/pii/S0042682206001280 doi: 10.1016/j.virol.2006.02.027 id: cord-269094-6aka052v author: Ortego, Javier title: Absence of E protein arrests transmissible gastroenteritis coronavirus maturation in the secretory pathway date: 2007-11-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A recombinant transmissible gastroenteritis coronavirus (rTGEV) in which E gene was deleted (rTGEV-ΔE) has been engineered. This deletion mutant only grows in cells expressing E protein (E(+) cells) indicating that E was an essential gene for TGEV replication. Electron microscopy studies of rTGEV-ΔE infected BHK-pAPN-E(−) cells showed that only immature intracellular virions were assembled. These virions were non-infectious and not secreted to the extracellular medium in BHK-pAPN-E(−) cells. RNA and protein composition analysis by RNase-gold and immunoelectron microscopy showed that rTGEV-ΔE virions contained RNA and also all the structural TGEV proteins, except the deleted E protein. Nevertheless, full virion maturation was blocked. Studies of the rTGEV-ΔE subcellular localization by confocal and immunoelectron microscopy in infected E(−) cells showed that in the absence of E protein virus trafficking was arrested in the intermediate compartment. Therefore, the absence of E protein in TGEV resulted in two actions, a blockade of virus trafficking in the membranes of the secretory pathway, and prevention of full virus maturation. url: https://www.ncbi.nlm.nih.gov/pubmed/17692883/ doi: 10.1016/j.virol.2007.05.032 id: cord-290282-oxyzndsj author: Ortego, Javier title: Transmissible gastroenteritis coronavirus gene 7 is not essential but influences in vivo virus replication and virulence date: 2003-03-30 words: 4287.0 sentences: 215.0 pages: flesch: 53.0 cache: ./cache/cord-290282-oxyzndsj.txt txt: ./txt/cord-290282-oxyzndsj.txt summary: Transmissible gastroenteritis coronavirus (TGEV) contains eight overlapping genes that are expressed from a 3′-coterminal nested set of leader-containing mRNAs. To facilitate the genetic manipulation of the viral genome, genes were separated by duplication of transcription regulating sequences (TRSs) and introduction of unique restriction endonuclease sites at the 5′ end of each gene using an infectious cDNA clone. All the rTGEV viruses conserved the modifications engineered in the cDNAs (data not shown), indicating that the ORF separation and the insertion of unique endonuclease restriction sites between genes were stably maintained in the rTGEV genomes. Interestingly, analysis of viral growth in the gut of infected piglets showed a 100-to 5000-fold reduction of recombinant viruses containing one or more restriction sites in relation to the rTGEV-wt virus ( Fig. 5D and E) . abstract: Transmissible gastroenteritis coronavirus (TGEV) contains eight overlapping genes that are expressed from a 3′-coterminal nested set of leader-containing mRNAs. To facilitate the genetic manipulation of the viral genome, genes were separated by duplication of transcription regulating sequences (TRSs) and introduction of unique restriction endonuclease sites at the 5′ end of each gene using an infectious cDNA clone. The recombinant TGEV (rTGEV) replicated in cell culture with similar efficiency to the wild-type virus and stably maintained the modifications introduced into the genome. In contrast, the rTGEV replication level in the lungs and gut of infected piglets and virulence were significantly reduced. rTGEV in which gene 7 expression was abrogated (rTGEV-Δ7) were recovered from cDNA constructs, indicating that TGEV gene 7 was a nonessential gene for virus replication. Interestingly, in vivo infections with rTGEV-Δ7 showed an additional reduction in virus replication in the lung and gut, and in virulence, indicating that TGEV gene 7 influences virus pathogenesis. url: https://www.ncbi.nlm.nih.gov/pubmed/12706086/ doi: 10.1016/s0042-6822(02)00096-x id: cord-008426-ktn8c0zx author: Othman, Yasmin title: Nucleotide sequence of the bean strain of southern bean mosaic virus() date: 1995-01-10 words: 5393.0 sentences: 276.0 pages: flesch: 57.0 cache: ./cache/cord-008426-ktn8c0zx.txt txt: ./txt/cord-008426-ktn8c0zx.txt summary: From a comparison of the predicted sequences of the ORFs of these three sobemoviruses and of the noncoding regions, it is suggested that the two SBMV strains differ from one another as much as they do from RYMV and that they should be considered as different viruses. Southern bean mosaic virus (SBMV) is the type member of the sobemovirus group of small icosahedral positive-strand RNA viruses (for reviews see Sehgal, 1981 ; Tremaine and Hamilton, 1983; Hull, 1988) . The recently published nucleotide sequence (4450 nt) of rice yellow mottle virus (RYMV), another sobemovirus (Ngon A Yassi et aL, 1994) , shows that it has a similar genome organization to SBMV-C (Fig. 1) . Amino acid sequence of southern bean mosaic virus coat protein and its relation to the three dimensional structure of the virus abstract: The genome of the bean strain of southern bean mosaic virus (SBMV-B) comprises 4109 nucleotides and thus is slightlyshorter than those of the two other sequenced sobemoviruses (southern bean mosaic virus, cowpea strain (SBMV-C) and rice yellow mottle virus (RYMV)). SBMV-B has an overall sequence similarity with SBMV-C of 55% and with RYMV of 45%. Three potential open reading frames (ORFs) were recognized in SBMV-B which were in similar positions in the genomes of SBMV-C and RYMV. However, there was no analog of SBMV-C and RYMV ORF 3. From a comparison of the predicted sequences of the ORFs of these three sobemoviruses and of the noncoding regions, it is suggested that the two SBMV strains differ from one another as much as they do from RYMV and that they should be considered as different viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7130989/ doi: 10.1016/s0042-6822(95)80044-1 id: cord-299976-36r794ow author: O’Brien, Amornrat title: Characterizing replication kinetics and plaque production of type I feline infectious peritonitis virus in three feline cell lines date: 2018-12-01 words: 6070.0 sentences: 306.0 pages: flesch: 56.0 cache: ./cache/cord-299976-36r794ow.txt txt: ./txt/cord-299976-36r794ow.txt summary: FCoVs are typically grouped into two biotypes (or pathotypes), which have been classified as feline enteric coronavirus (FECV) and feline infectious peritonitis virus (FIPV), based on tissue tropism, disease progression, and genetic markers (reviewed in Kipar and Meli, 2014; Pedersen, 2014 Pedersen, , 2009 , although the range of disease signs and clinical outcomes are likely to extend beyond these two basic definitions. As part of this study, we characterized three feline cell lines-two from the American Type Culture Collection (ATCC) and one from Cornell University-and evaluated the replication kinetics, efficiency of plaque formation, and responsiveness of these cells to interferon (IFN) in order to identify the optimal cell culture conditions for type I FIPV Black. After observing the rapid and uniform development of CPE and release of virus into cell supernatants during infection of AK-D and Fcwf-4 CU cells, we reasoned that these cells would be employable in a standardized plaque assay to consistently determine FIPV Black titer. abstract: Investigating type I feline coronaviruses (FCoVs) in tissue culture is critical for understanding the basic virology, pathogenesis, and virus-host interactome of these important veterinary pathogens. This has been a perennial challenge as type I FCoV strains do not easily adapt to cell culture. Here we characterize replication kinetics and plaque formation of a model type I strain FIPV Black in Fcwf-4 cells established at Cornell University (Fcwf-4 CU). We determined that maximum virus titers (>10(7) pfu/mL) were recoverable from infected Fcwf-4 CU cell-free supernatant at 20 hours post-infection. Type I FIPV Black and both biotypes of type II FCoV formed uniform and enumerable plaques on Fcwf-4 CU cells. Therefore, these cells were employable in a standardized plaque assay. Finally, we determined that the Fcwf-4 CU cells were morphologically distinct from feline bone marrow-derived macrophages and were less sensitive to exogenous type I interferon than were Fcwf-4 cells purchased from ATCC. url: https://doi.org/10.1016/j.virol.2018.08.022 doi: 10.1016/j.virol.2018.08.022 id: cord-260108-osg8q89i author: Park, Yon Mi title: Full genome analysis of a novel adenovirus from the South Polar skua (Catharacta maccormicki) in Antarctica date: 2012-01-05 words: 3039.0 sentences: 174.0 pages: flesch: 48.0 cache: ./cache/cord-260108-osg8q89i.txt txt: ./txt/cord-260108-osg8q89i.txt summary: Here, we report the entire 26,340-bp genome of a novel adenovirus, detected by PCR, in tissues of six of nine South Polar skuas (Catharacta maccormicki), collected in Lake King Sejong, King George Island, Antarctica, from 2007 to 2009. The DNA polymerase, penton base, hexon and fiber genes of the South Polar skua adenovirus (SPSAdV) exhibited 68.3%, 75.4%, 74.9% and 48.0% nucleotide sequence similarity with their counterparts in turkey hemorrhagic enteritis virus. Phylogenetic analysis based on the entire genome revealed that SPSAdV belonged to the genus Siadenovirus, family Adenoviridae. Using newly designed primers based on the obtained sequence, the full genome of the novel adenovirus (SPSAdV) was extended from the left-end inverted terminal repeat (ITR) region to the right-end ITR region. At the nucleotide level, the SPSAdV pol, penton base and hexon genes exhibited somewhat higher sequence similarity of 73.8%, 79.2% and 77.5% with RAdV-1 than with THEV (68.3%, 75.4% and 74.9%) ( Table 4 ). abstract: Adenoviruses have been identified in humans and a wide range of vertebrate animals, but not previously from the polar region. Here, we report the entire 26,340-bp genome of a novel adenovirus, detected by PCR, in tissues of six of nine South Polar skuas (Catharacta maccormicki), collected in Lake King Sejong, King George Island, Antarctica, from 2007 to 2009. The DNA polymerase, penton base, hexon and fiber genes of the South Polar skua adenovirus (SPSAdV) exhibited 68.3%, 75.4%, 74.9% and 48.0% nucleotide sequence similarity with their counterparts in turkey hemorrhagic enteritis virus. Phylogenetic analysis based on the entire genome revealed that SPSAdV belonged to the genus Siadenovirus, family Adenoviridae. This is the first evidence of a novel adenovirus, SPSAdV, from a large polar seabird (family Stercorariidae) in Antarctica. url: https://www.sciencedirect.com/science/article/pii/S0042682211004776 doi: 10.1016/j.virol.2011.10.008 id: cord-268341-103xf3dw author: Parra, Beatriz title: Kinetics of Cytokine mRNA Expression in the Central Nervous System Following Lethal and Nonlethal Coronavirus-Induced Acute Encephalomyelitis date: 1997-07-07 words: 5778.0 sentences: 316.0 pages: flesch: 49.0 cache: ./cache/cord-268341-103xf3dw.txt txt: ./txt/cord-268341-103xf3dw.txt summary: the plaque size and pathogenesis similar to the parental During JHMV infection of the CNS there is an abrupt suckling mouse brain pool of JHMV originally described increase in mRNA encoding interleukin-1 (a and b), ILby Weiner (1973) and produces a lethal encephalomyeli-6, tumor necrosis factor (TNF)-a, and interferon (IFN)-g, tis with minimal demyelination apparent at the time of at the time of maximal decrease in virus replication and death. Similar of mice through Day 5 postinfection, consistent with the to the kinetics of IFN-g, TNF-a mRNA increased until rapid accumulation of both NK and T cells in the CNS of death of lethally infected mice. Similarly, the adoptive transfer at the time most lethally infected mice were about to succumb to infection (Day 7), there was no difference in the of virus-specific CD4 / T cells to JHMV-infected mice demonstrates that some clones protect via reducing viral peak levels of IL-10 mRNA between the two groups. abstract: Abstract The potential role(s) of cytokines in the reduction of infectious virus and persistent viral infection in the central nervous system was examined by determining the kinetics of cytokine mRNA expression following infection with the neurotropic JHM strain of mouse hepatitis virus. Mice were infected with an antibody escape variant which produces a nonlethal encephalomyelitis and compared to a clonal virus population which produces a fulminant fatal encephalomyelitis. Infection with both viruses induced the accumulation of mRNAs associated with Th1- and Th2-type cytokines, including IFN-γ, IL-4, and IL-10. Peak mRNA accumulations were coincident with the clearance of virus and there was no obvious differences between lethally and nonlethally infected mice. TNF-α mRNA was induced more rapidly in lethally infected mice compared to mice undergoing a nonfatal encephalomyelitis. Rapid transient increases in the mRNAs encoding IL-12, iNOS, IL-1α, IL-1β, and IL-6 occurred following infection. Nonlethal infections were associated with increased IL-12, IL-1β, and earlier expression of IL-6, while lethal infections were associated with increased iNOS and IL-1α mRNA. These data suggest a rapid but differential response within the central nervous system cells to infection by different JHMV variants. However, neither the accumulation nor kinetics of induction provide evidence to distinguish lethal infections from nonlethal infections leading to a persistent infection. Accumulation of both Th1 and Th2 cytokines in the central nervous system of JHMV-infected mice is consistent with the participation of both cytokines and cell immune effectors during resolution of acute viral-induced encephalomyelitis. url: https://api.elsevier.com/content/article/pii/S004268229798613X doi: 10.1006/viro.1997.8613 id: cord-266617-z8uecyl6 author: Pavesi, Angelo title: Asymmetric evolution in viral overlapping genes is a source of selective protein adaptation date: 2019-04-03 words: 6677.0 sentences: 326.0 pages: flesch: 52.0 cache: ./cache/cord-266617-z8uecyl6.txt txt: ./txt/cord-266617-z8uecyl6.txt summary: Analysis of nucleotide and amino acid sequences revealed that half of overlaps undergo asymmetric evolution, as the protein from one frame shows a number of substitutions significantly higher than that of the protein from the other frame. I classified a pair of homologous overlaps as a case of symmetric evolution, if the number of amino acid substitutions in the Up1-Up2 alignment did not significantly differ from that in the Down1-Down2 alignment (chi-square < 3.84). In alternative, I classified a pair of homologous overlaps as a case of asymmetric evolution, if the number of amino acid substitutions in the Up1-Up2 alignment was significantly different from that in the Down1-Down2 alignment (chi-square > 3.84). The analysis of the pattern of nucleotide substitutions in the 75 pairs of homologous overlaps revealed 39 and 36 cases of symmetric and asymmetric evolution, respectively (Supplementary Table S2 ). abstract: Overlapping genes represent an intriguing puzzle, as they encode two proteins whose ability to evolve is constrained by each other. Overlapping genes can undergo “symmetric evolution” (similar selection pressures on the two proteins) or “asymmetric evolution” (significantly different selection pressures on the two proteins). By sequence analysis of 75 pairs of homologous viral overlapping genes, I evaluated their accordance with one or the other model. Analysis of nucleotide and amino acid sequences revealed that half of overlaps undergo asymmetric evolution, as the protein from one frame shows a number of substitutions significantly higher than that of the protein from the other frame. Interestingly, the most variable protein (often known to interact with the host proteins) appeared to be encoded by the de novo frame in all cases examined. These findings suggest that overlapping genes, besides to increase the coding ability of viruses, are also a source of selective protein adaptation. url: https://www.sciencedirect.com/science/article/pii/S0042682219300881 doi: 10.1016/j.virol.2019.03.017 id: cord-304421-xpj6c0vx author: Piñón, Josefina D. title: Further Requirements for Cleavage by the Murine Coronavirus 3C-like Proteinase: Identification of a Cleavage Site within ORF1b date: 1999-10-25 words: 7343.0 sentences: 346.0 pages: flesch: 57.0 cache: ./cache/cord-304421-xpj6c0vx.txt txt: ./txt/cord-304421-xpj6c0vx.txt summary: The coronavirus 3C-like proteinase (3CLpro), flanked on either side by hydrophobic, possibly membrane-spanning regions (HD1 and HD2), is believed to be the prinicipal viral proteinase responsible for the processing events leading to the formation of the viral replicase complex, with as many as 11 potential cleavage sites identified throughout pp1ab (Gorbalenya et al., 1989; Lee et al., 1991 ) (see Fig. 1 ). We therefore created several substrates of various lengths, encoding different putative cleavage sites in ORF1b, in order to investigate processing by the recombinant MBP-3CLpro. The effect of these cleavage site mutations on the autocatalytic cis release of the 29-kDa 3CLpro was assayed by the expression of the Radiolabeled, in vitro transcribed, and translated substrate from pET21-NX.3C was incubated with MBP-3CLpro (lane 2) or an equal volume of column buffer/20% glycerol (lane 1) and the processed products were separated on a 15% SDS-PAGE gel. abstract: Abstract The coronavirus mouse hepatitis virus strain A59 (MHV-A59) encodes a 3C-like proteinase (3CLpro) that is proposed to be responsible for the majority of the processing events that take place within the replicase polyproteins pp1a and pp1ab. In this study we demonstrate that the Q939↓S940 peptide bond, located between the polymerase and Zn-finger regions of pp1ab (the POL↓Zn site), is processed by the 3CLpro, albeit inefficiently. Mutagenesis of the POL↓Zn site, as well as the previously identified HD1↓3C site in the 1a region of pp1a and pp1ab, demonstrated that the amino acid residues at the P2 and P1 positions of the cleavage site, occupied by L and Q, respectively, were important determinants of 3CLpro substrate specificity. Finally, a direct comparison of the 3CLpro-mediated cleavages at the HD1↓3C and POL↓Zn sites was made by determining the rate constants using synthetic peptides. The results show that while a larger polypeptide substrate carrying the HD1↓3C site was processed more efficiently than a polypeptide substrate carrying the POL↓Zn site, cleavage of the synthetic peptide substrates containing these two cleavage sites occurred at similar efficiencies. This indicates that the overall conformation of a large polyprotein substrate is important in the accessibility of the cleavage site to the proteinase. url: https://www.sciencedirect.com/science/article/pii/S0042682299999543 doi: 10.1006/viro.1999.9954 id: cord-279924-09uwhxs9 author: Plaisted, Warren C. title: T cell mediated suppression of neurotropic coronavirus replication in neural precursor cells date: 2014-01-01 words: 5580.0 sentences: 280.0 pages: flesch: 48.0 cache: ./cache/cord-279924-09uwhxs9.txt txt: ./txt/cord-279924-09uwhxs9.txt summary: In this study, we demonstrate that cultured murine NPCs are infected by the neurotropic JHM strain of mouse hepatitis virus (JHMV), which induces acute encephalomyelitis and chronic demyelination when injected intracranially into immunocompetent mice. We co-cultured virus-specific CTLs at diminishing effectorto-target (E:T) ratios with NPCs pulsed with the immunodominant CD8 peptide specific for JHMV spike (S) glycoprotein spanning amino acids 510-518 (S510-518), and treated with IFN-γ to induce MHC class I expression. To confirm the role of IFN-γ as the major cytokine contributing to suppression of JHMV replication in infected NPC cultures, monoclonal antibody blockade against the IFN-γ receptor was performed on NPCs before and during treatment with virusspecific CD4þ T cell enriched media. Impaired expression of MHC class II following IFN-γ-treatment of infected NPCs may be a mechanism employed to subvert detection by infiltrating virus-specific CD4þ T cells. abstract: Neural precursor cells (NPCs) are the subject of intense investigation for their potential to treat neurodegenerative disorders, yet the consequences of neuroinvasive virus infection of NPCs remain unclear. This study demonstrates that NPCs support replication following infection by the neurotropic JHM strain of mouse hepatitis virus (JHMV). JHMV infection leads to increased cell death and dampens IFN-γ-induced MHC class II expression. Importantly, cytokines secreted by CD4+ T cells inhibit JHMV replication in NPCs, and CD8+ T cells specifically target viral peptide-pulsed NPCs for lysis. Furthermore, treatment with IFN-γ inhibits JHMV replication in a dose-dependent manner. Together, these findings suggest that T cells play a critical role in controlling replication of a neurotropic virus in NPCs, a finding which has important implications when considering immune modulation for NPC-based therapies for treatment of human neurologic diseases. url: https://api.elsevier.com/content/article/pii/S0042682213006478 doi: 10.1016/j.virol.2013.11.025 id: cord-260695-qwepi0we author: Postler, Thomas S. title: Identification and characterization of a long non-coding RNA up-regulated during HIV-1 infection date: 2017-11-01 words: 6315.0 sentences: 377.0 pages: flesch: 55.0 cache: ./cache/cord-260695-qwepi0we.txt txt: ./txt/cord-260695-qwepi0we.txt summary: Of the host-encoded lncRNAs reported to be differentially expressed upon HIV-1 infection, only nuclear enriched abundant transcript 1 (NEAT1) and noncoding repressor of nuclear factor of activated T cells (NRON) have been functionally characterized (Lazar et al., 2016) . In this report, we describe a meta-analysis of two independent RNA-seq studies of HIV-1-infected cells and show that, unexpectedly, only three lncRNAs are differentially expressed in both of these datasets (Chang et al., 2011; Mohammadi et al., 2013) . To obtain an unbiased understanding of any changes in lncRNA expression during HIV-1 infection, we performed a meta-analysis of two independent RNA-seq studies conducted by two different groups using two different virus strains ( Supplementary Fig. S1 ) (Chang et al., 2011; Mohammadi et al., 2013) . To validate the results of the in silico analysis of lnc173 expression, we isolated RNA from 4 human cell lines and probed for the presence of both transcript variants by quantitative RT-PCR (qRT-PCR; Fig. 3A -D). abstract: Long non-coding RNAs (lncRNAs) are rapidly emerging as important regulators of a diverse array of cellular functions. Here, we describe a meta-analysis of two independent RNA-seq studies to identify lncRNAs that are differentially expressed upon HIV-1 infection. Only three lncRNA genes exhibited altered expression of ≥2-fold in HIV-1-infected cells. Of these, the uncharacterized lncRNA LINC00173 was chosen for further study. Both transcript variants of LINC00173 (lnc173 TSV1 and 2) could be detected by qPCR, localized predominantly to the nucleus and were reproducibly up-regulated during infection. Knock-out of the LINC00173 locus did not have detectable effects on HIV-1 replication. Interestingly, however, stimulation of Jurkat T cells with PMA/ionomycin resulted in a decrease of lnc173 expression, and Jurkat cells deficient for lnc173 on average expressed higher levels of specific cytokines than control cells. These data suggest that lnc173 may have a role in the regulation of cytokines in T cells. url: https://doi.org/10.1016/j.virol.2017.08.006 doi: 10.1016/j.virol.2017.08.006 id: cord-274424-juj71nc5 author: Pulford, David J. title: Intracellular processing of the porcine coronavirus transmissible gastroenteritis virus spike protein expressed by recombinant vaccinia virus date: 1991-06-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract The Spike (S) protein from a virulent British field isolate of porcine transmissible gastroenteritis virus (TGEV) FS772/70 was constructed from cDNA and inserted into the vaccinia virus (VV) thymidine kinase gene locus under the control of the VV early/late gene P7.5K promoter. Recombinant S protein was synthesized as an endo-β-N-acetylglucosamini-dase H (Endo H)-sensitive glycoprotein with high mannose simple oligosaccharides (gp190) that underwent post-translational modification to an Endo H-resistant glycoprotein with complex oligosaccharides (gp210). Immunofluorescence analysis demonstrated that the majority of recombinant S protein was retained at the Golgi but some S protein was expressed on the plasma membrane. Monoclonal antibodies (mAbs) raised against native S protein reacted with this recombinant S protein; also, mice infected with the recombinant vaccinia virus (rVV) expressing the S protein induced TGEV neutralizing antibodies. A truncated S protein (SΔ) was also expressed in rVV-infected cells by introducing a deletion into the S protein cDNA that removed 292 amino acids from the C-terminus. The SΔ protein (gpl70) was shown to be antigenically similar to TGEV S protein by immunofluorescence and immunoprecipitation tests but was retained in the endoplasmic reticulum and not expressed on the cell surface. url: https://api.elsevier.com/content/article/pii/004268229190617K doi: 10.1016/0042-6822(91)90617-k id: cord-270814-krw8zmr5 author: Rao, Pasupuleti V. title: Identification of a Contiguous 6-Residue Determinant in the MHV Receptor That Controls the Level of Virion Binding to Cells date: 1997-03-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Murine carcinoembryonic antigens serve as receptors for the binding and entry of the enveloped coronavirus mouse hepatitis virus (MHV) into cells. Numerous receptor isoforms are now known, and each has extensive differences in its amino terminal immunoglobulin-like domain (NTD) to which MHV binds via its protruding spike proteins. Some of these receptor alterations may affect the ability to bind viral spikes. To identify individual residues controlling virus binding differences, we have used plasmid and vaccinia virus vectors to express two forms of MHV receptor differing only in their NTD. The two receptors, designated biliary glycoproteins (Bgp) 1aand 1b NTD, varied by 29 residues in the 107 amino acid NTD. When expressed from cDNAs in receptor-negative HeLa cells, these two Bgp molecules were displayed on cell surfaces to equivalent levels, as both were equally modified by a membrane-impermeant biotinylation reagent. Infectious center assays revealed that the 1aisoform was 10 to 100 times more effective than 1b NTDin its ability to confer sensitivity to MHV (strain A59) infection. Bgp1awas also more effective than Bgp1b NTDin comparative virus adsorption assays, binding 6 times more MHV (strain A59) and 2.5 times more MHV (strain JHMX). Bgp1awas similarly more effective in promoting the capacity of viral spikes to mediate intercellular membrane fusion as judged by quantitation of syncytia following cocultivation of spike and receptor-bearing cells. To identify residues influencing these differences, we inserted varying numbers of 1bresidues into the Bgp1abackground via restriction fragment exchange and site-directed mutagenesis. Analysis of the resulting chimeric receptors showed that residues 38 to 43 of the NTD were key determinants of the binding and fusion differences between the two receptors. These residues map to an exposed loop (C-C′ loop) in a structural model of the closely related human carcinoembryonic antigen. url: https://api.elsevier.com/content/article/pii/S0042682297984464 doi: 10.1006/viro.1997.8446 id: cord-269986-jdcw59r2 author: Regan, Andrew D. title: Activation of p38 MAPK by feline infectious peritonitis virus regulates pro-inflammatory cytokine production in primary blood-derived feline mononuclear cells date: 2009-02-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Feline infectious peritonitis (FIP) is an invariably fatal disease of cats caused by systemic infection with a feline coronavirus (FCoV) termed feline infectious peritonitis virus (FIPV). The lethal pathology associated with FIP (granulomatous inflammation and T-cell lymphopenia) is thought to be mediated by aberrant modulation of the immune system due to infection of cells such as monocytes and macrophages. Overproduction of pro-inflammatory cytokines occurs in cats with FIP, and has been suggested to play a significant role in the disease process. However, the mechanism underlying this process remains unknown. Here we show that infection of primary blood-derived feline mononuclear cells by FIPV WSU 79-1146 and FIPV-DF2 leads to rapid activation of the p38 MAPK pathway and that this activation regulates production of the pro-inflammatory cytokine tumor necrosis factor alpha (TNF-alpha) and interleukin-1 beta (IL-1 beta). FIPV-induced p38 MAPK activation and pro-inflammatory cytokine production was inhibited by the pyridinyl imidazole inhibitors SB 203580 and SC 409 in a dose-dependent manner. FIPV-induced p38 MAPK activation was observed in primary feline blood-derived mononuclear cells individually purified from multiple SPF cats, as was the inhibition of TNF-alpha production by pyridinyl imidazole inhibitors. url: https://www.sciencedirect.com/science/article/pii/S0042682208007356 doi: 10.1016/j.virol.2008.11.006 id: cord-316460-ibprgdh4 author: Rodríguez-Grille, Javier title: Avian reovirus-triggered apoptosis enhances both virus spread and the processing of the viral nonstructural muNS protein date: 2014-06-17 words: 7493.0 sentences: 334.0 pages: flesch: 49.0 cache: ./cache/cord-316460-ibprgdh4.txt txt: ./txt/cord-316460-ibprgdh4.txt summary: To assess whether muNS cleavage is promoted by avian reovirus proteins and/or by changes induced in the host during infection, we compared muNS-to-muNSC conversion in ARV-infected cells with that in transfected cells and in insect cells infected with a muNSexpressing recombinant baculovirus (Fig. 1A ). To verify that this putative caspase recognition sequence is a bona fide cleavage site we first examined whether the electrophoretic mobility of muNS, muNSC and muNSN matched with that of transiently expressed polypeptides comprising muNS residues 1-635, The resulting extracts were immunoprecipitated with polyclonal anti-muNS serum and the imunoprecipitated proteins were resolved on an electrophoresis gel system (8% tricine-SDS-PAGE gel) specifically designed to resolve small peptides (Schägger, 2006) . In the absence of an established reverse genetics system for ARV that would allow us to generate a recombinant virus that expresses an uncleavable muNS protein, like D154A, we examined the effect of Q-VD-OPh on ARV replication in CEF cells, since this compound had been shown to block both apoptosis and muNS processing. abstract: Avian reovirus non-structural protein muNS is partially cleaved in infected chicken embryo fibroblast cells to produce a 55-kDa carboxyterminal protein, termed muNSC, and a 17-kDa aminoterminal polypeptide, designated muNSN. In this study we demonstrate that muNS processing is catalyzed by a caspase 3-like protease activated during the course of avian reovirus infection. The cleavage site was mapped by site directed mutagenesis between residues Asp-154 and Ala-155 of the muNS sequence. Although muNS and muNSC, but not muNSN, are able to form inclusions when expressed individually in transfected cells, only muNS is able to recruit specific ARV proteins to these structures. Furthermore, muNSC associates with ARV factories more weakly than muNS, sigmaNS and lambdaA. Finally, the inhibition of caspase activity in ARV-infected cells does not diminish ARV gene expression and replication, but drastically reduces muNS processing and the release and dissemination of progeny viral particles. url: https://doi.org/10.1016/j.virol.2014.04.039 doi: 10.1016/j.virol.2014.04.039 id: cord-266230-ia04jc9j author: Rott, M. E. title: Comparison of the 5′ and 3′ termini of tomato ringspot virus RNA1 and RNA2: Evidence for RNA recombination date: 1991-11-30 words: 2003.0 sentences: 119.0 pages: flesch: 56.0 cache: ./cache/cord-266230-ia04jc9j.txt txt: ./txt/cord-266230-ia04jc9j.txt summary: It is possible that the similar sequences at both ends of TomRSV RNA1 and RNA2 are a result of recombination between these two genomic RNA components. Beginning from the first potential in-frame initiation site at AUG,B, the N-terminal regions of the TomRSV RNA1 and RNA2 polyproteins are identical for the first 132 amino acids, and of the next 145 amino acid residues 75.3% of the positions are identical (Fig. 3A ). The fact that these regions of similarity are present only at the N-termini of the TBRV and GCMV RNAl-encoded polyproteins but are present at the N-termini of both TomRSV RNA1 -and RNA2encoded pofyproteins suggests that a large portion of coding and noncoding sequences at the 5'' terminus of TomRSV RNA1 have been duplicated and are now present at the 5'' terrnini of both RNA1 and RNA2. abstract: Abstract The sequences of the 5′ terminal 1140 and 3′ terminal 1546 nt of tomato ringspot virus (TomRSV) RNA1 have been determined. These sequences share a high degree of nucleotide sequence similarity with the previously determined TomRSV RNA2 sequence. Eighty-eight percent of the 5' terminal 907 nt of TomRSV RNA1 and RNA2 contain identical nucleotide residues; the first 459 nt are identical at all positions, whereas the next 447 nt are identical at only 75.8% of the nucleotide positions. The region of similarity includes not only the 5' nontranslated leader but also sequence probably encoding polyproteins. The 3′ terminal 1533 nt of TomRSV RNA1 and RNA2 are identical and are noncoding. The sequences common to RNA1 and RNA2 account for almost 35% of the total genomic sequence. It is possible that the similar sequences at both ends of TomRSV RNA1 and RNA2 are a result of recombination between these two genomic RNA components. url: https://www.sciencedirect.com/science/article/pii/004268229190801H doi: 10.1016/0042-6822(91)90801-h id: cord-262441-slh52nxm author: Sakai, Yusuke title: Two-amino acids change in the nsp4 of SARS coronavirus abolishes viral replication date: 2017-07-21 words: 6120.0 sentences: 261.0 pages: flesch: 52.0 cache: ./cache/cord-262441-slh52nxm.txt txt: ./txt/cord-262441-slh52nxm.txt summary: To determine the crucial amino acid residue(s) in SARS-CoV nsp4 required to induce membrane rearrangements through the interaction with nsp3C, we constructed additional expression plasmids encoding deletion mutants of SARS-CoV nsp4, pCAG nsp4 Δ112-126-HA and pCAG nsp4 Δ126-164-HA, as shown in Fig. 1B . To determine the effect of the two amino acid residues, H120 and F121, in SARS-CoV nsp4 on the membrane rearrangements thorough interaction with nsp3C, 293T cells transfected with pCAG nsp4-HA or pCAG nsp4 H120N/F121L-HA together with pCAG nsp3C-3xFLAG at 30 h posttransfection were subjected to transmission electron microscopy (TEM) analysis. As we expected, expression of renilla luciferase was detected in cells transfected with pBAC-SARS-Rep-wt, but not in those with pBAC-SARS-Rep-H120N/F121L or pBAC-SARSRep-SAD (Fig. 7C) , suggesting that both H120 and F121 in SARS-CoV nsp4 play critical roles in the viral replication by remodeling the membrane through binding with nsp3. abstract: Infection with coronavirus rearranges the host cell membrane to assemble a replication/transcription complex in which replication of the viral genome and transcription of viral mRNA occur. Although coexistence of nsp3 and nsp4 is known to cause membrane rearrangement, the mechanisms underlying the interaction of these two proteins remain unclear. We demonstrated that binding of nsp4 with nsp3 is essential for membrane rearrangement and identified amino acid residues in nsp4 responsible for the interaction with nsp3. In addition, we revealed that the nsp3-nsp4 interaction is not sufficient to induce membrane rearrangement, suggesting the participation of other factors such as host proteins. Finally, we showed that loss of the nsp3-nsp4 interaction eliminated viral replication by using an infectious cDNA clone and replicon system of SARS-CoV. These findings provide clues to the mechanism of the replication/transcription complex assembly of SARS-CoV and could reveal an antiviral target for the treatment of betacoronavirus infection. url: https://www.ncbi.nlm.nih.gov/pubmed/28738245/ doi: 10.1016/j.virol.2017.07.019 id: cord-256036-gd53s4dv author: Sandmann, Lisa title: Barriers of hepatitis C virus interspecies transmission date: 2013-01-01 words: 7894.0 sentences: 373.0 pages: flesch: 40.0 cache: ./cache/cord-256036-gd53s4dv.txt txt: ./txt/cord-256036-gd53s4dv.txt summary: In contrast to human hepatocytes, murine cells do not support HCV entry thereby creating a first and important barrier for a broader host tropism of the virus. Utilizing blocking antibodies specific to CD81 or the viral envelope protein E2, expression of entry factor mutants and mice with a targeted disruption of the SCARB1 gene validated uptake of HCV into murine hepatocytes in an HCV glycoprotein-mediated fashion. Taking advantage of the high mutational plasticity of HCV, three adaptive mutations in the viral glycoproteins E1 and E2 were identified that allowed the virus to enter cells expressing human SCARB1, CLDN1, OCLN and mouse CD81. Recently, a genetically humanized mouse model was constructed utilizing cell culture produced recombinant hepatitis C virus to activate a cellular encoded reporter (Dorner et al., 2011, in press ). Human occludin is a hepatitis C virus entry factor required for infection of mouse cells A humanized mouse model to study Hepatitis C virus infection, immune response, and liver disease abstract: Hepatitis C virus (HCV) is a major causative agent of severe liver disease including fibrosis, cirrhosis and liver cancer. Therapy has improved over the years, but continues to be associated with adverse side effects and variable success rates. Furthermore, a vaccine protecting against HCV infection remains elusive. Development of more effective intervention measures has been delayed by the lack of a suitable animal model. Naturally, HCV infects only humans and chimpanzees. The determinants of this limited host range are poorly understood in part due to difficulties of studying HCV in cell culture. Some progress has been made elucidating the barriers for the HCV lifecycle in non-permissive species which will help in the future to construct animal models for HCV infection, immunity and pathogenesis. url: https://doi.org/10.1016/j.virol.2012.09.044 doi: 10.1016/j.virol.2012.09.044 id: cord-271359-dpa8zzc3 author: Sapats, S. I. title: Novel Variation in the N Protein of Avian Infectious Bronchitis Virus date: 1996-12-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract The nucleocapsid protein of coronaviruses has been considered highly conserved, showing greater than 94% conservation within strains of a given species. We determined the nucleotide sequence of the N gene and the 3′ untranslated region (UTR) of eight naturally occurring strains of IBV which differed in pathogenicity and tissue tropism. In pairwise comparisons, the deduced amino acid sequences of N of five strains Vic S, N1/62, N9/74, N2/75, and V5/90 (group I) shared 92.3–98.8% identity. The three strains N1/88, Q3/88, and V18/91 (group II) shared 85.8–89.2% identity with each other, but only 60.0–63.3% identity with viruses of group I. Amino acid substitutions, deletions, and insertions occurred throughout the N protein and involved regions previously identified as being conserved. Despite the considerable variation observed between the two virus groups, all N proteins contained a high proportion of basic residues, 80% of which were conserved in position. In addition, all strains contained approximately 30 serine residues of which 10 were conserved, the majority occurring between positions 168 and 194. As for all other coronaviruses, the region between positions 92 and 103 was highly conserved. Hence, a large number of amino acid changes can be tolerated within the N protein without affecting its integrity or functioning. The 3′ UTR immediately downstream from the N gene was highly heterogeneous with extensive deletions occurring in the group II strains. url: https://www.sciencedirect.com/science/article/pii/S0042682296906704 doi: 10.1006/viro.1996.0670 id: cord-259500-ndjbrtrv author: Satyanarayana, Tatineni title: Frameshift mutations in infectious cDNA clones of Citrus tristeza virus: a strategy to minimize the toxicity of viral sequences to Escherichia coli date: 2003-09-01 words: 6465.0 sentences: 322.0 pages: flesch: 60.0 cache: ./cache/cord-259500-ndjbrtrv.txt txt: ./txt/cord-259500-ndjbrtrv.txt summary: title: Frameshift mutations in infectious cDNA clones of Citrus tristeza virus: a strategy to minimize the toxicity of viral sequences to Escherichia coli These data demonstrate that, when hosts are sufficiently susceptible for infection by transcripts of reduced specific infectivity, introduction of frameshift mutations at "slippery sequences" near toxic regions of viral cDNAs can be used as an additional strategy to clone recalcitrant viral sequences in high-copy-number plasmids for reverse genetics. A similar frameshift mutation was also found in the derivative replicon pCTV-⌬Cla. However, the sequence of the progeny virion RNA of CTV9 from infected protoplasts or citrus plants did not contain the additional nt at position 3732 that occurred in the cDNA clones, suggesting that the frameshift mutation present in the original cDNA clone was repaired either during the in vitro transcription or during replication in the protoplasts. abstract: The advent of reverse genetics revolutionized the study of positive-stranded RNA viruses that were amenable for cloning as cDNAs into high-copy-number plasmids of Escherichia coli. However, some viruses are inherently refractory to cloning in high-copy-number plasmids due to toxicity of viral sequences to E. coli. We report a strategy that is a compromise between infectivity of the RNA transcripts and toxicity to E. coli effected by introducing frameshift mutations into “slippery sequences” near the viral “toxicity sequences” in the viral cDNA. Citrus tristeza virus (CTV) has cDNA sequences that are toxic to E. coli. The original full-length infectious cDNA of CTV and a derivative replicon, CTV-ΔCla, cloned into pUC119, resulted in unusually limited E. coli growth. However, upon sequencing of these cDNAs, an additional uridinylate (U) was found in a stretch of U’s between nts 3726 and 3731 that resulted in a change to a reading frame with a stop codon at nt 3734. Yet, in vitro produced RNA transcripts from these clones infected protoplasts, and the resulting progeny virus was repaired. Correction of the frameshift mutation in the CTV cDNA constructs resulted in increased infectivity of in vitro produced RNA transcripts, but also caused a substantial increase of toxicity to E. coli, now requiring 3 days to develop visible colonies. Frameshift mutations created in sequences not suspected to facilitate reading frame shifting and silent mutations introduced into oligo(U) regions resulted in complete loss of infectivity, suggesting that the oligo(U) region facilitated the repair of the frameshift mutation. Additional frameshift mutations introduced into other oligo(U) regions also resulted in transcripts with reduced infectivity similarly to the original clones with the +1 insertion. However, only the frameshift mutations introduced into oligo(U) regions that were near and before the toxicity region improved growth and stability in E. coli. These data demonstrate that, when hosts are sufficiently susceptible for infection by transcripts of reduced specific infectivity, introduction of frameshift mutations at “slippery sequences” near toxic regions of viral cDNAs can be used as an additional strategy to clone recalcitrant viral sequences in high-copy-number plasmids for reverse genetics. url: https://www.sciencedirect.com/science/article/pii/S0042682203003878 doi: 10.1016/s0042-6822(03)00387-8 id: cord-268467-btfz6ye8 author: Schreiber, Steven S. title: Sequence analysis of the nucleocapsid protein gene of human coronavirus 229E date: 1989-03-31 words: 5035.0 sentences: 343.0 pages: flesch: 59.0 cache: ./cache/cord-268467-btfz6ye8.txt txt: ./txt/cord-268467-btfz6ye8.txt summary: The 3′-noncoding region of the genome contains an 11-nucleotide sequence, which is relatively conserved throughout the Coronavirus family and lends support to the theory that this region is important for the replication of negative-strand RNA. This result suggested that the HCV229E subgenomic mRNAs possess a nested-set structure similar to other coronaviruses and that A34 represented a cDNA clone of either the 3''-end of the genomic RNA or the leader sequence. The 3''-noncoding region contains the sequence TGGAAGAGCCA, 75 nucleotides from the 3''-end (Fig. 4) which is relatively conserved among coronaviruses and is found at approximately the same location in all of these viral genomes (Kapke and Brian, 1986; Skinner and Siddell, 1984; Armstrong et a/., 1983; Lapps et al., 1987; Kamahora et a/., 1988; Boursnell et al., 1985) ( Table 1) . Three intergenic regions of coronavirus mouse hepatitis virus strain A59 genome RNA contain a common nucleotide sequence that is homologous to the 3''end of the viral mRNA leader sequence abstract: Abstract Human coronaviruses are important human pathogens and have also been implicated in multiple sclerosis. To further understand the molecular biology of human coronavirus 229E (HCV-229E), molecular cloning and sequence analysis of the viral RNA have been initiated. Following established protocols, the 3′-terminal 1732 nucleotides of the genome were sequenced. A large open reading frame encodes a 389 amino acid protein of 43,366 Da, which is presumably the nucleocapsid protein. The predicted protein is similar in size, chemical properties, and amino acid sequence to the nucleocapsid proteins of other coronaviruses. This is especially evident when the sequence is compared with that of the antigenically related porcine transmissible gastroenteritis virus (TGEV), with which a region of 46% amino acid sequence homology was found. Hydropathy profiles revealed the existence of several conserved domains which could have functional significance. An intergenic consensus sequence precedes the 5′-end of the proposed nucleocapsid protein gene. The consensus sequence is present in other coronaviruses and has been proposed as the site of binding of the leader sequence for mRNA transcriptional start. This region was also examined by primer extension analysis of mRNAs, which identified a 60-nucleotide leader sequence. The 3′-noncoding region of the genome contains an 11-nucleotide sequence, which is relatively conserved throughout the Coronavirus family and lends support to the theory that this region is important for the replication of negative-strand RNA. url: https://api.elsevier.com/content/article/pii/0042682289900500 doi: 10.1016/0042-6822(89)90050-0 id: cord-258327-03vk6enj author: Schultze, Beate title: Isolated HE-protein from hemagglutinating encephalomyelitis virus and bovine coronavirus has receptor-destroying and receptor-binding activity date: 1991-01-31 words: 4604.0 sentences: 267.0 pages: flesch: 52.0 cache: ./cache/cord-258327-03vk6enj.txt txt: ./txt/cord-258327-03vk6enj.txt summary: The purified HE protein retained acetylesterase activity and was able to function as a receptor-destroying enzyme rendering red blood cells resistant against agglutination by both coronaviruses. However, it was found to recognize glycoconjugates containing N-acetyl-9-O-acetylneuraminic acid as indicated by a binding assay with rat serum proteins blotted to nitrocellulose and by its ability to inhibit the hemagglutinating activity of BCV, HEV, and influenza C virus. The virus pellet was resuspended in PBS and used for (i) analysis by polyacrylamide gel electrophoresis ; (ii) determination of the esterase activity ; (iii) hemagglutination and hemagglutination-inhibition assays ; and (iv) purification of the viral glycoproteins . These erythrocytes and control cells, which had been incubated with PBS, were used to determine the HA titer of BCV, HEV, and influenza C virus . As shown in Table 1 , incubation of erythrocytes with purified acetylesterase from either BCV or HEV rendered the cells resistant to agglutination by both coronaviruses as well as by influenza C virus . abstract: Abstract Bovine coronavirus (BCV) and hemagglutinating encephalomyelitis virus (HEV) from swine were found to grow to high titers in MDCK I cells, a subline of Madin Darby canine kidney cells. Virus grown in these cells was used to isolate and purify the HE-protein. This protein has been shown recently to have acetylesterase activity and to function as the receptor-destroying enzyme of BCV. Here we show that HEV contains this enzyme, too. The glycoproteins were solubilized by treatment of virions with octylglucoside. Following centrifugation through a sucrose gradient the surface proteins S and HE (hemagglutinin-esterase) were obtained in purified form. After removal of the detergent by dialysis, HE formed rosettes as shown by electron microscopy. The purified HE protein retained acetylesterase activity and was able to function as a receptor-destroying enzyme rendering red blood cells resistant against agglutination by both coronaviruses. HE protein released from the viral membrane failed to agglutinate red blood cells. However, it was found to recognize glycoconjugates containing N-acetyl-9-O-acetylneuraminic acid as indicated by a binding assay with rat serum proteins blotted to nitrocellulose and by its ability to inhibit the hemagglutinating activity of BCV, HEV, and influenza C virus. The purified enzyme provides a useful tool for analyzing the cellular receptors for coronaviruses. url: https://api.elsevier.com/content/article/pii/0042682291900268 doi: 10.1016/0042-6822(91)90026-8 id: cord-253894-4u5yt7b7 author: Senkevich, Tatiana G. title: Vaccinia virus F16 protein, a predicted catalytically inactive member of the prokaryotic serine recombinase superfamily, is targeted to nucleoli date: 2011-09-01 words: 6253.0 sentences: 286.0 pages: flesch: 44.0 cache: ./cache/cord-253894-4u5yt7b7.txt txt: ./txt/cord-253894-4u5yt7b7.txt summary: VACV, by far the most intensively studied poxvirus, replicates entirely in the cytoplasm of infected cells and encodes many of the proteins required for its growth as well as numerous proteins modulating virus-host interactions. Here we provide a detailed computational analysis of the F16 protein indicating that it is unlikely to have serine recombinase activity, and experimental data showing that the F16L gene is not required for virus growth in cell culture. F16-3xflag was detected by Western blotting at 2 h after infection, only slightly increased in amount between 4 and 24 h, and accumulated in the presence of cytosine arabinoside (araC), an inhibitor of DNA synthesis that prevents VACV intermediate and late gene expression. Two other VAC proteins, I3 and B1, containing a C-terminal 3xflag tag and expressed from a transfected plasmid under the control of the CMV promoter were analyzed in parallel with F16-3xflag, and no nucleolar or nuclear membrane staining was detected (not shown). abstract: The F16L gene of vaccinia virus (VACV) is conserved in all chordopoxviruses except avipoxviruses. The crocodile poxvirus F16 protein ortholog has highly significant similarity to prokaryotic serine recombinases and contains all amino acids that comprise the catalytic site. In contrast, F16 orthologs encoded by other poxviruses show only marginally significant similarity to serine recombinases, lack essential amino acids of the active site and are most likely inactive derivatives of serine recombinases. Nevertheless, the conservation of F16L in non-avian poxviruses suggested an important function. However, a VACV mutant with the F16L gene knocked out replicated normally in dividing and quiescent cells. The F16 protein was synthesized early after infection and detected in virus cores. When expressed in infected or uninfected cells, F16 accumulated in nucleoli depending on the level of expression and confluency of cells. Evidence was obtained that F16 forms multimers, which might regulate concentration-dependent intracellular localization. url: https://www.ncbi.nlm.nih.gov/pubmed/21752417/ doi: 10.1016/j.virol.2011.06.017 id: cord-345088-krb1eidw author: Shen, S title: A single amino acid mutation in the spike protein of coronavirus infectious bronchitis virus hampers its maturation and incorporation into virions at the nonpermissive temperature date: 2004-09-01 words: 6949.0 sentences: 316.0 pages: flesch: 56.0 cache: ./cache/cord-345088-krb1eidw.txt txt: ./txt/cord-345088-krb1eidw.txt summary: title: A single amino acid mutation in the spike protein of coronavirus infectious bronchitis virus hampers its maturation and incorporation into virions at the nonpermissive temperature Here, we report the emergence and isolation of two temperature sensitive (ts) mutants and a revertant in the process of cold-adaptation of coronavirus infectious bronchitis virus (IBV) to a monkey kidney cell line. Evidence presented demonstrated that the Q(294)-to-L(294) mutation, located at a highly conserved domain of the S1 subunit, might hamper processing of the S protein to a matured 180-kDa, endo-glycosidase H-resistant glycoprotein and the translocation of the protein to the cell surface. In virus-infected cells, the Endo-H sensitive, 155-kDa form of ts291602 was abundant at the nonpermissive temperature, clearly indicating that the mutant S protein was trimmed in the ER and cis-Golgi but was not transported to the trans-Golgi. abstract: The spike (S) glycoprotein of coronavirus is responsible for receptor binding and membrane fusion. A number of variants with deletions and mutations in the S protein have been isolated from naturally and persistently infected animals and tissue cultures. Here, we report the emergence and isolation of two temperature sensitive (ts) mutants and a revertant in the process of cold-adaptation of coronavirus infectious bronchitis virus (IBV) to a monkey kidney cell line. The complete sequences of wild type (wt) virus, two ts mutants, and the revertant were compared and variations linked to phenotypes were mapped. A single amino acid reversion (L(294)-to-Q) in the S protein is sufficient to abrogate the ts phenotype. Interestingly, unlike wt virus, the revertant grows well at and below 32 °C, the permissive temperature, as it carries other mutations in multiple genes that might be associated with the cold-adaptation phenotype. If the two ts mutants were allowed to enter cells at 32 °C, the S protein was synthesized, core-glycosylated and at least partially modified at 40 °C. However, compared with wt virus and the revertant, no infectious particles of these ts mutants were assembled and released from the ts mutant-infected cells at 40 °C. Evidence presented demonstrated that the Q(294)-to-L(294) mutation, located at a highly conserved domain of the S1 subunit, might hamper processing of the S protein to a matured 180-kDa, endo-glycosidase H-resistant glycoprotein and the translocation of the protein to the cell surface. Consequently, some essential functions of the S protein, including mediation of cell-to-cell fusion and its incorporation into virions, were completely abolished. url: https://api.elsevier.com/content/article/pii/S0042682204003988 doi: 10.1016/j.virol.2004.06.016 id: cord-313091-ksrxsdpp author: Shirato, Kazuya title: Wild-type human coronaviruses prefer cell-surface TMPRSS2 to endosomal cathepsins for cell entry date: 2017-12-06 words: 4021.0 sentences: 217.0 pages: flesch: 58.0 cache: ./cache/cord-313091-ksrxsdpp.txt txt: ./txt/cord-313091-ksrxsdpp.txt summary: Studies using the ATCC isolate suggest that HCoV-229E enters cells via the late endosome using cathepsin L to cleave S protein, although it can enter cells via the cell surface or early endosome in the presence of transmembrane protease serine 2 (TMPRSS2) or trypsin (Bertram et al., 2013; Kawase et al., 2009) . In the present study, we found that field isolates of HCoV-OC43 and HCoV-HKU1 could be isolated using HBTE-ALI cell culture, and we then used these clinical isolates to assess whether the mode of virus entry found in HCoV-229E was also in play in other HCoVs. For isolation of HCoVs, nasal swabs were collected from outpatients who showed respiratory infection as a cardinal symptom when assessed at a hospital in Tokyo, Japan. To evaluate the entry routes of clinical isolates of HCoVs, viruses were inoculated onto HBTE-ALI in the presence of EST or camostat (10 μM) and the amounts virus that entered were estimated by detecting subgenomic mRNAs using real-time RT-PCR (Fig. 2) . abstract: Human coronaviruses (HCoVs) enter cells via two distinct pathways: the endosomal pathway using cathepsins to activate spike protein and the cell-surface or early endosome pathway using extracellular proteases such as transmembrane protease serine 2 (TMPRSS2). We previously reported that clinical isolates of HCoV-229E preferred cell-surface TMPRSS2 to endosomal cathepsin for cell entry, and that they acquired the ability to use cathepsin L by repeated passage in cultured cells and were then able to enter cells via the endosomal pathway. Here, we show that clinical isolates of HCoV-OC43 and -HKU1 preferred the cell-surface TMRRSS2 to endosomal cathepsins for cell entry, similar to HCoV-229E. In addition, the cell-culture-adapted HCoV-OC43 lost the ability to infect and replicate in air-liquid interface cultures of human bronchial tracheal epithelial cells. These results suggest that circulating HCoVs in the field generally use cell-surface TMPRSS2 for cell entry, not endosomal cathepsins, in human airway epithelial cells. url: https://doi.org/10.1016/j.virol.2017.11.012 doi: 10.1016/j.virol.2017.11.012 id: cord-325481-uzch2hwd author: Simmons, Graham title: Different host cell proteases activate the SARS-coronavirus spike-protein for cell-cell and virus-cell fusion date: 2011-05-01 words: 7139.0 sentences: 315.0 pages: flesch: 49.0 cache: ./cache/cord-325481-uzch2hwd.txt txt: ./txt/cord-325481-uzch2hwd.txt summary: For instance, the majority of strains of the murine coronavirus mouse hepatitis virus (MHV) contain Sproteins that are cleaved by furin in infected cells, and these viruses are believed to enter target cells by receptor-dependent, pH-independent fusion with the plasma membrane (de Haan et al., 2004; Nash and Buchmeier, 1997; Qiu et al., 2006) , although some of these findings are controversial (Eifart et al., 2007) . Treatment of cell-bound virus with trypsin was shown to allow infectious SARS-S-driven entry into ammonium chloride-treated cells (Simmons et al., 2005) , indicating that trypsin can functionally replace cathepsin L as a SARS-S-activating protease under these conditions ("trypsin bypass"). The fusion efficiency is then quantified by the addition of virions to leupeptin-treated (to exclude an impact of host cell proteases on SARS-S activation) HeLa cells, which express the EnvA receptor TvA, and which are not susceptible to SARS-S-driven infection (Simmons et al., 2005) . abstract: Severe acute respiratory syndrome coronavirus (SARS-CoV) poses a considerable threat to human health. Activation of the viral spike (S)-protein by host cell proteases is essential for viral infectivity. However, the cleavage sites in SARS-S and the protease(s) activating SARS-S are incompletely defined. We found that R667 was dispensable for SARS-S-driven virus-cell fusion and for SARS-S-activation by trypsin and cathepsin L in a virus-virus fusion assay. Mutation T760R, which optimizes the minimal furin consensus motif 758-RXXR-762, and furin overexpression augmented SARS-S-activity, but did not result in detectable SARS-S cleavage. Finally, SARS-S-driven cell-cell fusion was independent of cathepsin L, a protease essential for virus-cell fusion. Instead, a so far unknown leupeptin-sensitive host cell protease activated cellular SARS-S for fusion with target cells expressing high levels of ACE2. Thus, different host cell proteases activate SARS-S for virus-cell and cell-cell fusion and SARS-S cleavage at R667 and 758-RXXR-762 can be dispensable for SARS-S activation. url: https://www.sciencedirect.com/science/article/pii/S0042682211000924 doi: 10.1016/j.virol.2011.02.020 id: cord-264331-uvi8ucz4 author: Singh, Shailbala title: Avian influenza viral nucleocapsid and hemagglutinin proteins induce chicken CD8(+) memory T lymphocytes date: 2010-04-10 words: 5972.0 sentences: 295.0 pages: flesch: 51.0 cache: ./cache/cord-264331-uvi8ucz4.txt txt: ./txt/cord-264331-uvi8ucz4.txt summary: Following ex vivo co-culture with MHC matched B19/B19 APCs infected with H5N9 virus, memory responses were detected in T cell preparations obtained from all chickens receiving plasmids expressing either AIV protein by 3 weeks p.i. Since neither supernatants from the T cells cultured with uninfected APCs nor T cells from PBS inoculated birds cultured with infected MHC matched B19/B19 birds produced IFNγ (data not shown), the memory T lymphocyte activity was considered AIV specific. In order to evaluate the memory T lymphocyte responses of chickens inoculated with infectious AIV, chicks with the B19/B19 haplotype were inoculated with the low pathogenic H5N9/Turkey/Wis/68 strain and blood was collected at 5 weeks p.i. The ex vivo activation of T lymphocytes by AIV infected APCs was determined by the indirect IFNγ assay (Fig. 5) . abstract: The avian influenza viruses (AIVs) can be highly contagious to poultry and a zoonotic threat to humans. Since the memory CD8(+) T lymphocyte responses in chickens to AIV proteins have not been defined, these responses to H5N9 AIV hemagglutinin (HA) and nucleocapsid (NP) proteins were evaluated by ex vivo stimulation with virus infected non-professional antigen presenting cells. Secretion of IFNγ by activated T lymphocytes was evaluated through macrophage induction of nitric oxide. AIV specific, MHC-I restricted memory CD8(+) T lymphocyte responses to NP and HA were observed 3 to 9 weeks post-inoculation (p.i.). The responses specific to NP were greater than those to HA with maximum responses being observed at 5 weeks p.i. followed by a decline to weakly detectable levels by 9 weeks p.i. The cross-reaction of T lymphocytes to a heterologous H7N2 AIV strain demonstrated their ability to respond to a broader range of AIV. url: https://doi.org/10.1016/j.virol.2009.12.029 doi: 10.1016/j.virol.2009.12.029 id: cord-262574-gu0930s3 author: Slagle, Betty L. title: Identification and characterization of a mouse mammary tumor virus protein uniquely expressed on the surface of BALB/cV mammary tumor cells date: 1985-05-31 words: 7912.0 sentences: 407.0 pages: flesch: 53.0 cache: ./cache/cord-262574-gu0930s3.txt txt: ./txt/cord-262574-gu0930s3.txt summary: The BALB/cV subline was used to study the molecular basis of potential virus-host interactions involving cell surface-expressed MMTV proteins. Cell surface iodination identified virus-specific proteins expressed on BALB/cv primary mammary tumor cells grown in culture. Adsorption experiments have demonstrated that the anti-gp52/gp36 serum reacts specifically with MMTV glycoproteins and envelope-related precursors and does not react with normal cell proteins of BALB/c mammary tissue (Slagle et aQ, 1985) . Primary cultures of a BALB/cV tumor were analyzed for cell surface expression of viral proteins using the same iodination procedure. Primary cultures of BALB/cV tumor cells were starved for 2 hr in methionine-free media and were then metabolically labeled for 1 hr with r5S]Met. Intact cell monolayers were rinsed with cold TBS, placed on ice, and reacted with specific antisera to detect 35S-labeled MMTV proteins expressed on the cell surface. DISCUSSION This report describes a thorough analysis of the expression of MMTV-specific proteins on the surface of BALB/cV mammary tumor cells. abstract: Abstract A unique subline of BALB/c mice, designated BALB/cV, exhibits an intermediate mammary tumor incidence (47%) and harbors a distinct milk-transmitted mouse mammary tumor virus (MMTV). The BALB/cV subline was used to study the molecular basis of potential virus-host interactions involving cell surface-expressed MMTV proteins. Cell surface iodination identified virus-specific proteins expressed on BALB/cv primary mammary tumor cells grown in culture. In contrast to (C3H)MMTV-producing cell lines which expressed MMTV gp52, BALB/cV tumor cells lacked gp52 and expressed instead a 68K, env-related protein. The 68K env protein was also detected on the surface of metabolically labeled BALB/cV tumor cells by an external immunoprecipitation technique. The expression of 68K env was restricted to mammary tissues of BALB/cV mice that also expressed other MMTV proteins. Biochemical analysis established that 68K env was not modified by N-linked glycosylation. 125I-labeled 68K env was rapidly released into the media of tumor cell cultures and was recovered both in the form of a soluble protein and in a 100,000 g pellet. The biologic function of this cell surface-expressed viral protein remains unknown. url: https://api.elsevier.com/content/article/pii/0042682285901023 doi: 10.1016/0042-6822(85)90102-3 id: cord-340983-w219g6qs author: Smith, Mary Ellen title: Rabies Virus Glycoprotein as a Carrier for Anthrax Protective Antigen date: 2006-09-01 words: 7400.0 sentences: 376.0 pages: flesch: 50.0 cache: ./cache/cord-340983-w219g6qs.txt txt: ./txt/cord-340983-w219g6qs.txt summary: Using the rabies virus (RV) envelope protein as a carrier molecule we show here that inactivated RV particles can be utilized to present Bacillus anthracis protective antigen (PA) domain-4 in the viral membrane. Rabies virus is a promising vaccine vector able to induce humoral and cellular immune responses efficiently to foreign antigens (McGettigan et al., 2001a (McGettigan et al., , 2001b Schnell et al., 2000) . To evaluate the cell surface expression of the recombinant RV G-D4 fusion proteins, BSR cells were infected with recombinant vaccinia virus expressing T7 RNA polymerase for one h, transfected with 5 μg of each of the five plasmids and 24 h later fixed in paraformaldehyde, permeabilized, and immunostained with anti-PA monoclonal antibody. In contrast, PA expressed on the surface of virus particles induced potent humoral responses with either live or killed SPBN-D4-E51 particles stimulating antibody production after only a single dose. abstract: Live viral vectors expressing foreign antigens have shown great promise as vaccines against viral diseases. However, safety concerns remain a major problem regarding the use of even highly attenuated viral vectors. Using the rabies virus (RV) envelope protein as a carrier molecule we show here that inactivated RV particles can be utilized to present Bacillus anthracis protective antigen (PA) domain-4 in the viral membrane. In addition to the RV glycoprotein (G) transmembrane and cytoplasmic domains, a portion of the RV G ectodomain was required to express the chimeric RV G anthrax PA on the cell surface. The novel antigen was also efficiently incorporated into RV virions. Mice immunized with the inactivated recombinant RV virions exhibited seroconversion against both RV G and anthrax PA, and a second inoculation greatly increased these responses. These data demonstrate that a viral envelope protein can carry a bacterial protein and that a viral carrier can display whole polypeptides compared to the limited epitope presentation of previous viral systems. url: https://www.ncbi.nlm.nih.gov/pubmed/16820183/ doi: 10.1016/j.virol.2006.05.010 id: cord-274480-aywdmj6o author: Song, Wenfei title: Identification of residues on human receptor DPP4 critical for MERS-CoV binding and entry date: 2014-10-21 words: 2815.0 sentences: 147.0 pages: flesch: 57.0 cache: ./cache/cord-274480-aywdmj6o.txt txt: ./txt/cord-274480-aywdmj6o.txt summary: Middle East respiratory syndrome coronavirus (MERS-CoV) infects host cells through binding the receptor binding domain (RBD) on its spike glycoprotein to human receptor dipeptidyl peptidase 4 (hDPP4). Previously, we have generated a panel of MERS-CoV mutant RBD proteins at the residues D539, Y499, D510, E513, L506, W553 and V555 to characterize their impacts on binding activity to hDPP4 and the entry efficiency into target cells. To study the impacts of the substitutions of the critical residues on hDPP4 described above on the interaction between MERS-CoV RBD and hDDP4, we determined the binding efficiency between these two proteins by employing SPR technique. To further study the importance of the critical residues on hDPP4 on viral entry, we measured the entry efficiency of pseudovirus into COS7 cells expressing the wide-type and mutant forms of hDPP4. These results are consistent with our findings and suggest these residues play an important role in RBD binding and viral entry, and determining the tropism to MERS-CoV infection. abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) infects host cells through binding the receptor binding domain (RBD) on its spike glycoprotein to human receptor dipeptidyl peptidase 4 (hDPP4). Here, we report identification of critical residues on hDPP4 for RBD binding and virus entry through analysis of a panel of hDPP4 mutants. Based on the RBD–hDPP4 crystal structure we reported, the mutated residues were located at the interface between RBD and hDPP4, which potentially changed the polarity, hydrophobic or hydrophilic properties of hDPP4, thereby interfering or disrupting their interaction with RBD. Using surface plasmon resonance (SPR) binding analysis and pseudovirus infection assay, we showed that several residues in hDPP4–RBD binding interface were important on hDPP4–RBD binding and viral entry. These results provide atomic insights into the features of interactions between hDPP4 and MERS-CoV RBD, and also provide potential explanation for cellular and species tropism of MERS-CoV infection. url: https://www.sciencedirect.com/science/article/pii/S004268221400453X doi: 10.1016/j.virol.2014.10.006 id: cord-278578-vq5fy8m5 author: Stodola, Jenny K. title: The OC43 human coronavirus envelope protein is critical for infectious virus production and propagation in neuronal cells and is a determinant of neurovirulence and CNS pathology date: 2017-12-26 words: 10925.0 sentences: 469.0 pages: flesch: 50.0 cache: ./cache/cord-278578-vq5fy8m5.txt txt: ./txt/cord-278578-vq5fy8m5.txt summary: In this study, we demonstrate that the fully functional HCoV-OC43 E protein (harboring specific TMD and PBM) is critical in infectious virus production and dissemination in epithelial and neuronal cell cultures and in the murine CNS and that it is a determinant of neurovirulence, a first demonstration for this coronavirus species. However, in these primary cultures, low levels of infected cells were visualized by immunofluorescence (IFA) where we detect the viral S protein, suggesting that infection was possible even for the complemented rOC/E-Stop virus but that production of new infectious progeny and eventual propagation were severely inhibited compared to wild type virus (Fig. 2C ). Infection of human LA-N-5 cells and mixed primary cultures of mouse CNS cells showed a similar virus production kinetic Infectious viral titer differences observed between experiments, revealed, by sequencing (G), the appearance of reversions at the position in the E gene where a stop codon was introduced are indicated by bold and underline. abstract: The OC43 strain of human coronavirus (HCoV-OC43) is an ubiquitous respiratory tract pathogen possessing neurotropic capacities. Coronavirus structural envelope (E) protein possesses specific motifs involved in protein-protein interaction or in homo-oligomeric ion channel formation, which are known to play various roles including in virion morphology/assembly and in cell response to infection and/or virulence. Making use of recombinant viruses either devoid of the E protein or harboring mutations either in putative transmembrane domain or PDZ-binding motif, we demonstrated that a fully functional HCoV-OC43 E protein is first needed for optimal production of recombinant infectious viruses. Furthermore, HCoV-OC43 infection of human epithelial and neuronal cell lines, of mixed murine primary cultures from the central nervous system and of mouse central nervous system showed that the E protein is critical for efficient and optimal virus replication and propagation, and thereby for neurovirulence. url: https://www.sciencedirect.com/science/article/pii/S0042682217304361 doi: 10.1016/j.virol.2017.12.023 id: cord-256769-flfycl7i author: Stoermer, Kristina A. title: Complement and Viral Pathogenesis date: 2011-03-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The complement system functions as an immune surveillance system that rapidly responds to infection. Activation of the complement system by specific recognition pathways triggers a protease cascade, generating cleavage products that function to eliminate pathogens, regulate inflammatory responses, and shape adaptive immune responses. However, when dysregulated, these powerful functions can become destructive and the complement system has been implicated as a pathogenic effector in numerous diseases, including infectious diseases. This review highlights recent discoveries that have identified critical roles for the complement system in the pathogenesis of viral infection. url: https://www.sciencedirect.com/science/article/pii/S0042682210008135 doi: 10.1016/j.virol.2010.12.045 id: cord-286060-92lazxd7 author: Stohlman, Stephen A. title: Synthesis and subcellular localization of the murine coronavirus nucleocapsid protein date: 1983-10-30 words: 2012.0 sentences: 114.0 pages: flesch: 55.0 cache: ./cache/cord-286060-92lazxd7.txt txt: ./txt/cord-286060-92lazxd7.txt summary: Studies on the intracellular synthesis of MHV proteins by pulse-chase experiments have shown that the nucleocapsid protein, pp60, is a primary gene product (3, 12) . In addition, two-dimensional nonequilibrium isoelectric focusing of infected cell lysates indicated that the nucleocapsid protein was composed of multiple heterogeneously charged species which are homogeneous in size (1). In examining the kinetics of the appearance of JHMV proteins in infected DBT cells, we noted that the region of the gel which contains the pp60 protein also contained another protein of slightly lower molecular weight (Fig. 1A) . When infected cells were pulse-labeled with [%]methionine for 2 min and then chased with excess unlabeled methionine (20 m&Q for various lengths of time, only ~57 was detected within the pulse interval (Fig. 1B) . abstract: Abstract The synthesis and processing of the nucleocapsid protein (pp60) of the JHM strain of murine coronaviruses were examined. Pulse-chase experiments showed that pp60 was synthesized initially as a protein of approximately 57,000 in molecular weight (p57). Immunoprecipitation using mouse anti-JHMV antiserum indicated that p57 was virus specific. Immunoprecipitation with monoclonal antibodies specific for pp60 showed that p57 was antigenically related to pp60 and was not phosphorylated, while the intracellular protein that comigrated with the virion nucleocapsid protein, pp60, was phosphorylated. The p57 was found exclusively in the cytosol while the majority of pp60 was associated with the membrane fraction but pp60 was not an integral membrane protein. url: https://www.sciencedirect.com/science/article/pii/004268228390106X doi: 10.1016/0042-6822(83)90106-x id: cord-312210-3x9s3g8n author: Stoian, Ana title: The use of cells from ANPEP knockout pigs to evaluate the role of aminopeptidase N (APN) as a receptor for porcine deltacoronavirus (PDCoV) date: 2019-12-24 words: 3444.0 sentences: 199.0 pages: flesch: 59.0 cache: ./cache/cord-312210-3x9s3g8n.txt txt: ./txt/cord-312210-3x9s3g8n.txt summary: title: The use of cells from ANPEP knockout pigs to evaluate the role of aminopeptidase N (APN) as a receptor for porcine deltacoronavirus (PDCoV) However, lung fibroblast-like cells, derived from the ANPEP KO PAM cultures, supported PDCoV infection to high levels. In this study, we investigated the role of pAPN as a receptor for PDCoV by evaluating the permissiveness of different cell populations derived from the lungs of ANPEP KO and wild-type (WT) pigs. Porcine alveolar macrophages (PAMs) from ANPEP KO and WT pigs were used to evaluate the permissiveness of cells for infection with PDCoV and TGEV. The results showed that PAMs from pigs lacking a functional ANPEP gene are resistant to TGEV and PDCoV infection. The results from this study showed no PDCoV infection of PAMs obtained from ANPEP KO pigs (see Fig. 1A ), which supports the observations of Wang et al. abstract: The coronaviruses, porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and porcine deltacoronavirus (PDCoV) represent important sources of neonatal diarrhea on pig farms. The requirement for aminopeptidase N (APN) as a receptor for TGEV, but not for PEDV, is well established. In this study, the biological relevance of APN as a receptor for PDCoV was tested by using CRISPR/Cas9 to knockout the APN gene, ANPEP, in pigs. Porcine alveolar macrophages (PAMs) from ANPEP knockout (KO) pigs showed resistance to PDCoV infection. However, lung fibroblast-like cells, derived from the ANPEP KO PAM cultures, supported PDCoV infection to high levels. The results suggest that APN is a receptor for PDCoV in PAMs but is not necessary for infection of lung-derived fibroblast cells. The infection of the ANPEP KO pigs with PDCoV further confirmed that APN is dispensable as a receptor for PDCoV. url: https://api.elsevier.com/content/article/pii/S0042682219303496 doi: 10.1016/j.virol.2019.12.007 id: cord-332356-au7s3dmp author: Strandin, Tomas title: The cytoplasmic tail of hantavirus Gn glycoprotein interacts with RNA date: 2011-09-15 words: 6554.0 sentences: 329.0 pages: flesch: 53.0 cache: ./cache/cord-332356-au7s3dmp.txt txt: ./txt/cord-332356-au7s3dmp.txt summary: The results indicate that the binding ability of Gn-CT towards nucleic acids is rather unspecific since in addition to genomic RNA, also unrelated RNA as well as single-stranded DNA was able to interact with Gn-CTs of PUUV and TULV. Purified, lysed and micrococcal nuclease (MNase)-treated virus preparation and in vitro transcribed and radiolabeled genomic PUUV S segment were allowed to form RNA-protein complexes prior to UV cross-linking. The capability of structural proteins to bind RNA was analyzed by incubating purified, lysed and micrococcal nuclease (MNase)-treated virus preparations with radioactive PUUV S segment RNA in the case of PUUV ( The samples were immunoprecipitated with MAbs or PAbs specific to N, Gn or Gc and retained radioactivity on protein G beads after washing was measured by scintillation counting. The mapping indicated that the same peptides that were previously shown to interact with RNP and N protein (Hepojoki et al., 2010b) were capable of binding also nucleic acids (Fig. 5A ). abstract: We recently characterized the interaction between the intraviral domains of envelope glycoproteins (Gn and Gc) and ribonucleoprotein (RNP) of Puumala and Tula hantaviruses (genus Hantavirus, family Bunyaviridae). Herein we report a direct interaction between spike-forming glycoprotein and nucleic acid. We show that the envelope glycoprotein Gn of hantaviruses binds genomic RNA through its cytoplasmic tail (CT). The nucleic acid binding of Gn-CT is unspecific, as demonstrated by interactions with unrelated RNA and with single-stranded DNA. Peptide scan and protein deletions of Gn-CT mapped the nucleic acid binding to regions that overlap with the previously characterized N protein binding sites and demonstrated the carboxyl-terminal part of Gn-CT to be the most potent nucleic acid-binding site. We conclude that recognition of the RNP complex by the Gn-CT could be mediated by interactions with both genomic RNA and the N protein. This would provide the required selectivity for the genome packaging of hantaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/21807393/ doi: 10.1016/j.virol.2011.06.030 id: cord-293375-qcy56ui7 author: Strauss, Ellen G. title: Identification of the active site residues in the nsP2 proteinase of sindbis virus date: 1992-12-31 words: 5192.0 sentences: 265.0 pages: flesch: 56.0 cache: ./cache/cord-293375-qcy56ui7.txt txt: ./txt/cord-293375-qcy56ui7.txt summary: coma-, nepo-, and potyviruses; coronaviruses; and flaviviruses (and their proposed relatives pestiviruses and hepatitis C virus.) Originally these domains were predicted to have proteolytic activity based on the presence of certain conserved amino acid residues and on the basis of protein-modeling studies (Bazan and Fletterick, 1989; Boege et a/., 1981; Gorbalenya et al., 1989; Hahn eta/., 1985) . Furthermore, we present data to show that none of the asparagine residues in the proteinase domain of Sindbis nsP2 that are conserved among alphaviruses are absolutely required for proteolytic activity, but that Trp-559, adjacent to His-558, is essential for function. We also examined the effect of changing Cys-525, one of the two remaining conserved cysteine residues in the C-terminal half of nsP2, to serine or arginine, as well as changing Ser-535, which is found in a domain of limited similarity to the active site serine of serine proteinases, to threonine. abstract: Abstract The nonstructural polyproteins of Sindbis virus are processed by a virus-encoded proteinase which is located in the C-terminal domain of nsP2. Here we have performed a mutagenic analysis to identify the active site residues of this proteinase. Substitution of other amino acids for either Cys-481 or His-558 completely abolished proteolytic processing of Sindbis virus polyproteins in vitro. Substitutions within this domain for a second cysteine conserved among alphaviruses, for four other conserved histidines, or for a conserved serine did not affect the activity of the enzyme. These results suggest that nsP2 is a papain-like proteinase whose catalytic dyad is composed of Cys-481 and His-558. Since an asparagine residue has been implicated in the active site of papain, we changed the four conserved asparagine residues in the C-terminal half of nsP2 and found that all could be substituted without total loss of activity. Among papain-like proteinases, the residue following the catalytic histidine is alanine or glycine in the plant and animal enzymes, and the presence of Trp-559 in alphaviruses is unusual. A mutant enzyme containing Ala-559 was completely inactive, implying that Trp-559 is essential for a functional proteinase. All of these mutations were introduced into a full-length clone of Sindbis virus from which infectious RNA could be transcribed in vitro, and the effects of these changes on viability were tested. In all cases it was found that mutations which abolished proteolytic activity were lethal, whether or not these mutations were in the catalytic residues, indicating that proteolysis of the nonstructural polyprotein is essential for Sindbis replication. url: https://www.sciencedirect.com/science/article/pii/004268229290268T doi: 10.1016/0042-6822(92)90268-t id: cord-316134-lkd2mj27 author: Sungsuwan, Suttipun title: Nucleocapsid proteins from other swine enteric coronaviruses differentially modulate PEDV replication date: 2020-01-15 words: 9236.0 sentences: 495.0 pages: flesch: 52.0 cache: ./cache/cord-316134-lkd2mj27.txt txt: ./txt/cord-316134-lkd2mj27.txt summary: Investigation of possible molecular interactions between components of PEDV, PDCoV and TGEV and their influence on replication of each virus would provide a crucial insight into comprehensive understanding of these CoVs. Of all viral proteins, we have chosen to start with the N protein, as it is among the most abundant and ubiquitous structural proteins in infected cells. For viral infection in the transient CoV N expression experiment, VeroE6 cells were transfected with 1 or 2 μg of pCAGGS-PEDV N-Myc, pCAGGS-PDCoV N-HA, pCAGGS-TGEV N-FLAG, or the empty pCAGGS vector and were incubated for 24 h to allow for protein expression. To investigate how this protein-protein interaction might affect PEDV replication, we transiently transfected VeroE6 cells with varying amounts of the pCAGGS plasmid expressing N proteins from either PDCoV or TGEV for 24 h before infection with PEDV-mCherry (MOI = 0.0001) and followed the course of viral replication for each condition. abstract: Porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV) and porcine deltacoronavirus (PDCoV) share tropism for swine intestinal epithelial cells. Whether mixing of viral components during co-infection alters pathogenic outcomes or viral replication is not known. In this study, we investigated how different coronavirus nucleocapsid (CoV N) proteins interact and affect PEDV replication. We found that PDCoV N and TGEV N can competitively interact with PEDV N. However, the presence of PDCoV or TGEV N led to very different outcomes on PEDV replication. While PDCoV N significantly suppresses PEDV replication, overexpression of TGEV N, like that of PEDV N, increases production of PEDV RNA and virions. Despite partial interchangeability in nucleocapsid oligomerization and viral RNA synthesis, endogenous PEDV N cannot be replaced in the production of infectious PEDV particles. Results from this study give insights into functional compatibilities and evolutionary relationship between CoV viral proteins during viral co-infection and co-evolution. url: https://www.sciencedirect.com/science/article/pii/S0042682219303150 doi: 10.1016/j.virol.2019.11.007 id: cord-294260-g410mavp author: Sztuba-Solińska, Joanna title: Subgenomic messenger RNAs: Mastering regulation of (+)-strand RNA virus life cycle date: 2011-04-10 words: 9531.0 sentences: 506.0 pages: flesch: 54.0 cache: ./cache/cord-294260-g410mavp.txt txt: ./txt/cord-294260-g410mavp.txt summary: Arrow, RNA3 start site at nt 2721 (Lindenbach et al., 2002) ; (D) Schematic of the RCNMV genome showing the relative positions of the in trans interacting RNA elements: the loop portion of a stem-loop in RNA2 (termed trans-activator or TA) and a complementary sequence in RNA1 (termed TA binding site or TABS) located just upstream from the initiation site for SG mRNA transcription (Guenther et al., 2004) ; (E) Representation of CLSV genome and the proposed AS2 and RS2 interaction during regulation of SG RNA2 synthesis (Xu and White, 2008) ; (F) Overview of the BYDV genome and the in cisinteraction between genomic 5′-UTR stem-loop (BCL) and the genomic 3′-BTE, and the in trans interaction between the genomic 3′ BTE and the 5′ UTR of SG RNA1 . abstract: Many (+)-strand RNA viruses use subgenomic (SG) RNAs as messengers for protein expression, or to regulate their viral life cycle. Three different mechanisms have been described for the synthesis of SG RNAs. The first mechanism involves internal initiation on a (−)-strand RNA template and requires an internal SGP promoter. The second mechanism makes a prematurely terminated (−)-strand RNA which is used as template to make the SG RNA. The third mechanism uses discontinuous RNA synthesis while making the (−)-strand RNA templates. Most SG RNAs are translated into structural proteins or proteins related to pathogenesis: however other SG RNAs regulate the transition between translation and replication, function as riboregulators of replication or translation, or support RNA–RNA recombination. In this review we discuss these functions of SG RNAs and how they influence viral replication, translation and recombination. url: https://doi.org/10.1016/j.virol.2011.02.007 doi: 10.1016/j.virol.2011.02.007 id: cord-290883-r2744fb3 author: TORRES, JUAN M. title: Induction of Antibodies Protecting against Transmissible Gastroenteritis Coronavirus (TGEV) by Recombinant Adenovirus Expressing TGEV Spike Protein date: 1995-11-30 words: 7299.0 sentences: 390.0 pages: flesch: 54.0 cache: ./cache/cord-290883-r2744fb3.txt txt: ./txt/cord-290883-r2744fb3.txt summary: The antisera induced in swine by the Ad5 recombinants expressing the amino-terminal 26% of the spike protein (containing sites C and B) or the full-length spike protein, when mixed with a lethal dose of virus prior to administration to susceptible piglets, delayed or completely prevented the induction of symptoms of disease, respectively. Alternatively, S gene ces are determined rather than titers since in the first fragments were removed from the original plasmid or procedure virus-antibody mixtures are evaluated in the from pSV2X3-TS vectors without SV-40 Pr signal, or withplaque assay without further dilution of the antibody, proout both Pr and polyadenylation sequences, using the viding highly reproducible results and information about restriction endonucleases indicated in Fig. 1 . Infectious Ad-TS recombinants expressing S protein fragments were generated by cotransfecting 293 cells with pFG144K3-TS or pAB14-TS (which carry S gene sequences from TGEV and pFG173 plasmids). abstract: Abstract Ten recombinant adenoviruses expressing either fragments of 1135, 1587, or 3329 nt or the full-length spike gene of transmissible gastroenteritis coronavirus (TGEV) have been constructed. These recombinants produce S polypeptides with apparent molecular masses of 68, 86, 135, and 200 kDa, respectively. Expression of the recombinant antigen driven by Ad5 promoters was inhibited by the insertion of an exogenous SV-40 promoter. Most of the recombinant antigens remain intracytoplasmic in infected cells. All the recombinant-directed expression products contain functional antigenic sites C and B (Gebaueret al.,1991,Virology183, 225–238). The recombinant antigen of 135 kDa and that of 200 kDa, which represents the whole spike protein, also contain antigenic sites D and A, which have previously been shown to be the major inducers of TGEV-neutralizing antibodies. Interestingly, here we show that recombinant S protein fragments expressing only sites C and B also induced TGEV-neutralizing antibodies. The chimeric Ad5–TGEV recombinants elicited lactogenic immunity in hamsters, including the production of TGEV-neutralizing antibodies. The antisera induced in swine by the Ad5 recombinants expressing the amino-terminal 26% of the spike protein (containing sites C and B) or the full-length spike protein, when mixed with a lethal dose of virus prior to administration to susceptible piglets, delayed or completely prevented the induction of symptoms of disease, respectively. url: https://www.sciencedirect.com/science/article/pii/S0042682285700232 doi: 10.1006/viro.1995.0023 id: cord-315158-f6msh8od author: Taguchi, Fumihiro title: Comparison of six different murine coronavirus jhm variants by monoclonal antibodies against the e2 glycoprotein date: 1989-03-31 words: 1620.0 sentences: 86.0 pages: flesch: 58.0 cache: ./cache/cord-315158-f6msh8od.txt txt: ./txt/cord-315158-f6msh8od.txt summary: Abstract We have examined six different JHMV variants, sp-4 (recloned wt JHMV), cl-2, CNSV, DL, DS, and JHM-X, in terms of the sizes of the mRNA3 and E2 glycoprotein as well as their reactivity to a panel of monoclonal antibodies to the E2 glycoprotein. Recently, we have shown that the highly virulent variant viruses with larger E2 glycoproteins were preferentially isolated from rat brain (19) and cultured astrocytes (20) after infection by wild-type (wt) JHMV which contains a small mRNA3 and E2 glycoprotein. E2 glycoproteins produced by sp-4 and JHM-X, both of which synthesized a small mRNA3, were shown to be approximately 15,000 Da smaller than those produced by the other variant viruses with larger mRNA3.s. No significant differences were observed in the sizes of N proteins produced by the variants. As shown in Fig. 3 , the monoclonal antibodies uniformly had excellent binding to all the viruses tested, with the exception of sp-4 and JHM-X, the two variants with small mRNA3s and E2 proteins. abstract: Abstract We have examined six different JHMV variants, sp-4 (recloned wt JHMV), cl-2, CNSV, DL, DS, and JHM-X, in terms of the sizes of the mRNA3 and E2 glycoprotein as well as their reactivity to a panel of monoclonal antibodies to the E2 glycoprotein. Two of these variants, sp-4 and JHM-X, were found to have smaller mRNA3 and E2 glycoprotein species compared with those of the other four variants. In addition, sp-4 and JHM-X were distinguished from the other four variants by their inability to bind to monoclonal antibodies recognizing two antigenic domains of the E2 molecule. Thus, six JHMV variants could clearly be divided into two groups with respect to the size and antigenicity of their E2 glycoproteins. url: https://api.elsevier.com/content/article/pii/0042682289900615 doi: 10.1016/0042-6822(89)90061-5 id: cord-322062-nnefbeo6 author: Tam, Albert W. title: Hepatitis E virus (HEV): Molecular cloning and sequencing of the full-length viral genome date: 1991-11-30 words: 5738.0 sentences: 296.0 pages: flesch: 49.0 cache: ./cache/cord-322062-nnefbeo6.txt txt: ./txt/cord-322062-nnefbeo6.txt summary: We now report on the molecular cloning and sequencing of the complete HEV (Burma; B) viral genome together with the deduced amino acid sequences of viral-encoded proteins General perspectives on the genetic organization of the virus, as deduced from sequence and open reading frame analyses, indicate that HEV bears some similarity to the caliciviridae but may represent a new class of nonenveloped RNA virus. Bife was chosen as the RNA source for cDNA synthesis because it contained relatively large numbers of virus particles when HEV cDNA clones were identified from libraries made from randomly primed cyno bile (solid square), or from cyno liver after priming by oligo-dT (solid circle), random sequence hexamers (open circle) and HEV-sequence specific oligonucleotides (open square). The presence of HEV-specific subgenomic RNAs localized to the 3'' one-third of the genome suggests that these may be the transcripts from which these 3'' end ORFs are expressed and is indicative of a unique expression strategy among nonenveloped positive-sense RNA viruses infecting humans. abstract: Abstract We have recently described the cloning of a portion of the hepatitis E virus (HEV) and confirmed its etiologic association with enterically transmitted (waterborne, epidemic) non-A, non-B hepatitis. The virus consists of a single-stranded, positive-sense RNA genome of approximately 7.5 kb, with a polyadenylated 3' end. We now report on the cloning and nucleotide sequencing of an overlapping, contiguous set of cDNA clones representing the entire genome of the HEV Burma strain [HEV(B)]. The largest open reading frame extends approximately 5 kb from the Fend and contains the RNA-directed RNA polymerase and nucleoside triphosphate binding motifs. The second major open reading frame (ORF2) begins 37 by downstream of the first and extends approximately 2 kb to the termination codon present 65 by from the 3' terminal stretch of poly(A) residues. ORF2 contains a consensus signal peptide sequence at its amino terminus and a capsid-like region with a high content of basic amino acids similar to that seen with other virus capsid proteins. A third open reading frame partially overlaps the first and second and encompasses only 369 bp. In addition to the 7.5-kb full-length genomic transcript, two subgenomic polyadenylated messages of approximately 3.7 and 2.0 kb were detected in infected liver using a probe from the 3' third of the genome. The genomic organization of the virus is consistent with the Fend encoding nonstructural and the 3' end encoding the viral structural gene(s). The expression strategy of the virus involves the use of three different open reading frames and at least three different transcripts. HEV was previously determined to be a nonenveloped particle with a diameter of 27–34 nm. These findings on the genetic organization and expression strategy of HEV suggest that it is the prototype human pathogen for a new class of RNA virus or perhaps a separate genus within the Caliciviridae family url: https://www.ncbi.nlm.nih.gov/pubmed/1926770/ doi: 10.1016/0042-6822(91)90760-9 id: cord-283998-whwksoxt author: Tannock, Gregory A. title: The RNA of human coronavirus OC-43 date: 1977-12-31 words: 3978.0 sentences: 213.0 pages: flesch: 57.0 cache: ./cache/cord-283998-whwksoxt.txt txt: ./txt/cord-283998-whwksoxt.txt summary: Abstract A homogeneous RNA complex with a sedimentation coefficient of 70 S and an apparent molecular weight of approximately 6.1 × 106 was released from purified 32P-labeled, mouse-brain-derived OC-43 virus after treatment with 1% sodium dodecyl sulfate (SDS) for 15 min at 23°. This suggests that (a) extensive nicking of a large RNA molecule has occurred during viral growth, due to ribonucleases which are inactivated during phenol extractions; (b) heterogeneity for OC-43 RNA is not due to internal ribonuclease activity and fragments are held together by noncovalent linkages much weaker than those present in the 70 S retroviral RNA complex, or by small proteins; or, most probably, (c) a combination of extensive nicking and weak noncovalent linkages results in the heterogeneous denaturation products. The RNA of avian infectious bronchitis virus (IBV) was first described by Tannock (1973) , who obtained from purified virions a highly heterogeneous array of RNA fragments using a phenol-sodium dodecyl sulfate (SDS) extraction procedure. abstract: Abstract A homogeneous RNA complex with a sedimentation coefficient of 70 S and an apparent molecular weight of approximately 6.1 × 106 was released from purified 32P-labeled, mouse-brain-derived OC-43 virus after treatment with 1% sodium dodecyl sulfate (SDS) for 15 min at 23°. The complex was highly susceptible to heat, releasing 4 S RNA fragments at 37° and breaking down to fragments of 4–70 S at 60°; it was also degraded by centrifugation through dimethyl sulfoxide gradients. Unlike tobacco mosaic virus or Rous sarcoma virus RNA, OC-43 RNA prepared by extraction with phenol-SDS or phenol-chloroform degraded into a range of fragments with coefficients of 15–55 S; 4 S RNA was also present as a minor component. This suggests that (a) extensive nicking of a large RNA molecule has occurred during viral growth, due to ribonucleases which are inactivated during phenol extractions; (b) heterogeneity for OC-43 RNA is not due to internal ribonuclease activity and fragments are held together by noncovalent linkages much weaker than those present in the 70 S retroviral RNA complex, or by small proteins; or, most probably, (c) a combination of extensive nicking and weak noncovalent linkages results in the heterogeneous denaturation products. url: https://api.elsevier.com/content/article/pii/004268227790126X doi: 10.1016/0042-6822(77)90126-x id: cord-279813-mrei5kih author: Temeeyasen, G. title: Differential gene modulation of pattern-recognition receptor TLR and RIG-I-like and downstream mediators on intestinal mucosa of pigs infected with PEDV non S-INDEL and PEDV S-INDEL strains date: 2017-12-14 words: 6657.0 sentences: 337.0 pages: flesch: 49.0 cache: ./cache/cord-279813-mrei5kih.txt txt: ./txt/cord-279813-mrei5kih.txt summary: authors: Temeeyasen, G.; Sinha, A.; Gimenez-Lirola, L.G.; Zhang, J.Q.; Piñeyro, P.E. title: Differential gene modulation of pattern-recognition receptor TLR and RIG-I-like and downstream mediators on intestinal mucosa of pigs infected with PEDV non S-INDEL and PEDV S-INDEL strains The aim of this study was to investigate the differential gene modulation of pattern recognition TLR and RIG-I-like receptors and downstream mediators on the intestinal mucosa of neonatal pigs infected with PEDV non-S-INDEL and PEDV S-INDEL strains. We evaluated whether the differential modulatory effect observed in PRRs and downstream mediators in response to infection with the PEDV S-INDEL versus the non-S-INDEL strain was also translated into a differential modulation in the expression of gene coding for pro-inflammatory cytokines and type I interferons. Changes in TNF receptor associated factor (TRAF) 6 and interferon regulatory factor 7 (IRF7) genes mRNA expression induced by porcine epidemic diarrhea virus (PEDV) non S-INDEL and PEDV S-INDEL strains in intestinal mucosa (A-B). abstract: Porcine epidemic diarrhea virus (PEDV) strains can be divided into non-S-INDEL and S-INDEL strains. PEDV pathogenesis is strain-specific, and studies in neonatal pigs have demonstrated that the PEDV non-S-INDEL strains are more pathogenic than the PEDV S-INDEL strains. RNA viruses, including PEDV, can interact with a large number of pattern recognition receptors (PRRs) in the intestinal mucosa, including toll-like receptors (TLRs) and RIG-I-like receptors (RLRs). We investigated the differential gene modulation of TLRs, RIG-I, and downstream mediators on the intestinal mucosa of neonatal pigs infected with PEDV S-INDEL and non-S-INDEL strains. Ten five-day-old piglets were inoculated orally with 10 ml of 10(4) TCDI(50)/ml of either PEDV non-S-INDEL or S-INDEL strains. PEDV S-INDEL infection induced pro-inflammatory cytokines through the non-canonical NF-κB signaling pathway by activating RIG-I. In contrast, PEDV non-S-INDEL infection suppressed the induction of pro-inflammatory cytokines and type 1 interferon production by down-regulation of TLRs and downstream signaling molecules. url: https://www.ncbi.nlm.nih.gov/pubmed/29249266/ doi: 10.1016/j.virol.2017.11.024 id: cord-289045-vft163v0 author: Thackray, Larissa B. title: Substitutions of conserved amino acids in the receptor-binding domain of the spike glycoprotein affect utilization of murine CEACAM1a by the murine coronavirus MHV-A59 date: 2005-03-30 words: 7779.0 sentences: 345.0 pages: flesch: 56.0 cache: ./cache/cord-289045-vft163v0.txt txt: ./txt/cord-289045-vft163v0.txt summary: Cell lines from host species that are normally resistant to MHV, porcine coronavirus [transmissible gastroenteritis virus (TGEV)] or human coronavirus strain 229E (HCoV-229E) are rendered susceptible to infection by transfection with cDNA encoding the specific coronavirus receptors mCEACAM1a, porcine aminopeptidase N (pAPN) (Delmas et al., 1992; Dveksler et al., 1991; Yeager et al., 1992) . Since some of the aa substitutions in the RBD of S were chosen to reflect residues found in S330 of related rat, bovine or human coronaviruses in group II (Fig. 1A) , we examined the ability of the SA59 B, S33R A, S33G C, T62S A, T62A A, L65H C, L65A C, L79M/T82M A, L79A/ T82A B, Y162F A, K183R A and K183G A viruses to infect non-murine cells lines that are normally resistant to MHV-A59 infection. abstract: The host range of the murine coronavirus (MHV) is limited to susceptible mice and murine cell lines by interactions of the spike glycoprotein (S) with its receptor, mCEACAM1a. We identified five residues in S (S33, L79, T82, Y162 and K183) that are conserved in the receptor-binding domain of MHV strains, but not in related coronaviruses. We used targeted RNA recombination to generate isogenic viruses that differ from MHV-A59 by amino acid substitutions in S. Viruses with S33R and K183R substitutions had wild type growth, while L79A/T82A viruses formed small plaques. Viruses with S33G, L79M/T82M or K183G substitutions could only be recovered from cells that over-expressed a mutant mCEACAM1a. Viruses with Y162H or Y162Q substitutions were never recovered, while Y162A viruses formed minute plaques. However, viruses with Y162F substitutions had wild type growth, suggesting that Y162 may comprise part of a hydrophobic domain that contacts the MHV-binding site of mCEACAM1a. url: https://www.ncbi.nlm.nih.gov/pubmed/15749126/ doi: 10.1016/j.virol.2005.01.016 id: cord-283035-tpqf458q author: Thanthrige-Don, Niroshan title: Analyses of the spleen proteome of chickens infected with Marek's disease virus date: 2009-08-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Marek's disease virus (MDV), which causes a lymphoproliferative disease in chickens, is known to induce host responses leading to protection against disease in a manner dependent on genetic background of chickens and virulence of the virus. In the present study, changes in the spleen proteome at 7, 14 and 21 days post-infection in response to MDV infection were studied using two-dimensional polyacrylamide gel electrophoresis. Differentially expressed proteins were identified using one-dimensional liquid chromatography electrospray ionization tandem mass spectrometry (1D LC ESI MS/MS). Comparative analysis of multiple gels revealed that the majority of changes had occurred at early stages of the disease. In total, 61 protein spots representing 48 host proteins were detected as either quantitatively (false discovery rate (FDR) ≤ 0.05 and fold change ≥ 2) or qualitatively differentially expressed at least once during different sampling points. Overall, the proteins identified in the present study are involved in a variety of cellular processes such as the antigen processing and presentation, ubiquitin–proteasome protein degradation (UPP), formation of the cytoskeleton, cellular metabolism, signal transduction and regulation of translation. Notably, early stages of the disease were characterized by changes in the UPP, and antigen presentation. Furthermore, changes indicative of active cell proliferation as well as apoptosis together with significant changes in cytoskeletal components that were observed throughout the experimental period suggested the complexity of the pathogenesis. The present findings provide a basis for further studies aimed at elucidation of the role of these proteins in MDV interactions with its host. url: https://doi.org/10.1016/j.virol.2009.05.020 doi: 10.1016/j.virol.2009.05.020 id: cord-294990-jdjbjkcp author: Thuy, Nguyen Thanh title: A new nidovirus (NamDinh virus NDiV): Its ultrastructural characterization in the C6/36 mosquito cell line date: 2013-07-25 words: 3319.0 sentences: 154.0 pages: flesch: 50.0 cache: ./cache/cord-294990-jdjbjkcp.txt txt: ./txt/cord-294990-jdjbjkcp.txt summary: The viral nucleocapside-like particles detected in the cytoplasm (white arrows) and accumulated in the ER vesicles (Ves) of 48 h NDiV-infected C6/36 cells, appear immunoglod-labeled on ultrathin sections with anti-NDiV polyclonal antibodies, as shown in Fig. 5 . In this study, the nucleocapsid-like particle of NDiV was identified in the host cell cytoplasm as possessing a round shape and an inner core observed in several types of vesicles and in the ER and its viral nature was confirmed by immunogold labeling on thin sections. By EM analyses, we show that replication and assembly of NDiV was only detected in the cytoplasm of the host cells in which viral nucleocapsid-like particles appeared in the cytoplasm and in the endoplasmic compartments such as vacuoles, ER, and vesicles, but not in mitochondria. abstract: We describe the ultrastructure of the NamDinh virus (NDiV), a new member of the order Nidovirales grown in the C6/36 mosquito cell line. Uninfected and NDiV-infected cells were investigated by electron microscopy 24–48 h after infection. The results show that the viral nucleocapsid-like particles form clusters concentrated in the vacuoles, the endoplasmic reticulum, and are scattered in the cytoplasm. Mature virions of NDiV were released as budding particles on the cell surface where viral components appear to lie beneath and along the plasma membrane. Free homogeneous virus particles were obtained by ultracentrifugation on sucrose gradients of culture fluids. The size of the round-shaped particles with a complete internal structure was 80 nm in diameter. This is the first study to provide information on the morphogenesis and ultrastructure of the first insect nidovirus NDiV, a missing evolutionary link in the emergence of the viruses with the largest RNA genomes. url: https://www.sciencedirect.com/science/article/pii/S0042682213004005 doi: 10.1016/j.virol.2013.06.030 id: cord-266018-8bhnlsgy author: Trifilo, Matthew J. title: The CC chemokine ligand 3 regulates CD11c(+)CD11b(+)CD8α(−) dendritic cell maturation and activation following viral infection of the central nervous system: implications for a role in T cell activation date: 2004-09-15 words: 5101.0 sentences: 272.0 pages: flesch: 60.0 cache: ./cache/cord-266018-8bhnlsgy.txt txt: ./txt/cord-266018-8bhnlsgy.txt summary: The major findings of this study are (i) MHV infection of the CNS results in the appearance of two distinct populations of CD11c + cells each expressing markers characteristic of lymphoid (CD11c + CD11b À CD8a + DEC205 + ) and myeloid dendritic cells (CD11c + CD11b + CD8a À DEC205 À ), (ii) the accumulation of CD8a À DCs within the draining CLN is reduced in the absence of CCL3 signaling, (iii) expression of co-stimulatory molecules such as CD40 by CD8a À DCs within either the brain and CLN of MHV-infected CCL3 À/À mice is diminished suggesting that CCL3 signaling enhances expression of these molecules, and (iv) absence of CCL3 signaling results in the re-direction of the T cell response to viral antigens as determined by cytokine production. Our studies clearly indicate that CD8a À DCs isolated from the draining CLN of MHV-infected CCL3 +/+ mice secrete IL-12 suggesting that these cells help influence a protective Th1-mediated immune response characterized by the majority of antigen-specific T cells expressing IFN-g rather than IL-10 (Table 1 ). abstract: The role of CC chemokine ligand 3 (CCL3) in activation of dendritic cells (DCs) following mouse hepatitis virus (MHV) infection of the central nervous system (CNS) was examined. The results indicate that CCL3 participates in an effective host response to MHV infection by contributing to CD11c(+)CD11b(+)CD8α(−) DC maturation, activation, and migration to cervical lymph nodes (CLN). Diminished CD8α(−) DC activation correlated with reduced IFN-γ expression by virus-specific T cells accompanied by increased IL-10 production suggesting that CCL3 contributes to an effective host response to viral infection by enhancing the T cell activation potential of DC. url: https://www.sciencedirect.com/science/article/pii/S004268220400409X doi: 10.1016/j.virol.2004.06.027 id: cord-265173-70wyecwj author: Trujillo-Uscanga, Adrian title: Host cell p53 associates with the feline calicivirus major viral capsid protein VP1, the protease-polymerase NS6/7, and the double-stranded RNA playing a role in virus replication date: 2020-08-27 words: 5671.0 sentences: 282.0 pages: flesch: 53.0 cache: ./cache/cord-265173-70wyecwj.txt txt: ./txt/cord-265173-70wyecwj.txt summary: title: Host cell p53 associates with the feline calicivirus major viral capsid protein VP1, the protease-polymerase NS6/7, and the double-stranded RNA playing a role in virus replication Viruses modulate p53 functions in different manners: single-stranded RNA viruses such as the human coronavirus NL63 (HCoV-NL63) induces its degradation of p53 (Yuan et al., 2015) to ensure viral growth in infected cells (Ma-Lauer et al., 2016) , Zika (ZIKV) and West Nile (WNV) activate p53 to facilitate their replication (El Ghouzzi et al., 2016) (Teng et al., 2017) (Yang et al., 2008) while Adenovirus Even though p53 is implicated in the induction of apoptosis and in many viral infections, its role during calicivirus infection has not been studied. Here we found that p53 interacts with FCV dsRNA, the protease-polymerase NS6/7, and VP1 in the RC; moreover, knockdown of p53 resulted in a significant reduction of the NS viral protein synthesis and virus production, indicating its role for efficient viral replication. abstract: p53 is implicated in several cellular pathways such as induction of cell-cycle arrest, differentiation, senescence, and apoptosis. p53 is activated by a broad range of stress signals, including viral infections. While some viruses activate p53, others induce its inactivation, and occasionally p53 is differentially modulated during the replicative cycle. During calicivirus infections, apoptosis is required for virus exit and spread into the host; yet, the role of p53 during infection is unknown. By confocal microscopy, we found that p53 associates with FCV VP1, the protease-polymerase NS6/7, and the dsRNA. This interaction was further confirmed by proximity ligation assays, suggesting that p53 participates in the FCV replication. Knocked-down of p53 expression in CrFK cells before infection, resulted in a strong reduction of the non-structural protein levels and a decrease of the viral progeny production. These results indicate that p53 is associated with the viral replication complex and is required for an efficient FCV replication. url: https://api.elsevier.com/content/article/pii/S0042682220301616 doi: 10.1016/j.virol.2020.08.008 id: cord-267014-3vi7pgvr author: Vennema, H. title: Genomic organization and expression of the 3′ end of the canine and feline enteric coronaviruses date: 1992-11-30 words: 3543.0 sentences: 210.0 pages: flesch: 59.0 cache: ./cache/cord-267014-3vi7pgvr.txt txt: ./txt/cord-267014-3vi7pgvr.txt summary: Abstract The genomic organization at the 3′ end of canine coronavirus (CCV) and feline enteric coronavirus (FECV) was determined by sequence analysis and compared to that of feline infectious peritonitis virus (FIPV) and transmissible gastroenteritis virus (TGEV) of swine. Amplification of cDNA was performed by the polymerase chain reaction (PCR) as described (Kawasaki and Wang, 1989) , after the addition of synthetic oligonucleotide 178, 5''-GATGACACACAGGlTGAG-3'', which is identical to the carboxyl-terminus of the nucleocapsid (N) protein gene of FIPV (nucleotides 1945-l 962; Vennema et a/., 1991) . The nucleotide sequences flanking the ORFs 6a and 6b of FIPV and CCV and ORF 7 of TGEV were aligned to design primers for cDNA synthesis and polymerase chain reaction (PCR) amplification. The recombinant expression products were compared to the proteins produced in CCV-, FECV-, and FIPV-infected cells, which were analyzed similarly (Fig. 6) . abstract: Abstract The genomic organization at the 3′ end of canine coronavirus (CCV) and feline enteric coronavirus (FECV) was determined by sequence analysis and compared to that of feline infectious peritonitis virus (FIPV) and transmissible gastroenteritis virus (TGEV) of swine. Comparison of the latter two has previously revealed an extra open reading frame (ORF) at the 3′ end of the FIPV genome, lacking in TGEV, which is currently designated ORF 6b. Both CCV and FECV possess 6b-related ORFs at the 3′ ends of their genomes. The presence of ORF 6b in three of four viruses in this antigenic cluster strongly suggests that TGEV has lost this ORF by deletion. The CCV ORF 6b is collinear with that of FIPV, but the predicted amino acid sequences are only 58% identical. The FECV ORF 6b contains a large deletion compared to that of FIPV, reducing the collinear part to 60%. The sequence homologies were highest between CCV and TGEV on the one hand and between FECV and FIPV on the other. Previously, we showed that the expression product of the FIPV ORF 6b can be detected in infected cells by immunoprecipitation (Vennema et al., 1992). In the present study we have performed similar experiments with CCV and FECV. In infected cells both viruses produced proteins related to but different from the FIPV 6b protein. url: https://www.sciencedirect.com/science/article/pii/004268229290174N doi: 10.1016/0042-6822(92)90174-n id: cord-291306-g9qmmugg author: Vey, Martin title: Hemagglutinin activation of pathogenic avian influenza viruses of serotype H7 requires the protease recognition motif R-X-K/R-R date: 1992-05-31 words: 2436.0 sentences: 131.0 pages: flesch: 54.0 cache: ./cache/cord-291306-g9qmmugg.txt txt: ./txt/cord-291306-g9qmmugg.txt summary: It has long been known that the hemagglutinins activated by these enzymes have multiple lysine and arginine residues at theircleavage sites, and it has been shown that most of these basic amino acids are critical for cleavage activation (7). Comparison of the published hemagglutinin sequences of the pathogenic avian influenza-A-viruses of serotype H7 reveals a number of conserved amino acids upstream of the cleavage site, notably a series of arginine and lysine residues in positions -1 to -6 and two proline residues in positions -7 or -8 and in position -10 (Table 1) . To determine whether these conserved regions are important for the cleavability of the H7 hemagglutinin, we subjected a cDNA clone of the hemagglutinin of influenza virus AIFPV/Rostock/34 to site-directed mutagenesis at the cleavage site and from the panel of mutants obtained, we have selected two groups. In previous work, pathogenic variants with increased hemagglutinin cleavability could be obtained, when apathogenic avian influenza virus strains were adapted to non-permissive host cells (11, 9, 16) . abstract: Abstract The hemagglutinin of influenza virus A/FPV/Rostock/34 (H7) was altered at its multibasic cleavage site by site-directed mutagenesis and assayed for proteolytic activation after expression in CV-1 cells. The results indicated that the cellular protease responsible for activation recognizes the tetrapeptide motif R-X-K/R-R that must be presented in the correct sequence position. Studies on plaque variants of influenza virus A/fowINictoria/75 (H7N7) showed that alteration of the consensus sequence resulted in a loss of pathogenicity for chickens. url: https://api.elsevier.com/content/article/pii/004268229290775K doi: 10.1016/0042-6822(92)90775-k id: cord-344515-e0g911le author: Voss, Kelsey title: Inhibition of host extracellular signal-regulated kinase (ERK) activation decreases new world alphavirus multiplication in infected cells date: 2014-11-30 words: 9184.0 sentences: 499.0 pages: flesch: 54.0 cache: ./cache/cord-344515-e0g911le.txt txt: ./txt/cord-344515-e0g911le.txt summary: title: Inhibition of host extracellular signal-regulated kinase (ERK) activation decreases new world alphavirus multiplication in infected cells Our previous studies have indicated that host kinases including IKK-β and GSK-3β were modulated in VEEV-infected cells and that inhibition of these kinases with small molecule inhibitors resulted in decreased viral multiplication (Amaya et al., 2014; Kehn-Hall et al., 2012) . Cumulatively, the data included in Fig. 1 suggest that infection of U87MGs with the attenuated TC-83 strain of VEEV results in an activation of the ERK signaling cascade and phosphorylation of ERK1/2 at early time points after infection. Therefore, to confirm that Ag-126 treatment indeed resulted in decreased phosphorylation of ERK1/2 in U87MG cells, we investigated the intracellular p-ERK1/2 localization during VEEV infection in the presence or absence of Ag-126 at different time points using confocal microscopy as described previously (Amaya et al., 2014) . abstract: Abstract New World alphaviruses belonging to the family Togaviridae are classified as emerging infectious agents and Category B select agents. Our study is focused on the role of the host extracellular signal-regulated kinase (ERK) in the infectious process of New World alphaviruses. Infection of human cells by Venezuelan equine encephalitis virus (VEEV) results in the activation of the ERK-signaling cascade. Inhibition of ERK1/2 by the small molecule inhibitor Ag-126 results in inhibition of viral multiplication. Ag-126-mediated inhibition of VEEV was due to potential effects on early and late stages of the infectious process. While expression of viral proteins was down-regulated in Ag-126 treated cells, we did not observe any influence of Ag-126 on the nuclear distribution of capsid. Finally, Ag-126 exerted a broad-spectrum inhibitory effect on New World alphavirus multiplication, thus indicating that the host kinase, ERK, is a broad-spectrum candidate for development of novel therapeutics against New World alphaviruses. url: https://doi.org/10.1016/j.virol.2014.09.005 doi: 10.1016/j.virol.2014.09.005 id: cord-264359-m9j3pcj1 author: Vrijsen, R. title: Resolution of the major poliovirus capsid polypeptides into doublets date: 1978-05-15 words: 3862.0 sentences: 223.0 pages: flesch: 57.0 cache: ./cache/cord-264359-m9j3pcj1.txt txt: ./txt/cord-264359-m9j3pcj1.txt summary: The VPl-VP3 group of poliovirion polypeptides can be resolved into multiple components by normal polyacrylamide gel electrophoresis (PAGE) in the presence of sodium dodecyl sulfate (SDS) (Vanden Berghe and Boeye, 1972) ; however, resolution into six components is achieved more easily and reproducibly in the presence of a pH gradient. In summary, fine resolution of the poliovirus capsid polypeptides was achieved by pH gradient electrophoresis and the results were independent of (i) the virus purification or (ii) protein extraction procedures, (iii) the state of maturation (procapsid or mature virion), and (iv) the serotype (type 1 or 2). DISCUSSION The improved resolution of poliovirus capsid polypeptides by pH gradient electrophoresis reported by Vrijsen and Boeye (1978) was confirmed and shown to be independent of the serotype and of the methods used for virus purification and protein extraction. abstract: Abstract Using the pH gradient electrophoretic technique of Vrijsen and Boeyé, the coat protein of poliovirus types 1 and 2 was resolved into six components, Cl to C6, instead of the classical VP1-2-3 (the much smaller polypeptide VP4 was excluded from this study). The multiple components ran true upon reelectrophoresis, and there were no technical artifacts. Their resolution did not depend on a particular method for the preparation or disruption of the virion. The C1–C6 components of pH gradient electrophoresis and the classical VP1–VP3 polypeptides were examined with regard to (i) their migration in normal and pH gradient reelectrophoresis and (ii) their kinetics of leucine incorporation in emetine-stopped pulses. It is concluded that C1 and C2 were both derived from VPl, C3 and C4 from VP2, and C5 and C6 from VP3. url: https://www.ncbi.nlm.nih.gov/pubmed/27002/ doi: 10.1016/0042-6822(78)90093-4 id: cord-301755-fxfsr9bj author: Wang, F.-I. title: Sequence analysis of the spike protein gene of murine coronavirus variants: Study of genetic sites affecting neuropathogenicity date: 1992-02-29 words: 5594.0 sentences: 290.0 pages: flesch: 54.0 cache: ./cache/cord-301755-fxfsr9bj.txt txt: ./txt/cord-301755-fxfsr9bj.txt summary: authors: Wang, F.-I.; Fleming, John O.; Lai, Michael M.C. title: Sequence analysis of the spike protein gene of murine coronavirus variants: Study of genetic sites affecting neuropathogenicity To understand the molecular basis of MHV neuropathogenesis, we studied the spike protein gene sequences of several neutralization-resistant variants of the JHM strain of MHV, which were selected with monoclonal antibodies (MAbs) specific for the S protein. We found that variant 2.2-V-1, which was selected with MAb J.2.2 and primarily caused demyelination, had a single point mutation at nucleotide (NT) 3340, as compared to the parental JHM virus, which predominantly caused encephalitis. The viruses used in this study included several JHM variants which were selected for their resistance to neutralizing MAbs specific for the S protein (Fleming et a/., 1983) . abstract: Abstract Mouse hepatitis virus (MHV), a coronavirus, causes encephalitis and demyelination in susceptible rodents. Previous investigations have shown that the MHV spike (S) protein is a critical determinant of viral tropism and pathogenicity in mice and rats. To understand the molecular basis of MHV neuropathogenesis, we studied the spike protein gene sequences of several neutralization-resistant variants of the JHM strain of MHV, which were selected with monoclonal antibodies (MAbs) specific for the S protein. We found that variant 2.2-V-1, which was selected with MAb J.2.2 and primarily caused demyelination, had a single point mutation at nucleotide (NT) 3340, as compared to the parental JHM virus, which predominantly caused encephalitis. This site was in the S2 subunit of the S protein. In contrast, variant 7.2-V-1, which was selected with MAb J.7.2 and primarily caused encephalitis, had two point mutations at NT 1766 and 1950, which were in the S1 subunit. Finally, the double mutant 2.2/7.2-V-2, which was selected with both MAbs J.2.2 and J.7.2, and was attenuated with respect to both virulence and the ability to cause demyelination, had a deletion spanning from NT 1523 to 1624 in the S1 and a point mutation at NT 3340 in the S2. We conclude that at least two regions of the S protein contribute to neuropathogenicity of MHV. We have also isolated a partial revertant of 2.2-V-1, which was partially resistant to MAb 1.2.2 but retained the same neuropathogenicity as the variant 2.2-V-1. This revenant retained the mutation at NT 3340, but had a second-site mutation at NT 1994, further confirming that NT 3340 contributed to the pathogenic phenotype of MHV. By comparing these results with MHV variants isolated in other laboratories, which had mutations in other sites on the S gene and yet retained the demyelinating ability, we suggest that the ability of JHM viruses to induce demyelination is determined by the interaction of multiple sites on the S gene, rather than the characteristics of a single, unique site. Our study also revealed the possible presence of microheterogeneity of S gene sequence, particularly in the S1 region, in these viruses. The sequence microheterogeneity may also contribute to the differences in their biological properties. url: https://api.elsevier.com/content/article/pii/004268229290041M doi: 10.1016/0042-6822(92)90041-m id: cord-269862-krcu3hfa author: Wang, Shui-Mei title: APOBEC3G cytidine deaminase association with coronavirus nucleocapsid protein date: 2009-05-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We previously reported that replacing HIV-1 nucleocapsid (NC) domain with SARS-CoV nucleocapsid (N) residues 2–213, 215–421, or 234–421 results in efficient virus-like particle (VLP) production at a level comparable to that of wild-type HIV-1. In this study we demonstrate that these chimeras are capable of packaging large amounts of human APOBEC3G (hA3G), and that an HIV-1 Gag chimera containing the carboxyl-terminal half of human coronavirus 229E (HCoV-229E) N as a substitute for NC is capable of directing VLP assembly and efficiently packaging hA3G. When co-expressed with SARS-CoV N and M (membrane) proteins, hA3G was efficiently incorporated into SARS-CoV VLPs. Data from GST pull-down assays suggest that the N sequence involved in N–hA3G interactions is located between residues 86 and 302. Like HIV-1 NC, the SARS-CoV or HCoV-229E N-associated with hA3G depends on the presence of RNA, with the first linker region essential for hA3G packaging into both HIV-1 and SARS-CoV VLPs. The results raise the possibility that hA3G is capable of associating with different species of viral structural proteins through a potentially common, RNA-mediated mechanism. url: https://api.elsevier.com/content/article/pii/S0042682209001834 doi: 10.1016/j.virol.2009.03.010 id: cord-289248-6mx4o0eb author: Wang, Yilong title: Enhancement of safety and immunogenicity of the Chinese Hu191 measles virus vaccine by alteration of the S-adenosylmethionine (SAM) binding site in the large polymerase protein date: 2018-05-01 words: 7018.0 sentences: 388.0 pages: flesch: 59.0 cache: ./cache/cord-289248-6mx4o0eb.txt txt: ./txt/cord-289248-6mx4o0eb.txt summary: These two mutants grew to high titer in Vero cells, were genetically stable, and were significantly more attenuated in vitro and in vivo compared to the parental rMV-Hu191 vaccine strain. We next compared the replication kinetics of the rMV-Hu191 mutants and the parental virus in Vero cells in the time course of 120 h after infection (Fig. 5 ). These data suggest that rMVs carrying mutations in the SAM binding site were more attenuated in Vero cells than the parental MV vaccine strain. In this study, we successfully generated two recombinant measles viruses with amino acid substitutions in the SAM binding site of L protein and examined the effects of these mutations on viral replication, safety, and immunogenicity. We generated two recombinant MV-Hu191 carrying mutations in the SAM binding site, which not only grew to high titer in Vero cells and were genetically stable but also were significantly more attenuated and immunogenic compared to the currently used Chinese MV vaccine strain. abstract: The live-attenuated measles virus (MV) vaccine based on the Hu191 strain has played a significant role in controlling measles in China. However, it has considerable adverse effects that may cause public health burden. We hypothesize that the safety and efficacy of MV vaccine can be improved by altering the S-adeno- sylmethionine (SAM) binding site in the conserved region VI of the large polymerase protein. To test this hypothesis, we established an efficient reverse genetics system for the rMV-Hu191 strain and generated two recombinant MV-Hu191 carrying mutations in the SAM binding site. These two mutants grew to high titer in Vero cells, were genetically stable, and were significantly more attenuated in vitro and in vivo compared to the parental rMV-Hu191 vaccine strain. Importantly, both MV-Hu191 mutants triggered a higher neutralizing antibody than rMV-Hu191 vaccine and provided complete protection against MV challenge. These results demonstrate its potential for an improved MV vaccine candidate. url: https://doi.org/10.1016/j.virol.2018.02.022 doi: 10.1016/j.virol.2018.02.022 id: cord-320590-irybhp4j author: Wang, Zhitao title: Host Src controls gallid alpha herpesvirus 1 intercellular spread in a cellular fatty acid metabolism-dependent manner date: 2019-08-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viral spread is considered a promising target for antiviral therapeutics, but the associated mechanisms remain unclear for gallid alpha herpesvirus 1 (ILTV). We previously identified proto-oncogene tyrosine-protein kinase Src (Src) as a crucial host determinant of ILTV infection. The present study revealed accelerated spread of ILTV upon Src inhibition. This phenomenon was independent of either viral replication or the proliferation of infected cells and could not be compromised by neutralizing antibody. Neither extracellular vesicles nor the direct cytosol-to-cytosol connections between adjacent cells contributed to the enhanced spread of ILTV upon Src inhibition. Further genome-wide transcriptional profile analyses in combination with functional validation identified fatty acid metabolism as an essential molecular event during modulation of the intercellular spread and subsequent cytopathic effect of ILTV by Src. Overall, these data suggest that Src controls the cell-to-cell spread of ILTV in a cellular fatty acid metabolism-dependent manner, which determines the virus's cytopathic effect. url: https://doi.org/10.1016/j.virol.2019.08.011 doi: 10.1016/j.virol.2019.08.011 id: cord-281820-oltqsd6n author: Watanabe, Rie title: Heparan sulfate is a binding molecule but not a receptor for CEACAM1-independent infection of murine coronavirus date: 2007-09-15 words: 3700.0 sentences: 183.0 pages: flesch: 58.0 cache: ./cache/cord-281820-oltqsd6n.txt txt: ./txt/cord-281820-oltqsd6n.txt summary: A highly neurovirulent mouse hepatitis virus (MHV) JHMV strain (wt) with receptor (MHVR)-independent infection activity and its low-virulent mutant srr7 without such activity were found to attach to MHVR-negative, non-permissive BHK cells. To identify the molecule that interacts with JHMV, we focused on heparan sulfate (HS) since it works as a receptor of a mutant MHV-rec1 that infects in an MHVR-independent fashion. To evaluate the infectivity of the attached virus, 50 nM of soMHVR was added to the culture of BHK cells inoculated with wt JHMV and srr7 and those cells were further incubated for 14 h at 37°C. Binding of JHMV to HS on the cell surface HS is the major glycosaminoglycan (GAG) found on most cells and was recently reported as an entry receptor for MHV-BHK, a strain that has an extended host range and infects MHVR-negative cells (de Haan et al., 2005) . abstract: A highly neurovirulent mouse hepatitis virus (MHV) JHMV strain (wt) with receptor (MHVR)-independent infection activity and its low-virulent mutant srr7 without such activity were found to attach to MHVR-negative, non-permissive BHK cells. To identify the molecule that interacts with JHMV, we focused on heparan sulfate (HS) since it works as a receptor of a mutant MHV-rec1 that infects in an MHVR-independent fashion. The present study indicates that HS interacts with both wt JHMV and srr7 but it does not function as an entry receptor as it apparently does for MHV-rec1. Furthermore, HS failed to serve as an entry receptor in the MHVR-independent infection of wt JHMV, indicating that HS is not a host factor that wt JHMV utilizes in an MHVR-independent infection. url: https://www.ncbi.nlm.nih.gov/pubmed/17692355/ doi: 10.1016/j.virol.2007.06.034 id: cord-275664-qbafkxtr author: Wei, Li title: Porcine circovirus type 2 replication is impaired by inhibition of the extracellular signal-regulated kinase (ERK) signaling pathway date: 2009-03-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Postweaning multisystemic wasting syndrome, which is primarily caused by porcine circovirus type 2 (PCV2), is an emerging and important swine disease. We have recently shown that PCV2 induces nuclear factor kappa B activation and its activation is required for active replication, but the other cellular factors involved in PCV2 replication are not well defined. The extracellular signal-regulated kinase (ERK) which served as an important component of cellular signal transduction pathways has been shown to regulate many viral infections. In this report, we show that PCV2 activates ERK1/2 in PCV2-infected PK15 cells dependent on viral replication. The PCV2-induced ERK1/2 leads to phosphorylation of the ternary complex factor Elk-1, which kinetically paralleled ERK1/2 activation. Inhibition of ERK activation with U0126, a specific MEK1/2 inhibitor, significantly reduced viral progeny release. Investigations into the mechanism of ERK1/2 regulation revealed that inhibition of ERK activation leads to decreased viral transcription and lower virus protein expression. These data indicate that the ERK signaling pathway is involved in PCV2 infection and beneficial to PCV2 replication in the cultured cells. url: https://www.sciencedirect.com/science/article/pii/S0042682209000348 doi: 10.1016/j.virol.2009.01.010 id: cord-337976-c2auspti author: Weiss, Susan R. title: Coronaviruses SD and SK share extensive nucleotide homology with murine coronavirus MHV-A59, more than that shared between human and murine coronaviruses date: 1983-04-30 words: 3818.0 sentences: 267.0 pages: flesch: 61.0 cache: ./cache/cord-337976-c2auspti.txt txt: ./txt/cord-337976-c2auspti.txt summary: A cDNA probe representing the genome of mouse hepatitis virus (MHV) strain A59 (MHV-A59) was used to measure nucleotide sequence homologies among murine and human coronaviruses and the SD and SK coronaviruses isolated by Burks et al. Since SD and SK were isolated by inoculation of multiple sclerosis (MS) central nervous system (CNS) tissue into mice or cultured mouse cells, it is important to determine their relationships to other murine and human coronavirus isolates. Some strains of HCV such as 0C43, are antigenically related to murine coronaviruses such as MHV strain JHM (McIntosh, 1974; Gerdes et al., 1981a, b) and may be grown in the brains of suckling mice (McIntosh et al., 1967) . We have further compared murine and human coronaviruses and SD and SK by using molecular hybridization of virus-specific RNA with cDNA probes. RNA extracted either from brain homogenates of OC43-infected suckling mice or from HRT cells infected with OC43 shows homology with A59 cDNA when assayed by blot hybridization. abstract: A cDNA probe representing the genome of mouse hepatitis virus (MHV) strain A59 (MHV-A59) was used to measure nucleotide sequence homologies among murine and human coronaviruses and the SD and SK coronaviruses isolated by Burks et al. Since SD and SK were isolated by inoculation of multiple sclerosis (MS) central nervous system (CNS) tissue into mice or cultured mouse cells, it is important to determine their relationships to other murine and human coronavirus isolates. Our results indicate that SD and SK share almost complete nucleotide homology (approximately 90%) with MHV-A59 and generate subgenomic RNAs of the same sizes as MHV-A59. The human coronavirus (HCV) strains tested show less homology with MHV-A59. The immunologically unrelated HCV-229 E shows no nucleotide homology with MHV-A59. The immunologically crossreactive HCV-OC43 shows nucleotide homology with MHV-A59 by blot hybridization but not when hybridized in solution and assayed by S1 nuclease digestion. url: https://api.elsevier.com/content/article/pii/S0042682283800221 doi: 10.1016/s0042-6822(83)80022-1 id: cord-272871-gu9ptt9y author: White, K.Andrew title: Defective RNAs of clover yellow mosaic virus encode nonstructural/coat protein fusion products date: 1991-08-31 words: 4609.0 sentences: 241.0 pages: flesch: 60.0 cache: ./cache/cord-272871-gu9ptt9y.txt txt: ./txt/cord-272871-gu9ptt9y.txt summary: Abstract A small group of 1.2-kb RNAs present on polyribosoes from clover yellow mosaic virus (CYMV)-infected tissue contains sequences from the genomic RNA (gRNA) of CYMV and is encapsidated by CYMV coat protein. Figure 2 shows Northern blots of polyribosomal RNA extracted from CYMV-infected tissue containing the 1.2-kb RNAs. The 7.0-kb gRNA is identified by all probes (Fig. 2 , lanes a, c, e, g, i, and k; probes 1 to 6), but the 1 .O-kb sgRNA encoding coat protein hybridizes only to probes corresponding to the 3'' region of the gRNA (Fig. 2 , lanes i and k; probes 5 and 6). The majority of the sequence of the prototype 1.2-kb RNA (Fig. 4) and of additional 1.2-kb RNAs is identical WHITE, BANCROFT, AND MACKIE with the corresponding region of CYMV gRNA reported by Sit et al. abstract: Abstract A small group of 1.2-kb RNAs present on polyribosoes from clover yellow mosaic virus (CYMV)-infected tissue contains sequences from the genomic RNA (gRNA) of CYMV and is encapsidated by CYMV coat protein. Some features of these RNAs suggest that they are similar to defective interfering (DI) RNAs, and would be the first to be reported for the potexvirus group. The prototype 1.2-kb RNA is 1172 nucleotides in length excluding a probable poly(A) tail and is composed of two noncontiguous regions corresponding to 757 nucleotides of the 5′ and 415 nucleotides of the 3′ terminal of CYMV's gRNA. The sequence of the prototype 1.2-kb RNA reveals that the two terminal gRNA regions present in this RNA encode a single open reading frame (ORF) joining the N-terminus of the 191-kDa nonstructural product and the C-terminus of the coat protein to form a 35-kDa 191-kDa/coat protein fusion product. The coding properties of this prototype RNA have been confirmed by translation in vitro of native and synthetic transcripts of the 1.2-kb RNAs, both of which direct the synthesis of the anticipated 35-kDa product which reacts with anti-CYMV antiserum. Three additional 1.2-kb RNA species, each of which contains a unique junction site, have been characterized. In all cases, a fusion ORF encoding a 191-kDa/coat protein fusion product is encoded on the RNA. The presence of a fusion ORF in all members of the 1.2-kb RNA species analyzed suggests that maintenance of this ORF may be important for the survival of this class of RNA within the plant. This coding strategy represents a novel property of plant virus defective RNAs. url: https://www.sciencedirect.com/science/article/pii/004268229190977J doi: 10.1016/0042-6822(91)90977-j id: cord-258691-cd83w9o6 author: Whitman, Lucia title: IFN-γ-mediated suppression of coronavirus replication in glial-committed progenitor cells date: 2009-02-01 words: 4938.0 sentences: 257.0 pages: flesch: 40.0 cache: ./cache/cord-258691-cd83w9o6.txt txt: ./txt/cord-258691-cd83w9o6.txt summary: IFN-γ-mediated control of JHMV replication is dampened in glial cultures derived from the neural progenitor cells of type I receptor knock-out mice. These data indicate that JHMV is capable of infecting glial cells generated from neural progenitor cells and that IFN-γ-mediated control of viral replication is dependent, in part, on type I IFN secretion. In the present study, we demonstrate that primary cultures of glia derived from neural progenitor cells are susceptible to JHMV infection and support viral replication. Therefore, these findings provide, to our knowledge, the first demonstration that glia-committed cells derived from neural precursors are susceptible to JHMV infection as well as identify a potential mechanism responsible for controlling viral replication. These findings indicate that differentiated cells derived from neural progenitors are susceptible to JHMV infection and are capable of supporting replicating virus which results in extensive cytopathology. abstract: The neurotropic JHM strain of mouse hepatitis virus (JHMV) replicates primarily within glial cells following intracranial inoculation of susceptible mice, with relative sparing of neurons. This study demonstrates that glial cells derived from neural progenitor cells are susceptible to JHMV infection and that treatment of infected cells with IFN-γ inhibits viral replication in a dose-dependent manner. Although type I IFN production is muted in JHMV-infected glial cultures, IFN-β is produced following IFN-γ-treatment of JHMV-infected cells. Also, direct treatment of infected glial cultures with recombinant mouse IFN-α or IFN-β inhibits viral replication. IFN-γ-mediated control of JHMV replication is dampened in glial cultures derived from the neural progenitor cells of type I receptor knock-out mice. These data indicate that JHMV is capable of infecting glial cells generated from neural progenitor cells and that IFN-γ-mediated control of viral replication is dependent, in part, on type I IFN secretion. url: https://api.elsevier.com/content/article/pii/S0042682208006971 doi: 10.1016/j.virol.2008.10.036 id: cord-272045-v1wt5t7m author: Wilson, Lauren title: Hexamethylene amiloride blocks E protein ion channels and inhibits coronavirus replication date: 2006-09-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: All coronaviruses encode a small hydrophobic envelope (E) protein, which mediates viral assembly and morphogenesis by an unknown mechanism. We have previously shown that the E protein from Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) forms cation-selective ion channels in planar lipid bilayers (Wilson, L., McKinlay, C., Gage, P., Ewart, G., 2004. SARS coronavirus E protein forms cation-selective ion channels. Virology 330(1), 322–331). We now report that three other E proteins also form cation-selective ion channels. These E proteins were from coronaviruses representative of taxonomic groups 1–3: human coronavirus 229E (HCoV-229E), mouse hepatitis virus (MHV), and infectious bronchitis virus (IBV), respectively. It appears, therefore, that coronavirus E proteins in general, belong to the virus ion channels family. Hexamethylene amiloride (HMA) – an inhibitor of the HIV-1 Vpu virus ion channel – inhibited the HCoV-229E and MHV E protein ion channel conductance in bilayers and also inhibited replication of the parent coronaviruses in cultured cells, as determined by plaque assay. Conversely, HMA had no antiviral effect on a recombinant MHV with the entire coding region of E protein deleted (MHVΔE). Taken together, the data provide evidence of a link between inhibition of E protein ion channel activity and the antiviral activity of HMA. url: https://www.sciencedirect.com/science/article/pii/S004268220600359X doi: 10.1016/j.virol.2006.05.028 id: cord-270929-utn21ce1 author: Wise, Annabel G. title: Molecular characterization of a novel coronavirus associated with epizootic catarrhal enteritis (ECE) in ferrets date: 2006-05-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A novel coronavirus, designated as ferret enteric coronavirus (FECV), was identified in feces of domestic ferrets clinically diagnosed with epizootic catarrhal enteritis (ECE). Initially, partial sequences of the polymerase, spike, membrane protein, and nucleocapsid genes were generated using coronavirus consensus PCR assays. Subsequently, the complete sequences of the nucleocapsid gene and the last two open reading frames at the 3′ terminus of the FECV genome were obtained. Phylogenetic analyses based on predicted partial amino acid sequences of the polymerase, spike, and membrane proteins, and full sequence of the nucleocapsid protein showed that FECV is genetically most closely related to group 1 coronaviruses. FECV is more similar to feline coronavirus, porcine transmissible gastroenteritis virus, and canine coronavirus than to porcine epidemic diarrhea virus and human coronavirus 229E. Molecular data presented in this study provide the first genetic evidence for a new coronavirus associated with clinical cases of ECE. url: https://www.ncbi.nlm.nih.gov/pubmed/16499943/ doi: 10.1016/j.virol.2006.01.031 id: cord-282947-3hgku2e4 author: Wong, Hui Hui title: Accessory proteins 8b and 8ab of severe acute respiratory syndrome coronavirus suppress the interferon signaling pathway by mediating ubiquitin-dependent rapid degradation of interferon regulatory factor 3 date: 2017-12-30 words: 8714.0 sentences: 423.0 pages: flesch: 46.0 cache: ./cache/cord-282947-3hgku2e4.txt txt: ./txt/cord-282947-3hgku2e4.txt summary: title: Accessory proteins 8b and 8ab of severe acute respiratory syndrome coronavirus suppress the interferon signaling pathway by mediating ubiquitin-dependent rapid degradation of interferon regulatory factor 3 Through the construction of recombinant IBV expressing proteins 8a, 8b and 8ab encoded by SARS-CoV ORF8, we demonstrate that expression of 8b and 8ab enables the corresponding recombinant viruses to partially overcome the inhibitory actions of IFN activation to achieve higher replication efficiencies in cells. Compared to wild type and rIBV8a/b, however, rIBV8b and rIBV8ab were observed to replicate significantly better and express higher levels of N protein in cells stimulated by poly (I:C) (Fig. 2a) . In view of the central role of IRF3 in regulating IFN activation during virus infection, 8b and 8ab with Flag epitope-tagged to their Ntermini were co-expressed with Myc-tagged IRF3 (Fig. 3a) in Cos-7 cells using the vaccinia/T7 expression system (Anderson et al., 1996; Lim and Liu, 2001) for co-immunoprecipitation assays to determine if there is any physical interaction between the proteins. abstract: Severe acute respiratory syndrome coronavirus (SARS-CoV) is an inefficient inducer of interferon (IFN) response. It expresses various proteins that effectively circumvent IFN production at different levels via distinct mechanisms. Through the construction of recombinant IBV expressing proteins 8a, 8b and 8ab encoded by SARS-CoV ORF8, we demonstrate that expression of 8b and 8ab enables the corresponding recombinant viruses to partially overcome the inhibitory actions of IFN activation to achieve higher replication efficiencies in cells. We also found that proteins 8b and 8ab could physically interact with IRF3. Overexpression of 8b and 8ab resulted in the reduction of poly (I:C)-induced IRF3 dimerization and inhibition of the IFN-β signaling pathway. This counteracting effect was partially mediated by protein 8b/8ab-induced degradation of IRF3 in a ubiquitin-proteasome-dependent manner. Taken together, we propose that SARS-CoV may exploit the unique functions of proteins 8b and 8ab as novel mechanisms to overcome the effect of IFN response during virus infection. url: https://api.elsevier.com/content/article/pii/S0042682217304427 doi: 10.1016/j.virol.2017.12.028 id: cord-331807-ooym5eh3 author: Wu, Tao title: A reverse-transcription recombinase-aided amplification assay for the rapid detection of N gene of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) date: 2020-07-29 words: 556.0 sentences: 48.0 pages: flesch: 51.0 cache: ./cache/cord-331807-ooym5eh3.txt txt: ./txt/cord-331807-ooym5eh3.txt summary: title: A reverse-transcription recombinase-aided amplification assay for the rapid detection of N gene of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) The current outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China firstly. Here, we established a real-time reverse-transcription recombinase-aided amplification assay (RT-RAA) to detect SARS-CoV-2 rapidly. These results indicated that this real-time RT-RAA assay may be a valuable tool for detecting SARS-CoV-2. The minimum detection limit of real-time RAA assay was 10 copies / reaction. Use of a rapid 207 reverse-transcription recombinase aided amplification assay for respiratory syncytial virus detection Detection of 2019 novel coronavirus (2019-nCoV) by real-time 214 RT-PCR A rapid 235 and sensitive recombinase aided amplification assay to detect hepatitis B virus without DNA 236 extraction Development of a reverse 248 transcription recombinase-aided amplification assay for the detection of coxsackievirus A10 and 249 coxsackievirus A6 RNA abstract: The current outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China firstly. A rapid, highly sensitive, specific, and simple operational method was needed for the detection of SARS-CoV-2. Here, we established a real-time reverse-transcription recombinase-aided amplification assay (RT-RAA) to detect SARS-CoV-2 rapidly. The primers and probe were designed based on the nucleocapsid protein gene (N gene) sequence of SARS-CoV-2. The detection limit was 10 copies per reaction in this assay, which could be conducted within 15 min at a constant temperature (39 °C), without any cross-reactions with other respiratory tract pathogens, such as other coronaviruses. Furthermore, compared with commercial real-time RT-PCR assay, it showed a kappa value of 0.959 (p < 0.001) from 150 clinical specimens. These results indicated that this real-time RT-RAA assay may be a valuable tool for detecting SARS-CoV-2. url: https://api.elsevier.com/content/article/pii/S0042682220301331 doi: 10.1016/j.virol.2020.07.006 id: cord-270487-m770a1rl author: Wurch, T. title: The cauliflower mosaic virus reverse transcriptase is not produced by the mechanism of ribosomal frameshifting in Saccharomyces cerevisiae date: 1991-02-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract The capsid protein and the reverse transcriptase of cauliflower mosaic virus (CaMV) are encoded by two genes (ORF IV and ORF V) that lie in different translation reading frames. A comparison can be drawn between the synthesis of both CaMV proteins and the fusion protein in a yeast retrotransposon, Ty, resulting from a +1 frameshifting event which fuses two out-of-phase ORFs encoding the structural protein and the reverse transcriptase of Ty. For this reason, we constructed a yeast expression vector containing CaMV ORF VII fused to CaMV ORF III by a fragment of 452 bp including the overlapping region of ORF IV and ORF V, ORF VII and ORF III being used as reporter genes. We characterized two proteins (22 and 50 kDa) synthesized from this plasmid in the yeast expression system. We demonstrated that the 50-kDa polypeptide is not synthesized from a +1 frameshifting event but is probably a dimeric form of the 22-kDa protein. From this result we conclude that the CaMV reverse transcriptase is not produced by a mechanism of ribosomal frameshifting. url: https://api.elsevier.com/content/article/pii/004268229190103I doi: 10.1016/0042-6822(91)90103-i id: cord-328046-5us4se5o author: Xu, H. Y. title: Further Identification and Characterization of Novel Intermediate and Mature Cleavage Products Released from the ORF 1b Region of the Avian Coronavirus Infectious Bronchitis Virus 1a/1b Polyprotein date: 2001-09-30 words: 5643.0 sentences: 279.0 pages: flesch: 51.0 cache: ./cache/cord-328046-5us4se5o.txt txt: ./txt/cord-328046-5us4se5o.txt summary: In cells infected with avian coronavirus infectious bronchitis virus (IBV), three proteins of 100, 39, and 35 kDa, respectively, were previously identified as mature cleavage products released from the 1b region of the 1a/1b polyprotein by the 3C-like proteinase. Immunofluorescent staining of IBV-infected cells and cells expressing individual cleavage products showed that the 100-, 68-, and 58-kDa proteins were associated with the membranes of the endoplasmic reticulum, and the 39and 35-kDa proteins displayed diffuse distribution patterns. Taken together with the Q 3928 -S 2929 dipeptide bond (encoded by nucleotides 12310-12315) identified as the N-terminal cleavage site of the 100-kDa protein, cleavage at these positions would result in the release of five mature products with molecular masses of approximately 100, 68, 58, 39, and 35 kDa. Among them, the 100-, 39-, and 35-kDa proteins were specifically identified in IBV-infected cells (Liu et al., 1994 . abstract: Abstract The coronavirus 3C-like proteinase is one of the viral proteinases responsible for processing of the 1a and 1a/1b polyproteins to multiple mature products. In cells infected with avian coronavirus infectious bronchitis virus (IBV), three proteins of 100, 39, and 35 kDa, respectively, were previously identified as mature cleavage products released from the 1b region of the 1a/1b polyprotein by the 3C-like proteinase. In this report, we show the identification of two more cleavage products of 68 and 58 kDa released from the same region of the polyprotein. In addition, two stable intermediate cleavage products with molecular masses of 160 and 132 kDa, respectively, were identified in IBV-infected cells. The 160-kDa protein was shown to be an intermediate cleavage product covering the 100- and 68-kDa proteins, and the 132-kDa protein to be an intermediate cleavage product covering the 58-, 39-, and 35-kDa proteins. Immunofluorescent staining of IBV-infected cells and cells expressing individual cleavage products showed that the 100-, 68-, and 58-kDa proteins were associated with the membranes of the endoplasmic reticulum, and the 39- and 35-kDa proteins displayed diffuse distribution patterns. url: https://api.elsevier.com/content/article/pii/S0042682201910980 doi: 10.1006/viro.2001.1098 id: cord-286121-ltaxmp3u author: Xu, Ke title: Severe acute respiratory syndrome coronavirus accessory protein 9b is a virion-associated protein date: 2009-06-05 words: 5289.0 sentences: 287.0 pages: flesch: 56.0 cache: ./cache/cord-286121-ltaxmp3u.txt txt: ./txt/cord-286121-ltaxmp3u.txt summary: In this study, we demonstrate that 9b protein is translated from bicistronic mRNA9 via leaky ribosome scanning and it is incorporated into both virus-like particles (VLPs) and purified SARS-CoV virions. The expression of 9b protein in SARS-CoV infected cells was confirmed by Western blot analysis with anti-9b monoclonal antibody. To confirm that 9b protein can be translated from an mRNA corresponding to the SARS-CoV subgenomic RNA9, the sequence encoding ORFN which contains ORF9b was cloned into the eukaryotic expression vector pCAGGS and transfected into 293T cells. As 9b protein is present in virions, it is advantageous to characterize the role of other SARS-CoV structural proteins in incorporation of 9b protein into VLPs. Cultures of 293T cells were transfected with the indicated plasmids, and pCAGGS vector was added to adjust the total amount of DNA to equivalent levels. 9b protein was immunoprecipitated by anti-9b polyclonal antibody from SARS infected FRhK-4 cell lysates in RIPA buffer, the mass spectrometry analysis of the corresponding gel slices detected a specific peptide that represents 9b protein. abstract: Eight accessory proteins have been identified in severe acute respiratory syndrome-associated coronavirus (SARS-CoV). They are believed to play roles in the viral life cycle and may contribute to the pathogenesis and virulence. ORF9b as one of these accessory proteins is located in subgenomic mRNA9 and encodes a 98 amino acid protein. However, whether 9b protein is a structural component of SARS-CoV particles remains unknown. In this study, we demonstrate that 9b protein is translated from bicistronic mRNA9 via leaky ribosome scanning and it is incorporated into both virus-like particles (VLPs) and purified SARS-CoV virions. Further analysis shows that sufficient incorporation of 9b protein into VLPs is dependent upon the co-expression of E and M proteins, but not upon the presence of either S or N protein. Our data indicate that 9b protein of SARS-CoV is another virion-associated accessory protein. This finding will lead to a better understanding of the properties of the SARS-CoV 9b protein. url: https://doi.org/10.1016/j.virol.2009.03.032 doi: 10.1016/j.virol.2009.03.032 id: cord-273487-nfgjz6f9 author: Xu, Zaikun title: The helicase activity of DDX56 is required for its role in assembly of infectious West Nile virus particles date: 2012-11-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Although flaviviruses encode their own helicases, evidence suggests that cellular helicases are also required for replication and/or assembly of these viruses. By and large, the mechanisms of action for viral and cellular helicases are not known. Moreover, in some cases, enzymatic activity is not even required for their roles in virus biology. Recently, we showed that expression of the host nucleolar helicase DDX56 is important for infectivity of West Nile virus (WNV) particles. In the present study, we demonstrate that the helicase activity of this enzyme is essential for its role in assembly of infectious WNV virions. Over-expression of the capsid-binding region of DDX56 also reduces infectivity of WNV suggesting that interaction of DDX56 and capsid protein is an important step in the virion assembly pathway. To our knowledge, this is the first study showing that enzymatic activity of a cellular helicase is critical for infectivity of flaviviruses. url: https://api.elsevier.com/content/article/pii/S0042682212003923 doi: 10.1016/j.virol.2012.08.011 id: cord-283309-ovx5fzsg author: Yang, Yong-Le title: Characterization of a novel bat-HKU2-like swine enteric alphacoronavirus (SeACoV) infection in cultured cells and development of a SeACoV infectious clone date: 2019-08-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Swine enteric alphacoronavirus (SeACoV), also known as swine acute diarrhea syndrome coronavirus (SADS-CoV), belongs to the species Rhinolophus bat coronavirus HKU2. Herein, we report on the primary characterization of SeACoV in vitro. Four antibodies against the SeACoV spike, membrane, nucleocapsid and nonstructural protein 3 capable of reacting with viral antigens in SeACoV-infected Vero cells were generated. We established a DNA-launched SeACoV infectious clone based on the cell adapted passage-10 virus and rescued the recombinant virus with a unique genetic marker in cultured cells. Six subgenomic mRNAs containing the leader-body junction sites, including a bicistronic mRNA encoding the accessory NS7a and NS7b genes, were experimentally identified in SeACoV-infected cells. Cellular ultrastructural changes induced by SeACoV infection were visualized by electron microscopy. The availability of the SeACoV infectious clone and a panel of antibodies against different viral proteins will facilitate further studies on understanding the molecular mechanisms of SeACoV replication and pathogenesis. url: https://www.sciencedirect.com/science/article/pii/S0042682219302193 doi: 10.1016/j.virol.2019.08.006 id: cord-333525-67bbmo4m author: Yao, Qianqian title: Negatively charged residues in the endodomain are critical for specific assembly of spike protein into murine coronavirus date: 2013-07-01 words: 5251.0 sentences: 238.0 pages: flesch: 53.0 cache: ./cache/cord-333525-67bbmo4m.txt txt: ./txt/cord-333525-67bbmo4m.txt summary: In the current study, we analyzed the effects of the Endo charge-rich motif on virion incorporation of MHV S protein through substitutions of the homologous regions from the alphacoronavirus porcine transmissible gastroenteritis virus (TGEV), the betacoronaviruses bovine coronavirus (BCoV) and SARS-CoV, or the gammacoronavirus avian infectious bronchitis virus (IBV). Although the S2 portions of coronavirus S proteins show some degree of conservation, the Tm and Endo domains are highly divergent, with the exception of a conserved cluster of seven hydrophobic residues (WPWYVWL) at the start of Tm. To evaluate the functionality of different C-terminal sequence motifs in the MHV S protein, we constructed two sets of mutants in which the ectodomain of either S protein or HK protein was fused to the Tm and Endo domains from TGEV (an alphacoronavirus), BCoV (a betacoronavirus), SARS-CoV (a betacoronavirus), or IBV (a gammacoronavirus) ( Fig. 2A) . Reverting mutations in TGEV chimeras improved S assembly by eliminating positively charged residues in the endodomain MHV S protein mutants containing the entire carboxy terminus or just the charge-rich motif of TGEV S (Mut-TGEV and Mut-MMT) produced irregular plaques (Figs. abstract: Coronavirus spike (S) protein assembles into virions via its carboxy-terminus, which is composed of a transmembrane domain and an endodomain. Here, the carboxy-terminal charge-rich motif in the endodomain was verified to be critical for the specificity of S assembly into mouse hepatitis virus (MHV). Recombinant MHVs exhibited a range of abilities to accommodate the homologous S endodomains from the betacoronaviruses bovine coronavirus and human SARS-associated coronavirus, the alphacoronavirus porcine transmissible gastroenteritis virus (TGEV), and the gammacoronavirus avian infectious bronchitis virus respectively. Interestingly, in TGEV endodomain chimeras the reverting mutations resulted in stronger S incorporation into virions, and a net gain of negatively charged residues in the charge-rich motif accounted for the improvement. Additionally, MHV S assembly could also be rescued by the acidic carboxy-terminal domain of the nucleocapsid protein. These results indicate an important role for negatively charged endodomain residues in the incorporation of MHV S protein into assembled virions. url: https://api.elsevier.com/content/article/pii/S0042682213001955 doi: 10.1016/j.virol.2013.04.001 id: cord-310218-fky0cm5e author: Yoo, Dongwan title: The S2 subunit of the spike glycoprotein of bovine coronavirus mediates membrane fusion in insect cells date: 1991-01-31 words: 2384.0 sentences: 124.0 pages: flesch: 50.0 cache: ./cache/cord-310218-fky0cm5e.txt txt: ./txt/cord-310218-fky0cm5e.txt summary: Abstract The hemagglutinin/esterase (HE), spike precursor (S) and the S1 and S2 subunits of the spike precursor protein of bovine coronavirus were expressed in Spodoptera frugiperda (Sf9) cells, and the cell-fusing activity of each recombinant glycoprotein was examined. The hemagglutinin/esterase (HE), spike precursor (S) and the Sl and S2 subunits of the spike precursor protein of bovine coronavirus were expressed in Spodopfera frugperda (Sf9) cells, and the cell-fusing activity of each recombinant glycoprotein was examined. Thus, in order to identify the viral membrane glycoprotein which induces cell fusion by BCV, we expressed the HE, the S, and the Sl and S2 subunits of the S glycoprotein using recombinant baculoviruses, and examined the cell-fusing activity of each recombinant polypeptide. Therefore, it is clear that proteolytic cleavage is required to induce the fusion activity of both the recombinant S polypeptide in insect cells and the authentic S polypeptide produced in BCV-infected cells (14) . abstract: Abstract The hemagglutinin/esterase (HE), spike precursor (S) and the S1 and S2 subunits of the spike precursor protein of bovine coronavirus were expressed in Spodoptera frugiperda (Sf9) cells, and the cell-fusing activity of each recombinant glycoprotein was examined. Extensive syncytia formation was observed in cells infected with the S2 recombinant but not with the HE or S1 recombinant baculoviruses. Fusion of Sf9 cells expressing the intact S protein precursor was evident after trypsin treatment. These results demonstrate that proteolytic cleavage of the S spike precursor is required for fusion induction and that the fusion is mediated by the S2 subunit. These observations may reflect the biological role of the S2 subunit in fusion-penetration during bovine coronavirus infection. url: https://www.sciencedirect.com/science/article/pii/004268229190045D doi: 10.1016/0042-6822(91)90045-d id: cord-309015-t5v2sjus author: York, Joanne title: Genetic analysis of heptad-repeat regions in the G2 fusion subunit of the Junín arenavirus envelope glycoprotein date: 2005-12-20 words: 5071.0 sentences: 240.0 pages: flesch: 46.0 cache: ./cache/cord-309015-t5v2sjus.txt txt: ./txt/cord-309015-t5v2sjus.txt summary: The G2 fusion subunit of the Junín virus envelope glycoprotein GP-C contains two hydrophobic heptad-repeat regions that are postulated to form a six-helix bundle structure required for the membrane fusion activity of Class I viral fusion proteins. The mature envelope glycoprotein complex of the arenavirus consists of three noncovalently associated subunits derived from the GP-C precursor by proteolytic cleavage events: a stable myristoylated 58 amino-acid signal peptide (SSP), the receptor-binding G1 subunit and the transmembrane G2 fusion protein (Buchmeier, 2002; Eichler et al., 2003; York et al., 2004) . The molecular basis for envelope glycoprotein-mediated membrane fusion in the arenaviruses is largely unknown, however, sequence analysis of the G2 ectodomain of Lassa virus and lymphocytic choriomeningitis virus (LCMV) has revealed two heptad-repeat regions that can be represented to form amphipathic helices (Gallaher et al., 2001) . abstract: The G2 fusion subunit of the Junín virus envelope glycoprotein GP-C contains two hydrophobic heptad-repeat regions that are postulated to form a six-helix bundle structure required for the membrane fusion activity of Class I viral fusion proteins. We have investigated the role of these heptad-repeat regions and, specifically, the importance of the putative interhelical a and d position sidechains by using alanine-scanning mutagenesis. All the mutant glycoproteins were expressed and transported to the cell surface. Proteolytic maturation at the subtilisin kexin isozyme-1/site-1-protease (SKI-1/S1P) cleavage site was observed in all but two of the mutants. Among the adequately cleaved mutant glycoproteins, four positions in the N-terminal region (I333, L336, L347 and L350) and two positions in the C-terminal region (R392 and W395) were shown to be important determinants of cell–cell fusion. Taken together, our results indicate that α-helical coiled-coil structures are likely critical in promoting arenavirus membrane fusion. These findings support the inclusion of the arenavirus GP-C among the Class I viral fusion proteins and suggest pharmacologic and immunologic strategies for targeting arenavirus infection and hemorrhagic fever. url: https://api.elsevier.com/content/article/pii/S0042682205005209 doi: 10.1016/j.virol.2005.08.030 id: cord-329625-hx2rsi91 author: You, Jae-Hwan title: A model for the dynamic nuclear/nucleolar/cytoplasmic trafficking of the porcine reproductive and respiratory syndrome virus (PRRSV) nucleocapsid protein based on live cell imaging date: 2008-08-15 words: 5645.0 sentences: 271.0 pages: flesch: 46.0 cache: ./cache/cord-329625-hx2rsi91.txt txt: ./txt/cord-329625-hx2rsi91.txt summary: title: A model for the dynamic nuclear/nucleolar/cytoplasmic trafficking of the porcine reproductive and respiratory syndrome virus (PRRSV) nucleocapsid protein based on live cell imaging Porcine reproductive and respiratory syndrome virus (PRRSV), an arterivirus, in common with many other positive strand RNA viruses, encodes a nucleocapsid (N) protein which can localise not only to the cytoplasm but also to the nucleolus in virus-infected cells and cells over-expressing N protein. To investigate whether the trafficking of N protein between the cytoplasm and the nucleus/nucleolus was associated with microtubules or energy dependent, the mobility of EGFP-PRRSV-N protein was compared in 3D4/31 cells incubated at 37°C in the presence and absence of nocodazole (60ng/ml nocodazole (Sigma) for 16h), a microtubule inhibitor, or incubated at 10°C. In approximately 10% of cells expressing EGFP-PRRSV-N protein fluorescence was observed in the cytoplasm, but only if imaging was adjusted so that the fluorescent signal in the nucleus/nucleolus was above the linear range (for example Fig. 8C, lower panels) . abstract: Porcine reproductive and respiratory syndrome virus (PRRSV), an arterivirus, in common with many other positive strand RNA viruses, encodes a nucleocapsid (N) protein which can localise not only to the cytoplasm but also to the nucleolus in virus-infected cells and cells over-expressing N protein. The dynamic trafficking of positive strand RNA virus nucleocapsid proteins and PRRSV N protein in particular between the cytoplasm and nucleolus is unknown. In this study live imaging of permissive and non-permissive cell lines, in conjunction with photo-bleaching (FRAP and FLIP), was used to investigate the trafficking of fluorescent labeled (EGFP) PRRSV-N protein. The data indicated that EGFP-PRRSV-N protein was not permanently sequestered to the nucleolus and had equivalent mobility to cellular nucleolar proteins. Further the nuclear import of N protein appeared to occur faster than nuclear export, which may account for the observed relative distribution of N protein between the cytoplasm and the nucleolus. url: https://www.ncbi.nlm.nih.gov/pubmed/18550142/ doi: 10.1016/j.virol.2008.04.037 id: cord-296364-7rp60d2m author: Youn, Soonjeon title: In vitro assembled, recombinant infectious bronchitis viruses demonstrate that the 5a open reading frame is not essential for replication date: 2005-02-05 words: 5112.0 sentences: 270.0 pages: flesch: 56.0 cache: ./cache/cord-296364-7rp60d2m.txt txt: ./txt/cord-296364-7rp60d2m.txt summary: Molecular clones of infectious bronchitis virus (IBV), derived from the Vero cell adapted Beaudette strain, were constructed, using an in vitro assembly method. Direct sequencing of RT-PCR products derived from cells infected with the plaque-purified virus, which had lost expression of EGFP, confirmed loss of the EGFP ORF. This strategy was further modified to construct an infectious cDNA clone of MHV with their bno see''mQ technology, in which restriction endonuclease sequences were incorporated into amplicons, such that upon enzyme treatment, the endonuclease sites were eliminated prior to in vitro ligation. In the current study, molecular clones of IBV were generated using the in vitro assembly of cDNA fragments as a template for transcription of full-length genomic RNA. Interestingly, the size of plaques with the 5a deletions, including a revertant that had completely lost the EGFP ORF, was comparable to plaques generated by our standard Beaudette cell-adapted Beaudette virus (Fig. 6B ). abstract: Molecular clones of infectious bronchitis virus (IBV), derived from the Vero cell adapted Beaudette strain, were constructed, using an in vitro assembly method. In vitro transcribed RNA from a cDNA template that had been constructed from seven cDNA fragments, encompassing the entire genome of IBV, was electroporated into BHK-21 cells. The cells were overlaid onto the susceptible Vero cells and viable virus was recovered from the molecular clone. The molecularly cloned IBV (MIBV) demonstrated growth kinetics, and plaque size and morphology that resembled the parental Beaudette strain IBV. The recombinant virus was further manipulated to express enhanced green fluorescent protein (EGFP) by replacing an open reading frame (ORF) of the group-specific gene, ORF 5a, with the EGFP ORF. The rescued recombinant virus, expressing EGFP (GIBV), replicated to lower viral titers and formed smaller plaques compared to the parental virus and the MIBV. After six passages of GIBV, a minority of plaques were observed that had reverted to the larger plaque size and virus from these plaques no longer expressed EGFP. Direct sequencing of RT-PCR products derived from cells infected with the plaque-purified virus, which had lost expression of EGFP, confirmed loss of the EGFP ORF. The loss of EGFP expression (Δ5a IBV) was also accompanied by reversion to growth kinetics resembling the standard virus and intact recombinant virus. This study demonstrates that the 5a ORF is not essential for viral multiplication in Vero cells. url: https://www.sciencedirect.com/science/article/pii/S0042682204007421 doi: 10.1016/j.virol.2004.10.045 id: cord-299122-djfj4262 author: Yu, Hua title: Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice() date: 2007-03-15 words: 5459.0 sentences: 273.0 pages: flesch: 52.0 cache: ./cache/cord-299122-djfj4262.txt txt: ./txt/cord-299122-djfj4262.txt summary: title: Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice() Using the phage-displayed peptide library screening method and purified Fab fragments of immunoglobulin G (IgG Fab) from normal human sera and convalescent sera from SARS-CoV-infected patients as targets, 11 B cell epitopes of SARS-CoV spike glycoprotein (S protein) and membrane protein (M protein) were screened. Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice ☆ Therefore, in the present study, we screened and identified specific B cell epitopes of SARS-CoV using phagedisplayed peptide library, Fab fragments from anti-SARS-CoV immunoglobulin G (IgG) and normal human IgG as targets, and an improved biopanning procedure. Splenic lymphocytes from mice on day 42 still exhibited significant proliferative responses to specific antigen, demonstrating that the four epitope-based peptides induced long-term immune responses (data not shown). abstract: Antibodies to SARS-Coronavirus (SARS-CoV)-specific B cell epitopes might recognize the pathogen and interrupt its adherence to and penetration of host cells. Hence, these epitopes could be useful for diagnosis and as vaccine constituents. Using the phage-displayed peptide library screening method and purified Fab fragments of immunoglobulin G (IgG Fab) from normal human sera and convalescent sera from SARS-CoV-infected patients as targets, 11 B cell epitopes of SARS-CoV spike glycoprotein (S protein) and membrane protein (M protein) were screened. After a bioinformatics tool was used to analyze these epitopes, four epitope-based S protein dodecapeptides corresponding to the predominant epitopes were chosen for synthesis. Their antigenic specificities and immunogenicities were studied in vitro and in vivo. Flow cytometry and ELISPOT analysis of lymphocytes as well as a serologic analysis of antibody showed that these peptides could trigger a rapid, highly effective, and relatively safe immune response in BALB/c mice. These findings might aid development of SARS diagnostics and vaccines. Moreover, the role of S and M proteins as important surface antigens is confirmed. url: https://www.ncbi.nlm.nih.gov/pubmed/17055022/ doi: 10.1016/j.virol.2006.09.016 id: cord-300884-rqfxe0x1 author: Zhang, Jianqiang title: Genomic characterization of equine coronavirus date: 2007-12-05 words: 6804.0 sentences: 378.0 pages: flesch: 56.0 cache: ./cache/cord-300884-rqfxe0x1.txt txt: ./txt/cord-300884-rqfxe0x1.txt summary: Analysis of the sequence identified 11 open reading frames which encode two replicase polyproteins, five structural proteins (hemagglutinin esterase, spike, envelope, membrane, and nucleocapsid) and four accessory proteins (NS2, p4.7, p12.7, and I). In contrast to the replicase proteins which are directly translated from the genomic RNA, coronavirus structural and accessory proteins are expressed from a nested set of 3′ coterminal subgenomic (sg) mRNAs that also possess a common 5′ leader sequence derived from the 5′ end of the genome (Pasternak et al., 2006; Sawicki et al., 2007) . Following multiple alignments with the S proteins of other group 2a coronaviruses, a potential cleavage recognition sequence (RRQRR) was identified at residues 764-768 which would predict a cleavage between amino acids 768 and 769, separating the ECoV S protein into S1 and S2 subunits (Fig. 1) . abstract: The complete genome sequence of the first equine coronavirus (ECoV) isolate, NC99 strain was accomplished by directly sequencing 11 overlapping fragments which were RT–PCR amplified from viral RNA. The ECoV genome is 30,992 nucleotides in length, excluding the polyA tail. Analysis of the sequence identified 11 open reading frames which encode two replicase polyproteins, five structural proteins (hemagglutinin esterase, spike, envelope, membrane, and nucleocapsid) and four accessory proteins (NS2, p4.7, p12.7, and I). The two replicase polyproteins are predicted to be proteolytically processed by three virus-encoded proteases into 16 non-structural proteins (nsp1–16). The ECoV nsp3 protein had considerable amino acid deletions and insertions compared to the nsp3 proteins of bovine coronavirus, human coronavirus OC43, and porcine hemagglutinating encephalomyelitis virus, three group 2 coronaviruses phylogenetically most closely related to ECoV. The structure of subgenomic mRNAs was analyzed by Northern blot analysis and sequencing of the leader–body junction in each sg mRNA. url: https://www.sciencedirect.com/science/article/pii/S0042682207004655 doi: 10.1016/j.virol.2007.06.035 id: cord-255773-b4re5bky author: Zhang, Qingzhan title: Suppression of type I interferon production by porcine epidemic diarrhea virus and degradation of CREB-binding protein by nsp1 date: 2016-01-14 words: 9880.0 sentences: 584.0 pages: flesch: 52.0 cache: ./cache/cord-255773-b4re5bky.txt txt: ./txt/cord-255773-b4re5bky.txt summary: title: Suppression of type I interferon production by porcine epidemic diarrhea virus and degradation of CREB-binding protein by nsp1 We showed that PEDV suppressed the type I interferon production and ISGs expression in these cells, and identified nsp1, nsp3, nsp7, nsp14, nsp15, nsp16, E, M, N and ORF3 as the viral IFN antagonists. The CBP degradation is a novel mechanism of coronavirus nsp1 for IFN suppression and our study provides a new insight into the immune modulation and evasion strategy of PEDV. MARC-145 cells have been used to study type I IFN signaling of porcine arterivirus (Kim et al., 2010; Overend et al., 2007; Patel et al., 2010) , and thus infection of these cells One μg of each of the cloned genes was transfected to HeLa cells in 12-well plates, and protein expression was determined by immunofluorescence (B) and abstract: Type I interferons (IFN-α/β) are the major components of the innate immune response of hosts, and in turn many viruses have evolved to modulate the host response during infection. We found that the IFN-β production was significantly suppressed during PEDV infection in cells. To identify viral IFN antagonists and to study their suppressive function, viral coding sequences for the entire structural and nonstructural proteins were cloned and expressed. Of 16 PEDV nonstructural proteins (nsps), nsp1, nsp3, nsp7, nsp14, nsp15 and nsp16 were found to inhibit the IFN-β and IRF3 promoter activities. The sole accessory protein ORF3, structure protein envelope (E), membrane (M), and nucleocapsid (N) protein were also shown to inhibit such activities. PEDV nsp1 did not interfere the IRF3 phosphorylation and nuclear translocation but interrupted the enhanceosome assembly of IRF3 and CREB-binding protein (CBP) by degrading CBP. A further study showed that the CBP degradation by nsp1 was proteasome-dependent. Our data demonstrate that PEDV modulates the host innate immune responses by degrading CBP and suppressing ISGs expression. url: https://api.elsevier.com/content/article/pii/S0042682215005310 doi: 10.1016/j.virol.2015.12.010 id: cord-258286-lodjcj8c author: Zhang, Xuming title: Expression of Interferon-γ by a Coronavirus Defective-Interfering RNA Vector and Its Effect on Viral Replication, Spread, and Pathogenicity date: 1997-07-07 words: 5866.0 sentences: 296.0 pages: flesch: 54.0 cache: ./cache/cord-258286-lodjcj8c.txt txt: ./txt/cord-258286-lodjcj8c.txt summary: Previous studies have shown that immunocoma large plaque variant derived from the parental JHM petent mice infected with MHV exhibited increased exstrain (Stohlman et al., 1982) ; the small plaque variant pression of a number of cytokines, including IL-1, IL-6, DS (Stohlman et al., 1982) ; the neutralization-escape mu-TNF-a, and IFN-g, in the CNS at the time of viral cleartant 2.2-V-1 (Fleming et al., 1987; Wang et al., 1992) , and ance (Pearce et al., 1994) . The expressed IFNg exhibited antiviral activity, prevented virus spread in layers of DBT cells grown at approximately 70% confluence in 60-mm petri dishes were infected with MHV at vitro, and altered viral pathogenesis in mice. Expression of IFN-g using an MHV DI RNA vector cell metabolism prior to infection or it may be that interferon acts at an early stage of viral replication. abstract: Abstract A defective-interfering (DI) RNA of the murine coronavirus mouse hepatitis virus (MHV) was developed as a vector for expressing interferon-γ (IFN-γ). The murine IFN-γ gene was cloned into the DI vector under the control of an MHV transcriptional promoter and transfected into MHV-infected cells. IFN-γ was secreted into culture medium as early as 6 hr posttransfection and reached a peak level (up to 180 U/ml) at 12 hr posttransfection. The DI-expressed IFN-γ (DE-IFN-γ) exhibited an antiviral activity comparable to that of recombinant IFN-γ and was blocked by a neutralizing monoclonal antibody against IFN-γ. Treatment of macrophages with DE-IFN-γ selectively induced the expression of the cellular inducible nitric oxide synthase and the IFN-γ-inducing factor (IGIF) but did not affect the amounts of the MHV receptor mRNA. Antiviral activity was detected only when cells were pretreated with IFN-γ for 24 hr prior to infection; no inhibition of virus replication was detected when cells were treated with IFN-γ during or after infection. Furthermore, addition of IFN-γ together with MHV did not prevent infection, but appeared to prevent subsequent viral spread. MHV variants with different degrees of neurovirulence in mice had correspondingly different levels of sensitivities to IFN-γ treatmentin vitro,with the most virulent strain being most resistant to IFN-γ treatment. Infection of susceptible mice with DE-IFN-γ-containing virus caused significantly milder disease, accompanied by more pronounced mononuclear cell infiltrates into the CNS and less virus replication, than that caused by virus containing a control DI vector. This study thus demonstrates the feasibility and usefulness of this MHV DI vector for expressing cytokines and may provide a model for studying the role of cytokines in MHV pathogenesis. url: https://api.elsevier.com/content/article/pii/S0042682297985986 doi: 10.1006/viro.1997.8598 id: cord-263302-z5uhrta5 author: Zhang, Xuming title: Identification of a Noncanonical Signal for Transcription of a Novel Subgenomic mRNA of Mouse Hepatitis Virus: Implication for the Mechanism of Coronavirus RNA Transcription date: 2000-12-05 words: 7944.0 sentences: 411.0 pages: flesch: 58.0 cache: ./cache/cord-263302-z5uhrta5.txt txt: ./txt/cord-263302-z5uhrta5.txt summary: Transfection of the reporter RNA into MHV-infected cells resulted in synthesis of a CAT-specific subgenomic mRNA detected by reverse transcription-polymerase chain reaction (RT-PCR). Further sequencing on cDNA clones derived from JHM2c mRNAs by reserve transcription-polymerase chain reaction (RT-PCR) has shown that the leader-body joining sites in subgenomic mRNA2-1 are more heterogeneous . When it was placed in front of the chloramphenicol acetyl-transferase (CAT) gene in the defective-interfering (DI) RNA-CAT reporter plasmid, the IG5-1, which is devoid of any known IRES sequence, can direct the synthesis of a subgenomic CAT-containing mRNA and expression of the CAT activity, thus confirming that the IG5-1 serves as a promoter for transcription of a subgenomic mRNA. To identify the minimal sequence required for subgenomic mRNA transcription, three deletions within the 140-nt sequence were made by PCR, and the deletion fragments were cloned into the DI RNA-CAT reporter vector in place of the wild-type, full-length (140-nt) se, and MHV-1 (F), respectively. abstract: Abstract Subgenomic RNA transcription of coronaviruses involves the interaction between the leader (or antileader) and the intergenic (IG) sequences. However, it is not clear how these two sequences interact with each other. In this report, a previously unrecognized minor species of subgenomic mRNA, termed mRNA5–1, was identified in cells infected with mouse hepatitis virus (MHV) strains JHM2c, JHM(2), JHM(3), A59, and MHV-1. Sequence analysis revealed that the leader-body fusion site of the mRNA is located at approximately 150 nucleotides (nt) downstream of the consensus IG sequence for mRNA 5 and did not have sequence homology with any known IG consensus sequences. To determine whether this sequence functions independently as a promoter, we cloned a 140-nt sequence (from ≈70 nt upstream to ≈70 nt downstream of the fusion site) from viral genomic RNA and placed it in front of a reporter gene in the defective-interfering (DI) RNA-chloramphenicol acetyltransferase (CAT) reporter vector. Transfection of the reporter RNA into MHV-infected cells resulted in synthesis of a CAT-specific subgenomic mRNA detected by reverse transcription-polymerase chain reaction (RT-PCR). The strength of this promoter was similar to that of the IG7 (for mRNA 7) as measured by the CAT activity. Deletion analysis showed that the sequence as few as 13 nt was sufficient to initiate mRNA transcription, while mutations within the 13-nt abolished mRNA transcription. In vitro translation study confirmed that the envelope (E) protein was translated from mRNA5–1, which encodes the open reading frame (ORF) 5b at its 5′-end, indicating that mRNA5–1 is a functional message. Furthermore, when the ORF5b was replaced with the CAT gene and placed in the DI in the context of viral mini-genome, CAT was expressed not only from the first ORF of mRNA5–1 but also from the second and third ORF of mRNA5 and genomic DI RNA, respectively, suggesting that more than one mechanism is involved in regulation of ORF5b expression. Our findings thus support the notion that base-pairing between the leader (or antileader) and the IG is not the sole mechanism in subgenomic RNA transcription. url: https://api.elsevier.com/content/article/pii/S0042682200906378 doi: 10.1006/viro.2000.0637 id: cord-267532-5rnqd9mb author: Zhang, Xuming title: Expression of Hemagglutinin/Esterase by a Mouse Hepatitis Virus Coronavirus Defective–Interfering RNA Alters Viral Pathogenesis date: 1998-03-01 words: 6892.0 sentences: 357.0 pages: flesch: 55.0 cache: ./cache/cord-267532-5rnqd9mb.txt txt: ./txt/cord-267532-5rnqd9mb.txt summary: HEor CAT-specific subgenomic mRNAs were detected in the brains at days 1 and 2 p.i. but not later, indicating that the genes in the DI vector were expressed only in the early stage of viral infection. In the present study, we used this DI RNA vector system to express the viral HE gene in the CNS of mice in the presence of an HE-deficient helper virus. To determine the basis for the reduction in mortality following A59-DE-HE infection compared to other viruses ( Fig. 2) , virus titers in the brains of mice infected with A59-DE-HE were initially compared to mice infected with the parental A59 or A59-DE-CAT at 6 days p.i. Based on the survival of most mice infected with A59-DE-HE, reduced viral replication in the CNS was anticipated. IL-6 mRNA was also increased in the CNS of mice infected with A59-DE-HE virus (Fig. 5B) ; however, no differences were detected in the liver between the two groups. abstract: Abstract A defective-interfering (DI) RNA of mouse hepatitis virus (MHV) was developed as a vector for expressing MHV hemagglutinin/esterase (HE) protein. The virus containing an expressed HE protein (A59-DE-HE) was generated by infecting cells with MHV-A59, which does not express HE, and transfecting thein vitro-transcribed DI RNA containing the HE gene. A similar virus (A59-DE-CAT) expressing the chloramphenicol acetyltransferase (CAT) was used as a control. These viruses were inoculated intracerebrally into mice, and the role of the HE protein in viral pathogenesis was evaluated. Results showed that all mice infected with parental A59 or A59-DE-CAT succumbed to infection by 9 days postinfection (p.i.), demonstrating that inclusion of the DI did not by itself alter pathogenesis. In contrast, 60% of mice infected with A59-DE-HE survived infection. HE- or CAT-specific subgenomic mRNAs were detected in the brains at days 1 and 2 p.i. but not later, indicating that the genes in the DI vector were expressed only in the early stage of viral infection. No significant difference in virus titer or viral antigen expression in brains was observed between A59-DE-HE- and A59-DE-CAT-infected mice, suggesting that virus replication in brain was not affected by the expression of HE. However, at day 3 p.i. there was a slight increase in the extent of inflammatory cell infiltration in the brains of the A59-DE-HE-infected mice. Surprisingly, virus titers in the livers of A59-DE-HE-infected mice were 3 log10lower than that of the A59-DE-CAT-infected mice at day 6 p.i. Also, substantially less necrosis and viral antigen were detected in the livers of the A59-DE-HE-infected mice. This may account for the reduced mortality of these mice. The possible contribution of the host immune system to this difference in pathogenesis was analyzed by comparing the expression of four cytokines. Results showed that both tumor necrosis factor-α and interleukin-6 mRNAs increased in the brains of the A59-DE-HE-infected mice at day 2 p.i., whereas interferon-γ and interleukin-1α mRNAs were similar between A59-DE-HE- and A59-DE-CAT-infected mice. These data suggest that the transient expression of HE protein enhances an early innate immune response, possibly contributing to the eventual clearance of virus from the liver. This study indicates the feasibility of the DI expression system for studying roles of viral proteins during MHV infection. url: https://api.elsevier.com/content/article/pii/S0042682297989935 doi: 10.1006/viro.1997.8993 id: cord-291611-cfe8yujp author: Zhang, Xuming title: Comparison of the nucleotide and deduced amino acid sequences of the S genes specified by virulent and avirulent strains of bovine coronaviruses date: 1991-07-31 words: 2769.0 sentences: 149.0 pages: flesch: 60.0 cache: ./cache/cord-291611-cfe8yujp.txt txt: ./txt/cord-291611-cfe8yujp.txt summary: title: Comparison of the nucleotide and deduced amino acid sequences of the S genes specified by virulent and avirulent strains of bovine coronaviruses Abstract The entire nucleotide sequences of the spike glycoprotein (S) genes of the highly virulent bovine coronavirus (BCV) strain BCV-LY138, the avirulent BCV-L9 and related Norden Vaccine (BCV-Vaccine) strains were determined using the polymerase chain reaction (PCR) to amplify cDNAs obtained by reverse transcription of viral RNA, and to produce single strand cDNAs for DNA sequencing. Substitutions of few amino acids in the putative fusogenic domains and two prolines at 507 and 567 in the antigenic domains may cause altered immunogenic and other functional properties of the S proteins specified by the virulent and avirulent BCV strains. abstract: Abstract The entire nucleotide sequences of the spike glycoprotein (S) genes of the highly virulent bovine coronavirus (BCV) strain BCV-LY138, the avirulent BCV-L9 and related Norden Vaccine (BCV-Vaccine) strains were determined using the polymerase chain reaction (PCR) to amplify cDNAs obtained by reverse transcription of viral RNA, and to produce single strand cDNAs for DNA sequencing. The S gene sequences of these viral strains were compared with those of recently published strains BCV-Mebus, BCV-Quebec, and BCV-F15. An open reading frame of 4092 nucleotides, encoding a protein of 1363 amino acid residues, was found in all six strains. Frameshifts and insertions or deletions were not observed except for the BCV-Fl 5. The S gene sequences were more than 98% conserved overall inspite of different origins of the six viruses. There were 45 to 56 nt differences between the virulent and avirulent groups while there were 6 to 14 nt differences among four avirulent strains. Comparison of the deduced amino acid sequences indicated that the S proteins had typical properties of membrane glycoproteins. Nineteen Winked glycosylation sites were predicted in five strains, and 18 of them were conserved in the avirulent strain BCV-L9. The sequence KRRSRR at the predicted proteolytic cleavage site was identified in five strains while the sequence KRRSVR was found in BCV-Fl 5. Substitutions of few amino acids in the putative fusogenic domains and two prolines at 507 and 567 in the antigenic domains may cause altered immunogenic and other functional properties of the S proteins specified by the virulent and avirulent BCV strains. Nine amino acid substitutions between the virulent and avirulent groups may correlate with BCV virulence. url: https://www.ncbi.nlm.nih.gov/pubmed/2053289/ doi: 10.1016/0042-6822(91)90154-4 id: cord-324054-d71rj29o author: Zhang, Xuming title: The hemagglutinin/esterase gene of human coronavirus strain OC43: Phylogenetic relationships to bovine and murine coronaviruses and influenza C virus date: 1992-01-31 words: 2355.0 sentences: 147.0 pages: flesch: 64.0 cache: ./cache/cord-324054-d71rj29o.txt txt: ./txt/cord-324054-d71rj29o.txt summary: Abstract The complete nucleotide sequences of the hemagglutinin/esterase (HE) genes of human coronavirus (HCV) strain OC43 and bovine respiratory coronavirus (BRCV) strain G95 were determined from single-stranded cDNA fragments generated by reverse transcription of virus-specific mRNAs and amplified by polymerase chain reaction. Phylogenetic analysis suggests that the HE genes of coronaviruses and influenza C virus have a common ancestral origin, and that bovine coronaviruses and HCV-OC43 are closely related. We report here the complete nucleotide sequence of the HE genes of HCV-OC43 and BRCV-G95, and their phylogenetic relatedness to BCVs, MHV, and ICV. The predicted amino acid sequences of the HE genes from HCV-OC43 and BRCV-G95 (Fig. l) , BCVMost importantly, the putative acetylesterase active site (F-G-D-S) (at amino acids 72 to 75 in Fig. 2) is conserved in all HE proteins of human, bovine, and murine coronaviruses and ICV. abstract: Abstract The complete nucleotide sequences of the hemagglutinin/esterase (HE) genes of human coronavirus (HCV) strain OC43 and bovine respiratory coronavirus (BRCV) strain G95 were determined from single-stranded cDNA fragments generated by reverse transcription of virus-specific mRNAs and amplified by polymerase chain reaction. An open reading frame of 1272 nucleotides was identified as the putative HE gene by homology to the bovine coronavirus HE gene. This open reading frame encodes a protein of 424 amino acids with an estimated molecular weight of 47.7 kDa. Ten potential N-linked glycosylation sites were predicted in the HE protein of HCV-OC43 while nine of them were present in BRCV-G95. Fourteen cysteine residues were conserved in the HE proteins of both viruses. Two hydrophobic sequences at the N-terminus and the C-terminus may serve as signal peptide and transmembrane anchoring domain, respectively. The predicted HE protein of HCV-OC43 was 95% identical to the HEs of BRCV-G95 and other bovine coronaviruses, and 60% identical to the HEs of mouse hepatitis viruses. Phylogenetic analysis suggests that the HE genes of coronaviruses and influenza C virus have a common ancestral origin, and that bovine coronaviruses and HCV-OC43 are closely related. url: https://api.elsevier.com/content/article/pii/0042682292900898 doi: 10.1016/0042-6822(92)90089-8 id: cord-272437-gvzfl8c3 author: Zhao, Jing title: Replicase 1a gene plays a critical role in pathogenesis of avian coronavirus infectious bronchitis virus date: 2020-08-20 words: 565.0 sentences: 51.0 pages: flesch: 57.0 cache: ./cache/cord-272437-gvzfl8c3.txt txt: ./txt/cord-272437-gvzfl8c3.txt summary: title: Replicase 1a gene plays a critical role in pathogenesis of avian coronavirus infectious bronchitis virus Avian coronavirus infectious bronchitis virus (IBV) is an important pathogen threatening poultry production worldwide. Our findings demonstrate that the replicase 1a gene of avian coronavirus IBV is a determinant of pathogenicity. In this study, we used an IBV reverse genetics system based on virulent strain Fig. 2. Recombinant live attenuated avian coronavirus 431 vaccines with deletions in the accessory genes 3ab and/or 5ab protect against infectious 432 bronchitis in chickens attenuated Chinese QX-like infectious bronchitis virus strain as a candidate vaccine S gene and 5a accessory gene 455 are responsible for the attenuation of virulent infectious bronchitis coronavirus abstract: Avian coronavirus infectious bronchitis virus (IBV) is an important pathogen threatening poultry production worldwide. Here, two recombinant IBVs (rYN-1a-aYN and rYN-1b-aYN) were generated in which ORF1a or ORF1b of the virulent YN genome were replaced by the corresponding regions from the attenuated strain aYN. The pathogenicity and virulence of rIBVs were evaluated in ovo and in vivo. The results revealed that mutations in the ORF1a gene during passage in embryonated eggs caused the decreased pathogenicity of virulent IBV YN strain, proven by determination of virus replication in ECEs and CEK cells, the observation of clinical signs, gross lesions, microscopic lesions, tracheal ciliary activity and virus distribution in chickens following exposure to rIBVs. However, mutations in ORF1b had no obvious effect on virus replication in both ECEs and CEK cells, or pathogenicity in chickens. Our findings demonstrate that the replicase 1a gene of avian coronavirus IBV is a determinant of pathogenicity. url: https://api.elsevier.com/content/article/pii/S0042682220301628 doi: 10.1016/j.virol.2020.08.009 id: cord-276034-a8pixbuc author: Zhi, Yan title: Identification of murine CD8 T cell epitopes in codon-optimized SARS-associated coronavirus spike protein date: 2005-04-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The causative agent of severe acute respiratory syndrome (SARS) has been identified as a new type of coronavirus, SARS-associated coronavirus (SARS-CoV). CD8 T cells play an important role in controlling diseases caused by other coronaviruses and in mediating vaccine-induced protective immunity in corresponding animal models. The spike protein, a main surface antigen of SARS-CoV, is one of the most important antigen candidates for vaccine design. Overlapping peptides were used to identify major histocompatibility complex class I-restricted epitopes in mice immunized with vectors encoding codon-optimized SARS-CoV spike protein. CD8 T-cell responses were mapped to two H-2(b)-restricted epitopes (S436–443 and S525–532) and one H-2(d)-restricted epitope (S366–374). The identification of these epitopes will facilitate the evaluation of vaccine strategies in murine models of SARS-CoV infection. Furthermore, codon and promoter optimizations can greatly enhance the overall immunogenicity of spike protein in the context of replication-defective human and simian adenoviral vaccine carriers. The optimized recombinant adenoviral vaccine vectors encoding spike can generate robust antigen-specific cellular immunity in mice and may potentially be useful for control of SARS-CoV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/15823604/ doi: 10.1016/j.virol.2005.01.050 id: cord-297712-yy4g5npi author: Zhu, Xinyu title: Porcine deltacoronavirus nsp5 inhibits interferon-β production through the cleavage of NEMO date: 2016-12-13 words: 3284.0 sentences: 190.0 pages: flesch: 57.0 cache: ./cache/cord-297712-yy4g5npi.txt txt: ./txt/cord-297712-yy4g5npi.txt summary: Here, we demonstrate that nonstructural protein 5 (nsp5) of PDCoV, the 3C-like protease, significantly inhibits Sendai virus (SEV)-induced IFN-β production by targeting the NF-κB essential modulator (NEMO), confirmed by the diminished function of NEMO cleaved by PDCoV. A study published by our lab also demonstrated that nsp5, the 3C-like protease of porcine epidemic diarrhea virus (PEDV), which is classified into the Alphacoronavirus family, antagonizes IFN-β production by cleavage of NEMO . In this study, we reveal that nsp5 of PDCoV antagonizes the type I IFN signaling pathway through the cleavage of NEMO, a critical constituent of the IKK complex, thus representing a newly identified mechanism by which PDCoV evades the innate immune response. In contrast, TBK1induced activation of the IFN-β promoter was not affected by nsp5 (Fig. 3A) , suggesting that PDCoV nsp5 inhibits RIG-I/MDA5 signaling by targeting NEMO or other upstream proteins. abstract: Porcine deltacoronavirus (PDCoV) causes acute enteric disease and mortality in seronegative neonatal piglets. Previously we have demonstrated that PDCoV infection suppresses the production of interferon-beta (IFN-β), while the detailed mechanisms are poorly understood. Here, we demonstrate that nonstructural protein 5 (nsp5) of PDCoV, the 3C-like protease, significantly inhibits Sendai virus (SEV)-induced IFN-β production by targeting the NF-κB essential modulator (NEMO), confirmed by the diminished function of NEMO cleaved by PDCoV. The PDCoV nsp5 cleavage site in the NEMO protein was identified as glutamine 231, and was identical to the porcine epidemic diarrhea virus nsp5 cleavage site, revealing the likelihood of a common target in NEMO for coronaviruses. Furthermore, this cleavage impaired the ability of NEMO to activate the IFN response and downstream signaling. Taken together, our findings reveal PDCoV nsp5 to be a newly identified IFN antagonist and enhance the understanding of immune evasion by deltacoronaviruses. url: https://www.sciencedirect.com/science/article/pii/S0042682216303786 doi: 10.1016/j.virol.2016.12.005 id: cord-305143-mqd4ioj4 author: Zmasek, Christian M. title: Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO) date: 2019-01-06 words: 7266.0 sentences: 367.0 pages: flesch: 44.0 cache: ./cache/cord-305143-mqd4ioj4.txt txt: ./txt/cord-305143-mqd4ioj4.txt summary: Coupled with their genome complexity and the availability of numerous complete genome sequences, this deep evolutionary history makes herpesviruses a tractable and informative model to study virus genome evolution at the levels of gene duplication and protein domain rearrangement. In addition, the gene tree for human herpesvirus uracil DNA glycosylases ( Fig. 1B ) precisely recapitulates the herpesvirus species tree (Fig. 1A) ; therefore, this protein family can be inferred to have evolved from a single common ancestor and without any gene duplications or domain rearrangements (see Table 2 for virus-specific gene names). Phylogenetic analysis of human herpesvirus DNA polymerase proteins, plus related proteins from selected mammalian herpesviruses, shows that, similar to the glycoprotein B family, DNA polymerases of the Herpesviride evolved without gene duplication. abstract: We developed a computational approach called Domain-architecture Aware Inference of Orthologs (DAIO) for the analysis of protein orthology by combining phylogenetic and protein domain-architecture information. Using DAIO, we performed a systematic study of the proteomes of all human Herpesviridae species to define Strict Ortholog Groups (SOGs). In addition to assessing the taxonomic distribution for each protein based on sequence similarity, we performed a protein domain-architecture analysis for every protein family and computationally inferred gene duplication events. While many herpesvirus proteins have evolved without any detectable gene duplications or domain rearrangements, numerous herpesvirus protein families do exhibit complex evolutionary histories. Some proteins acquired additional domains (e.g., DNA polymerase), whereas others show a combination of domain acquisition and gene duplication (e.g., betaherpesvirus US22 family), with possible functional implications. This novel classification system of SOGs for human Herpesviridae proteins is available through the Virus Pathogen Resource (ViPR, www.viprbrc.org). url: https://www.sciencedirect.com/science/article/pii/S0042682219300054 doi: 10.1016/j.virol.2019.01.005 id: cord-265156-u1re7983 author: de Wilde, Adriaan H. title: Coronaviruses and arteriviruses display striking differences in their cyclophilin A-dependence during replication in cell culture date: 2017-12-15 words: 6306.0 sentences: 327.0 pages: flesch: 53.0 cache: ./cache/cord-265156-u1re7983.txt txt: ./txt/cord-265156-u1re7983.txt summary: Here, we investigated the CypA dependence of three distantly related nidoviruses that can all replicate in Huh7 cells: the arterivirus equine arteritis virus (EAV), the alphacoronavirus human coronavirus 229E (HCoV-229E), and the betacoronavirus Middle East respiratory syndrome coronavirus (MERS-CoV). The replication in cell culture of the arterivirus equine arteritis virus (EAV; de Wilde et al., 2013a) and the alphacoronaviruses feline coronavirus (FCoV; Tanaka et al., 2017) , human coronavirus (HCoV) NL63 (Carbajo-Lozoya et al., 2014), and HCoV-229E (von Brunn et al., 2015) was reported to be affected by CypA knockdown (KD) or knockout (KO), although the level of CypA dependence of these viruses, which was not compared directly, appeared to be quite different. Using different cell lines, the replication of two of these viruses, the arterivirus EAV (de Wilde et al., 2013a) and the alphacoronavirus HCoV-229E , was previously concluded to depend on CypA. abstract: Cyclophilin A (CypA) is an important host factor in the replication of a variety of RNA viruses. Also the replication of several nidoviruses was reported to depend on CypA, although possibly not to the same extent. These prior studies are difficult to compare, since different nidoviruses, cell lines and experimental set-ups were used. Here, we investigated the CypA dependence of three distantly related nidoviruses that can all replicate in Huh7 cells: the arterivirus equine arteritis virus (EAV), the alphacoronavirus human coronavirus 229E (HCoV-229E), and the betacoronavirus Middle East respiratory syndrome coronavirus (MERS-CoV). The replication of these viruses was compared in the same parental Huh7 cells and in CypA-knockout Huh7 cells generated using CRISPR/Cas9-technology. CypA depletion reduced EAV yields by ~ 3-log, whereas MERS-CoV progeny titers were modestly reduced (3-fold) and HCoV-229E replication was unchanged. This study reveals that the replication of nidoviruses can differ strikingly in its dependence on cellular CypA. url: https://doi.org/10.1016/j.virol.2017.11.022 doi: 10.1016/j.virol.2017.11.022 ==== 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