# ent

id: cord-252397-qlu7dilh
type: ORG
entity:
  Armed Forces Health Surveillance Center Division of Global Emerging Infections Surveillance and Response System


id: cord-252397-qlu7dilh
type: DISEASE
entity:
  Mia R Cornish Joseph P Yellayi Srikanth Huzella Louis Postnikova Elena Oberlander Nicholas Bartos Christopher


id: cord-253351-b36g09r0
type: PROTEIN
entity:
  enzyme Ϫ Wildtype S gene lanes 1 2 L1102K mutant lanes 3 4 V1103K mutant lanes 5 6 P1107K mutant lanes 7 8 L1110K mutant lanes 9


id: cord-008407-jbp8bxjz
type: CHEMICAL
entity:
  alphavirus genome Rubella virus RNA Effect of high multiplicity passage Construction of rubella virus genome length cDNA clones and synthesis of


id: cord-259717-e8ljkv2y
type: ORG
entity:
  the Menzies School of Health Research the Northern Territory Department of Health and Families the Royal Children s Hospital


id: cord-256036-gd53s4dv
type: SO
entity:
  RNA ER endoplasmatic reticulum hu human IFN interferon IFNAR interferon alpha receptor IL interleukin IRF interferon regulatory


id: cord-265173-70wyecwj
type: ORG
entity:
  Entry of Feline Calicivirus Is Dependent on Clathrin Mediated Endocytosis and Acidification in Endosomes VPg


id: cord-265173-70wyecwj
type: DISEASE
entity:
  human immunodeficiency virus type 1 reverse transcriptase The feline calicivirus leader of the capsid protein causes survivin and XIAP downregulation


id: cord-253894-4u5yt7b7
type: ORG
entity:
  the Division of Intramural Research National Institute of Allergy and Infectious Diseases National Institutes of Health


id: cord-255738-r8zfdsix
type: CHEMICAL
entity:
  N genes The N gene probe detected replicon RNA and replicon RNA derived Gb N and N RNAs The Gb probe detected only those RNAs containing the Gb gene replicon RNA and replicon RNA derived Gb N mRNA Fig 2B GFP expression of SCR 1 has


id: cord-259095-mfptcw8t
type: CHEBI
entity:
  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


id: cord-255453-7e40rj1y
type: PROTEIN
entity:
  2C helicase 93 amino acid 81 nucleotide 3C protease 89 amino acid 80 nucleotide and 3D polymerase 90 amino acid 78 nucleotide


id: cord-255453-7e40rj1y
type: PROTEIN
entity:
  Norwalk virus capsid Hepatitis E virus Picornaviridae the viruses and their replication Microbiology of calf diarrhoea in southern Britain TREE PUZZLE maximum likelihood phylogenetic analysis using quartets and parallel computing Human rhinovirus 2 complete nucleotide sequence


id: cord-255453-7e40rj1y
type: CHEMICAL
entity:
  Norwalk virus capsid Hepatitis E virus Picornaviridae the viruses and their replication Microbiology of calf diarrhoea


id: cord-262441-slh52nxm
type: CELL_LINE
entity:
  293T human kidney BHK 21 hamster kidney Huh7 human hepatocellular carcinoma and VeroE6 monkey kidney cells


id: cord-262574-gu0930s3
type: DNA
entity:
  mouse mammary tumor virus envelope protein gp52 Mouse mammary tumor virus and murine leukemia virus cell surface antigens


id: cord-262574-gu0930s3
type: ORG
entity:
  the Biological Carcinogenesis Branch Division of Cancer Cause and Prevention National Cancer Institute


id: cord-260108-osg8q89i
type: CHEMICAL
entity:
  bovine adenovirus 2 Adenovirus structure Hum Characterization of a new species of adenovirus in falcons


id: cord-253024-b393ea2u
type: PROTEIN
entity:
  RNA mutants LA7 LA1 2 3 0 x lo7 1 0 x 103 3 3 x 1o 4 1 1 x lo 1 0 x lo2 1 0 x 10 6 5 5 x 107 1 3 x lo 2 4 X 1O 6 5 5 x lo7 9 5 x lo4 1 7 x 10 3 3 5 x 10 4 3 x lo3 1 2 x 1o 4 7 8 x 10 1 4 x lo4 1 8 x 1O 4 6 9 X 10 8 7 x 10 1 2 x loo 7 3 x lo7 7 2 X 10 1 0 x loo 9 1 x 10 9 5 x lo7 1 0 x loo 2 1 x lo7 2 0 x 10 9 5 x 10 l 8 5 X lo 5 5 x 10 6 4 X lo 9 1 x lo7 7 2 X 10 7 9 x 10 Z 2 2 x 10 2 4 X lo7 1 1 x loo 4 0 x 10 2 0 x lo6 5 0 x 10 2 8 6 x 10 8 4 X 10 9 7 x 10 l 1 2 x lo8 1 2 x lo8 1 0 x lo0 1 2 x lo8 1 2 x 108 1 0 x loo 9 4 x 10 1 2 x 108 1 2 x loo 8 2 X lo7 9 2 x lo7 1 1 x lo0 1 0 x 108 9 0 x lo7 9 0 x 10 l 9 2 x 10 8 5 x 10 9 2 x 10 l 2 8 X 10 3 2 X 10 1 1 x loo 5 2 x lo7 4 5 x 10 8 6 x 10 J 4 7 x 10 4 6 X 10 9 7 x 10 l 5 9 x 10 4 8 X 10 8 1 x 10


id: cord-253024-b393ea2u
type: PROTEIN
entity:
  monoclonal antibodies 1 Viral Poliovirus genetics Coronavirus transcription subgenomic mouse hepatitis virus


id: cord-256316-1odgm6hm
type: DNA
entity:
  bovine enteric coronavirus BECV F15 mRNA 5 and mRNA 6 unique regions Influenza A virus M protein Monoclonal antibody


id: cord-256316-1odgm6hm
type: CHEMICAL
entity:
  N terminal part of the protein are needed for a definite assignment of the transmembrane orientation of ORF4 The possible role of the cysteine cluster


id: cord-256316-1odgm6hm
type: CHEMICAL
entity:
  Autographa californica nuclear polyhedrosis virus expression vectors The 1A protein of respiratory syncytial virus is an integral membrane protein present as multiple structurally distinct species Nucleotide sequence of the human coronavirus HCV 229E mRNA 4 and mRNA 5 unique regions Porcine respiratory coronavirus


id: cord-254747-vox5xsgd
type: WORK_OF_ART
entity:
  An Old Protein with A New Story Coronavirus Endoribonuclease Is Important for Evading Host Antiviral Defenses


id: cord-260782-1lm8tzbc
type: DISEASE
entity:
  liver spleen kidney forebrain hindbrain lumbar spinal cord salivary gland retropharyngeal lymph node and bladder


id: cord-008426-ktn8c0zx
type: PROTEIN
entity:
  GUUAUAAGG AGAUCGAUGUUGGUUGGCGUCGUGGCCUAAAACUCUGUUUAAAUACUUGUCUGAGGGCAAGUGGUUCUUUGAGGACUUAGAGCGAGAGCU 833 K I RG 2 Nucleotide sequence


id: cord-007373-livz5zuu
type: PROTEIN
entity:
  heparinbinding protein 1a7s Bacillus intermedius glutamyl endopeptidase 1p3c bovine beta trypsin 5ptp


id: cord-255773-b4re5bky
type: PROTEIN
entity:
  PEDV nonstructural and structural genes PEDV strain USA Colorado 2013 Restriction enzyme recognition sequences


id: cord-264331-uvi8ucz4
type: DNA
entity:
  eukaryotic expression vector pcDNA3 1 V5 His TOPO TA Invitrogen Carlsbad CA Big Dye terminator v1 1cycle sequencing kit Applied Biosystems Foster City CA


id: cord-258232-br4z3na6
type: PROTEIN
entity:
  anti E protein antibody Fraction 11 fractions 6 10 and fractions 1 4 represent 67 65 and 10 sucrose respectively Fraction 5


id: cord-254950-y6kayxie
type: CELL_LINE
entity:
  AR42J rat glandular epithelium BALB CL 7 mouse fibroblast BALB 3T3 fibroblast Cl271 mouse mammary tumor J774A l mouse macrophage NCTC 1469 mouse liver SC l feral mouse embryo TCMK 1 mouse kidney 32 Ill A rat hepatoma A549 human lung carcinoma HEp 2 human epidermoid carcinoma MDCK canine kidney epithelium Vero African green monkey kidney WISH diploid human amniotic epithelium 324K human kidney and primary cultures


id: cord-269986-jdcw59r2
type: GGP
entity:
  p38 c Jun N terminal mitogen activated protein kinase pathways and activates transcription factor AP 1 Leptin


id: cord-267027-diwm1940
type: DISEASE
entity:
  enteroviruses and rhinoviruses The predicted pseudoknots K2 tertiary interactions between the region


id: cord-263302-z5uhrta5
type: DNA
entity:
  5Ј SpeIG5 1 63 and 3ЈCAT542 and 5Ј SpeIG5 1 76 and 3ЈCAT542 respectively 5Ј SpeIG5 1 63 5Ј TTA CTA GTG CTT CCA ATT TAA 3Ј


id: cord-266585-jfjrk9gy
type: DNA
entity:
  nucleotides 1 5751 lane 2 5752 8693 lane 3 8694 15 520 lane 4 15 521 20 900 lane 5 and 20 901 27 608 lane 6


id: cord-266585-jfjrk9gy
type: GGP
entity:
  proteins i e spike glycoprotein S envelope protein E membrane protein M and nucleocapsid protein N The 5 two third region of mRNA 1


id: cord-266018-8bhnlsgy
type: DNA
entity:
  APCconjugated rat anti mouse CD8 PERCP conjugated rat anti mouse CD4 Pharmingen San Diego CA PE conjugated D b S510 518 MHC class I tetramer Beckman Coulter San Diego CA


id: cord-266018-8bhnlsgy
type: GGP
entity:
  Th2 associated cytokine IL 10 Table 1 Therefore the data indicate that cytokine production rather than the type of CD11c cell


id: cord-255828-jrqdyfbg
type: DNA
entity:
  GP4 http mobyle pasteur fr cgi bin portal py forms toppred Claros and von Heijne 1994 and the GPI anchor attachment signal http gpi unibe ch Fankhauser and Mäser 2005 Eisenhaber et al 1998


id: cord-262347-ejhz9rra
type: ORG
entity:
  Industry Study Assessment of the Economic Impact of Porcine Reproductive and Respiratory Syndrome Virus


id: cord-268467-btfz6ye8
type: PROTEIN
entity:
  I1 I II I III __ 1 III1 I llil I II II I I I III I II 2 J I I 111111 II I1111111 lllll III I II 1111 I Ill1 IIII I 3 I I I I Ill I I I11 I I I I I


id: cord-269419-68kja6bg
type: DNA
entity:
  3 11n01 6 25n01 4n01 9 121 3 15n01 2n01 8 109 1D2 1 69n09 4 17n01 4n02 7 121 3 15n01 2n01 4 108 1E1 a 3 23n04 1 1n01 4n02 7 121 3 11n01 5n01 0 108 1F2 a 3 23n04 5 5n01 5n02 6 121 3 15n01 5n01 2 108 1F4


id: cord-266230-ia04jc9j
type: DNA
entity:
  nepovirus CLRV 19 x AALTAPWLLCSYKSGVSSPPpPMTQRQQFAAIKRRLVQKGQQ IRELIRARKAAKYAlbFAARKKA AAITAPWLLRPCK GEAPPPPPLTQRQQFAALKKRLAVKGQQIIREHIRARKAAKYAAIAKAKKA X R x AAVAAQKARAEAPRLAAQKAAIAKILRDRQLVSLPPPPPPS RL A SKSASLQRL FH AALfLAVKAAQEAPRLAAQKISKILRDRDRDVAALPPPPPPS RL EABLASKAESLRRLKAFK RANRVRPVLNNSFPSPP TFSRVRPALNTSFPPPP shows 3 noncoding sequence


id: cord-270586-ohs8z91m
type: PROTEIN
entity:
  S1 subunit porcine respiratory coronavirus VIIIth International Congress of Virolof the spike protein


id: cord-271763-cual2qv4
type: CELL_LINE
entity:
  TATAGGCAC YAQHCFKAPSNFCPCKLDGSLC VGNGPGIDAGYKNSGIGT T T 1570 1580 1590 1600 1610 1620 1630 1640 1650 1660 1670


id: cord-271763-cual2qv4
type: PROTEIN
entity:
  GACTC G AC G LvGIGEHCScLAIKsDYC cNPCTCPPqAFLGWSVDSELQ _ _ _ 56b 1810 1820 1830 1840 1850 1860 1870 1880 1890 1900 1910 1920 GGGATAGGTGTAATAmTTGCTAATmATmGCATGATGATGTTAATAGTGGTACTACTTG CTACTGA AC ATC ACACAGACAT


id: cord-271763-cual2qv4
type: PROTEIN
entity:
  SPKVTIDCSAFVCGDY 800 2530 2540 2550 2560 2570 2580 2590 2600 2610 2620 2630 2640 CAGCATGTAAATCACAGTTGG G TATGGTAGCTTCTGTGACAATATTAATGCTATACTCACAGAAGTAAATGAACTACTTGACACTACACAGTTGCAAGTAGCT TA T GA


id: cord-271763-cual2qv4
type: CHEMICAL
entity:
  1670 1680 52b 1690 1700 1710 1720 1730 1740 1750 1760 1770 1780 1790 1800 TAGTTGGCATAGGTGAGCACTGTTCGGGGTC


id: cord-270814-krw8zmr5
type: PROTEIN
entity:
  measles virus hemagglutinin and CD46 Pathogenic murine coronaviruses murine coronavirus spike protein


id: cord-271526-14nfqusv
type: PROTEIN
entity:
  coronavirus packaging signal J Virol 66 3522 3530 Holmes K V 1991 In Fundamental Virology B N Fields and D M Sequence specific sequences


id: cord-275993-isff6lp2
type: DNA
entity:
  antisense primer 5V AAT GAA GCG GAT CCCGGG TTA GTG ATG GTG GTG ATG ATG TTG CTC ATA TTT TCC CAA 3V Base pairing region nts 3553 3570


id: cord-272051-arz8r204
type: WORK_OF_ART
entity:
  A R Castrucci and A M Ciccaglione Department of Infectious Parasitic and Immunomediated Diseases Istituto Superiore


id: cord-267014-3vi7pgvr
type: PROTEIN
entity:
  FIPV 6b protein Canine coronavirus CCV feline enteric coronavirus FECV feline infectious peritonitis virus


id: cord-269094-6aka052v
type: FAC
entity:
  the Comisión Interministerial de Ciencia y Tecnología CICYT the Consejería de Educación y Cultura de la Comunidad de Madrid


id: cord-272260-88l9bq4i
type: PROTEIN
entity:
  46 enzyme families 13 channel transporter families 4 RNA binding protein families DNA binding proteins G protein


id: cord-274480-aywdmj6o
type: CELL_LINE
entity:
  human non human primate porcine and bat de Wit et al 2013 Traditional small laboratory animals such as mice Coleman et al 2014 hamsters de Wit et al 2013 and ferrets Raj


id: cord-279813-mrei5kih
type: GGP
entity:
  NF kappa B p65 subunit RELA interferon regulatory transcription factor IRF TNF receptor associated factor TRAF interleukin IL tumor necrosis factor TNF Interferons IFN domain


id: cord-268139-tgpsu4qz
type: DNA
entity:
  fragments B and C NciI and BsmBI for fragments D and E BsmBI for F and SfiI and BsmBI for fragment G Gel purified restriction fragments


id: cord-276034-a8pixbuc
type: DISEASE
entity:
  human immunodeficiency virus type 1 Gag protein A simian replication defective adenoviral recombinant vaccine


id: cord-280287-t7uozjml
type: GGP
entity:
  sphingosine 2 sphingosine 1 phosphate 3 phytosphingosine 4 ceramide 5 sphingomyeline 6 sphingosyl phosphocholine 7 lysophosphatidic acid 8


id: cord-280287-t7uozjml
type: GGP
entity:
  monosialoganglioside G M1 10 disialoganglioside G D3 11 sulfatide 12 sphingosylgalactoside psychosine


id: cord-279346-7del8d2p
type: PROTEIN
entity:
  SARS associated coronavirus spike protein Woodchuck hepatitis virus posttranscriptional regulatory element


id: cord-278578-vq5fy8m5
type: PROTEIN
entity:
  secondary antibody AlexaFluor 488 donkey anti mouse IgG H L 1 1000 Life Technologies Molecular probes


id: cord-280957-cdd6ngf1
type: GGP
entity:
  host CPSF30 30 kDa subunit of the cleavage and polyadenylation specificity factor interaction and NS1


id: cord-280957-cdd6ngf1
type: GGP
entity:
  BST 2 NS1 of A WSN 33 H1N1 and A Texas 36 91 were previously reported to prevent the induction of BST 2


id: cord-283309-ovx5fzsg
type: DNA
entity:
  Spike S ORF3 Envelope E Membrane M Nucleocapsid N NS7a NS7b 3 SeACoV shared 95 nucleotide nt sequence


id: cord-270929-utn21ce1
type: TAXON
entity:
  transmissible gastroenteritis coronavirus nucleocapsid protein gene Cellular composition coronavirus


id: cord-277838-931sco95
type: DNA
entity:
  laryngotracheitis PHYLIP Phylogeny Inference Package Version 3 2c Avian infectious bronchitis virus Canine tracheobronchitis


id: cord-272871-gu9ptt9y
type: DNA
entity:
  YPNVYSLSYHKPSKFRRKAL AUAUCCAAACGUGUACUCCCUCUCAUACCBUARACCCUCCGC 720 FSYAPGGHKGAENWASQNYR C C C A GCACCAGGGGGACAAAGGAGCUGAGC GAAAAC GGG CC


id: cord-272871-gu9ptt9y
type: DNA
entity:
  GGAG C CA CC CCGC GCCC 840 SPPGGLIREPSPNERMANET I AGCCCCCCAGGAGGCC I CCGAGAACCAAGCCCAAAC 900 NKN HLYQT SRGSNLATTS AACI AGAI CG


id: cord-272871-gu9ptt9y
type: DNA
entity:
  ACGG AGGCCACCAAAGGAGC A C M GCG CG GG C A AC 1020 G P E l AGGCCCGGAG AI CCARCCACCRACCACUCAC CA A G C CGCCCCCGC 1060


id: cord-283035-tpqf458q
type: PROTEIN
entity:
  NKEF eukaryotic elongation factor 2 EEF2 aldolase B ALDOB membrane associated guanylate kinase MAGI3


id: cord-283035-tpqf458q
type: CL
entity:
  Mannheimia haemolytica virulence factor expression A statistical model for identifying proteins by tandem mass spectrometry Marek s disease virus


id: cord-284581-fl2nt4ak
type: DNA
entity:
  AlexaFlour488 conjugated anti human antibody goat 1 500 ThermoFisher Scientific were used ligand and antibody


id: cord-289248-6mx4o0eb
type: DNA
entity:
  GeneArt High Order Genetic Assembly System The traditional method for assembly of an infectious cDNA


id: cord-289248-6mx4o0eb
type: DNA
entity:
  GeneArt Seamless Cloning and Assembly Kit Invitrogen Fig 1A creating plasmid p107109 MV The primer sequences


id: cord-281309-c9y7m5do
type: CELL_TYPE
entity:
  lung tracheobronchial lymph node trachea thymus heart tonsil spleen iliac lymph node mesenteric lymph nodes ileum bone marrow kidneys liver inguinal lymph node cerebrum brainstem cerebellum and ventral midbrain


id: cord-279924-09uwhxs9
type: PROTEIN
entity:
  rabbit monoclonal anti Sox2 Epitomics and Alexa Fluor 568 goat anti rabbit IgG 1 secondary antibody Life


id: cord-279924-09uwhxs9
type: CELL_LINE
entity:
  EasySep Mouse T Cell Isolation kit Stemcell technologies This enriched fraction was treated with 50 μg mL mitomycin C AG Scientific and 35 Â 10 6 cells


id: cord-279924-09uwhxs9
type: GGP
entity:
  NPCs 2 6 Â 10 5 75 4 Â 10 4 PFU mL Under normal culture conditions expression of MHC classes I and II


id: cord-285869-jwflooop
type: DNA
entity:
  murine coronavirus MHV A59 Analysis of murine hepatitis virus strain A59 temperature sensitive mutant TS LA6


id: cord-286121-ltaxmp3u
type: CHEMICAL
entity:
  virus infected FRhK 4 cells using the RNesay Mini Kit Qiagen following the manufacturer s protocol The cDNA was prepared by reverse transcription using M MLV reverse transcriptase Invitrogen with oligonucleotide primers S E M N 3a


id: cord-275403-g4rohhtt
type: DNA
entity:
  adapter primers 5Ј 30 ApaI 5Ј ACTAG GGCCCTTAACAAAAAAAAAAAAAAAAAAA 3Ј UTR NdeI 5Ј ACTAGCATATGGCACTAGTGATTCCGGAAT 5Ј 65 ApaI 5Ј


id: cord-275403-g4rohhtt
type: GGP
entity:
  PRRSV 14 nsp 9 10 and 11 described below After optimal conditions were determined soluble recombinant proteins


id: cord-275403-g4rohhtt
type: ORG
entity:
  Functional Properties of the Predicted Helicase of Porcine Reproductive and Respiratory Syndrome Virus


id: cord-293375-qcy56ui7
type: GGP
entity:
  cathepsins B and H and stem bromelain Structure of papain refined at 1 65 A resolution 1 MO Nucleotide sequence


id: cord-286232-jo24ia4s
type: CHEMICAL
entity:
  disodium 3 4 methoxyspiro 1 2 dioxetane 3 2 5 chloro tricyclo 3 3 1 1 3 7 decan 4 yl phenyl phosphate


id: cord-290640-kh2t0kfz
type: DNA
entity:
  Coronavirus TGEV Gene 3b date 2000 03 30 journal Virology DOI 10 1006 viro 2000 0218 sha 96454b22b4c649398a3d7763603fec0faa9beb4f doc_id 290640 cord_uid kh2t0kfz Abstract Gene 3b ORF 3b


id: cord-290640-kh2t0kfz
type: ORG
entity:
  the University of Tennessee College of Veterinary Medicine Center of Excellence Program for Livestock Diseases and Human Health


id: cord-291611-cfe8yujp
type: ORG
entity:
  the United States Department of Agriculture and Louisiana Education Quality Support Fund of the Board of Regents State


id: cord-292019-rfu0bkag
type: DNA
entity:
  glycoprotein S gene sense primer 5Ј GCGCGGATCCATGAA AAACTATTTGTGG 3Ј antisense primer 5Ј GCGCGG TACCCGATGTGAAGCTATTG 3Ј Glycoprotein S mRNA


id: cord-293790-7hyelm88
type: RNA
entity:
  HCV NS5B RNAdependent RNA polymerase RdRp Here we report that ATG5 a protein required for the formation of DMV


id: cord-290282-oxyzndsj
type: PROTEIN
entity:
  light boxes 1b replicase 1b gene S spike gene E envelope gene M membrane gene N nucleoprotein gene Gene Rep 1b termination codon


id: cord-292751-tk1oggi9
type: DISEASE
entity:
  blood pressure diabetes heart diseases respiratory diseases cerebrovascular diseases endocrine system disorders digestive system disorders


id: cord-291306-g9qmmugg
type: DNA
entity:
  protease recognition motif R X K R R date 1992 05 31 journal Virology DOI 10 1016 0042 6822 92 90775 k sha fd3f6d68a7e654613b5f153454c943a9cac0bd12 doc_id 291306 cord_uid g9qmmugg Abstract The hemagglutinin of influenza virus A FPV Rostock 34 H7


id: cord-289045-vft163v0
type: DNA
entity:
  MHV JHM X04797 MHV 1 D83333 MHV 2 D83334 MHV 3 D83335 MHV S D83337 MHV U D83336 MHV BHK AY497331 RCoV AAF97738 BCoV strain L9 P25191 and HCoV


id: cord-289045-vft163v0
type: PROTEIN
entity:
  murine coronaviruses Purified soluble recombinant mouse hepatitis virus receptor bgp1 b and bgp2 murine coronavirus receptors


id: cord-289045-vft163v0
type: GGP
entity:
  carcinoembryonic antigen related cell adhesion molecule cellular receptors Angiotensin converting enzyme 2


id: cord-289045-vft163v0
type: ORG
entity:
  Susan Weiss Department of Microbiology University of Pennsylvania School of Medicine Philadelphia PA S


id: cord-288669-46tkedw7
type: DNA
entity:
  A12062G mutation E KO Fwd 5 GAATTGAAATGAAgTGGGGTCTATAC 3 nucleotide positions 12 049 to 12 074 and E KO Rev 5 GTATA GACCCCAcTTCATTTCAATTC 3 nucleotide positions 12 049 to 12 074


id: cord-288669-46tkedw7
type: DNA
entity:
  positive sense genomic RNA negative sense genomic RNA positive sense subgenomic mRNA7 or negative sense subgenomic mRNA7 PCR


id: cord-288669-46tkedw7
type: GGP
entity:
  small hydrophobic nonstructural proteins of Japanese encephalitis virus Hepatitis C virus E1 protein


id: cord-294260-g410mavp
type: CHEMICAL
entity:
  defective Citrus tristeza virus molecules Translational control of the subgenomic RNAs of severe acute


id: cord-299994-1ksfo0pr
type: PROTEIN
entity:
  dimer mate forming 6 hydrogen bonds A2 B147 A5 B136 A5 B136 A7 B147 A10 B134 2x and 1 salt bridge A1 B296


id: cord-296075-8axbkyyz
type: CELL_TYPE
entity:
  CD8 T cells 6 9 10 11 12 13 14 15 16 17 18 19 20 21 22 This chronic neurological disease one of the two epitopes


id: cord-300470-vgd1ol2z
type: RNA
entity:
  multi segmented dsRNA genomes Komoto and Taniguchi 2013 Trask et al 2013 Nevertheless in recent years reverse genetics systems


id: cord-300470-vgd1ol2z
type: DNA
entity:
  S9F GTTAAATAAGTTGTCTCATGTCTTCGGC S9R GTAAGTTTTAAGTTGCCTGCAAG S10F GTTAATTATCCCTTGTCATGAATCTAGC S10R GTAAGTTGTTATCCCACCCCCTAG The pJAD1


id: cord-300470-vgd1ol2z
type: GGP
entity:
  CGAAGgtttaaacGGCTCACCTTCGGGTGGGCCTTTCTGCGCAAAAAACCCCTCAAGACCCGTTTAG InvF GGCCGGCATGGTCCCAGC Linearization of


id: cord-300470-vgd1ol2z
type: PRODUCT
entity:
  CGAAGgtttaaacGGCTCACCTTCGGGTGGGCCTTTCTGCGCAAAAAACCCCTCAAGACCCGTTTAG InvF GGCCGGCATGGTCCCAGC Linearization of pJAD1


id: cord-300884-rqfxe0x1
type: DNA
entity:
  ORF2 hemagglutinin esterase HE ORF3 spike protein S ORF4 p4 7 protein ORF5 p12 7 protein ORF6 envelope protein E ORF7 membrane protein M ORF8 nucleocapsid protein N ORF9a and


id: cord-300884-rqfxe0x1
type: PROTEIN
entity:
  RNA polymerase Z zinc binding domain HEL helicase domain ExoN exonuclease N nidoviral uridylatespecific endoribonuclease NendoU MT 2 O ribose methyltransferase 2 O MT Domains


id: cord-300884-rqfxe0x1
type: PROTEIN
entity:
  N terminal signal peptide amino acid residues 1 14 or 17 the heptad repeat 1 HR1 amino acid residues 991 1902 the heptad repeat 2 HR2 amino acid residues 1259 1304 the transmembrane domain amino acid residues 1308 1330 and the cytoplasmic domain amino acid residues 1331 1363


id: cord-300884-rqfxe0x1
type: PROTEIN
entity:
  RNA polymerase ZBD zinc binding domain HEL helicase domain NendoU nidoviral uridylate specific endoribonuclease 2 O MT 2 O ribose methyltransferase


id: cord-300884-rqfxe0x1
type: GGP
entity:
  ORF2 hemagglutinin esterase HE ORF3 spike protein S ORF4 p4 7 protein ORF5 p12 7 protein ORF6 envelope protein E ORF7 membrane protein M ORF8 nucleocapsid protein N ORF9a and I protein


id: cord-303497-s3zs1oxf
type: SO
entity:
  Segment 4 hemagglutinin gene segment 5 nucleoprotein gene segment 6 neuraminidase gene segment 7 membrane protein gene segment 8 nonstructural protein gene


id: cord-299122-djfj4262
type: PROTEIN
entity:
  surface molecules fluorescein isothiocyanate FITC conjugated CD3e phycoerythrin PE conjugated CD19 CD4 CD8a allophycocyanin APC conjugated CD44


id: cord-301755-fxfsr9bj
type: CELL_LINE
entity:
  mouse cell line DBT culture Mouse hepatitis virus type 4 JHM strain induced fatal central nervous system disease I Genetic control and the murine neuron


id: cord-301755-fxfsr9bj
type: ORG
entity:
  Departments of Neurology and Medical Microbiology and Immunology School of Medicine University of Wisconsin


id: cord-301293-jqy7lcbk
type: ORG
entity:
  the National Institute of Allergy and Infectious Diseases National Institutes of Health Department of Health and Human Services


id: cord-305564-dj3vj4tk
type: DNA
entity:
  plasmids psl1190 BamHI SacII SARS CoV Δ 6 9b and psl1190 BamHI SacII SARS CoV Δ E 6 9b Finally fragment BamHI SacII


id: cord-304421-xpj6c0vx
type: CHEMICAL
entity:
  N terminal ORF 1a proteins of the coronavirus MHV A59 requires multiple proteolytic events Identification of polypeptides encoded in open reading frame 1b of the putative polymerase gene of the murine


id: cord-312210-3x9s3g8n
type: ORG
entity:
  the Federation of Animal Science Societies Guide for the Care and Use of Agricultural Animals in Research and Teaching the USDA Animal Welfare Act and Animal Welfare Regulations


id: cord-307354-dkwcheu0
type: DISEASE
entity:
  herpes simplex virus 1 vhs protein enhances translation of viral true late mRNAs and virus production


id: cord-319403-5qyc0wsz
type: DISEASE
entity:
  influenza A H5N1 viruses in primary human alveolar and bronchial epithelial cells Chemokine cytokine cross talk The ELR CXC chemokine LIX


id: cord-310967-15mv5yx7
type: PROTEIN
entity:
  G26 24 murjne oligodendroglioma cell line Sundarraj eta 1975 Lucas eta 1977 Bignami and Stoolmiller 1979 Two or ten day old Wistar


id: cord-325423-d212h4bp
type: PROTEIN
entity:
  MARV glycoprotein MAGP F 5 GGCCTTCAGGG CAGGTGTA 3 MAGP R 5 CCTGTGCATGAGGGTTTTGA 3 MMGP Probe 5 FAM CCTTGCTGTTAGATCCTCCTACCAA TAMRA 3


id: cord-324054-d71rj29o
type: DNA
entity:
  human coronavirus strain OC43 Phylogenetic relationships to bovine and murine coronaviruses and influenza C virus date 1992 01 31 journal Virology DOI 10 1016 0042 6822 92 90089 8 sha f0383dfc986d198dd48125704827db59270605f0 doc_id 324054 cord_uid d71rj29o


id: cord-317333-unrd76bo
type: GGP
entity:
  STAT1 MX1 OAS1 OAS2 ISG15 IFI44 suppressor of cytokine signaling 1 SOCS1 radical S adenosyl methionine domain


id: cord-317333-unrd76bo
type: DISEASE
entity:
  influenza and respiratory syncytial virus in the United States Mechanisms of type I interferon signal transduction Social and environmental risk factors in the emergence


id: cord-329819-dpgexphf
type: PROTEIN
entity:
  rabbit anti human EGFR rabbit anti human phospho EGFR Tyr1068 rabbit anti human AKT rabbit anti human phospho AKT rabbit anti human phospho ERK1 2


id: cord-329819-dpgexphf
type: ORG
entity:
  the Priority Academic Program Development of Jiangsu Higher Education Institutions PAPD Supplementary


id: cord-322062-nnefbeo6
type: DNA
entity:
  u1111Jul1uuluI111u lll1uuuul1 11111 JUI I 11 b iu UUUU IU 1 11 P I UJ L IUIU I I UII I u UUULII ui uu Computer generated open reading frame


id: cord-302486-z36hcvrx
type: TAXON
entity:
  human herpesviruses HHV 6 HHV 7 HHV 8 Epstein Barr virus herpes simplex virus parvovirus B19 TTV virus


id: cord-310748-ao29zx1u
type: CHEBI
entity:
  protein region of FMDV 1 The approach described in this report should provide a useful tool to study these possibilities Proc Natl Acad SC


id: cord-334133-61om170g
type: PROTEIN
entity:
  Y AP 1 preferences AP 2 preferences AP 3 preferences HIV 1 tyrosine dependent sorting signal sequences


id: cord-334133-61om170g
type: DISEASE
entity:
  human immunodeficiency virus type 1 transmembrane glycoprotein gp41 Interactions of the cytoplasmic domains of human and simian retroviral transmembrane


id: cord-334133-61om170g
type: DISEASE
entity:
  human immunodeficiency virus type 1 envelope protein Human immunodeficiency virus type 1 envelope protein


id: cord-305143-mqd4ioj4
type: PROTEIN
entity:
  cytoplasmic egress tegument protein cytoplasmic egress facilitator 1 cytoplasmic egress facilitator 2 encapsidation chaperone protein glycoprotein N Pfam clan Herpes_glyco CL0146 LTP binding protein


id: cord-305143-mqd4ioj4
type: PROTEIN
entity:
  HHV 6A HHV 6B HHV 7 Roseolovirus Protein U3 Tegument protein UL23 Protein U3_B Similarly CMV Tegument protein UL43


id: cord-305143-mqd4ioj4
type: CHEMICAL
entity:
  N terminal DNA_ pol_B_exo1 and C terminal DNA_pol_B denoted as DNA_pol_B_ex o1 DNA_pol_B of DNA polymerases


id: cord-305143-mqd4ioj4
type: DISEASE
entity:
  herpes simplex virus type 1 DNA polymerase contains a nuclear localization signal in the UL42 binding region


id: cord-319179-gqaxf7mz
type: DISEASE
entity:
  infectious cycle 4 5 The polymerase detected at early times p i synthesizes RNA complementary to virion RNA whereas the late appearing polymerase synthesizes subgenomic and genomic RNA of the same polarity as virion RNA positive strand RNA 6 The viral RNA polymerase


id: cord-289152-w5ynbewh
type: PROTEIN
entity:
  pro inflammatory cytokines chemokines adhesion molecules matrix metalloproteinases MMPs cyclooxygenase 2 COX2


id: cord-289152-w5ynbewh
type: PROTEIN
entity:
  anti NF nB p65 Santa Cruz Biotechnology Santa Cruz CA anti InBa Cell Signaling Beverly MA anti InBh Santa Cruz Biotechnology Santa Cruz CA anti InBq Santa Cruz Biotechnology Santa Cruz CA anti rabbit IgG HRP Amersham Biosciences Piscataway NJ


id: cord-289152-w5ynbewh
type: PROTEIN
entity:
  kinases TGF beta activated kinase 1 mitogenactivated kinase extracellular signal regulated kinase kinase 1


id: cord-289152-w5ynbewh
type: GGP
entity:
  EBV gp350 activate NF nB signaling pathway through binding to CD4 and CD21 Bossis et al 2002 D Addario et al 1999 Sugano et al 1997 However it is unlikely that NF nB activation by PRRSV


id: cord-330847-a84pcc9z
type: DNA
entity:
  ND1 8 A Southern blot of 15 putative BSMV strain CV17 7 cDNA clones lanes 1 l 5 a Type strain y cDNA clone lane 16


id: cord-330847-a84pcc9z
type: ORG
entity:
  CUAUGUAAGUUGCCUUUGGG UGU AAAAUUUCUUGCAUGCACAUAAUCGUAA UCGAUUCUUCUUGAUCUCUAAACAACACUUUCCCGUUAGC GCUAGCGAUGAGAUUGUCCGCAAUCUGAUCUCCCGUGAGAGGU


id: cord-325481-uzch2hwd
type: PROTEIN
entity:
  cathepsin L and B inhibitor MDL 28170 Calbiochem Darmstadt Germany for 30 min Thereafter pseudotypes of comparable infectivity


id: cord-346514-vyo8l14p
type: DNA
entity:
  BamHI BaMV5 1 5 GAATTCGAAAACCACTCCAAACGAAA3 and T7 13T BaMV3 end 5 GGTACCTAATACGACTCACTATAGGGTTTTT TTTTTTTTGGAAAA3 primers


id: cord-346514-vyo8l14p
type: DNA
entity:
  noA 5 GGAAAAAACTGTAGA AACCAAAAG3 BaMV 3 end 4A 5 TTTTGGAAAA AACTGTAGAAACC3 BaMV 3 end 7 A 5 TTT TTTTGGAAAAAACTGTAGAAA3 and BaMV 3


id: cord-353748-y1a52z8e
type: PROTEIN
entity:
  hACE2 SARS CoV 2 hACE2 nisin A hACE2 nisin Z hACE2 nisin H hACE2 nisin Q hACE2 nisin U hACE2 nisin U2 hACE2nisin F


id: cord-353748-y1a52z8e
type: PROTEIN
entity:
  T13 K31 C19 K31 K12 K31 T8 K31 P9 K31 K12 E35 K22 D38 N20 E35 C26 D38 H27 D38 C28 K353 T23 K353 Fig 2


id: cord-353748-y1a52z8e
type: GGP
entity:
  hACE2 SARS CoV 2 hACE2 nisin A hACE2 nisin Z hACE2 nisin H hACE2 nisin Q hACE2 nisin U hACE2 nisin U2


id: cord-353467-wbtzvm4i
type: CHEMICAL
entity:
  peptide N glycosidase F PNGase F which converted the gp27 form of S to its faster migrating p24 form The GFP S and S YFP


id: cord-337976-c2auspti
type: RNA
entity:
  intracellular RNA 5 0 0 5 and 0 05 g were used and in the case of purified genome RNA 0 1 0 01 and 0 001 ug were used The filter was hybridized with 106 cpm 10 s cpm g of 229E 32P cDNA


id: cord-344515-e0g911le
type: PROTEIN
entity:
  ERK 1 2 Thr 202 Tyr 204 Cell Signaling Technology Catalogue no 4370 ERK 1 2 Antibody Cell Signaling Technology Catalogue


id: cord-345630-bam3pa70
type: PROTEIN
entity:
  I I I I I I I I I I I I 1 2000 2500 3000 3500 3 ORF la lb 0 ORF lb I I I I I I I I I I I I I 1000 1500 2000 2500 FIG 2 Hydropathy


# bib

id: cord-007373-livz5zuu
author: Gayathri, P.
date: 2006-03-15
txt: ./txt/cord-007373-livz5zuu.txt
cache: ./cache/cord-007373-livz5zuu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7111806/
doi: 10.1016/j.virol.2005.11.011
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.

title:
  Crystal structure of the serine protease domain of Sesbania mosaic virus polyprotein and mutational analysis of residues forming the S1-binding pocket

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.


id: cord-008407-jbp8bxjz
author: Derdeyn, Cynthia A.
date: 1995-01-10
txt: ./txt/cord-008407-jbp8bxjz.txt
cache: ./cache/cord-008407-jbp8bxjz.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7130850/
doi: 10.1016/s0042-6822(95)80036-0
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.

title:
  Characterization of defective-interfering RNAs of rubella virusgenerated during serial undiluted passage

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.


id: cord-008426-ktn8c0zx
title: Nucleotide sequence of the bean strain of southern bean mosaic virus()
author: Othman, Yasmin
date: 1995-01-10
txt: ./txt/cord-008426-ktn8c0zx.txt
cache: ./cache/cord-008426-ktn8c0zx.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7130989/
doi: 10.1016/s0042-6822(95)80044-1
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.


id: cord-252397-qlu7dilh
author: Johnson, Reed F.
date: 2015-11-01
txt: ./txt/cord-252397-qlu7dilh.txt
cache: ./cache/cord-252397-qlu7dilh.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682215003323
doi: 10.1016/j.virol.2015.07.013
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).

title:
  Intratracheal exposure of common marmosets to MERS-CoV Jordan-n3/2012 or MERS-CoV EMC/2012 isolates does not result in lethal disease

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.


id: cord-252615-ajyv95pu
author: Lu, Yanfang
date: 2016-05-27
txt: ./txt/cord-252615-ajyv95pu.txt
cache: ./cache/cord-252615-ajyv95pu.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2016.05.013
doi: 10.1016/j.virol.2016.05.013
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) .

title:
  ATP1B3: a virus-induced host factor against EV71 replication by up-regulating the production of type-I interferons

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.


id: cord-253024-b393ea2u
title: Evidence for variable rates of recombination in the MHV genome
author: Fu, Kaisong
date: 1992-07-31
txt: ./txt/cord-253024-b393ea2u.txt
cache: ./cache/cord-253024-b393ea2u.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/004268229290684H
doi: 10.1016/0042-6822(92)90684-h
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.


id: cord-253351-b36g09r0
author: Luo, Zongli
date: 1998-05-10
txt: ./txt/cord-253351-b36g09r0.txt
cache: ./cache/cord-253351-b36g09r0.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682298991218
doi: 10.1006/viro.1998.9121
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.

title:
  Roles in Cell-to-Cell Fusion of Two Conserved Hydrophobic Regions in the Murine Coronavirus Spike Protein

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.


id: cord-253894-4u5yt7b7
author: Senkevich, Tatiana G.
date: 2011-09-01
txt: ./txt/cord-253894-4u5yt7b7.txt
cache: ./cache/cord-253894-4u5yt7b7.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/21752417/
doi: 10.1016/j.virol.2011.06.017
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).

title:
  Vaccinia virus F16 protein, a predicted catalytically inactive member of the prokaryotic serine recombinase superfamily, is targeted to nucleoli

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.


id: cord-254558-gvo0gwjf
author: Guo, Yan Xiang
date: 2003-03-30
txt: ./txt/cord-254558-gvo0gwjf.txt
cache: ./cache/cord-254558-gvo0gwjf.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682202000983
doi: 10.1016/s0042-6822(02)00098-3
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.

title:
  Induction of caspase-dependent apoptosis by betanodaviruses GGNNV and demonstration of protein α as an apoptosis inducer

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.


id: cord-254747-vox5xsgd
author: Deng, Xufang
date: 2018-04-01
txt: ./txt/cord-254747-vox5xsgd.txt
cache: ./cache/cord-254747-vox5xsgd.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29307596/
doi: 10.1016/j.virol.2017.12.024
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.

title:
  An “Old” Protein with A New Story: Coronavirus Endoribonuclease Is Important for Evading Host Antiviral Defenses

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.


id: cord-254950-y6kayxie
author: Morse, Stephen S.
date: 1988-03-31
txt: ./txt/cord-254950-y6kayxie.txt
cache: ./cache/cord-254950-y6kayxie.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/0042682288902620
doi: 10.1016/0042-6822(88)90262-0
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.

title:
  Mouse thymic virus (MTLV; Murid Herpesvirus 3) infection in athymic nude mice: Evidence for a T lymphocyte requirement

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.


id: cord-255453-7e40rj1y
author: Oliver, S.L.
date: 2006-06-20
txt: ./txt/cord-255453-7e40rj1y.txt
cache: ./cache/cord-255453-7e40rj1y.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682206001280
doi: 10.1016/j.virol.2006.02.027
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) .

title:
  Genomic characterization of the unclassified bovine enteric virus Newbury agent-1 (Newbury1) endorses a new genus in the family Caliciviridae

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.


id: cord-255738-r8zfdsix
author: Ge, Feng
date: 2007-03-30
txt: ./txt/cord-255738-r8zfdsix.txt
cache: ./cache/cord-255738-r8zfdsix.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682206007410
doi: 10.1016/j.virol.2006.10.016
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.

title:
  Derivation of a novel SARS–coronavirus replicon cell line and its application for anti-SARS drug screening

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.


id: cord-255773-b4re5bky
author: Zhang, Qingzhan
date: 2016-01-14
txt: ./txt/cord-255773-b4re5bky.txt
cache: ./cache/cord-255773-b4re5bky.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682215005310
doi: 10.1016/j.virol.2015.12.010
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

title:
  Suppression of type I interferon production by porcine epidemic diarrhea virus and degradation of CREB-binding protein by nsp1

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.


id: cord-255828-jrqdyfbg
author: Du, Yijun
date: 2012-03-01
txt: ./txt/cord-255828-jrqdyfbg.txt
cache: ./cache/cord-255828-jrqdyfbg.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682211005691
doi: 10.1016/j.virol.2011.12.009
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.

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

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.


id: cord-255841-3laov764
author: Duquerroy, Stéphane
date: 2005-05-10
txt: ./txt/cord-255841-3laov764.txt
cache: ./cache/cord-255841-3laov764.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15840526/
doi: 10.1016/j.virol.2005.02.022
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.

title:
  Central ions and lateral asparagine/glutamine zippers stabilize the post-fusion hairpin conformation of the SARS coronavirus spike glycoprotein()

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.


id: cord-256036-gd53s4dv
title: Barriers of hepatitis C virus interspecies transmission
author: Sandmann, Lisa
date: 2013-01-01
txt: ./txt/cord-256036-gd53s4dv.txt
cache: ./cache/cord-256036-gd53s4dv.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2012.09.044
doi: 10.1016/j.virol.2012.09.044
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.


id: cord-256316-1odgm6hm
title: TGEV corona virus ORF4 encodes a membrane protein that is incorporated into virions
author: Godet, Murielle
date: 1992-06-30
url: https://www.ncbi.nlm.nih.gov/pubmed/1316677/
doi: 10.1016/0042-6822(92)90521-p
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).


id: cord-256703-eaj63c2k
title: Intracellular accumulation of punta toro virus glycoproteins expressed from cloned cDNA
author: Matsuoka, Yumiko
date: 1988-11-30
txt: ./txt/cord-256703-eaj63c2k.txt
cache: ./cache/cord-256703-eaj63c2k.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/3142146/
doi: 10.1016/0042-6822(88)90075-x
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.


id: cord-256737-ptjng78b
author: McBride, Corrin E.
date: 2010-09-01
txt: ./txt/cord-256737-ptjng78b.txt
cache: ./cache/cord-256737-ptjng78b.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2010.05.031
doi: 10.1016/j.virol.2010.05.031
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.

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

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.


id: cord-256769-flfycl7i
title: Complement and Viral Pathogenesis
author: Stoermer, Kristina A.
date: 2011-03-01
url: https://www.sciencedirect.com/science/article/pii/S0042682210008135
doi: 10.1016/j.virol.2010.12.045
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.


id: cord-258232-br4z3na6
author: Maeda, Junko
date: 1999-10-25
txt: ./txt/cord-258232-br4z3na6.txt
cache: ./cache/cord-258232-br4z3na6.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682299999555
doi: 10.1006/viro.1999.9955
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.

title:
  Release of Coronavirus E Protein in Membrane Vesicles from Virus-Infected Cells and E Protein-Expressing Cells

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.


id: cord-258286-lodjcj8c
author: Zhang, Xuming
date: 1997-07-07
txt: ./txt/cord-258286-lodjcj8c.txt
cache: ./cache/cord-258286-lodjcj8c.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682297985986
doi: 10.1006/viro.1997.8598
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.

title:
  Expression of Interferon-γ by a Coronavirus Defective-Interfering RNA Vector and Its Effect on Viral Replication, Spread, and Pathogenicity

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.


id: cord-258327-03vk6enj
author: Schultze, Beate
date: 1991-01-31
txt: ./txt/cord-258327-03vk6enj.txt
cache: ./cache/cord-258327-03vk6enj.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/0042682291900268
doi: 10.1016/0042-6822(91)90026-8
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 .

title:
  Isolated HE-protein from hemagglutinating encephalomyelitis virus and bovine coronavirus has receptor-destroying and receptor-binding activity

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.


id: cord-258379-v3lceirh
title: Association of the infectious bronchitis virus 3c protein with the virion envelope
author: Liu, D. X.
date: 1991-12-31
txt: ./txt/cord-258379-v3lceirh.txt
cache: ./cache/cord-258379-v3lceirh.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/1962461/
doi: 10.1016/0042-6822(91)90572-s
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.


id: cord-258691-cd83w9o6
title: IFN-γ-mediated suppression of coronavirus replication in glial-committed progenitor cells
author: Whitman, Lucia
date: 2009-02-01
txt: ./txt/cord-258691-cd83w9o6.txt
cache: ./cache/cord-258691-cd83w9o6.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682208006971
doi: 10.1016/j.virol.2008.10.036
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.


id: cord-259095-mfptcw8t
title: Determinants of Mouse Hepatitis Virus 3C-like Proteinase Activity
author: Lu, Yiqi
date: 1997-04-14
txt: ./txt/cord-259095-mfptcw8t.txt
cache: ./cache/cord-259095-mfptcw8t.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/9143289/
doi: 10.1006/viro.1997.8479
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.


id: cord-259500-ndjbrtrv
author: Satyanarayana, Tatineni
date: 2003-09-01
txt: ./txt/cord-259500-ndjbrtrv.txt
cache: ./cache/cord-259500-ndjbrtrv.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682203003878
doi: 10.1016/s0042-6822(03)00387-8
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.

title:
  Frameshift mutations in infectious cDNA clones of Citrus tristeza virus: a strategy to minimize the toxicity of viral sequences to Escherichia coli

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.


id: cord-259717-e8ljkv2y
title: Geographic variation in the eukaryotic virome of human diarrhea
author: Holtz, Lori R.
date: 2014-11-01
txt: ./txt/cord-259717-e8ljkv2y.txt
cache: ./cache/cord-259717-e8ljkv2y.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25262473/
doi: 10.1016/j.virol.2014.09.012
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.


id: cord-260108-osg8q89i
author: Park, Yon Mi
date: 2012-01-05
txt: ./txt/cord-260108-osg8q89i.txt
cache: ./cache/cord-260108-osg8q89i.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682211004776
doi: 10.1016/j.virol.2011.10.008
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 ).

title:
  Full genome analysis of a novel adenovirus from the South Polar skua (Catharacta maccormicki) in Antarctica

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.


id: cord-260177-xu0elmak
author: Collins, Arlene R.
date: 1982-06-30
txt: ./txt/cord-260177-xu0elmak.txt
cache: ./cache/cord-260177-xu0elmak.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/0042682282900952
doi: 10.1016/0042-6822(82)90095-2
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.

title:
  Monoclonal antibodies to murine hepatitis virus-4 (strain JHM) define the viral glycoprotein responsible for attachment and cell-cell 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.


id: cord-260376-29ih5c9v
title: SARS corona virus peptides recognized by antibodies in the sera of convalescent cases
author: Guo, Jian-Ping
date: 2004-07-01
txt: ./txt/cord-260376-29ih5c9v.txt
cache: ./cache/cord-260376-29ih5c9v.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15207612/
doi: 10.1016/j.virol.2004.04.017
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.


id: cord-260695-qwepi0we
title: Identification and characterization of a long non-coding RNA up-regulated during HIV-1 infection
author: Postler, Thomas S.
date: 2017-11-01
txt: ./txt/cord-260695-qwepi0we.txt
cache: ./cache/cord-260695-qwepi0we.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2017.08.006
doi: 10.1016/j.virol.2017.08.006
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.


id: cord-260782-1lm8tzbc
author: Giles, Julia
date: 2018-07-14
txt: ./txt/cord-260782-1lm8tzbc.txt
cache: ./cache/cord-260782-1lm8tzbc.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30014860/
doi: 10.1016/j.virol.2018.07.003
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.

title:
  Viral RNA load and histological changes in tissues following experimental infection with an arterivirus of possums (wobbly possum disease virus)

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.


id: cord-262226-7kwkla73
author: Fang, Shouguo
date: 2013-07-09
url: https://api.elsevier.com/content/article/pii/S0042682213003632
doi: 10.1016/j.virol.2013.06.014
title:
  Identification of two ATR-dependent phosphorylation sites on coronavirus nucleocapsid protein with nonessential functions in viral replication and infectivity in cultured cells

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.


id: cord-262245-eb7g9p1x
author: Monica, Nicola La
date: 1991-06-30
txt: ./txt/cord-262245-eb7g9p1x.txt
cache: ./cache/cord-262245-eb7g9p1x.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/004268229190635O
doi: 10.1016/0042-6822(91)90635-o
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).

title:
  Localization of extensive deletions in the structural genes of two neurotropic variants of murine coronavirus JHM

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.


id: cord-262347-ejhz9rra
title: PRRSV structure, replication and recombination: Origin of phenotype and genotype diversity
author: Kappes, Matthew A.
date: 2015-03-07
url: https://doi.org/10.1016/j.virol.2015.02.012
doi: 10.1016/j.virol.2015.02.012
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.


id: cord-262441-slh52nxm
title: Two-amino acids change in the nsp4 of SARS coronavirus abolishes viral replication
author: Sakai, Yusuke
date: 2017-07-21
txt: ./txt/cord-262441-slh52nxm.txt
cache: ./cache/cord-262441-slh52nxm.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28738245/
doi: 10.1016/j.virol.2017.07.019
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.


id: cord-262574-gu0930s3
author: Slagle, Betty L.
date: 1985-05-31
txt: ./txt/cord-262574-gu0930s3.txt
cache: ./cache/cord-262574-gu0930s3.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/0042682285901023
doi: 10.1016/0042-6822(85)90102-3
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.

title:
  Identification and characterization of a mouse mammary tumor virus protein uniquely expressed 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.


id: cord-263302-z5uhrta5
author: Zhang, Xuming
date: 2000-12-05
txt: ./txt/cord-263302-z5uhrta5.txt
cache: ./cache/cord-263302-z5uhrta5.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682200906378
doi: 10.1006/viro.2000.0637
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.

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

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.


id: cord-263334-wwkdum94
author: Li, Chen
date: 2014-01-20
txt: ./txt/cord-263334-wwkdum94.txt
cache: ./cache/cord-263334-wwkdum94.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2013.11.008
doi: 10.1016/j.virol.2013.11.008
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

title:
  Cellular DDX3 regulates Japanese encephalitis virus replication by interacting with viral un-translated regions

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.


id: cord-264331-uvi8ucz4
author: Singh, Shailbala
date: 2010-04-10
txt: ./txt/cord-264331-uvi8ucz4.txt
cache: ./cache/cord-264331-uvi8ucz4.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2009.12.029
doi: 10.1016/j.virol.2009.12.029
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) .

title:
  Avian influenza viral nucleocapsid and hemagglutinin proteins induce chicken CD8(+) memory T lymphocytes

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.


id: cord-264359-m9j3pcj1
title: Resolution of the major poliovirus capsid polypeptides into doublets
author: Vrijsen, R.
date: 1978-05-15
txt: ./txt/cord-264359-m9j3pcj1.txt
cache: ./cache/cord-264359-m9j3pcj1.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27002/
doi: 10.1016/0042-6822(78)90093-4
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.


id: cord-265156-u1re7983
author: de Wilde, Adriaan H.
date: 2017-12-15
txt: ./txt/cord-265156-u1re7983.txt
cache: ./cache/cord-265156-u1re7983.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2017.11.022
doi: 10.1016/j.virol.2017.11.022
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.

title:
  Coronaviruses and arteriviruses display striking differences in their cyclophilin A-dependence during replication in cell culture

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.


id: cord-265173-70wyecwj
author: Trujillo-Uscanga, Adrian
date: 2020-08-27
txt: ./txt/cord-265173-70wyecwj.txt
cache: ./cache/cord-265173-70wyecwj.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682220301616
doi: 10.1016/j.virol.2020.08.008
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.

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

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.


id: cord-265895-ck7eto16
author: Baric, Ralph S.
date: 1987-02-28
txt: ./txt/cord-265895-ck7eto16.txt
cache: ./cache/cord-265895-ck7eto16.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/0042682287904144
doi: 10.1016/0042-6822(87)90414-4
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.

title:
  Analysis of intracellular small RNAs of mouse hepatitis virus: evidence for discontinuous transcription

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.


id: cord-266018-8bhnlsgy
author: Trifilo, Matthew J.
date: 2004-09-15
txt: ./txt/cord-266018-8bhnlsgy.txt
cache: ./cache/cord-266018-8bhnlsgy.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S004268220400409X
doi: 10.1016/j.virol.2004.06.027
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 ).

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

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.


id: cord-266230-ia04jc9j
author: Rott, M. E.
date: 1991-11-30
txt: ./txt/cord-266230-ia04jc9j.txt
cache: ./cache/cord-266230-ia04jc9j.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/004268229190801H
doi: 10.1016/0042-6822(91)90801-h
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.

title:
  Comparison of the 5′ and 3′ termini of tomato ringspot virus RNA1 and RNA2: Evidence for RNA recombination

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.


id: cord-266585-jfjrk9gy
author: Fang, Shouguo
date: 2007-02-05
txt: ./txt/cord-266585-jfjrk9gy.txt
cache: ./cache/cord-266585-jfjrk9gy.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682206005745
doi: 10.1016/j.virol.2006.08.020
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.

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

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.


id: cord-266617-z8uecyl6
title: Asymmetric evolution in viral overlapping genes is a source of selective protein adaptation
author: Pavesi, Angelo
date: 2019-04-03
txt: ./txt/cord-266617-z8uecyl6.txt
cache: ./cache/cord-266617-z8uecyl6.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682219300881
doi: 10.1016/j.virol.2019.03.017
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.


id: cord-266861-t5h133lp
title: Phosphatidylserine receptors: enhancers of enveloped virus entry and infection
author: Moller-Tank, Sven
date: 2014-11-01
url: https://www.ncbi.nlm.nih.gov/pubmed/25277499/
doi: 10.1016/j.virol.2014.09.009
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.


id: cord-267014-3vi7pgvr
title: Genomic organization and expression of the 3′ end of the canine and feline enteric coronaviruses
author: Vennema, H.
date: 1992-11-30
txt: ./txt/cord-267014-3vi7pgvr.txt
cache: ./cache/cord-267014-3vi7pgvr.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/004268229290174N
doi: 10.1016/0042-6822(92)90174-n
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.


id: cord-267027-diwm1940
author: Le, Shu-Yun
date: 1992-12-31
url: https://www.sciencedirect.com/science/article/pii/004268229290261M
doi: 10.1016/0042-6822(92)90261-m
title:
  Conserved tertiary structure elements in the 5′ untranslated region of human enteroviruses and rhinoviruses

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.


id: cord-267377-wyhsxj6g
title: Coat protein expression strategy of oat blue dwarf virus()
author: Edwards, Michael C.
date: 2014-01-14
txt: ./txt/cord-267377-wyhsxj6g.txt
cache: ./cache/cord-267377-wyhsxj6g.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2013.12.018
doi: 10.1016/j.virol.2013.12.018
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.


id: cord-267532-5rnqd9mb
author: Zhang, Xuming
date: 1998-03-01
txt: ./txt/cord-267532-5rnqd9mb.txt
cache: ./cache/cord-267532-5rnqd9mb.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682297989935
doi: 10.1006/viro.1997.8993
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.

title:
  Expression of Hemagglutinin/Esterase by a Mouse Hepatitis Virus Coronavirus Defective–Interfering RNA Alters Viral Pathogenesis

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.


id: cord-267718-t47i8hui
title: Evolutionary dynamics of recent peste des petits ruminants virus epidemic in China during 2013–2014
author: Bao, Jingyue
date: 2017-07-19
txt: ./txt/cord-267718-t47i8hui.txt
cache: ./cache/cord-267718-t47i8hui.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682217302362
doi: 10.1016/j.virol.2017.07.018
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.


id: cord-268139-tgpsu4qz
author: Brockway, Sarah M.
date: 2005-09-30
url: https://api.elsevier.com/content/article/pii/S0042682205003776
doi: 10.1016/j.virol.2005.06.035
title:
  Mutagenesis of the murine hepatitis virus nsp1-coding region identifies residues important for protein processing, viral RNA synthesis, and viral replication

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.


id: cord-268341-103xf3dw
author: Parra, Beatriz
date: 1997-07-07
txt: ./txt/cord-268341-103xf3dw.txt
cache: ./cache/cord-268341-103xf3dw.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S004268229798613X
doi: 10.1006/viro.1997.8613
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.

title:
  Kinetics of Cytokine mRNA Expression in the Central Nervous System Following Lethal and Nonlethal Coronavirus-Induced Acute Encephalomyelitis

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.


id: cord-268416-8hw80qx8
title: The coronavirus nucleocapsid protein is ADP-ribosylated
author: Grunewald, Matthew E.
date: 2018-04-01
txt: ./txt/cord-268416-8hw80qx8.txt
cache: ./cache/cord-268416-8hw80qx8.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2017.11.020
doi: 10.1016/j.virol.2017.11.020
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.


id: cord-268467-btfz6ye8
title: Sequence analysis of the nucleocapsid protein gene of human coronavirus 229E
author: Schreiber, Steven S.
date: 1989-03-31
txt: ./txt/cord-268467-btfz6ye8.txt
cache: ./cache/cord-268467-btfz6ye8.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/0042682289900500
doi: 10.1016/0042-6822(89)90050-0
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.


id: cord-269094-6aka052v
author: Ortego, Javier
date: 2007-11-25
url: https://www.ncbi.nlm.nih.gov/pubmed/17692883/
doi: 10.1016/j.virol.2007.05.032
title:
  Absence of E protein arrests transmissible gastroenteritis coronavirus maturation in the secretory pathway

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.


id: cord-269193-a647hwu9
author: Lin, Debby A.
date: 1991-05-31
txt: ./txt/cord-269193-a647hwu9.txt
cache: ./cache/cord-269193-a647hwu9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/2024457/
doi: 10.1016/0042-6822(91)90641-n
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) .

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

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.


id: cord-269204-kajws5xo
author: Nitschke, Matthias
date: 2008-08-01
txt: ./txt/cord-269204-kajws5xo.txt
cache: ./cache/cord-269204-kajws5xo.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2008.04.041
doi: 10.1016/j.virol.2008.04.041
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.

title:
  Equine arteritis virus is delivered to an acidic compartment of host cells via clathrin-dependent endocytosis

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.


id: cord-269419-68kja6bg
author: Hu, Weibin
date: 2013-01-20
txt: ./txt/cord-269419-68kja6bg.txt
cache: ./cache/cord-269419-68kja6bg.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/23084424/
doi: 10.1016/j.virol.2012.09.034
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.

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

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.


id: cord-269862-krcu3hfa
title: APOBEC3G cytidine deaminase association with coronavirus nucleocapsid protein
author: Wang, Shui-Mei
date: 2009-05-25
url: https://api.elsevier.com/content/article/pii/S0042682209001834
doi: 10.1016/j.virol.2009.03.010
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.


id: cord-269866-3tpyj04y
author: Liu, D. X.
date: 1992-01-31
txt: ./txt/cord-269866-3tpyj04y.txt
cache: ./cache/cord-269866-3tpyj04y.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/0042682292900946
doi: 10.1016/0042-6822(92)90094-6
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.

title:
  Identification of two new polypeptides encoded by mRNA5 of the coronavirus infectious bronchitis virus

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.


id: cord-269986-jdcw59r2
author: Regan, Andrew D.
date: 2009-02-05
url: https://www.sciencedirect.com/science/article/pii/S0042682208007356
doi: 10.1016/j.virol.2008.11.006
title:
  Activation of p38 MAPK by feline infectious peritonitis virus regulates pro-inflammatory cytokine production in primary blood-derived feline mononuclear cells

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.


id: cord-270487-m770a1rl
author: Wurch, T.
date: 1991-02-28
url: https://api.elsevier.com/content/article/pii/004268229190103I
doi: 10.1016/0042-6822(91)90103-i
title:
  The cauliflower mosaic virus reverse transcriptase is not produced by the mechanism of ribosomal frameshifting in Saccharomyces cerevisiae

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.


id: cord-270534-ebkwv4zo
author: Bodmer, Bianca S.
date: 2018-06-11
txt: ./txt/cord-270534-ebkwv4zo.txt
cache: ./cache/cord-270534-ebkwv4zo.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682218301697
doi: 10.1016/j.virol.2018.05.028
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.

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

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.


id: cord-270586-ohs8z91m
author: Ballesteros, M. L.
date: 1997-01-20
url: https://www.sciencedirect.com/science/article/pii/S0042682296983440
doi: 10.1006/viro.1996.8344
title:
  Two Amino Acid Changes at the N-Terminus of Transmissible Gastroenteritis Coronavirus Spike Protein Result in the Loss of Enteric Tropism

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.


id: cord-270814-krw8zmr5
author: Rao, Pasupuleti V.
date: 1997-03-17
url: https://api.elsevier.com/content/article/pii/S0042682297984464
doi: 10.1006/viro.1997.8446
title:
  Identification of a Contiguous 6-Residue Determinant in the MHV Receptor That Controls the Level of Virion Binding to Cells

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.


id: cord-270929-utn21ce1
author: Wise, Annabel G.
date: 2006-05-25
url: https://www.ncbi.nlm.nih.gov/pubmed/16499943/
doi: 10.1016/j.virol.2006.01.031
title:
  Molecular characterization of a novel coronavirus associated with epizootic catarrhal enteritis (ECE) in ferrets

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.


id: cord-271359-dpa8zzc3
title: Novel Variation in the N Protein of Avian Infectious Bronchitis Virus
author: Sapats, S. I.
date: 1996-12-15
url: https://www.sciencedirect.com/science/article/pii/S0042682296906704
doi: 10.1006/viro.1996.0670
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.


id: cord-271526-14nfqusv
author: Molenkamp, Richard
date: 1997-12-08
txt: ./txt/cord-271526-14nfqusv.txt
cache: ./cache/cord-271526-14nfqusv.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S004268229798867X
doi: 10.1006/viro.1997.8867
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.

title:
  Identification of a Specific Interaction between the Coronavirus Mouse Hepatitis Virus A59 Nucleocapsid Protein and Packaging Signal

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.


id: cord-271763-cual2qv4
author: Abraham, Sushma
date: 1990-05-31
url: https://www.ncbi.nlm.nih.gov/pubmed/2184576/
doi: 10.1016/0042-6822(90)90257-r
title:
  Deduced sequence of the bovine coronavirus spike protein and identification of the internal proteolytic cleavage site

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).


id: cord-272045-v1wt5t7m
title: Hexamethylene amiloride blocks E protein ion channels and inhibits coronavirus replication
author: Wilson, Lauren
date: 2006-09-30
url: https://www.sciencedirect.com/science/article/pii/S004268220600359X
doi: 10.1016/j.virol.2006.05.028
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.


id: cord-272050-0u62j7nj
author: Okamoto, Kimiyuki
date: 2008-05-25
txt: ./txt/cord-272050-0u62j7nj.txt
cache: ./cache/cord-272050-0u62j7nj.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2008.02.004
doi: 10.1016/j.virol.2008.02.004
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

title:
  cis-Preferential requirement of a − 1 frameshift product p88 for the replication 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.


id: cord-272051-arz8r204
author: Federico, Maurizio
date: 2011-08-15
url: https://www.sciencedirect.com/science/article/pii/S0042682211002157
doi: 10.1016/j.virol.2011.05.002
title:
  HIV-protease inhibitors block the replication of both vesicular stomatitis and influenza viruses at an early post-entry replication step

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.


id: cord-272260-88l9bq4i
author: Han, L.Y.
date: 2005-01-05
url: https://api.elsevier.com/content/article/pii/S0042682204006907
doi: 10.1016/j.virol.2004.10.020
title:
  Prediction of functional class of novel viral proteins by a statistical learning method irrespective of sequence similarity

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.


id: cord-272437-gvzfl8c3
author: Zhao, Jing
date: 2020-08-20
txt: ./txt/cord-272437-gvzfl8c3.txt
cache: ./cache/cord-272437-gvzfl8c3.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682220301628
doi: 10.1016/j.virol.2020.08.009
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

title:
  Replicase 1a gene plays a critical role in pathogenesis of avian coronavirus infectious bronchitis virus

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.


id: cord-272871-gu9ptt9y
title: Defective RNAs of clover yellow mosaic virus encode nonstructural/coat protein fusion products
author: White, K.Andrew
date: 1991-08-31
txt: ./txt/cord-272871-gu9ptt9y.txt
cache: ./cache/cord-272871-gu9ptt9y.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/004268229190977J
doi: 10.1016/0042-6822(91)90977-j
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.


id: cord-272925-xag1yaie
title: HIV entry in macrophages is dependent on intact lipid rafts
author: Carter, Gemma C.
date: 2009-03-30
url: https://www.sciencedirect.com/science/article/pii/S0042682208008556
doi: 10.1016/j.virol.2008.12.031
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.


id: cord-273246-4s54jrww
author: Niu, Shengniao
date: 2014-01-20
txt: ./txt/cord-273246-4s54jrww.txt
cache: ./cache/cord-273246-4s54jrww.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/24418557/
doi: 10.1016/j.virol.2013.11.021
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).

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

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.


id: cord-273379-w8vy5rl8
author: Mizutani, Tetsuya
date: 2000-09-30
txt: ./txt/cord-273379-w8vy5rl8.txt
cache: ./cache/cord-273379-w8vy5rl8.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/10998322/
doi: 10.1006/viro.2000.0489
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.

title:
  Nascent Synthesis of Leader Sequence-Containing Subgenomic mRNAs in Coronavirus Genome-Length Replicative Intermediate RNA

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.


id: cord-273487-nfgjz6f9
author: Xu, Zaikun
date: 2012-11-10
url: https://api.elsevier.com/content/article/pii/S0042682212003923
doi: 10.1016/j.virol.2012.08.011
title:
  The helicase activity of DDX56 is required for its role in assembly of infectious West Nile virus particles

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.


id: cord-273745-mwjh5se7
author: Meng, Fandan
date: 2014-03-25
url: https://www.sciencedirect.com/science/article/pii/S0042682214000130
doi: 10.1016/j.virol.2014.01.010
title:
  A phage-displayed peptide recognizing porcine aminopeptidase N is a potent small molecule inhibitor of PEDV entry

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.


id: cord-274122-n9jnu2ah
title: MERS-CoV papain-like protease has deISGylating and deubiquitinating activities
author: Mielech, Anna M.
date: 2014-02-01
url: https://www.sciencedirect.com/science/article/pii/S0042682213006624
doi: 10.1016/j.virol.2013.11.040
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.


id: cord-274172-3dctmmfe
author: Lucas, Alexandra
date: 1978-07-15
txt: ./txt/cord-274172-3dctmmfe.txt
cache: ./cache/cord-274172-3dctmmfe.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/0042682278902891
doi: 10.1016/0042-6822(78)90289-1
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.

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

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.


id: cord-274424-juj71nc5
author: Pulford, David J.
date: 1991-06-30
url: https://api.elsevier.com/content/article/pii/004268229190617K
doi: 10.1016/0042-6822(91)90617-k
title:
  Intracellular processing of the porcine coronavirus transmissible gastroenteritis virus spike protein expressed by recombinant vaccinia virus

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.


id: cord-274480-aywdmj6o
title: Identification of residues on human receptor DPP4 critical for MERS-CoV binding and entry
author: Song, Wenfei
date: 2014-10-21
txt: ./txt/cord-274480-aywdmj6o.txt
cache: ./cache/cord-274480-aywdmj6o.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S004268221400453X
doi: 10.1016/j.virol.2014.10.006
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.


id: cord-274673-tjzlssal
author: De Groot, Raoul J.
date: 1989-08-31
txt: ./txt/cord-274673-tjzlssal.txt
cache: ./cache/cord-274673-tjzlssal.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/2548329/
doi: 10.1016/0042-6822(89)90619-3
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.

title:
  Stably expressed FIPV peplomer protein induces cell fusion and elicits neutralizing antibodies in mice

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.


id: cord-275234-t6e7vr9y
author: Leone, Gustavo
date: 1991-05-31
url: https://api.elsevier.com/content/article/pii/0042682291906774
doi: 10.1016/0042-6822(91)90677-4
title:
  The N-terminal heptad repeat region of reovirus cell attachment protein σ1 is responsible for σ1 oligomer stability and possesses intrinsic oligomerization function

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.


id: cord-275348-jna496x7
author: Kapadia, Sagar U.
date: 2008-06-20
txt: ./txt/cord-275348-jna496x7.txt
cache: ./cache/cord-275348-jna496x7.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682208001736
doi: 10.1016/j.virol.2008.03.002
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.

title:
  SARS vaccine based on a replication-defective recombinant vesicular stomatitis virus is more potent than one based on a replication-competent vector

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.


id: cord-275403-g4rohhtt
author: Bautista, Elida M.
date: 2002-07-05
txt: ./txt/cord-275403-g4rohhtt.txt
cache: ./cache/cord-275403-g4rohhtt.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/12127789/
doi: 10.1006/viro.2002.1495
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 .

title:
  Functional Properties of the Predicted Helicase of Porcine Reproductive and Respiratory Syndrome Virus

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.


id: cord-275664-qbafkxtr
author: Wei, Li
date: 2009-03-30
url: https://www.sciencedirect.com/science/article/pii/S0042682209000348
doi: 10.1016/j.virol.2009.01.010
title:
  Porcine circovirus type 2 replication is impaired by inhibition of the extracellular signal-regulated kinase (ERK) signaling pathway

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.


id: cord-275993-isff6lp2
title: Development of a safe neutralization assay for SARS-CoV and characterization of S-glycoprotein
author: Han, Dong P
date: 2004-08-15
url: https://www.ncbi.nlm.nih.gov/pubmed/15262502/
doi: 10.1016/j.virol.2004.05.017
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.


id: cord-276034-a8pixbuc
author: Zhi, Yan
date: 2005-04-25
url: https://www.ncbi.nlm.nih.gov/pubmed/15823604/
doi: 10.1016/j.virol.2005.01.050
title:
  Identification of murine CD8 T cell epitopes in codon-optimized SARS-associated coronavirus spike protein

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.


id: cord-276358-so390gp4
author: Nieto-Torres, Jose L.
date: 2015-11-30
url: https://doi.org/10.1016/j.virol.2015.08.010
doi: 10.1016/j.virol.2015.08.010
title:
  Severe acute respiratory syndrome coronavirus E protein transports calcium ions and activates the NLRP3 inflammasome

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.


id: cord-277838-931sco95
title: Detection of a group 2 coronavirus in dogs with canine infectious respiratory disease
author: Erles, Kerstin
date: 2003-06-05
url: https://api.elsevier.com/content/article/pii/S0042682203001600
doi: 10.1016/s0042-6822(03)00160-0
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.


id: cord-278578-vq5fy8m5
author: Stodola, Jenny K.
date: 2017-12-26
txt: ./txt/cord-278578-vq5fy8m5.txt
cache: ./cache/cord-278578-vq5fy8m5.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682217304361
doi: 10.1016/j.virol.2017.12.023
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.

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

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.


id: cord-279346-7del8d2p
author: Callendret, Benoît
date: 2007-07-05
url: https://www.ncbi.nlm.nih.gov/pubmed/17331558/
doi: 10.1016/j.virol.2007.01.012
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

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.


id: cord-279432-aik5bo6o
title: Complex formation between influenza virus polymerase proteins expressed in Xenopus oocytes
author: Digard, Paul
date: 1989-07-31
url: https://www.ncbi.nlm.nih.gov/pubmed/2741339/
doi: 10.1016/0042-6822(89)90523-0
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.


id: cord-279813-mrei5kih
author: Temeeyasen, G.
date: 2017-12-14
txt: ./txt/cord-279813-mrei5kih.txt
cache: ./cache/cord-279813-mrei5kih.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29249266/
doi: 10.1016/j.virol.2017.11.024
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).

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

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.


id: cord-279924-09uwhxs9
title: T cell mediated suppression of neurotropic coronavirus replication in neural precursor cells
author: Plaisted, Warren C.
date: 2014-01-01
txt: ./txt/cord-279924-09uwhxs9.txt
cache: ./cache/cord-279924-09uwhxs9.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682213006478
doi: 10.1016/j.virol.2013.11.025
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.


id: cord-280287-t7uozjml
author: Favier, Anne-Laure
date: 2004-04-25
txt: ./txt/cord-280287-t7uozjml.txt
cache: ./cache/cord-280287-t7uozjml.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15063120/
doi: 10.1016/j.virol.2004.01.020
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) .

title:
  Unique physicochemical properties of human enteric Ad41 responsible for its survival and replication in the gastrointestinal tract

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.


id: cord-280795-wtrt13ij
title: Mutational analysis of a helicase motif-based RNA 5′-triphosphatase/NTPase from bamboo mosaic virus
author: Han, Yu-Tsung
date: 2007-10-10
txt: ./txt/cord-280795-wtrt13ij.txt
cache: ./cache/cord-280795-wtrt13ij.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682207003492
doi: 10.1016/j.virol.2007.05.013
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.


id: cord-280957-cdd6ngf1
title: The avian influenza virus PA segment mediates strain-specific antagonism of BST-2/tetherin
author: Narkpuk, Jaraspim
date: 2018-10-02
url: https://doi.org/10.1016/j.virol.2018.09.016
doi: 10.1016/j.virol.2018.09.016
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.


id: cord-281237-asnpuami
author: Garten, Wolfgang
date: 1989-09-30
txt: ./txt/cord-281237-asnpuami.txt
cache: ./cache/cord-281237-asnpuami.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/0042682289901037
doi: 10.1016/0042-6822(89)90103-7
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.

title:
  Inhibition of proteolytic activation of influenza virus hemagglutinin by specific peptidyl chloroalkyl ketones

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


id: cord-281309-c9y7m5do
author: Guo, Baoqing
date: 2013-01-20
txt: ./txt/cord-281309-c9y7m5do.txt
cache: ./cache/cord-281309-c9y7m5do.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682212004540
doi: 10.1016/j.virol.2012.09.013
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.

title:
  Experimental infection of United States swine with a Chinese highly pathogenic strain of porcine reproductive and respiratory syndrome virus

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.


id: cord-281820-oltqsd6n
author: Watanabe, Rie
date: 2007-09-15
txt: ./txt/cord-281820-oltqsd6n.txt
cache: ./cache/cord-281820-oltqsd6n.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/17692355/
doi: 10.1016/j.virol.2007.06.034
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) .

title:
  Heparan sulfate is a binding molecule but not a receptor for CEACAM1-independent infection of murine coronavirus

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.


id: cord-282947-3hgku2e4
author: Wong, Hui Hui
date: 2017-12-30
txt: ./txt/cord-282947-3hgku2e4.txt
cache: ./cache/cord-282947-3hgku2e4.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682217304427
doi: 10.1016/j.virol.2017.12.028
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.

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

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.


id: cord-283035-tpqf458q
title: Analyses of the spleen proteome of chickens infected with Marek's disease virus
author: Thanthrige-Don, Niroshan
date: 2009-08-01
url: https://doi.org/10.1016/j.virol.2009.05.020
doi: 10.1016/j.virol.2009.05.020
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.


id: cord-283309-ovx5fzsg
author: Yang, Yong-Le
date: 2019-08-09
url: https://www.sciencedirect.com/science/article/pii/S0042682219302193
doi: 10.1016/j.virol.2019.08.006
title:
  Characterization of a novel bat-HKU2-like swine enteric alphacoronavirus (SeACoV) infection in cultured cells and development of a SeACoV infectious clone

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.


id: cord-283998-whwksoxt
title: The RNA of human coronavirus OC-43
author: Tannock, Gregory A.
date: 1977-12-31
txt: ./txt/cord-283998-whwksoxt.txt
cache: ./cache/cord-283998-whwksoxt.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/004268227790126X
doi: 10.1016/0042-6822(77)90126-x
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.


id: cord-284581-fl2nt4ak
author: Kleine-Weber, Hannah
date: 2019-07-19
txt: ./txt/cord-284581-fl2nt4ak.txt
cache: ./cache/cord-284581-fl2nt4ak.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682219301916
doi: 10.1016/j.virol.2019.07.016
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.

title:
  Spike proteins of novel MERS-coronavirus isolates from North- and West-African dromedary camels mediate robust viral entry into human target cells

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.


id: cord-284646-fhruiw23
author: Jaeger, Anna S.
date: 2020-05-24
txt: ./txt/cord-284646-fhruiw23.txt
cache: ./cache/cord-284646-fhruiw23.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682220300921
doi: 10.1016/j.virol.2020.05.005
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) .

title:
  Spondweni virus causes fetal harm in Ifnar1(-/-) mice and is transmitted by Aedes aegypti mosquitoes

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.


id: cord-284707-72vx11aq
title: Synthesis of virus-specific RNA in permeabilized murine coronavirus-infected cells
author: Leibowitz, Julian L.
date: 1988-09-30
txt: ./txt/cord-284707-72vx11aq.txt
cache: ./cache/cord-284707-72vx11aq.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/004268228890147X
doi: 10.1016/0042-6822(88)90147-x
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.


id: cord-284968-eymvj6k3
title: Processing of virus-specific glycoproteins of varicella zoster virus
author: Namazue, Junko
date: 1985-05-31
txt: ./txt/cord-284968-eymvj6k3.txt
cache: ./cache/cord-284968-eymvj6k3.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/0042682285901126
doi: 10.1016/0042-6822(85)90112-6
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.


id: cord-285869-jwflooop
title: Mutation in murine coronavirus replication protein nsp4 alters assembly of double membrane vesicles
author: Clementz, Mark A.
date: 2008-05-01
txt: ./txt/cord-285869-jwflooop.txt
cache: ./cache/cord-285869-jwflooop.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682208000378
doi: 10.1016/j.virol.2008.01.018
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.


id: cord-286060-92lazxd7
title: Synthesis and subcellular localization of the murine coronavirus nucleocapsid protein
author: Stohlman, Stephen A.
date: 1983-10-30
txt: ./txt/cord-286060-92lazxd7.txt
cache: ./cache/cord-286060-92lazxd7.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/004268228390106X
doi: 10.1016/0042-6822(83)90106-x
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.


id: cord-286121-ltaxmp3u
title: Severe acute respiratory syndrome coronavirus accessory protein 9b is a virion-associated protein
author: Xu, Ke
date: 2009-06-05
txt: ./txt/cord-286121-ltaxmp3u.txt
cache: ./cache/cord-286121-ltaxmp3u.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2009.03.032
doi: 10.1016/j.virol.2009.03.032
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.


id: cord-286232-jo24ia4s
title: Infectious entry of equine herpesvirus-1 into host cells through different endocytic pathways
author: Hasebe, Rie
date: 2009-10-25
txt: ./txt/cord-286232-jo24ia4s.txt
cache: ./cache/cord-286232-jo24ia4s.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S004268220900470X
doi: 10.1016/j.virol.2009.07.032
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.


id: cord-287620-vuvgi8xx
author: Butler, Noah
date: 2006-04-10
txt: ./txt/cord-287620-vuvgi8xx.txt
cache: ./cache/cord-287620-vuvgi8xx.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16413043/
doi: 10.1016/j.virol.2005.11.044
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.

title:
  Murine encephalitis caused by HCoV-OC43, a human coronavirus with broad species specificity, is partly immune-mediated

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.


id: cord-287777-ogs4mq0v
title: Deubiquitination in virus infection
author: Lindner, Holger A.
date: 2007-06-05
txt: ./txt/cord-287777-ogs4mq0v.txt
cache: ./cache/cord-287777-ogs4mq0v.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/17291557/
doi: 10.1016/j.virol.2006.12.035
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.


id: cord-288669-46tkedw7
author: Lee, Changhee
date: 2006-11-10
txt: ./txt/cord-288669-46tkedw7.txt
cache: ./cache/cord-288669-46tkedw7.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682206004521
doi: 10.1016/j.virol.2006.07.013
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) .

title:
  The small envelope protein of porcine reproductive and respiratory syndrome virus possesses ion channel protein-like properties

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.


id: cord-289045-vft163v0
author: Thackray, Larissa B.
date: 2005-03-30
txt: ./txt/cord-289045-vft163v0.txt
cache: ./cache/cord-289045-vft163v0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15749126/
doi: 10.1016/j.virol.2005.01.016
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.

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

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.


id: cord-289152-w5ynbewh
title: Porcine arterivirus activates the NF-κB pathway through IκB degradation
author: Lee, Sang-Myeong
date: 2005-11-10
txt: ./txt/cord-289152-w5ynbewh.txt
cache: ./cache/cord-289152-w5ynbewh.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16129468/
doi: 10.1016/j.virol.2005.07.034
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.


id: cord-289248-6mx4o0eb
author: Wang, Yilong
date: 2018-05-01
txt: ./txt/cord-289248-6mx4o0eb.txt
cache: ./cache/cord-289248-6mx4o0eb.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2018.02.022
doi: 10.1016/j.virol.2018.02.022
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.

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

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.


id: cord-289712-w1y0lc5c
author: Flintoff, Wayne F.
date: 1984-04-30
url: https://api.elsevier.com/content/article/pii/004268228490312X
doi: 10.1016/0042-6822(84)90312-x
title:
  Replication of murine coronaviruses in somatic cell hybrids between murine fibroblasts and rat Schwannoma cells

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.


id: cord-289991-wx4rsr4g
title: Rotavirus infection induces G1 to S phase transition in MA104 cells via Ca(+2)/Calmodulin pathway
author: Bhowmick, Rahul
date: 2014-03-21
txt: ./txt/cord-289991-wx4rsr4g.txt
cache: ./cache/cord-289991-wx4rsr4g.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S004268221400083X
doi: 10.1016/j.virol.2014.03.001
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.


id: cord-290231-4m9lj0uq
author: Guirakhoo, Farshad
date: 1992-12-31
txt: ./txt/cord-290231-4m9lj0uq.txt
cache: ./cache/cord-290231-4m9lj0uq.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/1280384/
doi: 10.1016/0042-6822(92)90267-s
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.

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

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.


id: cord-290282-oxyzndsj
author: Ortego, Javier
date: 2003-03-30
txt: ./txt/cord-290282-oxyzndsj.txt
cache: ./cache/cord-290282-oxyzndsj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/12706086/
doi: 10.1016/s0042-6822(02)00096-x
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) .

title:
  Transmissible gastroenteritis coronavirus gene 7 is not essential but influences in vivo virus replication and virulence

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.


id: cord-290640-kh2t0kfz
title: Downstream Ribosomal Entry for Translation of Coronavirus TGEV Gene 3b
author: O''Connor, Jennifer Black
date: 2000-03-30
txt: ./txt/cord-290640-kh2t0kfz.txt
cache: ./cache/cord-290640-kh2t0kfz.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682200902186
doi: 10.1006/viro.2000.0218
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.


id: cord-290883-r2744fb3
author: TORRES, JUAN M.
date: 1995-11-30
txt: ./txt/cord-290883-r2744fb3.txt
cache: ./cache/cord-290883-r2744fb3.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682285700232
doi: 10.1006/viro.1995.0023
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).

title:
  Induction of Antibodies Protecting against Transmissible Gastroenteritis Coronavirus (TGEV) by Recombinant Adenovirus Expressing TGEV Spike Protein

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.


id: cord-290993-bsnja161
author: McAuliffe, Josephine
date: 2004-12-05
url: https://www.ncbi.nlm.nih.gov/pubmed/15527829/
doi: 10.1016/j.virol.2004.09.030
title:
  Replication of SARS coronavirus administered into the respiratory tract of African Green, rhesus and cynomolgus monkeys

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.


id: cord-291192-wm2eyaam
title: Antigenic structures stably expressed by recombinant TGEV-derived vectors
author: Becares, Martina
date: 2014-08-09
txt: ./txt/cord-291192-wm2eyaam.txt
cache: ./cache/cord-291192-wm2eyaam.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682214003353
doi: 10.1016/j.virol.2014.07.027
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.


id: cord-291306-g9qmmugg
author: Vey, Martin
date: 1992-05-31
txt: ./txt/cord-291306-g9qmmugg.txt
cache: ./cache/cord-291306-g9qmmugg.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/004268229290775K
doi: 10.1016/0042-6822(92)90775-k
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) .

title:
  Hemagglutinin activation of pathogenic avian influenza viruses of serotype H7 requires the protease recognition motif R-X-K/R-R

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.


id: cord-291611-cfe8yujp
author: Zhang, Xuming
date: 1991-07-31
txt: ./txt/cord-291611-cfe8yujp.txt
cache: ./cache/cord-291611-cfe8yujp.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/2053289/
doi: 10.1016/0042-6822(91)90154-4
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.

title:
  Comparison of the nucleotide and deduced amino acid sequences of the S genes specified by virulent and avirulent strains of bovine coronaviruses

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.


id: cord-292019-rfu0bkag
author: Gómez, N.
date: 1998-09-30
txt: ./txt/cord-292019-rfu0bkag.txt
cache: ./cache/cord-292019-rfu0bkag.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/9791026/
doi: 10.1006/viro.1998.9315
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.

title:
  Expression of Immunogenic Glycoprotein S Polypeptides from Transmissible Gastroenteritis Coronavirus in Transgenic Plants

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.


id: cord-292751-tk1oggi9
author: Hosseini, Elahe Seyed
date: 2020-09-24
txt: ./txt/cord-292751-tk1oggi9.txt
cache: ./cache/cord-292751-tk1oggi9.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2020.08.011
doi: 10.1016/j.virol.2020.08.011
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

title:
  The novel coronavirus Disease-2019 (COVID-19): Mechanism of action, detection and recent therapeutic strategies

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.


id: cord-293248-8vtd9e4n
title: Determination and analysis of the full-length chicken parvovirus genome
author: Day, J. Michael
date: 2010-03-30
txt: ./txt/cord-293248-8vtd9e4n.txt
cache: ./cache/cord-293248-8vtd9e4n.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/20097398/
doi: 10.1016/j.virol.2009.12.027
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.


id: cord-293375-qcy56ui7
title: Identification of the active site residues in the nsP2 proteinase of sindbis virus
author: Strauss, Ellen G.
date: 1992-12-31
txt: ./txt/cord-293375-qcy56ui7.txt
cache: ./cache/cord-293375-qcy56ui7.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/004268229290268T
doi: 10.1016/0042-6822(92)90268-t
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.


id: cord-293635-36pmai6s
title: Differential roles of CCL2 and CCR2 in host defense to coronavirus infection
author: Held, Katherine S.
date: 2004-11-24
txt: ./txt/cord-293635-36pmai6s.txt
cache: ./cache/cord-293635-36pmai6s.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15518805/
doi: 10.1016/j.virol.2004.09.006
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.


id: cord-293790-7hyelm88
author: Guévin, Carl
date: 2010-09-01
txt: ./txt/cord-293790-7hyelm88.txt
cache: ./cache/cord-293790-7hyelm88.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682210003764
doi: 10.1016/j.virol.2010.05.032
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.

title:
  Autophagy protein ATG5 interacts transiently with the hepatitis C virus RNA polymerase (NS5B) early during infection

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.


id: cord-294056-7e477y1x
author: La Monica, Nicola
date: 1992-05-31
txt: ./txt/cord-294056-7e477y1x.txt
cache: ./cache/cord-294056-7e477y1x.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/1566582/
doi: 10.1016/0042-6822(92)90774-j
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.

title:
  Coronavirus mRNA synthesis: Identification of novel transcription initiation signals which are differentially regulated by different leader sequences

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.


id: cord-294260-g410mavp
title: Subgenomic messenger RNAs: Mastering regulation of (+)-strand RNA virus life cycle
author: Sztuba-Solińska, Joanna
date: 2011-04-10
txt: ./txt/cord-294260-g410mavp.txt
cache: ./cache/cord-294260-g410mavp.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2011.02.007
doi: 10.1016/j.virol.2011.02.007
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.


id: cord-294990-jdjbjkcp
author: Thuy, Nguyen Thanh
date: 2013-07-25
txt: ./txt/cord-294990-jdjbjkcp.txt
cache: ./cache/cord-294990-jdjbjkcp.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682213004005
doi: 10.1016/j.virol.2013.06.030
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.

title:
  A new nidovirus (NamDinh virus NDiV): Its ultrastructural characterization in the C6/36 mosquito cell line

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.


id: cord-296075-8axbkyyz
author: Castro, Raymond F.
date: 1996-08-01
txt: ./txt/cord-296075-8axbkyyz.txt
cache: ./cache/cord-296075-8axbkyyz.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682296904158
doi: 10.1006/viro.1996.0415
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.

title:
  Differential Antigen Recognition by T Cells from the Spleen and Central Nervous System of Coronavirus-Infected 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.


id: cord-296364-7rp60d2m
author: Youn, Soonjeon
date: 2005-02-05
txt: ./txt/cord-296364-7rp60d2m.txt
cache: ./cache/cord-296364-7rp60d2m.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682204007421
doi: 10.1016/j.virol.2004.10.045
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 ).

title:
  In vitro assembled, recombinant infectious bronchitis viruses demonstrate that the 5a open reading frame is not essential for replication

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.


id: cord-296416-q0rsfzgw
author: LAVI, EHUD
date: 1996-07-15
txt: ./txt/cord-296416-q0rsfzgw.txt
cache: ./cache/cord-296416-q0rsfzgw.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/8661443/
doi: 10.1006/viro.1996.0382
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.

title:
  Syncytia Formation Induced by Coronavirus Infection Is Associated with Fragmentation and Rearrangement of the Golgi Apparatus

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.


id: cord-297712-yy4g5npi
title: Porcine deltacoronavirus nsp5 inhibits interferon-β production through the cleavage of NEMO
author: Zhu, Xinyu
date: 2016-12-13
txt: ./txt/cord-297712-yy4g5npi.txt
cache: ./cache/cord-297712-yy4g5npi.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682216303786
doi: 10.1016/j.virol.2016.12.005
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.


id: cord-298847-szezd2vb
title: Vacuolating encephalitis in mice infected by human coronavirus OC43
author: Jacomy, Hélène
date: 2003-10-10
txt: ./txt/cord-298847-szezd2vb.txt
cache: ./cache/cord-298847-szezd2vb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/14592756/
doi: 10.1016/s0042-6822(03)00323-4
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.


id: cord-298934-vtrfqozl
title: Primary structure and translation of a defective interfering rna of murine coronavirus
author: Makino, Shinji
date: 1988-10-31
txt: ./txt/cord-298934-vtrfqozl.txt
cache: ./cache/cord-298934-vtrfqozl.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/0042682288905260
doi: 10.1016/0042-6822(88)90526-0
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.


id: cord-299122-djfj4262
author: Yu, Hua
date: 2007-03-15
txt: ./txt/cord-299122-djfj4262.txt
cache: ./cache/cord-299122-djfj4262.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/17055022/
doi: 10.1016/j.virol.2006.09.016
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).

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()

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.


id: cord-299976-36r794ow
author: O’Brien, Amornrat
date: 2018-12-01
txt: ./txt/cord-299976-36r794ow.txt
cache: ./cache/cord-299976-36r794ow.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2018.08.022
doi: 10.1016/j.virol.2018.08.022
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.

title:
  Characterizing replication kinetics and plaque production of type I feline infectious peritonitis virus in three feline cell lines

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.


id: cord-299994-1ksfo0pr
author: Kanitz, Manuel
date: 2019-05-02
txt: ./txt/cord-299994-1ksfo0pr.txt
cache: ./cache/cord-299994-1ksfo0pr.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682219301151
doi: 10.1016/j.virol.2019.05.001
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) .

title:
  Structural basis for catalysis and substrate specificity of a 3C-like cysteine protease from a mosquito mesonivirus

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.


id: cord-300372-h5g4z8ts
author: Kelvin, Alyson A.
date: 2014-04-01
txt: ./txt/cord-300372-h5g4z8ts.txt
cache: ./cache/cord-300372-h5g4z8ts.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682214000439
doi: 10.1016/j.virol.2014.01.030
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).

title:
  Lack of Group X Secreted Phospholipase A(2) Increases Survival Following Pandemic H1N1 Influenza Infection

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.


id: cord-300470-vgd1ol2z
author: Conradie, Andelé M.
date: 2016-09-19
txt: ./txt/cord-300470-vgd1ol2z.txt
cache: ./cache/cord-300470-vgd1ol2z.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2016.07.010
doi: 10.1016/j.virol.2016.07.010
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.

title:
  Establishment of different plasmid only-based reverse genetics systems for the recovery of African horse sickness virus

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.


id: cord-300810-a1skdp67
author: Lafay, F.
date: 1991-07-31
txt: ./txt/cord-300810-a1skdp67.txt
cache: ./cache/cord-300810-a1skdp67.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/0042682291901452
doi: 10.1016/0042-6822(91)90145-2
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.

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:
  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.


