Typing tool
|
Complete norovirus genomes
OR262327 | GII.4 San Francisco | ||
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GII.P31 |
ORF1: 1..5088 ORF2: 5069..6694 ORF3: 6694..7500LOCUS OR262327 7546 bp RNA linear VRL 11-DEC-2023 DEFINITION Norovirus GII isolate Hu/GII.4 San Francisco[P31]/WT-NORO-1808/2021/UK nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION OR262327 VERSION OR262327.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7546) AUTHORS Chhabra,P., Tully,D.C., Mans,J., Niendorf,S., Barclay,L., Cannon,J.L., Montmayeur,A.M., Pan,C.Y., Page,N., Williams,R., Tutill,H., Roy,S., Celma,C., Beard,S., Mallory,M.L., Manouana,G.P., Velavan,T.P., Adegnika,A.A., Kremsner,P.G., Lindesmith,L.C., Hue,S., Baric,R.S., Breuer,J. and Vinje,J. TITLE Emergence of Novel Norovirus GII.4 Variant JOURNAL Emerg Infect Dis 30 (1) (2023) In press PUBMED 38063078 REMARK Publication Status: Available-Online prior to print REFERENCE 2 (bases 1 to 7546) AUTHORS Tutill,H.J., Williams,R.J., Roy,S. and Breuer,J. TITLE Direct Submission JOURNAL Submitted (12-JUL-2023) Viral Gastroenteritis Branch, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, USA COMMENT ##Assembly-Data-START## Assembly Method :: CLC Genomics Workbench v. 11.0.01 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7546 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="Hu/GII.4 San Francisco[P31]/WT-NORO-1808/2021/UK" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="Jul-2021" /note="genotype: GII.4 San Francisco[P31]" gene <1..5088 /gene="ORF1" CDS <1..5088 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="WKD81254.1" /translation="SNDASAAAAANSNNDIEKSSSDGVFSNMAVTFKRALGARPKQPP PKEIPPRPPRPPTPELAKKIPPPPPNGEDELVVSYSAKGGVSGLPELTTVSQPEENNT AFSVPPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAKV ELAPLSLFWRPVYTPQYLISPDTLKRLHGELFPYTAFDNNCYAFCCWVLDLNDSWLSR RMIQRTTGFFRPCQEWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLKPL NILNILATCDWTFPGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE ANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSAS PDIVGTINALLARIAAARSLVHRAKEELSSRLRPVVVMISGKPGIGKTHLARELAKKI AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL NCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPGVEKAKHD FPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL HERLDEYELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMSDLK QALKNVSIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLRCARI RYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEETTNKDGCPKPK EDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSE IRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLFI TSTHVIPQGANEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVAT LLIKRPTGELMPLAARMGTHATMRIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCP YIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSA PKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKP PRPSVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGES FTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMI RCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQ RDVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQILISEGLPSGVPCTSQWN SIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGL KPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHED PSETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVIAELKEGGMDFYVPRQEPMFR WMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide <1..978 /gene="ORF1" /product="p48" mat_peptide 979..2076 /gene="ORF1" /product="NTPase" mat_peptide 2077..2613 /gene="ORF1" /product="p22" mat_peptide 2614..3012 /gene="ORF1" /product="VPg" mat_peptide 3013..3555 /gene="ORF1" /product="Pro" mat_peptide 3556..5085 /gene="ORF1" /product="RdRp" gene 5069..6694 /gene="ORF2" CDS 5069..6694 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="WKD81255.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSTFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGSVTQTATGSHNYTMNLASQNWNSYDPTEDIPAPLGTPDFVGKIQGV LTQTTRGDGSTRGHKATLYTGSNDFTPKLGRVQFETDTNHDFEANQNTKFTPVGVIQN GDTAHRNEPQQWVLPSYSGRNTHNVHLAPVVAPTFPGEQLLFFRSTLPGCSGYPNMDL DCLLPQEWVQYFYQEAAPAQSEVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDL VIPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6694..7500 /gene="ORF3" CDS 6694..7500 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="WKD81256.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANFRNAAPARGSSSTPS NSSIATSVYSNQTASTRLGSTAGSGTSVSSPPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTHRQPLFAHIRRRGESRV" ORIGIN 1 tctaacgacg cttccgctgc cgctgctgct aacagcaaca acgacatcga aaaatcttca 61 agtgacggtg tgttttctaa catggctgtc acttttaagc gggccctcgg ggcgcggccc 121 aaacagccgc ccccgaagga aataccaccc agacccccac gaccacccac accagagttg 181 gccaaaaaga tcccacctcc cccacccaat ggggaggatg aactagtggt ttcttacagc 241 gccaaaggcg gcgtttccgg attgcctgag ctcaccaccg tcagccaacc agaagaaaac 301 aacacggcgt tcagtgttcc cccgctcaat caaagggaga atagggacgc taaggaacca 361 ctaactggaa cgatcattga gatgtgggat ggggaaatct atcattacgg cctgtacgta 421 gaacgaggcc ttatacttgg tgtgcacaag ccaccggcag ccatcagcct tgccaaagtt 481 gagctagcac cactctctct gttctggaga cctgtgtata ccccccagta cctcatctct 541 ccagacactc ttaagagact acatggagag ttattcccct acaccgcatt tgacaacaac 601 tgctacgcct tctgctgttg ggtgttagac ctaaacgact catggttaag taggagaatg 661 attcagagaa caacaggttt cttcaggcca tgccaagagt ggaacaggaa acccctcccc 721 actatggatg actccaaatt gaagaaggta gccaacatat tcttgtgcac tttgtcttca 781 ctattcacca ggcccattaa ggacataata ggaaaattga aacctctcaa catcctcaat 841 attctggcca catgtgattg gaccttccca ggcatagtgg aatccctgat actcttggca 901 gaactctttg gagttttctg gacaccccca gatgtgtctg cgatgatcgc ccccttacta 961 ggtgattatg aactgcaagg gcctgaggac cttgcagtag aactggtccc agtggtaatg 1021 ggggggatag gtttggtgct aggattcacc aaagagaaaa ttggaaagat gctgtcgtcc 1081 gctgcatcca ccttgagagc ttgcaaagac cttggtgcat acggactgga aattttgaaa 1141 ctagtcatga agtggttctt tccaaagaaa gaggaagcaa atgaactggc tatggtgaga 1201 tccatcgagg acgcagtgct agacctcgag gcaatcgaaa acaaccatat gaccaccctg 1261 ctcaaggaca aagacagctt ggcaacctac atgagaaccc ttgaccttga ggaggagaaa 1321 gccagaaaac tctcaaccaa gtccgcttca cctgatattg tgggcacaat caacgctctt 1381 ctggcacgaa tcgccgctgc acgctcccta gtgcatcggg cgaaagagga gctctccagc 1441 aggctgagac ctgttgttgt gatgatatcg ggaaaaccag ggatagggaa aactcacctt 1501 gccagggagt tggccaaaaa gatcgcagcc tccctcacag gggaccagcg tgtgggtttg 1561 atcccacgca acggcgtcga ccactgggat gcatacaagg gtgaaagagt tgtcctttgg 1621 gacgactatg ggatgagtaa ccccatacac gatgccctca ggttgcagga acttgctgac 1681 acttgccccc tcacactaaa ttgtgatagg attgagaaca aaggaaaagt ctttgatagc 1741 gatgccataa ttattaccac caatctggcc aacccagcac cactggatta tgtcaatttt 1801 gaagcgtgtt cgaggcgcat tgacttcctc gtgtacgcgg aagctcctgg ggtggagaag 1861 gcaaaacacg acttcccagg ccaacctgac atgtggaaga acgctttcag ctctgacttc 1921 tcacacataa aactggcatt ggctccacag ggtggttttg acaagaacgg taacaccccg 1981 catggaaaag gtgtcatgaa gaccctcacc actggctctc tcatcgcccg agcatcaggg 2041 ttactccacg agaggctaga tgaatatgaa ttacaaggcc ctgccctcac cactttcaac 2101 tttgaccgca ataaggtact tgcttttagg cagctcgctg ctgaaaacaa gtatggtcta 2161 atggacacaa tgagagttgg aaaacagctc aaggatgtca aaactatgtc agaccttaaa 2221 caagcactca agaatgtttc gatcaagaaa tgccagatag tgtacaatgg tggcacctac 2281 acacttgaag ccgacggcaa gggtagtgtg aaagttgaca aggtgcaaag tgccaccgtg 2341 caaaccaaca atgaactagc cggcgccctg caccacctaa ggtgcgccag aattaggtat 2401 tatgtcaagt gtgtccagga ggcgctgtac tccatcatcc aaatcgctgg ggctgcgttt 2461 gtcaccacgc gcatcgccaa gcgcatgaat atacaaaatc tctggtccaa gccacaggtg 2521 gaagacacag aagagacaac caacaaagat ggttgcccaa aacccaaaga ggatgaagag 2581 ttcgtcgttt catccgacga cattaaaact gagggcaaga aagggaagaa caagtccggc 2641 cgtggcaaga agcacacagc cttctcaagt aaagggctca gtgatgaaga gtacgatgag 2701 tacaagagaa ttagagaaga gaggaatggt aagtactcca ttgaggagta cctccaggac 2761 agagacaaat actatgagga agtggccatt gccagggcaa ctgaagagga cttctgtgaa 2821 gaagaagagg ccaaaatccg gcagagaatc ttcaggccaa caaggaaaca acgtaaagaa 2881 gagagggcct ctctaggctt ggtcacaggc tcagaaatca ggaagagaaa cccagaagac 2941 ttcaaaccca agggaaagct gtgggctgat gatgacagaa gtgttgacta caacgagaag 3001 ctcaactttg aggccccacc aagcatctgg tcgcggatag tcaactttgg ttcaggttgg 3061 ggtttctggg tctcccccag tctgtttata acgtcaaccc atgtcatacc ccaaggtgca 3121 aacgagttct tcggagtccc catcaaacaa atccagatac acaaatcagg tgaattctgc 3181 cgactgagat tcccaaaacc aatcagaact gatgtgacgg gcatgattct ggaagaaggt 3241 gcgccagaag gaaccgtggc cacactgctc atcaagagac caactggaga gctcatgcct 3301 ttggcagcca gaatgggaac ccatgcaacc atgaggattc aggggcgcac ggttggagga 3361 caaatgggta tgctcttgac aggatccaac gccaagagta tggacttggg cacaacgcca 3421 ggcgactgtg gctgtcccta catctacaaa agagggaacg actacgtggt tataggagtc 3481 catacagccg ctgcccgtgg agggaacact gtcatctgcg ccacccaggg tagtgaagga 3541 gaagccacac ttgaaggagg tgacaataaa ggaacgtact gtggtgcacc aattttgggc 3601 ccagggagtg ctccgaaact cagtactaaa accaagtttt ggagatcatc cacaacgcca 3661 ctcccaccag gcacctacga accagcctac ctcggtggca aggaccccag agtcaaaggt 3721 ggcccttcat tgcaacaagt tatgagggac caactaaaac cattcacaga acccagaggc 3781 aaaccgccaa gaccaagtgt gttggaagct gccaagaaaa ccatcattaa tgtccttgag 3841 caaacaattg acccacccca aaaatggtcg ttcgcgcaag cttgcgcatc ccttgacaaa 3901 accacctcca gcggccatcc gcatcacatg cggaaaaacg actgctggaa tggggaatcc 3961 tttacaggaa aattggcaga tcaggcctcc aaggccaacc taatgtttga agagggtaag 4021 aacatgactc cagtctacac aggtgcgctt aaagatgaat tagtgaagac tgacaagatt 4081 tatggtaaga tcaagaagag gctcctgtgg ggctcggacc tggcgaccat gatacggtgc 4141 gcccgggctt tcgggggcct tatggatgaa ctcaaggcac attgtgtcac ccttcctgtc 4201 agagttggta tgaacatgaa tgaagatggc cccataatct ttgagaagca ctccagatat 4261 aagtatcatt atgatgctga ttactccagg tgggactcga cacaacaaag ggatgtgcta 4321 gcagcagcac tagaaatcat ggttaagttt tctccagaac cacacttggc ccagatagtt 4381 gcagaagacc tcctttcccc tagtgtaatg gatgtgggtg acttccagat attaataagt 4441 gaaggactcc cctctggagt accttgcacc tcccagtgga actccatcgc ccactggctc 4501 ctcacccttt gtgcactctc tgaagtcacg gacctgtccc ctgacatcat tcaggccaac 4561 tcccttttct ccttctatgg tgatgatgag attgtgagta cagacataaa gttggaccca 4621 gagaagctga cggcaaaact caaggagtac gggctgaagc caacccgccc cgacaaaact 4681 gaaggacccc ttgtcatctc tgaagatctg gatggcctga cattcctccg gaggactgtg 4741 acccgtgacc cagctggctg gtttggaaaa ttggaacaaa gttcgattct caggcaaatg 4801 tactggacca ggggtcccaa ccatgaagac ccatctgaaa caatgatacc acactcccaa 4861 aggcccatac aattgatgtc cttgctaggc gaggctgcac tccacggccc atcattttac 4921 agcaaaatta gcaaattggt cattgcagaa ttgaaggaag gtggcatgga tttttacgtg 4981 cccagacaag agccaatgtt cagatggatg agattctcag atctgagcac gtgggagggc 5041 gatcgcaatc tggctcccag ttttgtgaat gaagatggcg tcgagtgacg ccaacccatc 5101 tgatgggtcc gcagccaacc tcgtcccaga ggtcaacaat gaggttatgg ctctggagcc 5161 cgttgttggt gccgctattg cggcgcctgt agcgggccaa caaaatgtga ttgacccctg 5221 gattagaaat aattttgtgc aagcccctgg tggagagttt acagtatccc ctagaaacgc 5281 tccaggtgaa atactatgga gcgcaccctt aggccctgat ctaaacccct acctatccca 5341 tttggctaga atgtataatg gttatgcagg tggttttgaa gtgcaggtaa ttcttgcggg 5401 gaatgcgttc accgccggaa agatcatatt tgcagcagtc ccaccaaatt tcccaactga 5461 aggcttgagc ccaagccagg tcactatgtt cccccatata atagtagatg ttagacaact 5521 ggagcctgtg ttgatcccct tacccgatgt taggaataat ttctatcact ataaccaatc 5581 aaatgacccc accattaagt tgatagcaat gttgtataca ccacttaggg ctaataatgc 5641 tggggatgat gtcttcacgg tttcttgccg agtcctcacg agaccatccc ctgattttga 5701 tttcatattc ttagtaccac ccacagttga atcaagaact aaaccattct ctgtcccaat 5761 tttaactgtt gaggagatga ctaattcaag attccccatt cctttggaaa aattgttcac 5821 aggtcccagc agtacctttg ttgttcaacc acagaatggt aggtgtacga ctgatggcgt 5881 gctcctaggt accacccaat tgtcacctgt caacatctgc accttcagag ggagtgtcac 5941 ccaaacagcg acaggtagtc ataactacac aatgaatctg gcttcccaaa attggaacag 6001 ttatgatcca acagaagaca tcccagcccc tctaggaact ccagatttcg tagggaagat 6061 tcaaggtgtg ctcacccaga ccacaagagg agatggctca acacgcggcc acaaagccac 6121 attgtatact gggagcaacg atttcactcc aaaactgggt agggtccaat ttgaaactga 6181 cacaaaccac gattttgagg ccaaccaaaa cacaaagttc actccggtcg gcgtcatcca 6241 gaacggagac actgcccacc gaaatgaacc tcaacaatgg gtgctcccaa gttattcagg 6301 cagaaacact cataatgtgc atctggcccc cgttgtagct cccacttttc cgggcgagca 6361 gctcctcttc ttcagatcta ccttgcctgg atgcagcggg tatcccaaca tggatttgga 6421 ttgtctactc ccccaggaat gggtgcagta cttctatcaa gaggcagccc cagcacaatc 6481 tgaagtggct ctgttgaggt ttgtgaatcc agacacaggt agggttttgt ttgagtgtaa 6541 gctccacaaa tcgggctatg tcacagtggc ccacactggc caacatgatt tggttatccc 6601 ccccaatggt tatttcagat ttgattcctg ggtcaaccaa ttctacacgc ttgcccccat 6661 gggaaatgga acggggcgca gacgtgcatt ataatggctg gagctttctt tgctggattg 6721 gcatctgatg tccttggctc tggacttggt tccctgatca acgctggggc tggggccatc 6781 aatcaaaaga ttgaatttga aaacaacaga aaattgcaac aagcttcatt ccaatttagt 6841 agcaacctac aacaggcttc ctttcaacat gacaaagaga tgctccaagc acaaattgag 6901 gccaccaaaa agctgcaaca ggaaatgatg aaagttaagc aggcagtgct cctagagggt 6961 gggttttctg agacagatgc agcccgcgga gcaatcaacg cccctatgac aaaagctttg 7021 gactggagcg gtacaaggta ttgggcaccc gatgctagga ctacaacata caatgcaggc 7081 cgcttctcta ccccccaacc atcgggggca ctgccaggaa gagctaactt caggaatgct 7141 gcccccgctc ggggttcctc tagtacaccc tccaattcct ctattgctac ttctgtgtac 7201 tcaaatcaaa ctgcttcaac gagacttggt tctacagccg gttctgggac cagtgtctcg 7261 agccccccgt caactgcaag gactaggagc tgggttgagg atcaaaacag gaatctgtcg 7321 cctttcatga ggggggccca caacatatcg tttgtcaccc caccatctag cagatcctct 7381 agccaaggca cagtctcaac cgtgcctaaa gaagttttgg actcctggac tggtgctttc 7441 aacacgcaca ggcagcctct cttcgctcac attcgtaggc gaggggagtc acgggtgtaa 7501 tgtgaaaaga caaaattgat tatctttctt ttctttagtg tctttt //