Typing tool
|
Complete norovirus genomes
OR262329 | GII.4 San Francisco | ||
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GII.P31 |
ORF1: 1..5078 ORF2: 5059..6684 ORF3: 6684..7490LOCUS OR262329 7500 bp RNA linear VRL 11-DEC-2023 DEFINITION Norovirus GII isolate Hu/GII.4 San Francisco[P31]/WT-NORO-2177/2021/UK nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION OR262329 VERSION OR262329.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7500) 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 7500) 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..7500 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="Hu/GII.4 San Francisco[P31]/WT-NORO-2177/2021/UK" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="02-Nov-2021" /note="genotype: GII.4 San Francisco[P31]" gene <1..5078 /gene="ORF1" CDS <1..5078 /gene="ORF1" /codon_start=3 /product="nonstructural polyprotein" /protein_id="WKD81260.1" /translation="SAAAAANSNNDIEKSSGDGVFSNMAVTFKRALGARPKQPSPREK PPRPPRPPTPELVKRIPSPPPNGEDELVVSYSAKDGISGLPELTTVSQPEENNTAFSV PPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAKVELAP LSLFWRPVYTPQYLISPDTLKRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQ RTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLKPLNILN ILATCDWTFPGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPV VMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEETNEL AMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMKTLDLEEEKARKLSTKSASPDIV GTINALLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLARELAKKIAASL TGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDR IENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPGVEKAKHDFPGQ PDMWKNAFSPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERL DEYELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPDLKQALK NVAIKKCQIVYNGGTYTLEADGKGGVRVDKVQSATVQTNNELAGALHHLRCARIRYYV KCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEETTSKDGCPKPKDDEE FVVSSDDIRTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYL QDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKR NPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTH VIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLLIK RPTGELMPLAARMGTHATMRIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYK RGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSAPKLS TKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPN VLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGK LADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCAR AFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRDVL AAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCTSQWNSIAH WLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTR PDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSET MIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRF SDLSTWEGDRNLAPSFVNEDGVE" mat_peptide <1..968 /gene="ORF1" /product="p48" mat_peptide 969..2066 /gene="ORF1" /product="NTPase" mat_peptide 2067..2603 /gene="ORF1" /product="p22" mat_peptide 2604..3002 /gene="ORF1" /product="VPg" mat_peptide 3003..3545 /gene="ORF1" /product="Pro" mat_peptide 3546..5075 /gene="ORF1" /product="RdRp" gene 5059..6684 /gene="ORF2" CDS 5059..6684 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="WKD81261.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALDPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGSVTQTAAGSHNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGM LTQTTRGDGSTRGHKATVYTGSNDFAPKLGRVQFETDTTNDFETNQNTKFTPVGVIQN GDTAHRNEPQQWVLPSYSGRDTHNVHLAPAVAPTFPGEQLLFFRSTLPGCSGYPNMDL DCLLPQEWVQYFYQEAAPAQSEVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDL VIPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6684..7490 /gene="ORF3" CDS 6684..7490 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="WKD81262.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPPGALPGRANLRNAVPARGSSNTPS NSSIATSVYSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTHRQPLFAHIRRRGESRV" ORIGIN 1 cttccgctgc cgctgctgct aacagcaaca acgacatcga aaaatcttca ggtgacggtg 61 tgttttctaa catggctgtc acttttaagc gggccctcgg ggcgcggcct aaacagccgt 121 ccccgaggga aaaaccaccc agacccccac gaccacccac accagagttg gtcaaaagga 181 tcccatctcc cccacccaac ggggaggatg aactagtggt ttcttacagc gccaaagacg 241 gcatttccgg attgcctgag ctcaccaccg tcagccaacc ggaagaaaac aacacggcgt 301 tcagtgttcc cccgctcaat caaagggaga acagggacgc taaggaacca ctaactggaa 361 caatcattga gatgtgggat ggggaaatct atcattatgg cctgtacgta gaacgaggcc 421 ttatacttgg tgtgcataag ccaccggcag ccatcagtct tgccaaagtt gagctagcac 481 cactctcttt gttctggaga cctgtgtaca cccctcagta cctcatctct ccagacactc 541 ttaagagact acatggagag tcatttccct acaccgcatt tgacaacaat tgctacgcct 601 tttgctgttg ggtgttggac ctaaacgact catggctaag taggagaatg attcagagga 661 caacaggttt ctttagacca taccaagaat ggaacaggaa acccctcccc actatggatg 721 actccaaatt gaagaaggtg gccaacatat ttttgtgcac cttgtcttca ctattcacca 781 gacccattaa ggacataata ggaaaattga aacctcttaa catcctcaat attctggcca 841 catgtgattg gaccttccca ggtatagtgg agtccctaat actcttggca gaactctttg 901 gagttttctg gacaccccca gatgtgtctg cgatgatcgc ccccttacta ggtgattatg 961 aactacaagg acctgaggac cttgcagtag aactggtccc agtggtgatg ggggggatag 1021 gtttggtgct aggattcacc aaagagaaaa ttggaaagat gctgtcatcc gctgcatcca 1081 ccttgagagc ttgcaaagac cttggtgcat acggactgga aattttgaaa ctagtcatga 1141 agtggttctt cccaaagaaa gaggaaacaa atgaactggc tatggtaaga tccatcgagg 1201 acgcagtact agacctcgag gcaattgaaa acaaccacat gaccgccctg ctcaaagaca 1261 aagacagctt ggcaacctac atgaaaaccc ttgatcttga ggaggagaaa gccagaaaac 1321 tctcaactaa atccgcttca cctgatattg tgggcacaat caacgctctc ctggcacgaa 1381 tcgccgctgc acgttcccta gtgcatcggg cgaaagaaga gctctccagc aggccgagac 1441 ctgttgttgt gatgatatcg ggaaaaccag ggatagggaa aactcacctt gccagggagt 1501 tggccaaaaa gattgcagcc tccctcacag gggaccagcg tgtgggtttg atcccacgca 1561 acggcgtcga ccactgggat gcatacaagg gtgaaagagt tgtcctatgg gacgactatg 1621 ggatgagcaa ccccatacac gatgccctca ggttgcagga acttgctgac acttgccccc 1681 tcacactaaa ttgtgatagg attgagaaca aagggaaagt ctttgatagt gatgccataa 1741 ttattaccac caacctggcc aacccagcac cactggatta tgtcaacttt gaagcgtgtt 1801 cgaggcgcat tgacttcctc gtgtatgcgg aagctcctgg ggtggagaag gcaaaacacg 1861 acttcccagg ccaacctgac atgtggaaga acgctttcag ccctgacttc tcacacataa 1921 aactagcatt ggctccacag ggtggttttg acaagaacgg caacaccccg catggaaaag 1981 gtgtcatgaa gaccctcacc actggctccc tcatcgcccg agcatcaggg ttgctccatg 2041 agagactaga tgaatatgaa ttgcaaggcc cagccctcac cactttcaac ttcgaccgca 2101 acaaggtgct tgcttttaga cagctcgctg ctgaaaacaa gtatggtcta atggacacga 2161 tgagagttgg aaaacagctc aaggacgtta agactatgcc agaccttaaa caagcactca 2221 agaatgtcgc gatcaagaaa tgccagatag tgtacaatgg tggcacctac acacttgagg 2281 ccgacggtaa gggtggtgtg agagttgaca aagtgcaaag tgccaccgtg caaaccaaca 2341 atgaactagc cggcgccctg caccacctaa ggtgcgccag gatcaggtat tatgttaagt 2401 gcgtccagga agcactgtac tccatcatcc aaatcgctgg ggctgcgttt gtcaccacgc 2461 gcatcgccaa gcgcatgaat atacaaaatc tctggtccaa gccacaggtg gaagacacag 2521 aagagacaac cagcaaggat ggttgcccaa aacccaaaga tgatgaagag ttcgtcgttt 2581 catccgacga catcagaact gagggcaaga aagggaagaa caagtccggc cgtggcaaga 2641 agcacacagc cttctcaagc aaagggctca gtgatgaaga gtacgatgag tacaagagaa 2701 ttagagaaga gaggaatggt aagtactcca tagaggagta cctccaggac agagacaagt 2761 actatgagga agtggccatt gccagggcaa ctgaagagga cttctgtgaa gaagaagagg 2821 ctaaaatccg gcagagaatt ttcagaccaa caaggaaaca acgtaaagaa gagagggcct 2881 ccctaggctt ggtcacaggt tcagaaatca ggaaaagaaa cccagaagac ttcaaaccca 2941 agggaaaact atgggctgat gatgacagaa gtgttgacta caatgagaag ctcaactttg 3001 aggccccacc aagcatctgg tcgcggatag tcaactttgg ttcaggttgg ggtttctggg 3061 tctcccccag tctgtttata acatcaaccc atgtcatacc tcaaggtgca aaagagttct 3121 tcggagtccc catcaaacaa atccagatac acaaatcagg tgaattctgc cgactgagat 3181 tcccaaaacc aatcagaact gatgtgacgg gcatgattct ggaagaaggc gcgccagaag 3241 gaaccgtggc cacactgctc attaagagac caactggaga actcatgcct ttggcagcca 3301 gaatggggac ccatgcaacc atgaggattc aggggcgcac ggttggagga caaatgggta 3361 tgctcttgac aggatccaac gccaagagta tggacttggg cacaacacca ggcgactgtg 3421 gctgtcccta catctacaag agagggaatg actacgtggt tataggagtc catacagccg 3481 ctgcccgtgg aggaaacact gtcatctgcg ccacccaggg tagtgaagga gaagccacac 3541 ttgaaggagg tgacaacaaa ggaacgtact gtggtgcacc gattttgggc ccagggagtg 3601 ctccgaaact cagcactaaa actaagtttt ggagatcatc cacgacgcca ctcccaccag 3661 gcacctacga accagcttac ctcggtggca aggaccctag agtcaaaggt ggcccttcat 3721 tgcaacaagt tatgagggac caactaaaac cattcacaga acccaggggc aaaccgccaa 3781 gaccaaatgt gttggaagct gccaagaaaa ccatcattaa tgttcttgag caaacaattg 3841 acccacccca aaaatggtca ttcgcgcaag cttgcgcatc cctcgacaaa accacctcca 3901 gcggccatcc gcaccacatg cggaaaaacg actgctggaa tggggagtcc tttacaggaa 3961 aattggcaga tcaggcctct aaggccaacc taatgttcga agagggaaag aacatgactc 4021 cagtttacac aggtgcactt aaagatgagt tagtgaagac tgacaaaatt tatggtaaga 4081 tcaagaagag gctcctgtgg ggctcggacc tggcgaccat gatacggtgc gcccgggcct 4141 tcggaggcct tatggatgaa ctcaaggcgc attgtgtcac ccttcctgtc agagttggta 4201 tgaatatgaa tgaagatggc cccataatct ttgagaagca ctccagatat aaataccatt 4261 atgatgctga ttactccagg tgggactcga cacagcaaag ggatgtgtta gcagcagcac 4321 tagaaatcat ggttaagttc tctccagaac cacacttggc ccagatagtt gcagaagacc 4381 tcctttcccc tagtgtaatg gatgtgggtg actttcaaat atcaataagt gaaggactcc 4441 cctccggggt gccttgcacc tcccagtgga attccatcgc ccactggctc ctcacccttt 4501 gtgcactctc tgaagtcacg gacctgtccc ctgacatcat tcaggccaat tcccttttct 4561 ccttttatgg cgatgatgag attgtgagta cagacataaa gttggaccca gagaagctga 4621 cggcaaaact caaagagtac gggctaaagc caacccgccc cgacaagact gaaggacccc 4681 ttgtcatctc tgaagatctg gatggcctga cattcctccg gaggactgtg acccgtgacc 4741 cagctggctg gtttgggaaa ttggaacaaa gttcaatcct caggcaaatg tattggacca 4801 ggggtcccaa ccatgaagac ccatctgaaa caatgatacc acactcccaa agacccatac 4861 aattgatgtc cttgctaggc gaggctgcac tccacggccc agcattttac agcaaaatta 4921 gcaaattggt cattgcagaa ttaaaggagg gtggcatgga tttttacgtg cccaggcagg 4981 aaccaatgtt cagatggatg agattctcag atctgagcac gtgggagggc gatcgcaatc 5041 tggctcccag ttttgtgaat gaagatggcg tcgagtgacg ccaacccatc tgatgggtcc 5101 gcagccaacc tcgtcccaga ggtcaacaat gaggttatgg ctctggatcc cgttgttggt 5161 gccgctattg cggcgcctgt agcgggccaa caaaatgtaa ttgacccctg gattagaaat 5221 aattttgtgc aagcccctgg tggagagttt acagtgtcac ctagaaatgc tccaggtgaa 5281 atactatgga gcgctccctt aggccctgat ctaaacccct acctatccca tttggccaga 5341 atgtacaatg gttatgcagg tggttttgaa gtgcaggtaa tccttgcggg gaacgcgttc 5401 accgccggaa agatcatatt tgcagcagtc ccacctaatt ttccaactga aggtctgagc 5461 cccagccagg tcactatgtt cccccatata atagtagatg ttagacaact ggaacctgtg 5521 ttgattcccc tgcccgatgt taggaataat ttctatcact ataaccaatc aaacgatccc 5581 accattaagt tgatagcaat gttgtataca ccacttaggg ctaataatgc tggggatgat 5641 gtcttcacag tttcttgtcg agtcctcacg agaccatccc ctgattttga ctttatattc 5701 ttagtgccac ccacagttga gtcaagaact aaaccatttt ctgtcccaat tttaactgtt 5761 gaggagatga ctaattcaag attccccatt cctttggaaa agttgttcac aggtcccagc 5821 agtgcctttg ttgttcaacc acaaaatggc aggtgcacga ctgatggcgt gctcctaggt 5881 accacccaat tgtcccctgt caacatctgc accttcagag ggagtgtcac ccaaacagca 5941 gcaggtagtc ataactacac aatgaatttg gcctcccaaa attggaacag ttatgatcca 6001 acagaagaaa tcccagcccc tttaggaact ccagatttcg tagggaagat tcaaggtatg 6061 ctcacccaaa ccacaagagg agatggctca acacgcggcc acaaagccac agtgtacact 6121 gggagcaacg actttgctcc aaaactgggt agggttcaat ttgaaactga cacaaccaac 6181 gattttgaaa ctaaccaaaa cacaaagttc accccggtcg gcgtcatcca gaatggtgac 6241 actgcccacc gaaatgaacc ccaacaatgg gtgctcccaa gttattcagg cagagacact 6301 cataatgtgc acctggcccc cgctgtagct cccacttttc cgggagagca actcctcttc 6361 ttcagatcta ccttgcccgg atgcagcggg taccccaaca tggatttgga ttgtctgctt 6421 ccccaggagt gggtgcagta cttctatcaa gaggcagccc cagcacaatc cgaagtggct 6481 ctgttaagat ttgtgaatcc agacacaggt agggttttgt ttgagtgcaa gctccacaaa 6541 tcgggctatg tcacagtggc tcacactggc cagcatgatt tggttatccc ccccaatggt 6601 tatttcagat ttgattcctg ggttaatcaa ttctacacgc ttgcccccat gggaaatgga 6661 acggggcgta gacgtgcatt ataatggctg gagctttctt tgctggattg gcatctgatg 6721 tccttggctc tggacttggt tccctgatca atgctggggc tggggccatc aaccaaaaga 6781 ttgaatttga aaataacaga aaattgcaac aagcttcctt ccaattcagt agcaacctac 6841 aacaggcttc ctttcaacat gacaaagaga tgctccaagc acaaattgag gccaccaaaa 6901 agctgcaaca ggaaatgatg aaagttaagc aggcagtgct cttagagggc gggttctctg 6961 agacagatgc agcccgcggg gcaatcaatg cccccatgac aaaagctttg gattggagcg 7021 gtacaaggta ttgggcccct gatgctagaa ctacaacata caatgcaggc cgcttctcca 7081 caccccaacc accgggggca ctgccaggaa gagctaacct caggaatgct gtccctgctc 7141 ggggttcctc taatacacct tccaattcct ctattgctac ttctgtgtac tcaaatcaaa 7201 ctgcttcaac gagacttggt tctacagctg gttctgggac cagtgtctcg agtctcccgt 7261 caactgcaag gactaggagt tgggttgagg atcaaaatag gaatctgtca cctttcatga 7321 ggggggccca caacatatcg tttgtcaccc caccatctag cagatcctct agccaaggca 7381 cagtctcaac cgtgcctaaa gaagttttgg actcctggac tggtgctttc aacacgcaca 7441 ggcagcctct cttcgctcac attcgtaggc gaggggagtc acgggtgtaa tgtgaaaaga //