Typing tool
|
Complete norovirus genomes
OR262328 | GII.4 San Francisco | ||
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GII.P31 |
ORF1: 1..5093 ORF2: 5074..6699 ORF3: 6699..7505LOCUS OR262328 7551 bp RNA linear VRL 11-DEC-2023 DEFINITION Norovirus GII isolate Hu/GII.4 San Francisco[P31]/WT-NORO-1954/2019/UK nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION OR262328 VERSION OR262328.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7551) 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 7551) 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..7551 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="Hu/GII.4 San Francisco[P31]/WT-NORO-1954/2019/UK" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="21-Nov-2019" /note="genotype: GII.4 San Francisco[P31]" gene <1..5093 /gene="ORF1" CDS <1..5093 /gene="ORF1" /codon_start=3 /product="nonstructural polyprotein" /protein_id="WKD81257.1" /translation="ASNDASAAAAANSNNDIEKSSSDGVFSNMAVTFKRALGARPKQP PPREKPPRPPRPPTPELVKRIPPPPPNGEDELVVSYNAKDGVSGLPELTTVSQPEENN TAFSVPPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAK VELTPLSLFWRPVYTPQYLISPDTLKRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLS RRMIQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLKP LNILNILATCDWTFPGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAV ELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKE ETNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMKTLDLEEEKARKLSTKSA SPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLARELAKK IAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLT LNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPGVEKAKH DFPGQPDMWKNAFSPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGL LHERLDEYELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPDL KQALKNVAIKKCQIVYNGGTYTLEADGKGGVRVDKVQSATVQTNNELAGALHHLRCAR IRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEETTSKDGCPKP KDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYS IEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGS EIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLF ITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVA TLLIKRPTGELMPLAARMGTHATMRIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGC PYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGS APKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGK PPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGE SFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATM IRCARAFGGLMDELKAHCVTLPVRVGMSMNEDGPIIFEKHSRYKYHYDADYSRWDSTQ QRDVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCTSQW NSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYG LKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHE DPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMF RWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide <1..983 /gene="ORF1" /product="p48" mat_peptide 984..2081 /gene="ORF1" /product="NTPase" mat_peptide 2082..2618 /gene="ORF1" /product="p22" mat_peptide 2619..3017 /gene="ORF1" /product="VPg" mat_peptide 3018..3560 /gene="ORF1" /product="Pro" mat_peptide 3561..5090 /gene="ORF1" /product="RdRp" gene 5074..6699 /gene="ORF2" CDS 5074..6699 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="WKD81258.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPNQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSTFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGSVTQTAAGTHNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIRGM LTQTTRGNGSTRGHIATVYTGSNDFAPKLGRVQFETDTTNDFETNQNTKFTPVGVIQD GDTAHRNEPLQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTLPGCSGYPNMDL DCLLPQEWVQYFYQEAAPAQSEVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDL VIPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6699..7505 /gene="ORF3" CDS 6699..7505 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="WKD81259.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRNVVPARGSSSTPS NSSIATSVHSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTHRQPLFAHIRRRGESRV" ORIGIN 1 tggcgtctaa cgacgcttcc gctgccgctg ctgctaacag caacaacgac atcgaaaaat 61 cttcaagtga cggtgtgttt tctaacatgg ctgtcacttt taagcgggcc ctcggggcgc 121 ggcctaaaca gccgcccccg agggaaaaac cacccagacc cccacgacca cccacaccag 181 agttggtcaa aaggatccca cctcccccac ccaacgggga ggatgaacta gtggtttctt 241 acaacgccaa agacggcgtt tccggattgc ctgagctcac caccgtcagc caaccggaag 301 aaaacaacac ggcgttcagt gttcccccgc tcaatcaaag ggagaacagg gacgctaagg 361 aaccactaac tggaacaatc attgagatgt gggatgggga aatctatcac tacggcctgt 421 acgtagaacg aggtcttata cttggtgtgc ataagccacc ggcggccatc agtcttgcca 481 aagttgagct aacaccactc tctttgttct ggagacctgt gtataccccc cagtacctca 541 tctctccaga cactcttaag agactacatg gagagtcatt cccctacacc gcatttgaca 601 acaattgcta tgccttctgc tgttgggtgc tagacctaaa cgactcatgg ctaagtagga 661 gaatgattca gaggacaaca ggtttcttca gaccatacca agaatggaac aggaaacccc 721 tccccactat ggatgactcc aaattgaaga aggtagccaa catattcttg tgcaccttgt 781 cttcactatt caccagaccc attaaggaca taatagggaa attgaaacct cttaacatcc 841 tcaatattct ggccacatgt gattggacct tcccaggcat agtggaatcc ctaatactct 901 tggcagaact ctttggagtt ttctggacac ccccagatgt gtctgcgatg atcgccccct 961 tactaggtga ttatgaactg caaggacctg aggaccttgc agtagaactg gtcccagtgg 1021 tgatgggggg gataggtttg gtgctaggat tcaccaaaga gaaaattgga aagatgctgt 1081 cgtccgctgc atccaccttg agagcttgca aagaccttgg tgcatacgga ctggaaattt 1141 tgaaactagt catgaagtgg ttcttcccaa agaaagagga aacaaatgaa ctggctatgg 1201 tgagatccat cgaggacgca gtactagatc tcgaggcaat tgaaaacaac cacatgaccg 1261 ccctgctcaa agacaaagac agtttggcaa cctacatgaa aacccttgat cttgaggagg 1321 agaaagccag aaaactctca actaaatccg cttcacctga tattgtgggc acaatcaacg 1381 ctcttctggc acgaatcgcc gctgcacgct ccctagtgca tcgggcgaaa gaagagctct 1441 ccagcaggcc gagacctgtt gtcgtgatga tatcgggaaa accagggata gggaaaactc 1501 accttgccag ggagttggcc aaaaagatcg cagcctccct cacaggggac cagcgtgtgg 1561 gtttgatccc acgcaacggc gtcgaccact gggatgcata caagggtgaa agagttgtcc 1621 tatgggacga ctatgggatg agcaacccca tacacgatgc cctcaggttg caggaacttg 1681 ctgacacttg ccccctcaca ctaaattgtg ataggattga gaataaagga aaagtctttg 1741 atagcgatgc cataattatt accaccaatc tggccaaccc agcaccactg gactatgtta 1801 actttgaagc gtgttcgagg cgcattgact tcctcgtgta cgcggaagct cctggggtgg 1861 agaaggcaaa acacgacttc ccaggccaac ctgacatgtg gaagaacgct ttcagccctg 1921 acttctcaca cataaaactg gcattggctc cacagggagg ttttgacaag aacggcaaca 1981 ccccgcatgg aaaaggtgtc atgaagaccc tcaccactgg ctccctcatc gcccgagcat 2041 cagggttact ccatgagagg ctagatgaat atgaattgca aggcccagcc ctcaccactt 2101 tcaacttcga ccgcaacaag gtacttgctt ttagacagct tgctgctgaa aacaagtatg 2161 gcctaatgga cacaatgaga gttggaaaac agctaaagga tgttaagact atgccagacc 2221 ttaaacaagc actcaagaat gtcgcgatca agaagtgcca gatagtgtac aatggtggca 2281 cctacacact tgaggccgac ggcaagggtg gtgtgagagt tgataaagtg caaagtgcca 2341 ccgtacaaac caacaatgag ctagccggcg ccctgcacca cctaaggtgc gccagaatca 2401 ggtattatgt taagtgtgtc caggaggcac tgtactccat catccaaatc gctggggctg 2461 cgtttgtcac tacgcgcatc gccaagcgca tgaatataca aaatctctgg tctaagccac 2521 aggtggaaga cacagaagag acaaccagca aagatggttg cccaaaaccc aaagatgatg 2581 aagagttcgt cgtttcatcc gacgacatca aaactgaggg caagaaaggg aagaacaagt 2641 ccggccgtgg caagaagcac acagccttct caagtaaagg actcagtgat gaagagtatg 2701 atgagtacaa gaggattagg gaagagagga atggtaagta ctccatagag gagtacctcc 2761 aggacagaga caagtactat gaggaagtgg ccattgccag ggcaactgaa gaggacttct 2821 gtgaagaaga agaggccaaa atccggcaga gaattttcag accaacaagg aaacaacgta 2881 aagaagagag ggcctctcta ggcttggtca caggctcaga aatcaggaag agaaacccag 2941 aagacttcaa acccaaggga aagctgtggg ctgatgatga cagaagtgtt gactacaatg 3001 agaagctcaa ctttgaggcc ccaccaagca tctggtcgcg gatagtcaac tttggttcag 3061 gttggggttt ctgggtctcc cccagtctgt ttataacatc aacccatgtc ataccccaag 3121 gtgcaaaaga gttcttcgga gtccccatca aacaaatcca gatacacaaa tcaggtgaat 3181 tctgccgact gagattccca aaaccaatca gaactgatgt gacgggcatg attctggaag 3241 aaggtgcgcc agaaggaacc gtggccacac tgctcatcaa gagaccaact ggagagctca 3301 tgcctttggc agccagaatg ggaacccatg caaccatgag gattcagggg cgcacggttg 3361 gaggacaaat gggcatgctc ttgacaggat ccaacgccaa gagtatggac ttgggcacaa 3421 caccaggcga ttgtggctgt ccctacatct acaaaagagg gaatgactac gtggttatag 3481 gagtccatac agccgctgcc cgtggaggaa acactgtcat ctgcgccacc cagggtagtg 3541 aaggagaagc cacacttgaa ggaggtgaca acaaaggaac gtactgtggt gcaccaattt 3601 tgggcccagg gagtgctccg aaactcagca ctaaaactaa gttttggaga tcatccacaa 3661 cgccactccc accaggcacc tacgaaccag cttacctcgg tggcaaggac cctagagtca 3721 aaggtggccc ttcattgcaa caagttatga gggaccaact aaaaccattc acagaaccta 3781 gaggcaaacc gccaagacca aatgtgttgg aagctgccaa gaaaaccatc attaatgttc 3841 ttgagcaaac aattgaccca ccccaaaaat ggtcattcgc gcaagcttgc gcatccctcg 3901 acaaaaccac ctccagcggc catccgcacc acatgcggaa aaacgactgc tggaatgggg 3961 aatcctttac aggaaaattg gcagaccagg cctctaaggc caacctaatg tttgaagagg 4021 gaaagaacat gactccagtt tacacaggtg cacttaaaga tgagttagtg aagactgata 4081 aaatttatgg taagatcaag aagaggctcc tgtggggctc ggacctggcg accatgatac 4141 ggtgcgcccg ggctttcgga ggccttatgg atgaactcaa ggcacattgt gtcacccttc 4201 ctgttagagt tggtatgagt atgaatgaag atggccctat aatctttgag aagcactcca 4261 gatataaata tcattatgat gctgattact ccaggtggga ctcgacacaa cagagggatg 4321 tgttagcagc agcactagaa atcatggtta aattctctcc agaaccacac ttggcccaga 4381 tagttgcaga agacctcctt tcccctagtg taatggatgt gggtgacttt caaatatcaa 4441 taagcgaagg acttccctcc ggggtacctt gcacctccca gtggaattcc atcgcccact 4501 ggctcctcac cctttgtgca ctctctgaag tcacggacct gtcccctgac attattcagg 4561 ccaactccct tttctccttc tatggtgatg acgagattgt gagtacagac ataaagttgg 4621 acccagagaa gctgacggca aaactcaagg agtacggact gaagccaacc cgccccgaca 4681 agactgaagg accccttgtc atctctgaag atctggatgg cctgacattc ctccggagga 4741 ctgtgacccg tgacccagct ggctggtttg gcaaattgga acaaagttca atcctcaggc 4801 aaatgtactg gaccaggggt cccaaccatg aagacccatc tgaaacaatg ataccacact 4861 ctcaaagacc catacaattg atgtccctgc taggcgaggc tgcactccac ggcccagcat 4921 tttacagcaa aattagcaaa ttggtcatcg cagaattgaa ggaaggtggt atggactttt 4981 acgtgcccag acaagaacca atgttcagat ggatgagatt ctcagatctg agcacgtggg 5041 agggcgatcg caatctggct cccagttttg tgaatgaaga tggcgtcgag tgacgccaac 5101 ccatctgatg ggtccgcagc caacctcgtc ccagaggtca acaatgaggt tatggctctg 5161 gagcccgttg ttggtgccgc tattgcggca cctgtagcgg gccaacaaaa tgtaattgac 5221 ccctggatta gaaataattt tgtgcaagcc cctggtggag agtttacagt atcccctaga 5281 aacgctccag gtgaaatact atggagcgct cccctaggcc ctgatctaaa cccctaccta 5341 tcccatttgg ccagaatgta taatggttat gcaggtggtt ttgaagtgca ggtaatcctt 5401 gcggggaacg cgttcaccgc cggaaagatc atatttgcag cagtcccacc taattttcca 5461 actgaaggtt tgagccccaa ccaggtcact atgttccccc atataatagt agatgttaga 5521 caactggaac ctgtgttgat tcccctaccc gatgttagga ataatttcta tcactataac 5581 caatcaaacg accccaccat taagttgata gcaatgttgt atacaccact tagggctaat 5641 aatgctgggg atgatgtctt cacggtttct tgccgagtcc tcacgagacc atcccctgat 5701 tttgacttca tattcttggt gccacccaca gttgagtcaa gaactaaacc attctctgtc 5761 ccaattttaa ctgttgagga gatgactaat tcaagattcc ccattccttt ggaaaagttg 5821 ttcacaggtc ccagcagcac ctttgttgtt caaccacaaa atggcaggtg cacgactgat 5881 ggcgtgctcc tgggcaccac ccaattgtcc cctgtcaaca tctgcacctt cagagggagt 5941 gtcacccaaa cagcggcagg tactcataac tacacaatga atttggcttc ccaaaattgg 6001 aatagctatg atccaacaga agaaatccca gcccctttag gaaccccaga tttcgtaggt 6061 aagattcgag gtatgctcac ccaaaccaca aggggaaatg gctcaacacg tggccacata 6121 gccacagtgt acactgggag caacgacttt gctccaaaac tgggtagggt ccaatttgaa 6181 actgacacaa ccaacgattt tgaaactaac caaaacacaa agttcacccc ggttggcgtc 6241 atccaggatg gtgacactgc tcaccgaaat gaacccctac aatgggtgct cccaagttat 6301 tcaggcagaa atactcataa tgtgcatctg gcccccgctg tagctcccac ttttccgggc 6361 gagcagctcc tcttctttag atctaccttg cccggatgca gcgggtaccc caacatggat 6421 ttggattgtc tgcttcccca ggaatgggtg cagtacttct atcaagaggc agccccagca 6481 caatctgaag tggctctgtt aagatttgtg aatccagata caggtagggt tttgtttgag 6541 tgtaagctcc acaaatcggg ctatgtcaca gtggctcata ctggccaaca tgatttggtt 6601 atccccccca atggttattt tagatttgat tcctgggtca atcaattcta cacgcttgcc 6661 cccatgggaa atggaacggg gcgtagacgt gcattgtaat ggctggagct ttctttgctg 6721 gattggcatc tgatgtcctt ggctctggac ttggttccct gatcaacgct ggggctgggg 6781 ccatcaacca aaagattgaa tttgaaaata acagaaaatt gcaacaggca tccttccaat 6841 ttagtagcaa cctacaacag gcttcctttc aacatgacaa agagatgctc caagcacaaa 6901 ttgaggccac caaaaagctg caacaggaaa tgatgaaagt taagcaggca gtgctcttag 6961 agggcgggtt ctctgagaca gatgcagccc gcggggcaat caacgcccct atgacaaaag 7021 ctttggattg gagcggtaca aggtattggg cccctgatgc tagaactaca acatacaatg 7081 caggccgttt ctccacaccc caaccatcgg gggcactgcc aggaagagct aatctcagga 7141 atgttgtccc cgctcggggt tcctctagta caccttctaa ttcctctatt gctacttctg 7201 tgcactcaaa tcaaactgct tcaacgagac ttggttctac agctggttct gggaccagtg 7261 tctcgagcct cccgtcaact gcaaggacta ggagctgggt tgaggatcaa aataggaatc 7321 tgtcaccttt catgaggggg gcccacaaca tatcgtttgt caccccacca tctagcagat 7381 cctctagcca aggcacagtc tcaaccgtgc ctaaagaagt tttggactcc tggactggtg 7441 cttttaacac gcacaggcag cctctcttcg ctcacattcg taggcgaggg gagtcacggg 7501 tgtaatgtga aaagacaaaa ttgattatct ttctcatctt tagtgtcttt t //