Typing tool
|
Complete norovirus genomes
MT725762 | GII.4 Sydney | ||
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GII.P4 New Orleans |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7510LOCUS MT725762 7566 bp RNA linear VRL 12-JUL-2020 DEFINITION Norovirus GII isolate Hu/US/2017/GII.4 Sydney[P4 New Orleans]/CA-RGDS-1091, complete genome. ACCESSION MT725762 VERSION MT725762.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7566) AUTHORS Pan,C.-Y., Huynh,T., Padilla,T., Montmayear,A.M., Chhabra,P., Barclay,L., Vinje,J. and Morales,C. TITLE Direct Submission JOURNAL Submitted (07-JUL-2020) Viral and Rickettsial Disease Laboratory, California Department of Public Health, 850 Marina Bay Parkway, Richmond, CA 94804, USA COMMENT ##Assembly-Data-START## Assembly Method :: SPAdes v. 3.6; Geneious v. R10 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7566 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="Hu/US/2017/GII.4 Sydney[P4 New Orleans]/CA-RGDS-1091" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA: California" /collection_date="Dec-2017" /note="genotype: GII.4 Sydney[P4 New Orleans]" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="QLD97902.1" /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP KQPPPREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVTYSVKDGVSGLPDLSTVRQPE ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTM PELKQALKNVSIKKCQIVYNGCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENIEETTSKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV TGSEIRKRNPDDFKPKGRLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQDAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPERWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIRKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 5..994 /gene="ORF1" /product="p48" mat_peptide 995..2092 /gene="ORF1" /product="NTPase" mat_peptide 2093..2629 /gene="ORF1" /product="p22" mat_peptide 2630..3028 /gene="ORF1" /product="VPg" mat_peptide 3029..3571 /gene="ORF1" /product="Pro" mat_peptide 3572..5101 /gene="ORF1" /product="RdRp" gene 5085..6707 /gene="ORF2" CDS 5085..6707 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QLD97903.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGAPDFVGKIQGML TQTTRADGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG NTTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6707..7510 /gene="ORF3" CDS 6707..7510 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QLD97904.1" /translation="MAGAFFAELASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQVEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSAPQPSGVLPGRTNLRDAAPARGSSKSSN SSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNIS FVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRA" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga 61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc 121 cctcggggcg cggcctaaac agcccccccc gagggaaaaa ccacaaagac ccccacgacc 181 acccacacca gaactggtta aaaatattcc ccccccccca cccaacggag aggatgaaat 241 agtggttact tatagtgtta aggatggtgt ttccggcttg cctgaccttt ccaccgtcag 301 acagccggaa gaatccaaca cggccttcag tgtccctcca ctcaatcaga gggagaacag 361 agatgctaag gaaccactca ctggaacaat tctggaaatg tgggacgggg aaatctacca 421 ttatggcctg tatgtggagc gaggtcttgt actaggcgta cacaagccac cagctgccat 481 cagcctcgct aaggttgagt tggcaccact ctccttatac tggaggcctg tgtacactcc 541 tcagtacctc atctctccag acactctcaa gaaattgtct ggggaaacgt tcccctacac 601 agcatttgac aacaactgct atgccttttg ttgctgggtt ctggacctaa atgactcgtg 661 gctgagcagg agaatgatcc agaggacaac tggtttcttc aggccctacc aagactggaa 721 taggaaaccc cttcccacta tggatgactc caaaataaag aaggtggcca atatatttct 781 gtgtgccctg tcctcgctat ttaccaggcc cataaaagac ataataggga aaataaggcc 841 tcttaacatc ctcaacatct tggcctcatg tgattggacc tttgcgggca tagtagagtc 901 cctgatactc ttagcagagc tctttggagt tttctggaca cccccagatg tgtctgcaat 961 gattgccccc ttacttggtg actacgagct acaaggacct gaggaccttg cagtggagct 1021 cgtccccgtg gtgatggggg gaattggttt ggtgctagga ttcaccaaag aaaaaattgg 1081 gaaaatgttg tcatcagctg cgtccacctt gagagcttgc aaagaccttg gtgcatatgg 1141 gctagagatc ctaaagctag tcatgaagtg gttcttcccg aagaaggagg aggcaaatga 1201 gctggctatg gtgaggtcca tcgaggatgc agtcctggat ctcgaagcaa ttgaaaacaa 1261 tcatatgacc accttgctta aagataaaga cagtctggca acctacatga gaacactcga 1321 ccttgaagag gagaaagcca ggaaactctc aaccaagtct gcctcacctg acatcgtggg 1381 cacaatcaac gccctcctgg cgagaatcgc tgccgcacgt tctctggtgc atcgagcgaa 1441 ggaggagctt tccagcagac caagacctgt ggtgttgatg atatcaggta ggccaggaat 1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcagcctccc ttacaggtga 1561 ccagcgtgtt ggtctcatcc cacgcaatgg cgtcgaccac tgggatgcgt ataaggggga 1621 gagggtcgtc ctatgggacg attatggaat gagcaaccct attcacgatg ccctcaggct 1681 gcaagaactc gctgacactt gccccctcac tctgaactgt gacaggattg aaaataaggg 1741 gaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagccccact 1801 ggactatgtc aactttgaag catgctcgag gcgcattgac ttcctcgtat atgcagaagc 1861 ccctgatgtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc 1921 tttcagttcc gatttctcac acataaaact agcactggcc ccacagggtg gtttcgacaa 1981 gaacgggaac accccacacg ggaagggcgt catgaagact ctcaccactg gctcccttat 2041 tgcccgggca tcagggctac tccatgagag gttagatgaa tttgaactgc agggcccagc 2101 tctcaccacc ttcaatttcg atcgcaataa agtgcttgcc tttagacagc ttgctgctga 2161 aaacaaatat ggactgatgg acacaatgag ggttgggaaa cagctcaagg acgtcaaaac 2221 catgccagaa ctcaaacaag cactcaaaaa tgtctcaatc aagaagtgtc aaatagtgta 2281 taatggttgc acctacatgc ttgagtctga tggcaagggc aatgtgaaag ttgacaggat 2341 ccagagcgcc gccgtgcaga ccaacaatga gctggctggt gccctgcacc acttgaggtg 2401 cgccagaatc agatactatg tcaagtgtgt ccaggaagcc ctgtattcca tcattcaaat 2461 tgctggggct gcatttgtca ccacgcgcat tgccaagcgc atgaacatac aggatctatg 2521 gtccaagcca caagtggaaa acatagagga aactaccagc aaggacgggt gcccaaaacc 2581 caaggatgat gaggagtttg tcatttcatc cgacgacatc aaaactgagg gcaagaaagg 2641 gaagaacaag actggccgtg gcaagaagca cacagcattt tcaagcaaag gcctcagtga 2701 tgaagagtac gatgaataca agaggatcag agaagaaagg aatggcaagt actctataga 2761 agagtacctc caggacaggg acaaatatta tgaggaggtg gccattgcca gagcgactga 2821 ggaagacttc tgtgaagagg aggaagccaa gatccggcaa aggatcttta ggccaacaag 2881 gaaacaacgc aaggaggaaa gagtctctct cggtttagtc acgggctctg aaattaggaa 2941 aagaaaccca gatgacttca aacccaaagg gagattgtgg gctgacgatg acaggagtgt 3001 ggactacaat gagaaactca gttttgaggc cccgccaagc atttggtcaa gaatagtcaa 3061 ctttggttca ggctggggat tctgggtctc ccccagcttg ttcataacat caacccatgt 3121 tataccccag gacgcaaagg agttctttgg agtccccatc aaacaaatac aggtacacaa 3181 gtcaggcgag ttctgtcgct tgagattccc taaaccaatc aggactgatg tgacgggcat 3241 gatcttagaa gaaggcgcac ctgagggcac cgtggttaca ctactcatca aaaggtccac 3301 cggggaactt atgcccctag cagctaggat ggggacccat gcgaccatga agatccaagg 3361 gcgcactgtt gggggccaga tgggcatgct tctgacagga tccaacgcca agagtatgga 3421 cctgggtact acaccaggtg attgtggctg cccctacatc tacaagagag gtaatgacta 3481 tgtggtcatt ggagtccaca cggctgccgc acgtgggggg aacactgtca tatgtgccac 3541 ccaggggagt gaaggagagg ccacacttga gggtggtgac aacaagggga cttactgtgg 3601 tgcaccaatc ctaggcccag ggagtgcccc aacacttagc accaagacca aattctggag 3661 atcgtccaca gcatcactcc cacctggcac ctatgaacca gcctaccttg gtggcaagga 3721 ccctagagtc aagggtggcc cttcactaca gcaagtcatg agggaacagt tgaagccatt 3781 cacagagccc agaggtaagc caccaaaacc aagtgtgtta gaagctgcca agaaaaccat 3841 catcaatgtt cttgagcaaa caattgatcc acctgagaga tggtcgttcg cacaagcttg 3901 cgcgtctctt gacaagacca cttccagtgg tcatccgcat cacatgcgga aaaacgactg 3961 ctggaacggg gagtccttca caggcaagct ggcagaccag gcttctaagg ccaacctgat 4021 gtttgaagaa ggaaagaaca tgaccccagt ctacacagct gcgctcaagg atgagctagt 4081 taaaactgac aaaatttatg gtaagatcag gaagagactt ctttggggct cggacttggc 4141 gaccatgatc cggtgtgctc gggcattcgg aggcctaatg gatgaactca aagcacactg 4201 tgtcacactt cccgttagag ttggcatgaa tatgaatgag gatggcccca tcatcttcga 4261 gaggcattcc aggtacacgt accactatga tgctgattac tctcgatggg attcaacaca 4321 acagagagcc gtgttggcgg cagctctaga aatcatggta aaattctccc cagaaccaca 4381 tttggcccag gtagtcgctg aagaccttct ttctcctagc gtggtggacg tgggcgactt 4441 cacaatatca atcaacgagg gtcttccctc tggggtgccc tgcacctccc aatggaactc 4501 catcgcccac tggcttctca ctctctgcgc gctctccgaa gtcacaaacc tgtctcctga 4561 taccatacag gctaattctc tcttttcttt ttatggcgat gatgaaattg ttagcacaga 4621 cataaaattg gacccagaga aattgacagc aaaactcaaa gaatacgggt taaaaccaac 4681 ccgccctgac aaaactgaag gaccccttgt catctctgaa gacctgaatg gcctaacttt 4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc 4801 aatactcagg caaatgtact ggactagggg acccaaccat ggagacccat ctgaaacaat 4861 gattccacat tcccaaagac ccatacaatt gatgtcccta ctgggggagg ccgctctcca 4921 cggcccagca ttttacagta agattagcaa attggtcatt gcagagctaa aagaaggtgg 4981 tatggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg 5161 ttatggctct ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa 5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag 5281 tgtcccccag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatttaa 5341 atccctacct atcccacttg gccagaatgt ataatggtta tgcaggtggt tttgaagtgc 5401 aggtgattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac 5461 caaattttcc aactgaaggc ttgagcccca gccaggtcac tatgttcccc catatagtag 5521 tggatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataatttct 5581 accattacaa tcaatcaaat gaccccacca ttaagttgat agcaatgtta tatacaccac 5641 ttagggctaa taatgctggg gatgatgtct tcacagtttc ttgccgagtt ctcacgaggc 5701 catcccccga ttttgatttc atatttctag tgccacccac agttgagtct agaaccaaac 5761 cattttccgt cccagttttg actgttgagg agatgaccaa ttcaagattc cccattcctt 5821 tggaaaagtt gttcacgggc cccagtagtg cctttgttgt tcaaccacaa aacggtaggt 5881 gcacgactga cggcgtgctc ctaggcacca cccaattgtc tcctgtcaac atctgcacct 5941 tcagagggga tgtcacccac attacaggta gtcgtaacta cacaatgaat ttggcttctc 6001 aaaactggaa caattatgat ccaacagaag aaatcccagc ccctctagga gctccagatt 6061 ttgtggggaa gattcaaggc atgctcaccc aaaccacaag ggcagatggc tcaacacgcg 6121 gccacaaggc tacggtgtac actgggagcg ccgacttcgc tccaaaactg ggcagagttc 6181 aatttgaaac tgacacagac catgattttg aagctaacca aaacacaaag ttcactccag 6241 tcggtgtcat ccaagatggc aacaccaccc accgaaatga accccaacag tgggtgctcc 6301 caagttactc aggcagaaat actcataatg ttcatctggc ccccgctgtg gcccccactt 6361 ttccgggtga acaacttctc ttctttagat ccaccatgcc cggatgtagc gggtatccca 6421 acatggattt ggactgtttg ctcccccagg aatgggtgca gtacttctac caagaggcag 6481 ccccagcgca atctgatgtg gccctgctaa gatttgtgaa tccagacaca ggtagggttt 6541 tgtttgaatg caaacttcat aaatcaggct atgttacagt ggctcacact ggccaacatg 6601 atttggtcat cccccccaat ggttatttta ggtttgattc ctgggtcaac cagttctaca 6661 cgcttgcccc catgggaaat ggaacggggc gtagacgcgt agtataatgg ctggagcttt 6721 ctttgctgag ttagcatctg atgtcctcgg ctctggactt ggttccctta tcaatgctgg 6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc 6841 cttccaattt agcagcaatt tacaacaggc ttcctttcaa catgacaaag aaatgcttca 6901 agcacaagtt gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat 6961 gcttctagag ggtgggttct ctgaaacaga tgcagcccgc ggggcaatca acgcccccat 7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cctgatgcta ggactacaac 7081 ttataatgca ggccgctttt ccgcccctca accatcgggg gtactaccag gaaggactaa 7141 tcttagggat gctgcccctg ctcggggttc ctctaaatct tctaactctt ctactgctac 7201 ttctgtgtac tcaaatcaaa ccacttcaac gagacttggt tctacagctg gttctggcac 7261 cagtgtctcg agtctcccgt caactgcaag gaccaggagc tgggttgagg atcaaagtag 7321 gaatttgtct cctttcatga ggggggccca caacatatcg tttgtcaccc caccatctag 7381 cagatcctct agccaaggca cagtctcaac cgtgcctaaa gaggttttgg actcctggac 7441 tggcgctttc aacacgcgca ggcagcctct cttcgctcac attcgtaaac gaggggagtc 7501 acgggcgtaa tgtgaaaaga caaaattgat tatctttctt tttctttagt gtcttttaaa 7561 aaaaaa //