Typing tool
|
Complete norovirus genomes
MK753032 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7513LOCUS MK753032 7572 bp RNA linear VRL 11-APR-2019 DEFINITION Norovirus GII isolate Hu/US/2016/GII.P16-GII.4 Sydney/SanJoaquin0116, complete genome. ACCESSION MK753032 VERSION MK753032.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7572) AUTHORS Barclay,L., Cannon,J.L., Wikswo,M.E., Phillips,A., Browne,H., Montmayeur,A.M., Tatusov,R.L., Burke,R.M., Hall,A.J. and Vinje,J. TITLE Emergence and characterization of multiple viruses associated with a novel GII.P16 polymerase in the United States, 2015-2018 JOURNAL Unpublished REFERENCE 2 (bases 1 to 7572) AUTHORS Barclay,L., Cannon,J.L., Pan,C.-Y., Montmayeur,A.M., Tatusov,R.L., Chhabra,P. and Vinje,J. TITLE Direct Submission JOURNAL Submitted (05-APR-2019) Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, USA COMMENT ##Assembly-Data-START## Assembly Method :: Geneious v. R10; SPAdes v. 3.6 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7572 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="SanJoaquin0116" /isolate="Hu/US/2016/GII.P16-GII.4 Sydney/SanJoaquin0116" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA" /collection_date="08-Sep-2016" /note="genotype: GII.P16-GII.4 Sydney" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="QBS54666.1" /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP KQPAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYDVKSGISGLPELTTVPQ SDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA RASGLLHERMDEFELQGHTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK TMEELKQAIRNVTIKRCRIIYGGSVYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE ALKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYSQACASLDKTTSSGHPHHVRKNEFW NGETFTGKLADQASKANLMYEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLASALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE" mat_peptide 5..1000 /gene="ORF1" /product="p48" mat_peptide 1001..2098 /gene="ORF1" /product="NTPase" mat_peptide 2099..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="QBS54667.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6707..7513 /gene="ORF3" CDS 6707..7513 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QBS54668.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKTLDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS NPSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVSKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgctac cgttgccgtt gcttgcaaca acaacaacga 61 caaggaaaaa tcttcaggtg aaggcttatt cacaaatatg tcttccacct taaagaaagc 121 cctcggggct aggcccaaac agcctgcccc gagagacgaa ccacaaaaac ccccaagacc 181 accaactccc gagttggtca agaggatacc ccctcctcca cctaatggcg aagaagaaga 241 agaaccagtc attaggtatg atgttaagag tgggatctct ggcctgcccg agctcacaac 301 agtcccccaa tcggacgtgg ccaacacagc attcagtgtt ccaccactga gcctgagaga 361 aaacagggag gccaaggaac cgctaacagg ggcaatatta gagatgtggg acggagagat 421 ataccactat ggcctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc 481 agccataagc atggcaagag tggagctgac gccgctgtca ttgtactggc gtgtggtgta 541 cactccccaa tacctcatct cccctgaaac tctcaggagg ctcaacggag aggcgttccc 601 ttacaccgcc ttcgacaaca actgttatgc cttttgctgc tgggtgttag acctcaatga 661 ctcatggctt agcaggagga tggtgcaaag aacaacgggc ttcttcagac cttaccaaga 721 gtggaacaga aaacccctgc ctaccatgga tgactccaaa ataaagaagg tagcaaatat 781 attcctatgt tcattgtcca cattgtttac cagacccata aaagacctca taggaaaaat 841 caaaccatta aacatattga acatcctggc aacgtgtgac tggacgtttg ccggaatagt 901 ggagtctctg atattacttg ctgaactctt cggagttttc tggacacccc cagatgtgtc 961 tgctatgatc gctcccttac tcggggacta cgagttgcaa gggccagaag acctcgccgt 1021 tgaactcgta cctgtggtaa tgggagggat tggtttggtg ttgggattca ccaaagagaa 1081 aattggcaaa atgttgtcct cagcagcatc aacactcagg gcttgcaaag atcttggtgc 1141 ctatggctta gagatactca aattggtcat gaagtggttc ttcccaaaga aagaggaggc 1201 caatgaacta gccatggtga gggccataga ggatgccgta ctagatcttg aggcaataga 1261 aaataaccac atgacaaccc tgttgaaaga caaagacagc ttagcaacat acatgaaaac 1321 actggacatg gaggaggaga aagccagaag gttgtccaca aaatctgcat cccctgacat 1381 agttggaaca atcaacgccc tgctggctcg aatagcagcg gccaggtcat tagtccacag 1441 ggccaaggaa gagctatcta gcaggataag accagtagtt gttatgatat ctggcaaacc 1501 aggaataggt aaaactcatc tggccaggga ggtggcaaga aaagtggcat ccactctcac 1561 aggggatcaa agagtcggac tcataccaag aaacggtgtg gaccattggg atgcatacaa 1621 aggtgagaga gtcgtgctgt gggacgacta tggcatgagt aaccccattc atgatgctct 1681 tcgcatacag gaattggctg atacgtgtcc cctcacctta aattgtgaca gaattgaaaa 1741 taagggaaaa gtttttgaca gtgaagtcat aataatcaca acaaaccttg ccaacccagc 1801 cccacttgat tatgtcaact ttgaggcctg ttccaggaga attgatttcc tggtgtacgc 1861 tgaggcacca gaagtagaaa aggcaaaacg ggactttcct ggtcagccag atatgtggaa 1921 ggacgccttc aagccggact tttcacacat caagctacag cttgcacctc agggcggctt 1981 tgacaagaat ggcaacaccc cacatgggaa aggagtgatg aagaccctca ctaccggttc 2041 tctgattgcc cgtgcatcag gcctactgca tgagaggatg gatgaatttg aactccaagg 2101 tcacacaatc accaccttca atttcgaccg gaacagaatc acagcattca gacaattggc 2161 tgcagaaaac aagtatggat tggtggacac catgaaagtt ggcaatcaac taaaaggagt 2221 gaaaaccatg gaagaactca aacaagcaat caggaatgtg accatcaaga ggtgccggat 2281 catctatggt ggctccgtgt atgaccttga atctgatggc aagggcaaag ttttggtgga 2341 aaaggtcaag aacacctctg tacagaccaa caacgagttg gccggggccc tgcaccacct 2401 caaacacgcc cgaatcaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat 2461 acaaattgcc ggcgctgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga 2521 actctggtcg aagccacaat tagatcaaaa tgaatcagag actaaggaag aggccctcaa 2581 gtcagaagat gacgagttca tcatatcttc taaggacatc aaggaggaag gaaagaaggg 2641 caaaaacaaa actggtcgtg gtaagaaaca cactgcattc tccagcaagg gcttgagcga 2701 tgaggagtat gacgagtaca agaggataag agaagagaga aatgggaagt actctataga 2761 ggagtatctt caagacagag acaggtacta tgaggagcta gccattgcca aggccacgga 2821 agaagacttc tgtgaagagg aggagatcaa aatccgtcag agaattttcc gtcccaccag 2881 gaaacaaaga aaggaagaga gggccacatt agggctggta acaggttcag aaatcagaaa 2941 aagaaaccct gatgacttca aacccaaagg gaagctgtgg gccgatgaca acagaagtgt 3001 tgactacaat gagaaactgg actttgaggc ccccccaagc atatggtcta ggattgtgag 3061 ctttggttct ggctggggct tctgggtatc accaagcctg ttcataacat caactcatgt 3121 aatccccgca ggcataacag aagcatttgg agtccccatc aaacaaattc agatccacaa 3181 atcaggtgaa ttttgccgat tcagattccc aaaaccaatt agaccagatg tgacaggaat 3241 gatcttggaa gaaggtgcgc ctgaaggcac cgtggcaact gtgctcatca aacgccccac 3301 cggggagctc atgcctcttg cagccagaat gggaacacac gcaaccatga aaattcaagg 3361 ccgcatggtt ggcggacaga tgggtatgtt gctcactgga tcaaatgcta aaggaatgga 3421 tttgggaaca actcctggtg actgtggctg tccttacatc tataaaaggg gcaatgacta 3481 tatagtcatt ggggtgcaca ctgcagcagc ccgtggtgga aacaccgtca tctgtgccac 3541 acagggaagt gagggtgagg caactcttga gggtggagat gacaaaggaa catactgtgg 3601 ggcacccatt ctaggccctg ggggtgcacc aaaattgagc accaaaacca aattttggag 3661 gtcatcgaac acgccccttc caccagggac atatgagcct gcctacctcg gtggccgtga 3721 tccgcgtgtt aagggtgggc cctccttgca gcaggtgatg agagaccagt tgaagccatt 3781 cactgaaccc aggggcaaac ctccaagacc aagtgtattg gaggcagcca aacaaaccat 3841 tatcaatgtt ctcgaacaaa ccctggaccc tccacaaaaa tggacatact cacaggcgtg 3901 tgcctcactt gacaaaacca cctccagcgg gcatccccat cacgtccgaa agaatgaatt 3961 ctggaatggt gagaccttca ctggtaaatt ggcagaccaa gcatcaaaag caaacctaat 4021 gtatgaggaa gggaaacaca tgacaccagt gtatacagca gcactcaagg acgagctagt 4081 caagactgag aaaatctatg gaaagatcaa gaagagactg ctctggggct ctgacttgtc 4141 cactatgatc cggtgcgcta ggtcatttgg tgggctcatg gacgagatga aggcacactg 4201 catatcactc ccagtacgag ttggcatgaa tatgaatgaa gatggcccaa taatatttga 4261 gaaacattcc agatacaaat accactatga tgcagactac tctcgttggg attcaacaca 4321 acagagggca gtactagcat cagccttgga aatcatggtc agattctctg cagaaccaca 4381 attggcacaa atagtcgctg aggatctact ggcccctagt gtagtagatg taggagactt 4441 taaaatcaca ataaatgaag ggctcccatc tggtgtgcca tgcacttctc aatggaactc 4501 catcgcacac tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtcccctga 4561 cattatacaa gcaaattcca tgttctcatt ttacggtgat gacgagattg tcagcaccga 4621 cataaaattg gaccctgaac agttaaccgc caagctgaag gagtacggcc tgaaaccaac 4681 ccgcccagac aagaccgagg gacccctgat catcagtgaa gatttgaacg gactcacctt 4741 cctccgaagg acggtgactc gtgacccagc tggctggttt ggaaaactgg accaaagttc 4801 aattttgagg cagatgtact ggactagagg accaaatcat gaagacccca atgagacaat 4861 gataccccac tctcaaagac ccatacagct catggcactg cttggtgaag cctctcttca 4921 cggaccctct ttctacagta gaattagtaa attggtcata actgaactca aagaaggtgg 4981 gatggacttt tacgtgccaa ggcaggaacc catgttcagg tggatgaggt tttctgactt 5041 gagcacgtgg gagggcgatc gcaatctggc tcccaatttt gtgaatgaag atggcgtcga 5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt accagaggtc aacaatgagg 5161 ttatggcttt ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa 5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtggg gagtttacag 5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccctaggc cctgacctaa 5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc 5401 aggtaattct cgcggggaac gcgttcaccg ccgggaagat tatatttgca gctgtcccac 5461 caaattttcc aactgaaggc ttaagtccta gccaggtcac tatgttcccc catataatag 5521 tagatgttag acagttagaa cctgtgctga ttcccttacc cgatgttagg aataatttct 5581 atcattacaa tcagtcaaat gattccacta ttaagttgat agcaatgttg tatacaccac 5641 ttagggctaa taatgctggg gatgatgttt tcacagtttc gtgccgagtt ctcacgagac 5701 catcccccga ttttgatttc atatttttag tgccacccac ggttgagtca agaactaaac 5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccatccctt 5821 tggaaaagtt gttcacaggc cccagcagtg cctttgttgt tcaaccacaa aacggcaggt 5881 gcacaactga tggcgtgctc ctaggcacca cccaactttc tcctgtcaac atctgcacct 5941 tcagagggga tgtcacccac atcacaggta gtcgcaacta cacaatgaat ttggcttctc 6001 aaaattggaa caactatgac ccaacagaag aaatcccagc ccctctagga actccagatt 6061 ttgtggggaa gattcaaggc atgctcaccc aaactacaag gacagatggt tcaacacgcg 6121 gccacaaagc tacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc 6181 aatttgaaac tgacacagac catgattttg aagctaatca aaacacaaag ttcaccccag 6241 tcggtgtcat ccaagatggt agcaccaccc accgaaacga accccaacag tgggtgctcc 6301 caagttactc aggcagaaat actcacaatg tacatttggc ccccgctgta gcccccactt 6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca 6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag 6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt 6541 tgtttgagtg caagcttcac aaatcaggct acgttacagt ggctcacact ggccaacatg 6601 atttggtcat tccccccaat ggttacttta ggtttgattc ctgggtcaac cagttctaca 6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgt agtataatgg ctggagcttt 6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg 6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc 6841 cttccaattt agcagcaatc tgcaacaggc ttcctttcag catgataaag agatgctcca 6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat 6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatta acgcccccat 7021 gacaaaaact ttggactgga gcgggacaag gtactgggct ccagatgcta ggattacaac 7081 atacaatgca ggccactttt ccacccctca accatcgagg gcactgccag gaagagctaa 7141 tcttagggat gctgtccctg ctcggggacc ctccaacaaa tcttctaacc cttctactgc 7201 cacctctgtg tactcaaatc aaactatttc aacgagactt ggttctacag ctggttctgg 7261 aaccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa 7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcatttgtca ccccaccatc 7381 tagcagatcc tctagccaag gcacagtctc aaccgtgtct aaagagattt tggactcctg 7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga 7501 gtcacgggtg taatgtgaaa agacaaaact gattatttta ctttttcttt tctttagtgt 7561 cttttaaaaa aa //