Typing tool
|
Complete norovirus genomes
MK773585 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 2..5101 ORF2: 5082..6704 ORF3: 6704..7510LOCUS MK773585 7552 bp RNA linear VRL 14-APR-2019 DEFINITION Norovirus GII isolate Hu/US/2016/GII.P16-GII.4 Sydney/Olmsted0261 nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes, complete cds. ACCESSION MK773585 VERSION MK773585.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7552) 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characterization of multiple viruses associated with a novel GII.P16 polymerase in the United States, 2015-2018 JOURNAL Unpublished REFERENCE 2 (bases 1 to 7552) AUTHORS Barclay,L., Cannon,J.L., Cebelinski,E., Montmayeur,A.M., Tatusov,R.L., Chhabra,P. and Vinje,J. TITLE Direct Submission JOURNAL Submitted (09-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..7552 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Olmsted0261" /isolate="Hu/US/2016/GII.P16-GII.4 Sydney/Olmsted0261" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA" /collection_date="20-Nov-2016" /note="genotype: GII.P16-GII.4 Sydney" gene 2..5101 /gene="ORF1" CDS 2..5101 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="QBY34792.1" /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP KRPAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ PGVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGEYELQGP EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH LKHARIRYYVKCVQEAIYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRLRFPKPIRPDVTGMILEEGAPEG TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVVRDQLKPFTEP RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIVFEKHSRYKYHYDADYSRWD STQQRAVLASALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE" mat_peptide 2..997 /gene="ORF1" /product="p48" mat_peptide 998..2095 /gene="ORF1" /product="NTPase" mat_peptide 2096..2626 /gene="ORF1" /product="p22" mat_peptide 2627..3025 /gene="ORF1" /product="VPg" mat_peptide 3026..3568 /gene="ORF1" /product="Pro" mat_peptide 3569..5098 /gene="ORF1" /product="RdRp" gene 5082..6704 /gene="ORF2" CDS 5082..6704 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QBY34793.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6704..7510 /gene="ORF3" CDS 6704..7510 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QBY34794.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS NSSTVTSVYSNQTISTRLGSTAGSGTSVSSPPSTARTRSWVEDQSRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 aatgaagatg gcgtctaacg acgctaccgt tgccgttgct tgcaacaaca acaacgacaa 61 ggaaaaatct tcaggtgaag gcttattcac aaatatgtct tccaccttaa agaaagccct 121 cggggctagg cccaaacggc ccgccccgag agacgaacca caaaagcccc caagaccacc 181 aactcccgag ttggtcaaga ggataccccc tcctccacct aatggcgaag aagaagaaga 241 accagtcatt aggtatgagg ttaagagtgg gatctctggc ctgcccgagc tcacaacagt 301 cccccaaccg ggcgtggcca acacagcatt cagtgttcca ccactgagct tgagagaaaa 361 cagggaggcc aaggaaccgc taacaggggc aatattagag atgtgggatg gagagatata 421 ccactatggc ctgtacgtgg agaaaggctt agtgttgggt gtgcacaaac cacctgcagc 481 cataagcatg gcaagagtgg agctgacgcc gctgtcattg tactggcgtg tggtgtacac 541 tccccaatac ctcatctccc ctgaaactct caggaggctc aacggagagg cgttccctta 601 caccgccttc gacaacaact gctatgcctt ttgctgctgg gtgttagacc tcaatgactc 661 atggcttagc aggaggatgg tgcaaagaac aacgggcttc ttcagacctt accaagagtg 721 gaacagaaaa cccctgccca ccatggatga ctccaaaatt aagaaggtag caaatatatt 781 cctatgttca ttgtccacgt tattcaccag acccataaaa gacctcatag gaaaaattaa 841 accattaaac atattgaaca tcctggcaac gtgtgactgg acgtttgccg gaatagtgga 901 atctctgata ttacttgctg aactcttcgg agttttctgg acacccccag atgtgtctgc 961 tatgatcgct cccttactcg gggaatacga gttgcaaggg ccagaagacc tcgccgttga 1021 actcgtacct gtggtaatgg gagggattgg tttggtgttg ggattcacca aagagaaaat 1081 tggcaaaatg ttgtcctcag cagcatcaac actcagggct tgcaaagatc ttggtgccta 1141 tggcttagag atactcaaat tggtcatgaa gtggttcttc ccaaagaaag aggaggccaa 1201 tgagctagcc atggtgaggg ccatagagga tgccgtacta gatcttgagg caatagaaaa 1261 taaccacatg acaaccctgt tgaaagacaa agacagctta gcaacataca tgaaaacact 1321 ggacatggag gaggagaaag ccagaaggtt gtccacaaaa tctgcatccc ctgacatagt 1381 tgggacaatc aacgccctgc tggctcgaat agcagcggcc aggtcattag tccacagggc 1441 caaggaagag ctgtctagca ggataagacc agtagttgtt atgatatctg gcaaaccagg 1501 gataggcaaa actcatctgg ccagggaggt ggcaagaaag gtggcatcca ctctcacagg 1561 ggatcaaaga gtcggactca taccaagaaa cggtgtggac cattgggatg catacaaagg 1621 tgagagagtc gtgctgtggg acgactatgg catgagtaac cccattcatg atgctcttcg 1681 catacaagaa ttggctgata cgtgtcccct taccttaaat tgtgacagaa ttgaaaataa 1741 gggaaaagtt tttgacagtg aagtcataat aattacaaca aaccttgcca atccagcccc 1801 acttgattat gtcaactttg aggcctgttc caggagaatt gatttcctgg tgtacgctga 1861 ggcaccagaa gtagaaaagg caaaacggga ctttcctggt cagccagata tgtggaagga 1921 cgccttcaag ccggactttt cacacatcaa gctacagctt gcacctcagg gcggctttga 1981 caagaatggc aacaccccac atgggaaagg agtgatgaag accctcacca ccggttctct 2041 gattgcccgt gcatcaggcc tactgcatga aaggatggat gaatttgaac tccaaggtcc 2101 cacaatcacc accttcaatt tcgaccggaa cagaatcaca gcattcagac aattggctgc 2161 agaaaacaag tatggattgg tggataccat gaaagttggc aatcaactaa agggagtgaa 2221 aaccatggaa gaactcaaac aagcaatcag gaatgtgacc atcaagaggt gccggatcat 2281 ctacggtggc tccacgtacg accttgaatc tgatggcaag ggcaaagttt tggtggaaaa 2341 agtcaagaac acctctgtac agaccaacaa cgagttggcc ggggccctgc accatctcaa 2401 acacgcccga atcaggtact atgtcaaatg tgtgcaagaa gcaatctact ccatcataca 2461 aattgccggc gctgcgtttg tcaccacgcg cattgcacgc cgcatgaaca tacaagaact 2521 ctggtcgaag ccacaattag atcaaaatga atcagagact aaggaagagg cccccaagtc 2581 agaagacgac gagttcatca tatcttctaa ggacatcaag gaggaaggaa agaagggcaa 2641 aaacaaaact ggccgtggca agaaacacac tgcattctcc agcaagggtt tgagcgatga 2701 ggagtatgac gagtacaaga ggataagaga agagagaaat gggaagtact ctatagagga 2761 gtatcttcaa gatagagaca ggtactatga ggagctcgcc attgccaagg ccacagaaga 2821 agacttctgt gaagaggagg agatcaaaat ccgtcagaga attttccgtc ccaccaggaa 2881 acaaagaaag gaagagaggg ccacattagg gctagtaaca ggttcagaaa tcagaaaaag 2941 aaaccctgat gacttcaaac ccaaagggaa gctgtgggcc gatgacaaca gaagtgttga 3001 ctacaatgag aaactggact ttgaggcccc cccaagcata tggtctagga ttgtgagctt 3061 tggttctggc tggggcttct gggtatcacc aagcctgttc ataacatcaa ctcatgtaat 3121 ccccgcaggc ataacagaag cgtttggagt ccccatcaaa caaattcaga tccacaaatc 3181 aggtgaattt tgccgactca gattcccaaa accaattaga ccagatgtga caggaatgat 3241 cttggaagaa ggtgcgcctg aaggcaccgt ggcaactgtg ctcatcaaac gccccaccgg 3301 agagctcatg cctcttgcag ccagaatggg aacacacgca accatgaaaa ttcaaggccg 3361 catggttggc ggacagatgg gtatgttgct cactggatca aatgctaaag gaatggattt 3421 gggaacaact cctggtgact gtggctgccc ttacatctat aaaaggggca atgactacat 3481 agtcattggg gtgcacactg cagcagcccg tggtggaaac accgtcatct gtgccacaca 3541 gggaagtgag ggtgaggcaa ctcttgaggg tggagatgac aaaggaacat actgtggggc 3601 acccattcta ggccctgggg gtgcaccaaa attgagcacc aaaaccaaat tttggaggtc 3661 atcgaacacg ccccttccac cagggacata tgagcctgcc tacctcggtg gccgtgatcc 3721 gcgtgttaag ggtgggccct ccttgcagca ggtagtgaga gaccagttga agccattcac 3781 tgaacccagg ggcaaacctc caagaccaag tgtattggaa gcagccaaac aaaccattat 3841 caatgtcctc gaacaaaccc tggaccctcc acaaaaatgg acatacgcac aggcgtgtgc 3901 ctcacttgac aaaaccacct ccagcgggca tccccatcac gtccgaaaga atgaattctg 3961 gaatggtgag accttcactg gtaaattggc agaccaagca tcaaaagcaa acctaatgtt 4021 tgaggaaggg aaacacatga caccagtgta tacagcagca ctcaaggatg agctagtcaa 4081 gactgagaaa atctatggaa agatcaagaa gagactgctc tggggctctg acttgtccac 4141 catgatccgg tgcgctaggt catttggtgg gctcatggac gagatgaagg cacactgcat 4201 atcactccca gtacgagttg gcatgaatat gaatgaagat ggcccaatag tatttgagaa 4261 acattccaga tacaaatatc actatgatgc agactactct cgttgggatt caacacaaca 4321 gagggcagta ctagcatcag ctttggaaat catggtcaga ttctctgcag aaccacaatt 4381 ggcacaaata gtcgctgagg atctgctggc ccctagtgta gtagatgtag gagactttaa 4441 aatcacaata aatgaagggc tcccatctgg tgtaccatgc acttctcaat ggaactccat 4501 cgcacactgg ctgctaactc tctgtgcctt gtctgaagtc accaaactgt cccctgacat 4561 catacaagca aattccatgt tctcatttta cggtgatgac gagattgtca gcaccgacat 4621 aaaattggac cctgaacagt taaccgccaa gttgaaggag tacggcctga aaccaacccg 4681 cccagacaag accgagggac ccctgatcat cagtgaagat ttgaacggac tcactttcct 4741 ccgaaggacg gtgactcgtg acccagctgg ctggtttgga aaactggacc aaagctcaat 4801 tctgaggcag atgtactgga ctagaggacc aaatcatgaa gaccctaatg agacaatgat 4861 accccattct caaagaccca tacagctcat ggcactgctt ggtgaagcct ctcttcacgg 4921 accctctttc tacagtaaaa tcagtaaatt ggtcataact gaactcaaag aaggtgggat 4981 ggacttttac gtgccaaggc aggaacccat gttcaggtgg atgaggtttt ctgacttgag 5041 cacgtgggag ggcgatcgca atctggctcc caattttgtg aatgaagatg gcgtcgagtg 5101 acgccaaccc atctgatggg tccgcagcca acctcgtacc agaggtcaac aatgaggtta 5161 tggctttgga gcccgttgtt ggtgccgcta ttgcggcacc tgtagcgggc caacaaaatg 5221 taattgaccc ctggattaga aataattttg tacaagcccc tggaggggag tttacagtat 5281 cccctagaaa cgctccaggt gaaatactat ggagcgcgcc cctaggccct gacctaaatc 5341 cctacctatc ccatttggcc agaatgtaca atggttatgc aggtggtttt gaagtgcagg 5401 taattctcgc ggggaacgcg ttcaccgccg ggaagatcat atttgcagca gtcccaccaa 5461 attttccaac tgagggctta agtcctagcc aagtcactat gttcccccat ataatagtag 5521 atgttagaca attagaacct gtgctgattc ccttacccga tgttaggaat aatttctatc 5581 attataatca gtcaaatgac tccactatta agttgatagc aatgttgtat acaccactta 5641 gggctaataa tgctggggat gatgttttca cagtttcgtg ccgagttctc acgagaccat 5701 cccccgattt tgatttcata tttttagtgc cacccacagt tgagtcaaga actaaaccat 5761 tctctgtccc agttttaact gttgaggaga tgaccaattc aagattcccc attcctttgg 5821 aaaagttgtt cacgggcccc agcagtgcct ttgttgtcca accacaaaac ggcaggtgca 5881 caactgatgg cgtgctccta ggcaccactc aactgtctcc tgttaacatc tgcaccttca 5941 gaggggatgt cacccacatc acaggtagtc gcaactacac aatgaatttg gcttctcaaa 6001 attggaataa ttatgaccca acagaagaaa tcccagcccc tctaggaact ccagattttg 6061 tggggaagat tcaaggcatg ctcacccaaa ccacaaggac agatggttca acacgcggcc 6121 acaaagctac agtgtacact gggagcgccg actttgctcc aaaactgggt agagttcaat 6181 ttgaaactga cacagaccat gattttgaag ctaatcaaaa cacaaagttc accccagtcg 6241 gtgtcatcca agacggtagc accacccacc gaaacgaacc ccaacagtgg gtgctcccaa 6301 gttactcagg cagaaatacc cacaatgtac acctggcccc cgctgtagcc cccacctttc 6361 cgggtgagca acttctcttc ttcagatcca ccatgcccgg atgcagcggg taccccaaca 6421 tggatttgga ctgtctgctc ccccaggaat gggtgcagta tttctaccaa gaggcagccc 6481 cagcacaatc tgatgtggct ctgctaagat ttgtaaatcc agacacaggt agggttttgt 6541 ttgagtgcaa gcttcacaaa tcaggctatg ttacagtggc tcacactggc caacatgatt 6601 tggttatccc tcccaatggt tactttaggt ttgattcctg ggtcaaccag ttctacacgc 6661 ttgcccccat gggaaatgga acggggcgta gacgtgtagt ataatggctg gagctttctt 6721 tgctggattg gcatctgatg tccttggctc tggacttggt tccctcatca atgctggggc 6781 tggggccatc aaccaaaaag ttgagtttga aaataacaga aaattgcaac aagcatcctt 6841 ccaatttagc agtaatctgc aacaggcttc ctttcaacat gataaagaga tgctccaagc 6901 acaaattgag gccaccaaaa agctacaaca ggaaatgatg aaagttaagc aggcagtgct 6961 cctagagggt gggttctctg agacagatgc agcccgcggg gcaattaacg cccccatgac 7021 aaaagctttg gattggagcg ggacaaggta ctgggctccc gatgctagga ctacaacata 7081 caatgcaggc cgcttttcca cccctcaacc atcgggggca ctgccaggaa gagctaatct 7141 tagggatgct gtccctgctc ggggaccctc caacaaatct tctaactctt ctactgtcac 7201 ctctgtgtac tcaaatcaaa ctatttcaac gagacttggt tctacagctg gttctggaac 7261 cagtgtctcg agccccccgt caactgcaag gactaggagc tgggttgagg atcaaagtag 7321 gaatttgtca cctttcatga ggggggccca caacatatca tttgtcaccc caccatctag 7381 cagatcctct agccaaggca cagtctcaac cgtgcctaaa gagattttgg actcctggac 7441 tggcgctttc aacacgcgca ggcagcctct cttcgctcac attcgtaagc gaggggagtc 7501 acgggtgtaa tgtgaaaaga caaaactgat tatctttctt tttctttagt gt //