Typing tool
|
Complete norovirus genomes
KY947549 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 4..5103 ORF2: 5084..6706 ORF3: 6706..7512LOCUS KY947549 7530 bp ss-RNA linear VRL 18-MAY-2017 DEFINITION Norovirus GII strain Hu/USA/2016/GII.P16-GII.4 Sydney/CS4243 polyprotein, VP1, and VP2 genes, complete cds. ACCESSION KY947549 VERSION KY947549.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7530) AUTHORS Cannon,J.L., Barclay,L., Collins,N.R., Wikswo,M.E., Castro,C.J., Magana,L.C., Gregoricus,N., Marine,R.L., Chhabra,P. and Vinje,J. TITLE Genetic and Epidemiologic Trends of Norovirus Outbreaks in the US Demonstrated Emergence of Novel GII.4 Recombinant Viruses, 2013-2016 JOURNAL J. Clin. Microbiol. (2017) In press PUBMED 28490488 REMARK Publication Status: Available-Online prior to print REFERENCE 2 (bases 1 to 7530) AUTHORS Cannon,J.L., Barclay,L., Collins,N.R., Chhabra,P., Wikswo,M.E., Castro,C.J., Magana,L.C., Gregoricus,N. and Vinje,J. TITLE Direct Submission JOURNAL Submitted (14-APR-2017) Viral Gastroenteritis Branch/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. 8 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7530 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Hu/USA/2016/GII.P16-GII.4 Sydney/CS4243" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA" /collection_date="24-Mar-2016" /note="genotype: GII.P16-GII.4 Sydney" 5'UTR 1..3 CDS 4..5103 /note="nonstructural protein; ORF1" /codon_start=1 /product="polyprotein" /protein_id="ARR95963.1" /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP KQPAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD CGCPYIYKRGNDYIAIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE" CDS 5084..6706 /note="major capsid protein; ORF2" /codon_start=1 /product="VP1" /protein_id="ARR95964.1" /translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNAHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV" CDS 6706..7512 /note="minor structural protein; ORF3" /codon_start=1 /product="VP2" /protein_id="ARR95965.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGTLPGRANLRDAVPARGPSNKSS NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRRRGESRV" 3'UTR 7513..7530 ORIGIN 1 tgaatgaaga tggcgtctaa cgacgctacc gttgccgttg cttgcaacaa caacaacgac 61 aaggaaaaat cttcaggtga aggcttattc acaaatatgt cttccacctt aaagaaagcc 121 ctcggggcta ggcccaaaca gcctgccccg agagacgaac cacaaaagcc cccaagacca 181 ccaactcccg agttggtcaa gaggataccc cctcctccac ctaatggcga agaagaagaa 241 gaaccagtca ttaggtatga ggttaagagt gggatctctg gcctgcccga gctcacaaca 301 gtcccccaac cggacgtggc caacacagca ttcagtgttc caccactgag cttgagagaa 361 aacagggagg ccaaagaacc gctaacaggg gcaatattag agatgtggga tggagagata 421 taccactatg gcctgtacgt ggagaaaggc ttagtgttgg gtgtgcacaa accacctgca 481 gccataagca tggcaagagt ggagttgacg ccgctgtcat tgtactggcg tgtggtgtac 541 actccccaat acctcatctc ccctgaaact ctcaggaggc tcaacggaga ggcgttccct 601 tacaccgcct tcgacaacaa ctgctatgcc ttttgctgct gggtgttgga cctcaatgac 661 tcatggctta gcaggaggat ggtgcaaaga acaacgggct tcttcagacc ttaccaagag 721 tggaacagaa aacccctgcc taccatggat gactccaaaa ttaagaaggt agcaaatata 781 ttcctatgtt cattgtccac attattcacc agacccataa aagacctcat aggaaagatt 841 aaaccattaa acatattgaa catcctggca acgtgtgact ggacgtttgc cggaatagtg 901 gagtctctga tattacttgc tgaactcttc ggagttttct ggacaccccc agatgtgtct 961 gctatgatcg ctcccttact cggggactac gaattgcaag ggccagaaga cctcgccgtt 1021 gaactcgtac ctgtggtaat gggagggatt ggtttggtgt tgggattcac caaagagaaa 1081 attggcaaaa tgttgtcctc agcagcatca acactcaggg cttgcaaaga tcttggtgcc 1141 tatggcttag agatactcaa attggtcatg aagtggttct tcccaaagaa agaggaggcc 1201 aatgagctag ccatggtgag ggccatagag gatgccgtac tagatcttga ggcaatagaa 1261 aataaccaca tgacaaccct gttgaaagac aaagacagct tagcaacata catgaaaaca 1321 ctggacatgg aagaggagaa agccagaagg ttgtccacaa aatctgcatc ccctgacata 1381 gttgggacaa tcaacgccct gctggctcga atagcagcgg ccaggtcatt agtccacagg 1441 gccaaggaag agctgtctag caggataaga ccagtagttg ttatgatatc tggcaaacca 1501 ggaataggca aaactcatct ggccagggag gtggcaagaa aggtggcatc cactctcaca 1561 ggggatcaaa gagtcggact cataccaaga aacggtgtgg accattggga tgcatacaaa 1621 ggtgagagag tcgtgctgtg ggacgactat ggcatgagta accccattca tgatgctctt 1681 cgcatacaag aattggctga cacgtgtccc cttaccttaa attgtgacag aattgaaaat 1741 aagggaaaag tttttgacag tgaggtcata ataatcacaa caaaccttgc caatccagcc 1801 ccacttgatt atgtcaactt tgaggcctgt tccaggagaa ttgattttct ggtgtacgct 1861 gaggcaccag aagtagaaaa ggcaaaacgg gactttcctg gtcagccaga tatgtggaag 1921 gacgccttca agccggactt ctcacacatc aagctacagc ttgcacctca gggcggcttt 1981 gacaagaatg gcaacactcc acatgggaag ggagtgatga agaccctcac taccggttct 2041 ctgattgccc gcgcgtcagg cctactgcat gagaggatgg atgaatttga actccaaggt 2101 cccacaatca ccaccttcaa tttcgaccgg aacagaatca cagcattcag gcaattggct 2161 gcggaaaaca agtatggatt ggtggatacc atgaaagttg gcaatcaact aaaaggagtg 2221 aaaaccatgg aagaactcaa acaagcaatc aggaatgtga ccatcaagag gtgccggatc 2281 atctacggtg gctccacgta tgaccttgaa tctgatggca agggcaaagt tttggtggaa 2341 aaggtcaaga acacctctgt acagaccaac aacgagctgg ctggggccct gcaccatctc 2401 aaacacgccc gaatcaggta ctatgtcaaa tgtgtgcaag aagcagtcta ttccatcata 2461 caaattgccg gcgctgcgtt tgtcaccacg cgcattgcgc gccgcatgaa catacaggaa 2521 ctctggtcga agccacaatt agatcaaaat gaatcagaga ctaaggaaga ggcccccaag 2581 tcagaagatg acgagttcat catatcttct aaggacatca aggaggaagg aaagaagggc 2641 aaaaacaaga ctggccgtgg caagaaacac actgcattct ccagcaaggg cttgagcgat 2701 gaggagtacg acgagtacaa gaggataaga gaagagagaa atgggaagta ctctatagag 2761 gagtatcttc aagacagaga caggtactat gaggagctcg ccattgccaa ggccacggaa 2821 gaagacttct gtgaagagga ggagatcaaa atccgtcaga gaattttccg tcccaccagg 2881 aaacaaagaa aggaagagag ggccacatta gggctagtaa caggttcaga aatcagaaaa 2941 agaaaccctg atgacttcaa acccaaaggg aagctgtggg ccgatgacaa cagaagtgtt 3001 gactacaatg agaaactgga ctttgaggcc cccccaagca tatggtctag gattgtgagc 3061 tttggttctg gctggggctt ctgggtatca ccaagcctgt tcataacatc aactcatgta 3121 atccccgcag gcataacaga agcatttgga gtccccatca aacaaattca gattcacaaa 3181 tcaggtgaat tttgccgatt cagattccca aaaccaatta gaccagatgt gacaggaatg 3241 atcttagaag aaggtgcgcc tgaaggcacc gtagcaactg tgcttatcaa acgccccacc 3301 ggagagctca tgcctcttgc agccagaatg ggaacacacg caaccatgaa aattcaaggc 3361 cgcatggttg gcggacagat gggtatgttg ctcactggat caaatgctaa aggaatggat 3421 ttgggaacaa ctcctggtga ctgtggctgt ccttacatct ataaaagggg caatgactat 3481 atagccattg gggtgcacac tgcagcagcc cgtggtggaa acaccgtcat ctgtgccaca 3541 cagggaagtg agggtgaggc aactcttgag ggtggagatg acaaaggaac atactgtggg 3601 gcacctattc taggccctgg gggtgcacca aaattgagca ccaaaaccaa attttggagg 3661 tcatcgaaca cgccccttcc accagggaca tatgagcctg cctacctcgg tggccgtgat 3721 ccgcgtgtta agggtgggcc ctccttgcag caggtaatga gagaccagtt aaagccattc 3781 actgaaccca ggggcaaacc tccaagacca agtgtattgg aagcagccaa acaaaccatt 3841 atcaacgtcc tcgaacaaac cctggaccct ccacaaaaat ggacatacgc acaggcgtgt 3901 gcatcacttg acaaaaccac ctccagcggg catccccatc acgtccgaaa gaatgaattc 3961 tggaatggtg agaccttcac tggcaaattg gcagaccaag catcaaaagc aaacctaatg 4021 tttgaggaag ggaaacacat gacaccagtg tatacagcag cactcaagga cgagctagtc 4081 aagactgaga aaatctatgg aaagatcaag aagagactgc tctggggctc tgacttgtcc 4141 accatgatcc ggtgcgctag gtcatttggt gggctcatgg acgagatgaa ggcgcactgc 4201 atatcactcc cagtacgagt tggcatgaat atgaatgaag atggcccaat aatatttgag 4261 aaacattcca gatacaaata ccactatgat gcagactact ctcgttggga ttcaacacaa 4321 cagagggcag tgctagcagc agccttggaa atcatggtca gattctctgc agaaccacaa 4381 ttggcacaaa tagtcgctga ggatctgctg gcccctagtg tagtagatgt aggagacttt 4441 aaaatcacaa taaatgaagg gctcccatct ggtgtgccat gcacttctca atggaactcc 4501 atcgcacact ggctgctaac tctctgtgcc ttgtctgaag tcaccaaact gtcccctgac 4561 attatacaag caaattccat gttctcattt tacggtgatg acgagattgt cagcaccgac 4621 ataaaattgg accctgaaca gttaaccgcc aaattgaagg agtacggcct gaaaccaacc 4681 cgcccagaca agaccgaggg acccctgatt atcagtgaag atttgaacgg actcactttc 4741 ctccgaagga cggtgactcg tgacccagct ggctggtttg gaaaactgga ccaaagctca 4801 attttgaggc agatgtactg gactagagga ccaaatcatg aagaccccaa tgagacaatg 4861 ataccccatt ctcaaagacc catacagctc atggcactgc ttggtgaagc ctctcttcac 4921 ggaccctctt tctacagtaa aatcagtaaa ttggtcataa ctgaactcaa agaaggtggg 4981 atggactttt acgtgccaag gcaggaaccc atgttcagat ggatgaggtt ttctgacttg 5041 agcacgtggg agggcgatcg caatctggct cccaattttg tgaatgaaga tggcgtcgaa 5101 tgacgccaac ccatctgatg ggtccgcagc caacctcgta ccagaggtca acaatgaggt 5161 tatggctttg gagcccgttg ttggtgccgc tattgcggca cctgtagcgg gccaacaaaa 5221 tgtaattgac ccctggatta gaaataattt tgtacaagcc cctggtgggg agtttacagt 5281 atcccccaga aacgctccag gtgaaatact atggagcgcg cccctaggcc ctgacctaaa 5341 tccctaccta tcccatttgg ccagaatgta caatggttat gcaggtggtt ttgaagtgca 5401 ggtaattctc gcggggaacg cgttcactgc cgggaagatc atatttgcag cagtcccacc 5461 aaattttcca actgaaggct taagtcctag ccaggtcact atgttccccc atataatagt 5521 ggatgttaga caattagaac ctgtgctgat tcccttaccc gatgtcagga ataatttcta 5581 tcattataac cagtcaaatg attccactat taagttgata gcaatgttgt atacaccact 5641 tagggctaat aatgctgggg atgatgtttt cacagtttcg tgccgagttc tcacgagacc 5701 atcccccgat tttgatttca tatttttagt gccacccaca gttgagtcaa gaactaaacc 5761 attctctgtc ccagttttaa ctgttgagga gatgaccaat tcaagattcc ccattccttt 5821 ggaaaagttg ttcacgggcc ccagcagtgc ctttgttgtt caaccacaaa acggcaggtg 5881 cacaactgat ggcgtgctcc taggcaccac ccaattgtct cctgtcaata tctgcacctt 5941 cagaggggat gtcacccaca tcacaggtag tcgcaactac acaatgaatt tggcttctca 6001 aaattggaac aactatgacc caacagaaga aatcccagcc cctctaggaa ctccagattt 6061 tgtggggaag attcaaggca tgctcaccca aaccacaagg acagatggtt caacacgcgg 6121 ccacaaagct acagtgtaca ctgggagcgc cgactttgct ccaaaactgg gtagagttca 6181 atttgaaact gacacagacc atgattttga agctaatcaa aacacaaagt tcaccccagt 6241 cggtgtcatc caagatggta gcaccaccca tcgaaacgaa ccccaacagt gggtgctccc 6301 aagttactca ggcagaaatg ctcacaatgt acatctggcc cctgctgtag cccccacctt 6361 cccgggtgag caacttctct tcttcagatc caccatgccc ggatgcagcg ggtaccccaa 6421 catggatttg gactgtctgc ttccccagga atgggtgcag tacttctacc aagaggcagc 6481 cccagcacaa tctgatgtgg ctctgctaag atttgtgaac ccagacacag gtagggtttt 6541 gtttgagtgc aagcttcaca aatcaggcta tgttacagtg gctcacactg gccaacatga 6601 tttggttatc ccccccaatg gttactttag gtttgattcc tgggtcaacc agttctacac 6661 gcttgccccc atgggaaatg gaacggggcg tagacgtgca gtataatggc tggtgctttc 6721 tttgctggat tggcatccga tgtccttggc tctggacttg gttcccttat caatgctggg 6781 gctggggcca tcaaccaaaa agttgagttt gaaaataaca gaaaattgca acaagcatcc 6841 ttccaattta gcagcaatct gcaacaggct tcctttcaac atgataaaga gatgctccaa 6901 gcacaaattg aggccaccaa aaagctacaa caggaaatga tgaaagttaa gcaggcaatg 6961 ctcctagagg gtgggttctc tgagacagat gcagcccgcg gggcaattaa cgcccccatg 7021 acaaaagttt tggactggag cgggacaagg tactgggctc ccgatgctag gactacaaca 7081 tacaatgcag gtcgcttttc cacccctcaa ccatcgggga cactgccagg aagagctaat 7141 cttagggatg ctgtccctgc tcggggaccc tccaacaaat cttctaactc ttctactgcc 7201 acctctgtgt actcaaatca aactatctca acgagacttg gttctacagc tggttctgga 7261 accagtgtct cgagcctccc gtcaactgca aggactagga gctgggttga ggatcaaagt 7321 aggaatttgt cacctttcat gaggggggcc cacaacatat catttgtcac cccaccatct 7381 agcagatcct ctagccaagg cacagtctca accgtgccta aagagatttt ggactcctgg 7441 actggcgctt tcaacacgcg caggcagcct ctcttcgctc acattcgtag gcgaggggag 7501 tcacgggtgt aatgtgaaaa gacaaaactg //