Typing tool
|
Complete norovirus genomes
MK752938 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7513LOCUS MK752938 7573 bp RNA linear VRL 11-APR-2019 DEFINITION Norovirus GII isolate Hu/US/2017/GII.P16-GII.4 Sydney/Brown0441, complete genome. ACCESSION MK752938 VERSION MK752938.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7573) 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characterization of multiple viruses associated with a novel GII.P16 polymerase in the United States, 2015-2018 JOURNAL Unpublished REFERENCE 2 (bases 1 to 7573) AUTHORS Barclay,L., Cannon,J.L., Davis,T., Montmayeur,A.M., Tatusov,R.L. and Vinje,J. TITLE Direct Submission JOURNAL Submitted (04-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..7573 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Brown0441" /isolate="Hu/US/2017/GII.P16-GII.4 Sydney/Brown0441" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA" /collection_date="23-Mar-2017" /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="QBS47645.1" /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP KQPAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA ISMARVELAPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP EELAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV EKAKRDFPGQPDMWKDAFKSDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVAGMILEEGAPEG TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW NGETFTGKLADQASKANLMYEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK EYGLKPTRPDKTEGPLITSEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP 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="QBS47646.1" /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="QBS47647.1" /translation="MAGTFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQSTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgctac cgttgccgtt gcttgcaaca acaacaacga 61 caaggaaaaa tcttcaggtg agggattatt cacaaatatg tcttccacct taaagaaagc 121 cctcggggct aggcccaaac agcctgcccc gagagacgaa ccgcaaaagc ccccaagacc 181 accaactccc gagttggtca agaggatacc ccctcctcca cctaatggcg aagaagaaga 241 agaaccagtc attaggtatg aggttaagag tgggatctct ggcctgcccg aactcacaac 301 agtcccccaa ccggacgtgg ccaacacagc attcagtgtt ccaccactga gcttgagaga 361 aaacagggag gccaaggaac cgctaacagg ggcaatatta gagatgtggg acggagaaat 421 ataccactat ggcctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc 481 agccataagc atggcaagag tggagctggc gccgctgtca ctgtactggc gtgtggtgta 541 cactccccaa tacctaatct cccctgaaac tctcaggagg ctcaacggag aggcgttccc 601 ttacaccgcc ttcgacaaca actgctatgc cttttgctgc tgggtgttag acctcaatga 661 ctcgtggctt agcaggagga tggtgcaaag aacaacgggt ttcttcagac cttaccaaga 721 gtggaacaga aaacccctgc ctaccatgga tgactccaaa ataaagaagg tggcaaatat 781 attcctatgt tcattgtcca cattgtttac cagacccata aaagacctca taggaaaaat 841 taaaccatta aacatattga acatcctggc aacgtgtgat tggacgtttg ccggaatagt 901 ggagtctctg atattacttg ctgaactctt cggagttttc tggacacccc cagatgtgtc 961 tgctatgatc gctcccttac tcggggacta cgagttgcaa gggccagaag agctcgccgt 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 atatgaaaac 1321 actggacatg gaggaggaga aagccagaag gttgtccaca aaatctgcat cccctgacat 1381 agttggaaca atcaacgcct tgctggctcg aatagcagcg gccaggtcat tagtccacag 1441 ggccaaggaa gagctatcta gcaggataag accagtagtt gttatgatat ctggcaaacc 1501 aggaataggc aaaactcatc tggccaggga ggtggcaaga aaggtggcat ccaccctcac 1561 aggggatcaa agagtcggac tcataccaag aaacggtgtg gaccattggg atgcatacaa 1621 aggtgagaga gtcgtgctat gggacgacta tggcatgagt aaccccattc atgatgctct 1681 tcgcatacag gaattggctg atacgtgtcc ccttacctta aattgtgaca gaattgaaaa 1741 taagggaaaa gtttttgaca gtgaagtcat aataattaca acaaaccttg ccaacccagc 1801 cccacttgat tatgtcaact ttgaggcctg ttccaggaga attgatttcc tggtgtacgc 1861 tgaggcacca gaagtagaaa aggcaaaacg ggactttcct ggtcagccag atatgtggaa 1921 ggacgccttc aagtcggact tttcacacat caagctacag cttgcacctc agggcggctt 1981 tgacaagaat ggcaacaccc cacatgggaa aggagtgatg aagaccctca ctaccggttc 2041 tctgattgcc cgtgcatcag gcctactgca tgagaggatg gatgagtttg aactccaagg 2101 tcccacaatc accaccttca atttcgatcg gaacagaatc acagcattca gacaattggc 2161 tgcagaaaac aagtatggat tggtggacac catgaaagtt ggcaatcaac taaaaggagt 2221 gaaaaccatg gaagaactca aacaagcaat caggaatgtg accatcaaga ggtgccggat 2281 catctatggt ggctccacgt atgaccttga atctgatggc aagggcaaag ttttggtgga 2341 aaaggtcaag aacacctctg tacagaccaa caacgagttg gccggggccc tgcaccacct 2401 caaacacgcc cgaattaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat 2461 acaaattgcc ggcgctgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga 2521 actctggtcg aagccacaat tagatcaaaa tgaatcagag actaaggaag aggcccccaa 2581 gtcagaagat gacgagttca tcatatcttc taaggacatc aaggaggaag gaaagaaggg 2641 caaaaacaaa actggccgtg gcaagaaaca cactgcattc tccagcaagg gcttgagcga 2701 tgaggagtat gacgagtaca agaggataag agaagagaga aatgggaagt actctataga 2761 ggagtatctt caagacagag acaggtacta tgaggagctc gccattgcca aggccacgga 2821 agaagacttc tgtgaagagg aggagatcaa aatccgtcag agaattttcc gtcccaccag 2881 gaaacaaaga aaagaagaga gggctacatt 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 aagcgtttgg agtccccatc aaacaaattc agatccacaa 3181 atcaggtgaa ttttgccgat tcagattccc aaaaccaatt agaccagatg tggcaggaat 3241 gatcttggaa gaaggtgcgc ctgaaggcac cgtggcaact gtgctcatca aacgccccac 3301 cggagagctc atgcctcttg cagccagaat gggaacacac gcaaccatga aaattcaagg 3361 ccgcatggtt ggcggacaga tgggtatgtt gctcactgga tcaaatgcta aaggaatgga 3421 tttgggaaca actcctggtg actgtggctg cccttacatc 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 atacgagcct gcctacctcg gtggccgtga 3721 tccgcgtgtt aagggtgggc cctccttgca gcaggtgatg agagaccagt tgaaaccatt 3781 cactgaaccc aggggcaaac ctcctagacc aagtgtattg gaagcagcca agcaaaccat 3841 tatcaatgtt ctcgaacaaa ccctggaccc tccacaaaaa tggacatacg cacaggcgtg 3901 tgcctcactt gacaaaacca cctccagcgg gcatccccat cacgtccgaa agaatgaatt 3961 ctggaatggt gagaccttca ctggtaaatt ggcagaccaa gcttcaaaag caaacctaat 4021 gtatgaggaa gggaaacaca tgacaccagt gtatacagca gcactcaagg acgagctagt 4081 caagactgag aaaatctatg gaaagatcaa gaagagactg ctctggggct ctgacttgtc 4141 cactatgatc cggtgcgcta ggtcatttgg tgggctcatg gacgagatga aggcacactg 4201 catatcactc ccggtacgag ttggcatgaa tatgaatgaa gatggcccaa taatatttga 4261 gaaacactcc agatacaaat accactatga tgcagactac tctcgttggg attcaacaca 4321 acagagggca gtactagcag 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 caagttgaag gagtacggcc tgaaaccaac 4681 ccgcccagat aagaccgagg gacccctgat caccagtgaa 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 gaatcagtaa 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 gaacgctcca ggtgaaatac tatggagcgc gcccctaggc cctgacctaa 5341 acccctacct gtcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc 5401 aggtaattct cgcggggaac gcgttcaccg ccgggaagat tatatttgca gcagtcccac 5461 caaattttcc aactgaaggc ttaagtccta gccaggtcac tatgttcccc catataatag 5521 tagatgttag acaattagaa cctgtgttga ttcccttacc cgatgttagg aacaattttt 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 cttttgttgt ccaaccacaa 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 aaaccacaag 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 aggcagaaac actcacaatg tacatttggc ccccgctgta gcccccactt 6361 ttccaggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca 6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag 6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt 6541 tgtttgagtg caagcttcac aaatcaggct atgttacagt ggctcacact ggccaacatg 6601 atttggttat ccctcccaat ggttacttta gatttgattc ctgggttaat cagttctaca 6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgt agtataatgg ctggaacttt 6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg 6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaacaac agaaaattgc aacaagcatc 6841 cttccaattt agcagcaatc tacaacaggc ttcctttcaa catgataaag agatgctcca 6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat 6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatta acgcccccat 7021 gacaaaagct ttggactgga gcgggacaag gtactgggct ccagatgcta ggattacaac 7081 atacaatgca ggccactttt ccacccctca accatcgagg gcactgccag gaagagctaa 7141 tcttagggat gctgtccctg ctcggggacc ctccaacaaa tcttctaact cttctactgc 7201 cacctctgtg tactcaaatc aaaccatttc aacgagactt ggttctacag ctggttctgg 7261 aaccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa 7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcatttgtca ccccaccatc 7381 tagcagatcc tctagccaaa gcacagtctc aaccgtgcct aaagagattt tggactcctg 7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga 7501 gtcacgggtg taatgtgaaa agacaatact gattattttt cttttccttt ttctttagtg 7561 tctattaaaa aaa //