Typing tool
|
Complete norovirus genomes
MK762563 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5076 ORF2: 5057..6679 ORF3: 6679..7485LOCUS MK762563 7485 bp RNA linear VRL 13-APR-2019 DEFINITION Norovirus GII isolate Hu/US/2016/GII.P16-GII.4 Sydney/CS0194 nonstructural polyprotein (ORF1) gene, partial cds; VP1 (ORF2) gene, complete cds; and VP2 (ORF3) gene, partial cds. ACCESSION MK762563 VERSION MK762563.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7485) 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characterization of multiple viruses associated with a novel GII.P16 polymerase in the United States, 2015-2018 JOURNAL Unpublished REFERENCE 2 (bases 1 to 7485) AUTHORS Barclay,L., Cannon,J.L., Montmayeur,A.M., Tatusov,R.L., Chhabra,P. and Vinje,J. TITLE Direct Submission JOURNAL Submitted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..7485 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="CS0194" /isolate="Hu/US/2016/GII.P16-GII.4 Sydney/CS0194" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA" /collection_date="03-Mar-2016" /note="genotype: GII.P16-GII.4 Sydney" gene <1..5076 /gene="ORF1" CDS <1..5076 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="QBX91016.1" /translation="TVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPRGE PQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVANTAF SVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARVEL TPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRM VQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNI LNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELV PVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEAN ELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSASPD IVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVAS TLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNC DRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFP GQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHE RMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQA IRNVTIKRCQIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARIRY YVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSEDDE FIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYL QDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKR NPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTH VIPAGITEAFGVPIKQIQVHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIK RPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYK RGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLS TKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPS VLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFTGK LADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCAR SFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVL AAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAH WLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTR PDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQNSILRQMYWTRGPNHEDPNET MIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWMRF SDLSTWEGDRNLAPNFVNEDGVE" mat_peptide <1..972 /gene="ORF1" /product="p48" mat_peptide 973..2070 /gene="ORF1" /product="NTPase" mat_peptide 2071..2601 /gene="ORF1" /product="p22" mat_peptide 2602..3000 /gene="ORF1" /product="VPg" mat_peptide 3001..3543 /gene="ORF1" /product="Pro" mat_peptide 3544..5073 /gene="ORF1" /product="RdRp" gene 5057..6679 /gene="ORF2" CDS 5057..6679 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QBX91017.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFSPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6679..>7485 /gene="ORF3" CDS 6679..>7485 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QBX91018.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS NSSTVTSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRVR" ORIGIN 1 accgttgccg ttgcttgcaa caacaacaac gacaaggaaa aatcttcagg tgaaggctta 61 ttcacaaata tgtcttccac cttaaagaaa gccctcgggg ctaggcccaa acagcctgcc 121 ccgagaggcg aaccacaaaa gcccccaaga ccaccaactc ccgagttggt caagaggata 181 ccccctcctc cacctaatgg cgaagaagaa gaagaaccag tcattaggta tgaggttaag 241 agtgggatct ctggcctgcc cgagctcaca acagtccccc aaccggacgt ggccaacaca 301 gcattcagtg ttccaccact gagcttgaga gaaaacaggg aggccaagga accgttaaca 361 ggggcaatat tagagatgtg ggatggagag atataccact atggcctgta cgtggagaaa 421 ggcttagtgt tgggtgtgca caaaccacct gcagccataa gcatggcaag agtggagctg 481 acgccgctgt cattgtactg gcgtgtggtg tacactcccc aatacctcat ctcccctgaa 541 actctcagga ggctcaacgg agaggcgttc ccttacaccg cctttgacaa caactgctat 601 gccttttgct gctgggtgtt agacctcaat gactcatggc ttagcaggag gatggtgcaa 661 agaacaacgg gcttcttcag accttaccaa gagtggaaca gaaaacccct gcctaccatg 721 gatgactcca aaattaagaa ggtagcaaat atattcctat gttcattgtc cacattattc 781 accagaccca taaaagacct cataggaaaa attaaaccat taaacatatt gaacatcctg 841 gcaacgtgtg actggacgtt tgccggaata gtggagtccc tgatattact tgctgaactc 901 ttcggagttt tctggacacc cccagatgtg tctgctatga tcgctccctt actcggggac 961 tacgagttgc aagggccaga agacctcgcc gttgaactcg tacctgtggt aatgggaggg 1021 attggtttgg tgttgggatt caccaaagag aaaattggca aaatgttgtc ctcagcagca 1081 tcaacactca gggcttgcaa agatcttggt gcctatggct tagagatact caaactggtc 1141 atgaagtggt tcttcccaaa gaaagaggag gccaatgagc tagccatggt gagggccata 1201 gaggatgccg tactagatct tgaggcaata gaaaataacc acatgacaac cctgttgaaa 1261 gacaaagaca gcttagcaac atacatgaaa acactggaca tggaggagga gaaagccaga 1321 aggttgtcca caaaatctgc atcccctgac atagttggga caatcaacgc cctgctggct 1381 cgaatagcag cggccaggtc attagtccac agggccaagg aagagctatc tagcaggata 1441 agaccagtag ttgttatgat atctggcaaa ccaggaatag gcaaaactca cctggccagg 1501 gaggtggcaa gaaaggtggc atccactctc acaggggatc aaagagtcgg actcatacca 1561 agaaacggtg tggaccattg ggatgcatac aaaggtgaga gagtcgtgct gtgggacgac 1621 tatggcatga gtaaccccat tcatgatgct cttcgcatac aggaattggc tgatacgtgt 1681 ccccttacct taaattgtga cagaattgag aataagggaa aagtttttga cagtgaagtc 1741 ataataatta caacaaacct tgccaatcca gccccacttg attatgtcaa ctttgaggcc 1801 tgttccagga gaattgattt cctggtgtac gctgaggcac cagaagtaga aaaggcaaaa 1861 cgggactttc ctggtcagcc agatatgtgg aaggacgcct tcaagccgga cttttcacac 1921 atcaagctac agcttgcacc tcagggcggt tttgacaaga atggcaacac cccacatggg 1981 aaaggagtga tgaagaccct cactaccggt tctctgattg cccgtgcatc aggcctactg 2041 cacgagagga tggatgaatt tgaactccaa ggtcccacaa tcaccacctt caatttcgac 2101 cggaacagaa tcacagcatt cagacaattg gctgcagaaa acaagtatgg attggtggat 2161 accatgaaag ttggcaatca actaaaagga gtaaaaacca tggaagaact caaacaagca 2221 atcaggaatg tgaccatcaa gaggtgccag atcatctacg gtggctccac gtatgacctt 2281 gaatctgatg gcaagggcaa agttttggtg gaaaaggtca agaacacctc tgtacagacc 2341 aacaacgagt tggccggggc cctgcaccat ctcaaacacg cccgaatcag gtactatgtc 2401 aaatgtgtgc aagaagcagt ctattccatc atacaaattg ccggcgctgc gtttgtcacc 2461 acgcgcattg cacgccgcat gaacatacaa gaactctggt cgaagccaca attagatcaa 2521 aatgaatcag agactaagga agaggccccc aagtcagaag atgacgagtt catcatatct 2581 tctaaggaca tcaaggagga aggaaagaag ggcaaaaaca aaactggccg tggcaagaaa 2641 cacactgcat tctccagcaa gggcttgagc gatgaggagt atgacgagta caagaggata 2701 agagaagaga gaaatgggaa gtactctata gaggagtatc ttcaagacag agacaggtac 2761 tatgaggagc tcgccattgc caaggccacg gaagaagact tctgtgaaga ggaggagatc 2821 aaaatccgtc agagaatttt ccgtcccacc aggaaacaaa gaaaggaaga gagggccaca 2881 ttagggctag taacaggttc agaaatcaga aaaagaaacc ctgatgactt caaacccaaa 2941 gggaagctgt gggccgatga caatagaagt gttgactaca atgagaaact agactttgag 3001 gcccccccaa gcatatggtc taggattgtg agctttggtt ctggctgggg cttctgggta 3061 tcaccaagcc tgttcataac atcaactcat gtaatccccg caggcataac agaagcattt 3121 ggagtcccca tcaaacaaat tcaggtccac aaatcaggtg aattttgccg attcagattc 3181 ccaaaaccaa ttagaccaga tgtgacagga atgatcttgg aagaaggtgc gcctgaaggc 3241 accgtggcaa ctgtgctcat caaacgcccc accggagagc tcatgcctct tgcagccaga 3301 atgggaacac acgcaaccat gaaaattcaa ggccgcatgg ttggcggaca aatgggtatg 3361 ttgctcactg gatcaaatgc taaaggaatg gatttgggaa caactcctgg tgactgtggc 3421 tgtccttaca tctataaaag gggcaatgac tatatagtca ttggggtgca cactgcagca 3481 gcccgtggcg gaaacaccgt catctgtgcc acacagggaa gtgagggtga ggcaactctt 3541 gagggtggag atgacaaagg aacatactgt ggggcaccca ttctaggccc tgggggtgca 3601 ccaaaattga gcaccaaaac caaattttgg aggtcatcga acacgcctct tccaccaggg 3661 acatatgagc ctgcctacct cggtggccgt gatccgcgtg ttaagggtgg gccctccttg 3721 cagcaggtaa tgagagacca gttgaagcca ttcactgaac ccaggggcaa acctccaaga 3781 ccaagtgtat tggaagcagc caaacaaacc attatcaatg tcctcgaaca aaccctggat 3841 cctccacaaa aatggacata cgcacaggcg tgtgcctcac ttgacaaaac cacctccagc 3901 gggcatcccc atcacgtccg aaagaatgaa ttctggaatg gtgagacctt cactggtaaa 3961 ttggcagacc aagcatcaaa agcaaaccta atgtttgagg aagggaaaca catgacacca 4021 gtgtacacag cagcactcaa ggacgagcta gtcaagactg agaaaatcta tggaaagatc 4081 aagaagagac tgctctgggg ctctgacttg tccaccatga tccggtgcgc taggtcattt 4141 ggtgggctca tggatgagat gaaggcacac tgcatatcac tcccagtacg agttggcatg 4201 aatatgaatg aagatggccc aataatattt gagaaacatt ccagatacaa ataccactat 4261 gatgcagact actctcgttg ggattcaaca caacagaggg cagtactagc agcagccttg 4321 gaaatcatgg tcagattttc tgcagaacca caattggcac aaatagtcgc tgaggatctg 4381 ctggccccta gtgtagtaga tgtaggagac tttaaaatca caataaatga agggctccca 4441 tctggtgtgc catgcacttc tcaatggaac tccatcgcac actggctgct aactctctgt 4501 gccttgtctg aagtcaccaa actgtcccct gacattatac aagcaaattc catgttctca 4561 ttttacggtg atgacgagat tgttagcacc gacataaaat tggaccctga acagttaacc 4621 gccaaattga aggagtacgg cctgaaacca acccgcccag acaagaccga gggacccctg 4681 atcatcagtg aagatttgaa cggactcact ttcctccgaa ggacggtgac tcgtgaccca 4741 gctggctggt ttggaaaact ggaccaaaac tcaatattga ggcagatgta ctggactaga 4801 ggaccaaatc atgaagaccc caatgagaca atgatacccc attctcaaag acccatacag 4861 ctcatggcac tgcttggtga agcctctctt cacggaccct ctttctacag taaaatcagt 4921 aagttggtca taactgaact caaagaaggt gggatggact tttacgtgcc aaggcaggaa 4981 cccatgttca ggtggatgag gttttctgac ttgagcacgt gggagggcga tcgcaatctg 5041 gctcccaatt ttgtgaatga agatggcgtc gagtgacgcc aacccatctg atgggtccgc 5101 agccaacctc gtaccagagg tcaacaatga ggttatggct ttggagcccg ttgttggtgc 5161 cgctattgcg gcacctgtag cgggccaaca aaatgtaatt gacccctgga ttagaaataa 5221 ttttgtacaa gcccctggtg gggagtttac agtatcccct agaaacgctc caggtgaaat 5281 actatggagc gcgcccctag gccctgacct aaatccctac ctatcccatt tggccagaat 5341 gtacaatggt tatgcaggtg gttttgaagt gcaggtaatt ctcgcgggga acgcgttcac 5401 cgccgggaag atcatatttg cagcagtccc accaaatttt ccaactgaag gcttaagtcc 5461 tagccaggtc actatgttcc cccatataat agtagatgtt agacaattag aacctgtgct 5521 gattccctta cccgatgtca ggaataattt ctatcattac aatcagtcaa atgactccac 5581 tattaagttg atagcaatgt tgtacacacc acttagggct aataatgctg gggatgatgt 5641 tttcacagtt tcgtgccgag ttctcacgag accatccccc gattttgatt tcatattttt 5701 agtgccaccc acagttgagt caagaactaa accattctct gtcccagttt taactgttga 5761 ggagatgacc aattcaagat tccccattcc tttggaaaag ttgttcacgg gccccagcag 5821 tgcctttgtt gttcaaccac aaaacggcag gtgcacaact gatggcgtgc tcctaggcac 5881 cacccaactg tctcctgtca acatctgcac cttcagaggg gatgtcaccc acatcacagg 5941 tagtcgcaac tacacaatga atttggcttc tcaaaattgg aacaactatg acccaacaga 6001 agaaatccca gcccctctag gaactccaga ttttgtgggg aagattcaag gcatgctcac 6061 ccaaaccaca aggacagatg gttcaacacg cggccacaaa gctacagtgt acactgggag 6121 cgccgacttt tctccaaaac taggtagagt tcaatttgaa actgacacag accatgattt 6181 tgaagctaac caaaacacaa agttcacccc agtcggtgtc atccaagatg gtagcaccac 6241 ccaccgaaac gaaccccaac agtgggtgct cccaagttac tcaggcagaa atactcacaa 6301 tgtacacctg gcccccgctg tagcccccac ctttccgggt gagcaacttc tcttcttcag 6361 atccaccatg cccggatgca gcgggtaccc caacatggat ttggactgtc tgctccccca 6421 ggaatgggtg cagtacttct accaagaggc agccccagca caatctgatg tggctctgct 6481 aagatttgtg aatccagaca caggtagggt tttgtttgag tgcaagcttc acaaatcagg 6541 ctatgttaca gtggctcaca ctggccaaca tgatttggtt atccccccca atggttactt 6601 taggtttgat tcctgggtca accagttcta cacgcttgcc cccatgggaa atggaacggg 6661 gcgtagacgt gtagtataat ggctggagct ttctttgctg gattggcatc tgatgtcctt 6721 ggctctggac ttggttccct tatcaatgct ggggctgggg ccatcaacca aaaagttgag 6781 tttgaaaata acagaaaatt gcaacaagca tccttccaat ttagcagcaa tctgcaacag 6841 gcttcctttc aacatgataa agagatgctc caagcacaaa ttgaggccac caaaaagcta 6901 caacaggaaa tgatgaaagt taagcaggca atgctcctag agggtgggtt ctctgagaca 6961 gatgcagccc gcggggcaat taacgccccc atgacaaaag ctttggactg gagcgggaca 7021 aggtactggg ctcccgatgc taggactaca acatataatg caggccgctt ttccacccct 7081 caaccatcgg gggcactgcc aggaagagct aatcttaggg atgctgtccc tgctcgggga 7141 ccctccaaca aatcttccaa ctcttctact gtcacctctg tgtactcaaa tcaaactatt 7201 tcaacgaggc ttggttctac agctggttct ggaaccagtg tctcgagcct cccgtcaact 7261 gcaaggacta ggagctgggt tgaggatcaa agtaggaatt tgtcaccttt catgaggggg 7321 gcccacaaca tatcatttgt caccccacca tctagcagat cctctagcca aggcacagtc 7381 tcaaccgtgc ctaaagagat tttggactcc tggactggcg ctttcaacac gcgcaggcag 7441 cctctcttcg ctcacattcg taagcgaggg gagtcacggg tgagg //