Typing tool
|
Complete norovirus genomes
MK753029 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..4736 ORF2: 4717..6339 ORF3: 6339..7145LOCUS MK753029 7146 bp RNA linear VRL 11-APR-2019 DEFINITION Norovirus GII isolate Hu/US/2016/GII.P16-GII.4 Sydney/SanDiego0043 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION MK753029 VERSION MK753029.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7146) 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characterization of multiple viruses associated with a novel GII.P16 polymerase in the United States, 2015-2018 JOURNAL Unpublished REFERENCE 2 (bases 1 to 7146) AUTHORS Barclay,L., Cannon,J.L., Pan,C.-Y., Montmayeur,A.M., Tatusov,R.L., Chhabra,P. and Vinje,J. TITLE Direct Submission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..7146 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="SanDiego0043" /isolate="Hu/US/2016/GII.P16-GII.4 Sydney/SanDiego0043" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA" /collection_date="03-Jan-2016" /note="genotype: GII.P16-GII.4 Sydney" gene <1..4736 /gene="ORF1" CDS <1..4736 /gene="ORF1" /codon_start=3 /product="nonstructural polyprotein" /protein_id="QBS54657.1" /translation="AKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARV ELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSR RMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPL NILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE ANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSAS PDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKV ASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTL NCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD FPGQPDMWKDVFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL HERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELK QAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARI RYYVKCVQEAVYSIIQIAGAAFVTTRIVRRMNIQELWSKPQLDQNESETKEEAPKSED DEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE YLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIR KRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITS THVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVL IKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYI YKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPK LSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPR PSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFT GKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRC ARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRA VLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSI AHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKP TRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPN ETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWM RFSDLSTWEGDRNLAPNFVNEDGVE" mat_peptide <1..632 /gene="ORF1" /product="p48" mat_peptide 633..1730 /gene="ORF1" /product="NTPase" mat_peptide 1731..2261 /gene="ORF1" /product="p22" mat_peptide 2262..2660 /gene="ORF1" /product="VPg" mat_peptide 2661..3203 /gene="ORF1" /product="Pro" mat_peptide 3204..4733 /gene="ORF1" /product="RdRp" gene 4717..6339 /gene="ORF2" CDS 4717..6339 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QBS54658.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6339..7145 /gene="ORF3" CDS 6339..7145 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QBS54659.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 aggccaagga accgttaaca ggggcaatat tagagatgtg ggatggagag atataccact 61 atggcctgta cgtggagaaa ggcttagtgt tgggtgtgca caaaccacct gcagccataa 121 gcatggcaag agtggagctg acgccgctgt cattgtactg gcgtgtggtg tacactcccc 181 aatacctcat ctcccctgaa actctcagga ggctcaacgg agaggcgttc ccttacaccg 241 cctttgacaa caactgctat gccttttgct gctgggtgtt agacctcaat gactcatggc 301 ttagcaggag gatggtgcaa agaacaacgg gcttcttcag accttaccaa gagtggaaca 361 gaaaacccct gcctaccatg gatgactcca aaattaagaa ggtagcaaat atattcctat 421 gttcattgtc cacattattc accagaccca taaaagacct cataggaaaa attaaaccat 481 taaacatatt gaacatcctg gcaacgtgtg actggacgtt tgccggaata gtggagtctc 541 tgatattact tgctgaactc ttcggagttt tctggacacc cccagatgtg tctgctatga 601 tcgctccctt actcggggac tacgagttgc aagggccaga agacctcgcc gttgaactcg 661 tacctgtggt aatgggaggg attggtttgg tgttgggatt caccaaagag aaaattggca 721 aaatgttgtc ctcagcagca tcaacactca gggcttgcaa agatcttggt gcctatggct 781 tagagatact caaattggtc atgaagtggt tcttcccaaa gaaagaggag gccaatgagc 841 tagccatggt gagggccata gaggatgccg tactagatct tgaggcaata gaaaataacc 901 acatgacaac cctgttgaaa gacaaagaca gcttagcaac atacatgaaa acactggaca 961 tggaggagga gaaagccaga aggttgtcca caaaatctgc atcccctgac atagttggaa 1021 caatcaacgc cctgctggct cgaatagcag cggccaggtc attagtccac agggccaagg 1081 aagagctatc tagcaggata agaccagtag ttgttatgat atctggcaaa ccaggaatag 1141 gcaaaactca tctggccagg gaggtggcaa gaaaggtggc atccactctc acaggggatc 1201 aaagagtcgg actcatacca agaaacggtg tggaccattg ggatgcatac aaaggtgaga 1261 gagtcgtgct gtgggacgac tatggcatga gtaaccccat tcatgatgct cttcgcatac 1321 aggaattggc tgatacgtgt ccccttacct taaattgtga cagaattgag aataagggaa 1381 aagtttttga cagtgaagtc ataataatta caacaaacct tgccaatcca gccccacttg 1441 attatgtcaa ctttgaggcc tgttccagga gaattgattt cctggtgtac gctgaggcac 1501 cagaagtaga aaaggcaaaa cgggactttc ctggtcagcc agatatgtgg aaggacgtct 1561 tcaagccgga cttttcacac atcaagctac agcttgcacc tcagggcggt tttgacaaga 1621 atggcaacac cccacatggg aaaggagtga tgaagaccct cactaccggt tctctgattg 1681 cccgtgcatc aggcctactg catgagagga tggatgaatt tgaactccaa ggtcccacaa 1741 tcaccacctt caatttcgac cggaacagaa tcacagcatt cagacaattg gctgcagaaa 1801 acaagtatgg attggtggat accatgaaag ttggcaacca actaaaagga gtgaaaacca 1861 tggaagaact caaacaagca atcaggaatg tgaccatcaa gaggtgccgg atcatctacg 1921 gtggctccac gtatgacctt gaatctgatg gcaagggcaa agttttggtg gaaaaggtca 1981 agaacacctc tgtacagacc aacaacgagt tggccggggc cctgcaccat ctcaaacacg 2041 cccgaattag gtactatgtc aaatgtgtgc aagaagcagt ctattccatc atacaaattg 2101 ccggcgctgc gtttgtcacc acgcgcattg tacgccgcat gaacatacaa gaactctggt 2161 cgaagccaca attagatcaa aatgaatcag agactaagga agaggccccc aagtcagaag 2221 atgacgagtt catcatatct tctaaggaca tcaaggagga aggaaagaag ggcaaaaaca 2281 aaactggccg tggcaagaaa cacactgcat tctccagcaa gggcttgagc gatgaggagt 2341 atgacgagta caagaggata agagaagaga gaaatgggaa gtactctata gaggagtatc 2401 ttcaagacag agacaggtac tatgaggagc tcgccattgc caaggccacg gaagaagact 2461 tctgtgaaga ggaggaaatc aaaatccgtc agagaatttt ccgtcccacc aggaaacaaa 2521 gaaaggaaga gagggccaca ttagggctag taacaggttc agaaatcaga aaaagaaacc 2581 ctgatgactt caaacccaaa gggaagctgt gggccgatga caacagaagt gttgactaca 2641 atgagaaact agactttgag gcccccccaa gcatatggtc taggattgtg agctttggtt 2701 ctggctgggg cttctgggta tcaccaagcc tgttcataac atcaactcat gtaatccccg 2761 caggcataac agaagcattt ggagtcccca ttaaacaaat tcagatccac aaatcaggtg 2821 aattttgccg attcagattc ccaaaaccaa ttagaccaga tgtgacagga atgatcttgg 2881 aagaaggtgc gcctgaaggc accgtggcaa ctgtgctcat caaacgcccc accggagagc 2941 tcatgcctct tgcagccaga atgggaacac acgcaaccat gaaaattcaa ggccgcatgg 3001 ttggcggaca aatgggtatg ttgctcactg gatcaaatgc taaaggaatg gatttgggaa 3061 caactcctgg tgactgtggc tgtccttaca tctataaaag gggcaatgac tatatagtca 3121 ttggggtgca cactgcagca gcccgtggcg gaaacaccgt catctgtgcc acacagggaa 3181 gtgagggtga ggcaactctt gaaggtggag atgacaaagg aacatactgt ggggcaccca 3241 ttctaggccc tgggggtgca ccaaaattga gcaccaaaac caaattttgg aggtcatcga 3301 acacgcccct tccaccaggg acatatgagc ctgcctacct cggtggccgt gatccgcgtg 3361 ttaagggtgg gccctccttg cagcaggtaa tgagagacca gttgaagcca ttcactgaac 3421 ccaggggcaa acctccaaga ccaagtgtgt tggaagcagc caaacaaacc attatcaatg 3481 tcctcgaaca aaccctggac cctccacaaa aatggacata cgcacaggcg tgtgcctcac 3541 ttgacaaaac cacctccagc gggcatcccc atcacgtccg aaagaatgaa ttctggaatg 3601 gtgagacctt cactggtaaa ttggcagacc aagcatcaaa agcaaaccta atgtttgagg 3661 aagggaaaca catgacacca gtgtatacag cagcactcaa ggacgagcta gtcaagactg 3721 agaaaatcta tggaaagatc aagaagagac tgctctgggg ctctgacttg tccaccatga 3781 tccggtgcgc taggtcattt ggtgggctca tggatgagat gaaggcacac tgcatatcac 3841 tcccagtacg agttggcatg aatatgaatg aagatggccc aataatattt gagaaacatt 3901 ccagatacaa atatcactat gatgcagatt actctcgctg ggattcaaca caacaaaggg 3961 cagtactagc agcagccttg gaaatcatgg tcagattctc tgcagaacca caattggcac 4021 aaatagtcgc tgaggatctg ctggccccta gtgtagtaga tgtaggagac tttaaaatca 4081 caataaatga agggctccca tctggtgtgc catgcacttc tcaatggaac tccatcgcac 4141 actggctgct aactctctgt gccttgtctg aagtcaccaa actgtcccct gacattatac 4201 aagcaaattc catgttctca ttttacggtg atgacgagat tgtcagcacc gacataaaat 4261 tggaccctga acagttaacc gccaaattga aggagtacgg cctgaaacca acccgcccag 4321 acaagaccga gggacccctg atcatcagtg aagatttgaa cggactcact ttcctccgaa 4381 ggacggtgac tcgtgaccca gctggctggt ttggaaaact ggaccaaagc tcaattttga 4441 ggcagatgta ctggactaga ggaccaaatc atgaagaccc caatgagaca atgatacccc 4501 attctcaaag acccatacag ctcatggcac tgcttggtga agcctctctt cacggaccct 4561 ctttctacag taaaatcagt aaattggtca taactgaact caaagaaggt gggatggact 4621 tttacgtgcc aaggcaggaa cccatgttca ggtggatgag gttttctgac ttgagcacgt 4681 gggagggcga tcgcaatctg gctcccaatt ttgtgaatga agatggcgtc gagtgacgcc 4741 aacccatctg atgggtccgc agccaacctc gtaccagagg tcaacaatga ggttatggct 4801 ttggagcccg ttgttggtgc cgctattgcg gcacctgtag cgggccaaca aaatgtaatt 4861 gacccctgga ttagaaataa ttttgtacaa gcccctggtg gggagtttac agtatcccct 4921 agaaacgctc caggtgaaat actatggagc gcgcccctag gccctgacct aaatccctac 4981 ctatcccatt tggccagaat gtacaatggt tatgcaggtg gttttgaagt gcaggtaatt 5041 ctcgcgggga acgcgttcac cgccgggaag atcatatttg cagcagtccc accaaatttt 5101 ccaactgaag gcttaagtcc tagccaggtc actatgttcc cccatataat agtagatgtt 5161 agacaattag aacctgtgct gattccctta cccgatgtca ggaataattt ctatcattac 5221 aatcagtcaa atgactccac tattaagttg atagcaatgt tgtatacacc acttagggct 5281 aataatgctg gggatgatgt tttcacagtt tcgtgccgag ttctcacgag accatccccc 5341 gattttgatt ttatattttt agtgccaccc acagttgagt caagaactaa accattctct 5401 gtcccagttt taactgttga ggagatgacc aattcaagat tccccattcc tttggaaaag 5461 ttgttcacgg gccccagcag tgcctttgtt gttcaaccac aaaacggcag gtgcacaact 5521 gatggcgtgc tcctaggcac cacccaactg tctcctgtca acatctgcac cttcagaggg 5581 gatgtcaccc acatcacagg tagtcgcaac tacacaatga atttggcttc tcaaaattgg 5641 aacaactatg acccaacaga agaaatccca gctcctctag gaactccaga ttttgtgggg 5701 aagattcaag gcatgctcac ccaaaccaca agaacagatg gttcaacgcg cggccacaaa 5761 gctacagtgt acactgggag cgccgacttt gctccaaaac tgggtagagt tcaatttgaa 5821 actgacacag accatgattt tgaagctaat caaaacacaa agttcacccc agtcggtgtc 5881 atccaagatg gtagcaccac ccaccggaac gaaccccaac agtgggtgct cccaagttac 5941 tcaggcagaa atactcacaa tgtacatctg gcccccgctg tagcccccac ctttccgggt 6001 gagcaacttc tcttcttcag atccaccatg cccggatgca gcgggtaccc caacatggat 6061 ttggactgtc tgctccccca ggaatgggtg cagtacttct accaagaggc agccccagca 6121 caatctgatg tggctctgct aagatttgtg aatccagaca caggtagggt tttgtttgag 6181 tgcaagcttc acaaatcagg ctatgttaca gtggctcaca ctggccaaca tgatttggtt 6241 atccccccca atggttactt caggtttgat tcctgggtca accagttcta cacgcttgcc 6301 cccatgggaa atggaacggg gcgtagacgt gtagtataat ggctggagct ttctttgctg 6361 gattggcatc tgatgtcctt ggctctggac ttggttccct tatcaatgct ggggctgggg 6421 ccatcaacca aaaagttgag tttgaaaata acagaaaatt gcaacaagca tccttccaat 6481 ttagcagcaa tctgcaacag gcttcctttc aacatgataa agagatgctc caagcacaaa 6541 ttgaggccac caaaaggcta caacaggaaa tgatgaaagt taagcaggca atgctcctag 6601 agggtgggtt ctctgagaca gatgcagccc gcggggcaat taacgccccc atgacaaaag 6661 ctttggactg gagcgggaca aggtactggg ctcccgatgc taggactaca acatataatg 6721 caggccgctt ttccacccct caaccatcgg gggcactgcc aggaagagct aatcttaggg 6781 atgctgtccc tgctcgggga ccctccaaca aatcttctaa ctcttctact gccacctctg 6841 tgtactcaaa tcaaactatt tcaacgagac ttggttctac agctggttct ggaaccagtg 6901 tctcgagcct cccgtcaact gcaaggacta ggagctgggt tgaggatcaa agtaggaatt 6961 tgtcaccttt catgaggggg gcccacaaca tatcattcgt caccccacca tctagcagat 7021 cctctagcca aggcacagtc tcaaccgtgc ctaaagagat tttggactcc tggactggcg 7081 ctttcaacac gcgcaggcag cctctcttcg ctcacattcg taagcgaggg gagtcacggg 7141 tgtaat //